Published in Bioinformatics on January 22, 2003
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics (2010) 9.47
Coexpression analysis of human genes across many microarray data sets. Genome Res (2004) 9.38
Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res (2005) 4.41
Dedifferentiation of neurons and astrocytes by oncogenes can induce gliomas in mice. Science (2012) 4.14
Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res (2005) 3.36
Simple decision rules for classifying human cancers from gene expression profiles. Bioinformatics (2005) 3.24
Gitools: analysis and visualisation of genomic data using interactive heat-maps. PLoS One (2011) 2.74
Protein family expansions and biological complexity. PLoS Comput Biol (2006) 2.69
Transcriptional coordination of the metabolic network in Arabidopsis. Plant Physiol (2006) 2.36
INTERFEROME: the database of interferon regulated genes. Nucleic Acids Res (2008) 2.31
Systematic identification of type I and type II interferon-induced antiviral factors. Proc Natl Acad Sci U S A (2012) 2.18
Large-scale identification of yeast integral membrane protein interactions. Proc Natl Acad Sci U S A (2005) 2.03
Reduced cell proliferation by IKK2 depletion in a mouse lung-cancer model. Nat Cell Biol (2012) 1.87
Constitutive canonical NF-κB activation cooperates with disruption of BLIMP1 in the pathogenesis of activated B cell-like diffuse large cell lymphoma. Cancer Cell (2010) 1.85
Intestinal dysbiosis and depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea. J Clin Microbiol (2013) 1.79
Large-scale integration of cancer microarray data identifies a robust common cancer signature. BMC Bioinformatics (2007) 1.74
Bcl6 expressing follicular helper CD4 T cells are fate committed early and have the capacity to form memory. J Immunol (2013) 1.71
Construction of a genome-scale structural map at single-nucleotide resolution. Genome Res (2007) 1.69
Long-term survival of influenza virus infected club cells drives immunopathology. J Exp Med (2014) 1.64
The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Res (2006) 1.62
Jarid1b targets genes regulating development and is involved in neural differentiation. EMBO J (2011) 1.50
Defining estrogenic mechanisms of bisphenol A analogs through high throughput microscopy-based contextual assays. Chem Biol (2014) 1.49
Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. Bioinformatics (2008) 1.48
Merging microarray data from separate breast cancer studies provides a robust prognostic test. BMC Bioinformatics (2008) 1.48
Relationships between gene expression and brain wiring in the adult rodent brain. PLoS Comput Biol (2011) 1.47
Detection of DNA structural motifs in functional genomic elements. Genome Res (2007) 1.45
DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res (2010) 1.41
Conservation of trans-acting circuitry during mammalian regulatory evolution. Nature (2014) 1.38
Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites. Genome Res (2012) 1.37
Hematopoietic stem cell development requires transient Wnt/β-catenin activity. J Exp Med (2012) 1.35
Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein. RNA (2013) 1.34
Circulating microRNA is a biomarker of pediatric Crohn disease. J Pediatr Gastroenterol Nutr (2011) 1.29
Diverse epigenetic strategies interact to control epidermal differentiation. Nat Cell Biol (2012) 1.29
In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae. PLoS Genet (2012) 1.28
Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution. Genes Dev (2015) 1.28
Disrupted-in-schizophrenia 1 (DISC1) plays essential roles in mitochondria in collaboration with Mitofilin. Proc Natl Acad Sci U S A (2010) 1.28
Systems-level analysis of nitrogen starvation-induced modifications of carbon metabolism in a Chlamydomonas reinhardtii starchless mutant. Plant Cell (2013) 1.27
Influenza A virus hemagglutinin antibody escape promotes neuraminidase antigenic variation and drug resistance. PLoS One (2011) 1.24
Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action. Mol Syst Biol (2010) 1.23
Selective knockdown of ceramide synthases reveals complex interregulation of sphingolipid metabolism. J Lipid Res (2010) 1.23
Concurrent loss of Ezh2 and Tet2 cooperates in the pathogenesis of myelodysplastic disorders. J Exp Med (2013) 1.23
Genome-wide analysis of p63 binding sites identifies AP-2 factors as co-regulators of epidermal differentiation. Nucleic Acids Res (2012) 1.22
Common and unique elements of the ABA-regulated transcriptome of Arabidopsis guard cells. BMC Genomics (2011) 1.21
KIT oncogene inhibition drives intratumoral macrophage M2 polarization. J Exp Med (2013) 1.18
Tomato Expression Database (TED): a suite of data presentation and analysis tools. Nucleic Acids Res (2006) 1.17
