Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (scientific article published on August 25, 2010)

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Q34158533	CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences
Q42144375	CodonLogo: a sequence logo-based viewer for codon patterns.
Q37065921	Cofactors of LIM Domains Associate with Estrogen Receptor α to Regulate the Expression of Noncoding RNA H19 and Corneal Epithelial Progenitor Cell Function
Q37054248	Cold acclimation wholly reorganizes the Drosophila melanogaster transcriptome and metabolome
Q38365585	Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads.
Q57076021	Collaborative Tools to Accelerate Neglected Disease Research: Open-Source Drug Discovery Model
Q36870790	Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota
Q46241600	Colorful seashells: Identification of haem pathway genes associated with the synthesis of porphyrin shell color in marine snails
Q41628071	Combination scaffolds of salmon fibrin, hyaluronic acid, and laminin for human neural stem cell and vascular tissue engineering
Q92159592	Combinatorial action of NF-Y and TALE at embryonic enhancers defines distinct gene expression programs during zygotic genome activation in zebrafish
Q37699087	Combinatorial bZIP dimers display complex DNA-binding specificity landscapes.
Q36104408	Combinatorial complexity in a transcriptionally centered signaling hub in Arabidopsis.
Q42770081	Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits
Q27315050	Combinatorial gene regulation by modulation of relative pulse timing
Q36431578	Common Viral Integration Sites Identified in Avian Leukosis Virus-Induced B-Cell Lymphomas
Q30979411	Compact graphical representation of phylogenetic data and metadata with GraPhlAn
Q61799743	Comparative Analyses of Metabolomic Fingerprints and Cytotoxic Activities of Soft Corals from the Colombian Caribbean
Q91692967	Comparative Analysis of Strategies for De Novo Transcriptome Assembly in Prokaryotes: Streptomyces clavuligerus as a Case Study
Q41641548	Comparative Genomics Identifies a Potential Marker of Human-Virulent Anaplasma phagocytophilum
Q35757986	Comparative RNA-seq analysis of the Tritrichomonas foetus PIG30/1 isolate from pigs reveals close association with Tritrichomonas foetus BP-4 isolate 'bovine genotype'.
Q38435208	Comparative analysis of MBD-seq and MeDIP-seq and estimation of gene expression changes in a rodent model of schizophrenia
Q36714234	Comparative analysis of somatic copy-number alterations across different human cancer types reveals two distinct classes of breakpoint hotspots
Q38674649	Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions
Q39038992	Comparative and retrospective molecular analysis of Parapoxvirus (PPV) isolates
Q39587285	Comparative faecal microbiota of dogs with and without calcium oxalate stones
Q35093972	Comparative genomics of unintrogressed Campylobacter coli clades 2 and 3.
Q34057457	Comparative mechanistic studies of brilacidin, daptomycin, and the antimicrobial peptide LL16.
Q34778106	Comparative transcriptome analysis of obligately asexual and cyclically sexual rotifers reveals genes with putative functions in sexual reproduction, dormancy, and asexual egg production.
Q28703615	Comparative transcriptome analysis to investigate the high starch accumulation of duckweed (Landoltia punctata) under nutrient starvation
Q60043886	Comparative transcriptomic analysis of bovine papillomatosis
Q35943370	Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets.
Q34587095	Comparative transcriptomics reveals striking similarities between the bovine and feline isolates of Tritrichomonas foetus: consequences for in silico drug-target identification
Q48045941	Comparison between Listeria sensu stricto and Listeria sensu lato strains identifies novel determinants involved in infection
Q38637795	Comparison of Illumina de novo assembled and Sanger sequenced viral genomes: A case study for RNA viruses recovered from the plant pathogenic fungus Sclerotinia sclerotiorum.
Q37513014	Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut.
Q40907197	Comparison of gene activation by two TAL effectors from Xanthomonas axonopodis pv. manihotis reveals candidate host susceptibility genes in cassava
Q30580108	Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces
Q35070206	Comparison of ultra-conserved elements in drosophilids and vertebrates
Q91583914	Complementary DNA/RNA-Based Profiling: Characterization of Corrosive Microbial Communities and Their Functional Profiles in an Oil Production Facility
Q41619508	Complete Circular Genome Sequence and Temperature Independent Adaptation to Anaerobiosis of Listeria weihenstephanensis DSM 24698.
Q37190887	Complete Genome Sequence of Genotype VI Newcastle Disease Viruses Isolated from Pigeons in Pakistan
Q36990491	Complete Genome Sequence of Seoul Virus Strain Tchoupitoulas
Q27928024	Complete Genome Sequence of Zika Virus Isolated from Semen
Q36548230	Complete Genome Sequence of a Genotype XVII Newcastle Disease Virus, Isolated from an Apparently Healthy Domestic Duck in Nigeria
Q37138170	Complete Genome Sequence of an Avian Paramyxovirus Representative of Putative New Serotype 13.
Q42107793	CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments
Q39351743	Complex mixtures by NMR and complex NMR for mixtures: experimental and publication challenges
Q37303701	Composition and function of the pediatric colonic mucosal microbiome in untreated patients with ulcerative colitis
Q34120064	Compound-gene interaction mapping reveals distinct roles for Staphylococcus aureus teichoic acids.
Q37336776	Comprehensive analysis of human endogenous retrovirus group HERV-W locus transcription in multiple sclerosis brain lesions by high-throughput amplicon sequencing
Q33410276	Comprehensive genetic analysis of complement and coagulation genes in atypical hemolytic uremic syndrome
Q36698845	Comprehensive genetic testing in the clinical evaluation of 1119 patients with hearing loss
Q92134487	Computational Oncology in the Multi-Omics Era: State of the Art
Q42379515	Computational Population Biology: Linking the inner and outer worlds of organisms
Q37615429	Computational Tools for Genomic Studies in Plants
Q47664589	Computational approaches for discovery of mutational signatures in cancer.
Q35417365	Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput
Q45886254	Computational discovery of human coding and non-coding transcripts with conserved splice sites.
Q39480814	Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights
Q30317857	Computational predictions provide insights into the biology of TAL effector target sites
Q30617899	Computational solutions for omics data
Q30578985	Computational thinking in the era of big data biology
Q62727456	Computational tools to unmask transposable elements
Q57034124	Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes
Q47790761	Computer Analysis of Glioma Transcriptome Profiling: Alternative Splicing Events.
Q34897264	Concurrent transcriptional profiling of Dirofilaria immitis and its Wolbachia endosymbiont throughout the nematode life cycle reveals coordinated gene expression
Q35666136	Conditional CD8+ T cell escape during acute simian immunodeficiency virus infection
Q35208886	Conducting a microbiome study
Q30657932	Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data
Q30515384	Confirmation of an epilepsy modifier locus on mouse chromosome 11 and candidate gene analysis by RNA-Seq
Q36066303	Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME.
Q33656515	Connectivity of vertebrate genomes: Paired-related homeobox (Prrx) genes in spotted gar, basal teleosts, and tetrapods
Q34880496	Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes
Q28598276	Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals
Q42906922	Conservative sex and the benefits of transformation in Streptococcus pneumoniae
Q33819847	Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation
Q34357104	Construction of a stability landscape of the CH3 domain of human IgG1 by combining directed evolution with high throughput sequencing
Q35742594	Context influences on TALE-DNA binding revealed by quantitative profiling
Q35217155	Context-dependent individualization of nucleotides and virtual genomic hybridization allow the precise location of human SNPs
Q38919660	Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes
Q36439318	Contribution of global rare copy-number variants to the risk of sporadic congenital heart disease
Q35625332	Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus
Q33796395	Copy number variants are a common cause of non-syndromic hearing loss
Q55259259	Copy number variants implicate cardiac function and development pathways in earthquake-induced stress cardiomyopathy
Q36718985	Copy number variation prevalence in known asthma genes and their impact on asthma susceptibility
Q36628606	Correlates of relative resistance against low-dose rectal simian immunodeficiency virus challenges in peripheral blood mononuclear cells of vaccinated rhesus macaques
Q51803421	Corrigendum: Carbonic anhydrases, EPF2 and a novel protease mediate CO2 control of stomatal development.
Q34998386	Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries
Q92391860	CpG-related SNPs in the MS4A region have a dose-dependent effect on risk of late-onset Alzheimer disease
Q42692621	CpGislandEVO: a database and genome browser for comparative evolutionary genomics of CpG islands.
Q38048232	Creating reusable tools from scripts: the Galaxy Tool Factory
Q38910521	Cross-Comparison of Exome Analysis, Next-Generation Sequencing of Amplicons, and the iPLEX(®) ADME PGx Panel for Pharmacogenomic Profiling
Q34481688	Cross-organism analysis using InterMine
Q47140654	Cryptic genetic variation in an inbreeding and cosmopolitan pest, Xylosandrus crassiusculus, revealed using ddRADseq.
Q27317037	CsoR Is Essential for Maintaining Copper Homeostasis in Mycobacterium tuberculosis
Q28652027	Culture-independence for surveillance and epidemiology
Q34251827	Current challenges in de novo plant genome sequencing and assembly
Q34273183	Cyber-T web server: differential analysis of high-throughput data
Q38390303	Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.
Q34752212	Cytomegalovirus-mediated activation of pyrimidine biosynthesis drives UDP-sugar synthesis to support viral protein glycosylation
Q36931469	Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells
Q42792284	Cytoscape: the network visualization tool for GenomeSpace workflows
Q35787474	DAPPER: a data-mining resource for protein-protein interactions
Q35032224	DDBJ progress report: a new submission system for leading to a correct annotation
Q30622838	DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data
Q36090115	DISMISS: detection of stranded methylation in MeDIP-Seq data
Q30816604	DIVE: a graph-based visual-analytics framework for big data
Q31147210	DNA Data Bank of Japan.
Q35936655	DNA Subtraction of In Vivo Selected Phage Repertoires for Efficient Peptide Pathology Biomarker Identification in Neuroinflammation Multiple Sclerosis Model
Q34590458	DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly
Q34097863	DNA damage in plant herbarium tissue
Q31025244	DNA data bank of Japan (DDBJ) progress report
Q41836697	DNA hypermethylation of alternatively spliced and repeat sequences in humans
Q52608211	DNA metabarcoding of nestling feces reveals provisioning of aquatic prey and resource partitioning among Neotropical migratory songbirds in a riparian habitat.
Q34463678	DNA methylation profile of Aire-deficient mouse medullary thymic epithelial cells
Q35238487	DNA methylation transcriptionally regulates the putative tumor cell growth suppressor ZNF677 in non-small cell lung cancers
Q28287769	DNA polymerase ε and δ exonuclease domain mutations in endometrial cancer
Q51553614	DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes.
Q35047158	DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families
Q36199591	DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome
Q88538181	DNAp: A Pipeline for DNA-seq Data Analysis
Q38388740	DNAseq Workflow in a Diagnostic Context and an Example of a User Friendly Implementation
Q35086835	DRUMS: Disk Repository with Update Management and Select option for high throughput sequencing data
Q26776402	Data standards can boost metabolomics research, and if there is a will, there is a way
Q58027817	DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis
Q39099931	Database Search Engines: Paradigms, Challenges and Solutions
Q36668680	Database resources for the tuberculosis community
Q47209606	Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes
Q28306928	David Haussler
Q38474294	De novo characterisation of the greenlip abalone transcriptome (Haliotis laevigata) with a focus on the heat shock protein 70 (HSP70) family.
Q55260537	De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: narrowing the US origin(s) of the invasive kudzu.
Q33702797	Decoding human gene expression signatures in the brain
Q35182201	Deep evolutionary comparison of gene expression identifies parallel recruitment of trans-factors in two independent origins of C4 photosynthesis
Q34058885	Deep sequencing analysis reveals temporal microbiota changes associated with development of bovine digital dermatitis
Q45038635	Deep sequencing reveals persistence of intra- and inter-host genetic diversity in natural and greenhouse populations of zucchini yellow mosaic virus.
Q31078900	DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets
Q44657393	Defined Sensing Mechanisms and Signaling Pathways Contribute to the Global Inflammatory Gene Expression Output Elicited by Ionizing Radiation.
Q36079824	Defining bacterial regulons using ChIP-seq
Q35552136	Defining essential genes and identifying virulence factors of Porphyromonas gingivalis by massively parallel sequencing of transposon libraries (Tn-seq).
Q38846804	Defining the Clinical Value of a Genomic Diagnosis in the Era of Next-Generation Sequencing.
Q34487175	Defining the nociceptor transcriptome
Q37543961	Deletion of conserved protein phosphatases reverses defects associated with mitochondrial DNA damage in Saccharomyces cerevisiae
Q34590651	Deploying and sharing U-Compare workflows as web services
Q34117744	Design and implementation of degenerate microsatellite primers for the mammalian clade
Q34285275	Detailed comparison of two popular variant calling packages for exome and targeted exon studies
Q35828069	Detecting false-positive signals in exome sequencing
Q35671927	Detecting reticulate relationships among diploid Leucanthemum Mill. (Compositae, Anthemideae) taxa using multilocus species tree reconstruction methods and AFLP fingerprinting
Q38068938	Detection and interpretation of genomic structural variation in health and disease.
Q44012905	Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline
Q34281116	Developing and applying heterogeneous phylogenetic models with XRate
Q59799797	Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics
Q42369709	Developing science gateways for drug discovery in a grid environment
Q34981369	Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts
Q52651140	Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics.
Q36007873	Development of Persister-FACSeq: a method to massively parallelize quantification of persister physiology and its heterogeneity
Q28647984	Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp
Q36605561	Development of a High Resolution Virulence Allelic Profiling (HReVAP) Approach Based on the Accessory Genome of Escherichia coli to Characterize Shiga-Toxin Producing E. coli (STEC).
Q30489234	Development of a cloud-based Bioinformatics Training Platform
Q37180882	Developmental profiles of the murine palatal methylome
Q36990211	Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma
Q42006359	Diet of the insectivorous bat Pipistrellus nathusii during autumn migration and summer residence
Q34986661	Dietary competition between the alien Asian Musk Shrew (Suncus murinus) and a re-introduced population of Telfair's Skink (Leiolopisma telfairii).
Q39425449	Dietary overlap and seasonality in three species of mormoopid bats from a tropical dry forest
Q36143057	Differential Rickettsial Transcription in Bloodfeeding and Non-Bloodfeeding Arthropod Hosts
Q36055343	Differential Transcriptome Networks between IDO1-Knockout and Wild-Type Mice in Brain Microglia and Macrophages
Q28647202	Differential and coherent processing patterns from small RNAs
Q92777509	Differential basal expression of immune genes confers Crassostrea gigas resistance to Pacific oyster mortality syndrome
Q40253733	Differential distribution patterns of ammonia-oxidizing archaea and bacteria in acidic soils of Nanling National Nature Reserve forests in subtropical China
Q24633890	Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Q37430497	Differential inhibition of LINE1 and LINE2 retrotransposition by vertebrate AID/APOBEC proteins.
Q36293132	Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP
Q36528328	Digital detection of endonuclease mediated gene disruption in the HIV provirus.
Q34257320	Digital gene expression analysis based on integrated de novo transcriptome assembly of sweet potato [Ipomoea batatas (L.) Lam].
