Peer Bork

Q: What Schools Are Affiliated With Peer Bork

Peer Bork is affiliated with the following schools: Technical University of Denmark, Washington University in St. Louis, University of California, Berkeley, University of Manitoba, University of Copenhagen, University of Würzburg, Yonsei University

Peer Bork's AcademicInfluence.com Rankings

Peer Bork

Biology

#553

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#974

Historical Rank

Bioinformatics

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biology Degrees

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Biology

Why Is Peer Bork Influential?

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According to Wikipedia, Peer Bork is a German bioinformatician. He is Director of the European Molecular Biology Laboratory site in Heidelberg, in south-west Germany. Bork received his PhD in biochemistry in 1990 from the Leipzig University and his habilitation in theoretical biophysics in 1995 from the Humboldt University of Berlin. He was appointed a Group Leader at EMBL in 1995. He has worked on the microbiomes of humans and other animals.

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Peer Bork's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

A method and server for predicting damaging missense mutations (2010) (11439)
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets (2018) (9523)
A human gut microbial gene catalogue established by metagenomic sequencing (2010) (9177)
STRING v10: protein–protein interaction networks, integrated over the tree of life (2014) (8096)
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible (2016) (5417)
Enterotypes of the human gut microbiome (2011) (4920)
Functional organization of the yeast proteome by systematic analysis of protein complexes (2002) (4880)
Initial sequencing and comparative analysis of the mouse genome. (2002) (4609)
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees (2016) (3988)
Interactive Tree Of Life (iTOL) v4: recent updates and new developments (2019) (3903)
STRING v9.1: protein-protein interaction networks, with increased coverage and integration (2012) (3879)
SMART, a simple modular architecture research tool: identification of signaling domains. (1998) (3541)
Richness of human gut microbiome correlates with metabolic markers (2013) (3351)
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored (2010) (3277)
Proteome survey reveals modularity of the yeast cell machinery (2006) (2642)
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation (2007) (2493)
Comparative assessment of large-scale data sets of protein–protein interactions (2002) (2434)
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution (2004) (2417)
STRING 8—a global view on proteins and their functional interactions in 630 organisms (2008) (2396)
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets (2020) (2365)
Human non-synonymous SNPs: server and survey. (2002) (2348)
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments (2006) (2291)
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation (2021) (2278)
Initial sequence of the chimpanzee genome and comparison with the human genome (2005) (2222)
Genome sequence of the Brown Norway rat yields insights into mammalian evolution (2004) (2053)
The Genome Sequence of the Malaria Mosquito Anopheles gambiae (2002) (2020)
InterPro: the integrative protein signature database (2008) (1850)
STRING: a database of predicted functional associations between proteins (2003) (1756)
Structure and function of the global ocean microbiome (2015) (1716)
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences (2015) (1590)
Comparative Metagenomics of Microbial Communities (2004) (1588)
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper (2016) (1585)
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018) (1563)
SMART 7: recent updates to the protein domain annotation resource (2011) (1556)
Toward Automatic Reconstruction of a Highly Resolved Tree of Life (2006) (1516)
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy (2011) (1444)
An integrated catalog of reference genes in the human gut microbiome (2014) (1431)
STRING: known and predicted protein–protein associations, integrated and transferred across organisms (2004) (1427)
SMART: recent updates, new developments and status in 2015 (2014) (1360)
Insights into social insects from the genome of the honeybee Apis mellifera (2006) (1356)
Eukaryotic plankton diversity in the sunlit ocean (2015) (1309)
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data (2016) (1294)
The genome of the model beetle and pest Tribolium castaneum (2008) (1262)
Human gut microbes impact host serum metabolome and insulin sensitivity (2016) (1257)
20 years of the SMART protein domain annotation resource (2017) (1251)
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota (2015) (1243)
SMART: a web-based tool for the study of genetically mobile domains (2000) (1232)
InterPro in 2017—beyond protein family and domain annotations (2016) (1217)
Protein disorder prediction: implications for structural proteomics. (2003) (1197)
The InterPro protein families database: the classification resource after 15 years (2014) (1186)
The Ecoresponsive Genome of Daphnia pulex (2011) (1152)
Drug Target Identification Using Side-Effect Similarity (2008) (1120)
InterPro in 2019: improving coverage, classification and access to protein sequence annotations (2018) (1101)
InterPro in 2011: new developments in the family and domain prediction database (2011) (1100)