Sequential transcriptional changes dictate safe and effective antigen-specific immunotherapy. Nat Commun (2014) 1.15
Collagen architecture in pregnancy-induced protection from breast cancer. J Cell Sci (2013) 1.12
Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Nucleic Acids Res (2015) 1.12
Circulating tumor cell enumeration with a combination of epithelial cell adhesion molecule- and cell-surface vimentin-based methods for monitoring breast cancer therapeutic response. Clin Chem (2014) 1.12
NCI: A server to identify non-canonical interactions in protein structures. Nucleic Acids Res (2003) 1.10
Identification of drought-responsive universal stress proteins in viridiplantae. Bioinform Biol Insights (2011) 1.09
cGAS surveillance of micronuclei links genome instability to innate immunity. Nature (2017) 1.04
Transposable element derived DNaseI-hypersensitive sites in the human genome. Biol Direct (2006) 1.04
INVEX--a web-based tool for integrative visualization of expression data. Bioinformatics (2013) 1.04
Structural insights into selective histone H3 recognition by the human Polybromo bromodomain 2. Cell Res (2010) 1.02
Proteomic analysis of the supernatant of red blood cell units: the effects of storage and leucoreduction. Vox Sang (2013) 1.02
Multiple independent evolutionary solutions to core histone gene regulation. Genome Biol (2006) 1.00
TMKink: a method to predict transmembrane helix kinks. Protein Sci (2011) 0.98
PRMT5 modulates the metabolic response to fasting signals. Proc Natl Acad Sci U S A (2013) 0.98
The word landscape of the non-coding segments of the Arabidopsis thaliana genome. BMC Genomics (2009) 0.98
Overexpression of an activated REL mutant enhances the transformed state of the human B-lymphoma BJAB cell line and alters its gene expression profile. Oncogene (2009) 0.97
Comparative genomics allows the discovery of cis-regulatory elements in mosquitoes. Proc Natl Acad Sci U S A (2009) 0.97
ChroMoS: an integrated web tool for SNP classification, prioritization and functional interpretation. Bioinformatics (2013) 0.96
Naive CD4 t cell proliferation is controlled by mammalian target of rapamycin regulation of GRAIL expression. J Immunol (2009) 0.95
Bacterial superantigens promote acute nasopharyngeal infection by Streptococcus pyogenes in a human MHC Class II-dependent manner. PLoS Pathog (2014) 0.95
Epidermal barrier defects link atopic dermatitis with altered skin cancer susceptibility. Elife (2014) 0.95
Multiplex immunoassay of lower genital tract mucosal fluid from women attending an urban STD clinic shows broadly increased IL1ß and lactoferrin. PLoS One (2011) 0.95
Further insights into the antinociceptive potential of a peptide disrupting the N-type calcium channel-CRMP-2 signaling complex. Channels (Austin) (2011) 0.95
Inhibition of transmitter release and attenuation of anti-retroviral-associated and tibial nerve injury-related painful peripheral neuropathy by novel synthetic Ca2+ channel peptides. J Biol Chem (2012) 0.94
Caveolin-1 is a critical determinant of autophagy, metabolic switching, and oxidative stress in vascular endothelium. PLoS One (2014) 0.93
Biochemical profiling of histone binding selectivity of the yeast bromodomain family. PLoS One (2010) 0.93
A network of HMG-box transcription factors regulates sexual cycle in the fungus Podospora anserina. PLoS Genet (2013) 0.92
Screening for active small molecules in mitochondrial complex I deficient patient's fibroblasts, reveals AICAR as the most beneficial compound. PLoS One (2011) 0.92
Lipopolysaccharide priming enhances expression of effectors of immune defence while decreasing expression of pro-inflammatory cytokines in mammary epithelia cells from cows. BMC Genomics (2012) 0.92
The sodium channel β1 subunit mediates outgrowth of neurite-like processes on breast cancer cells and promotes tumour growth and metastasis. Int J Cancer (2014) 0.91
A new means to identify type 3 secreted effectors: functionally interchangeable class IB chaperones recognize a conserved sequence. MBio (2012) 0.91
Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage. PLoS One (2011) 0.91
Genome-wide identification of MAPKK and MAPKKK gene families in tomato and transcriptional profiling analysis during development and stress response. PLoS One (2014) 0.89
Rectal microRNAs are perturbed in pediatric inflammatory bowel disease of the colon. J Crohns Colitis (2014) 0.89
Genesis of avian influenza H9N2 in Bangladesh. Emerg Microbes Infect (2014) 0.88
HeatMapViewer: interactive display of 2D data in biology. F1000Res (2014) 0.88
Enhanced cardiac Akt/protein kinase B signaling contributes to pathological cardiac hypertrophy in part by impairing mitochondrial function via transcriptional repression of mitochondrion-targeted nuclear genes. Mol Cell Biol (2014) 0.87