Q35874860	Dintor: functional annotation of genomic and proteomic data.
Q102220209	Dinucleosome specificity and allosteric switch of the ISW1a ATP-dependent chromatin remodeler in transcription regulation
Q35853411	Direct Evidence for Packaging Signal-Mediated Assembly of Bacteriophage MS2
Q40507104	Directed evolution of artificial enzymes (XNAzymes) from diverse repertoires of synthetic genetic polymers
Q34825832	Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins.
Q33769472	Discovering cooperative relationships of chromatin modifications in human T cells based on a proposed closeness measure
Q34508525	Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum
Q93037409	Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing
Q36859420	Discovery of a potentially deleterious variant in TMEM87B in a patient with a hemizygous 2q13 microdeletion suggests a recessive condition characterized by congenital heart disease and restrictive cardiomyopathy.
Q35035877	Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses
Q28117728	Discovery of the β-barrel-type RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs
Q36032513	Discriminating somatic and germline mutations in tumor DNA samples without matching normals
Q28513515	Disruption of murine Adamtsl4 results in zonular fiber detachment from the lens and in retinal pigment epithelium dedifferentiation
Q34417606	Dissecting molecular stress networks: identifying nodes of divergence between life-history phenotypes
Q46293989	Dissecting the 'bacon and eggs' phenotype: transcriptomics of post-anthesis colour change in Lotus
Q35721274	Dissecting the target specificity of RNase H recruiting oligonucleotides using massively parallel reporter analysis of short RNA motifs.
Q28243453	Dissemination of scientific software with Galaxy ToolShed
Q34979578	DistMap: a toolkit for distributed short read mapping on a Hadoop cluster
Q33592436	Distilling structure in Taverna scientific workflows: a refactoring approach
Q90114569	Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF
Q34482091	Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic
Q38678210	Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor
Q36754737	Distinct mutational behaviors differentiate short tandem repeats from microsatellites in the human genome
Q42428268	Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells
Q46277779	Diversity and dynamics of lactic acid bacteria in Atole agrio, a traditional maize-based fermented beverage from South-Eastern Mexico, analysed by high throughput sequencing and culturing
Q39345823	Diversity and temporal patterns of planktonic protist assemblages at a Mediterranean Long Term Ecological Research site.
Q39098915	Do it yourself guide to genome assembly
Q42068405	Does base-pairing strength play a role in microRNA repression?
Q35994066	Dominance of ammonia-oxidizing archaea community induced by land use change from Masson pine to eucalypt plantation in subtropical China
Q37592373	Dormancy-specific imprinting underlies maternal inheritance of seed dormancy in Arabidopsis thaliana.
Q91623524	Dosage Compensation throughout the Schistosoma mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome
Q28660875	Draft Genome Sequence of the Alga-Aggregating Bacterium Bacillus sp. Strain RP1137
Q28652279	Draft Genome Sequence of the Cellulolytic Bacterium Clavibacter sp. CF11, a Strain Producing Cold-Active Cellulase
Q52653343	Draft Genome Sequences of Five Novel Ochrobactrum spp. Isolated from Different Avian Hosts in Nigeria.
Q90383462	Draft Genome Sequences of Three Novel Staphylococcus arlettae Strains Isolated from a Disused Biological Safety Cabinet
Q54236687	Draft Genome Sequences of Three Ochrobactrum spp. Isolated from Different Avian Hosts in Pakistan.
Q41834561	Draft Genome Sequences of Two New Zealand Xanthomonas campestris pv. campestris Isolates, ICMP 4013 and ICMP 21080.
Q41826174	Draft Genome of the Heterotrophic Iron-Oxidizing Bacterium "Acidibacillus ferroxidans" Huett2, Isolated from a Mine Drainage Ditch in Freiberg, Germany
Q36354873	Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains
Q40736188	DsrA regulatory RNA represses both hns and rbsD mRNAs through distinct mechanisms in Escherichia coli.
Q36637712	Dual RNA-Sequencing of Eucalyptus nitens during Phytophthora cinnamomi Challenge Reveals Pathogen and Host Factors Influencing Compatibility.
Q34256415	Dual transcriptional profiling of mice and Toxoplasma gondii during acute and chronic infection
Q34453834	Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease.
Q47094418	Dynamic DNA methylation regulates neuronal intrinsic membrane excitability
Q34341998	Dynamic changes in Ezh2 gene occupancy underlie its involvement in neural stem cell self-renewal and differentiation towards oligodendrocytes
Q36923350	Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle
Q34590410	Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis
Q35115893	Dynamics of GATA1 binding and expression response in a GATA1-induced erythroid differentiation system
Q35557723	Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study
Q37298457	Dysbiosis of small intestinal microbiota in liver cirrhosis and its association with etiology
Q64128808	Dysbiosis of the Gut Microbiota on the Inflammatory Background due to Lack of Suppressor of Cytokine Signalling-1 in Mice
Q58785910	EBV Associated Breast Cancer Whole Methylome Analysis Reveals Viral and Developmental Enriched Pathways
Q30597346	EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
Q34270499	ELK1 uses different DNA binding modes to regulate functionally distinct classes of target genes
Q34567072	EMEN2: an object oriented database and electronic lab notebook
Q30437064	EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics.
Q36942388	Early developmental gene enhancers affect subcortical volumes in the adult human brain
Q42314837	Early metabolic and transcriptional variations in fruit of natural white-fruited Fragaria vesca genotypes
Q40109156	Ebola virus encodes a miR-155 analog to regulate importin-α5 expression
Q37651510	Ecology of subglacial lake vostok (antarctica), based on metagenomic/metatranscriptomic analyses of accretion ice.
Q55081403	Effect of Bmi1 over-expression on gene expression in adult and embryonic murine neural stem cells.
Q36137250	Effects of Elevated Tropospheric Ozone Concentration on the Bacterial Community in the Phyllosphere and Rhizoplane of Rice.
Q28584597	Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation
Q33651238	Effects of cold-acclimation on gene expression in Fall field cricket (Gryllus pennsylvanicus) ionoregulatory tissues
Q48789186	Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9.
Q36250175	Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell
Q38379915	Embracing an integromic approach to tissue biomarker research in cancer: Perspectives and lessons learned.
Q57002849	Enabling cloud bursting for life sciences within Galaxy
Q24595911	Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas
Q36811520	Enantioselective Utilization of D-Amino Acids by Deep-Sea Microorganisms
Q30821128	Endoglin integrates BMP and Wnt signalling to induce haematopoiesis through JDP2.
Q35572231	Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution.
Q28606718	Enhanced reproducibility of SADI web service workflows with Galaxy and Docker
Q36317809	Enhancing knowledge discovery from cancer genomics data with Galaxy.
Q41430723	EpiExplorer: live exploration and global analysis of large epigenomic datasets
Q36154484	EpiMINE, a computational program for mining epigenomic data
Q41354790	EpiToolKit--a web-based workbench for vaccine design
Q36626342	Epigenetic Studies Point to DNA Replication/Repair Genes as a Basis for the Heritable Nature of Long Term Complications in Diabetes
Q36973678	Epimicrobiota Associated with the Decay and Recovery of Orbicella Corals Exhibiting Dark Spot Syndrome
Q30490545	Equipping Physiologists with an Informatics Tool Chest: Toward an Integerated Mitochondrial Phenome
Q27348830	Erbb2 is required for cardiac atrial electrical activity during development
Q33426304	Escherichia coli O157:H7 strains harbor at least three distinct sequence types of Shiga toxin 2a-converting phages
Q52624464	Ethylene-Related Gene Expression Networks in Wood Formation.
Q42663192	EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes
Q34313331	EuPathDB: the eukaryotic pathogen database
Q36319863	Evaluating alignment and variant-calling software for mutation identification in C. elegans by whole-genome sequencing.
Q37745041	Evaluation of copy-number variants as modifiers of breast and ovarian cancer risk for BRCA1 pathogenic variant carriers
Q48250267	Evaluation of the iron regulatory protein-1 interactome.
Q36231970	Evidence for Amino Acid Snorkeling from a High-Resolution, In Vivo Analysis of Fis1 Tail-Anchor Insertion at the Mitochondrial Outer Membrane
Q22037756	Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade
Q35923413	Evidence from Multiple Species that Spider Silk Glue Component ASG2 is a Spidroin
Q35009069	Evidence of coat color variation sheds new light on ancient canids
Q39099043	Evolution of gamete attraction molecules: evidence for purifying selection in speract and its receptor, in the pantropical sea urchin Diadema
Q35750653	Evolution of the unspliced transcriptome
Q50424275	Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
Q37983903	Evolutionary insight from whole-genome sequencing of experimentally evolved microbes.
Q37633388	Evolvix BEST Names for semantic reproducibility across code2brain interfaces.
Q38872885	Examination of Enterococcus faecalis Toxin-Antitoxin System Toxin Fst Function Utilizing a Pheromone-Inducible Expression Vector with Tight Repression and Broad Dynamic Range.
Q28654778	Executing SADI services in Galaxy
Q60630405	Exome sequencing and array-based comparative genomic hybridisation analysis of preferential 6-methylmercaptopurine producers
Q36272727	Exome sequencing reveals a high genetic heterogeneity on familial Hirschsprung disease
Q30858361	ExomeAI: detection of recurrent allelic imbalance in tumors using whole-exome sequencing data
Q28654543	Experiences Building Globus Genomics: A Next-Generation Sequencing Analysis Service using Galaxy, Globus, and Amazon Web Services
Q57002165	Experiences in integrated data and research object publishing using GigaDB
Q30987801	Experiences with workflows for automating data-intensive bioinformatics
Q35930289	Experimental analysis of sources of error in evolutionary studies based on Roche/454 pyrosequencing of viral genomes
Q35970261	Experimental flux measurements on a network scale
Q35897576	Exploration of Human Salivary Microbiomes--Insights into the Novel Characteristics of Microbial Community Structure in Caries and Caries-Free Subjects
Q30763134	Explorative search of distributed bio-data to answer complex biomedical questions
Q47104264	Explorative visual analytics on interval-based genomic data and their metadata
Q34058920	Exploratory analysis of genomic segmentations with Segtools
Q34413161	Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome-wide digital gene expression analysis.
Q60919447	Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment
Q35611113	Exploring the sheep rumen microbiome for carbohydrate-active enzymes
Q33906952	Exposure to hycanthone alters chromatin structure around specific gene functions and specific repeats in Schistosoma mansoni
Q64448563	Expression of Adhesive Pili and the Collagen-Binding Adhesin Ace Is Activated by ArgR Family Transcription Factors in Enterococcus faecalis
Q36545552	Expression of young HERV-H loci in the course of colorectal carcinoma and correlation with molecular subtypes
Q33974147	ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data
Q55261640	Extensive screening of microRNA populations identifies hsa-miR-375 and hsa-miR-133a-3p as selective markers for human rectal and colon cancer.
Q35161360	FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections.
Q34417579	FLI1 expression is correlated with breast cancer cellular growth, migration, and invasion and altered gene expression.
Q47302166	FROGS: Find, Rapidly, OTUs with Galaxy Solution.
Q93025673	FROM DESKTOP TO LARGE-SCALE MODEL EXPLORATION WITH SWIFT/T
Q33866995	Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny.
Q36720600	Fecal microbiota composition differs between children with β-cell autoimmunity and those without
Q31162688	Fibronectin and androgen receptor expression data in prostate cancer obtained from a RNA-sequencing bioinformatics analysis
Q36170695	Fine Mapping of a Dravet Syndrome Modifier Locus on Mouse Chromosome 5 and Candidate Gene Analysis by RNA-Seq
Q90599267	Fine-Grained Provenance for Matching & ETL
Q57661560	FireWorks: a dynamic workflow system designed for high-throughput applications
Q35319061	Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework
Q52310730	Flexible metagenome analysis using the MGX framework.
Q34321600	Fluorescence-based phenotypic selection allows forward genetic screens in haploid human cells
Q46242285	Formate hydrogenlyase and formate secretion ameliorate H2 inhibition in the hyperthermophilic archaeon Thermococcus paralvinellae
Q92859715	Forward Genetic Screen for Caenorhabditis elegans Mutants with a Shortened Locomotor Healthspan
Q30040556	Forward Genetics by Genome Sequencing Reveals That Rapid Cyanide Release Deters Insect Herbivory of Sorghum bicolor
Q35909543	Four broad temperament dimensions: description, convergent validation correlations, and comparison with the Big Five
Q40812076	Frequency and mitotic heritability of epimutations in Schistosoma mansoni
Q28647341	From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics
Q35527797	From benchtop to desktop: important considerations when designing amplicon sequencing workflows
Q36668920	From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software
Q34193716	From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems
Q40222639	FuMa: reporting overlap in RNA-seq detected fusion genes.
Q30935358	Fully automated pipeline for detection of sex linked genes using RNA-Seq data.
Q35108627	Functional analysis of C1 family cysteine peptidases in the larval gut of Тenebrio molitor and Tribolium castaneum
Q35590286	Functional and mechanistic studies of XPC DNA-repair complex as transcriptional coactivator in embryonic stem cells
Q37825465	Functional genomics of the brain: uncovering networks in the CNS using a systems approach
Q38705097	Functional interrelationship between TFII-I and E2F transcription factors at specific cell cycle gene loci
Q38930208	Functional redundancy in the nuclear compartmentalization of the late-replicating genome
Q61810756	Functional screening for triclosan resistance in a wastewater metagenome and isolates of Escherichia coli and Enterococcus spp. from a large Canadian healthcare region
Q33694702	Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes
Q36180589	Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology.
Q92153081	Fungal and Bacterial Communities Exhibit Consistent Responses to Reversal of Soil Acidification and Phosphorus Limitation over Time
Q38949047	Fungal compositions and diversities on indoor surfaces with visible mold growths in residential buildings in the Seoul Capital Area of South Korea
Q38228039	Fungal model systems and the elucidation of pathogenicity determinants
Q34273644	FusionAnalyser: a new graphical, event-driven tool for fusion rearrangements discovery
Q34089185	GCAT-SEEKquence: genome consortium for active teaching of undergraduates through increased faculty access to next-generation sequencing data
Q42129608	GRHL3 binding and enhancers rearrange as epidermal keratinocytes transition between functional states.
Q34350973	GRHL3/GET1 and trithorax group members collaborate to activate the epidermal progenitor differentiation program
Q38811023	GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome
Q27315849	GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research
Q42036390	Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics.
Q36967209	Galaxy Portal: interacting with the galaxy platform through mobile devices
Q28595781	Galaxy Workflows for Web-based Bioinformatics Analysis of Aptamer High-throughput Sequencing Data
Q37219358	Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology
Q37424925	Galaxy tools to study genome diversity.
Q31049058	Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data
Q28536855	Gathering and exploring scientific knowledge in pharmacovigilance
Q33844633	GeCo++: a C++ library for genomic features computation and annotation in the presence of variants
Q36375736	GeMSTONE: orchestrated prioritization of human germline mutations in the cloud
Q39436207	Gene Array Analyzer: alternative usage of gene arrays to study alternative splicing events
Q37567970	Gene conversion events and variable degree of homogenization of rDNA loci in cultivars of Brassica napus
Q35902166	Gene expression profiling in necrotizing enterocolitis reveals pathways common to those reported in Crohn's disease
Q35860667	Gene network inference and visualization tools for biologists: application to new human transcriptome datasets.