Extensive impact of non-antibiotic drugs on human gut bacteria (2018) (1099)
Prediction of deleterious human alleles. (2001) (1087)
Conservation of gene order: a fingerprint of proteins that physically interact. (1998) (1076)
mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. (2006) (1054)
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans (2008) (1032)
SMART 4.0: towards genomic data integration (2004) (1016)
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (2017) (990)
SMART 6: recent updates and new developments (2008) (989)
SMART 5: domains in the context of genomes and networks (2005) (986)
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract (2002) (958)
Structure and function of the global topsoil microbiome (2018) (940)
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. (2000) (926)
Immunity-Related Genes and Gene Families in Anopheles gambiae (2002) (909)
Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III (2000) (906)
STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data (2015) (895)
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment (2020) (894)
The InterPro protein families and domains database: 20 years on (2020) (858)
The SIDER database of drugs and side effects (2015) (824)
An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. (1992) (823)
Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species (2010) (819)
A side effect resource to capture phenotypic effects of drugs (2010) (819)
SMART: recent updates, new developments and status in 2020 (2020) (818)
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes (2014) (812)
Potential of fecal microbiota for early-stage detection of colorectal cancer (2014) (793)
A superfamily of conserved domains in DNA damage‐ responsive cell cycle checkpoint proteins (1997) (789)
Salt-responsive gut commensal modulates TH17 axis and disease (2017) (748)
Systematic Discovery of In Vivo Phosphorylation Networks (2007) (747)
The InterPro Database, 2003 brings increased coverage and new features (2003) (742)
The immunoglobulin fold. Structural classification, sequence patterns and common core. (1994) (735)
Genomic variation landscape of the human gut microbiome (2012) (715)
Enterotypes of the human gut microbiome (2011) (713)
Literature mining for the biologist: from information retrieval to biological discovery (2006) (695)
Recent improvements to the SMART domain-based sequence annotation resource (2002) (693)
Genome phylogeny based on gene content (1999) (679)
STRING 7—recent developments in the integration and prediction of protein interactions (2006) (673)
Determinants of community structure in the global plankton interactome (2015) (672)
The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data (2004) (672)
STITCH: interaction networks of chemicals and proteins (2007) (651)
The modular architecture of a new family of growth regulators related to connective tissue growth factor (1993) (635)
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins (2003) (635)
Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome (2018) (612)
HEAT repeats in the Huntington's disease protein (1995) (599)
The CUB domain. A widespread module in developmentally regulated proteins. (1993) (597)
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications (2011) (588)
Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching. (2001) (576)
InterPro, progress and status in 2005 (2004) (573)
Enterotypes in the landscape of gut microbial community composition (2017) (561)
Systematic identification of novel protein domain families associated with nuclear functions. (2002) (551)
New developments in the InterPro database (2007) (542)
Patterns and ecological drivers of ocean viral communities (2015) (539)
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer (2019) (538)
SuperTarget and Matador: resources for exploring drug-target relationships (2007) (537)
Comparative Genome and Proteome Analysis of Anopheles gambiae and Drosophila melanogaster (2002) (536)
Plankton networks driving carbon export in the oligotrophic ocean (2015) (532)
The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates (2012) (528)
Alternative splicing and genome complexity (2002) (521)
Polycystic kidney disease: The complete structure of the PKD1 gene and its protein (1995) (521)
Hundreds of ankyrin‐like repeats in functionally diverse proteins: Mobile modules that cross phyla horizontally? (1993) (521)
Identification and mutation analysis of the complete gene for Chediak–Higashi syndrome (1996) (511)
Comparison of ARM and HEAT protein repeats. (2001) (504)
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses (2016) (503)
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges (2011) (502)
Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. (2000) (492)
eggNOG v4.0: nested orthology inference across 3686 organisms (2013) (487)
Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children (2016) (487)
Metabolic dependencies drive species co-occurrence in diverse microbial communities (2015) (486)
Towards standards for human fecal sample processing in metagenomic studies (2017) (479)
The Human Gut Microbiome: From Association to Modulation (2018) (466)
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale (2021) (465)
eggNOG: automated construction and annotation of orthologous groups of genes (2007) (450)
KEGG Atlas mapping for global analysis of metabolic pathways (2008) (448)
Linear Motif Atlas for Phosphorylation-Dependent Signaling (2008) (442)