Development of an automated imaging pipeline for the analysis of the zebrafish larval kidney. PLoS One (2013) 0.87
Cross-reactivity virtual profiling of the human kinome by X-react(KIN): a chemical systems biology approach. Mol Pharm (2010) 0.86
Role of conserved non-coding regulatory elements in LMW glutenin gene expression. PLoS One (2011) 0.86
Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs. Mol Syst Biol (2014) 0.86
Structural requirements for recognition of major histocompatibility complex class II by membrane-associated RING-CH (MARCH) protein E3 ligases. J Biol Chem (2012) 0.86
Functional and structural analysis of five mutations identified in methylmalonic aciduria cblB type. Hum Mutat (2010) 0.86
The MoxR ATPase RavA and its cofactor ViaA interact with the NADH:ubiquinone oxidoreductase I in Escherichia coli. PLoS One (2014) 0.86
Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles. BMC Genomics (2013) 0.86
Mobility of the native Bacillus subtilis conjugative plasmid pLS20 is regulated by intercellular signaling. PLoS Genet (2013) 0.85
Diversity and history of the long-chain acyl-CoA synthetase (Acsl) gene family in vertebrates. BMC Evol Biol (2013) 0.85
Global Phosphoproteomic Mapping of Early Mitotic Exit in Human Cells Identifies Novel Substrate Dephosphorylation Motifs. Mol Cell Proteomics (2015) 0.85
Effects of β4 integrin expression on microRNA patterns in breast cancer. Biol Open (2012) 0.85
A key role for the endothelium in NOD1 mediated vascular inflammation: comparison to TLR4 responses. PLoS One (2012) 0.84
Integrative sequence and tissue expression profiling of chicken and mammalian aquaporins. BMC Genomics (2009) 0.84
Co-regulation of histone-modifying enzymes in cancer. PLoS One (2011) 0.83
Sex chromosome complement regulates expression of mood-related genes. Biol Sex Differ (2013) 0.83
Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29
Quantifying similarity between motifs. Genome Biol (2007) 9.27
Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods (2007) 8.94
FIMO: scanning for occurrences of a given motif. Bioinformatics (2011) 8.89
Searching for statistically significant regulatory modules. Bioinformatics (2003) 5.72
Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res (2007) 5.57
Nucleosome positioning signals in genomic DNA. Genome Res (2007) 4.99
The spectrum kernel: a string kernel for SVM protein classification. Pac Symp Biocomput (2002) 4.90
Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods (2012) 4.89
Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal Chem (2006) 4.16
Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res (2012) 3.80
A statistical framework for genomic data fusion. Bioinformatics (2004) 3.64
The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev (2006) 3.58
Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol (2008) 3.56
Kernel methods for predicting protein-protein interactions. Bioinformatics (2005) 3.52
Exploring gene expression data with class scores. Pac Symp Biocomput (2002) 3.51
Mismatch string kernels for discriminative protein classification. Bioinformatics (2004) 3.27
Learning gene functional classifications from multiple data types. J Comput Biol (2002) 2.65
Posterior error probabilities and false discovery rates: two sides of the same coin. J Proteome Res (2007) 2.61
The effect of replication on gene expression microarray experiments. Bioinformatics (2003) 2.49
Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinformatics (2006) 2.36
Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Res (2012) 2.24
A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J Proteome Res (2003) 2.16
Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. J Comput Biol (2003) 2.04
Large-scale identification of yeast integral membrane protein interactions. Proc Natl Acad Sci U S A (2005) 2.03
Peptide charge state determination for low-resolution tandem mass spectra. Proc IEEE Comput Syst Bioinform Conf (2005) 1.97
Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data. J Proteome Res (2010) 1.91
Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res (2008) 1.90
Learning to predict protein-protein interactions from protein sequences. Bioinformatics (2003) 1.84
Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets. J Proteome Res (2009) 1.80
Protein ranking: from local to global structure in the protein similarity network. Proc Natl Acad Sci U S A (2004) 1.67
Predicting human nucleosome occupancy from primary sequence. PLoS Comput Biol (2008) 1.66
Support vector machine classification on the web. Bioinformatics (2004) 1.65
High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions. PLoS Comput Biol (2010) 1.52
Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. Bioinformatics (2008) 1.48