Q90006461	Gene silencing by double-stranded RNA from C. elegans neurons reveals functional mosaicism of RNA interference
Q37595144	Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota
Q30686301	GeneProf data: a resource of curated, integrated and reusable high-throughput genomics experiments
Q83150406	GeneProf: analysis of high-throughput sequencing experiments
Q29547401	Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data
Q36029976	Generation of a synthetic GlcNAcylated nucleosome reveals regulation of stability by H2A-Thr101 GlcNAcylation
Q41074730	Genes related to antioxidant metabolism are involved in Methylobacterium mesophilicum-soybean interaction
Q35113112	Genetic dissection of Anopheles gambiae gut epithelial responses to Serratia marcescens
Q33944213	Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)
Q40238692	Genetic hurdles limit the arms race between Prochlorococcus and the T7-like podoviruses infecting them
Q39104263	Genetic predisposition to high anxiety- and depression-like behavior coincides with diminished DNA methylation in the adult rat amygdala.
Q91193621	Genetic stability of a Newcastle disease virus vectored infectious laryngotracheitis virus vaccine after serial passages in chicken embryos
Q30887423	GenoMetric Query Language: a novel approach to large-scale genomic data management.
Q35608246	Genome Sequence of Bacillus thuringiensis Strain Btm27, an Egyptian Isolate Highly Toxic to Cotton Leafworm
Q60912691	Genome Sequences of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Type t899 Strains Belonging to Three Different Sequence Types (ST398, ST9, and ST4034)
Q33361050	Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins
Q55426160	Genome data uncover four synergistic key regulators for extremely small body size in horses.
Q28709882	Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory
Q41577565	Genome sequences of two freshwater betaproteobacterial isolates, Limnohabitans species strains Rim28 and Rim47, indicate their capabilities as both photoautotrophs and ammonia oxidizers.
Q40211764	Genome-Wide Survey of Pseudomonas aeruginosa PA14 Reveals a Role for the Glyoxylate Pathway and Extracellular Proteases in the Utilization of Mucin.
Q36378673	Genome-Wide Transcriptional Profiling and Metabolic Analysis Uncover Multiple Molecular Responses of the Grass Species Lolium perenne Under Low-Intensity Xenobiotic Stress.
Q33863233	Genome-guided transcriptome assembly in the age of next-generation sequencing
Q50676759	Genome-wide Chromatin Mapping Defines AP2α in the Etiology of Craniofacial Disorders
Q47142220	Genome-wide DNase hypersensitivity, and occupancy of RUNX2 and CTCF reveal a highly dynamic gene regulome during MC3T3 pre-osteoblast differentiation
Q54220039	Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells.
Q35906122	Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion
Q57794275	Genome-wide analyses of miniature inverted-repeat transposable elements reveals new insights into the evolution of the Triticum-Aegilops group
Q54285779	Genome-wide analysis of Stowaway-like MITEs in wheat reveals high sequence conservation, gene association, and genomic diversification.
Q41514063	Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon.
Q34569617	Genome-wide analysis of human hotspot intersected genes highlights the roles of meiotic recombination in evolution and disease
Q36180219	Genome-wide analysis of p63 binding sites identifies AP-2 factors as co-regulators of epidermal differentiation
Q35134867	Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators.
Q37138522	Genome-wide association meta-analysis in Chinese and European individuals identifies ten new loci associated with systemic lupus erythematosus
Q34968567	Genome-wide association of mediator and RNA polymerase II in wild-type and mediator mutant yeast
Q40165187	Genome-wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress
Q35576105	Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line.
Q34649734	Genome-wide determinants of proviral targeting, clonal abundance and expression in natural HTLV-1 infection
Q36561507	Genome-wide endogenous DAF-16/FOXO recruitment dynamics during lowered insulin signalling in C. elegans
Q35131055	Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED.
Q37550517	Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene.
Q34660264	Genome-wide identification of Bacillus subtilis CodY-binding sites at single-nucleotide resolution
Q46554107	Genome-wide identification of novel genetic markers from RNA sequencing assembly of diverse Aegilops tauschii accessions
Q34356312	Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data
Q35588273	Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem
Q53073432	Genome-wide mutant profiling predicts the mechanism of a Lipid II binding antibiotic.
Q35956064	Genome-wide occupancy links Hoxa2 to Wnt-β-catenin signaling in mouse embryonic development
Q35667041	Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq.
Q34272305	Genome-wide recruitment to Polycomb-modified chromatin and activity regulation of the synovial sarcoma oncogene SYT-SSX2.
Q34760829	Genome-wide small RNA sequencing and gene expression analysis reveals a microRNA profile of cancer susceptibility in ATM-deficient human mammary epithelial cells.
Q33355813	Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy.
Q41722329	GenomeCons: a web server for manipulating multiple genome sequence alignments and their consensus sequences
Q35708487	GenomeRunner: automating genome exploration
Q36655724	Genome Sequences and Photosynthesis Gene Cluster Composition of a Freshwater Aerobic Anoxygenic Phototroph, Sandarakinorhabdus sp. Strain AAP62, Isolated from the Shahu Lake in Ningxia, China
Q46283374	Genomic Approaches to Analyze Alternative Splicing, A Key Regulator of Transcriptome and Proteome Diversity in Brachypodium distachyon.
Q38384099	Genomic Database Searching
Q36100788	Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals.
Q30828686	Genomic V exons from whole genome shotgun data in reptiles
Q39784125	Genomic analysis of mouse VL30 retrotransposons
Q42745731	Genomic data integration for ecological and evolutionary traits in non-model organisms
Q64376819	Genomic functions of developmental pluripotency associated factor 4 (Dppa4) in pluripotent stem cells and cancer
Q33801920	Genomic landscape of human, bat, and ex vivo DNA transposon integrations
Q28608430	Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud
Q60321312	Genomics of Phenotypic Plasticity in Aphids
Q30410093	Genomics: moving behavioural ecology beyond the phenotypic gambit
Q35388414	Genotype and cardiovascular phenotype correlations with TBX1 in 1,022 velo-cardio-facial/DiGeorge/22q11.2 deletion syndrome patients
Q34307655	Genotype of a historic strain of Mycobacterium tuberculosis
Q30487960	GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development.
Q35811393	Getting a full dose? Reconsidering sex chromosome dosage compensation in the silkworm, Bombyx mori
Q28657885	GigaDB: promoting data dissemination and reproducibility
Q64057626	Gigwa v2-Extended and improved genotype investigator
Q28547186	Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax
Q40639982	Global Tn-seq analysis of carbohydrate utilization and vertebrate infectivity of Borrelia burgdorferi
Q33419895	Global analysis of posttranscriptional regulation by GlmY and GlmZ in enterohemorrhagic Escherichia coli O157:H7
Q34389954	Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression
Q34058172	Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation
Q35122804	Global patterns of abundance, diversity and community structure of the Aminicenantes (candidate phylum OP8)
Q39076535	Global transcriptomic profiling in barramundi (Lates calcarifer) from rivers impacted by differing agricultural land uses
Q36199705	Glucose Starvation Alters Heat Shock Response, Leading to Death of Wild Type Cells and Survival of MAP Kinase Signaling Mutant.
Q28681837	GnpIS: an information system to integrate genetic and genomic data from plants and fungi
Q30660958	GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data
Q37171115	Groups: knowledge spreadsheets for symbolic biocomputing
Q64101576	Growth Kinetics, Carbon Isotope Fractionation, and Gene Expression in the Hyperthermophile during Hydrogen-Limited Growth and Interspecies Hydrogen Transfer
Q38297316	Guanine polynucleotides are self-antigens for human natural autoantibodies and are significantly reduced in the human genome
Q30671351	Guide: a desktop application for analysing gene expression data
Q35030160	Gut Lactobacillales are associated with higher CD4 and less microbial translocation during HIV infection
Q35847815	H2O2 production rate in Lactobacillus johnsonii is modulated via the interplay of a heterodimeric flavin oxidoreductase with a soluble 28 Kd PAS domain containing protein
Q38904000	H3 ubiquitination by NEDD4 regulates H3 acetylation and tumorigenesis
Q24294721	HIF1A employs CDK8-mediator to stimulate RNAPII elongation in response to hypoxia
Q90716768	HaTSPiL: A modular pipeline for high-throughput sequencing data analysis
Q30009105	Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets.
Q93223313	Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition
Q28969528	Harnessing Big Data for Systems Pharmacology
Q42200402	Harnessing cloud computing with Galaxy Cloud
Q38593158	Helitrons shaping the genomic architecture of Drosophila: enrichment of DINE-TR1 in α- and β-heterochromatin, satellite DNA emergence, and piRNA expression
Q37258798	Heme acquisition in the parasitic filarial nematode Brugia malayi
Q28111713	Hepatitis C virus RNA functionally sequesters miR-122
Q35682554	Heterologous expression and transcript analysis of gibberellin biosynthetic genes of grasses reveals novel functionality in the GA3ox family
Q35089644	HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization
Q31152971	HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking
Q34224677	Hidden treasures in unspliced EST data
Q64965726	High Resolution Mapping of Rph MBR1012 Conferring Resistance to Puccinia hordei in Barley (Hordeum vulgare L.).
Q35574840	High level of fecal calprotectin at age 2 months as a marker of intestinal inflammation predicts atopic dermatitis and asthma by age 6.
Q27026983	High throughput sequencing approaches to mutation discovery in the mouse
Q30856812	High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis.
Q51323498	High-Resolution Genome-Wide Mapping of Nucleosome Positioning and Occupancy Level Using Paired-End Sequencing Technology
Q36245801	High-Throughput Cloning of Temperature-Sensitive Caenorhabditis elegans Mutants with Adult Syncytial Germline Membrane Architecture Defects
Q36185593	High-Throughput Parallel Sequencing to Measure Fitness of Leptospira interrogans Transposon Insertion Mutants during Acute Infection.
Q34569184	High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology
Q48240056	High-resolution TADs reveal DNA sequences underlying genome organization in flies.
Q42151086	High-resolution genome-wide mapping of the primary structure of chromatin
Q47667039	High-throughput Parallel Sequencing to Measure Fitness of Leptospira interrogans Transposon Insertion Mutants During Golden Syrian Hamster Infection
Q37734818	High-throughput neuroimaging-genetics computational infrastructure
Q35022826	High-throughput sequencing of islet-infiltrating memory CD4+ T cells reveals a similar pattern of TCR Vβ usage in prediabetic and diabetic NOD mice
Q47551736	Higher sequence diversity in the vaginal tract than in blood at early HIV-1 infection.
Q33705946	Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.).
Q58708467	Highly efficient genome editing via CRISPR-Cas9 in human pluripotent stem cells is achieved by transient BCL-XL overexpression
Q46638570	Highly efficient heritable plant genome engineering using Cas9 orthologues from Streptococcus thermophilus and Staphylococcus aureus
Q36182106	Hippo signaling influences HNF4A and FOXA2 enhancer switching during hepatocyte differentiation
Q50762485	Histone acetyltransferase cofactor Trrap maintains self-renewal and restricts differentiation of embryonic stem cells.
Q55176668	Histone methylation changes are required for life cycle progression in the human parasite Schistosoma mansoni.
Q40867896	Histone methyltransferase Setd8 represses Gata2 expression and regulates erythroid maturation
Q37327621	Homology-mediated end-capping as a primary step of sister chromatid fusion in the breakage-fusion-bridge cycles
Q47098837	Host Genetic Variation Does Not Determine Spatio-Temporal Patterns of European Bat 1 Lyssavirus
Q37574219	Hox in motion: tracking HoxA cluster conformation during differentiation
Q38914351	Hoxa2 selectively enhances Meis binding to change a branchial arch ground state.
Q21563355	Hsp70-Hsp40 chaperone complex functions in controlling polarized growth by repressing Hsf1-driven heat stress-associated transcription
Q34105820	HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data
Q38794889	Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy
Q46259543	Human accelerated regions and other human-specific sequence variations in the context of evolution and their relevance for brain development
Q50882156	Hypoxia-Sensitive COMMD1 Integrates Signaling and Cellular Metabolism in Human Macrophages and Suppresses Osteoclastogenesis
Q58606523	I-SceI Meganuclease-mediated transgenesis in the acorn worm, Saccoglossus kowalevskii
Q34733135	IL-22-producing CD4+ cells are depleted in actively inflamed colitis tissue
Q52579987	IRProfiler - a software toolbox for high throughput immune receptor profiling.
Q47201380	IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform.
Q24701803	Identification and Characterization of Two Novel RNA Viruses from Anopheles gambiae Species Complex Mosquitoes
Q36518693	Identification and Complete Genome Sequence Analysis of a Genotype XIV Newcastle Disease Virus from Nigeria.
Q91725799	Identification and Quantification of Proteoforms by Mass Spectrometry
Q30559452	Identification and analysis of pig chimeric mRNAs using RNA sequencing data
Q46314363	Identification and characterization of a subtelomeric satellite DNA in Callitrichini monkeys
Q64109857	Identification and characterization of core abscisic acid (ABA) signaling components and their gene expression profile in response to abiotic stresses in Setaria viridis
Q35607096	Identification and characterization of rye genes not expressed in allohexaploid triticale
Q36667419	Identification of CodY targets in Bacillus anthracis by genome-wide in vitro binding analysis
Q30983929	Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data
Q40046347	Identification of a mouse Lactobacillus johnsonii strain with deconjugase activity against the FXR antagonist T-β-MCA.
Q30979217	Identification of a new marine algal species Pyropia nitida sp. nov. (Bangiales: Rhodophyta) from Monterey, California
Q58740126	Identification of a novel enhancer/chromatin opening element associated with high-level γ-globin gene expression
Q41127839	Identification of antisense long noncoding RNAs that function as SINEUPs in human cells
Q45326646	Identification of candidate effector genes in the transcriptome of the rice root knot nematode Meloidogyne graminicola.
Q61445099	Identification of candidate neoantigens produced by fusion transcripts in human osteosarcomas
Q35740642	Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites
Q35617343	Identification of cis-regulatory sequence variations in individual genome sequences
Q35125183	Identification of genes differentially expressed in myogenin knock-down bovine muscle satellite cells during differentiation through RNA sequencing analysis
Q37734734	Identification of in vivo regulators of the Vibrio cholerae xds gene using a high-throughput genetic selection
Q40612005	Identification of miRNAs in Bovine Endometrium through RNAseq and Prediction of Regulated Pathways
Q35089615	Identification of mutations in zebrafish using next-generation sequencing
Q30749239	Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases
Q40411649	Identification of sRNA interacting with a transcript of interest using MS2-affinity purification coupled with RNA sequencing (MAPS) technology
Q37126629	Identification of shared TCR sequences from T cells in human breast cancer using emulsion RT-PCR
Q28114916	Identification of the BRD1 interaction network and its impact on mental disorder risk
Q51051029	Identification of unknown RNA partners using MAPS.
Q28552694	Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla
Q31125439	Identifying Regions Enriched in a ChIP-seq Data Set (Peak Finding).