Prediction of potential GPI-modification sites in proprotein sequences. (1999) (431)
Predicting function: from genes to genomes and back. (1998) (431)
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation (2019) (430)
Transcriptome Complexity in a Genome-Reduced Bacterium (2009) (427)
The DNA sequence of human chromosome 7 (2003) (425)
Metagenomic species profiling using universal phylogenetic marker genes (2013) (421)
A Novel Class of RanGTP Binding Proteins (1997) (421)
Durable coexistence of donor and recipient strains after fecal microbiota transplantation (2016) (414)
Dynamic Complex Formation During the Yeast Cell Cycle (2005) (407)
Proteome Organization in a Genome-Reduced Bacterium (2009) (401)
Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer (2007) (392)
Association of genes to genetically inherited diseases using data mining (2002) (388)
The WW domain: a signalling site in dystrophin? (1994) (386)
REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export. (2000) (384)
Disentangling the effects of type 2 diabetes and metformin on the human gut microbiota (2015) (383)
Marine DNA Viral Macro- and Microdiversity from Pole to Pole (2019) (381)
Characterization of a novel protein‐binding module — the WW domain (1995) (377)
InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites (2002) (376)
Structure-Based Assembly of Protein Complexes in Yeast (2004) (372)
Recovery of gut microbiota of healthy adults following antibiotic exposure (2018) (372)
Genomes in flux: the evolution of archaeal and proteobacterial gene content. (2002) (371)
Convergent evolution of similar enzymatic function on different protein folds: The hexokinase, ribokinase, and galactokinase families of sugar kinases (1993) (370)
A Holistic Approach to Marine Eco-Systems Biology (2011) (365)
STITCH 4: integration of protein–chemical interactions with user data (2013) (364)
Protein interaction networks from yeast to human. (2004) (360)
Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients (2017) (358)
Molecular eco-systems biology: towards an understanding of community function (2008) (348)
Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi (2015) (348)
Country-specific antibiotic use practices impact the human gut resistome (2013) (347)
Towards a structural basis of human non-synonymous single nucleotide polymorphisms. (2000) (347)
Epidermal growth factor-like modules (1993) (338)
Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. (1999) (332)
Predicting functions from protein sequences—where are the bottlenecks? (1998) (329)
Characterization of the Mammalian YAP (Yes-associated Protein) Gene and Its Role in Defining a Novel Protein Module, the WW Domain (*) (1995) (328)
Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. (2007) (324)
EST comparison indicates 38% of human mRNAs contain possible alternative splice forms (2000) (321)
SMART: identification and annotation of domains from signalling and extracellular protein sequences (1999) (320)
Structure and distribution of modules in extracellular proteins (1996) (319)
NetworKIN: a resource for exploring cellular phosphorylation networks (2007) (315)
SAM as a protein interaction domain involved in developmental regulation (1997) (313)
iPath2.0: interactive pathway explorer (2011) (306)
Open science resources for the discovery and analysis of Tara Oceans data (2015) (305)
Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli (1996) (304)
Gut Microbiota Linked to Sexual Preference and HIV Infection (2016) (302)
In situ structural analysis of the human nuclear pore complex (2015) (300)
Nonsense‐mediated mRNA decay in Drosophila:at the intersection of the yeast and mammalian pathways (2003) (298)
Accurate and universal delineation of prokaryotic species (2013) (296)
STITCH 3: zooming in on protein–chemical interactions (2011) (289)
A genome-wide survey of human pseudogenes. (2003) (289)
Non-orthologous gene displacement. (1996) (288)
Impact of Genome Reduction on Bacterial Metabolism and Its Regulation (2009) (288)
Ancient animal microRNAs and the evolution of tissue identity (2010) (286)
Minimum Information about an Uncultivated Virus Genome (MIUViG) (2018) (286)
A large domain common to sperm receptors (Zp2 and Zp3) and TGF‐β type III receptor (1992) (283)
Prediction of effective genome size in metagenomic samples (2007) (277)
Environments shape the nucleotide composition of genomes (2005) (276)
Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children☆ (2015) (271)
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. (2005) (269)
Evolution and functional cross‐talk of protein post‐translational modifications (2013) (265)
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. (2014) (264)
The identification of functional modules from the genomic association of genes (2002) (264)
Pathway alignment: application to the comparative analysis of glycolytic enzymes. (1999) (260)
The rhodanese/Cdc25 phosphatase superfamily (2002) (259)
Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines (2013) (259)
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. (2000) (255)
A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development. (2006) (253)
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations (2009) (247)
Insight into Structure and Assembly of the Nuclear Pore Complex by Utilizing the Genome of a Eukaryotic Thermophile (2011) (244)
SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia (2002) (241)
Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs. (1997) (235)
Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase. (1998) (234)
TAP (NXF1) Belongs to a Multigene Family of Putative RNA Export Factors with a Conserved Modular Architecture (2000) (230)
A global ocean atlas of eukaryotic genes (2018) (229)
Evolution of biomolecular networks — lessons from metabolic and protein interactions (2009) (228)
Proposed acquisition of an animal protein domain by bacteria. (1992) (225)
STITCH 2: an interaction network database for small molecules and proteins (2009) (225)
Role for urea in nitrification by polar marine Archaea (2012) (223)
Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data (2012) (222)
Bioinformatics in the post-sequence era (2003) (220)
Gene context conservation of a higher order than operons. (2000) (218)
Microbial abundance, activity and population genomic profiling with mOTUs2 (2019) (218)
Comparison of computational methods for the identification of cell cycle-regulated genes (2005) (217)
BRCA1 protein products ... Functional motifs... (1996) (217)
Increase of functional diversity by alternative splicing. (2003) (217)
Extensive transmission of microbes along the gastrointestinal tract (2019) (215)
Information extraction from full text scientific articles: Where are the keywords? (2003) (214)
Vertebrate-Type Intron-Rich Genes in the Marine Annelid Platynereis dumerilii (2005) (213)
Frameshift peptide‐derived T‐cell epitopes: A source of novel tumor‐specific antigens (2001) (212)
Deciphering a global network of functionally associated post-translational modifications (2012) (212)
LotuS: an efficient and user-friendly OTU processing pipeline (2014) (211)
Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing (2016) (205)
Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19 (2020) (205)
Co-evolution of transcriptional and post-translational cell-cycle regulation (2006) (204)
Internal repeats in the BRCA2 protein sequence (1996) (202)
Homology-based method for identification of protein repeats using statistical significance estimates. (2000) (201)
iPath: interactive exploration of biochemical pathways and networks. (2008) (200)
SPRY domains in ryanodine receptors (Ca(2+)-release channels). (1997) (199)
The protein phosphatase 2C (PP2C) superfamily: Detection of bacterial homologues (1996) (198)
Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs (2004) (193)
G2D: a tool for mining genes associated with disease (2005) (193)
Genome evolution. Gene fusion versus gene fission. (2000) (192)
Quantifying environmental adaptation of metabolic pathways in metagenomics (2009) (191)
Global Trends in Marine Plankton Diversity across Kingdoms of Life (2019) (190)
Species-specific activity of antibacterial drug combinations (2018) (188)
Selective maternal seeding and environment shape the human gut microbiome (2018) (187)
The mahogany protein is a receptor involved in suppression of obesity (1999) (186)
Statin therapy is associated with lower prevalence of gut microbiota dysbiosis (2020) (186)
A phosphotyrosine interaction domain (1995) (185)
Variation and evolution of the citric-acid cycle: a genomic perspective. (1999) (184)
Standardized benchmarking in the quest for orthologs (2016) (184)
MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit (2012) (183)
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes (2013) (180)
Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes. (2001) (180)
SHOT: a web server for the construction of genome phylogenies. (2002) (180)
Molecular modelling of the Norrie disease protein predicts a cystine knot growth factor tertiary structure (1993) (179)
Medusa: a simple tool for interaction graph analysis (2005) (178)
Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data (2011) (178)
Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways. (2000) (176)
Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data (2011) (176)
Drosophila kelch motif is derived from a common enzyme fold. (1994) (175)
OGEE: an online gene essentiality database (2011) (174)
Get the most out of your metagenome: computational analysis of environmental sequence data. (2007) (173)
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome (2019) (172)
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome (2019) (172)
Similarity of the dog and human gut microbiomes in gene content and response to diet (2018) (172)
Systematic Association of Genes to Phenotypes by Genome and Literature Mining (2005) (172)
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium (2012) (171)
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. (2005) (171)
Alternative splicing and evolution. (2003) (170)
Extraction of regulatory gene/protein networks from Medline (2006) (167)
Common exon duplication in animals and its role in alternative splicing. (2002) (167)
The microbiome explored: recent insights and future challenges (2013) (166)
SMART, a simple modular architecture research tool (1998) (166)
Pathogenesis of DNA repair-deficient cancers: a statistical meta-analysis of putative Real Common Target genes (2003) (163)
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies (2018) (161)
Anopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines. (2000) (161)
An adhesive domain detected in functionally diverse receptors. (1993) (161)
Applying motif and profile searches. (1996) (158)
Function prediction and protein networks. (2003) (155)
HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources (2002) (155)
Quantification of insect genome divergence. (2007) (154)
