Multi-species integrative biclustering

scientific article

Multi-species integrative biclustering is …
instance of (P31):
scholarly articleQ13442814

External links are
P6179Dimensions Publication ID1046296680
P356DOI10.1186/GB-2010-11-9-R96
P2888exact matchhttps://scigraph.springernature.com/pub.10.1186/gb-2010-11-9-r96
P932PMC publication ID2965388
P698PubMed publication ID20920250
P5875ResearchGate publication ID47335465

P50authorRichard BonneauQ7324255
Daniel B. KearnsQ38325842
P2093author name stringDavid J Reiss
Daniel B Kearns
Patrick Eichenberger
Ashley R Bate
Peter Waltman
Thadeous Kacmarczyk
P2860cites workMolecular genetics of sporulation in Bacillus subtilis.Q41291273
Assessing performance of orthology detection strategies applied to eukaryotic genomesQ42025644
DNA microarray analysis of Bacillus subtilis sigma factors of extracytoplasmic function familyQ42595174
The Bacillus subtilis ywkA gene encodes a malic enzyme and its transcription is activated by the YufL/YufM two-component system in response to malateQ44569204
Systematic analysis of SigD-regulated genes in Bacillus subtilis by DNA microarray and Northern blotting analysesQ47918069
A predictive model for transcriptional control of physiology in a free living cell.Q51897861
The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis.Q52107363
Identification of sporulation genes by genome-wide analysis of the sigmaE regulon of Bacillus subtilis.Q52552179
Organization and expression of the Bacillus subtilis sigY operon.Q52553117
FlhF, a signal recognition particle-like GTPase, is involved in the regulation of flagellar arrangement, motility behaviour and protein secretion in Bacillus cereus.Q52580771
Construction of a cloning site near one end of Tn917 into which foreign DNA may be inserted without affecting transposition in Bacillus subtilis or expression of the transposon-borne erm geneQ54472807
Differential gene expression of Listeria monocytogenes during high hydrostatic pressure processing.Q54549170
Genome-wide analysis of temporally regulated and compartment-specific gene expression in sporulating cells of Bacillus subtilisQ59566917
Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA boxQ73567740
A genetic signature of interspecies variations in gene expressionQ79749665
A molecular clutch disables flagella in the Bacillus subtilis biofilmQ81485635
The forespore line of gene expression in Bacillus subtilisQ82645059
The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilisQ21146400
A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of landQ21283975
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networksQ21284254
The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1Q22065990
KEGG: kyoto encyclopedia of genes and genomesQ24515297
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a geneQ24523893
From genomics to chemical genomics: new developments in KEGGQ24538628
Spectral biclustering of microarray data: coclustering genes and conditionsQ24561940
Listeria monocytogenes regulates flagellar motility gene expression through MogR, a transcriptional repressor required for virulenceQ24563423
Genetic aspects of bacterial endospore formationQ24564182
Systematic discovery of nonobvious human disease models through orthologous phenotypesQ24600277
Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide dataQ24625913
KEGG for linking genomes to life and the environmentQ24650347
STRING 8--a global view on proteins and their functional interactions in 630 organismsQ24656073
Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysisQ38357042
The Mouse Genome Database (MGD): mouse biology and model systemsQ38393159
Transcriptional profiling of the Bacillus anthracis life cycle in vitro and an implied model for regulation of spore formationQ38501345
Comparing genomic expression patterns across species identifies shared transcriptional profile in agingQ38522233
Global functional profiling of gene expression.Q38522897
Comprehensive DNA microarray analysis of Bacillus subtilis two-component regulatory systems.Q39505684
LIGAND: chemical database of enzyme reactionsQ39541353
Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK.Q39678911
RSAT: regulatory sequence analysis toolsQ39786125
Mannitol-1-phosphate dehydrogenase (MtlD) is required for mannitol and glucitol assimilation in Bacillus subtilis: possible cooperation of mtl and gut operonsQ39793892
Regulatory sequence analysis toolsQ39804364
Deletion of the Bacillus subtilis isocitrate dehydrogenase gene causes a block at stage I of sporulationQ39846606
Characterization of the sigD transcription unit of Bacillus subtilisQ39931548
Induction of motility and capsulation in Bacillus anthracis.Q40313537
NCBI GEO: mining tens of millions of expression profiles--database and tools updateQ24675443
Stepwise formation of the bacterial flagellar systemQ24683633
A novel method for accurate operon predictions in all sequenced prokaryotesQ24791071
Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approachQ24796408
Similarities and differences in genome-wide expression data of six organismsQ24800747
Prolinks: a database of protein functional linkages derived from coevolutionQ24801555
Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription programQ24810484
A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservationQ25256951
Gene Expression Omnibus: NCBI gene expression and hybridization array data repositoryQ27860523
Fitting a mixture model by expectation maximization to discover motifs in biopolymersQ27860556
Biclustering of expression dataQ28138031
DNA binding sites: representation and discoveryQ28144459
Combining evidence using p-values: application to sequence homology searchesQ28265811
Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzeesQ28270561
Expression profiling in primates reveals a rapid evolution of human transcription factorsQ28300964
The MogR transcriptional repressor regulates nonhierarchal expression of flagellar motility genes and virulence in Listeria monocytogenesQ29346598
The H2O2 stress-responsive regulator PerR positively regulates srfA expression in Bacillus subtilisQ29346689
A gene-coexpression network for global discovery of conserved genetic modulesQ29614451
Identifying DNA and protein patterns with statistically significant alignments of multiple sequencesQ29615307
Automatic clustering of orthologs and in-paralogs from pairwise species comparisonsQ29615401
Singular value decomposition for genome-wide expression data processing and modelingQ29618495
Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organismsQ30776338
Iterative signature algorithm for the analysis of large-scale gene expression dataQ30784636
Discovering local structure in gene expression data: the order-preserving submatrix problemQ30820127
Defining transcription modules using large-scale gene expression dataQ30916115
A systematic comparison and evaluation of biclustering methods for gene expression dataQ31033002
Benchmarking ortholog identification methods using functional genomics dataQ31036627
Discovering biclusters in gene expression data based on high-dimensional linear geometriesQ31153461
Profiling and comprehensive expression analysis of ABC transporter solute-binding proteins of Bacillus subtilis membrane based on a proteomic approachQ33196937
BioNetBuilder: automatic integration of biological networksQ33265164
EDISA: extracting biclusters from multiple time-series of gene expression profilesQ33298681
Genomic and proteomic analysis of the Alkali-Tolerance Response (AlTR) in Listeria monocytogenes 10403SQ33346468
Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studiesQ33379705
Cross species analysis of microarray expression dataQ33428459
QUBIC: a qualitative biclustering algorithm for analyses of gene expression dataQ33464828
Detailing regulatory networks through large scale data integrationQ33510307
MicrobesOnline: an integrated portal for comparative and functional genomicsQ33600574
Catabolite regulation of the Bacillus subtilis ctaBCDEF gene clusterQ33742915
Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeastQ33780778
Metabolic imbalance and sporulation in an isocitrate dehydrogenase mutant of Bacillus subtilisQ33992122
Two ResD-controlled promoters regulate ctaA expression in Bacillus subtilisQ33996236
Predictome: a database of putative functional links between proteinsQ34010645
Role of FliF and FliI of Listeria monocytogenes in flagellar assembly and pathogenicityQ34033803
Automatic policing of biochemical annotations using genomic correlationsQ34110870
Hierarchical evolution of the bacterial sporulation networkQ34149232
How Bacteria Assemble FlagellaQ34194719
Swarming motility in undomesticated Bacillus subtilisQ34214577
Regulation of endospore formation in Bacillus subtilisQ34307580
Krebs cycle function is required for activation of the Spo0A transcription factor in Bacillus subtilisQ34508814
Overexpression of PrfA leads to growth inhibition of Listeria monocytogenes in glucose-containing culture media by interfering with glucose uptakeQ34697229
The KEGG database.Q35050215
The transcriptional profile of early to middle sporulation in Bacillus subtilis.Q35175821
Comparative analysis indicates regulatory neofunctionalization of yeast duplicatesQ35850302
Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumorsQ35906418
Origins of flagellar gene operons and secondary flagellar systemsQ36098399
An operon of Bacillus subtilis motility genes transcribed by the sigma D form of RNA polymeraseQ36113348
Comparative transcriptome analysis of Listeria monocytogenes strains of the two major lineages reveals differences in virulence, cell wall, and stress responseQ36137085
Transcriptional organization of a cloned chemotaxis locus of Bacillus subtilisQ36159903
Phenotypic and transcriptomic analyses demonstrate interactions between the transcriptional regulators CtsR and Sigma B in Listeria monocytogenesQ36313500
Transcriptomic and phenotypic analyses suggest a network between the transcriptional regulators HrcA and sigmaB in Listeria monocytogenesQ36313512
Comparative analysis of the sigma B-dependent stress responses in Listeria monocytogenes and Listeria innocua strains exposed to selected stress conditionsQ36420828
Loss of flagellum-based motility by Listeria monocytogenes results in formation of hyperbiofilmsQ36845573
Comparative biology: beyond sequence analysisQ36907995
DNA microarray analysis of Bacillus subtilis DegU, ComA and PhoP regulons: an approach to comprehensive analysis of B.subtilis two-component regulatory systems.Q38296966
Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis.Q38304662
Bacillus subtilis RghR (YvaN) represses rapG and rapH, which encode inhibitors of expression of the srfA operonQ38314827
Bacillus subtilis LmrA is a repressor of the lmrAB and yxaGH operons: identification of its binding site and functional analysis of lmrB and yxaGH.Q38337578
P4510describes a project that usesCytoscapeQ3699942
P433issue9
P304page(s)R96
P577publication date2010-09-29
P1433published inGenome BiologyQ5533480
P1476titleMulti-species integrative biclustering
P478volume11