Q34114670	Identifying elemental genomic track types and representing them uniformly
Q35022839	Identifying genes relevant to specific biological conditions in time course microarray experiments.
Q45906516	IgH loci of American alligator and saltwater crocodile shed light on IgA evolution.
Q37193174	Immune cell-specific transcriptional profiling highlights distinct molecular pathways controlled by Tob1 upon experimental autoimmune encephalomyelitis
Q34360686	Immune response of the Caribbean sea fan, Gorgonia ventalina, exposed to an Aplanochytrium parasite as revealed by transcriptome sequencing
Q57476539	Immune-suppression by OsHV-1 viral infection causes fatal bacteraemia in Pacific oysters
Q35509152	ImmunoGlobulin galaxy (IGGalaxy) for simple determination and quantitation of immunoglobulin heavy chain rearrangements from NGS
Q45976658	Immunoglobulin genes of the turtles.
Q42210618	Immunoglobulin heavy chains in medaka (Oryzias latipes).
Q33931390	Immunoglobulin light chains in medaka (Oryzias latipes)
Q36304147	Immunoinformatics and epitope prediction in the age of genomic medicine
Q35461867	Impact of analytic provenance in genome analysis
Q36115147	Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST.
Q46941770	Impact of primer choice on characterization of orchid mycorrhizal communities using 454 pyrosequencing
Q44754408	Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression.
Q47151248	Impact of the G84E variant on HOXB13 gene and protein expression in formalin-fixed, paraffin-embedded prostate tumours.
Q61883689	Impacts of a reduction in seawater pH mimicking ocean acidification on the structure and diversity of mycoplankton communities
Q90261799	Impacts of environmental complexity on respiratory and gut microbiome community structure and diversity in growing pigs
Q35178920	Implementation of Cloud based next generation sequencing data analysis in a clinical laboratory.
Q42557646	Improved binding site assignment by high-resolution mapping of RNA-protein interactions using iCLIP
Q34173632	Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information
Q39337607	Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias.
Q30491434	Improving data workflow systems with cloud services and use of open data for bioinformatics research.
Q42641947	Improving mRNA 5' coding sequence determination in the mouse genome
Q37291312	In Utero Caffeine Exposure Induces Transgenerational Effects on the Adult Heart
Q41748778	In Vitro selection of Neisseria gonorrhoeae mutants with elevated MIC values and increased resistance to cephalosporins
Q94471967	In memory of James Taylor: the birth of Galaxy
Q38831897	In silico dissection of miRNA targetome polymorphisms and their role in regulating miRNA-mediated gene expression in esophageal cancer.
Q38169846	In silico to in vivo splicing analysis using splicing code models
Q46468013	In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids.
Q41654100	In vitro reconstitution demonstrates the cell wall ligase activity of LCP proteins
Q64066504	In-depth human plasma proteome analysis captures tissue proteins and transfer of protein variants across the placenta
Q30536439	InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor
Q38260979	Incorporating computational resources in a cancer research program
Q37708268	Increased genomic burden of germline copy number variants is associated with early onset breast cancer: Australian breast cancer family registry
Q35904251	Increasing the Richness of Culturable Arsenic-Tolerant Bacteria from Theonella swinhoei by Addition of Sponge Skeleton to the Growth Medium
Q48147324	Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system
Q88348980	Inflammatory pathways are central to posterior cerebrovascular artery remodelling prior to the onset of congenital hypertension
Q35589786	Influence of a non-hospital medical care facility on antimicrobial resistance in wastewater
Q37620745	Influences of pH and Iron Concentration on the Salivary Microbiome in Individual Humans with and without Caries
Q40190073	Insect pathogenic fungus interacts with the gut microbiota to accelerate mosquito mortality.
Q38784610	Insect phylogenetics in the digital age.
Q39093572	Insight into the Genome of Brochothrix thermosphacta, a Problematic Meat Spoilage Bacterium.
Q34485099	Insulator function and topological domain border strength scale with architectural protein occupancy
Q37075888	Integrated genome browser: visual analytics platform for genomics
Q39960763	Integrated whole-genome sequencing and temporospatial analysis of a continuing Group A Streptococcus epidemic
Q91750411	Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks
Q28236549	Integrating diverse databases into an unified analysis framework: a Galaxy approach
Q35413415	Integrating omics technologies to study pulmonary physiology and pathology at the systems level
Q31116335	Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases
Q36354909	Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes
Q36871546	Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo.
Q37267384	Integration of genomic and functional approaches reveals enhancers at LMX1A and LMX1B
Q50732745	Integration-free induced pluripotent stem cells model genetic and neural developmental features of down syndrome etiology
Q42089762	Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse.
Q90371866	Integrative analysis of gut microbiome and metabolites revealed novel mechanisms of intestinal Salmonella carriage in chicken
Q30571380	InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data
Q35490223	Interaction between conjugative and retrotransposable elements in horizontal gene transfer
Q90715096	Interactions between antenatal sulfadoxine-pyrimethamine, drug-resistant Plasmodium falciparum parasites and delivery outcomes in Malawi
Q91742776	Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps
Q34036161	Interactive metagenomic visualization in a Web browser
Q35791522	Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease
Q62776588	Interoperable and scalable data analysis with microservices: Applications in Metabolomics
Q64113894	Interoperable and scalable data analysis with microservices: Applications in Metabolomics
Q55412306	Interplay of cell-cell contacts and RhoA/MRTF-A signaling regulates cardiomyocyte identity.
Q59798945	Intestinal Microbiome in Irritable Bowel Syndrome before and after Gut-Directed Hypnotherapy
Q57738908	Introducing DNA-based methods to compare fungal microbiota and concentrations in indoor, outdoor, and personal air
Q28597874	Investigating core genetic-and-epigenetic cell cycle networks for stemness and carcinogenic mechanisms, and cancer drug design using big database mining and genome-wide next-generation sequencing data
Q33901207	Investigating reproducibility and tracking provenance - A genomic workflow case study
Q42773885	Investigation of JAKs/STAT-3 in lipopolysaccharide-induced intestinal epithelial cells
Q40981648	In Vivo Regulation of the Zebrafish Endoderm Progenitor Niche by T-Box Transcription Factors
Q36648689	Isolation of a Hypomorphic skn-1 Allele That Does Not Require a Balancer for Maintenance
Q35747690	JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing
Q57002856	Jetstream
Q35802549	Jflow: a workflow management system for web applications
Q36380048	Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers.
Q55739128	KREAP: an automated Galaxy platform to quantify in vitro re-epithelialization kinetics
Q37000950	Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets
Q30301170	Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history
Q90391244	Kin28 depletionincreases association of TFIID subunits Taf1 and Taf4 with promoters in Saccharomyces cerevisiae
Q39681001	Knockdown of DNA methyltransferase 3a alters gene expression and inhibits function of embryonic cardiomyocytes
Q37229186	KnowEnG: a knowledge engine for genomics.
Q38430223	Kronos: a workflow assembler for genome analytics and informatics
Q42367988	LMO2 is required for TAL1 DNA binding activity and initiation of definitive haematopoiesis at the haemangioblast stage.
Q36225338	Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts
Q35635739	Large-scale discovery of enhancers from human heart tissue
Q37579830	Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline
Q38475800	Leaf phenomics: a systematic reverse genetic screen for Arabidopsis leaf mutants
Q57234033	Lessons learned from Galaxy, a Web-based platform for high-throughput genomic analyses
Q34782992	Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data
Q28658731	Leveraging the national cyberinfrastructure for biomedical research
Q35794357	Library Construction for Mutation Identification by Whole-Genome Sequencing
Q38160843	Life at high salt concentrations, intracellular KCl concentrations, and acidic proteomes
Q57716967	Life science data analysis workflow development using the bioextract server leveraging the iPlant collaborative cyberinfrastructure
Q90592172	Light affects tissue patterning of the hypocotyl in the shade-avoidance response
Q41620260	Lineage overwhelms environmental conditions in determining rhizosphere bacterial community structure in a cosmopolitan invasive plant
Q90219807	Linkage analysis and whole exome sequencing reveals AHNAK2 as a novel genetic cause for autosomal recessive CMT in a Malaysian family
Q37483033	Localization and Transcriptional Responses of Chrysoporthe austroafricana in Eucalyptus grandis Identify Putative Pathogenicity Factors.
Q91979174	Long non-coding RNA LncKdm2b regulates cortical neuronal differentiation by cis-activating Kdm2b
Q34670147	Long-range transcriptional regulation by the p110 CUX1 homeodomain protein on the ENCODE array
Q92264584	Loss of RNA Chaperone Hfq Unveils a Toxic Pathway in Pseudomonas aeruginosa
Q30854061	Lost in plasmids: next generation sequencing and the complex genome of the tick-borne pathogen Borrelia burgdorferi
Q36249999	Low temperature MBBR nitrification: Microbiome analysis
Q39294303	Low-grade and high-grade mammary carcinomas in WAP-T transgenic mice are independent entities distinguished by Met expression
Q28709381	MAPI: a software framework for distributed biomedical applications
Q39744452	MIRPIPE: quantification of microRNAs in niche model organisms
Q34452175	MOCAT: a metagenomics assembly and gene prediction toolkit
Q33662599	MOIRAI: a compact workflow system for CAGE analysis
Q37283260	MS-GF+ makes progress towards a universal database search tool for proteomics
Q28243703	Making whole genome multiple alignments usable for biologists
Q39022639	Male breast cancer precursor lesions: analysis of the EORTC 10085/TBCRC/BIG/NABCG International Male Breast Cancer Program
Q37485567	Male-Specific Transcription Factor Occupancy Alone Does Not Account for Differential Methylation at Imprinted Genes in the mouse Germ Cell Lineage.
Q27024732	Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectives
Q30572370	Mapping genetic modifiers of survival in a mouse model of Dravet syndrome
Q41545459	Mapping mutations in plant genomes with the user-friendly web application CandiSNP.
Q35541535	Mapping regulatory factors by immunoprecipitation from native chromatin
Q35870178	Mapping the CgrA regulon of Rhodospirillum centenum reveals a hierarchal network controlling Gram-negative cyst development.
Q27683918	Marine Rhodobacteraceae L-haloacid dehalogenase contains a novel His/Glu dyad that could activate the catalytic water
Q28583278	Marine and giant viruses as indicators of a marine microbial community in a riverine system
Q52567289	Maser: one-stop platform for NGS big data from analysis to visualization.
Q35008829	Massive depletion of bovine leukemia virus proviral clones located in genomic transcriptionally active sites during primary infection
Q52595091	Matchmaking in Bioinformatics.
Q37435273	MathIOmica: An Integrative Platform for Dynamic Omics
Q36642236	Mature microsatellites: mechanisms underlying dinucleotide microsatellite mutational biases in human cells
Q43343973	Meso and micro-scale response of post carbon removal nitrifying MBBR biofilm across carrier type and loading
Q38977206	Meta-Analysis of Arabidopsis KANADI1 Direct Target Genes Identifies a Basic Growth-Promoting Module Acting Upstream of Hormonal Signaling Pathways
Q30883144	MetaDB a Data Processing Workflow in Untargeted MS-Based Metabolomics Experiments.
Q37678008	MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets
Q36357346	MetaGenSense: A web-application for analysis and exploration of high throughput sequencing metagenomic data
Q38404566	MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation
Q50035710	Metabolomics of tomato xylem sap during bacterial wilt reveals Ralstonia solanacearum produces abundant putrescine, a metabolite that accelerates wilt disease.
Q35557728	Metagenomic biomarker discovery and explanation
Q35009233	Metagenomic profiling of antibiotic resistance genes and mobile genetic elements in a tannery wastewater treatment plant
Q26747593	Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis
Q30953199	Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies
Q35658689	Metaproteomic analysis using the Galaxy framework.
Q31112255	Metaproteomic data analysis at a glance: advances in computational microbial community proteomics
Q35162769	Metatranscriptome of an anaerobic benzene-degrading, nitrate-reducing enrichment culture reveals involvement of carboxylation in benzene ring activation
Q28114487	Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data
Q35837242	Methanosarcina Play an Important Role in Anaerobic Co-Digestion of the Seaweed Ulva lactuca: Taxonomy and Predicted Metabolism of Functional Microbial Communities
Q26766083	Methodological challenges and analytic opportunities for modeling and interpreting Big Healthcare Data
Q36539328	Methylated microRNA genes of the developing murine palate
Q41471467	MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution
Q52671205	MicroRNA duplication accelerates the recruitment of new targets during vertebrate evolution.
Q38709130	MicroRNA signatures associated with thioacetamide-induced liver fibrosis in mice
Q21245309	Microarrays, deep sequencing and the true measure of the transcriptome
Q35749049	Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula.
Q35889138	Microbial and Functional Diversity within the Phyllosphere of Espeletia Species in an Andean High-Mountain Ecosystem.
Q28081332	Microbial bioinformatics for food safety and production
Q34735225	Microbial diversity analysis of fermented mung beans (Lu-Doh-Huang) by using pyrosequencing and culture methods
Q39411191	Microbial diversity within the Trichodesmium holobiont
Q35944035	Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients
Q35818694	Microbiome shifts and the inhibition of quorum sensing by Black Band Disease cyanobacteria.
Q34525116	Microbiota diversity and gene expression dynamics in human oral biofilms
Q33739450	Microbiota-induced peritrophic matrix regulates midgut homeostasis and prevents systemic infection of malaria vector mosquitoes.
Q35929472	Microdissection of lampbrush chromosomes as an approach for generation of locus-specific FISH-probes and samples for high-throughput sequencing
Q28540820	Microsatellite interruptions stabilize primate genomes and exist as population-specific single nucleotide polymorphisms within individual human genomes
Q34583957	Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements
Q40275733	Minimally destructive sampling of type specimens of Pyropia (Bangiales, Rhodophyta) recovers complete plastid and mitochondrial genomes
Q46255546	Misexpression of Tbx18 in cardiac chambers of fetal mice interferes with chamber-specific developmental programs but does not induce a pacemaker-like gene signature
Q89306618	Mitochondrial DNA Variation and Heteroplasmy in Monozygotic Twins Clinically Discordant for Multiple Sclerosis
Q39140349	Mitochondrial DNA sequence and phylogenetic evaluation of geographically disparate Sus scrofa breeds.
Q30360077	Mitochondrial DNA, restoring Beethovens music.
Q47207584	Mobilization of Stowaway-like MITEs in newly formed allohexaploid wheat species.
Q33796448	Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics
Q36678678	Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models.
Q36070681	Modulating Molecular Chaperones Improves Mitochondrial Bioenergetics and Decreases the Inflammatory Transcriptome in Diabetic Sensory Neurons
Q34493715	Molecular analyses of juvenile granulosa cell tumors bearing AKT1 mutations provide insights into tumor biology and therapeutic leads.
Q36618241	Molecular classification of anaplastic oligodendroglioma using next-generation sequencing: a report of the prospective randomized EORTC Brain Tumor Group 26951 phase III trial.