Eukaryotic translation elongation factor 1γ contains a glutathione transferase domain—Study of a diverse, ancient protein super family using motif search and structural modeling (1994) (153)
The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly. (2001) (153)
A latrophilin/CL-1-like GPS domain in polycystin-1 (1999) (153)
Genome evolution reveals biochemical networks and functional modules (2003) (152)
A putative nucleic acid-binding domain in Bloom's and Werner's syndrome helicases. (1997) (152)
Protein sequence motifs. (1996) (152)
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat (2008) (151)
Friedreich's ataxia protein: phylogenetic evidence for mitochondrial dysfunction (1996) (150)
A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae (2010) (150)
Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats (2015) (147)
Operon structure and cotranslational subunit association direct protein assembly in bacteria (2015) (147)
Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages (2008) (146)
Pervasive Protein Thermal Stability Variation during the Cell Cycle (2018) (146)
Pleckstrin's repeat performance: a novel domain in G-protein signaling? (1996) (146)
Inter-individual differences in the gene content of human gut bacterial species (2015) (144)
Diversity within species: interpreting strains in microbiomes (2020) (144)
Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome. (2006) (144)
The SEA module: A new extracellular domain associated with O‐glycosylation (1995) (143)
The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia. (2003) (142)
Tara Oceans: towards global ocean ecosystems biology (2020) (140)
Tara Oceans: towards global ocean ecosystems biology (2020) (140)
Metabolites: a helping hand for pathway evolution? (2003) (140)
Temporal and technical variability of human gut metagenomes (2015) (139)
Systematic discovery of analogous enzymes in thiamin biosynthesis (2003) (137)
The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins. (1999) (137)
Environmental characteristics of Agulhas rings affect interocean plankton transport (2015) (135)
Evolutionarily mobile modules in proteins. (1993) (134)
MOCAT2: a metagenomic assembly, annotation and profiling framework (2016) (134)
Alternative splicing of human genes: more the rule than the exception? (1999) (133)
iPath3.0: interactive pathways explorer v3 (2018) (132)
Drug-Induced Regulation of Target Expression (2010) (132)
Orthology prediction methods: A quality assessment using curated protein families (2011) (131)
Shuffled domains in extracellular proteins (1991) (131)
Tara Oceans studies plankton at planetary scale (2015) (130)
NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria (2002) (130)
OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines (2016) (129)
Powers and pitfalls in sequence analysis: the 70% hurdle. (2000) (128)
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins (2012) (127)
Computational characterization of multiple Gag-like human proteins. (2006) (127)
An expanding family of helicases within the 'DEAD/H' superfamily. (1993) (124)
Luminal signalling links cell communication to tissue architecture during organogenesis (2014) (123)
Homology-based fold predictions for Mycoplasma genitalium proteins. (1998) (122)
Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition (2017) (121)
A P‐loop‐like motif in a widespread ATP pyrophosphatase domain: Implications for the evolution of sequence motifs and enzyme activity (1994) (119)
Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium (2015) (119)
Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients (2020) (119)
A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor. (1992) (118)
Wanted: subcellular localization of proteins based on sequence. (1998) (117)
Secreted Fringe-like Signaling Molecules May Be Glycosyltransferases (1997) (117)
Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota (2018) (115)
A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme? (1994) (114)
Predicting protein cellular localization using a domain projection method. (2002) (113)
Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution. (2001) (113)
ASTD: The Alternative Splicing and Transcript Diversity database. (2009) (112)
Automated annotation of GPI anchor sites: case study C. elegans. (2000) (112)
A new family of carbon‐nitrogen hydrolases (1994) (111)
Go hunting in sequence databases but watch out for the traps. (1996) (111)
High-resolution transcription atlas of the mitotic cell cycle in budding yeast (2010) (110)
Automated extraction of information in molecular biology (2000) (108)
Systematic identification of proteins that elicit drug side effects (2013) (108)
The p150-Spir protein provides a link between c-Jun N-terminal kinase function and actin reorganization (2000) (108)
Year : 2013 STRING v 9 . 1 : protein-protein interaction networks , with increased coverage and integration (2017) (108)
Complex genomic rearrangements lead to novel primate gene function. (2005) (107)
Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding (2013) (106)
Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) (2001) (106)
GeneQuiz: A Workbench for Sequence Analysis (1994) (103)
Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes (2012) (101)
A complex prediction: three‐dimensional model of the yeast exosome (2002) (100)
Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III (1992) (98)
Challenging times for bioinformatics (1995) (98)
