Published in Bioinformatics on September 23, 2004
An analysis of human microRNA and disease associations. PLoS One (2008) 5.21
Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biol (2005) 5.19
Tissue-specific genetic control of splicing: implications for the study of complex traits. PLoS Biol (2008) 5.08
Patterns of positive selection in six Mammalian genomes. PLoS Genet (2008) 4.69
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res (2010) 3.34
The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature (2014) 2.93
Identification of new genetic risk variants for type 2 diabetes. PLoS Genet (2010) 2.62
Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol (2010) 2.60
Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator. Curr Biol (2012) 2.50
A CRISPR-Cas9 gene drive system targeting female reproduction in the malaria mosquito vector Anopheles gambiae. Nat Biotechnol (2015) 2.21
Global organization of replication time zones of the mouse genome. Genome Res (2008) 2.11
HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Mol Syst Biol (2010) 2.05
Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genet (2009) 1.97
Cancer evolution is associated with pervasive positive selection on globally expressed genes. PLoS Genet (2014) 1.94
A comprehensive gene expression atlas of sex- and tissue-specificity in the malaria vector, Anopheles gambiae. BMC Genomics (2011) 1.88
Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples. Nature (2015) 1.86
Widespread ectopic expression of olfactory receptor genes. BMC Genomics (2006) 1.80
Large-scale integration of cancer microarray data identifies a robust common cancer signature. BMC Bioinformatics (2007) 1.74
A genome-wide association study identifies CDHR3 as a susceptibility locus for early childhood asthma with severe exacerbations. Nat Genet (2013) 1.70
Rare ADH variant constellations are specific for alcohol dependence. Alcohol Alcohol (2012) 1.66
A trans-species missense SNP in Amhr2 is associated with sex determination in the tiger pufferfish, Takifugu rubripes (fugu). PLoS Genet (2012) 1.58
Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent. Genome Res (2011) 1.58
Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis. PLoS One (2011) 1.53
Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells. Proc Natl Acad Sci U S A (2008) 1.53
An integrative transcriptomic atlas of organogenesis in human embryos. Elife (2016) 1.50
Sex-biased transcriptome evolution in Drosophila. Genome Biol Evol (2012) 1.48
Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. RNA (2009) 1.44
Genome-wide association identifies a deletion in the 3' untranslated region of striatin in a canine model of arrhythmogenic right ventricular cardiomyopathy. Hum Genet (2010) 1.43
Disentangling the relationship between sex-biased gene expression and X-linkage. Genome Res (2012) 1.40
A complex suite of forces drives gene traffic from Drosophila X chromosomes. Genome Biol Evol (2009) 1.32
Towards a more nuanced understanding of the relationship between sex-biased gene expression and rates of protein-coding sequence evolution. Mol Biol Evol (2011) 1.32
Human gene copy number spectra analysis in congenital heart malformations. Physiol Genomics (2012) 1.30
Comparison of human solute carriers. Protein Sci (2010) 1.29
HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis. Nucleic Acids Res (2012) 1.29
Cadherin-related family member 3, a childhood asthma susceptibility gene product, mediates rhinovirus C binding and replication. Proc Natl Acad Sci U S A (2015) 1.26
A computational approach for genome-wide mapping of splicing factor binding sites. Genome Biol (2009) 1.25
Origin and spread of de novo genes in Drosophila melanogaster populations. Science (2014) 1.22
Switch-like genes populate cell communication pathways and are enriched for extracellular proteins. BMC Genomics (2008) 1.21
Digital sorting of complex tissues for cell type-specific gene expression profiles. BMC Bioinformatics (2013) 1.18
Tissue-specific control of brain-enriched miR-7 biogenesis. Genes Dev (2013) 1.18
Little evidence for demasculinization of the Drosophila X chromosome among genes expressed in the male germline. Genome Biol Evol (2012) 1.16
Of mice and men: divergence of gene expression patterns in kidney. PLoS One (2012) 1.15
SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis. PLoS Comput Biol (2015) 1.14
Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing. BMC Genomics (2011) 1.11
Digital gene expression analysis of the zebra finch genome. BMC Genomics (2010) 1.10
Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human. Bioinformatics (2012) 1.10
Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer. Nucleic Acids Res (2015) 1.09
Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biol Evol (2011) 1.09
Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective. Genome Biol (2008) 1.08
Genome-wide genetic associations with IFNγ response to smallpox vaccine. Hum Genet (2012) 1.08
Gene expression during Drosophila melanogaster egg development before and after reproductive diapause. BMC Genomics (2009) 1.07
Nonrandom gene loss from the Drosophila miranda neo-Y chromosome. Genome Biol Evol (2011) 1.07
Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biol Evol (2009) 1.07
Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation. Genome Biol (2011) 1.07
Genome-wide methylomic analysis of monozygotic twins discordant for adolescent depression. Biol Psychiatry (2014) 1.07
The TissueNet database of human tissue protein-protein interactions. Nucleic Acids Res (2012) 1.07
Are sex-biased genes more dispensable? Biol Lett (2009) 1.07
Distribution of miRNA expression across human tissues. Nucleic Acids Res (2016) 1.04
Nuclear myosin is ubiquitously expressed and evolutionary conserved in vertebrates. Histochem Cell Biol (2006) 1.03
Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. PLoS Genet (2009) 1.03
Mutation bias is the driving force of codon usage in the Gallus gallus genome. DNA Res (2011) 1.03
XenomiRs and miRNA homeostasis in health and disease: evidence that diet and dietary miRNAs directly and indirectly influence circulating miRNA profiles. RNA Biol (2012) 1.02
Genes overexpressed in different human solid cancers exhibit different tissue-specific expression profiles. Proc Natl Acad Sci U S A (2007) 1.02
Alanine aminotransferase-old biomarker and new concept: a review. Int J Med Sci (2014) 1.01
Faster-X evolution of gene expression in Drosophila. PLoS Genet (2012) 1.01
The rs10993994 risk allele for prostate cancer results in clinically relevant changes in microseminoprotein-beta expression in tissue and urine. PLoS One (2010) 1.01
A computational framework to infer human disease-associated long noncoding RNAs. PLoS One (2014) 1.00
Runs of homozygosity identify a recessive locus 12q21.31 for human adult height. J Clin Endocrinol Metab (2010) 1.00
Proinflammatory actions of glucocorticoids: glucocorticoids and TNFα coregulate gene expression in vitro and in vivo. Endocrinology (2012) 1.00
Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa. BMC Genomics (2013) 1.00
Interspecific Y chromosome introgressions disrupt testis-specific gene expression and male reproductive phenotypes in Drosophila. Proc Natl Acad Sci U S A (2011) 0.99
Whole transcriptome RNA-Seq allelic expression in human brain. BMC Genomics (2013) 0.99
Functional relevance of CpG island length for regulation of gene expression. Genetics (2011) 0.99
The complex jujube genome provides insights into fruit tree biology. Nat Commun (2014) 0.98
Human growth is associated with distinct patterns of gene expression in evolutionarily conserved networks. BMC Genomics (2013) 0.98
Novel association of APC with intermediate filaments identified using a new versatile APC antibody. BMC Cell Biol (2009) 0.97
SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences. BMC Res Notes (2008) 0.97
MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering. BMC Bioinformatics (2009) 0.97
Integrated systems analysis reveals a molecular network underlying autism spectrum disorders. Mol Syst Biol (2014) 0.97
CRX is a diagnostic marker of retinal and pineal lineage tumors. PLoS One (2009) 0.97
Transcriptome sequencing reveals the character of incomplete dosage compensation across multiple tissues in flycatchers. Genome Biol Evol (2013) 0.96
Organismal complexity, cell differentiation and gene expression: human over mouse. Nucleic Acids Res (2007) 0.96
What are the determinants of gene expression levels and breadths in the human genome? Hum Mol Genet (2011) 0.96
The roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression. Genome Res (2013) 0.95
Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants. Plant Physiol (2013) 0.95
Defining the gene expression signature of rhabdomyosarcoma by meta-analysis. BMC Genomics (2006) 0.95
A tour through the transcriptional landscape of platelets. Blood (2014) 0.94
Gene expression profiles identify inflammatory signatures in dendritic cells. PLoS One (2010) 0.94
Genes encoding hub and bottleneck enzymes of the Arabidopsis metabolic network preferentially retain homeologs through whole genome duplication. BMC Evol Biol (2010) 0.93