Q27329732	Molecular evolution of multiple-level control of heme biosynthesis pathway in animal kingdom
Q38495290	Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach
Q35749760	Molgenis-impute: imputation pipeline in a box
Q57041792	Monitoring of microbial dynamics in a drinking water distribution system using the culture-free, user-friendly, MYcrobiota platform
Q63246327	Mosquito Small RNA Responses to West Nile and Insect-Specific Virus Infections in and Mosquito Cells
Q30826166	Motif-based analysis of large nucleotide data sets using MEME-ChIP.
Q57326733	Mouse Genetic and Phenotypic Resources as Tools for Human Genetics
Q26829673	Mouse Genome Database: From sequence to phenotypes and disease models
Q37057166	Mouse Models of NMNAT1-Leber Congenital Amaurosis (LCA9) Recapitulate Key Features of the Human Disease
Q102058995	Multi-level analysis of reproduction in an Antarctic midge identifies female and male accessory gland products that are altered by larval stress and impact progeny viability
Q30888756	Multi-omic data analysis using Galaxy.
Q40085595	Multi-omics enrichment analysis using the GeneTrail2 web service
Q38755858	Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial.
Q34597785	Multiple influenza A (H3N2) mutations conferring resistance to neuraminidase inhibitors in a bone marrow transplant recipient
Q38305450	Multiple regulatory mechanisms control the expression of the Geobacillus stearothermophilus gene for extracellular xylanase
Q35913042	MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics
Q35993287	MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes.
Q95441508	Mutation in the AP4B1 gene cause hereditary spastic paraplegia type 47 (SPG47)
Q37128670	Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast
Q30444518	Mutations in KARS, encoding lysyl-tRNA synthetase, cause autosomal-recessive nonsyndromic hearing impairment DFNB89
Q52342708	Mutations in PMPCB Encoding the Catalytic Subunit of the Mitochondrial Presequence Protease Cause Neurodegeneration in Early Childhood.
Q28258055	Mutations in the NHEJ component XRCC4 cause primordial dwarfism
Q36106723	Mutations in the Plasmodium falciparum chloroquine resistance transporter, PfCRT, enlarge the parasite's food vacuole and alter drug sensitivities
Q35763834	NCBI BLAST+ integrated into Galaxy.
Q35910335	NEAT: a framework for building fully automated NGS pipelines and analyses
Q28278914	NGS analyses by visualization with Trackster
Q41233070	NGS population genetics analyses reveal divergent evolution of a Lyme Borreliosis agent in Europe and Asia
Q34787758	NGS-Trex: Next Generation Sequencing Transcriptome profile explorer
Q30743446	NGSANE: a lightweight production informatics framework for high-throughput data analysis.
Q34476716	NRE: a tool for exploring neutral loci in the human genome
Q58389953	Nationwide buildings energy research enabled through an integrated data intensive
Q48202968	Natural Variation of Molecular and Morphological Gibberellin Responses.
Q34350802	Nebula--a web-server for advanced ChIP-seq data analysis
Q35789407	Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center
Q34071155	Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs
Q35734661	Neglected role of fungal community composition in explaining variation in wood decay rates.
Q51734245	Neonatal exposure to hyperoxia leads to persistent disturbances in pulmonary histone signatures associated with NOS3 and STAT3 in a mouse model.
Q39297356	Neonatal maternal separation stress elicits lasting DNA methylation changes in the hippocampus of stress-reactive Wistar Kyoto rats
Q57806417	Network of GRAS transcription factors involved in the control of arbuscule development in Lotus japonicus
Q38475233	New insights into polar overdominance in callipyge sheep
Q38014423	Next generation quantitative genetics in plants
Q36375758	Next generation sequence analysis and computational genomics using graphical pipeline workflows
Q34941781	Next generation sequencing analysis of nine Corynebacterium ulcerans isolates reveals zoonotic transmission and a novel putative diphtheria toxin-encoding pathogenicity island
Q51761085	Next-Generation Sequencing Analysis of the Human TCRγδ+ T-Cell Repertoire Reveals Shifts in Vγ- and Vδ-Usage in Memory Populations upon Aging.
Q35950446	Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications.
Q44853811	Next-generation sequencing data interpretation: enhancing reproducibility and accessibility
Q42330162	Next-generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia
Q64108799	Next-generation sequencing-guided identification and reconstruction of antibody CDR combinations from phage selection outputs
Q35799615	Next-generation-based targeted sequencing as an efficient tool for the study of the genetic background in Hirschsprung patients
Q48290835	Nextflow enables reproducible computational workflows
Q35288509	Nfkb1 activation by the E26 transformation-specific transcription factors PU.1 and Spi-B promotes Toll-like receptor-mediated splenic B cell proliferation.
Q34621976	NightShift: NMR shift inference by general hybrid model training--a framework for NMR chemical shift prediction
Q35066023	Nitrifying moving bed biofilm reactor (MBBR) biofilm and biomass response to long term exposure to 1 °C.
Q35648966	No evidence for Fabaceae Gametophytic self-incompatibility being determined by Rosaceae, Solanaceae, and Plantaginaceae S-RNase lineage genes
Q28601391	Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells
Q36374700	Non-canonical TAF complexes regulate active promoters in human embryonic stem cells
Q30742924	Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data
Q37409237	Noncoding Subgenomic Flavivirus RNA Is Processed by the Mosquito RNA Interference Machinery and Determines West Nile Virus Transmission by Culex pipiens Mosquitoes
Q38967649	NorWood: a gene expression resource for evo-devo studies of conifer wood development
Q35686982	Novel Degenerate PCR Method for Whole-Genome Amplification Applied to Peru Margin (ODP Leg 201) Subsurface Samples
Q61500416	Novel Methods for Correcting Next Generation Sequencing Errors in the $$\beta $$ Chain of T Cell Receptors
Q36446199	Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq
Q30590421	Nozzle: a report generation toolkit for data analysis pipelines
Q36814898	OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows
Q63565679	Obesity-associated inflammation promotes angiogenesis and breast cancer via angiopoietin-like 4
Q27324569	Ocular and extraocular expression of opsins in the rhopalium of Tripedalia cystophora (Cnidaria: Cubozoa)
Q30886785	Omics Pipe: a community-based framework for reproducible multi-omics data analysis
Q110949992	On-demand virtual research environments using microservices
Q35001781	Oncogenic mutation profiling in new lung cancer and mesothelioma cell lines
Q61805925	One tool to find them all: a case of data integration and querying in a distributed LIMS platform
Q28650700	Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines
Q27687756	Open source libraries and frameworks for biological data visualisation: a guide for developers
Q28598346	Open source molecular modeling
Q28278187	OpenMS: a flexible open-source software platform for mass spectrometry data analysis
Q24289255	Opinion: Reproducible research can still be wrong: adopting a prevention approach
Q40136060	Opposing roles of Toll-like receptor and cytosolic DNA-STING signaling pathways for Staphylococcus aureus cutaneous host defense.
Q54285098	Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations.
Q37169624	Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes
Q28315778	Optimization of tomographic reconstruction workflows on geographically distributed resources
Q97570307	Optimizing parameter sensitivity analysis of large-scale microscopy image analysis workflows with multilevel computation reuse
Q45753231	Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data
Q28084527	Orchestrating high-throughput genomic analysis with Bioconductor
Q35561953	Organelle DNA rearrangement mapping reveals U-turn-like inversions as a major source of genomic instability in Arabidopsis and humans
Q89531829	Organizing genome engineering for the gigabase scale
Q28657611	Orione, a web-based framework for NGS analysis in microbiology
Q92802028	Oropouche virus cases identified in Ecuador using an optimised qRT-PCR informed by metagenomic sequencing
Q38623694	Overexpression of DEMETER, a DNA demethylase, promotes early apical bud maturation in poplar
Q47577234	P-MartCancer-Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets
Q35053478	PD5: a general purpose library for primer design software.
Q34532804	PFunkel: efficient, expansive, user-defined mutagenesis.
Q34242994	PHYTOCHROME C is an essential light receptor for photoperiodic flowering in the temperate grass, Brachypodium distachyon
Q91473584	PIPE-T: a new Galaxy tool for the analysis of RT-qPCR expression data
Q47122790	PITDB: a database of translated genomic elements.
Q47204760	PIVOT: platform for interactive analysis and visualization of transcriptomics data.
Q35265891	PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme
Q35074751	POMO--Plotting Omics analysis results for Multiple Organisms
Q21133922	PPARG binding landscapes in macrophages suggest a genome-wide contribution of PU.1 to divergent PPARG binding in human and mouse
Q39746910	PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments
Q35171523	PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration
Q63407249	PaDuA: A Python Library for High-Throughput (Phospho)proteomics Data Analysis
Q28708794	Parallel evolutionary dynamics of adaptive diversification in Escherichia coli
Q35195589	Parallel faster-X evolution of gene expression and protein sequences in Drosophila: beyond differences in expression properties and protein interactions
Q57810092	Parallelizing the execution of native data mining algorithms for computational biology
Q28743743	ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia
Q58611540	Partial loss of psychiatric risk gene Mir137 in mice causes repetitive behavior and impairs sociability and learning via increased Pde10a
Q37971380	Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics.
Q92719071	Pathogenicity and transmission of virulent Newcastle disease virus from the 2018-2019 California outbreak and related viruses in young and adult chickens
Q94464356	Pathogenomes of Atypical Non-shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive Phylogenomic Analysis Using Closed Genomes
Q35880903	Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform
Q35604396	Patterns of histone H3 lysine 27 monomethylation and erythroid cell type-specific gene expression
Q56999071	Patterns of natural fungal community assembly during initial decay of coniferous and broadleaf tree logs
Q49024658	PeptideShaker enables reanalysis of MS-derived proteomics data sets.
Q36312190	Peptidomic and transcriptomic profiling of four distinct spider venoms
Q61446744	Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes
Q40322671	PerC Manipulates Metabolism and Surface Antigens in Enteropathogenic Escherichia coli
Q33850998	Performance studies on distributed virtual screening
Q34488242	PeroxiBase: a database for large-scale evolutionary analysis of peroxidases.
Q28744652	Persistence and availability of Web services in computational biology
Q34530068	Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package.
Q109383060	Perspectives on automated composition of workflows in the life sciences
Q35209312	Phage-bacteria network analysis and its implication for the understanding of coral disease
Q36117686	Pharmacoethnicity in Paclitaxel-Induced Sensory Peripheral Neuropathy
Q57278386	PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud
Q61660063	PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud
Q33292411	Phosphorylation regulates FOXC2-mediated transcription in lymphatic endothelial cells
Q34455526	Phylodynamic analysis of clinical and environmental Vibrio cholerae isolates from Haiti reveals diversification driven by positive selection
Q28607149	Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription
Q34559797	Phylogenetic and DNA methylation analysis reveal novel regions of variable methylation in the mouse IAP class of transposons
Q38372719	Phylogenetics of Kingsnakes, Lampropeltis getula Complex (Serpentes: Colubridae), in Eastern North America
Q28683167	Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
Q47397308	PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool
Q91972037	Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines
Q39040171	Planning bioinformatics workflows using an expert system
Q35972059	Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland
Q34532235	Plasmodium falciparum var genes expressed in children with severe malaria encode CIDRα1 domains
Q45915554	Plastid genome instability leads to reactive oxygen species production and plastid-to-nucleus retrograde signaling in Arabidopsis.
Q31148953	Platforms and Pipelines for Proteomics Data Analysis and Management
Q35896543	Pliocene-Pleistocene lineage diversifications in the Eastern Indigo Snake (Drymarchon couperi) in the Southeastern United States
Q44197854	Polycomb Cbx family members mediate the balance between haematopoietic stem cell self-renewal and differentiation.
Q37528887	Polycomb recruitment attenuates retinoic acid-induced transcription of the bivalent NR2F1 gene
Q30848182	Polyglot programming in applications used for genetic data analysis
Q35631187	PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits
Q56981739	Polymorphic NumtS trace human population relationships
Q52836198	Population diversity and adaptive evolution in keratinization genes: impact of environment in shaping skin phenotypes.
Q28547754	Porphyromonas gingivalis Type IX Secretion Substrates Are Cleaved and Modified by a Sortase-Like Mechanism
Q48243209	Positively selected enhancer elements endow osteosarcoma cells with metastatic competence.
Q42609408	Post-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation
Q30834395	Potential Environmental Factors Affecting Oil-Degrading Bacterial Populations in Deep and Surface Waters of the Northern Gulf of Mexico
Q34944670	Potential role of viruses in white plague coral disease
Q34364373	Pou5f1 transcription factor controls zygotic gene activation in vertebrates.
Q21563477	Practical guidelines for the comprehensive analysis of ChIP-seq data
Q26767338	Pre-early functions of bacteriophage T5 and its relatives
Q34558011	Predicting mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies
Q34770821	Prediction of Gene Activity in Early B Cell Development Based on an Integrative Multi-Omics Analysis
Q30581456	Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study
Q30743735	Prevention, diagnosis and treatment of high-throughput sequencing data pathologies
Q34247976	Primates and mouse NumtS in the UCSC Genome Browser
Q34690154	Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial
Q34033294	Prioritizing disease-linked variants, genes, and pathways with an interactive whole-genome analysis pipeline
Q31038696	Proceedings of the Tenth Annual UT-ORNL-KBRIN Bioinformatics Summit 2011.
Q90043893	Programmed Chromosome Deletion in the Ciliate Oxytricha trifallax
Q90029329	Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA
Q57032491	Progression of ductal carcinoma in situ to invasive breast cancer: comparative genomic sequencing
Q28649512	Proliferation of endogenous retroviruses in the early stages of a host germ line invasion
Q36008871	Pronounced and extensive microtubule defects in a Saccharomyces cerevisiae DIS3 mutant.
Q33614650	Properties of human disease genes and the role of genes linked to Mendelian disorders in complex disease aetiology
Q21285082	Protein adaptations in archaeal extremophiles.
Q35314189	ProteoAnnotator--open source proteogenomics annotation software supporting PSI standards.
Q38918710	Proteogenomic studies on cancer drug resistance: towards biomarker discovery and target identification
Q38660073	Proteogenomics approaches for studying cancer biology and their potential in the identification of acute myeloid leukemia biomarkers
Q38670152	Proteogenomics from a bioinformatics angle: A growing field.
Q31041085	Proteome Scale-Protein Turnover Analysis Using High Resolution Mass Spectrometric Data from Stable-Isotope Labeled Plants.
Q35884862	Proteome-wide Identification of Novel Ceramide-binding Proteins by Yeast Surface cDNA Display and Deep Sequencing
Q52692051	Proteomic analysis of the human retina reveals region-specific susceptibilities to metabolic- and oxidative stress-related diseases.
Q57251411	Proteomics
Q59635336	Provenance and data differencing for workflow reproducibility analysis
Q36705958	Pseudo-De Novo Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveal Novel Gene Content
Q33465439	Pseudomonas aeruginosa Biofilm Response and Resistance to Cold Atmospheric Pressure Plasma Is Linked to the Redox-Active Molecule Phenazine
Q28554516	PubMedPortable: A Framework for Supporting the Development of Text Mining Applications
Q42115496	Putting epigenome comparison into practice
Q45013057	QDD version 3.1: a user-friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate
Q61443038	Qresp, a tool for curating, discovering and exploring reproducible scientific papers
Q33663633	Quality control on the frontier
Q41984352	QualitySNPng: a user-friendly SNP detection and visualization tool
Q35060267	Quantifying reproducibility in computational biology: the case of the tuberculosis drugome
Q36202258	Quantitative Transcriptomics Reveals the Growth- and Nutrient-Dependent Response of a Streamlined Marine Methylotroph to Methanol and Naturally Occurring Dissolved Organic Matter.
