| scholarly article | Q13442814 |
| P8978 | DBLP publication ID | journals/bioinformatics/GrantBN11 |
| P356 | DOI | 10.1093/BIOINFORMATICS/BTR064 |
| P932 | PMC publication ID | 3065696 |
| P698 | PubMed publication ID | 21330290 |
| P5875 | ResearchGate publication ID | 49844689 |
| P50 | author | Timothy L. Bailey | Q57958471 |
| William S. Noble | Q29053213 | ||
| P2093 | author name string | Charles E Grant | |
| P2860 | cites work | Searching for statistically significant regulatory modules. | Q50787972 |
| Staden: searching for motifs in nucleic acid sequences | Q71996333 | ||
| CTCF: master weaver of the genome | Q24621388 | ||
| Combining evidence using p-values: application to sequence homology searches | Q28265811 | ||
| MEME SUITE: tools for motif discovery and searching | Q29547204 | ||
| CisML: an XML-based format for sequence motif detection software | Q38450427 | ||
| P275 | copyright license | Creative Commons Attribution-NonCommercial 2.5 Generic | Q19113746 |
| P6216 | copyright status | copyrighted | Q50423863 |
| P433 | issue | 7 | |
| P407 | language of work or name | English | Q1860 |
| P304 | page(s) | 1017-1018 | |
| P577 | publication date | 2011-02-16 | |
| P1433 | published in | Bioinformatics | Q4914910 |
| P1476 | title | FIMO: scanning for occurrences of a given motif | |
| P478 | volume | 27 |
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| Q35713972 | Database of RNA binding protein expression and disease dynamics (READ DB). |
| Q38929176 | Dataset for distribution of INGI/RIME and SLACS CRE transposable elements in Trypanosoma brucei genome |
| Q37010390 | De novo mutations in the genome organizer CTCF cause intellectual disability. |
| Q36228906 | DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter |
| Q90066018 | Deciphering epigenomic code for cell differentiation using deep learning |
| Q89531327 | Deciphering the Rules Underlying Xenogeneic Silencing and Counter-Silencing of Lsr2-like Proteins Using CgpS of Corynebacterium glutamicum as a Model |
| Q101569793 | Decoding myofibroblast origins in human kidney fibrosis |
| Q92962725 | Deep learning models predict regulatory variants in pancreatic islets and refine type 2 diabetes association signals |
| Q33878855 | Defining the 5΄ and 3΄ landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq. |
| Q38623186 | Defining the DNA Binding Site Recognized by the Fission Yeast Zn2Cys6 Transcription Factor Pho7 and Its Role in Phosphate Homeostasis |
| Q88886393 | Deletion of the Clostridium thermocellum recA gene reveals that it is required for thermophilic plasmid replication but not plasmid integration at homologous DNA sequences |
| Q59809252 | Dempster-Shafer Theory for the Prediction of Auxin-Response Elements (AuxREs) in Plant Genomes |
| Q92619198 | Depicting the Core Transcriptome Modulating Multiple Abiotic Stresses Responses in Sesame (Sesamum indicum L.). |
| Q35968181 | Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains |
| Q58605199 | Detection of long non-coding RNA homology, a comparative study on alignment and alignment-free metrics |
| Q39039082 | Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties |
| Q35057918 | Developmental expression of the Nfe2-related factor (Nrf) transcription factor family in the zebrafish, Danio rerio |
| Q90689201 | Developmental regulation of cell type-specific transcription by novel promoter-proximal sequence elements |
| Q38667242 | Differences in DNA-binding specificity of floral homeotic protein complexes predict organ-specific target genes |
| Q35604281 | Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription |
| Q89802978 | Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations |
| Q45753212 | Differential Expression of miR-93 and miR-21 in Granulosa Cells and Follicular Fluid of Polycystic Ovary Syndrome Associating with Different Phenotypes |
| Q64071897 | Differential regulation of CpG island methylation within divergent and unidirectional promoters in colorectal cancer |
| Q90389884 | Differential regulation of OCT4 targets facilitates reacquisition of pluripotency |
| Q52690497 | Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch. |
| Q92430868 | Direct and Specific Functional Evaluation of the Nrf2 and MafG Heterodimer by Introducing a Tethered Dimer into Small Maf-Deficient Cells |
| Q36454627 | Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome. |
| Q93085427 | Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays |
| Q52349662 | Discovery of enzymes for toluene synthesis from anoxic microbial communities. |
| Q97424865 | Discovery of regulatory noncoding variants in individual cancer genomes by using cis-X |
| Q108126987 | Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network |
| Q62660641 | Disrupting the IL-36 and IL-23/IL-17 loop underlies the efficacy of calcipotriol and corticosteroid therapy for psoriasis |
| Q36431439 | Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development |
| Q90546424 | Dissecting the role of PfAP2-G in malaria gametocytogenesis |
| Q92351344 | Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells |
| Q38803510 | Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer |
| Q37579115 | Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain. |
| Q90260424 | Distinct Roles for BET Family Members in Estrogen Receptor α Enhancer Function and Gene Regulation in Breast Cancer Cells |
| Q54947840 | Distinct gene networks modulate floral induction of autonomous maize and photoperiod-dependent teosinte. |
| Q35921265 | Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer |
| Q36619840 | Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions |
| Q35476240 | Distinguishing between productive and abortive promoters using a random forest classifier in Mycoplasma pneumoniae |
| Q33839459 | Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster |
| Q48880001 | Diversification of C. elegans Motor Neuron Identity via Selective Effector Gene Repression. |
| Q83225257 | Diversification of the heat shock response by Helitron transposable elements |
| Q33357617 | Diversity of Prdm9 zinc finger array in wild mice unravels new facets of the evolutionary turnover of this coding minisatellite |
| Q33861803 | Dosage compensation via transposable element mediated rewiring of a regulatory network |
| Q36093984 | Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters. |
| Q91794142 | Draft genome assembly and transcriptome data of the icefish Chionodraco myersi reveal the key role of mitochondria for a life without hemoglobin at subzero temperatures |
| Q34536097 | Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease |
| Q38862967 | Dynamic Gene Regulatory Networks of Human Myeloid Differentiation |
| Q58834917 | Dynamic and spatial restriction of Polycomb activity by plant histone demethylases |
| Q30855589 | Dynamic regulation of Nanog and stem cell-signaling pathways by Hoxa1 during early neuro-ectodermal differentiation of ES cells |
| Q34590410 | Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis |
| Q34543685 | Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapy |
| Q42363811 | Dynamic transcription factor activity networks in response to independently altered mechanical and adhesive microenvironmental cues |
| Q40620169 | Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development |
| Q33624348 | Dysregulated IER3 Expression is Associated with Enhanced Apoptosis in Titin-Based Dilated Cardiomyopathy |
| Q64062624 | EAT-Rice: A predictive model for flanking gene expression of T-DNA insertion activation-tagged rice mutants by machine learning approaches |
| Q28590260 | EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments |
| Q30370914 | EMX1 regulates NRP1-mediated wiring of the mouse anterior cingulate cortex. |
| Q58560751 | ENHO, RXRA, and LXRA polymorphisms and dyslipidaemia, related comorbidities and survival in haemodialysis patients |
| Q41876293 | ERG promotes the maintenance of hematopoietic stem cells by restricting their differentiation |
| Q93229380 | ERα activity depends on interaction and target site corecruitment with phosphorylated CREB1 |
| Q38696706 | ETV4 and AP1 Transcription Factors Form Multivalent Interactions with three Sites on the MED25 Activator-Interacting Domain |
| Q37388827 | Early B-cell factor-1 (EBF1) is a key regulator of metabolic and inflammatory signaling pathways in mature adipocytes |
| Q91639109 | Early Stage Adaptation of a Mesophilic Green Alga to Antarctica: Systematic Increases in Abundance of Enzymes and LEA Proteins |
| Q46425223 | Ecotype diversification of an abundant Roseobacter lineage |
| Q90650590 | Effector mining from the Erysiphe pisi haustorial transcriptome identifies novel candidates involved in pea powdery mildew pathogenesis |
| Q57173895 | Effects of liquid cultivation on gene expression and phenotype of C. elegans |
| Q94545188 | Elucidating the Regulon of a Fur-like Protein in Mycobacterium avium subsp. paratuberculosis (MAP) |
| Q35185286 | Elucidation of sigma factor-associated networks in Pseudomonas aeruginosa reveals a modular architecture with limited and function-specific crosstalk. |
| Q90009739 | Embryonic ethanol exposure alters expression of sox2 and other early transcripts in zebrafish, producing gastrulation defects |
| Q38390479 | Embryonic lethal abnormal vision proteins and adenine and uridine-rich element mRNAs after global cerebral ischemia and reperfusion in the rat. |
| Q64057963 | Enabling cell-type-specific behavioral epigenetics in Drosophila: a modified high-yield INTACT method reveals the impact of social environment on the epigenetic landscape in dopaminergic neurons |
| Q90024786 | Enhancer Architecture and Essential Core Regulatory Circuitry of Chronic Lymphocytic Leukemia |
| Q35036393 | Enhancer evolution across 20 mammalian species |
| Q95328259 | Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance |
| Q58755746 | Enhancer reprogramming in mammalian genomes |
| Q42597586 | Enhancer transcripts mark active estrogen receptor binding sites |
| Q91495371 | Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease |
| Q60045652 | Enhancers in the Peril lincRNA locus regulate distant but not local genes |
| Q34652607 | Environmentally induced epigenetic transgenerational inheritance of altered Sertoli cell transcriptome and epigenome: molecular etiology of male infertility |
| Q90428496 | Epigenetic engineering of yeast reveals dynamic molecular adaptation to methylation stress and genetic modulators of specific DNMT3 family members |
