Peer Bork

发表

Martin Vingron, Yan P. Yuan, Oliver Eulenstein, 1997, German Conference on Bioinformatics.

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

Davide Heller, Damian Szklarczyk, Christian von Mering, 2018, Nucleic Acids Res..

Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine-learning toolbox

Peer Bork, Jakob Wirbel, Konrad Zych, 2020, bioRxiv.

Comparing genes and genomes (abstract): from polymorphism to phylogeny

Peer Bork, P. Bork, 1999, RECOMB.

Drug-Induced Regulation of Target Expression

Peer Bork, Lars Juhl Jensen, Michael Kuhn, 2010, PLoS Comput. Biol..

LSAT: learning about alternative transcripts in MEDLINE

Peer Bork, Parantu K. Shah, P. Bork, 2006, Bioinform..

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources

Martin Vingron, Christian von Mering, Ines Liebich, 2004, Bioinform..

Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication"

Xing-Ming Zhao, Peer Bork, Vera van Noort, 2014, PLoS Comput. Biol..

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data

Julio Saez-Rodriguez, Peer Bork, Emanuel J. V. Gonçalves, 2012, Bioinform..

Identifying Single Copy Orthologs in Metazoa

Peer Bork, Julie Dawn Thompson, Jean Muller, 2011, PLoS Comput. Biol..

Open science resources for the discovery and analysis of Tara Oceans data

Peer Bork, Shinichi Sunagawa, Daniele Iudicone, 2015, Scientific Data.

SMART: recent updates, new developments and status in 2015

Peer Bork, Ivica Letunic, Tobias Doerks, 2014, Nucleic Acids Res..

SMART 7: recent updates to the protein domain annotation resource

Peer Bork, Ivica Letunic, Tobias Doerks, 2011, Nucleic Acids Res..

GeneQuiz: A Workbench for Sequence Analysis

Chris Sander, Alfonso Valencia, Reinhard Schneider, 1994, ISMB.

SmashCell: a software framework for the analysis of single-cell amplified genome sequences

Peer Bork, Jeroen Raes, Manimozhiyan Arumugam, 2010, Bioinform..

Review Process File

Peer Bork, Kiran Raosaheb Patil, Jeroen Raes, 2012 .

Computational Analysis of Modular Protein Architectures

Peer Bork, Ivica Letunic, Toby J. Gibson, 2008 .

A novel sequence motif highlights a functional link between spartin and spastin, mutated in hereditary spastic paraplegia.

Peer Bork, Francesca D. Ciccarelli, Christos Proukakis, 2002 .

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language

Peer Bork, Jaime Huerta-Cepas, Ana T. Freitas, 2019, Microbiome.

Pathway alignment: Application in the comparative analysis of glycolysis

Peer Bork, Stefan Schuster, Martijn A. Huynen, 1998, German Conference on Bioinformatics.

ArrayProspector: a web resource of functional associations inferred from microarray expression data

Christian von Mering, Julien Lagarde, Peer Bork, 2004, Nucleic Acids Res..

Sequences and topology

Peer Bork, David Eisenberg, P. Bork, 2000 .

Towards detection of orthologues in sequence databases

Martin Vingron, Yan P. Yuan, Oliver Eulenstein, 1998, Bioinform..

SMART 6: recent updates and new developments

Peer Bork, Ivica Letunic, Tobias Doerks, 2008, Nucleic Acids Res..

20 years of the SMART protein domain annotation resource

Peer Bork, Ivica Letunic, P. Bork, 2017, Nucleic Acids Res..

Applying Logic Programming to Derive Novel Functional Information of Genomes

Peer Bork, Arvind K. Bansal, P. Bork, 1999, International Symposium on Practical Aspects of Declarative Languages.

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes

Peer Bork, Jaime Huerta-Cepas, Daniel R. Mende, 2016, Nucleic Acids Res..

STITCH: interaction networks of chemicals and proteins

Christian von Mering, Peer Bork, Lars Juhl Jensen, 2007, Nucleic Acids Res..

eggNOG v4.0: nested orthology inference across 3686 organisms

Damian Szklarczyk, Christian von Mering, Peer Bork, 2013, Nucleic Acids Res..

Recent improvements to the SMART domain-based sequence annotation resource

Peer Bork, Francesca D. Ciccarelli, Ivica Letunic, 2002, Nucleic Acids Res..

SuperTarget and Matador: resources for exploring drug-target relationships

Robert B. Russell, Philip E. Bourne, Reinhard Schneider, 2007, Nucleic Acids Res..

Extraction of regulatory gene/protein networks from Medline

Peer Bork, Lars Juhl Jensen, Jasmin Saric, 2006, Bioinform..

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

Peer Bork, David Torrents, Mikita Suyama, 2006, Nucleic Acids Res..

InterPro: the integrative protein signature database

Robert D. Finn, Cathy H. Wu, Alex Bateman, 2008, Nucleic Acids Res..

The Sequence Alerting Server - a new WEB server

Peer Bork, Hedvig Hegyi, J. M. Lai, 1997, Comput. Appl. Biosci..

ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins

Leszek Rychlewski, Peer Bork, Allegra Via, 2003, Nucleic Acids Res..

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

Damian Szklarczyk, Christian von Mering, Andrea Franceschini, 2012, Nucleic Acids Res..

HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources

Yan P. Yuan, Peer Bork, D. Fredman, 2002, Nucleic Acids Res..

Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs

Xing-Ming Zhao, Peer Bork, Vera van Noort, 2013, PLoS Comput. Biol..