Q40258161	Quantitative analysis of the tomato nuclear proteome during Phytophthora capsici infection unveils regulators of immunity
Q38284619	Quantitative bacterial transcriptomics with RNA-seq
Q61875313	Quantum chemical meta-workflows in MoSGrid
Q64230137	Queuine links translational control in eukaryotes to a micronutrient from bacteria
Q37514131	RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS.
Q61814916	RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes
Q40067139	RNA Sequencing of Murine Norovirus-Infected Cells Reveals Transcriptional Alteration of Genes Important to Viral Recognition and Antigen Presentation
Q36060828	RNA regulatory networks diversified through curvature of the PUF protein scaffold
Q35541156	RNA-Rocket: an RNA-Seq analysis resource for infectious disease research
Q41918164	RNA-Seq analysis of differential gene expression in electroporated chick embryonic spinal cord.
Q35232930	RNA-Seq analysis reveals a six-gene SoxR regulon in Streptomyces coelicolor
Q34209332	RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts
Q36367279	RNA-mediated paternal heredity of diet-induced obesity and metabolic disorders
Q59280342	RNA-seq analysis in forest tree species: bioinformatic problems and solutions
Q28684802	RNA-seq analysis of single bovine blastocysts
Q45721922	RNA-seq and Tn-seq reveal fitness determinants of vancomycin-resistant Enterococcus faecium during growth in human serum
Q36732466	RNA-seq-based mapping and candidate identification of mutations from forward genetic screens
Q38443525	RNA-sequencing profiles hippocampal gene expression in a validated model of cancer-induced depression.
Q35167784	RNAbrowse: RNA-Seq de novo assembly results browser
Q39174680	RNAi-mediated endogene silencing in strawberry fruit: detection of primary and secondary siRNAs by deep sequencing.
Q35810270	RSAT 2015: Regulatory Sequence Analysis Tools.
Q56894370	RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting
Q27322512	RSR-2, the Caenorhabditis elegans ortholog of human spliceosomal component SRm300/SRRM2, regulates development by influencing the transcriptional machinery
Q57248452	RUbioSeq+: An Application that Executes Parallelized Pipelines to Analyse Next-Generation Sequencing Data
Q36238101	Rampant software errors may undermine scientific results
Q35081115	Random or stochastic monoallelic expressed genes are enriched for neurodevelopmental disorder candidate genes.
Q35618848	Rapid and efficient human mutation detection using a bench-top next-generation DNA sequencer
Q30870516	Rapid evaluation and quality control of next generation sequencing data with FaQCs.
Q34317507	Rapid genome-scale mapping of chromatin accessibility in tissue
Q46465136	Rapid identification of causal mutations in tomato EMS populations via mapping-by-sequencing.
Q30447155	Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing
Q36272490	Rapid start-up of nitrifying MBBRs at low temperatures: nitrification, biofilm response and microbiome analysis
Q34488679	Rapid transcriptome characterization and parsing of sequences in a non-model host-pathogen interaction; pea-Sclerotinia sclerotiorum
Q51102391	Rare germline copy number deletions of likely functional importance are implicated in endometrial cancer predisposition
Q64039390	Rare missense variants in the ALPK1 gene may predispose to periodic fever, aphthous stomatitis, pharyngitis and adenitis (PFAPA) syndrome
Q35425270	Rare nonsynonymous variants in alpha-4 nicotinic acetylcholine receptor gene protect against nicotine dependence
Q38482790	Rates of evolution of hominoid seminal proteins are correlated with function and expression, rather than mating system
Q38840691	ReGaTE: Registration of Galaxy Tools in Elixir.
Q106196264	Realizing virtual research environments for the agri‐food community: The AGINFRA PLUS experience
Q57716950	Recipes 2.0: building for today and tomorrow
Q41959212	Recognition memory-induced gene expression in the perirhinal cortex: A transcriptomic analysis
Q28602618	Recommendations for open data science
Q38146618	Recommendations for the design and analysis of epigenome-wide association studies
Q27851991	Recurrent SETBP1 mutations in atypical chronic myeloid leukemia
Q28830094	Recurrent evolution of host and vector association in bacteria of the Borrelia burgdorferi sensu lato species complex
Q35116209	Redefining the human oral mycobiome with improved practices in amplicon-based taxonomy: discovery of Malassezia as a prominent commensal
Q36414237	Reduced infectivity of adenovirus type 5 particles and degradation of entering viral genomes associated with incomplete processing of the preterminal protein
Q36924136	Reducing the Cost of the Diagnostic Odyssey in Early Onset Epileptic Encephalopathies.
Q33556609	Reduction in fecundity and shifts in cellular processes by a native virus on an invasive insect
Q34010252	Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling
Q36826668	Region of difference 4 in alpine Mycobacterium caprae isolates indicates three variants
Q38324240	Regulation of alternative splicing by the circadian clock and food related cues
Q36070422	Regulation of gene expression dynamics during developmental transitions by the Ikaros transcription factor.
Q36097780	Regulatory Divergence among Beta-Keratin Genes during Bird Evolution
Q44576507	Relationship between Gingival Crevicular Fluid Microbiota and Cytokine Profile in Periodontal Host Homeostasis
Q35850909	Reliably Detecting Clinically Important Variants Requires Both Combined Variant Calls and Optimized Filtering Strategies
Q33741138	Removing bias against short sequences enables northern blotting to better complement RNA-seq for the study of small RNAs
Q36307373	Removing the needle from the haystack: Enrichment of Wolbachia endosymbiont transcripts from host nematode RNA by Cappable-seq™.
Q37065222	Repair of adjacent single-strand breaks is often accompanied by the formation of tandem sequence duplications in plant genomes
Q51266258	RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads.
Q35763503	ReproPhylo: An Environment for Reproducible Phylogenomics
Q36337411	Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System.
Q36461896	Reproducible features of small RNAs in C. elegans reveal NU RNAs and provide insights into 22G RNAs and 26G RNAs
Q36367151	Research resource: interplay between the genomic and transcriptional networks of androgen receptor and estrogen receptor α in luminal breast cancer cells
Q37207611	Research resource: progesterone receptor targetome underlying mammary gland branching morphogenesis
Q37604333	Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations
Q35556375	Restriction Site-Associated DNA Sequencing (RAD-seq) Reveals an Extraordinary Number of Transitions among Gecko Sex-Determining Systems
Q36067801	Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis.
Q37262010	Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats
Q30857788	Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing
Q37318588	Review of general algorithmic features for genome assemblers for next generation sequencers
Q30987292	Review: High-performance computing to detect epistasis in genome scale data sets
Q41154492	RiboTools: a Galaxy toolbox for qualitative ribosome profiling analysis
Q64267830	Rice Galaxy: an open resource for plant science
Q58782835	Riluzole reduces amyloid beta pathology, improves memory, and restores gene expression changes in a transgenic mouse model of early-onset Alzheimer's disease
Q51504406	Ring chromosomes, breakpoint clusters, and neocentromeres in sarcomas.
Q36088542	RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
Q56976305	Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis
Q50642121	Role of STAT5 and epigenetics in lactation-associated upregulation of multidrug transporter ABCG2 in the mammary gland
Q35802055	Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses
Q31106793	SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data
Q28727279	SAVoR: a server for sequencing annotation and visualization of RNA structures
Q35802135	SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks
Q56754943	SCRAM–CK: applying a collaborative requirements engineering process for designing a web based e-science toolkit
Q52573956	SECIMTools: a suite of metabolomics data analysis tools.
Q36254978	SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology
Q27313564	SIV genome-wide pyrosequencing provides a comprehensive and unbiased view of variation within and outside CD8 T lymphocyte epitopes
Q61807225	SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis
Q34540539	SNP detection from de novo transcriptome sequencing in the bivalve Macoma balthica: marker development for evolutionary studies
Q35810285	SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations.
Q30684791	SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species.
Q47343155	SOAPnuke: A MapReduce Acceleration supported Software for integrated Quality Control and Preprocessing of High-Throughput Sequencing Data
Q28645968	SOCR data dashboard: an integrated big data archive mashing medicare, labor, census and econometric information
Q34535082	SOLiD-SAGE of endophyte-infected red fescue reveals numerous effects on host transcriptome and an abundance of highly expressed fungal secreted proteins
Q50062529	SOX2 regulates common and specific stem cell features in the CNS and endoderm derived organs.
Q41839302	START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries.
Q47398620	STAT3 controls COL1A2 enhancer activation cooperatively with JunB, regulates type I collagen synthesis posttranscriptionally, and is essential for lung myofibroblast differentiation
Q37366527	STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B-cell lymphoma
Q30486640	STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud
Q31105044	SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis
Q42126101	Savant Genome Browser 2: visualization and analysis for population-scale genomics
Q35809152	Scalable and cost-effective NGS genotyping in the cloud
Q35114409	Scanning of transposable elements and analyzing expression of transposase genes of sweet potato [Ipomoea batatas].
Q58971524	Science gateways today and tomorrow: positive perspectives of nearly 5000 members of the research community
Q38409331	Scientific workflows for bibliometrics
Q57004775	Scientific workflows for process mining: building blocks, scenarios, and implementation
Q30362814	Screening of Living Kidney Donors for Genetic Diseases Using a Comprehensive Genetic Testing Strategy.
Q39744699	SePIA: RNA and small RNA sequence processing, integration, and analysis.
Q34070504	Segtor: rapid annotation of genomic coordinates and single nucleotide variations using segment trees.
Q56890144	Selecting Fully-Modified XNA Aptamers Using Synthetic Genetics
Q45325336	Selection for avian leukosis virus integration sites determines the clonal progression of B-cell lymphomas
Q88774862	Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH)
Q24607867	Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros
Q36108383	Self-renewing diploid Axin2(+) cells fuel homeostatic renewal of the liver
Q36561721	Sense-antisense gene-pairs in breast cancer and associated pathological pathways
Q30994226	SeqMule: automated pipeline for analysis of human exome/genome sequencing data
Q52707741	Sequanix: A Dynamic Graphical Interface for Snakemake Workflows.
Q42620212	Sequence shortening in the rodent ancestor
Q38696935	Sequence-specific DNA binding by MYC/MAX to low-affinity non-E-box motifs.
Q28256164	Sequence-specific cleavage of dsRNA by Mini-III RNase
Q26824068	Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics
Q36133874	Sequential Binding of MEIS1 and NKX2-5 on the Popdc2 Gene: A Mechanism for Spatiotemporal Regulation of Enhancers during Cardiogenesis
Q39348159	Sequential Monte Carlo multiple testing
Q36215010	Serological and Virological Evidence of Crimean-Congo Haemorrhagic Fever Virus Circulation in the Human Population of Borno State, Northeastern Nigeria.
Q28554367	Sex-Biased Transcriptome of Schistosoma mansoni: Host-Parasite Interaction, Genetic Determinants and Epigenetic Regulators Are Associated with Sexual Differentiation
Q38809600	Short DNA Hairpins Compromise Recombinant Adeno-Associated Virus Genome Homogeneity.
Q36685774	Short-Term Dynamics of North Sea Bacterioplankton-Dissolved Organic Matter Coherence on Molecular Level
Q33617888	Should we build "obese" or "lean" anaerobic digesters?
Q41440565	Shrimp miR-10a Is Co-opted by White Spot Syndrome Virus to Increase Viral Gene Expression and Viral Replication.
Q42233195	Similar recombination-activating gene (RAG) mutations result in similar immunobiological effects but in different clinical phenotypes
Q57113360	Single Nucleotide Polymorphism Analysis Indicates Genetic Distinction and Reduced Diversity of Swine-Associated Methicillin Resistant (MRSA) ST5 Isolates Compared to Clinical MRSA ST5 Isolates
Q26858911	Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database
Q28710245	Single-nucleotide polymorphisms reveal patterns of allele sharing across the species boundary between rhesus (Macaca mulatta) and cynomolgus (M. fascicularis) macaques
Q36889612	Sir2/Sirt1 Links Acute Inebriation to Presynaptic Changes and the Development of Alcohol Tolerance, Preference, and Reward
Q41455914	Site-specific genome editing in Plasmodium falciparum using engineered zinc-finger nucleases
Q47122778	Small RNA-mediated regulation of DNA dosage in the ciliate Oxytricha
Q34505062	Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma
Q34394442	Small interfering RNA-producing loci in the ancient parasitic eukaryote Trypanosoma brucei
Q34386337	Snakemake--a scalable bioinformatics workflow engine
Q35772860	Social Regulation of Gene Expression in Threespine Sticklebacks
Q92005041	Social support for collaboration and group awareness in life science research teams
Q43030207	Soda pans of the Pannonian steppe harbor unique bacterial communities adapted to multiple extreme conditions
Q35586971	Soil microbiome responses to the short-term effects of Amazonian deforestation.
Q42075142	Some phenotype association tools in Galaxy: looking for disease SNPs in a full genome
Q57104956	Spatiotemporal and demographic variation in the diet of New Zealand lesser short-tailed bats ()
Q36155435	Specific CD8+ T cell responses correlate with control of simian immunodeficiency virus replication in Mauritian cynomolgus macaques
Q48020178	Specific Inhibition of the Bifunctional Farnesyl/Geranylgeranyl Diphosphate Synthase in Malaria Parasites via a New Small-Molecule Binding Site
Q91920431	Specificity of protein-DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR
Q46576979	Spectral classification of short numerical exon and intron sequences
Q58743077	Spfy: an integrated graph database for real-time prediction of bacterial phenotypes and downstream comparative analyses
Q35411691	SpliceTrap: a method to quantify alternative splicing under single cellular conditions
Q36932889	Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression
Q30861981	SraTailor: graphical user interface software for processing and visualizing ChIP-seq data.
Q36877024	Strand-Specific RNA-Seq Provides Greater Resolution of Transcriptome Profiling.
Q40095881	Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat.
Q55543246	Stream acidification and reduced aquatic prey availability are associated with dietary shifts in an obligate riparian Neotropical migratory songbird.
Q30633779	Streaming support for data intensive cloud-based sequence analysis
Q47548145	Streamlined ex vivo and in vivo genome editing in mouse embryos using recombinant adeno-associated viruses.
Q30574042	Streamlined ion torrent PGM-based diagnostics: BRCA1 and BRCA2 genes as a model
Q57465697	Streptococcal Lancefield polysaccharides are critical cell wall determinants for human Group IIA secreted phospholipase A2 to exert its bactericidal effects
Q47871475	Strobilurins as growth-promoting compounds: how Stroby regulates Arabidopsis leaf growth.
Q39023262	Structural and Functional Annotation of Long Noncoding RNAs
Q35888854	Structural bias in T4 RNA ligase-mediated 3'-adapter ligation
Q54978872	Structure and Function of the Transmembrane Domain of NsaS, an Antibiotic Sensing Histidine Kinase in Staphylococcus aureus.