| Q36051153 | Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots |
| Q38432674 | Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation. |
| Q24623379 | Epigenetic priors for identifying active transcription factor binding sites |
| Q92397301 | Epigenome-wide association study reveals methylation pathways associated with childhood allergic sensitization |
| Q64087985 | Epigenomic profiling of retinal progenitors reveals LHX2 is required for developmental regulation of open chromatin |
| Q92183823 | Epigenomics and Single-Cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis |
| Q110951440 | Episodes of Rapid Recovery of the Functional Activity of the ras85D Gene in the Evolutionary History of Phylogenetically Distant Drosophila Species |
| Q93015633 | Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes |
| Q45048407 | Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors. |
| Q92126665 | Ethanolamine Utilization and Bacterial Microcompartment Formation Are Subject to Carbon Catabolite Repression |
| Q36180626 | Evaluating tools for transcription factor binding site prediction. |
| Q28603870 | Evidence for a common evolutionary rate in metazoan transcriptional networks |
| Q36619825 | Evidence that a consensus element found in naturally intronless mRNAs promotes mRNA export |
| Q46330116 | Evidence that auxin is required for normal seed size and starch synthesis in pea. |
| Q35974552 | Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants |
| Q38696648 | Evolution and multiple roles of the Pancrustacea specific transcription factor zelda in insects |
| Q52316984 | Evolution of DNAaseI Hypersensitive Sites in MHC Regulatory Regions of Primates. |
| Q28550139 | Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression |
| Q36975138 | Evolutionarily conserved long intergenic non-coding RNAs in the eye |
| Q36271594 | Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing. |
| Q90658037 | Evolutionary flexibility in flooding response circuitry in angiosperms |
| Q35591746 | Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis. |
| Q36851106 | ExactSearch: a web-based plant motif search tool |
| Q28552633 | Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation |
| Q50302255 | Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility. |
| Q42697227 | Exploiting sequence-based features for predicting enhancer-promoter interactions |
| Q90727635 | Exploring novel herbicidin analogues by transcriptional regulator overexpression and MS/MS molecular networking |
| Q28314339 | Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice |
| Q89864883 | Expression of E93 provides an instructive cue to control dynamic enhancer activity and chromatin accessibility during development |
| Q38322713 | Expression of nuclear factor one A and -B in the olfactory bulb |
| Q47377031 | Expression of sf1 and dax-1 are regulated by thyroid hormones and androgens during Silurana tropicalis early development |
| Q47282615 | Expression of the arsenite oxidation regulatory operon in Rhizobium sp. str. NT-26 is under the control of two promoters that respond to different environmental cues |
| Q34479374 | Expression profile in rice panicle: insights into heat response mechanism at reproductive stage |
| Q35349449 | Expression profiling during arabidopsis/downy mildew interaction reveals a highly-expressed effector that attenuates responses to salicylic acid |
| Q36219899 | Extensive Regulation of Diurnal Transcription and Metabolism by Glucocorticoids |
| Q59096611 | Extensive sex differences at the initiation of genetic recombination |
| Q48284512 | Extracytoplasmic function sigma factor σD confers resistance to environmental stress by enhancing mycolate synthesis and modifying peptidoglycan structures in Corynebacterium glutamicum. |
| Q89543505 | Extreme clustering of type-1 NF1 deletion breakpoints co-locating with G-quadruplex forming sequences |
| Q93053616 | FOXA1 mutations alter pioneering activity, differentiation and prostate cancer phenotypes |
| Q91770771 | FOXA2 Is Required for Enhancer Priming during Pancreatic Differentiation |
| Q90429904 | Factor cooperation for chromosome discrimination in Drosophila |
| Q28280461 | Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium |
| Q64084483 | FeatSNP: An Interactive Database for Brain-Specific Epigenetic Annotation of Human SNPs |
| Q35246463 | Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast |
| Q92480972 | Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes |
| Q38872766 | Form and function of topologically associating genomic domains in budding yeast |
| Q44326729 | Formation of a functional maize centromere after loss of centromeric sequences and gain of ectopic sequences |
| Q37355138 | Four Inducible Promoters for Controlled Gene Expression in the Oleaginous Yeast Rhodotorula toruloides |
| Q42359739 | Foxp transcription factors suppress a non-pulmonary gene expression program to permit proper lung development |
| Q36256189 | From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data |
| Q91924473 | From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy |
| Q89514321 | From reads to insight: a hitchhiker's guide to ATAC-seq data analysis |
| Q92700438 | Functional Analysis of the PgCesA3 White Spruce Cellulose Synthase Gene Promoter in Secondary Xylem |
| Q57187699 | Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence |
| Q57340009 | Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells |
| Q91799108 | Functional annotation of noncoding causal variants in autoimmune diseases |
| Q37681763 | Functional annotation of sixty-five type-2 diabetes risk SNPs and its application in risk prediction |
| Q46261346 | Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease. |
| Q42223900 | Functional characterisation of cis-regulatory elements governing dynamic Eomes expression in the early mouse embryo |
| Q90472702 | Functional characterization of enhancer evolution in the primate lineage |
| Q61660344 | Functional dissection of the ARGONAUTE7 promoter |
| Q35757936 | Functional diversity of CTCFs is encoded in their binding motifs. |
| Q89948870 | Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters |
| Q98176913 | Functional fine-mapping of noncoding risk variants in amyotrophic lateral sclerosis utilizing convolutional neural network |
| Q61797539 | Functional genomics reveal gene regulatory mechanisms underlying schizophrenia risk |
| Q90212560 | Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification |
| Q34629093 | Functional knowledge transfer for high-accuracy prediction of under-studied biological processes |
| Q36745020 | Functional screen identifies regulators of murine hematopoietic stem cell repopulation |
| Q34539468 | G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch. |
| Q38746800 | G-quadruplex structures mark human regulatory chromatin |
| Q35588343 | GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters |
| Q37141721 | GATA1 Binding Kinetics on Conformation-Specific Binding Sites Elicit Differential Transcriptional Regulation |
| Q35112992 | GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris |
| Q36185343 | GENE REGULATION. Discrete functions of nuclear receptor Rev-erbα couple metabolism to the clock. |
| Q55322458 | GKAP Acts as a Genetic Modulator of NMDAR Signaling to Govern Invasive Tumor Growth. |
| Q46284217 | Gain and Loss of Small RNA Classes-Characterization of Small RNAs in the Parasitic Nematode Family Strongyloididae |
| Q58615807 | Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency |
| Q36023271 | Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus |
| Q88984520 | Gastrointestinal stromal tumor enhancers support a transcription factor network predictive of clinical outcome |
| Q52720862 | Gcn4 Binding in Coding Regions Can Activate Internal and Canonical 5' Promoters in Yeast. |
| Q35644844 | Gene Regulation by the LiaSR Two-Component System in Streptococcus mutans |
| Q45069937 | Gene Regulation, Two Component Regulatory Systems, and Adaptive Responses in Treponema Denticola |
| Q46292737 | Gene Regulatory Enhancers with Evolutionarily Conserved Activity Are More Pleiotropic than Those with Species-Specific Activity |
| Q47095688 | Gene Regulatory Network Rewiring in the Immune Cells Associated with Cancer. |
| Q31121565 | Gene Slider: sequence logo interactive data-visualization for education and research |
| Q57793623 | Gene expression variability across cells and species shapes innate immunity |
| Q38788399 | Gene regulatory mechanisms underpinning prostate cancer susceptibility |
| Q92631135 | General and Genomic DNA-Binding Specificity for the Thermus thermophilus HB8 Transcription Factor TTHB023 |
| Q64299325 | Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies |
| Q48190630 | Genetic determinants and epigenetic effects of pioneer-factor occupancy. |
| Q34501150 | Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci |
| Q36277126 | Genetic variants alter T-bet binding and gene expression in mucosal inflammatory disease. |
| Q34224429 | Genetic variants in transcription factors are associated with the pharmacokinetics and pharmacodynamics of metformin. |
| Q38696563 | Genome Organization Drives Chromosome Fragility |
| Q22122068 | Genome and transcriptome of the porcine whipworm Trichuris suis |
| Q35967692 | Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes |
| Q36258695 | Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility |
| Q36253774 | Genome-Wide Binding of Posterior HOXA/D Transcription Factors Reveals Subgrouping and Association with CTCF. |
| Q38849869 | Genome-Wide Identification of MESP1 Targets Demonstrates Primary Regulation Over Mesendoderm Gene Activity. |
| Q37592700 | Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans |
| Q47813986 | Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood |
| Q55362433 | Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation. |
| Q61797820 | Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation |
| Q38456475 | Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells |
| Q89514417 | Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana |
| Q33741869 | Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B |
| Q36044879 | Genome-wide analyses reveal the extent of opportunistic STAT5 binding that does not yield transcriptional activation of neighboring genes |
| Q37609654 | Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types |
| Q40537164 | Genome-wide analysis of p53 transcriptional programs in B cells upon exposure to genotoxic stress in vivo |
