Published in Nat Protoc on January 01, 2007
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
A PGC1-α-dependent myokine that drives brown-fat-like development of white fat and thermogenesis. Nature (2012) 14.67
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res (2007) 13.81
IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res (2012) 12.03
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res (2011) 8.18
A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc (2010) 6.64
IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res (2013) 6.14
The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res (2009) 6.07
A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria. Cell Host Microbe (2010) 4.98
Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics (2009) 4.67
The Transporter Classification Database: recent advances. Nucleic Acids Res (2008) 4.26
The IGS Standard Operating Procedure for Automated Prokaryotic Annotation. Stand Genomic Sci (2011) 3.62
Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS One (2008) 3.41
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J (2011) 2.97
A comprehensive assessment of N-terminal signal peptides prediction methods. BMC Bioinformatics (2009) 2.85
IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res (2011) 2.76
Ergatis: a web interface and scalable software system for bioinformatics workflows. Bioinformatics (2010) 2.69
Genome sequence of the recombinant protein production host Pichia pastoris. Nat Biotechnol (2009) 2.67
Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. PLoS Biol (2011) 2.38
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol (2010) 2.36
A comprehensive comparison of transmembrane domains reveals organelle-specific properties. Cell (2010) 2.35
Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence. Curr Biol (2009) 2.35
GLK transcription factors coordinate expression of the photosynthetic apparatus in Arabidopsis. Plant Cell (2009) 2.35
A defined transposon mutant library and its use in identifying motility genes in Vibrio cholerae. Proc Natl Acad Sci U S A (2008) 2.27
Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. PLoS Biol (2009) 2.25
Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans. Genome Res (2009) 2.24
Communication between viruses guides lysis-lysogeny decisions. Nature (2017) 2.23
A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis. PLoS One (2008) 2.17
Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathog (2011) 2.13
Diverse type VI secretion phospholipases are functionally plastic antibacterial effectors. Nature (2013) 2.11
Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. Nucleic Acids Res (2009) 2.09
Proteomics reveals novel Drosophila seminal fluid proteins transferred at mating. PLoS Biol (2008) 2.09
Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathog (2011) 2.09
A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407. J Bacteriol (2010) 2.08
Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Genome Res (2012) 2.04
Genetic variation in Staphylococcus aureus surface and immune evasion genes is lineage associated: implications for vaccine design and host-pathogen interactions. BMC Microbiol (2010) 1.92
Identification of a novel Staphylococcus aureus two-component leukotoxin using cell surface proteomics. PLoS One (2010) 1.89
TarO: a target optimisation system for structural biology. Nucleic Acids Res (2008) 1.89
Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana. Nat Commun (2012) 1.83
Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. Proc Natl Acad Sci U S A (2008) 1.78
Global view of the Clostridium thermocellum cellulosome revealed by quantitative proteomic analysis. J Bacteriol (2007) 1.77
Recognition of a signal peptide by the signal recognition particle. Nature (2010) 1.77
AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. Nucleic Acids Res (2007) 1.76
Comparative analysis of two complete Corynebacterium ulcerans genomes and detection of candidate virulence factors. BMC Genomics (2011) 1.75
Identification and functional characterization of gene components of Type VI Secretion system in bacterial genomes. PLoS One (2008) 1.73
Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains. PLoS One (2008) 1.72
The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS One (2010) 1.71
The cytochrome P450 enzyme CYP96A15 is the midchain alkane hydroxylase responsible for formation of secondary alcohols and ketones in stem cuticular wax of Arabidopsis. Plant Physiol (2007) 1.71
