Published in Bioinformatics on January 01, 2002
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science (2009) 6.07
Learning a prior on regulatory potential from eQTL data. PLoS Genet (2009) 3.31
CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity. Cell (2015) 1.38
DNA microarray data and contextual analysis of correlation graphs. BMC Bioinformatics (2003) 1.07
A scale-free structure prior for graphical models with applications in functional genomics. PLoS One (2010) 0.97
Validating module network learning algorithms using simulated data. BMC Bioinformatics (2007) 0.94
Regulatory module network of basic/helix-loop-helix transcription factors in mouse brain. Genome Biol (2007) 0.93
Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells. BMC Genomics (2012) 0.88
Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data. BMC Bioinformatics (2013) 0.87
Interspecies translation of disease networks increases robustness and predictive accuracy. PLoS Comput Biol (2011) 0.86
Identification of functional modules based on transcriptional regulation structure. BMC Proc (2008) 0.84
Discovering conditional co-regulated protein complexes by integrating diverse data sources. BMC Syst Biol (2010) 0.83
Reprogramming of lysosomal gene expression by interleukin-4 and Stat6. BMC Genomics (2013) 0.82
Coherent functional modules improve transcription factor target identification, cooperativity prediction, and disease association. PLoS Genet (2014) 0.81
Robustness of transcriptional regulatory program influences gene expression variability. BMC Genomics (2009) 0.79
Compartmentalized gene regulatory network of the pathogenic fungus Fusarium graminearum. New Phytol (2016) 0.77
Estimation of Gene Regulatory Networks. Postdoc J (2013) 0.75
Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A (2009) 20.66
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat Genet (2008) 17.67
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev (2011) 16.77
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet (2003) 14.56
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell (2010) 12.27
lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature (2011) 11.31
Three-dimensional folding and functional organization principles of the Drosophila genome. Cell (2012) 9.19
Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods (2010) 9.09
A module map showing conditional activity of expression modules in cancer. Nat Genet (2004) 8.57
SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat Genet (2009) 7.48
Natural history and evolutionary principles of gene duplication in fungi. Nature (2007) 7.26
Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell (2011) 7.03
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature (2013) 6.50
A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature (2012) 6.34
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science (2009) 6.07
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A (2009) 6.01
Comparative functional genomics of the fission yeasts. Science (2011) 6.00
Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet (2011) 5.97
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature (2010) 5.79
Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci U S A (2006) 5.62
Deterministic direct reprogramming of somatic cells to pluripotency. Nature (2013) 5.18
A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell (2009) 4.98
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science (2014) 4.91
Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1. Nature (2013) 4.74
Induction and molecular signature of pathogenic TH17 cells. Nat Immunol (2012) 4.43
From signatures to models: understanding cancer using microarrays. Nat Genet (2005) 4.29
Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line. Proc Natl Acad Sci U S A (2008) 4.20
Dynamic single-cell imaging of direct reprogramming reveals an early specifying event. Nat Biotechnol (2010) 3.98
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol (2011) 3.81
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res (2011) 3.81
A global view of pleiotropy and phenotypically derived gene function in yeast. Mol Syst Biol (2005) 3.70
Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet (2009) 3.59
Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc Natl Acad Sci U S A (2005) 3.58
High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science (2011) 3.53
EXPANDER--an integrative program suite for microarray data analysis. BMC Bioinformatics (2005) 3.43
Proto-genes and de novo gene birth. Nature (2012) 3.43
Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos. PLoS Biol (2009) 3.24
BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24
Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell (2011) 3.20
Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol (2010) 3.09
Dynamic regulatory network controlling TH17 cell differentiation. Nature (2013) 3.07
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell (2012) 3.04
Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression. Proc Natl Acad Sci U S A (2004) 2.99
The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. Cell (2012) 2.78
Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science (2014) 2.77
Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nat Methods (2013) 2.71
Structure and function of a transcriptional network activated by the MAPK Hog1. Nat Genet (2008) 2.67
Chromatin signature of embryonic pluripotency is established during genome activation. Nature (2010) 2.64
Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science (2014) 2.63
Transcriptional regulatory circuits: predicting numbers from alphabets. Science (2009) 2.61
The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol (2010) 2.53
Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics (2007) 2.52
Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J (2013) 2.48
Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods (2012) 2.42
High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell (2013) 2.35
Dissecting timing variability in yeast meiosis. Cell (2007) 2.35
Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods (2009) 2.26
Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. Nat Genet (2012) 2.20
Expander: from expression microarrays to networks and functions. Nat Protoc (2010) 2.12
Conservation and divergence in the transcriptional programs of the human and mouse immune systems. Proc Natl Acad Sci U S A (2013) 1.94
H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Mol Cell (2010) 1.85
Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection. Cell (2011) 1.84
Digital transcriptome profiling from attomole-level RNA samples. Genome Res (2010) 1.83
Systematic discovery of TLR signaling components delineates viral-sensing circuits. Cell (2011) 1.83
Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network. Nat Biotechnol (2008) 1.82
Impulse control: temporal dynamics in gene transcription. Cell (2011) 1.79
Identification of transcriptional regulators in the mouse immune system. Nat Immunol (2013) 1.79
A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation. Dev Cell (2012) 1.72
Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture. PLoS Genet (2010) 1.68
The transcriptional landscape of αβ T cell differentiation. Nat Immunol (2013) 1.61
Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs. Development (2013) 1.54
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
Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting. PLoS Genet (2006) 1.48
A probabilistic methodology for integrating knowledge and experiments on biological networks. J Comput Biol (2006) 1.47
Systematic dissection of roles for chromatin regulators in a yeast stress response. PLoS Biol (2012) 1.44
Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Res (2011) 1.37
Gene duplication and the evolution of ribosomal protein gene regulation in yeast. Proc Natl Acad Sci U S A (2010) 1.33
Integrative genomic analysis implicates gain of PIK3CA at 3q26 and MYC at 8q24 in chronic lymphocytic leukemia. Clin Cancer Res (2012) 1.33
Revealing targeted therapy for human cancer by gene module maps. Cancer Res (2008) 1.29
Addiction of t(8;21) and inv(16) acute myeloid leukemia to native RUNX1. Cell Rep (2013) 1.22
Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells. Stem Cell Reports (2013) 1.19
Dynamic combinatorial interactions of RUNX1 and cooperating partners regulates megakaryocytic differentiation in cell line models. Blood (2010) 1.18
Genome-wide identification and characterization of replication origins by deep sequencing. Genome Biol (2012) 1.18
Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations. Curr Biol (2010) 1.15
Strategies to discover regulatory circuits of the mammalian immune system. Nat Rev Immunol (2011) 1.10
Revisiting the Saccharomyces cerevisiae predicted ORFeome. Genome Res (2008) 1.07
Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast. PLoS Comput Biol (2010) 1.07
Evolutionary principles of modular gene regulation in yeasts. Elife (2013) 1.05
Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis. BMC Genomics (2012) 1.05
Modeling and analysis of heterogeneous regulation in biological networks. J Comput Biol (2004) 1.03
Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli. Nat Biotechnol (2013) 1.03
Convergent Evolution of Calcineurin Pathway Roles in Thermotolerance and Virulence in Candida glabrata. G3 (Bethesda) (2012) 1.02
From elements to modules: regulatory evolution in Ascomycota fungi. Curr Opin Genet Dev (2009) 1.02
Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia. Nano Lett (2012) 1.01
A functional selection model explains evolutionary robustness despite plasticity in regulatory networks. Mol Syst Biol (2012) 0.99
DNA methylation programming and reprogramming in primate embryonic stem cells. Genome Res (2009) 0.99