Q41980729	Structure of the CRISPR interference complex CSM reveals key similarities with cascade
Q30533216	Structure of the type IV secretion system in different strains of Anaplasma phagocytophilum
Q27694724	Structure of two crystal forms of sheep β-lactoglobulin with EF-loop in closed conformation
Q41051803	StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo.
Q28249096	Structuring research methods and data with the research object model: genomics workflows as a case study
Q34768900	Study of the viral and microbial communities associated with Crohn's disease: a metagenomic approach.
Q93132934	Subgenomic flavivirus RNA binds the mosquito DEAD/H-box helicase ME31B and determines Zika virus transmission by Aedes aegypti
Q21089770	Subglacial Lake Vostok (Antarctica) accretion ice contains a diverse set of sequences from aquatic, marine and sediment-inhabiting bacteria and eukarya
Q46067109	Summary of talks and papers at ISCB-Asia/SCCG 2012.
Q34727635	Superresolution modeling of calcium release in the heart
Q57810111	Supporting biodiversity studies with the EUBrazilOpenBio Hybrid Data Infrastructure
Q64286663	Surface sterilization methods impact measures of internal microbial diversity in ticks
Q40162665	Swarm v2: highly-scalable and high-resolution amplicon clustering
Q58605203	SyNDI: synchronous network data integration framework
Q30362250	SymD webserver: a platform for detecting internally symmetric protein structures
Q35118594	Synergistic and antagonistic interplay between myostatin gene expression and physical activity levels on gene expression patterns in triceps Brachii muscles of C57/BL6 mice
Q64915998	System for Quality-Assured Data Analysis: Flexible, reproducible scientific workflows.
Q31104377	Systematic analysis of microRNA targeting impacted by small insertions and deletions in human genome
Q34746460	Systematic identification and quantification of phase variation in commensal and pathogenic Escherichia coli
Q38537092	Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective
Q59103406	Systems Biology and Synthetic Biology: A New Epoch for Toxicology Research
Q37661327	Systems toxicology: from basic research to risk assessment
Q35834802	T cell deficiency in spinal cord injury: altered locomotor recovery and whole-genome transcriptional analysis.
Q55514652	TALE factors use two distinct functional modes to control an essential zebrafish gene expression program.
Q35826318	TARDIS, a targeted RNA directional sequencing method for rare RNA discovery
Q36781316	TDP-43 repression of nonconserved cryptic exons is compromised in ALS-FTD.
Q35836443	TOGGLE: toolbox for generic NGS analyses.
Q37326100	TP53 gene mutation analysis in chronic lymphocytic leukemia by nanopore MinION sequencing
Q31035530	TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation
Q40855944	TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing.
Q33762828	Tailing and degradation of Argonaute-bound small RNAs protect the genome from uncontrolled RNAi.
Q34270708	Tangram: a comprehensive toolbox for mobile element insertion detection
Q33575868	TargetOrtho: a phylogenetic footprinting tool to identify transcription factor targets
Q47841428	Targeted deletion of a 170 kb cluster of LINE1 repeats: implications for regional control
Q33840084	Targeted metagenomic sequencing data of human gut microbiota associated with Blastocystis colonization
Q30467733	Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis
Q48320125	Targeted sequencing for gene discovery and quantification using RNA CaptureSeq
Q52683959	Targeting AR Variant-Coactivator Interactions to Exploit Prostate Cancer Vulnerabilities.
Q36439781	Targeting of >1.5 Mb of human DNA into the mouse X chromosome reveals presence of cis-acting regulators of epigenetic silencing
Q91638141	Targeting the BRD4-HOXB13 Coregulated Transcriptional Networks with Bromodomain-Kinase Inhibitors to Suppress Metastatic Castration-Resistant Prostate Cancer
Q44832215	Technical challenges in metatranscriptomic studies applied to the bacterial communities of freshwater ecosystems
Q55510151	Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology.
Q38933098	Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa
Q30986262	Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure
Q27084103	Ten Simple Rules for Taking Advantage of Git and GitHub
Q28974707	Ten simple rules for providing a scientific Web resource
Q28974699	Ten simple rules for reproducible computational research
Q34376714	Testing potential effects of maize expressing the Bacillus thuringiensis Cry1Ab endotoxin (Bt maize) on mycorrhizal fungal communities via DNA- and RNA-based pyrosequencing and molecular fingerprinting.
Q34426620	Tethering of the conserved piggyBac transposase fusion protein CSB-PGBD3 to chromosomal AP-1 proteins regulates expression of nearby genes in humans.
Q28076577	Text mining resources for the life sciences
Q28705183	The "fossilized" mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate
Q34016311	The 2010 Rosetta developers meeting: macromolecular prediction and design meets reproducible publishing
Q28603708	The 2015 Bioinformatics Open Source Conference (BOSC 2015)
Q27975975	The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
Q26744240	The A, C, G, and T of Genome Assembly
Q38677249	The Antisense Transcriptome and the Human Brain.
Q29580544	The BioExtract Server: a web-based bioinformatic workflow platform
Q51041496	The CRISPR/Cas system can be used as nuclease for in planta gene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny
Q33797000	The Cavβ1a subunit regulates gene expression and suppresses myogenin in muscle progenitor cells
Q31143300	The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data
Q41813155	The Complete Genome Sequence of Proteus mirabilis Strain BB2000 Reveals Differences from the P. mirabilis Reference Strain.
Q34084439	The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes
Q24426218	The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data
Q57752878	The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops
Q35042495	The Drosophila early ovarian transcriptome provides insight to the molecular causes of recombination rate variation across genomes
Q27990296	The Dutch Techcentre for Life Sciences: Enabling data-intensive life science research in the Netherlands
Q36246291	The Effect of a Novel c.820C>T (Arg274Trp) Mutation in the Mitofusin 2 Gene on Fibroblast Metabolism and Clinical Manifestation in a Patient.
Q58070318	The Essential Components of a Successful Galaxy Service
Q37348855	The Ets transcription factor EHF as a regulator of cornea epithelial cell identity
Q36453042	The Eucalyptus grandis NBS-LRR Gene Family: Physical Clustering and Expression Hotspots.
Q34524689	The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
Q30620627	The Genomic HyperBrowser: an analysis web server for genome-scale data
Q39691591	The Glycome Analytics Platform: an integrative framework for glycobioinformatics.
Q52679212	The HAP Complex Governs Fumonisin Biosynthesis and Maize Kernel Pathogenesis in Fusarium verticillioides.
Q30750828	The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data
Q28604193	The Human Toxome Collaboratorium: A Shared Environment for Multi-Omic Computational Collaboration within a Consortium
Q35488562	The MET gene is a common integration target in avian leukosis virus subgroup J-induced chicken hemangiomas
Q33787328	The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button
Q36809538	The Myb-p300-CREB axis modulates intestine homeostasis, radiosensitivity and tumorigenesis
Q28030951	The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability
Q34313744	The NSL complex regulates housekeeping genes in Drosophila.
Q35896180	The Notch-mediated hyperplasia circuitry in Drosophila reveals a Src-JNK signaling axis
Q30540388	The PinkThing for analysing ChIP profiling data in their genomic context
Q36689975	The Pokeweed Leaf mRNA Transcriptome and Its Regulation by Jasmonic Acid
Q28743714	The Reactome BioMart
Q35810134	The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community.
Q26770644	The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics
Q38370905	The Role of Free/Libre and Open Source Software in Learning Health Systems.
Q27499246	The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation
Q35630951	The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons
Q35064871	The Strategies WDK: a graphical search interface and web development kit for functional genomics databases
Q28290043	The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud
Q38463526	The Transcriptome and Terpene Profile of Eucalyptus grandis Reveals Mechanisms of Defense Against the Insect Pest, Leptocybe invasa
Q34424493	The Tribolium castaneum cell line TcA: a new tool kit for cell biology.
Q28740969	The UCSC Archaeal Genome Browser: 2012 update
Q35253526	The UCSC Cancer Genomics Browser: update 2015
Q57306437	The UCSC Genome Browser
Q57306438	The UCSC Genome Browser
Q30872157	The UCSC Genome Browser database: 2015 update
Q36434956	The UCSC Genome Browser database: 2016 update
Q46580891	The Urinary Microbiome Differs Significantly Between Patients With Chronic Prostatitis/Chronic Pelvic Pain Syndrome and Controls as Well as Between Patients With Different Clinical Phenotypes.
Q30560932	The Wasp System: an open source environment for managing and analyzing genomic data.
Q34586929	The ability to suppress macrophage-mediated inflammation in orbital fat stem cells is controlled by miR-671-5p
Q29303030	The amino acid composition of proteins from anaerobic halophilic bacteria of the order Halanaerobiales
Q40990473	The banana genome hub.
Q91704023	The barley stripe mosaic virus expression system reveals the wheat C2H2 zinc finger protein TaZFP1B as a key regulator of drought tolerance
Q34342864	The cell of origin and subtype of K-Ras-induced lung tumors are modified by Notch and Sox2.
Q34643010	The challenges of delivering bioinformatics training in the analysis of high-throughput data
Q34143940	The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes
Q35976881	The compact genome of the plant pathogen Plasmodiophora brassicae is adapted to intracellular interactions with host Brassica spp
Q46244233	The complete genome sequence of the rumen bacterium Butyrivibrio hungatei MB2003.
Q36427004	The decrease in histone methyltransferase EZH2 in response to fluid shear stress alters endothelial gene expression and promotes quiescence
Q35052467	The diet of Myotis lucifugus across Canada: assessing foraging quality and diet variability
Q47269349	The dynamic recruitment of TRBP to neuronal membranes mediates dendritogenesis during development
Q28659455	The eGenVar data management system--cataloguing and sharing sensitive data and metadata for the life sciences
Q48045527	The ecological and genetic basis of convergent thick-lipped phenotypes in cichlid fishes
Q46245365	The effects of pastoral intensification on the feeding interactions of generalist predators in streams.
Q35092095	The evidence for increased L1 activity in the site of human adult brain neurogenesis.
Q42092879	The evolution and functional impact of human deletion variants shared with archaic hominin genomes
Q28651512	The evolutionary fate of the horizontally transferred agrobacterial mikimopine synthase gene in the genera Nicotiana and Linaria
Q56894874	The evolutionary landscape of alternative splicing in vertebrate species
Q41965408	The flagellar set Fla2 in Rhodobacter sphaeroides is controlled by the CckA pathway and is repressed by organic acids and the expression of Fla1.
Q39443034	The forkhead transcription factor FOXK2 promotes AP-1-mediated transcriptional regulation
Q47290844	The function of two type II metacaspases in woody tissues of Populus trees
Q35358397	The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing
Q114868265	The future of metabolomics in ELIXIR
Q38882086	The future of metabolomics in ELIXIR.
Q92593160	The genomic landscape of estrogen receptor α binding sites in mouse mammary gland
Q57753804	The helicase Ded1p controls use of near-cognate translation initiation codons in 5' UTRs
Q33637319	The highly buffered Arabidopsis immune signaling network conceals the functions of its components
Q39013777	The histone demethylase PHF8 is a molecular safeguard of the IFNγ response.
Q31036204	The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences
Q33994847	The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize.
Q91861345	The invasive Asian bush mosquito Aedes japonicus found in the Netherlands can experimentally transmit Zika virus and Usutu virus
Q37590649	The marriage of nutrigenomics with the microbiome: the case of infant-associated bifidobacteria and milk
Q68414290	The metaRbolomics Toolbox in Bioconductor and beyond
Q28292064	The missing graphical user interface for genomics
Q35021853	The mitochondrial RNA landscape of Saccharomyces cerevisiae
Q50215819	The modulatory effect of infusions of green tea, oolong tea, and black tea on gut microbiota in high-fat-induced obese mice
Q33691022	The multiplicity of alternative splicing decisions in Caenorhabditis elegans is linked to specific intronic regulatory motifs and minisatellites
Q33856754	The murine appendiceal microbiome is altered in spontaneous colitis and its pathological progression
Q35650544	The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard.
Q46564717	The novel fungal-specific gene FUG1 has a role in pathogenicity and fumonisin biosynthesis in Fusarium verticillioides.
Q30663360	The perfect neuroimaging-genetics-computation storm: collision of petabytes of data, millions of hardware devices and thousands of software tools
Q35866979	The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows
Q35632563	The real cost of sequencing: higher than you think!
Q28818366	The rearranged mitochondrial genome of Leptopilina boulardi (Hymenoptera: Figitidae), a parasitoid wasp of Drosophila
Q24634193	The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
Q37181184	The severity of hereditary porphyria is modulated by the porphyrin exporter and Lan antigen ABCB6.
Q42773924	The synovial microenvironment of osteoarthritic joints alters RNA-seq expression profiles of human primary articular chondrocytes
Q111347958	The transcriptome of the lone star tick, Amblyomma americanum, reveals molecular changes in response to infection with the pathogen, Ehrlichia chaffeensis
Q35820376	The unique transcriptional response produced by concurrent estrogen and progesterone treatment in breast cancer cells results in upregulation of growth factor pathways and switching from a Luminal A to a Basal-like subtype
Q34480065	The uniqueome: a mappability resource for short-tag sequencing
Q57255886	The unseen world: environmental microbial sequencing and identification methods for ecologists
Q34123744	The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms
Q35073265	The utility of shallow RNA-Seq for documenting differential gene expression in genes with high and low levels of expression
Q38917975	The within-host dynamics of infection in trans-generationally primed flour beetles
Q27936820	The yeast Snt2 protein coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress
Q21131388	Therapeutic helminth infection of macaques with idiopathic chronic diarrhea alters the inflammatory signature and mucosal microbiota of the colon
Q38656006	Time to Spread Your Wings: A Review of the Avian Ancient DNA Field
Q35838815	Tissue-specific transcriptomics and proteomics of a filarial nematode and its Wolbachia endosymbiont
Q30833466	Titin-truncating variants affect heart function in disease cohorts and the general population.
Q36343067	Toil enables reproducible, open source, big biomedical data analyses
Q29002201	Tools and techniques for computational reproducibility
Q40990458	Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling
Q30363613	Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow
Q33837397	Towards a new generation of agricultural system data, models and knowledge products: Information and communication technology
Q37440490	Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles
Q94335553	Towards reproducible computational drug discovery
Q34487014	ToxDBScan: Large-scale similarity screening of toxicological databases for drug candidates
Q34854752	Tracking fungal community responses to maize plants by DNA- and RNA-based pyrosequencing
Q36666759	Trans-Atlantic exchanges have shaped the population structure of the Lyme disease agent Borrelia burgdorferi sensu stricto
Q36118451	Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions
Q48731754	Transcription elongation factors represent in vivo cancer dependencies in glioblastoma
Q34066561	Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs
Q37003094	Transcription start site evolution in Drosophila.
