Published in Nucleic Acids Res on October 25, 2007
DiRE: identifying distant regulatory elements of co-expressed genes. Nucleic Acids Res (2008) 1.42
Transcriptional programs: modelling higher order structure in transcriptional control. BMC Bioinformatics (2009) 0.83
Deriving transcriptional programs and functional processes from gene expression databases. Bioinformatics (2012) 0.79
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res (2006) 22.20
JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res (2004) 19.32
Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell (2002) 17.32
Transcriptional activation by recruitment. Nature (1997) 10.44
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Transcriptional regulation and function during the human cell cycle. Nat Genet (2001) 5.89
A predictive model for regulatory sequences directing liver-specific transcription. Genome Res (2001) 5.16
oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes. Nucleic Acids Res (2005) 4.52
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res (2006) 4.32
Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell (2004) 3.82
Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res (2003) 3.79
Toucan: deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Res (2003) 3.68
Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J Mol Biol (2004) 3.54
A probabilistic method to detect regulatory modules. Bioinformatics (2003) 3.24
Myogenic regulatory factors and the specification of muscle progenitors in vertebrate embryos. Annu Rev Cell Dev Biol (2002) 3.21
Pbx marks genes for activation by MyoD indicating a role for a homeodomain protein in establishing myogenic potential. Mol Cell (2004) 3.15
E2Fs link the control of G1/S and G2/M transcription. EMBO J (2004) 2.81
Megabase deletions of gene deserts result in viable mice. Nature (2004) 2.68
Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res (2003) 2.50
CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics (2003) 2.42
DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PLoS Comput Biol (2007) 2.37
Conservation of regulatory elements between two species of Drosophila. BMC Bioinformatics (2003) 2.06
CREME: Cis-Regulatory Module Explorer for the human genome. Nucleic Acids Res (2004) 1.96
Modulation of hepatic gene expression by hepatocyte nuclear factor 1. Science (1997) 1.79
ETO-2 associates with SCL in erythroid cells and megakaryocytes and provides repressor functions in erythropoiesis. Mol Cell Biol (2005) 1.70
The Hox cofactor and proto-oncogene Pbx1 is required for maintenance of definitive hematopoiesis in the fetal liver. Blood (2001) 1.67
The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation. Mol Syst Biol (2005) 1.60
Phosphorylation controls Ikaros's ability to negatively regulate the G(1)-S transition. Mol Cell Biol (2004) 1.53
The human synMuv-like protein LIN-9 is required for transcription of G2/M genes and for entry into mitosis. EMBO J (2006) 1.51
CONFAC: automated application of comparative genomic promoter analysis to DNA microarray datasets. Nucleic Acids Res (2004) 1.44
Muscle cachexia is regulated by a p53-PW1/Peg3-dependent pathway. Genes Dev (2006) 1.42
Cyclic amplification and selection of targets for multicomponent complexes: myogenin interacts with factors recognizing binding sites for basic helix-loop-helix, nuclear factor 1, myocyte-specific enhancer-binding factor 2, and COMP1 factor. Proc Natl Acad Sci U S A (1992) 1.41
Tumor suppressor activity of AP2alpha mediated through a direct interaction with p53. J Biol Chem (2002) 1.40
Androgen receptor remains critical for cell-cycle progression in androgen-independent CWR22 prostate cancer cells. Am J Pathol (2006) 1.33
Apigenin-induced cell cycle arrest is mediated by modulation of MAPK, PI3K-Akt, and loss of cyclin D1 associated retinoblastoma dephosphorylation in human prostate cancer cells. Cell Cycle (2007) 1.30
Smads, TAK1, and their common target ATF-2 play a critical role in cardiomyocyte differentiation. J Cell Biol (2001) 1.20