Reverse relations

cites work (P2860)
Q55379249A Hierarchical Framework for State-Space Matrix Inference and Clustering.
Q30971184A hierarchical Bayesian model for flexible module discovery in three-way time-series data
Q30572998A novel biclustering approach with iterative optimization to analyze gene expression data
Q40312082An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network.
Q41251692Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules
Q89997489BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus
Q39535857Comparative microbial modules resource: generation and visualization of multi-species biclusters.
Q97646056High-Throughput Screen for Cell Wall Synthesis Network Module in Mycobacterium tuberculosis Based on Integrated Bioinformatics Strategy
Q34366411Identifying multi-layer gene regulatory modules from multi-dimensional genomic data
Q38000683Integrated inference and analysis of regulatory networks from multi-level measurements
Q26824897Integrative approaches for finding modular structure in biological networks
Q30844373Inter-species pathway perturbation prediction via data-driven detection of functional homology
Q52681322It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data.
Q61810617Multi-study inference of regulatory networks for more accurate models of gene regulation
Q34189620QServer: a biclustering server for prediction and assessment of co-expressed gene clusters
Q40413653Reconstruction and Analysis of the Evolution of Modular Transcriptional Regulatory Programs Using Arboretum
Q36337384Reverse engineering systems models of regulation: discovery, prediction and mechanisms
Q31092338Sparse group factor analysis for biclustering of multiple data sources
Q34020907Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees
Q40891278xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model

Search more.