Correction to ‘The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets’ (2021) (98)
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Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton (2016) (59)
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More than 1,000 putative new human signalling proteins revealed by EST data mining (2000) (51)
Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair‐deficient cancer cells (2001) (49)
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An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum (2014) (49)
Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes. (2003) (48)
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Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox (2021) (47)
Fibronectin type III modules in the receptor phosphatase CD45 and tapeworm antigens (1993) (46)
Complement components C1r/C1s, bone morphogenic protein 1 and Xenopus laevis developmentally regulated protein UVS.2 share common repeats (1991) (46)
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More von Willebrand factor type A domains? Sequence similarities with malaria thrombospondin-related anonymous protein, dihydropyridine-sensitive calcium channel and inter-alpha-trypsin inhibitor. (1991) (46)
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Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation (2008) (45)
Biosynthetic potential of the global ocean microbiome (2022) (44)
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Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs (2013) (42)
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Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox (2020) (40)
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Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome (2019) (25)
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Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs)* (2015) (25)
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Circular reasoning rather than cyclic expression (2008) (6)
A protocol for the update of references to scientific literature in biological databases. (2003) (6)
[The gut microbiome in Parkinson's disease]. (2019) (6)
Estimating rates of alternative splicing in mammals and invertebrates (2004) (6)
Discovery and validation of the antimetastatic activity of citalopram in colorectal cancer (2015) (5)
Evolution and regulation of cellular periodic processes: a role for paralogues (2010) (5)
Experimental characterization of the human non-sequence-specific nucleic acid interactome (2013) (5)
On the classification of modular proteins. (1996) (5)
Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology (2019) (5)
Individuality and temporal stability of the human gut microbiome (2014) (5)
Conservation of gene co-regulation in prokaryotes and eukaryotes (2002) (5)
Consent insufficient for data release—Response (2019) (4)
Extraction of regulatory gene/protein networks (2005) (4)
FMN- or DNA-binding? (1994) (4)
Protein Intake, Metabolic Status and the Gut Microbiota in Different Ethnicities: Results from Two Independent Cohorts (2021) (4)
Literature and Genome Data Mining for Prioritizing Disease-Associated Genes (2006) (4)
Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments (2022) (4)
Coupling proteomics and metabolomics for the unsupervised identification of protein–metabolite interactions in Chaetomium thermophilum (2021) (4)
Supplementary Information for : Co-evolution of transcriptional and posttranslational cell cycle regulation (2006) (4)
MIACA – Minimum Information About a Cellular Assay: Standardized description of cell-based functional assay projects (2013) (4)
Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology (2020) (4)
The breast cancer gene product TSG101 (1997) (4)
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes (2022) (3)
Sequences and topology: Genes and structures in context (2004) (3)
A 12‐genus bacterial signature identifies a group of severe autistic children with differential sensory behavior and brain structures (2021) (3)
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes (2022) (3)
Lipidomics profiling reveals a distinct pattern of selective lipid depletion in the circulation and liver tissue in patients with progressive alcohol-associated liver fibrosis: a biopsy-controlled study in 400 people (2020) (3)
Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses (2022) (3)
[Microbial Biomarkers for Early Cancer Detection]. (2017) (3)
Quality analysis and integration of large-scale molecular data sets (2004) (3)
Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication" (2014) (3)
(Phospho)proteomic Profiling of Microsatellite Unstable CRC Cells Reveals Alterations in Nuclear Signaling and Cholesterol Metabolism Caused by Frameshift Mutation of NMD Regulator UPF3A (2020) (3)
The Functional Composition of Living Machines as a Design Principle for Artificial Organisms (1995) (3)
Molecular characterization of a cDNA encoding functional human CLK4 kinase and localization to chromosome 5q35 [correction of 4q35]. (2001) (3)
Phospholipases A2 and Wnts are unlikely to share a common ancestor. (1999) (3)
Human nuclear pore complex (2015) (2)
Insights into biotic and abiotic modulation of ocean mesopelagic communities (2021) (2)
The Sequence Alerting Server - a new WEB server (1997) (2)
Exploitation of gene context to infer evolution and to predict function (2000) (2)
Microbiome Determinants and Physiological Effects of the Benzoate-Hippurate Microbial-Host Co-Metabolic Pathway (2019) (2)
