Published in Genome Res on April 01, 2003
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Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets. Plant Cell (2011) 1.08
Lineage specificity of gene expression patterns. Proc Natl Acad Sci U S A (2004) 1.07
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A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data. J Math Biol (2011) 0.97
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Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae. BMC Bioinformatics (2006) 0.95
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Discovery and visualization of miRNA-mRNA functional modules within integrated data using bicluster analysis. Nucleic Acids Res (2013) 0.86
Extracting expression modules from perturbational gene expression compendia. BMC Syst Biol (2008) 0.86
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Transcription factor network reconstruction using the living cell array. J Theor Biol (2008) 0.83
Dual activation of pathways regulated by steroid receptors and peptide growth factors in primary prostate cancer revealed by Factor Analysis of microarray data. BMC Genomics (2005) 0.83
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Linking Genes to Cardiovascular Diseases: Gene Action and Gene-Environment Interactions. J Cardiovasc Transl Res (2015) 0.80
A search engine to identify pathway genes from expression data on multiple organisms. BMC Syst Biol (2007) 0.79
ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants. Plant Methods (2006) 0.79
Extracting regulatory modules from gene expression data by sequential pattern mining. BMC Genomics (2011) 0.79
Comparative microbial modules resource: generation and visualization of multi-species biclusters. PLoS Comput Biol (2011) 0.78
UNCLES: method for the identification of genes differentially consistently co-expressed in a specific subset of datasets. BMC Bioinformatics (2015) 0.78
UniBic: Sequential row-based biclustering algorithm for analysis of gene expression data. Sci Rep (2016) 0.78
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eMBI: Boosting Gene Expression-based Clustering for Cancer Subtypes. Cancer Inform (2014) 0.78
An efficient voting algorithm for finding additive biclusters with random background. J Comput Biol (2008) 0.77
Nonlinear dependence in the discovery of differentially expressed genes. ISRN Bioinform (2012) 0.77
A systematic comparative evaluation of biclustering techniques. BMC Bioinformatics (2017) 0.77
Categories and Functional Units: An Infinite Hierarchical Model for Brain Activations. Adv Neural Inf Process Syst (2010) 0.77
Model validation for gene selection and regulation maps. Funct Integr Genomics (2007) 0.76
A composite model for subgroup identification and prediction via bicluster analysis. PLoS One (2014) 0.75
A GPU-accelerated algorithm for biclustering analysis and detection of condition-dependent coexpression network modules. Sci Rep (2017) 0.75
Clustering Algorithms: Their Application to Gene Expression Data. Bioinform Biol Insights (2016) 0.75
Biclustering of linear patterns in gene expression data. J Comput Biol (2012) 0.75
Clustering cancer gene expression data by projective clustering ensemble. PLoS One (2017) 0.75
Identifying Multi-Dimensional Co-Clusters in Tensors Based on Hyperplane Detection in Singular Vector Spaces. PLoS One (2016) 0.75
Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering. PLoS Comput Biol (2016) 0.75
Two-way learning with one-way supervision for gene expression data. BMC Bioinformatics (2017) 0.75
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Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36
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Genomic and proteomic analysis of the myeloid differentiation program. Blood (2001) 1.55
CLIFF: clustering of high-dimensional microarray data via iterative feature filtering using normalized cuts. Bioinformatics (2001) 1.52
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
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The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
Landscape of transcription in human cells. Nature (2012) 20.18
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
Divergence of transcription factor binding sites across related yeast species. Science (2007) 7.10
Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
Relating whole-genome expression data with protein-protein interactions. Genome Res (2002) 5.78
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev (2007) 4.62
Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A (2003) 3.89
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res (2006) 3.62
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61
Genomic analysis of essentiality within protein networks. Trends Genet (2004) 3.52
Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A (2006) 3.51
Modeling ChIP sequencing in silico with applications. PLoS Comput Biol (2008) 3.48
GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc Natl Acad Sci U S A (2002) 3.41
Structured digital abstract makes text mining easy. Nature (2007) 3.38
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol (2008) 3.34
Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A (2010) 3.28
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev (2002) 3.27
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res (2005) 3.23
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) 3.22
The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. Am J Med Genet A (2012) 3.12
Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature (2012) 3.09
Getting connected: analysis and principles of biological networks. Genes Dev (2007) 3.03
Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00
Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches. Cell (2007) 2.95
Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. Curr Opin Microbiol (2004) 2.92
Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A (2010) 2.90
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res (2005) 2.89
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res (2002) 2.89
PubNet: a flexible system for visualizing literature derived networks. Genome Biol (2005) 2.89
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res (2002) 2.88
PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics (2006) 2.85
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res (2003) 2.85
Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A (2009) 2.83
The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. Dev Cell (2005) 2.81
Modeling gene expression using chromatin features in various cellular contexts. Genome Biol (2012) 2.76
Genomics. Defining genes in the genomics era. Science (2003) 2.73
Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins (2002) 2.72
MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes Dev (2008) 2.66
DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci U S A (2004) 2.66
Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 2.66
Major molecular differences between mammalian sexes are involved in drug metabolism and renal function. Dev Cell (2004) 2.65
Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends Genet (2002) 2.65
Actions as space-time shapes. IEEE Trans Pattern Anal Mach Intell (2007) 2.62
Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium. Methods Enzymol (2005) 2.54
Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet (2004) 2.51
Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol (2007) 2.48
Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet (2010) 2.46
TOS9 regulates white-opaque switching in Candida albicans. Eukaryot Cell (2006) 2.42
Target hub proteins serve as master regulators of development in yeast. Genes Dev (2006) 2.39
Large-scale analysis of pseudogenes in the human genome. Curr Opin Genet Dev (2004) 2.38
Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet (2003) 2.38
Personal genome sequencing: current approaches and challenges. Genes Dev (2010) 2.38
Conformational changes associated with protein-protein interactions. Curr Opin Struct Biol (2004) 2.37
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet (2005) 2.36
Assessing the limits of genomic data integration for predicting protein networks. Genome Res (2005) 2.33
Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J Mol Biol (2005) 2.32
The protein target list of the Northeast Structural Genomics Consortium. Proteins (2004) 2.31
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res (2010) 2.30
CREB binds to multiple loci on human chromosome 22. Mol Cell Biol (2004) 2.28
RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics (2010) 2.26
Modelling the recent common ancestry of all living humans. Nature (2004) 2.22
3V: cavity, channel and cleft volume calculator and extractor. Nucleic Acids Res (2010) 2.20
Regulation of gene expression by a metabolic enzyme. Science (2004) 2.15
Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proc Natl Acad Sci U S A (2007) 2.15
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Information assessment on predicting protein-protein interactions. BMC Bioinformatics (2004) 2.14
Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. Genome Biol (2010) 2.12
Studying genomes through the aeons: protein families, pseudogenes and proteome evolution. J Mol Biol (2002) 2.07
Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies. Nat Struct Mol Biol (2008) 2.07
A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Res (2002) 2.07
Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. BMC Genomics (2010) 2.03
A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation. Genome Res (2008) 2.01
Global changes in STAT target selection and transcription regulation upon interferon treatments. Genes Dev (2005) 2.01
Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinformatics (2002) 2.00