| Q39018172 | Genome-wide analysis of p53-regulated transcription in Myc-driven lymphomas. |
| Q92864303 | Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption |
| Q37264405 | Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1. |
| Q28586104 | Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions |
| Q35889279 | Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus |
| Q38451538 | Genome-wide bioinformatics analysis of steroid metabolism-associated genes in Nocardioides simplex VKM Ac-2033D. |
| Q35619449 | Genome-wide co-occupancy of AML1-ETO and N-CoR defines the t(8;21) AML signature in leukemic cells |
| Q104471929 | Genome-wide correlation analysis to identify amplitude regulators of circadian transcriptome output |
| Q35042993 | Genome-wide discovery of human splicing branchpoints |
| Q38456974 | Genome-wide disruption of 5-hydroxymethylcytosine in a mouse model of autism |
| Q35935489 | Genome-wide footprinting: ready for prime time? |
| Q36134892 | Genome-wide identification and characterisation of HOT regions in the human genome. |
| Q38808041 | Genome-wide identification and characterization of Notch transcription complex-binding sequence-paired sites in leukemia cells. |
| Q91650737 | Genome-wide identification and comparative analysis of drought-related microRNAs in two maize inbred lines with contrasting drought tolerance by deep sequencing |
| Q35554891 | Genome-wide identification of Bacillus subtilis Zur-binding sites associated with a Zur box expands its known regulatory network. |
| Q37286069 | Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis. |
| Q60048618 | Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators |
| Q38598206 | Genome-wide identification of histone H2A and histone variant H2A.Z-interacting proteins by bPPI-seq |
| Q48352274 | Genome-wide identification of regulatory elements in Sertoli cells. |
| Q41331086 | Genome-wide identification of target genes of a mating-type α-domain transcription factor reveals functions beyond sexual development |
| Q30525712 | Genome-wide in silico prediction of gene expression. |
| Q36268817 | Genome-wide map of RNA degradation kinetics patterns in dendritic cells after LPS stimulation facilitates identification of primary sequence and secondary structure motifs in mRNAs. |
| Q51419224 | Genome-wide mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and high-throughput sequencing. |
| Q38667699 | Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize |
| Q57902778 | Genome-wide measurement of local nucleosome array regularity and spacing by nanopore sequencing |
| Q28277540 | Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder |
| Q93020234 | Genome-wide response on phytosterol in 9-hydroxyandrostenedione-producing strain of Mycobacterium sp. VKM Ac-1817D |
| Q50420630 | Genome-wide strategies identify downstream target genes of connective tissue-associated transcription factors. |
| Q35091848 | Genome-wide tissue-specific gene expression, co-expression and regulation of co-expressed genes in adult nematode Ascaris suum |
| Q37548484 | Genome-wide uniformity of human 'open' pre-initiation complexes |
| Q30855594 | Genome-wide use of high- and low-affinity Tbrain transcription factor binding sites during echinoderm development |
| Q34999326 | Genome-wide view of TGFβ/Foxh1 regulation of the early mesendoderm program. |
| Q38384099 | Genomic Database Searching |
| Q54213249 | Genomic Organization and Expression of Iron Metabolism Genes in the Emerging Pathogenic Mold Scedosporium apiospermum. |
| Q101476372 | Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm |
| Q37701475 | Genomic binding of PAX8-PPARG fusion protein regulates cancer-related pathways and alters the immune landscape of thyroid cancer. |
| Q28820976 | Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining |
| Q38749638 | Genomic footprinting |
| Q42027899 | Genomic landscape of cutaneous T cell lymphoma |
| Q55710805 | Gestational exposure to chlordecone promotes transgenerational changes in the murine reproductive system of males. |
| Q60908065 | Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons |
| Q92421670 | Global Mapping of H3K4 Trimethylation (H3K4me3) and Transcriptome Analysis Reveal Genes Involved in the Response to Epidemic Diarrhea Virus Infections in Pigs |
| Q89531517 | Global Network Analysis of Neisseria gonorrhoeae Identifies Coordination between Pathways, Processes, and Regulators Expressed during Human Infection |
| Q37627911 | Global analysis of cell cycle gene expression of the legume symbiont Sinorhizobium meliloti. |
| Q55020711 | Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling. |
| Q29346753 | Global analysis of the regulon of the transcriptional repressor LexA, a key component of SOS response in Mycobacterium tuberculosis. |
| Q37076970 | Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts |
| Q90124729 | Global insight into the distribution of velvet-like B protein in Cochliobolus species and implication in pathogenicity and fungicide resistance |
| Q38457012 | Global poplar root and leaf transcriptomes reveal links between growth and stress responses under nitrogen starvation and excess |
| Q47096901 | Global role of the bacterial post-transcriptional regulator CsrA revealed by integrated transcriptomics |
| Q58776576 | Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding |
| Q57286596 | Glucocorticoids Induce Stress Oncoproteins Associated with Therapy-Resistance in African American and European American Prostate Cancer Cells |
| Q64234927 | Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes |
| Q90009333 | Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data |
| Q64101729 | Greedy de novo motif discovery to construct motif repositories for bacterial proteomes |
| Q64265772 | HCP5 is a SMAD3-responsive long non-coding RNA that promotes lung adenocarcinoma metastasis via miR-203/SNAI axis |
| Q26314404 | Hairy and Groucho mediate the action of juvenile hormone receptor Methoprene-tolerant in gene repression |
| Q92478425 | Hallmarks and Determinants of Oncogenic Translation Revealed by Ribosome Profiling in Models of Breast Cancer |
| Q92217593 | Hand2 Selectively Reorganizes Chromatin Accessibility to Induce Pacemaker-like Transcriptional Reprogramming |
| Q50110862 | Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements. |
| Q27694804 | HemR is an OmpR/PhoB-like response regulator from Leptospira, which simultaneously effects transcriptional activation and repression of key haem metabolism genes |
| Q92548360 | Heterochromatin drives compartmentalization of inverted and conventional nuclei |
| Q47104096 | Hfq links translation repression to stress-induced mutagenesis in E. coli |
| Q47159941 | HiTAD: detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions |
| Q89625549 | Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data |
| Q61444339 | High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue |
| Q36024968 | High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases. |
| Q54089688 | High-Throughput Sequencing of microRNAs in Glucocorticoid Sensitive Paediatric Inflammatory Bowel Disease Patients. |
| Q34296849 | High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression |
| Q43658331 | High-intensity UV laser ChIP-seq for the study of protein-DNA interactions in living cells |
| Q48240056 | High-resolution TADs reveal DNA sequences underlying genome organization in flies. |
| Q33767447 | High-resolution promoter map of human limbal epithelial cells cultured with keratinocyte growth factor and rho kinase inhibitor |
| Q103043791 | High-resolution temporal transcriptome sequencing unravels ERF and WRKY as the master players in the regulatory networks underlying sesame responses to waterlogging and recovery |
| Q63352310 | High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity |
| Q34350068 | High-throughput functional testing of ENCODE segmentation predictions. |
| Q47731283 | High-throughput identification of RNA nuclear enrichment sequences |
| Q57030072 | High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites |
| Q36835735 | Holo-TFIID controls the magnitude of a transcription burst and fine-tuning of transcription |
| Q33701686 | Homo-trimerization is essential for the transcription factor function of Myrf for oligodendrocyte differentiation |
| Q58792891 | Human cardiac -regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants |
| Q33863026 | Human immunodeficiency virus Tat associates with a specific set of cellular RNAs |
| Q89984705 | Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus |
| Q96303311 | IHF stabilizes pathogenicity island I of uropathogenic Escherichia coli strain 536 by attenuating integrase I promoter activity |
| Q64100618 | IKZF1 Deletions with COBL Breakpoints Are Not Driven by RAG-Mediated Recombination Events in Acute Lymphoblastic Leukemia |
| Q93344389 | IKZF2 Drives Leukemia Stem Cell Self-Renewal and Inhibits Myeloid Differentiation |
| Q90703128 | IRF2 is a master regulator of human keratinocyte stem cell fate |
| Q91716094 | Identification and Characterization of Preferred DNA-Binding Sites for the Thermus thermophilus HB8 Transcriptional Regulator TTHA0973 |
| Q36958129 | Identification and Characterization of a cis-Regulatory Element for Zygotic Gene Expression in Chlamydomonas reinhardtii. |
| Q36253752 | Identification of AMPK Phosphorylation Sites Reveals a Network of Proteins Involved in Cell Invasion and Facilitates Large-Scale Substrate Prediction |
| Q90132222 | Identification of C2CD4A as a human diabetes susceptibility gene with a role in β cell insulin secretion |
| Q92115848 | Identification of DNA motifs that regulate DNA methylation |
| Q92217667 | Identification of Pparγ-modulated miRNA hubs that target the fibrotic tumor microenvironment |
| Q49721248 | Identification of Single Nucleotide Non-coding Driver Mutations in Cancer. |
| Q98735805 | Identification of Transcription Factor/Gene Axis in Colon Cancer Using a Methylome Approach |
| Q64064611 | Identification of a novel strong promoter from the anhydrobiotic midge, Polypedilum vanderplanki, with conserved function in various insect cell lines |
| Q39197388 | Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits. |
| Q89237242 | Identification of epigenetic modulators in human breast cancer by integrated analysis of DNA methylation and RNA-Seq data |
| Q64271784 | Identification of genes underlying phenotypic plasticity of wing size via insulin signaling pathway by network-based analysis in Sogatella furcifera |