Q37303724	Transcriptional Fingerprint of Hypomyelination in Zfp191null and Shiverer (Mbpshi) Mice
Q58063616	Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce
Q34261528	Transcriptional enhancers in protein-coding exons of vertebrate developmental genes
Q37038076	Transcriptional plasticity promotes primary and acquired resistance to BET inhibition
Q50319958	Transcriptional response of Prochlorococcus to co-culture with a marine Alteromonas: differences between strains and the involvement of putative infochemicals
Q36230430	Transcriptome Profiling of Trypanosoma brucei Development in the Tsetse Fly Vector Glossina morsitans
Q35121971	Transcriptome analysis of cyst formation in Rhodospirillum centenum reveals large global changes in expression during cyst development
Q48465555	Transcriptome analysis of grey and white matter cortical tissue in multiple system atrophy
Q35519403	Transcriptome and hormone profiling reveals Eucalyptus grandis defence responses against Chrysoporthe austroafricana
Q48147113	Transcriptome portrait of cellulose-enriched flax fibres at advanced stage of specialization
Q33940022	Transcriptome-wide discovery of microRNA binding sites in human brain.
Q36619854	Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing
Q35456862	Transcriptomic events associated with internal browning of apple during postharvest storage
Q33716778	Transcriptomic evidence for a dramatic functional transition of the malpighian tubules after a blood meal in the Asian tiger mosquito Aedes albopictus
Q28486092	Transcriptomic study reveals widespread spliced leader trans-splicing, short 5'-UTRs and potential complex carbon fixation mechanisms in the euglenoid Alga Eutreptiella sp
Q39298486	Transcriptomics-based analysis using RNA-Seq of the coconut (Cocos nucifera) leaf in response to yellow decline phytoplasma infection.
Q34897615	Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology
Q38764222	Transferrin receptor mRNA interactions contributing to iron homeostasis
Q36247396	Transient In Vivo Resistance Mechanisms of Burkholderia pseudomallei to Ceftazidime and Molecular Markers for Monitoring Treatment Response
Q57797065	Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding
Q30384862	Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC).
Q34410261	Translocations at 8q24 juxtapose MYC with genes that harbor superenhancers resulting in overexpression and poor prognosis in myeloma patients
Q30653831	Transposable Element Insertions in Long Intergenic Non-Coding RNA Genes
Q34699808	Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs
Q37445042	Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues
Q42775603	Treatment of potato tubers with the synthetic cytokinin 1-(α-ethylbenzyl)-3-nitroguanidine results in rapid termination of endodormancy and induction of transcripts associated with cell proliferation and growth.
Q28648484	Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies
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Q42143984	TrioVis: a visualization approach for filtering genomic variants of parent-child trios
Q34035535	Tripal: a construction toolkit for online genome databases
Q21192760	True lemurs…true species - species delimitation using multiple data sources in the brown lemur complex
Q39442604	Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription.
Q40057209	Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses
Q24624409	Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV
Q33364506	UNBRANCHED3 regulates branching by modulating cytokinin biosynthesis and signaling in maize and rice
Q37484911	Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in early Drosophila embryos reveals hundreds of conserved translated sORFs
Q27322324	Unbiased identification of signal-activated transcription factors by barcoded synthetic tandem repeat promoter screening (BC-STAR-PROM)
Q36970890	Understanding barriers to Borrelia burgdorferi dissemination during infection using massively parallel sequencing
Q30866842	Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems
Q28647841	Unexpected evolutionary diversity in a recently extinct Caribbean mammal radiation
Q30869286	Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses
Q28534652	Unique transcriptome patterns of the white and grey matter corroborate structural and functional heterogeneity in the human frontal lobe
Q34690771	Unscrambling butterfly oogenesis.
Q35847204	Unusually Large Number of Mutations in Asexually Reproducing Clonal Planarian Dugesia japonica
Q92753384	Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus
Q35618038	UrQt: an efficient software for the Unsupervised Quality trimming of NGS data.
Q34390623	Use of allele-specific FAIRE to determine functional regulatory polymorphism using large-scale genotyping arrays
Q92437153	Use of high throughput amplicon sequencing and ethidium monoazide dye to track microbiota changes in an equol-producing menopausal woman receiving a long-term isoflavones treatment
Q34304668	Using Galaxy to perform large-scale interactive data analyses
Q28246542	Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations
Q37400072	Using Genome Query Language to uncover genetic variation
Q34038636	Using RNA-seq and targeted nucleases to identify mechanisms of drug resistance in acute myeloid leukemia
Q56988462	Using a suite of ontologies for preserving workflow-centric research objects
Q38415751	Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy
Q28277397	Using galaxy to perform large-scale interactive data analyses
Q38167615	Using genetic findings in autism for the development of new pharmaceutical compounds.
Q30315549	Using intron position conservation for homology-based gene prediction.
Q38241426	Using next-generation sequencing to isolate mutant genes from forward genetic screens
Q34630150	Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms
Q42034064	Utilizing ethnic-specific differences in minor allele frequency to recategorize reported pathogenic deafness variants.
Q41670301	VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.
Q36216675	VDR regulation of microRNA differs across prostate cell models suggesting extremely flexible control of transcription
Q41869702	VISPA: a computational pipeline for the identification and analysis of genomic vector integration sites
Q35586852	Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers
Q34115271	VarSifter: visualizing and analyzing exome-scale sequence variation data on a desktop computer
Q28584522	Variable Autosomal and X Divergence Near and Far from Genes Affects Estimates of Male Mutation Bias in Great Apes
Q55710066	Variable retention harvesting influences belowground plant-fungal interactions of Nothofagus pumilio seedlings in forests of southern Patagonia.
Q31119209	Variant detection and runs of homozygosity in next generation sequencing data elucidate the genetic background of Lundehund syndrome
Q30865154	VariantDB: a flexible annotation and filtering portal for next generation sequencing data
Q34518645	Variation Interpretation Predictors: Principles, Types, Performance, and Choice
Q38911800	Variation in Biological Soil Crust Bacterial Abundance and Diversity as a Function of Climate in Cold Steppe Ecosystems in the Intermountain West, USA.
Q37550216	Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects
Q30316429	Varying levels of complexity in transcription factor binding motifs
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Q37949696	Viral metagenomics as an emerging and powerful tool in veterinary medicine.
Q36262823	Viral variants that initiate and drive maturation of V1V2-directed HIV-1 broadly neutralizing antibodies
Q36060571	Virtual Reference Environments: a simple way to make research reproducible.
Q30235426	Virulence factor activity relationships (VFARs): a bioinformatics perspective
Q35093820	Virus-independent and common transcriptome responses of leafhopper vectors feeding on maize infected with semi-persistently and persistent propagatively transmitted viruses.
Q30990975	VisRseq: R-based visual framework for analysis of sequencing data
Q26749009	Visual programming for next-generation sequencing data analytics
Q37715451	Vitamin D Deficiency Is Associated With Increased Risk of Non-alcoholic Steatohepatitis in Adults With Non-alcoholic Fatty Liver Disease: Possible Role for MAPK and NF-κB?
Q64114999	Volatile Evolution of Long Non-Coding RNA Repertoire in Retinal Pigment Epithelium: Insights from Comparison of Bovine and Human RNA Expression Profiles
Q34569215	WGS Analysis and Interpretation in Clinical and Public Health Microbiology Laboratories: What Are the Requirements and How Do Existing Tools Compare?
Q85281790	We are all individuals... bioinformatics in the personalized medicine era
Q28658396	Web Apollo: a web-based genomic annotation editing platform
Q31133475	Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species
Q28292552	Web-based visual analysis for high-throughput genomics
Q50330914	Western Indian Rural Gut Microbial Diversity in Extreme Prakriti Endo-Phenotypes Reveals Signature Microbes
Q38153062	When cloud computing meets bioinformatics: a review
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Q36079032	Where next for the reproducibility agenda in computational biology?
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Q40376521	Whole Genome Sequence of the Soybean Aphid Endosymbiont Buchnera aphidicola and Genetic Differentiation among Biotype-Specific Strains
Q37054221	Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks
Q47595282	Whole genome sequencing identifies influenza A H3N2 transmission and offers superior resolution to classical typing methods
Q33640755	Whole genome sequencing identifies missense mutation in MTBP in Shar-Pei affected with Autoinflammatory Disease (SPAID)
Q38705023	Whole transcriptome analysis reveals dysregulated oncogenic lncRNAs in natural killer/T-cell lymphoma and establishes MIR155HG as a target of PRDM1.
Q36756706	Whole-Genome Sequences of an Aerobic Anoxygenic Phototroph, Blastomonas sp. Strain AAP53, Isolated from a Freshwater Desert Lake in Inner Mongolia, China
Q40123609	Whole-genome characterization of Uruguayan strains of avian infectious bronchitis virus reveals extensive recombination between the two major South American lineages
Q47660195	Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf
Q28704285	Whole-genome sequence of a freshwater aerobic anoxygenic phototroph, Porphyrobacter sp. strain AAP82, isolated from the Huguangyan Maar Lake in Southern China
Q34160591	Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare
Q37231213	Whole-genome sequencing in bacteriology: state of the art.
Q42320445	Whole-genome sequencing investigation of animal-skin-drum-associated UK anthrax cases reveals evidence of mixed populations and relatedness to a US case
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Q35128358	Widespread FRA1-dependent control of mesenchymal transdifferentiation programs in colorectal cancer cells
Q28652843	Widespread intron retention in mammals functionally tunes transcriptomes
Q40696181	Wolbachia from Drosophila incompta: just a hitchhiker shared by Drosophila in the New and Old World?
Q59854560	WorkWays: interacting with scientific workflows
Q38393076	Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics
Q57005102	Workflows for Heliophysics
Q57393488	Workflows for Information Integration in the Life Sciences
Q34272531	Workflows for microarray data processing in the Kepler environment
Q30768491	Wrangling Galaxy's reference data
Q33788900	X-MATE: a flexible system for mapping short read data
Q34459008	XiP: a computational environment to create, extend and share workflows.
Q37306053	Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction
Q31046381	ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis
Q31116678	biosigner: A New Method for the Discovery of Significant Molecular Signatures from Omics Data
Q41166217	dNTP pools determine fork progression and origin usage under replication stress
Q30681790	dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data
Q33860863	deepTools: a flexible platform for exploring deep-sequencing data.
Q35173843	edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens
Q42728000	gff2sequence, a new user friendly tool for the generation of genomic sequences
Q30870544	glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data
Q36932925	hnRNP A1 and secondary structure coordinate alternative splicing of Mag.
Q39016298	hppRNA-a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples
Q64055617	iGEAK: an interactive gene expression analysis kit for seamless workflow using the R/shiny platform
Q42975797	iReport: a generalised Galaxy solution for integrated experimental reporting.
Q30648830	kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets
Q34447540	lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis
Q38671556	m6aViewer: software for the detection, analysis and visualization of N6-methyl-adenosine peaks from m6A-seq/ME-RIP sequencing data
Q30660885	metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research
Q34928893	miRNA and miRNA target genes in copy number variations occurring in individuals with intellectual disability
Q35422390	microRNA-34c is a novel target to treat dementias
Q28646557	microRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs in the brown alga Ectocarpus
Q39067522	myGenomeBrowser: building and sharing your own genome browser.
Q42697060	nmrML: a community supported open data standard for the description, storage, and exchange of NMR data
Q36196099	oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets
Q28732175	openBIS: a flexible framework for managing and analyzing complex data in biology research
Q61447535	p.E95K mutation in Indian hedgehog causing brachydactyly type A1 impairs IHH/Gli1 downstream transcriptional regulation
Q30316862	plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants
Q47569590	pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment.
Q47722568	qPortal: A platform for data-driven biomedical research
Q30398727	repo: an R package for data-centered management of bioinformatic pipelines
Q34401341	siSPOTR: a tool for designing highly specific and potent siRNAs for human and mouse.
Q92328374	snakePipes: facilitating flexible, scalable and integrative epigenomic analysis
Q36138772	systemPipeR: NGS workflow and report generation environment
Q91924522	uap: reproducible and robust HTS data analysis
Q42129589	wANNOVAR: annotating genetic variants for personal genomes via the web.
Q27318208	xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud
Q35861638	xQTL workbench: a scalable web environment for multi-level QTL analysis

P6179	Dimensions Publication ID	1046347776
P356	DOI	10.1186/GB-2010-11-8-R86
P953	full work available at URL	http://www.biomedcentral.com/1465-6906/11/R86
		https://genomebiology.biomedcentral.com/counter/pdf/10.1186/gb-2010-11-8-r86
		https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20738864/?tool=EBI
		http://genomebiology.com/2010/11/8/R86
		http://genomebiology.com/2010/11/8/R86/abstract
		http://genomebiology.com/content/pdf/gb-2010-11-8-R86.pdf
		http://www.biomedcentral.com/1465-6906/11/R86/abstract
		http://www.biomedcentral.com/content/pdf/1465-6906-11-R86.pdf
		https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20738864/pdf/?tool=EBI
		https://europepmc.org/articles/PMC2945788
		https://europepmc.org/articles/PMC2945788?pdf=render
P3181	OpenCitations bibliographic resource ID	80268
P932	PMC publication ID	2945788
P698	PubMed publication ID	20738864
P5875	ResearchGate publication ID	45951138

P50	author	Anton Nekrutenko	Q30004030
		James Taylor	Q30362443
		Jeremy Goecks	Q57068417
P2093	author name string	Galaxy Team
P2860	cites work	Bioconductor: open software development for computational biology and bioinformatics	Q21194861
		Mapping and quantifying mammalian transcriptomes by RNA-Seq	Q22122035
		The Bioperl toolkit: Perl modules for the life sciences	Q24682183
		Basic local alignment search tool	Q25938991
		EMBOSS: the European Molecular Biology Open Software Suite	Q27860491
		ChIP-seq accurately predicts tissue-specific activity of enhancers	Q28235102
		Taverna: a tool for the composition and enactment of bioinformatics workflows	Q28267254
		Galaxy: a web-based genome analysis tool for experimentalists	Q28270252
		Using galaxy to perform large-scale interactive data analyses	Q28277397
		myExperiment: a repository and social network for the sharing of bioinformatics workflows	Q28283335
		A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly	Q28306159
		Repeatability of published microarray gene expression analyses	Q28307780
		InterProScan--an integration platform for the signature-recognition methods in InterPro	Q29547336
		GenePattern 2.0	Q29614171
		Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing	Q29618021
		A map of open chromatin in human pancreatic islets	Q33687905
		Computation for ChIP-seq and RNA-seq studies	Q33999125
		Altered histone acetylation is associated with age-dependent memory impairment in mice.	Q34114011
		Mobyle: a new full web bioinformatics framework	Q37411747
		Windshield splatter analysis with the Galaxy metagenomic pipeline	Q37417294
		Reproducible research: a bioinformatics case study	Q38453401
		Computer science. Accessible reproducible research	Q41845628
		Genome-wide analysis of epigenetic signatures for kidney-specific transporters	Q84424502
P433	issue	8
P407	language of work or name	English	Q1860
P921	main subject	Internet	Q75
		life sciences	Q864928
		reproducibility	Q1425625
		computational research	Q113990498
P304	page(s)	R86
P577	publication date	2010-01-01
		2010-08-25
P1433	published in	Genome Biology	Q5533480
P1476	title	Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
P478	volume	11

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

scientific article published on August 25, 2010

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