Hierarchical modeling identifies novel lung cancer susceptibility variants in inflammation pathways among 10,140 cases and 11,012 controls. Hum Genet (2013) 0.93
Oxidative stress and adult neurogenesis--effects of radiation and superoxide dismutase deficiency. Semin Cell Dev Biol (2012) 0.92
Adaptive history of single copy genes highly expressed in the term human placenta. Genomics (2008) 0.92
Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases. PLoS Comput Biol (2014) 0.91
The amyloid precursor protein/protease nexin 2 Kunitz inhibitor domain is a highly specific substrate of mesotrypsin. J Biol Chem (2009) 0.91
Initiation of BMP2 signaling in domains on the plasma membrane. J Cell Physiol (2012) 0.91
Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression. Mob DNA (2014) 0.91
Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs. Proc Natl Acad Sci U S A (2011) 0.90
Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans. PLoS Genet (2015) 0.90
Evolution of a cluster of innate immune genes (beta-defensins) along the ancestral lines of chicken and zebra finch. Immunome Res (2010) 0.90
A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster. Genome Res (2014) 0.90
Serum microRNAs are promising novel biomarkers. PLoS One (2008) 8.69
Outcome signature genes in breast cancer: is there a unique set? Bioinformatics (2004) 7.96
MicroRNAs accurately identify cancer tissue origin. Nat Biotechnol (2008) 7.27
Stem cell-related "self-renewal" signature and high epidermal growth factor receptor expression associated with resistance to concomitant chemoradiotherapy in glioblastoma. J Clin Oncol (2008) 6.41
Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci U S A (2006) 6.26
GeneCards Version 3: the human gene integrator. Database (Oxford) (2010) 6.05
The genome of a songbird. Nature (2010) 5.90
Genome analysis of the platypus reveals unique signatures of evolution. Nature (2008) 5.74
A module of negative feedback regulators defines growth factor signaling. Nat Genet (2007) 4.35
Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE. Nucleic Acids Res (2003) 4.29
GeneCards 2002: towards a complete, object-oriented, human gene compendium. Bioinformatics (2002) 4.24
Diagnostic assay based on hsa-miR-205 expression distinguishes squamous from nonsquamous non-small-cell lung carcinoma. J Clin Oncol (2009) 3.47
Transcription control reprogramming in genetic backup circuits. Nat Genet (2005) 3.36
Relationship of gene expression and chromosomal abnormalities in colorectal cancer. Cancer Res (2006) 3.32
A distinctive DNA damage response in human hematopoietic stem cells reveals an apoptosis-independent role for p53 in self-renewal. Cell Stem Cell (2010) 2.95
GeneNote: whole genome expression profiles in normal human tissues. C R Biol (2004) 2.92
The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming. Nature (2012) 2.80
PML, YAP, and p73 are components of a proapoptotic autoregulatory feedback loop. Mol Cell (2008) 2.66
Network analysis of protein structures identifies functional residues. J Mol Biol (2004) 2.61
Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates. PLoS Biol (2004) 2.56
Genetic elucidation of human hyperosmia to isovaleric acid. PLoS Biol (2007) 2.47
Mutant p53 oncogenic functions are sustained by Plk2 kinase through an autoregulatory feedback loop. Cell Cycle (2011) 2.46
Natural selection on the olfactory receptor gene family in humans and chimpanzees. Am J Hum Genet (2003) 2.44
Intron retention is a major phenomenon in alternative splicing in Arabidopsis. Plant J (2004) 2.42
Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. OMICS (2004) 2.40
Novel definition files for human GeneChips based on GeneAnnot. BMC Bioinformatics (2007) 2.32
Human specific loss of olfactory receptor genes. Proc Natl Acad Sci U S A (2003) 2.23
Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. Nat Genet (2012) 2.20
Classification of human astrocytic gliomas on the basis of gene expression: a correlated group of genes with angiogenic activity emerges as a strong predictor of subtypes. Cancer Res (2003) 2.15
Different noses for different people. Nat Genet (2003) 2.10
In-silico human genomics with GeneCards. Hum Genomics (2011) 2.10
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res (2007) 2.07
GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes. Bioinformatics (2004) 1.92
Two phases of mitogenic signaling unveil roles for p53 and EGR1 in elimination of inconsistent growth signals. Mol Cell (2011) 1.89
Transcriptional programs following genetic alterations in p53, INK4A, and H-Ras genes along defined stages of malignant transformation. Cancer Res (2005) 1.86