| Q28388119 | Identification of genomic features in environmentally induced epigenetic transgenerational inherited sperm epimutations |
| Q64092199 | Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression |
| Q94502096 | Identification of new pentatricopeptide repeat proteins, MREF1 and 2, involved in mitochondrial RNA editing, using computational target RNA prediction |
| Q61446248 | Identification of new signalling peptides through a genome-wide survey of 250 fungal secretomes |
| Q41908345 | Identification of the alternative sigma factor SigX regulon and its implications for Pseudomonas aeruginosa pathogenicity |
| Q89171869 | Identification, characterization, and expression analysis of auxin response factor (ARF) gene family in Brachypodium distachyon |
| Q36008410 | Identifying Network Perturbation in Cancer |
| Q36033384 | Impact of the N-Terminal Domain of STAT3 in STAT3-Dependent Transcriptional Activity |
| Q37534309 | Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes |
| Q88766650 | In Silico Analysis of Natural Resistance-Associated Macrophage Protein (NRAMP) Family of Transporters in Rice |
| Q89722721 | In situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila |
| Q98164580 | Index and biological spectrum of human DNase I hypersensitive sites |
| Q42503475 | Induced Genome-Wide Binding of Three Arabidopsis WRKY Transcription Factors during Early MAMP-Triggered Immunity. |
| Q38763605 | Inference and Evolutionary Analysis of Genome-Scale Regulatory Networks in Large Phylogenies |
| Q36019746 | Inferring RBP-Mediated Regulation in Lung Squamous Cell Carcinoma |
| Q31153687 | Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data |
| Q35702332 | Inferring regulatory element landscapes and transcription factor networks from cancer methylomes |
| Q90713168 | Inferring targeting modes of Argonaute-loaded tRNA fragments |
| Q57165634 | Inherited DNA methylation primes the establishment of accessible chromatin during genome activation |
| Q90631958 | Inherited variants at 3q13.33 and 3p24.1 are associated with risk of diffuse large B-cell lymphoma and implicate immune pathways |
| Q35819673 | Insm1 cooperates with Neurod1 and Foxa2 to maintain mature pancreatic β-cell function |
| Q64994676 | Integrated Functional Genomic Analysis Enables Annotation of Kidney Genome-Wide Association Study Loci. |
| Q64295966 | Integrated Omic Analyses Provide Evidence that a " Accumulibacter phosphatis" Strain Performs Denitrification under Microaerobic Conditions |
| Q45943015 | Integrated analysis of motif activity and gene expression changes of transcription factors. |
| Q36310757 | Integrated analysis of promoter mutation, methylation and expression of AKT1 gene in Chinese breast cancer patients |
| Q64075921 | Integrated epigenomic profiling reveals endogenous retrovirus reactivation in renal cell carcinoma |
| Q35022270 | Integrated module and gene-specific regulatory inference implicates upstream signaling networks |
| Q36296882 | Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism. |
| Q31114011 | Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens |
| Q35195359 | Integrating diverse datasets improves developmental enhancer prediction |
| Q34493813 | Integrating multiple oestrogen receptor alpha ChIP studies: overlap with disease susceptibility regions, DNase I hypersensitivity peaks and gene expression |
| Q39757220 | Integration host factor and LuxR synergistically bind DNA to coactivate quorum-sensing genes in Vibrio harveyi |
| Q93055036 | Integration of Biological Networks for Acidithiobacillus thiooxidans Describes a Modular Gene Regulatory Organization of Bioleaching Pathways |
| Q42075255 | Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis |
| Q48089880 | Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci. |
| Q89081238 | Integrative Genome-Wide Analysis of Long Noncoding RNAs in Diverse Immune Cell Types of Melanoma Patients |
| Q49913571 | Integrative genomic analysis predicts causative cis-regulatory mechanisms of the breast cancer-associated genetic variant rs4415084. |
| Q57181843 | Integrative genomic analysis reveals novel regulatory mechanisms of eyeless during Drosophila eye development |
| Q55263060 | Interactions between genetic variation and cellular environment in skeletal muscle gene expression. |
| Q36022868 | Interactions between pluripotency factors specify cis-regulation in embryonic stem cells |
| Q43151067 | Interplay among Drosophila transcription factors Ets21c, Fos and Ftz-F1 drives JNK-mediated tumor malignancy |
| Q59349974 | Interpretation of an individual functional genomics experiment guided by massive public data |
| Q36501199 | Irx3 is required for postnatal maturation of the mouse ventricular conduction system |
| Q59770869 | Joint profiling of chromatin accessibility and gene expression in thousands of single cells. |
| Q39550924 | Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments |
| Q37500984 | K63-polyubiquitinated HAUSP deubiquitinates HIF-1α and dictates H3K56 acetylation promoting hypoxia-induced tumour progression |
| Q46244893 | Kiwifruit SVP2 controls developmental and drought-stress pathways |
| Q90621927 | KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors |
| Q55485409 | Landscape of transcriptional deregulation in lung cancer. |
| Q99353748 | Large domains of heterochromatin direct the formation of short mitotic chromosome loops |
| Q36022356 | Large-Scale Gene Relocations following an Ancient Genome Triplication Associated with the Diversification of Core Eudicots |
| Q41709160 | Large-scale detection and analysis of adenosine-to-inosine RNA editing during development in Plutella xylostella |
| Q36338647 | Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo |
| Q39005713 | Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex. |
| Q64077219 | Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells |
| Q88802197 | Leveraging epigenomics and contactomics data to investigate SNP pairs in GWAS |
| Q41577826 | Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb. |
| Q53841958 | Lineage-Determining Transcription Factor TCF-1 Initiates the Epigenetic Identity of T Cells. |
| Q64119190 | Linking Terpene Synthases to Sesquiterpene Metabolism in Grapevine Flowers |
| Q36111569 | Lipopolysaccharide treatment induces genome-wide pre-mRNA splicing pattern changes in mouse bone marrow stromal stem cells |
| Q47203571 | Local sequence features that influence AP-1 cis-regulatory activity |
| Q43924342 | Loci associated with skin pigmentation identified in African populations. |
| Q47137076 | Locus-specific hypomethylation of the mouse IAP retrotransposon is associated with transcription factor-binding sites. |
| Q33789606 | Long noncoding RNAs are spatially correlated with transcription factors and regulate lung development |
| Q33813325 | Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1. |
| Q45939332 | Long-Read Sequencing of Human Cytomegalovirus Transcriptome Reveals RNA Isoforms Carrying Distinct Coding Potentials. |
| Q89637953 | Long-range single-molecule mapping of chromatin accessibility in eukaryotes |
| Q91338211 | Lung morphogenesis is orchestrated through Grainyhead-like 2 (Grhl2) transcriptional programs |
| Q34489641 | MACE: model based analysis of ChIP-exo |
| Q56894111 | MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations |
| Q92296143 | MAPCap allows high-resolution detection and differential expression analysis of transcription start sites |
| Q64114728 | MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments |
| Q38664271 | MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics |
| Q34958598 | MEF2 transcription factors regulate distinct gene programs in mammalian skeletal muscle differentiation |
| Q91179083 | MERIT: Systematic Analysis and Characterization of Mutational Effect on RNA Interactome Topology |
| Q93060625 | MPRAnalyze: statistical framework for massively parallel reporter assays |
| Q57903251 | Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities |
| Q40749005 | Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. |
| Q37629625 | Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq |
| Q30620797 | Mapping functional transcription factor networks from gene expression data |
| Q42339238 | Mapping the chromatin landscape and Blimp1 transcriptional targets that regulate trophoblast differentiation. |
| Q36833119 | Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding |
| Q37695019 | Massively parallel functional annotation of 3' untranslated regions |
| Q34354921 | Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks. |
| Q45944363 | Maximum entropy methods for extracting the learned features of deep neural networks. |
| Q38308757 | Members of the barley NAC transcription factor gene family show differential co-regulation with senescence-associated genes during senescence of flag leaves. |
| Q92313571 | Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types |
| Q64110406 | Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow |
| Q57297931 | MicroRNA expression profile of urinary exosomes in Type IV lupus nephritis complicated by cellular crescent |
| Q34986572 | Minimal metabolic pathway structure is consistent with associated biomolecular interactions |
| Q39165584 | Mining Bacterial Genomes for Secondary Metabolite Gene Clusters. |
| Q61796276 | Mismatch repair-signature mutations activate gene enhancers across human colorectal cancer epigenomes |
| Q93162035 | Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements |
| Q90260233 | Mitochondrial Pentatricopeptide Repeat Protein, EMB2794, Plays a Pivotal Role in NADH Dehydrogenase Subunit nad2 mRNA Maturation in Arabidopsis thaliana |
| Q42426838 | Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation |
| Q38882162 | Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility |
| Q37451136 | Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast |
| Q38797962 | Modeling Gene Regulation in Liver Hepatocellular Carcinoma with Random Forests. |
| Q30618656 | Models incorporating chromatin modification data identify functionally important p53 binding sites |
| Q34512262 | Models of human core transcriptional regulatory circuitries |
| Q36266144 | Modifiers of solid RNP granules control normal RNP dynamics and mRNA activity in early development |
| Q46485872 | Molecular Anatomy of the Developing Human Retina. |