Associative database of protein sequences (1999) (2)
Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation (2019) (2)
Bacterium Proteome Organization in a Genome-Reduced (2009) (2)
Genome analysis MOCAT 2 : a metagenomic assembly , annotation and profiling framework (2016) (2)
Computational Analysis of Modular Protein Architectures (2008) (2)
Functional and evolutionary significance of unknown genes from uncultivated taxa (2022) (2)
Cytoplasmic signalling domains (1997) (2)
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes (2022) (2)
High rate of gene displacement in vitamin biosynthesis pathways. (2003) (2)
Recovery of gut microbiota of healthy adults following antibiotic exposure (2018) (1)
Applying Logic Programming to Derive Novel Functional Information of Genomes (1999) (1)
PLOS Computational Biology 2017 Reviewer and Editorial Board Thank You (2018) (1)
Author Correction: Macroscale patterns of oceanic zooplankton composition and size structure (2021) (1)
Genetic gradients and convergence (2008) (1)
STRING and STITCH: known and predicted interactions between proteins and chemicals (2008) (1)
PLOS Computational Biology 2016 Reviewer and Editorial Board Thank You (2017) (1)
A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links (2018) (1)
No Sec7-homology domain in guanine-nucleotide-exchange factors that act on Ras and Rho. (1999) (1)
Entschlüsselung von Proteinfunktionen mit Hilfe des Computers: Erkennung und Interpretation entfernter Sequenzähnlichkeiten (1993) (1)
, Metabolism and Its Regulation Impact of Genome Reduction on Bacterial (2009) (1)
Reference genome-independent taxonomic profiling of microbiomes with mOTUs3 (2022) (1)
Experimental characterization of the human non-sequence-specific nucleic acid interactome (2013) (1)
Discovery of Analogous Enzymes in Thiamin Biosynthesis by Anticorrelation (2002) (1)
A lipid-binding domain in Wnt (1999) (1)
On alpha-helices terminated by glycine. 2. Recognition by sequence patterns. (1991) (1)
Microbial abundance, activity and population genomic profiling with mOTUs2 (2019) (1)
Author response: Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes (2017) (1)
Quest for Orthologs ( QfO ) entails Quest for Tree of Life ( QfToL ) : in Search of the Gene Stream (2015) (1)
Vast human gut virus diversity uncovered by combined short- and long-read sequencing (2022) (1)
InterPro in 2011 (2012) (1)
C. difficile is overdiagnosed in adults and a commensal in infants (2022) (1)
Consistent mutational paths predict eukaryotic thermostability (2013) (1)
Disentangling disease- and drug signatures of the human gut microbiome: the case of type 2 diabetes mellitus (2016) (1)
Bioinformatics and molecular medicine--introduction and call for papers. (1997) (1)
AMPSphere : the worldwide survey of prokaryotic antimicrobial peptides (2021) (0)
Spatiotemporal variation of mammalian protein complex stoichiometries (2016) (0)
The signalling domain repertoire - (TIBSC 04) (1997) (0)
Similarity of the dog and human gut microbiomes in gene content and response to diet (2018) (0)
Discussion: Conservation of gene co-regulation in prokaryotes and eukaryotes (2002) (0)
Abstract 717: Mouse model for the development of preventive and therapeutic vaccines against microsatellite-unstable cancers (2018) (0)
Correction. (2021) (0)
Resource Lipid Cooperativity as a Ge neral Membrane-Recruitment Principle for PH Domains Graphical (2015) (0)
Sequences and topology. Genome and proteome informatics - Editorial overview (2000) (0)
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies (2018) (0)
A point of entry into genomics (1999) (0)
Associative Data Base of Biomolecuiar Sequences (1997) (0)
1 Genome-wide experimental determination of barriers to horizontal gene transfer (2008) (0)
function Complex genomic rearrangements lead to novel primate gene data (2005) (0)
Maintenance of EGFR plasma membrane levels involves cargo-specific COPII components of the early secretory pathway machinery (2016) (0)
Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress (2007) (0)
Pseudogenes and genomes. (2003) (0)
Review Process File (2012) (0)
Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties(2011 JGI User Meeting) (2011) (0)
Temporal and technical variability of human gut metagenomes (2015) (0)
50 The Rise of Bioinformatics in Data-driven Cancer Research (2012) (0)
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities (2021) (0)
A novel sequence motif highlights a functional link between spartin and spastin, mutated in hereditary spastic paraplegia. (2002) (0)
Unveiling the metabolism of polar archaea through metagenomics and single-cell approaches (2012) (0)
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, August 6-10, 1999, Heidelberg, Germany (1999) (0)
Proteomics Analysis of Cellular Network in Human Bone Marrow Reveals Lineage Skewing Towards Megakaryocytes and Decrease in Lymphoid Development upon Aging (2016) (0)
Enterotypes of thehumangutmicrobiome (2011) (0)
Structure and function of DNA transposition assemblies involved in antibiotic resistance spreading (2022) (0)
The current understanding of protein – lipid recognition comes from the study of a limited number of lipids , principally (2010) (0)
Efficient recovery of complete gut phage genomes by combined short- and long-sequencing (2022) (0)
Association of the Liver and Plasma Lipidomes with the Histological Stage of Alcohol-Related Liver Disease (2021) (0)