The role of STAT1/IRF-1 on synergistic ROS production and loss of mitochondrial transmembrane potential during hepatic cell death induced by LPS/d-GalN. J Mol Biol (2007) 1.10
Identification of muscle-specific regulatory modules in Caenorhabditis elegans. Genome Res (2007) 1.07
Gene expression profiling reveals progesterone-mediated cell cycle and immunoregulatory roles of Hoxa-10 in the preimplantation uterus. Mol Endocrinol (2003) 1.06
Lymphoid enhancer factor 1 makes cells resistant to transforming growth factor beta-induced repression of c-myc. Cancer Res (2003) 1.00
Enhanced position weight matrices using mixture models. Bioinformatics (2005) 0.94
The adenovirus oncoprotein E1a stimulates binding of transcription factor ETF to transcriptionally activate the p53 gene. J Biol Chem (1999) 0.93
Signalling cross-talk between hepatocyte nuclear factor 4alpha and growth-hormone-activated STAT5b. Biochem J (2006) 0.90
Transcriptional regulation of protein complexes and biological pathways. Mamm Genome (2003) 0.90
CDP and AP-2 mediated repression mechanism of the replication-dependent hamster histone H3.2 promoter. J Cell Biochem (2002) 0.89
NF-Y and Sp1 are involved in transcriptional regulation of rat SND p102 gene. Biochem Biophys Res Commun (2007) 0.83
Delayed liver regeneration in mice lacking liver serum response factor. Am J Physiol Gastrointest Liver Physiol (2006) 0.83
Ubiquitous factors that interact simultaneously with two distinct cis-elements on the rat aldolase B gene promoter. Biochim Biophys Acta (1993) 0.82
Involvement of an AFP1-binding site in cell-specific transcription of the pre-S1 region of the human hepatitis B virus surface antigen gene. Nucleic Acids Res (1989) 0.81
SREBP inhibits VEGF expression in human smooth muscle cells. Biochem Biophys Res Commun (2006) 0.80
Functional activity of hepatocyte nuclear factor-1 is specifically decreased in amino acid-limited hepatoma cells. Biochim Biophys Acta (1999) 0.79
Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature (2012) 13.71
Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. Nat Genet (2011) 10.07
Enhancing CD8 T-cell memory by modulating fatty acid metabolism. Nature (2009) 8.09
Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A (2004) 6.08
Common variants at 7p21 are associated with frontotemporal lobar degeneration with TDP-43 inclusions. Nat Genet (2010) 5.52
Genome-wide analysis of retroviral DNA integration. Nat Rev Microbiol (2005) 3.98
Retroviral DNA integration: viral and cellular determinants of target-site selection. PLoS Pathog (2006) 3.67
Selection of target sites for mobile DNA integration in the human genome. PLoS Comput Biol (2006) 3.21
Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy. Nat Genet (2011) 2.97
The microRNA miR-34 modulates ageing and neurodegeneration in Drosophila. Nature (2012) 2.94
Meta-analysis confirms CR1, CLU, and PICALM as alzheimer disease risk loci and reveals interactions with APOE genotypes. Arch Neurol (2010) 2.91
Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E ϵ4,and the risk of late-onset Alzheimer disease in African Americans. JAMA (2013) 2.58
Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders. Neuron (2013) 2.45
Novel late-onset Alzheimer disease loci variants associate with brain gene expression. Neurology (2012) 2.08
Identification of transcription factor binding sites in the human genome sequence. Mamm Genome (2002) 2.00
Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae. Nucleic Acids Res (2007) 1.98
The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol (2005) 1.79
Genomic analysis of sleep deprivation reveals translational regulation in the hippocampus. Physiol Genomics (2012) 1.64
Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet (2010) 1.56
Global analysis of RNA secondary structure in two metazoans. Cell Rep (2012) 1.50
Evidence for a role of the rare p.A152T variant in MAPT in increasing the risk for FTD-spectrum and Alzheimer's diseases. Hum Mol Genet (2012) 1.46
Gene coexpression network topology of cardiac development, hypertrophy, and failure. Circ Cardiovasc Genet (2010) 1.46
Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential. Nucleic Acids Res (2009) 1.44
Comparison of cerebrospinal fluid levels of tau and Aβ 1-42 in Alzheimer disease and frontotemporal degeneration using 2 analytical platforms. Arch Neurol (2012) 1.42
Statistically based postprocessing of phylogenetic analysis by clustering. Bioinformatics (2002) 1.41
GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo. Development (2007) 1.39
CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features. Genome Biol (2009) 1.38
Hopx and Hdac2 interact to modulate Gata4 acetylation and embryonic cardiac myocyte proliferation. Dev Cell (2010) 1.38
Gene profiling of human adipose tissue during evoked inflammation in vivo. Diabetes (2009) 1.34
Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development. Development (2008) 1.32
Genome-wide association reveals genetic effects on human Aβ42 and τ protein levels in cerebrospinal fluids: a case control study. BMC Neurol (2010) 1.32
Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acids Res (2007) 1.28
HAMR: high-throughput annotation of modified ribonucleotides. RNA (2013) 1.24
SORL1 is genetically associated with late-onset Alzheimer's disease in Japanese, Koreans and Caucasians. PLoS One (2013) 1.23
Functional analysis of Hes-1 in preadipocytes. Mol Endocrinol (2005) 1.21
Young proteins experience more variable selection pressures than old proteins. Genome Res (2010) 1.19
Differential transcriptional response to nonassociative and associative components of classical fear conditioning in the amygdala and hippocampus. Learn Mem (2006) 1.14
Regulation of lung endoderm progenitor cell behavior by miR302/367. Development (2011) 1.14
Design of comprehensive Alzheimer's disease centers to address unmet national needs. Alzheimers Dement (2010) 1.14
Genomic landscape of a three-generation pedigree segregating affective disorder. PLoS One (2009) 1.13
Genetic and physiological activation of osmosensitive gene expression mimics transcriptional signatures of pathogen infection in C. elegans. PLoS One (2010) 1.13
A mammalian promoter model links cis elements to genetic networks. Biochem Biophys Res Commun (2006) 1.11
Correcting population stratification in genetic association studies using a phylogenetic approach. Bioinformatics (2010) 1.08
ABCC9 gene polymorphism is associated with hippocampal sclerosis of aging pathology. Acta Neuropathol (2014) 1.07
A Bayesian approach to efficient differential allocation for resampling-based significance testing. BMC Bioinformatics (2009) 1.07
Why transcription factor binding sites are ten nucleotides long. Genetics (2012) 1.07
Age-correlated gene expression in normal and neurodegenerative human brain tissues. PLoS One (2010) 1.06
Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex. Genome Biol (2007) 1.05
Cellular, synaptic, and biochemical features of resilient cognition in Alzheimer's disease. Neurobiol Aging (2012) 1.04
Genome-wide analysis of natural selection on human cis-elements. PLoS One (2008) 1.00
Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expression. PLoS One (2008) 0.99
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. J Comput Biol (2014) 0.99
Potent obatoclax cytotoxicity and activation of triple death mode killing across infant acute lymphoblastic leukemia. Blood (2013) 0.99
DACTAL: divide-and-conquer trees (almost) without alignments. Bioinformatics (2012) 0.98
Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach. BMC Evol Biol (2006) 0.98
Recurring genomic breaks in independent lineages support genomic fragility. BMC Evol Biol (2006) 0.96
Sex and age dimorphism of myocardial gene expression in nonischemic human heart failure. Circ Cardiovasc Genet (2008) 0.96
High-throughput identification of long-range regulatory elements and their target promoters in the human genome. Nucleic Acids Res (2013) 0.96
Enhanced position weight matrices using mixture models. Bioinformatics (2005) 0.94
SAVoR: a server for sequencing annotation and visualization of RNA structures. Nucleic Acids Res (2012) 0.94