| Q47387947 | Molecular basis for the differential expression of the global regulator VieA in Vibrio cholerae biotypes directed by H-NS, LeuO and quorum sensing. |
| Q36084323 | Molecular mechanisms of ribosomal protein gene coregulation. |
| Q59795532 | Molecular pathway analysis towards understanding tissue vulnerability in spinocerebellar ataxia type 1 |
| Q91677421 | Molecular signature of an ancient organizer regulated by Wnt/β-catenin signalling during primary body axis patterning in Hydra |
| Q41891132 | Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress. |
| Q39231609 | Most brain disease-associated and eQTL haplotypes are not located within transcription factor DNase-seq footprints in brain |
| Q41867668 | Mot1 redistributes TBP from TATA-containing to TATA-less promoters. |
| Q35852366 | Motif signatures in stretch enhancers are enriched for disease-associated genetic variants |
| Q30586232 | MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis |
| Q33615189 | Mouse Dux is myotoxic and shares partial functional homology with its human paralog DUX4. |
| Q35111710 | Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution |
| Q92304149 | Multi-species annotation of transcriptome and chromatin structure in domesticated animals |
| Q61810617 | Multi-study inference of regulatory networks for more accurate models of gene regulation |
| Q91828683 | Multilevel regulation of the glass locus during Drosophila eye development |
| Q52390187 | Multiplatform next-generation sequencing identifies novel RNA molecules and transcript isoforms of the endogenous retrovirus isolated from cultured cells. |
| Q91863553 | Multiple SCN5A variant enhancers modulate its cardiac gene expression and the QT interval |
| Q30002315 | Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs |
| Q37086508 | Multiple layers of transcriptional regulation by PLZF in NKT-cell development |
| Q91650105 | Multivariable regulation of gene expression plasticity in metazoans |
| Q52691469 | Mutation hotspots at CTCF binding sites coupled to chromosomal instability in gastrointestinal cancers. |
| Q36095027 | Mutational Biases Drive Elevated Rates of Substitution at Regulatory Sites across Cancer Types |
| Q41627960 | MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation |
| Q37061160 | NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors |
| Q59301309 | NF-κB-Dependent Lymphoid Enhancer Co-option Promotes Renal Carcinoma Metastasis |
| Q36098789 | NFIX Regulates Proliferation and Migration Within the Murine SVZ Neurogenic Niche |
| Q37390226 | NFIX regulates neural progenitor cell differentiation during hippocampal morphogenesis |
| Q97643468 | NFYB-1 regulates mitochondrial function and longevity via lysosomal prosaposin |
| Q30008748 | NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions. |
| Q41652826 | NODULE INCEPTION antagonistically regulates gene expression with nitrate in Lotus japonicus |
| Q83224631 | Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and mA modification |
| Q90099983 | Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression |
| Q57817834 | Natural variation for gene expression responses to abiotic stress in maize |
| Q41551345 | Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100. |
| Q35279380 | Neomorphic effects of recurrent somatic mutations in Yin Yang 1 in insulin-producing adenomas |
| Q42696593 | NetProphet 2.0: Mapping Transcription Factor Networks by Exploiting Scalable Data Resources. |
| Q48171311 | Network analysis of SRC-1 reveals a novel transcription factor hub which regulates endocrine resistant breast cancer |
| Q36319623 | Network perturbation by recurrent regulatory variants in cancer |
| Q42776375 | Neuronal identity genes regulated by super-enhancers are preferentially down-regulated in the striatum of Huntington's disease mice |
| Q33703205 | Nicotinamide metabolism regulates glioblastoma stem cell maintenance |
| Q49819293 | Non-B-form DNA is enriched at centromeres. |
| Q57791261 | Non-canonical Drosophila X chromosome dosage compensation and repressive topologically associated domains |
| Q35621452 | Noncoding RNAs that associate with YB-1 alter proliferation in prostate cancer cells |
| Q37297706 | Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer. |
| Q93052238 | Nonmutational mechanism of inheritance in the Archaeon Sulfolobus solfataricus |
| Q93101128 | Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors |
| Q38715088 | Notch1 maintains dormancy of olfactory horizontal basal cells, a reserve neural stem cell. |
| Q37488426 | Novel mechanism of positive versus negative regulation by thyroid hormone receptor β1 (TRβ1) identified by genome-wide profiling of binding sites in mouse liver |
| Q48009521 | Nuclear factor one X regulates Bobby sox during development of the mouse forebrain |
| Q36563212 | Nuclear hormone receptor DHR96 mediates the resistance to xenobiotics but not the increased lifespan of insulin-mutant Drosophila |
| Q36002014 | Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors |
| Q33669183 | Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells |
| Q60922632 | Nucleosome remodeling at origins of global genome-nucleotide excision repair occurs at the boundaries of higher-order chromatin structure |
| Q33741021 | ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data. |
| Q45985278 | On the necessity and biological significance of threshold-free regulon prediction outputs. |
| Q37166444 | Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes |
| Q90427431 | Oncogenic hijacking of the stress response machinery in T cell acute lymphoblastic leukemia |
| Q92666113 | Open Chromatin Profiling in Adipose Tissue Marks Genomic Regions with Functional Roles in Cardiometabolic Traits |
| Q34180708 | Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes. |
| Q36426572 | Oxytocin-stimulated NFAT transcriptional activation in human myometrial cells. |
| Q28817926 | PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond |
| Q37027516 | PEDLA: predicting enhancers with a deep learning-based algorithmic framework. |
| Q40201338 | PGBD5 promotes site-specific oncogenic mutations in human tumors |
| Q55024329 | PHB Biosynthesis Counteracts Redox Stress in Herbaspirillum seropedicae. |
| Q91619737 | POSTAR2: deciphering the post-transcriptional regulatory logics |
| Q28584439 | POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins |
| Q41627029 | PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis. |
| Q63979688 | PTBP1-Mediated Alternative Splicing Regulates the Inflammatory Secretome and the Pro-tumorigenic Effects of Senescent Cells |
| Q36392356 | PTEN deficiency reprogrammes human neural stem cells towards a glioblastoma stem cell-like phenotype |
| Q64064136 | Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk |
| Q63664483 | PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data |
| Q92202805 | Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics |
| Q64799902 | Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons. |
| Q34559489 | Pax6 interactions with chromatin and identification of its novel direct target genes in lens and forebrain |
| Q30828757 | PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data. |
| Q59804292 | Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome |
| Q58617453 | Pervasive Gene Conversion in Chromosomal Inversion Heterozygotes |
| Q93051373 | Pervasive Positive and Negative Feedback Regulation of Insulin-Like Signaling in Caenorhabditis elegans |
| Q30048292 | PfSR1 controls alternative splicing and steady-state RNA levels in Plasmodium falciparum through preferential recognition of specific RNA motifs |
| Q112715271 | Phosphor-IWS1-dependent U2AF2 splicing regulates trafficking of CAR-E-positive intronless gene mRNAs and sensitivity to viral infection |
| Q37245968 | Photoreceptor phagocytosis is mediated by phosphoinositide signaling |
| Q37960377 | Phylogenetic footprinting: a boost for microbial regulatory genomics |
| Q33767733 | PipX, the coactivator of NtcA, is a global regulator in cyanobacteria |
| Q36619534 | Piwi maintains germline stem cells and oogenesis in Drosophila through negative regulation of Polycomb group proteins |
| Q91856140 | PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System |
| Q55487757 | Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0. |
| Q28818092 | PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants |
| Q58087062 | Plau and Tgfbr3 are YAP-regulated genes that promote keratinocyte proliferation |
| Q37271996 | Pleiotropic regulatory genes bldA, adpA and absB are implicated in production of phosphoglycolipid antibiotic moenomycin |
| Q33631279 | Pol II docking and pausing at growth and stress genes in C. elegans |
| Q35212253 | Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype |
| Q52319669 | Polymer physics predicts the effects of structural variants on chromatin architecture. |
| Q36000058 | Positional distribution of transcription factor binding sites in Arabidopsis thaliana |
| Q57698394 | Positional specificity of different transcription factor classes within enhancers |
| Q51401747 | Positive selection of the TRIM family regulatory region in primate genomes. |
| Q47141351 | Post-transcriptional gene silencing mediated by microRNAs is controlled by nucleoplasmic Sfpq |
| Q31115343 | Post-transcriptional regulation of the trypanosome heat shock response by a zinc finger protein |
| Q45023662 | Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos. |
| Q90348513 | Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions |
| Q21563477 | Practical guidelines for the comprehensive analysis of ChIP-seq data |
| Q100526343 | Predicting 3D genome folding from DNA sequence with Akita |
| Q57476557 | Predicting CTCF-mediated chromatin interactions by integrating genomic and epigenomic features |
| Q55514170 | Predicting CTCF-mediated chromatin loops using CTCF-MP. |
| Q36407816 | Predicting Transcription Factor Binding Sites and Their Cognate Transcription Factors Using Gene Expression Data |
| Q21128766 | Predicting effective microRNA target sites in mammalian mRNAs |
| Q38755095 | Predicting gene expression in massively parallel reporter assays: A comparative study |
| Q90059865 | Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features |
| Q36212204 | Predicting the recurrence of noncoding regulatory mutations in cancer |
| Q33740989 | Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data |
| Q100737123 | Prediction of genome-wide effects of single nucleotide variants on transcription factor binding |
