Published in BMC Bioinformatics on July 19, 2010
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Model-based deconvolution of genome-wide DNA binding. Bioinformatics (2007) 1.70
Prevalence of transcription promoters within archaeal operons and coding sequences. Mol Syst Biol (2009) 1.62
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The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol (2006) 5.22
CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A (2008) 4.89
Visualization of omics data for systems biology. Nat Methods (2010) 4.59
The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics (2006) 4.05
A predictive model for transcriptional control of physiology in a free living cell. Cell (2007) 3.35
Peroxiredoxins are conserved markers of circadian rhythms. Nature (2012) 2.95
BioNetBuilder: automatic integration of biological networks. Bioinformatics (2006) 2.76
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics (2006) 2.57
BayGO: Bayesian analysis of ontology term enrichment in microarray data. BMC Bioinformatics (2006) 2.13
Catabolite control protein A (CcpA) contributes to virulence and regulation of sugar metabolism in Streptococcus pneumoniae. J Bacteriol (2005) 2.09
Model-based deconvolution of genome-wide DNA binding. Bioinformatics (2007) 1.70
Prevalence of transcription promoters within archaeal operons and coding sequences. Mol Syst Biol (2009) 1.62
The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. BMC Bioinformatics (2007) 1.51
General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A (2007) 1.42
A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Genome Res (2012) 1.37
A systems view of haloarchaeal strategies to withstand stress from transition metals. Genome Res (2006) 1.35
The anatomy of microbial cell state transitions in response to oxygen. Genome Res (2007) 1.26
Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biol (2004) 1.25
HTself: self-self based statistical test for low replication microarray studies. DNA Res (2005) 1.21
Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1. Mol Cell Proteomics (2003) 1.15
Parallel evolution of transcriptome architecture during genome reorganization. Genome Res (2011) 1.14
Low-pass sequencing for microbial comparative genomics. BMC Genomics (2004) 1.11
An integrated systems approach for understanding cellular responses to gamma radiation. Mol Syst Biol (2006) 1.11
metaXCMS: second-order analysis of untargeted metabolomics data. Anal Chem (2010) 1.10
A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability. Mol Syst Biol (2009) 1.07
miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling. Nucleic Acids Res (2011) 1.04
Coordination of frontline defense mechanisms under severe oxidative stress. Mol Syst Biol (2010) 1.04
Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. J Proteome Res (2008) 1.03
Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network. Genome Biol (2014) 0.99
Multi-species integrative biclustering. Genome Biol (2010) 0.99
Global analysis of mRNA stability in Mycobacterium tuberculosis. Nucleic Acids Res (2012) 0.98
The role of predictive modelling in rationally re-engineering biological systems. Nat Rev Microbiol (2009) 0.96
Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana. Proc Natl Acad Sci U S A (2013) 0.95
Diurnally entrained anticipatory behavior in archaea. PLoS One (2009) 0.94
A major role for nonenzymatic antioxidant processes in the radioresistance of Halobacterium salinarum. J Bacteriol (2011) 0.93
Site-directed gene disruption in Xylella fastidiosa. FEMS Microbiol Lett (2002) 0.93
Niche adaptation by expansion and reprogramming of general transcription factors. Mol Syst Biol (2011) 0.92
A role for programmed cell death in the microbial loop. PLoS One (2013) 0.92
Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon. Nucleic Acids Res (2010) 0.90
Learning transcriptional networks from the integration of ChIP-chip and expression data in a non-parametric model. Bioinformatics (2010) 0.88
A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen. Genome Res (2013) 0.87
Effects of H2 and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis. J Bacteriol (2013) 0.87
The single extracytoplasmic-function sigma factor of Xylella fastidiosa is involved in the heat shock response and presents an unusual regulatory mechanism. J Bacteriol (2006) 0.86
Molecular mechanisms of system responses to novel stimuli are predictable from public data. Nucleic Acids Res (2013) 0.85
Genome sequence of "Candidatus Microthrix parvicella" Bio17-1, a long-chain-fatty-acid-accumulating filamentous actinobacterium from a biological wastewater treatment plant. J Bacteriol (2012) 0.84
Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis. BMC Syst Biol (2010) 0.84
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Metallochaperones regulate intracellular copper levels. PLoS Comput Biol (2013) 0.81
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Specificity of anion binding in the substrate pocket of bacteriorhodopsin. Biochemistry (2004) 0.80
Role of sigma54 in the regulation of genes involved in type I and type IV pili biogenesis in Xylella fastidiosa. Arch Microbiol (2007) 0.80
Intracytoplasmic copper homeostasis controls cytochrome c oxidase production. MBio (2014) 0.80
An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Mol Microbiol (2014) 0.80
Global gene expression analysis during germination in the chytridiomycete Blastocladiella emersonii. Eukaryot Cell (2008) 0.79
Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon. BMC Microbiol (2010) 0.78
Model organisms retain an "ecological memory" of complex ecologically relevant environmental variation. Appl Environ Microbiol (2014) 0.78
Modeling the evolution of C4 photosynthesis. Cell (2013) 0.76
Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea. RNA Biol (2015) 0.76
The F-box protein FBXO25 promotes the proteasome-dependent degradation of ELK-1 protein. J Biol Chem (2013) 0.76
Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions. BMC Syst Biol (2015) 0.75
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GTC: A web server for integrating systems biology data with web tools and desktop applications. Source Code Biol Med (2010) 0.75
Reverse engineering systems models of regulation: discovery, prediction and mechanisms. Curr Opin Biotechnol (2011) 0.75
Harnessing the power of human tumor-derived cell lines for the rational design of cancer therapies. Pigment Cell Melanoma Res (2012) 0.75
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