Functional annotation, genome organization and phylogeny of the grapevine (Vitis vinifera) terpene synthase gene family based on genome assembly, FLcDNA cloning, and enzyme assays. BMC Plant Biol (2010) 1.71
The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome Res (2011) 1.70
An Arabidopsis GPI-anchor plasmodesmal neck protein with callose binding activity and potential to regulate cell-to-cell trafficking. Plant Cell (2009) 1.65
LocateP: genome-scale subcellular-location predictor for bacterial proteins. BMC Bioinformatics (2008) 1.64
Structural diversity of bacterial flagellar motors. EMBO J (2011) 1.63
An integrated transcriptomics and proteomics analysis of the secretome of the helminth pathogen Fasciola hepatica: proteins associated with invasion and infection of the mammalian host. Mol Cell Proteomics (2009) 1.63
Genome comparison of barley and maize smut fungi reveals targeted loss of RNA silencing components and species-specific presence of transposable elements. Plant Cell (2012) 1.61
Comparative genomics of Lactobacillus. Microb Biotechnol (2010) 1.60
Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer. Proc Natl Acad Sci U S A (2011) 1.59
Proteomic analysis of the secretome of Leishmania donovani. Genome Biol (2008) 1.54
Computational Identification and Systematic Classification of Novel Cytochrome P450 Genes in Salvia miltiorrhiza. PLoS One (2014) 1.53
The making of a new pathogen: insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species. Genome Res (2011) 1.53
T4-related bacteriophage LIMEstone isolates for the control of soft rot on potato caused by 'Dickeya solani'. PLoS One (2012) 1.52
Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Hum Mol Genet (2014) 1.51
Reconstruction of the complete human cytomegalovirus genome in a BAC reveals RL13 to be a potent inhibitor of replication. J Clin Invest (2010) 1.50
Protein identification using top-down. Mol Cell Proteomics (2011) 1.50
Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective. Brief Bioinform (2012) 1.50
Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. Proc Natl Acad Sci U S A (2011) 1.50
Nuclear outsourcing of RNA interference components to human mitochondria. PLoS One (2011) 1.49
Induction of lignocellulose-degrading enzymes in Neurospora crassa by cellodextrins. Proc Natl Acad Sci U S A (2012) 1.48
The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist. PLoS One (2011) 1.48
Approaches to Fungal Genome Annotation. Mycology (2011) 1.47
Unity in variety--the pan-genome of the Chlamydiae. Mol Biol Evol (2011) 1.47
Biochemical characterization, localization, and tissue distribution of the longer form of mouse SIRT3. Protein Sci (2009) 1.46
A dynamic interface for capsaicinoid systems biology. Plant Physiol (2009) 1.46
Negative feedback control of HIF-1 through REDD1-regulated ROS suppresses tumorigenesis. Proc Natl Acad Sci U S A (2010) 1.46
A stromal heat shock protein 70 system functions in protein import into chloroplasts in the moss Physcomitrella patens. Plant Cell (2010) 1.46
Identification of adropin as a secreted factor linking dietary macronutrient intake with energy homeostasis and lipid metabolism. Cell Metab (2008) 1.45
Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process. Plant Physiol (2008) 1.45
Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers. BMC Genomics (2016) 1.45
Chapter 12: Human microbiome analysis. PLoS Comput Biol (2012) 1.44
Genome sequence of the versatile fish pathogen Edwardsiella tarda provides insights into its adaptation to broad host ranges and intracellular niches. PLoS One (2009) 1.44
The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PLoS Comput Biol (2008) 1.44
Characterizing the anaerobic response of Chlamydomonas reinhardtii by quantitative proteomics. Mol Cell Proteomics (2010) 1.43
YLoc--an interpretable web server for predicting subcellular localization. Nucleic Acids Res (2010) 1.43
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BMC Bioinformatics (2009) 1.41
Mechanisms and evolution of oxidative sulfur metabolism in green sulfur bacteria. Front Microbiol (2011) 1.38
YuaB functions synergistically with the exopolysaccharide and TasA amyloid fibers to allow biofilm formation by Bacillus subtilis. J Bacteriol (2011) 1.38
Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors. BMC Genomics (2013) 1.37
Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. Elife (2015) 1.36
Duox maturation factors form cell surface complexes with Duox affecting the specificity of reactive oxygen species generation. FASEB J (2008) 1.36
The secreted and surface proteomes of the adult stage of the carcinogenic human liver fluke Opisthorchis viverrini. Proteomics (2010) 1.35
Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans. BMC Genomics (2010) 1.35
Cildb: a knowledgebase for centrosomes and cilia. Database (Oxford) (2009) 1.35
Sequential delivery of host-induced virulence effectors by appressoria and intracellular hyphae of the phytopathogen Colletotrichum higginsianum. PLoS Pathog (2012) 1.35
The DegraBase: a database of proteolysis in healthy and apoptotic human cells. Mol Cell Proteomics (2012) 1.34
Insights into the venom composition of the ectoparasitoid wasp Nasonia vitripennis from bioinformatic and proteomic studies. Insect Mol Biol (2010) 1.34
Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust. PLoS One (2011) 1.33
Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic bacteroidetes. J Biol Chem (2010) 1.32
Global profiling of protease cleavage sites by chemoselective labeling of protein N-termini. Proc Natl Acad Sci U S A (2009) 1.32
The Caenorhabditis elegans A beta 1-42 model of Alzheimer disease predominantly expresses A beta 3-42. J Biol Chem (2009) 1.32
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods (2011) 33.90
Enterotypes of the human gut microbiome. Nature (2011) 24.36
A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal (2010) 8.61
Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics (2004) 7.76
Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature (2005) 7.72
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
Preoperative staging of lung cancer with combined PET-CT. N Engl J Med (2009) 7.38
A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol (2002) 7.12
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci (2003) 6.85
Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology (2004) 6.13
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci (2003) 5.94
Analysis and prediction of leucine-rich nuclear export signals. Protein Eng Des Sel (2004) 5.15
Dynamic complex formation during the yeast cell cycle. Science (2005) 5.11
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature (2007) 4.60
Feature-based prediction of non-classical and leaderless protein secretion. Protein Eng Des Sel (2004) 4.54
Mining electronic health records: towards better research applications and clinical care. Nat Rev Genet (2012) 4.42
Global topology analysis of the Escherichia coli inner membrane proteome. Science (2005) 4.11
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Linear motif atlas for phosphorylation-dependent signaling. Sci Signal (2008) 3.77
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics (2004) 3.72
A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A (2008) 3.57
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation. J Virol (2002) 3.38
Membrane insertion of a potassium-channel voltage sensor. Science (2005) 3.30
Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature (2006) 3.28
Non-classical protein secretion in bacteria. BMC Microbiol (2005) 3.17
Reliability measures for membrane protein topology prediction algorithms. J Mol Biol (2003) 3.13
Identification and evolution of dual-topology membrane proteins. Nat Struct Mol Biol (2006) 3.12
Prediction of proprotein convertase cleavage sites. Protein Eng Des Sel (2004) 3.05
Prediction of twin-arginine signal peptides. BMC Bioinformatics (2005) 3.03
Emulating membrane protein evolution by rational design. Science (2007) 2.96
Interface connections of a transmembrane voltage sensor. Proc Natl Acad Sci U S A (2005) 2.92
Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Res (2005) 2.89
Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics (2004) 2.83
Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. EMBO J (2013) 2.58
Increased short- and long-term risk of inflammatory bowel disease after salmonella or campylobacter gastroenteritis. Gastroenterology (2009) 2.57
Prediction of membrane-protein topology from first principles. Proc Natl Acad Sci U S A (2008) 2.55
Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods (2013) 2.51
Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction. Plant Cell (2002) 2.48
Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae. Genome Biol (2006) 2.43
Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics (2004) 2.39
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics (2005) 2.34
Risk for myocardial infarction and stroke after community-acquired bacteremia: a 20-year population-based cohort study. Circulation (2014) 2.29
Prediction of glycosylation across the human proteome and the correlation to protein function. Pac Symp Biocomput (2002) 2.29
Control of membrane protein topology by a single C-terminal residue. Science (2010) 2.28