| Q33563017 | Predictive long-range allele-specific mapping of regulatory variants and target transcripts |
| Q90696893 | Preferences in a trait decision determined by transcription factor variants |
| Q60916259 | Pregnancy Epigenetic Signature in T Helper 17 and T Regulatory Cells in Multiple Sclerosis |
| Q30421140 | Primate evolution of the recombination regulator PRDM9 |
| Q61802081 | Probing transcription factor combinatorics in different promoter classes and in enhancers |
| Q45956551 | Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules. |
| Q37690705 | Progesterone receptor assembly of a transcriptional complex along with activator protein 1, signal transducer and activator of transcription 3 and ErbB-2 governs breast cancer growth and predicts response to endocrine therapy |
| Q42334610 | Progressive Loss of Function in a Limb Enhancer during Snake Evolution |
| Q61876944 | Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer |
| Q37038710 | Promoter directionality is controlled by U1 snRNP and polyadenylation signals |
| Q58695766 | PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence |
| Q34622766 | Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas. |
| Q36030567 | Prosaposin activates the androgen receptor and potentiates resistance to endocrine treatment in breast cancer |
| Q34631463 | Protection of CpG islands against de novo DNA methylation during oogenesis is associated with the recognition site of E2f1 and E2f2. |
| Q90480895 | Proteome-level assessment of origin, prevalence and function of leucine-aspartic acid (LD) motifs |
| Q42960061 | Pseudomonas putida AlkA and AlkB proteins comprise different defense systems for the repair of alkylation damage to DNA - in vivo, in vitro, and in silico studies |
| Q60935253 | Pure early zygotic genes in the Asian malaria mosquito Anopheles stephensi |
| Q47150528 | PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data |
| Q47099525 | Put3 Positively Regulates Proline Utilization in Candida albicans. |
| Q55339380 | Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits. |
| Q92264369 | QTG-Finder: A Machine-Learning Based Algorithm To Prioritize Causal Genes of Quantitative Trait Loci in Arabidopsis and Rice |
| Q59327243 | Quantifying post-transcriptional regulation in the development of Drosophila melanogaster |
| Q38284619 | Quantitative bacterial transcriptomics with RNA-seq |
| Q21563285 | Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association |
| Q99568243 | RAB13 mRNA compartmentalisation spatially orients tissue morphogenesis |
| Q97527964 | RALF1-FERONIA complex affects splicing dynamics to modulate stress responses and growth in plants |
| Q38698829 | RBM25 is a global splicing factor promoting inclusion of alternatively spliced exons and is itself regulated by lysine mono-methylation |
| Q50518029 | REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis. |
| Q96136661 | RIC-seq for global in situ profiling of RNA-RNA spatial interactions |
| Q35216351 | RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer |
| Q28661337 | RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi |
| Q35086192 | RNA polymerase III transcriptomes in human embryonic stem cells and induced pluripotent stem cells, and relationships with pluripotency transcription factors |
| Q33741954 | RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome |
| Q59136284 | RRAD, IL4I1, CDKN1A, and SERPINE1 genes are potentially co-regulated by NF-κB and p53 transcription factors in cells exposed to high doses of ionizing radiation |
| Q38716029 | RTA Occupancy of the Origin of Lytic Replication during Murine Gammaherpesvirus 68 Reactivation from B Cell Latency. |
| Q39691584 | RTFBSDB: an integrated framework for transcription factor binding site analysis |
| Q93064580 | Reactivation of super-enhancers by KLF4 in human Head and Neck Squamous Cell Carcinoma |
| Q36399385 | Recent computational developments on CLIP-seq data analysis and microRNA targeting implications. |
| Q47735172 | Recent development of Ori-Finder system and DoriC database for microbial replication origins |
| Q47141782 | Recombination rate variation in mice from an isolated island |
| Q36701985 | Recombination rates and genomic shuffling in human and chimpanzee--a new twist in the chromosomal speciation theory |
| Q47719683 | Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines |
| Q89367601 | Recovering Gene Interactions from Single-Cell Data Using Data Diffusion |
| Q36109396 | Recruitment of RAG1 and RAG2 to Chromatinized DNA during V(D)J Recombination |
| Q40171028 | Red Blood Cell Invasion by the Malaria Parasite Is Coordinated by the PfAP2-I Transcription Factor |
| Q37254115 | Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines. |
| Q64945872 | Refining the Pneumococcal Competence Regulon by RNA Sequencing. |
| Q89924369 | Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility |
| Q50421570 | Regeneration of the lung alveolus by an evolutionarily conserved epithelial progenitor. |
| Q45261331 | Regulation of V-nitrogenase genes in Anabaena variabilis by RNA processing and by dual repressors |
| Q90754732 | Regulation of lifespan by neural excitation and REST |
| Q47107984 | Regulation of ribonucleotide synthesis by the Pseudomonas aeruginosa two-component system AlgR in response to oxidative stress |
| Q34516863 | Regulatory evolution of innate immunity through co-option of endogenous retroviruses |
| Q90665100 | Regulatory mechanisms of major depressive disorder risk variants |
| Q40045181 | Regulatory network changes between cell lines and their tissues of origin |
| Q35272189 | Regulatory network decoded from epigenomes of surface ectoderm-derived cell types |
| Q48257532 | Relationship between histone modifications and transcription factor binding is protein family specific |
| Q92513745 | Remodeling of the Caenorhabditis elegans non-coding RNA transcriptome by heat shock |
| Q97527937 | Remote modulation of lncRNA GCLET by risk variant at 16p13 underlying genetic susceptibility to gastric cancer |
| Q30982599 | Removing reference mapping biases using limited or no genotype data identifies allelic differences in protein binding at disease-associated loci |
| Q41428658 | Reorganization of enhancer patterns in transition from naive to primed pluripotency |
| Q33920597 | Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates |
| Q36197536 | Repression by H-NS of genes required for the biosynthesis of the Vibrio cholerae biofilm matrix is modulated by the second messenger cyclic diguanylic acid |
| Q64056933 | Reproducible big data science: A case study in continuous FAIRness |
| Q50453578 | Resolving Heart Regeneration by Replacement Histone Profiling. |
| Q89497668 | Retinoic Acid Induces Embryonic Stem Cells (ESCs) Transition to 2 Cell-Like State Through a Coordinated Expression of Dux and Duxbl1 |
| Q91173501 | Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions |
| Q35070297 | Reverse engineering the neuroblastoma regulatory network uncovers MAX as one of the master regulators of tumor progression |
| Q103028516 | Robustness and lethality in multilayer biological molecular networks |
| Q35770624 | Role of intragenic binding of cAMP responsive protein (CRP) in regulation of the succinate dehydrogenase genes Rv0249c-Rv0247c in TB complex mycobacteria |
| Q41827311 | Roles of cofactors and chromatin accessibility in Hox protein target specificity |
| Q97531015 | SARS-CoV-2 contributes to altering the post-transcriptional regulatory networks across human tissues by sponging RNA binding proteins and micro-RNAs |
| Q48349026 | SMiLE-seq identifies binding motifs of single and dimeric transcription factors. |
| Q35185463 | STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer |
| Q30699640 | Saccharomyces genome database provides new regulation data |
| Q93059715 | SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes |
| Q47576712 | Salt Stress and CTD PHOSPHATASE-LIKE4 Mediate the Switch between Production of Small Nuclear RNAs and mRNAs. |
| Q30979730 | Saturation analysis of ChIP-seq data for reproducible identification of binding peaks |
| Q92761494 | Secondary nucleotide messenger c-di-GMP exerts a global control on natural product biosynthesis in streptomycetes |
| Q64114801 | Secreted frizzled related protein is a target of PaxB and plays a role in aquiferous system development in the freshwater sponge, Ephydatia muelleri |
| Q47169628 | Secretome Characterization and Correlation Analysis Reveal Putative Pathogenicity Mechanisms and Identify Candidate Avirulence Genes in the Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici |
| Q30391792 | Secretome weaponries of Cochliobolus lunatus interacting with potato leaf at different temperature regimes reveal a CL[xxxx]LHM - motif |
| Q37133454 | Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans |
| Q53406877 | Selection on the regulation of sympathetic nervous activity in humans and chimpanzees. |
| Q37200073 | Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers |
| Q34172714 | Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA. |
| Q37248390 | Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing |
| Q34079283 | Sequence-based classification using discriminatory motif feature selection |
| Q35098003 | Sequence-dependent off-target inhibition of TLR7/8 sensing by synthetic microRNA inhibitors |
| Q33983578 | Serial number tagging reveals a prominent sequence preference of retrotransposon integration |
| Q91511901 | Shared distal regulatory regions may contribute to the coordinated expression of human ribosomal protein genes |
| Q57295515 | Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates |
| Q33909150 | Short DNA sequence patterns accurately identify broadly active human enhancers |
| Q30830810 | Silencing of cryptic prophages in Corynebacterium glutamicum |
| Q40106239 | Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii |
| Q92720716 | Single-Cell Analysis Reveals Regional Reprogramming During Adaptation to Massive Small Bowel Resection in Mice |
| Q64107545 | Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development |
| Q36291431 | Single-Nucleotide-Specific Targeting of the Tf1 Retrotransposon Promoted by the DNA-Binding Protein Sap1 of Schizosaccharomyces pombe |
| Q97421905 | Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation |
| Q89580541 | Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures |
| Q91618808 | Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation |
| Q59329462 | Siroheme Is Essential for Assimilation of Nitrate and Sulfate as Well as Detoxification of Nitric Oxide but Dispensable for Murine Virulence of |
| Q40605206 | Site-specific association with host and viral chromatin by Kaposi's sarcoma-associated herpesvirus LANA and its reversal during lytic reactivation. |
| Q36723404 | Sleep-active neuron specification and sleep induction require FLP-11 neuropeptides to systemically induce sleep |
| Q39311703 | Solanum tuberosum StCDPK1 is regulated by miR390 at the posttranscriptional level and phosphorylates the auxin efflux carrier StPIN4 in vitro, a potential downstream target in potato development |
| Q48142600 | SoxNeuro and Shavenbaby act cooperatively to shape denticles in the embryonic epidermis of Drosophila. |
| Q41328427 | SoxNeuro orchestrates central nervous system specification and differentiation in Drosophila and is only partially redundant with Dichaete |
| Q58084808 | Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic |
| Q98164628 | Spatiotemporal DNA methylome dynamics of the developing mouse fetus |
| Q35927876 | Specific tagging of the egress-related osmiophilic bodies in the gametocytes of Plasmodium falciparum |
| Q62788210 | Splicing factor controls ER-positive breast cancer by altering metabolic pathways |
| Q89837706 | Splicing of enhancer-associated lincRNAs contributes to enhancer activity |
| Q26782206 | Spotting the enemy within: Targeted silencing of foreign DNA in mammalian genomes by the Krüppel-associated box zinc finger protein family |
| Q38690389 | Structural and biochemical analyses indicate that a bacterial persulfide dioxygenase-rhodanese fusion protein functions in sulfur assimilation |
| Q34579681 | Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers |
| Q34491255 | Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions |
| Q31135205 | Subpallial Enhancer Transgenic Lines: a Data and Tool Resource to Study Transcriptional Regulation of GABAergic Cell Fate. |
| Q38429466 | Super-lncRNAs: Identification of lncRNAs that target super-enhancers via RNA:DNA:DNA triplex formation |
| Q35786148 | Survey of protein-DNA interactions in Aspergillus oryzae on a genomic scale |
| Q33574553 | Symbolic extensions applied to multiscale structure of genomes |
| Q36068731 | Symmetrical Dose-Dependent DNA-Methylation Profiles in Children with Deletion or Duplication of 7q11.23 |
| Q58090917 | Synaptogyrin-2 influences replication of Porcine circovirus 2 |
| Q35446103 | Synergy: a web resource for exploring gene regulation in Synechocystis sp. PCC6803 |
| Q89648967 | Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells |
| Q57162652 | Systematic Dissection of the Evolutionarily Conserved WetA Developmental Regulator across a Genus of Filamentous Fungi |
| Q36107248 | Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana |
| Q37658966 | Systematic dissection of genomic features determining transcription factor binding and enhancer function |
| Q35933400 | Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection |
| Q40125796 | Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses. |
| Q42653906 | Systematic identification of regulatory variants associated with cancer risk |
| Q29614895 | Systematic localization of common disease-associated variation in regulatory DNA |
| Q33709312 | Systematic mapping of functional enhancer-promoter connections with CRISPR interference |
| Q63804672 | Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development |
| Q93209177 | T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide-MHC complexes |
| Q103804126 | TERT promoter alterations could provide a solution for Peto's paradox in rodents |
| Q37661734 | TFBSshape: a motif database for DNA shape features of transcription factor binding sites |
| Q91812163 | TFutils: Data structures for transcription factor bioinformatics |
| Q35052645 | TGF-β/Smad signaling through DOCK4 facilitates lung adenocarcinoma metastasis |
| Q104064332 | TGFβ promotes widespread enhancer chromatin opening and operates on genomic regulatory domains |
| Q47227853 | THiCweed: fast, sensitive detection of sequence features by clustering big datasets |
| Q34480931 | TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins |
| Q38429142 | TSS-Seq analysis of low pH-induced gene expression in intercalated cells in the renal collecting duct |
| Q28655699 | TSSAR: TSS annotation regime for dRNA-seq data |
| Q64115610 | Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development |
| Q91951347 | Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection |
| Q33575868 | TargetOrtho: a phylogenetic footprinting tool to identify transcription factor targets |
| Q38774302 | Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. |
| Q28269737 | Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves |
| Q57047042 | Targeting nuclear receptor NR4A1-dependent adipocyte progenitor quiescence promotes metabolic adaptation to obesity |
| Q59329522 | Targets and genomic constraints of ectopic Dnmt3b expression |
| Q92147754 | Tcf1 and Lef1 are required for the immunosuppressive function of regulatory T cells |
| Q37126836 | Temperate phages both mediate and drive adaptive evolution in pathogen biofilms |
| Q57289942 | Temporal dynamics of Wnt-dependent transcriptome reveals an oncogenic Wnt/MYC/ribosome axis |
| Q63345312 | Temporal enhancer profiling of parallel lineages identifies AHR and GLIS1 as regulators of mesenchymal multipotency |
| Q52644711 | Tetramerization of MADS family transcription factors SEPALLATA3 and AGAMOUS is required for floral meristem determinacy in Arabidopsis. |
| Q41911201 | The APSES transcription factor Efg1 is a global regulator that controls morphogenesis and biofilm formation in Candida parapsilosis. |
| Q89790189 | The African Swine Fever Virus Transcriptome |
| Q58691724 | The Amino Acid Composition of Quadruplex Binding Proteins Reveals a Shared Motif and Predicts New Potential Quadruplex Interactors |
| Q39093205 | The Bio-Analytic Resource for Plant Biology |
| Q90279780 | The CAF-1 complex couples Hippo pathway target gene expression and DNA replication |
| Q90050753 | The Cancer-Associated Genetic Variant Rs3903072 Modulates Immune Cells in the Tumor Microenvironment |
| Q33649701 | The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension |
| Q34995029 | The DNA-binding network of Mycobacterium tuberculosis |
| Q35808875 | The DYW Subgroup PPR Protein MEF35 Targets RNA Editing Sites in the Mitochondrial rpl16, nad4 and cob mRNAs in Arabidopsis thaliana |
| Q90239343 | The Dm-Myb Oncoprotein Contributes to Insulator Function and Stabilizes Repressive H3K27me3 PcG Domains |
| Q40991157 | The Global Redox Responding RegB/RegA Signal Transduction System Regulates the Genes Involved in Ferrous Iron and Inorganic Sulfur Compound Oxidation of the Acidophilic Acidithiobacillus ferrooxidans |
| Q57817108 | The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication |
| Q46321733 | The Ground State and Evolution of Promoter Region Directionality |
| Q38975496 | The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement |
| Q64979973 | The Identification and Interpretation of cis-Regulatory Noncoding Mutations in Cancer. |
| Q64107571 | The Integrity of piRNA Clusters is Abolished by Insulators in the Germline |
| Q93047910 | The Length of the Expressed 3' UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases |
| Q35810173 | The MEME Suite |
| Q28602228 | The Mouse Solitary Odorant Receptor Gene Promoters as Models for the Study of Odorant Receptor Gene Choice |
| Q38762769 | The NANCI-Nkx2.1 gene duplex buffers Nkx2.1 expression to maintain lung development and homeostasis |
| Q55431830 | The PGRS Domain of Mycobacterium tuberculosis PE_PGRS Protein Rv0297 Is Involved in Endoplasmic Reticulum Stress-Mediated Apoptosis through Toll-Like Receptor 4. |
| Q44511470 | The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function. |
| Q41628128 | The SmAP2 RNA binding motif in the 3'UTR affects mRNA stability in the crenarchaeum Sulfolobus solfataricus |
| Q40208191 | The Time Scale of Recombination Rate Evolution in Great Apes |
| Q64084979 | The Transcriptional Landscape of Marek's Disease Virus in Primary Chicken B Cells Reveals Novel Splice Variants and Genes |
| Q42881926 | The Treponema denticola AtcR LytTR domain-containing response regulator interacts with three architecturally distinct promoter elements: implications for understanding the molecular signaling mechanisms that drive the progression of periodontal dise |
| Q37389551 | The Two-Component System RsrS-RsrR Regulates the Tetrathionate Intermediate Pathway for Thiosulfate Oxidation in Acidithiobacillus caldus |
| Q90068812 | The WT1-like transcription factor Klumpfuss maintains lineage commitment of enterocyte progenitors in the Drosophila intestine |
| Q24595581 | The accessible chromatin landscape of the human genome |
| Q46215237 | The analysis of Gene Regulatory Networks in plant evo-devo. |
| Q92319646 | The androgen receptor regulates a druggable translational regulon in advanced prostate cancer |
| Q91895462 | The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements |
| Q37416713 | The caste- and sex-specific DNA methylome of the termite Zootermopsis nevadensis. |
| Q52655776 | The cis-regulatory dynamics of embryonic development at single-cell resolution. |
| Q92867236 | The dyslexia susceptibility KIAA0319 gene shows a specific expression pattern during zebrafish development supporting a role beyond neuronal migration |
| Q35050230 | The epigenome of evolving Drosophila neo-sex chromosomes: dosage compensation and heterochromatin formation |
| Q51554035 | The extracytoplasmic function σ factor σ(C) regulates expression of a branched quinol oxidation pathway in Corynebacterium glutamicum. |
| Q118108008 | The functional and evolutionary impacts of human-specific deletions in conserved elements |
| Q61797755 | The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes |
| Q36991107 | The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. |
| Q35539843 | The global regulatory architecture of transcription during the Caulobacter cell cycle |
| Q33728316 | The histone demethylase KDM3A regulates the transcriptional program of the androgen receptor in prostate cancer cells |
| Q38849899 | The iron stimulon and fur regulon of Geobacter sulfurreducens and their role in energy metabolism |
| Q58786841 | The landscape of the A-to-I RNA editome from 462 human genomes |
| Q22000593 | The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation |
| Q36775463 | The long noncoding RNA Gm15055 represses Hoxa gene expression by recruiting PRC2 to the gene cluster |
| Q47237663 | The modERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors |
| Q91720970 | The murine IgH locus contains a distinct DNA sequence motif for the chromatin regulatory factor CTCF |
| Q35945288 | The orientation of transcription factor binding site motifs in gene promoter regions: does it matter? |
| Q33741148 | The pentatricopeptide repeat protein MTSF2 stabilizes a nad1 precursor transcript and defines the 3΄ end of its 5΄-half intron. |
| Q27977592 | The primary transcriptome of the Escherichia coli O104:H4 pAA plasmid and novel insights into its virulence gene expression and regulation |
| Q93116736 | The protein secretion modulator TMED9 drives CNIH4/TGFα/GLI signaling opposing TMED3-WNT-TCF to promote colon cancer metastases |
| Q92883800 | The purine biosynthesis regulator PurR moonlights as a virulence regulator in Staphylococcus aureus |
| Q39142026 | The quorum-sensing regulator ComA from Bacillus subtilis activates transcription using topologically distinct DNA motifs |
| Q56770267 | The role of Twist1 in mutant huntingtin-induced transcriptional alterations and neurotoxicity |
| Q92439389 | The structural basis for cohesin-CTCF-anchored loops |
| Q37595312 | The systematic analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury. |
| Q90006426 | The transcription factors ActR and SoxR differentially affect the phenazine tolerance of Agrobacterium tumefaciens |
| Q21128760 | The transcriptional cofactor TRIM33 prevents apoptosis in B lymphoblastic leukemia by deactivating a single enhancer |
| Q54964931 | The ΦBT1 large serine recombinase catalyzes DNA integration at pseudo-attB sites in the genus Nocardia. |
| Q28483962 | ThioFinder: a web-based tool for the identification of thiopeptide gene clusters in DNA sequences |
| Q89499082 | Thyroid hormones and androgens differentially regulate gene expression in testes and ovaries of sexually mature Silurana tropicalis |
| Q48358053 | Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo. |
| Q37666053 | Tissue-specific RNA-Seq in human evoked inflammation identifies blood and adipose LincRNA signatures of cardiometabolic diseases |
| Q89263132 | Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers |
| Q30386790 | ToxR Antagonizes H-NS Regulation of Horizontally Acquired Genes to Drive Host Colonization |
| Q91045843 | Transcription factor Foxp1 regulates Foxp3 chromatin binding and coordinates regulatory T cell function |
| Q35530039 | Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells |
| Q39454422 | Transcription factor PRO1 targets genes encoding conserved components of fungal developmental signaling pathways. |
| Q36766594 | Transcription factor motif quality assessment requires systematic comparative analysis |
| Q38823710 | Transcription factor trapping by RNA in gene regulatory elements |
| Q30276192 | Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation |
| Q42152864 | Transcription of Sialic Acid Catabolism Genes in Corynebacterium glutamicum Is Subject to Catabolite Repression and Control by the Transcriptional Repressor NanR. |
| Q55263322 | Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities. |
| Q36035522 | Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs |
| Q91598803 | Transcriptional profiling of Zygosaccharomyces bailii early response to acetic acid or copper stress mediated by ZbHaa1 |
| Q92149978 | Transcriptional regulation of a gonococcal gene encoding a virulence factor (L-lactate permease) |
| Q46604576 | Transcriptional regulation of the Nkx3.1 gene in prostate luminal stem cell specification and cancer initiation via its 3' genomic region. |
| Q48149649 | Transcriptional regulatory control of mammalian nephron progenitors revealed by multi-factor cistromic analysis and genetic studies. |
| Q36348389 | Transcriptional regulatory logic of the diurnal cycle in the mouse liver |
| Q51415889 | Transcriptional regulatory networks underlying gene expression changes in Huntington's disease. |
| Q41186921 | Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti. |
| Q37054369 | Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish |
| Q35616234 | Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors |
| Q41311269 | Transcriptome profiling of mouse brains with qkI-deficient oligodendrocytes reveals major alternative splicing defects including self-splicing. |
| Q55657573 | Transcriptomic Analysis of the Campylobacter jejuni Response to T4-Like Phage NCTC 12673 Infection. |
| Q33364382 | Transcriptomic Effects of the Cell Cycle Regulator LGO in Arabidopsis Sepals |
| Q64101044 | Transcriptomic analysis reveals novel downstream regulatory motifs and highly transcribed virulence factor genes of Entamoeba histolytica |
| Q52731208 | Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells. |
| Q64066516 | Transitions in cell potency during early mouse development are driven by Notch |
| Q54964020 | Translatome Regulation in Neuronal Injury and Axon Regrowth. |
| Q89105578 | Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints |
| Q92709268 | Transposable elements drive widespread expression of oncogenes in human cancers |
| Q36559305 | Transposon integration enhances expression of stress response genes |
| Q35995673 | Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners |
| Q38844877 | Tumorigenesis by Meis1 overexpression is accompanied by a change of DNA target-sequence specificity which allows binding to the AP-1 element |
| Q38886775 | Two new loci and gene sets related to sex determination and cancer progression are associated with susceptibility to testicular germ cell tumor |
| Q90546773 | Two paralogous EcfG σ factors hierarchically orchestrate the activation of the General Stress Response in Sphingopyxis granuli TFA |
| Q47865708 | Two-Element Transcriptional Regulation in the Canonical Wnt Pathway. |
| Q64243846 | TyrR is involved in the transcriptional regulation of biofilm formation and D-alanine catabolism in Azospirillum brasilense Sp7 |
| Q48164547 | Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat |
| Q35591884 | Ubiquitous promoter-localization of essential virulence regulators in Francisella tularensis |
| Q42211716 | Unbiased identification of substrates of protein tyrosine phosphatase ptp-3 in C. elegans |
| Q41329937 | Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity |
| Q93019818 | Uncovering a mitochondrial unfolded protein response in corals and its role in adapting to a changing world |
| Q33768214 | Uncovering the transcriptomic and epigenomic landscape of nicotinic receptor genes in non-neuronal tissues |
| Q50082931 | Understanding Tissue-Specific Gene Regulation. |
| Q36790036 | Understanding multicellular function and disease with human tissue-specific networks |
| Q34165431 | Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing |
| Q35923331 | Unsupervised pattern discovery in human chromatin structure through genomic segmentation |
| Q52657307 | Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival. |
| Q64096876 | Up-regulation of FOXD1 by YAP alleviates senescence and osteoarthritis |
| Q36285408 | Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci. |
| Q34815644 | Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease |
| Q48227408 | WRINKLED1 Rescues Feedback Inhibition of Fatty Acid Synthesis in Hydroxylase-Expressing Seeds |
| Q52719273 | Warming Induces Significant Reprogramming of Beige, but Not Brown, Adipocyte Cellular Identity. |
| Q90524923 | Whole-genome sequencing of Puccinia striiformis f. sp. tritici mutant isolates identifies avirulence gene candidates |
| Q34590420 | Widespread contribution of transposable elements to the innovation of gene regulatory networks |
| Q37197823 | Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development |
| Q60922627 | Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions |
| Q33790871 | Wild tobacco genomes reveal the evolution of nicotine biosynthesis |
| Q46277313 | Xenbase: a genomic, epigenomic and transcriptomic model organism database. |
| Q26773792 | Yersinia Type III Secretion System Master Regulator LcrF |
| Q92685972 | ZIC3 Controls the Transition from Naive to Primed Pluripotency |
| Q41686713 | ZNF516 suppresses EGFR by targeting the CtBP/LSD1/CoREST complex to chromatin |
| Q27304341 | Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control |
| Q53176450 | Zinc-finger protein 471 suppresses gastric cancer through transcriptionally repressing downstream oncogenic PLS3 and TFAP2A. |
| Q58118301 | and , Two Genes Controlling Stationary Phase, Sexual Development and Cell Degeneration in |
| Q36276489 | atSNP: transcription factor binding affinity testing for regulatory SNP detection |
| Q37631864 | c-Jun/c-Fos heterodimers regulate cellular genes via a newly identified class of methylated DNA sequence motifs. |
| Q92380913 | c-MYC regulates mRNA translation efficiency and start-site selection in lymphoma |
| Q89206172 | c-Myc is a novel Leishmania virulence factor by proxy that targets the host miRNA system and is essential for survival in human macrophages |
| Q35885874 | cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism |
| Q47294799 | circlncRNAnet: An integrated web-based resource for mapping functional networks of long or circular forms of non-coding RNAs |
| Q92708007 | cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel |
| Q33966726 | coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq data |
| Q47336496 | dRNA-seq implicates sulfide as master regulator of S(0) metabolism in Chlorobaculum tepidum and other green sulfur bacteria |
| Q46077296 | dbCoRC: a database of core transcriptional regulatory circuitries modeled by H3K27ac ChIP-seq signals. |
| Q42365362 | iDamIDseq and iDEAR: an improved method and computational pipeline to profile chromatin-binding proteins. |
| Q36228406 | iFORM: Incorporating Find Occurrence of Regulatory Motifs |
| Q43518926 | miREval 2.0: a web tool for simple microRNA prediction in genome sequences |
| Q31058957 | p53 transcriptional programs in B cells upon exposure to genotoxic stress in vivo: Computational analysis of next-generation sequencing data |
| Q34487194 | piRNAQuest: searching the piRNAome for silencers |
| Q98771607 | regSNPs-ASB: A Computational Framework for Identifying Allele-Specific Transcription Factor Binding From ATAC-seq Data |
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