Published in Genome Res on May 01, 2004
Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res (2006) 3.67
Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc Natl Acad Sci U S A (2005) 3.58
Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network. Nat Biotechnol (2008) 1.82
Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence. Genome Res (2005) 1.44
Coding limits on the number of transcription factors. BMC Genomics (2006) 1.38
CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features. Genome Biol (2009) 1.38
Functional characterization of variations on regulatory motifs. PLoS Genet (2008) 0.99
Tree-based position weight matrix approach to model transcription factor binding site profiles. PLoS One (2011) 0.96
Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites. PLoS Comput Biol (2008) 0.96
Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus. Mol Biol Evol (2011) 0.92
Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis. BMC Bioinformatics (2005) 0.89
Impact of DNA-binding position variants on yeast gene expression. Nucleic Acids Res (2009) 0.81
Evidence that purifying selection acts on promoter sequences. Genetics (2011) 0.79
Computational identification of transcriptionally co-regulated genes, validation with the four ANT isoform genes. BMC Genomics (2012) 0.78
Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast. PLoS One (2012) 0.75
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol (1994) 37.96
Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell (2000) 36.09
TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res (2003) 29.26
Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science (2001) 17.11
Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science (2003) 16.49
DNA binding sites: representation and discovery. Bioinformatics (2000) 16.01
Detection of regulatory variation in mouse genes. Nat Genet (2002) 5.76
Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res (2001) 4.22
Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science (2001) 3.69
Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol Biol (2003) 2.67
Rapid evolution of cis-regulatory sequences via local point mutations. Mol Biol Evol (2001) 2.51
Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities. J Mol Biol (2002) 1.60
Positive and negative autoregulation of REB1 transcription in Saccharomyces cerevisiae. Mol Cell Biol (1998) 1.29
SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat Genet (2009) 7.48
Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in culture. Cell Stem Cell (2011) 6.82
Discovering statistically significant biclusters in gene expression data. Bioinformatics (2002) 6.17
Network-based prediction of protein function. Mol Syst Biol (2007) 6.13
Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci U S A (2006) 5.62
Regulatory networks define phenotypic classes of human stem cell lines. Nature (2008) 4.98
A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell (2009) 4.98
GERBIL: Genotype resolution and block identification using likelihood. Proc Natl Acad Sci U S A (2004) 4.36
Modelling and analysis of gene regulatory networks. Nat Rev Mol Cell Biol (2008) 4.36
How prevalent is functional alternative splicing in the human genome? Trends Genet (2004) 3.81
Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res (2003) 3.79
A global view of pleiotropy and phenotypically derived gene function in yeast. Mol Syst Biol (2005) 3.70
Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc Natl Acad Sci U S A (2005) 3.58
Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc Natl Acad Sci U S A (2004) 3.49
Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. Genome Res (2008) 3.09
CLICK and EXPANDER: a system for clustering and visualizing gene expression data. Bioinformatics (2003) 3.07
Identification of functional modules using network topology and high-throughput data. BMC Syst Biol (2007) 3.00
A fast method for computing high-significance disease association in large population-based studies. Am J Hum Genet (2006) 2.84
Computing has changed biology--biology education must catch up. Science (2009) 2.58
Comprehensive microRNA profiling reveals a unique human embryonic stem cell signature dominated by a single seed sequence. Stem Cells (2008) 2.52
A block-free hidden Markov model for genotypes and its application to disease association. J Comput Biol (2005) 2.52
A non-EST-based method for exon-skipping prediction. Genome Res (2004) 2.15
Expander: from expression microarrays to networks and functions. Nat Protoc (2010) 2.12
Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol (2005) 2.02
Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks. Mol Syst Biol (2007) 1.83
Systematic discovery of TLR signaling components delineates viral-sensing circuits. Cell (2011) 1.83
Tag SNP selection in genotype data for maximizing SNP prediction accuracy. Bioinformatics (2005) 1.73
A randomization test for controlling population stratification in whole-genome association studies. Am J Hum Genet (2007) 1.73
Accurate identification of alternatively spliced exons using support vector machine. Bioinformatics (2004) 1.66
DEGAS: de novo discovery of dysregulated pathways in human diseases. PLoS One (2010) 1.59
The canine olfactory subgenome. Genomics (2004) 1.55
A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription. Nat Genet (2007) 1.53
Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing. Nat Genet (2013) 1.52
A probabilistic methodology for integrating knowledge and experiments on biological networks. J Comput Biol (2006) 1.47
The degenerate primer design problem. Bioinformatics (2002) 1.46
A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking. Nat Struct Mol Biol (2010) 1.44
Refinement and expansion of signaling pathways: the osmotic response network in yeast. Genome Res (2007) 1.39
Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium. Mol Syst Biol (2005) 1.36
Identifying functional modules using expression profiles and confidence-scored protein interactions. Bioinformatics (2009) 1.35
From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. Mol Syst Biol (2008) 1.35