Epigenetic priors for identifying active transcription factor binding sites. Bioinformatics (2011) 1.47
Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. Bioinformatics (2008) 1.47
Predicting co-complexed protein pairs from heterogeneous data. PLoS Comput Biol (2008) 1.44
Statistical calibration of the SEQUEST XCorr function. J Proteome Res (2009) 1.43
Semi-supervised protein classification using cluster kernels. Bioinformatics (2005) 1.42
Ranking predicted protein structures with support vector regression. Proteins (2008) 1.41
QVALITY: non-parametric estimation of q-values and posterior error probabilities. Bioinformatics (2009) 1.38
Faster SEQUEST searching for peptide identification from tandem mass spectra. J Proteome Res (2011) 1.33
Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure. Bioinformatics (2006) 1.27
Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions. Anal Chem (2007) 1.19
Riboproteomics of the hepatitis C virus internal ribosomal entry site. J Proteome Res (2004) 1.19
Consistent probabilistic outputs for protein function prediction. Genome Biol (2008) 1.17
On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements. Nucleic Acids Res (2012) 1.13
Improved similarity scores for comparing motifs. Bioinformatics (2011) 1.10
Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs. J Proteome Res (2010) 1.09
Crux: rapid open source protein tandem mass spectrometry analysis. J Proteome Res (2014) 1.06
The Genomedata format for storing large-scale functional genomics data. Bioinformatics (2010) 1.05
On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics. J Proteome Res (2011) 1.03
Exploratory analysis of genomic segmentations with Segtools. BMC Bioinformatics (2011) 1.02
Learning kernels from biological networks by maximizing entropy. Bioinformatics (2004) 1.01
Automated mapping of large-scale chromatin structure in ENCODE. Bioinformatics (2008) 0.99
Estimating relative abundances of proteins from shotgun proteomics data. BMC Bioinformatics (2012) 0.98
Kernel hierarchical gene clustering from microarray expression data. Bioinformatics (2003) 0.98
Direct maximization of protein identifications from tandem mass spectra. Mol Cell Proteomics (2011) 0.98
A structural alignment kernel for protein structures. Bioinformatics (2007) 0.97
Assessing phylogenetic motif models for predicting transcription factor binding sites. Bioinformatics (2009) 0.95
Protein ranking by semi-supervised network propagation. BMC Bioinformatics (2006) 0.95
A thermodynamic approach to PCR primer design. Nucleic Acids Res (2009) 0.94
RANKPROP: a web server for protein remote homology detection. Bioinformatics (2008) 0.90
Motif-based protein ranking by network propagation. Bioinformatics (2005) 0.90
On the importance of well-calibrated scores for identifying shotgun proteomics spectra. J Proteome Res (2014) 0.88
Improved network-based identification of protein orthologs. Bioinformatics (2008) 0.88
Multiple functional categories of proteins identified in an in vitro cellular ubiquitin affinity extract using shotgun peptide sequencing. J Proteome Res (2003) 0.87
Faster mass spectrometry-based protein inference: junction trees are more efficient than sampling and marginalization by enumeration. IEEE/ACM Trans Comput Biol Bioinform (2012) 0.86
Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens. PLoS Comput Biol (2010) 0.86
A cross-validation scheme for machine learning algorithms in shotgun proteomics. BMC Bioinformatics (2012) 0.85
A unified multitask architecture for predicting local protein properties. PLoS One (2012) 0.84
A learned comparative expression measure for affymetrix genechip DNA microarrays. Proc IEEE Comput Syst Bioinform Conf (2005) 0.83
Protein family classification using sparse markov transducers. J Comput Biol (2003) 0.82
Detecting remote evolutionary relationships among proteins by large-scale semantic embedding. PLoS Comput Biol (2011) 0.82
Efficient identification of DNA hybridization partners in a sequence database. Bioinformatics (2006) 0.81
Learning score function parameters for improved spectrum identification in tandem mass spectrometry experiments. J Proteome Res (2012) 0.77
Using substitution matrices to estimate probability distributions for biological sequences. J Comput Biol (2002) 0.76
Data hoarding is harming proteomics. Nat Biotechnol (2004) 0.75
Automated validation of polymerase chain reaction amplicon melting curves. J Bioinform Comput Biol (2006) 0.75
Correction to "Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics". J Proteome Res (2016) 0.75
Automated validation of polymerase chain reactions using amplicon melting curves. Proc IEEE Comput Syst Bioinform Conf (2005) 0.75
Correction to "On the Importance of Well-Calibrated Scores for Identifying Shotgun Proteomics Spectra". J Proteome Res (2016) 0.75