A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell (2013) 2.28
Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis. Mol Cell Proteomics (2008) 2.24
Membrane protein structure: prediction versus reality. Annu Rev Biochem (2007) 2.21
NESbase version 1.0: a database of nuclear export signals. Nucleic Acids Res (2003) 2.21
An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur J Immunol (2005) 2.19
Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis. Proc Natl Acad Sci U S A (2002) 2.17
High-throughput fluorescent-based optimization of eukaryotic membrane protein overexpression and purification in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2007) 2.15
Using electronic patient records to discover disease correlations and stratify patient cohorts. PLoS Comput Biol (2011) 2.14
Macrophage serum markers in pneumococcal bacteremia: Prediction of survival by soluble CD163. Crit Care Med (2006) 2.06
GFP-based optimization scheme for the overexpression and purification of eukaryotic membrane proteins in Saccharomyces cerevisiae. Nat Protoc (2008) 2.06
How translocons select transmembrane helices. Annu Rev Biophys (2008) 2.03
Intrauterine exposure to mild analgesics is a risk factor for development of male reproductive disorders in human and rat. Hum Reprod (2010) 1.97
Modeling the adaptive immune system: predictions and simulations. Bioinformatics (2007) 1.95
Impact of hepatitis C virus coinfection on response to highly active antiretroviral therapy and outcome in HIV-infected individuals: a nationwide cohort study. Clin Infect Dis (2006) 1.87
Human gut microbes impact host serum metabolome and insulin sensitivity. Nature (2016) 1.85
Prediction of the human membrane proteome. Proteomics (2010) 1.85
Prediction of proteasome cleavage motifs by neural networks. Protein Eng (2002) 1.81
Protein complexes of the Escherichia coli cell envelope. J Biol Chem (2005) 1.69
A study of the membrane-water interface region of membrane proteins. J Mol Biol (2004) 1.68
Evidence for a protein transported through the secretory pathway en route to the higher plant chloroplast. Nat Cell Biol (2005) 1.66
Transmembrane helices before, during, and after insertion. Curr Opin Struct Biol (2005) 1.64
Continuum secondary structure captures protein flexibility. Structure (2002) 1.63
Biogenesis of inner membrane proteins in Escherichia coli. Annu Rev Microbiol (2005) 1.61
Somatic acquisition and signaling of TGFBR1*6A in cancer. JAMA (2005) 1.59
Arginine in membranes: the connection between molecular dynamics simulations and translocon-mediated insertion experiments. J Membr Biol (2010) 1.58
The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion polymorphisms in the PMEL17 gene. Genetics (2004) 1.57
Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes. Proteins (2005) 1.57
Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry. J Proteome Res (2004) 1.57
Photocross-linking of nascent chains to the STT3 subunit of the oligosaccharyltransferase complex. J Cell Biol (2003) 1.54
Protein interaction-based genome-wide analysis of incident coronary heart disease. Circ Cardiovasc Genet (2011) 1.54
A nine-transmembrane domain topology for presenilin 1. J Biol Chem (2005) 1.52
Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Res (2007) 1.50
New weakly expressed cell cycle-regulated genes in yeast. Yeast (2005) 1.49
Membrane topology of the human seipin protein. FEBS Lett (2006) 1.48
Clarithromycin for 2 weeks for stable coronary heart disease: 6-year follow-up of the CLARICOR randomized trial and updated meta-analysis of antibiotics for coronary heart disease. Cardiology (2008) 1.47
A global topology map of the Saccharomyces cerevisiae membrane proteome. Proc Natl Acad Sci U S A (2006) 1.45
Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes. Am J Hum Genet (2013) 1.43
Molecular recognition of a single sphingolipid species by a protein's transmembrane domain. Nature (2012) 1.42
K65R with and without S68: a new resistance profile in vivo detected in most patients failing abacavir, didanosine and stavudine. Antivir Ther (2003) 1.42
Topology models for 37 Saccharomyces cerevisiae membrane proteins based on C-terminal reporter fusions and predictions. J Biol Chem (2003) 1.40
A systematic study of site-specific GalNAc-type O-glycosylation modulating proprotein convertase processing. J Biol Chem (2011) 1.40
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol (2007) 1.39
Dissecting spatio-temporal protein networks driving human heart development and related disorders. Mol Syst Biol (2010) 1.35