SPIKE--a database, visualization and analysis tool of cellular signaling pathways. BMC Bioinformatics (2008) 1.35
Towards computational prediction of microRNA function and activity. Nucleic Acids Res (2010) 1.32
Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis. Genome Biol (2005) 1.31
A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs. Genome Biol (2005) 1.31
Transcriptional modulation induced by ionizing radiation: p53 remains a central player. Mol Oncol (2011) 1.23
SPIKE: a database of highly curated human signaling pathways. Nucleic Acids Res (2010) 1.23
Integration of transcriptomics, proteomics, and microRNA analyses reveals novel microRNA regulation of targets in the mammalian inner ear. PLoS One (2011) 1.15
Dissection of regulatory networks that are altered in disease via differential co-expression. PLoS Comput Biol (2013) 1.14
Deciphering transcriptional regulatory elements that encode specific cell cycle phasing by comparative genomics analysis. Cell Cycle (2005) 1.12
Allegro: analyzing expression and sequence in concert to discover regulatory programs. Nucleic Acids Res (2009) 1.11
Two notes on genome rearrangement. J Bioinform Comput Biol (2003) 1.10
SlimPLS: a method for feature selection in gene expression-based disease classification. PLoS One (2009) 1.07
Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy. Genome Biol (2011) 1.07
Gene expression signature of human cancer cell lines treated with the ras inhibitor salirasib (S-farnesylthiosalicylic acid). Cancer Res (2007) 1.05
Constructing logical models of gene regulatory networks by integrating transcription factor-DNA interactions with expression data: an entropy-based approach. J Comput Biol (2012) 1.05
Modeling and analysis of heterogeneous regulation in biological networks. J Comput Biol (2004) 1.03
Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments. Mol Syst Biol (2009) 1.03
A computational method for resequencing long DNA targets by universal oligonucleotide arrays. Proc Natl Acad Sci U S A (2002) 1.02
The degenerate primer design problem: theory and applications. J Comput Biol (2005) 1.02
Digital cell quantification identifies global immune cell dynamics during influenza infection. Mol Syst Biol (2014) 1.02
Pediatric onset Crohn's colitis is characterized by genotype-dependent age-related susceptibility. Inflamm Bowel Dis (2007) 1.01
Different sets of QTLs influence fitness variation in yeast. Mol Syst Biol (2010) 1.00
Environmental stresses disrupt telomere length homeostasis. PLoS Genet (2013) 1.00
A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data. Nucleic Acids Res (2014) 0.99
Topology-free querying of protein interaction networks. J Comput Biol (2010) 0.99
GEVALT: an integrated software tool for genotype analysis. BMC Bioinformatics (2007) 0.98
In silico identification of transcriptional regulators associated with c-Myc. Nucleic Acids Res (2004) 0.98
Functional genomic delineation of TLR-induced transcriptional networks. BMC Genomics (2007) 0.97
Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites. PLoS Comput Biol (2008) 0.96
The restriction scaffold problem. J Comput Biol (2003) 0.96
Degenerate primer design: theoretical analysis and the HYDEN program. Methods Mol Biol (2007) 0.95
Towards accurate imputation of quantitative genetic interactions. Genome Biol (2009) 0.93
DEFOG: a practical scheme for deciphering families of genes. Genomics (2002) 0.92
MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data. Genome Biol (2008) 0.92
Assessment of algorithms for inferring positional weight matrix motifs of transcription factor binding sites using protein binding microarray data. PLoS One (2012) 0.91
RAP: accurate and fast motif finding based on protein-binding microarray data. J Comput Biol (2013) 0.90
Systematic inference of highways of horizontal gene transfer in prokaryotes. Bioinformatics (2013) 0.90
Fast lossless compression via cascading Bloom filters. BMC Bioinformatics (2014) 0.90
PrtT-regulated proteins secreted by Aspergillus fumigatus activate MAPK signaling in exposed A549 lung cells leading to necrotic cell death. PLoS One (2011) 0.88
Multilevel modeling and inference of transcription regulation. J Comput Biol (2004) 0.88
Assessing the number of ancestral alternatively spliced exons in the human genome. BMC Genomics (2006) 0.87
Understanding gene sequence variation in the context of transcription regulation in yeast. PLoS Genet (2010) 0.87
Network-induced classification kernels for gene expression profile analysis. J Comput Biol (2012) 0.86
Risk factors for perianal Crohn's disease: the role of genotype, phenotype, and ethnicity. Am J Gastroenterol (2007) 0.86
Detecting excess radical replacements in phylogenetic trees. Gene (2003) 0.85
The MORPH algorithm: ranking candidate genes for membership in Arabidopsis and tomato pathways. Plant Cell (2012) 0.85
Sorting cancer karyotypes by elementary operations. J Comput Biol (2009) 0.85
Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case. BMC Syst Biol (2010) 0.82
Detecting highways of horizontal gene transfer. J Comput Biol (2011) 0.82
E2F1 identified by promoter and biochemical analysis as a central target of glioblastoma cell-cycle arrest in response to Ras inhibition. Int J Cancer (2006) 0.82
TORQUE: topology-free querying of protein interaction networks. Nucleic Acids Res (2009) 0.81
Detecting pathways transcriptionally correlated with clinical parameters. Comput Syst Bioinformatics Conf (2008) 0.81
Ras inhibits endoplasmic reticulum stress in human cancer cells with amplified Myc. Int J Cancer (2010) 0.80
A novel candidate cis-regulatory motif pair in the promoters of germline and oogenesis genes in C. elegans. Genome Res (2011) 0.80
PIVOT: protein interacions visualizatiOn tool. Bioinformatics (2004) 0.80
A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.80
A faster algorithm for simultaneous alignment and folding of RNA. J Comput Biol (2010) 0.80
Transcriptional and proteomic analysis of the Aspergillus fumigatus ΔprtT protease-deficient mutant. PLoS One (2012) 0.79