Viral photosynthetic reaction center genes and transcripts in the marine environment. ISME J (2007) 1.84
Accurate classification of non-small cell lung carcinoma using a novel microRNA-based approach. Clin Cancer Res (2010) 1.81
Widespread ectopic expression of olfactory receptor genes. BMC Genomics (2006) 1.80
Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. BMC Genomics (2006) 1.80
MOPED: Model Organism Protein Expression Database. Nucleic Acids Res (2011) 1.79
Evidence for positive selection and population structure at the human MAO-A gene. Proc Natl Acad Sci U S A (2002) 1.79
Systems medicine and integrated care to combat chronic noncommunicable diseases. Genome Med (2011) 1.78
Glycolytic strategy as a tradeoff between energy yield and protein cost. Proc Natl Acad Sci U S A (2013) 1.75
eQuilibrator--the biochemical thermodynamics calculator. Nucleic Acids Res (2011) 1.73
Potential photosynthesis gene recombination between Prochlorococcus and Synechococcus via viral intermediates. Environ Microbiol (2005) 1.72
Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites. PLoS Pathog (2013) 1.72
Association of survival and disease progression with chromosomal instability: a genomic exploration of colorectal cancer. Proc Natl Acad Sci U S A (2009) 1.72
Microarray analysis of the abscission-related transcriptome in the tomato flower abscission zone in response to auxin depletion. Plant Physiol (2010) 1.70
Functional immunomics: microarray analysis of IgG autoantibody repertoires predicts the future response of mice to induced diabetes. Proc Natl Acad Sci U S A (2004) 1.69
Human olfaction: from genomic variation to phenotypic diversity. Trends Genet (2009) 1.66
Autosomal-recessive hypophosphatemic rickets is associated with an inactivation mutation in the ENPP1 gene. Am J Hum Genet (2010) 1.65
Plant respiratory burst oxidase homologs impinge on wound responsiveness and development in Lycopersicon esculentum. Plant Cell (2004) 1.64
High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution. PLoS Genet (2008) 1.60
Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms. Nat Genet (2005) 1.60
The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation. Mol Syst Biol (2005) 1.60
Transcriptomic profiling of heat-stress response in potato periderm. J Exp Bot (2009) 1.59
Signaling to transcription networks in the neuronal retrograde injury response. Sci Signal (2010) 1.57
The canine olfactory subgenome. Genomics (2004) 1.55
CATSPER2, a human autosomal nonsyndromic male infertility gene. Eur J Hum Genet (2003) 1.54
MalaCards: an integrated compendium for diseases and their annotation. Database (Oxford) (2013) 1.52
RNF20 and USP44 regulate stem cell differentiation by modulating H2B monoubiquitylation. Mol Cell (2012) 1.52
GeneDecks: paralog hunting and gene-set distillation with GeneCards annotation. OMICS (2009) 1.51
Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity. PLoS Comput Biol (2010) 1.51
Identification of a proliferation gene cluster associated with HPV E6/E7 expression level and viral DNA load in invasive cervical carcinoma. Oncogene (2005) 1.50
Primary ciliary dyskinesia caused by homozygous mutation in DNAL1, encoding dynein light chain 1. Am J Hum Genet (2011) 1.49
Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. OMICS (2014) 1.49
Automated assignment of SCOP and CATH protein structure classifications from FSSP scores. Proteins (2002) 1.48
Prediction of the odorant binding site of olfactory receptor proteins by human-mouse comparisons. Protein Sci (2004) 1.48
Transcriptional profiling of maturing tomato (Solanum lycopersicum L.) microspores reveals the involvement of heat shock proteins, ROS scavengers, hormones, and sugars in the heat stress response. J Exp Bot (2009) 1.47
Expression of L1-CAM and ADAM10 in human colon cancer cells induces metastasis. Cancer Res (2007) 1.46
A critical role for ceramide synthase 2 in liver homeostasis: II. insights into molecular changes leading to hepatopathy. J Biol Chem (2010) 1.41
Is the G72/G30 locus associated with schizophrenia? single nucleotide polymorphisms, haplotypes, and gene expression analysis. Biol Psychiatry (2004) 1.41
Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. PLoS One (2007) 1.40
The execution of the transcriptional axis mutant p53, E2F1 and ID4 promotes tumor neo-angiogenesis. Nat Struct Mol Biol (2009) 1.39
Comprehensive gene and microRNA expression profiling reveals a role for microRNAs in human liver development. PLoS One (2009) 1.37
USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses. Eur J Hum Genet (2002) 1.36