Evidence for coregulation of myocardial gene expression by MEF2 and NFAT in human heart failure. Circ Cardiovasc Genet (2009) 0.94
MetaProm: a neural network based meta-predictor for alternative human promoter prediction. BMC Genomics (2007) 0.94
Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic Caucasians. Clin Endocrinol (Oxf) (2008) 0.93
Intrinsically disordered proteins and conformational noise: implications in cancer. Cell Cycle (2012) 0.92
Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus. Mol Biol Evol (2011) 0.92
CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation. Nucleic Acids Res (2013) 0.92
Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons. Genome Biol (2009) 0.90
Determinants of expression variability. Nucleic Acids Res (2014) 0.89
CoRAL: predicting non-coding RNAs from small RNA-sequencing data. Nucleic Acids Res (2013) 0.88
Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes. Virology (2007) 0.88
Epigenomic and RNA structural correlates of polyadenylation. RNA Biol (2011) 0.87
Derepression of Cancer/testis antigens in cancer is associated with distinct patterns of DNA hypomethylation. BMC Cancer (2013) 0.87
Dense subgraph computation via stochastic search: application to detect transcriptional modules. Bioinformatics (2006) 0.86
Generalizations of Markov model to characterize biological sequences. BMC Bioinformatics (2005) 0.86
Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families. Nucleic Acids Res (2009) 0.85
Widespread evidence of viral miRNAs targeting host pathways. BMC Bioinformatics (2013) 0.85
Rap1 relocalization contributes to the chromatin-mediated gene expression profile and pace of cell senescence. Genes Dev (2013) 0.84
Frequency and clinicopathological characteristics of presenilin 1 Gly206Ala mutation in Puerto Rican Hispanics with dementia. J Alzheimers Dis (2013) 0.84
Patterns of sequence conservation in presynaptic neural genes. Genome Biol (2006) 0.84
DRAW+SneakPeek: analysis workflow and quality metric management for DNA-seq experiments. Bioinformatics (2013) 0.83
PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. Nucleic Acids Res (2008) 0.83
Three independent determinants of protein evolutionary rate. J Mol Evol (2013) 0.83
Comparative survey of the topographical distribution of signature molecular lesions in major neurodegenerative diseases. J Comp Neurol (2013) 0.83
Reassessment of risk genotypes (GRN, TMEM106B, and ABCC9 variants) associated with hippocampal sclerosis of aging pathology. J Neuropathol Exp Neurol (2015) 0.83
Selection of individual VH genes occurs at the pro-B to pre-B cell transition. J Immunol (2011) 0.82
Regulating the regulators: modulators of transcription factor activity. Methods Mol Biol (2010) 0.82
Computational approaches to the detection and analysis of sequences with intramolecular G-quadruplex forming potential. Methods Mol Biol (2010) 0.81
A note on efficient computation of haplotypes via perfect phylogeny. J Comput Biol (2004) 0.81
Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity. PLoS One (2008) 0.81
A tutorial of the poisson random field model in population genetics. Adv Bioinformatics (2008) 0.81
Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers. Nucleic Acids Res (2013) 0.80
Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis. Nucleic Acids Res (2011) 0.80
Myocardin-like protein 2 regulates TGFβ signaling in embryonic stem cells and the developing vasculature. Development (2012) 0.79
Polyploidy, aneuploidy and the evolution of cancer. Adv Exp Med Biol (2010) 0.78
Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6. BMC Evol Biol (2012) 0.77
Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagation. BMC Genomics (2013) 0.77
Analyzing copy number variation using SNP array data: protocols for calling CNV and association tests. Curr Protoc Hum Genet (2013) 0.76
Epigenomic model of cardiac enhancers with application to genome wide association studies. Pac Symp Biocomput (2013) 0.76
Correlated evolution of positions within mammalian cis elements. PLoS One (2013) 0.76