Multiomics and quantitative modelling disentangle diet, host, and microbiota contributions to the host metabolome (2022) (0)
Enterotypes in the landscape of gut microbial community composition (2017) (0)
Complex genomic rearrangements lead to novel primate gene Material Supplemental (2005) (0)
Quality assessment of orthology prediction methods using curated protein families (2011) (0)
Novel function in light-mediated microbial processes (2008) (0)
Systematic genomic screening and analysis of mRNA in the 5' and 3' untranslated region (1997) (0)
Towards detection of sequence orthologs (1997) (0)
Genome comparisons to monitor molecular evolution (1999) (0)
Nephrology Dialysis Transplantation Structural motifs of the PKD 1 protein (2005) (0)
Von Genomsequenzen zu Proteinfunktionen (1996) (0)
Publisher Correction: Visualizing translation dynamics at atomic detail inside a bacterial cell (2022) (0)
Publisher Correction: Enterotypes in the landscape of gut microbial community composition (2018) (0)
Statin therapy is associated with lower prevalence of gut microbiota dysbiosis (2020) (0)
Inter-individual differences in the gene content of human gut bacterial species (2015) (0)
Ice-Age Climate Adaptatio ns Trap the AlpineMarmot in a State of Low Genetic Diversity Highlights (0)
Genome speak (2001) (0)
Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation (2019) (0)
Title: BLAST2GENE: a comprehensive conversion of BLAST output into independent (2004) (0)
Glycogen accumulation, central carbon metabolism, and aging of hematopoietic stem and progenitor cells (2020) (0)
Table of Contents (1994) (0)
Dissecting the intracellular pancreatic tumor microbiome at single-cell level. (2022) (0)
Bioinformatics: Bits and Bytes (1999) (0)
Comparing genes and genomes (abstract): from polymorphism to phylogeny (1999) (0)
Second International Meeting on Single Nucleotide Polymorphism and Complex Genome Analysis (2018) (0)
Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans (2018) (0)
Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline (2018) (0)
Comparative sequence analysis (2000) (0)
The Tenth Asia Pacific Bioinformatics Conference (APBC 2012) (2012) (0)
Abstract A40: The SIAMCAT R package enables statistical and machine learning analyses for case-control microbiome datasets (2020) (0)
Circular reasoning rather than cyclic expression Lars Juhl Jensen* †¤ , Ulrik de Lichtenberg ‡¤ , Thomas Skøt Jensen § , (2008) (0)
Databases and ontologies LSAT : learning about alternative transcripts in MEDLINE (2006) (0)
THE SOLUTION STRUCTURE OF SAM DOMAIN FROM THE RECEPTOR TYROSINE KINASE EPHB2, NMR, 10 STRUCTURES (1999) (0)
Aus tumorzellen isolierbare gene mit kodierenden mononucleotid- oder dinucleotid-mikrosatelliten (2001) (0)
SPHINGOLIPIDS ARE DEPLETED IN ALCOHOL-RELATED LIVER FIBROSIS. (2023) (0)
First Tara Oceans V9 rDNA metabarcoding dataset. (2015) (0)
Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by multi-omic analysis (2022) (0)
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity (2020) (0)
Chemicals in context: from SuperTarget and Matador (2008) (0)
different lineages reveal highly variable rates of genomic rearrangements across Comparative architectures of mammalian and chicken genomes data (2004) (0)
Just-in-time assembly of cell-cycle protein complexes (2008) (0)
LotuS: an efficient and user-friendly OTU processing pipeline (2014) (0)
Proteome Analyses and Single-Cell RNA Sequencing Reveal Age-Dependent Re-Wiring of Central Carbon Metabolism in Myeloid-Biased Subsets of Human Hematopoietic Stem Cells (2018) (0)
Structure and function of the global topsoil microbiome (2018) (0)
Transcription start site associated RNAs in bacteria This article has been corrected since Online Publication. The name of the seventh author has been corrected. (2012) (0)
Mikrobielle Biomarker zur Krebsfrüherkennung (2017) (0)
The microbiomes of blowflies and houseflies as bacterial transmission reservoirs (2017) (0)
NMR STRUCTURE OF THE HRDC DOMAIN FROM SACCHAROMYCES CEREVISIAE RECQ HELICASE (2000) (0)
Polarization of microbial communities between competitive and cooperative metabolism (2021) (0)
Enterotypes of the human gut microbiome (Addendum) (2014) (0)
Environmental High-content Fluorescence Microscopy (e-HCFM) of Tara Oceans Samples Provides a View of Global Ocean Protist Biodiversity (2016) (0)
Lawrence Berkeley National Laboratory Recent Work Title Plankton networks driving carbon export in the oligotrophic ocean Permalink (2016) (0)
Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients (2017) (0)
Bacterium Transcriptome Complexity in a Genome-Reduced (2009) (0)
Global cross-domain diversity patterns of picoplankton in the photic and aphotic ocean (2014) (0)
Consistency across multi-omics layers in a drug-perturbed gut microbial community (2023) (0)
A global ocean atlas of eukaryotic genes (2018) (0)
Mikrobielle Biomarker zur Krebsfrüherkennung (2018) (0)
Partial gene catalog of deep samples (4000m) from a Global Metagenomics Expedition (Malaspina 2010) (2017) (0)
Tara Oceans' approach and new challenges in studying the ocean microbiome at global scale (2016) (0)
Pathway alignment: Application in the comparative analysis of glycolysis (1998) (0)
Author response: Extensive transmission of microbes along the gastrointestinal tract (2018) (0)
Erratum to: LotuS: an efficient and user-friendly OTU processing pipeline (2014) (0)
Of Roman roads , train yards and inspectors : recent discoveries in RNA research (0)

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