A Versatile Structural Domain Analysis Server Using Profile Weight Matrices

Peer Bork, Thomas Dandekar, Steffen Schmidt, 2002, J. Chem. Inf. Comput. Sci..

Gene annotation from scientific literature using mappings between keyword systems

Miguel A. Andrade-Navarro, Peer Bork, Carolina Perez-Iratxeta, 2004, Bioinform..

STRING: known and predicted protein–protein associations, integrated and transferred across organisms

Christian von Mering, Peer Bork, Sean D. Hooper, 2004, Nucleic Acids Res..

Large-scale Extraction of Protein/Gene Relations for Model Organisms

Peer Bork, Lars Juhl Jensen, Jasmin Saric, 2005 .

A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links

Matej Oresic, Falk Hildebrand, Peer Bork, 2018, Nature Protocols.

STRING and STITCH: known and predicted interactions between proteins and chemicals

Christian von Mering, Peer Bork, Lars Juhl Jensen, 2008 .

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins

Joaquín Dopazo, Peer Bork, Jaime Huerta-Cepas, 2014, Nucleic Acids Res..

STRING v10: protein–protein interaction networks, integrated over the tree of life

Davide Heller, Damian Szklarczyk, Christian von Mering, 2014, Nucleic Acids Res..

InterPro, progress and status in 2005

Cathy H. Wu, Alex Bateman, Rolf Apweiler, 2004, Nucleic Acids Res..

PLOS Computational Biology 2016 Reviewer and Editorial Board Thank You

Matthias Bethge, Gunnar Blohm, Kevin Bretonnel Cohen, 2017, PLoS Comput. Biol..

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

Damian Szklarczyk, Christian von Mering, Andrea Franceschini, 2010, Nucleic Acids Res..

The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold

Peer Bork, Francesca D. Ciccarelli, Elisa Izaurralde, 2003, BMC Bioinformatics.

New developments in the InterPro database

Robert D. Finn, Robert Petryszak, Cathy H. Wu, 2007, Nucleic Acids Res..

Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data

Xing-Ming Zhao, Peer Bork, Georg Zeller, 2011, PLoS Comput. Biol..

NetworKIN: a resource for exploring cellular phosphorylation networks

Tony Pawson, Peer Bork, Lars Juhl Jensen, 2007, Nucleic Acids Res..

HGBASE: a database of SNPs and other variations in and around human genes

Yan P. Yuan, Peer Bork, Marianne Siegfried, 2000, Nucleic Acids Res..

STRING 7—recent developments in the integration and prediction of protein interactions

Christian von Mering, Peer Bork, Berend Snel, 2006, Nucleic Acids Res..

Medusa: a simple tool for interaction graph analysis

Peer Bork, Sean D. Hooper, P. Bork, 2005, Bioinform..

SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology

Yan P. Yuan, Peer Bork, Axel Benner, 2009, Nucleic Acids Res..

BIOINFORMATICS APPLICATIONS

Peer Bork, Julie Dawn Thompson, Jean Muller, 2022 .

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

Peer Bork, Ivica Letunic, P. Bork, 2007, Bioinform..

iPath3.0: interactive pathways explorer v3

Peer Bork, Ivica Letunic, Takuji Yamada, 2018, Nucleic Acids Res..

BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments

Peer Bork, David Torrents, Mikita Suyama, 2004, Bioinform..

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features

Peer Bork, Michael Kuhn, Yuanyue Li, 2019, bioRxiv.

Associative Data Base of Biomolecuiar Sequences

Peer Bork, Jens G. Reich, Jens Hanke, 1997, German Conference on Bioinformatics.

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

Peer Bork, Ivica Letunic, P. Bork, 2016, Nucleic Acids Res..

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

Davide Heller, Damian Szklarczyk, Christian von Mering, 2015, Nucleic Acids Res..

DCD – a novel plant specific domain in proteins involved in development and programmed cell death

Peer Bork, Tobias Doerks, Raimund Tenhaken, 2005, BMC Bioinformatics.

Comparative analysis of protein interaction networks

Peer Bork, 2002, ECCB.

PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins

Peer Bork, Pablo Minguez, Ivica Letunic, 2012, Nucleic Acids Res..

RTK: efficient rarefaction analysis of large datasets

Falk Hildebrand, Peer Bork, Kristoffer Forslund, 2017, Bioinform..

Frame: detection of genomic sequencing errors

Chris Sander, Peer Bork, N. P. Brown, 1998, Bioinform..

Identification and Analysis of Genes and Pseudogenes within Duplicated Regions in the Human and Mouse Genomes

Peer Bork, David Torrents, Eoghan D. Harrington, 2006, PLoS Comput. Biol..

A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens

Christian von Mering, Peer Bork, Roland Krause, 2003, Bioinform..

The Tenth Asia Pacific Bioinformatics Conference (APBC 2012)

Yi-Ping Phoebe Chen, Peer Bork, 2012, BMC Genomics.

Extracting Regulatory Gene Expression Networks From Pubmed

Peer Bork, Lars Juhl Jensen, Jasmin Saric, 2004, ACL.

A fast, sensitive pattern-matching approach for protein sequences

Peer Bork, K. Rohde, P. Bork, 1993, Comput. Appl. Biosci..

The SIDER database of drugs and side effects

Peer Bork, Ivica Letunic, Lars Juhl Jensen, 2015, Nucleic Acids Res..

Extraction of Transcript Diversity from Scientific Literature

Peer Bork, Lars Juhl Jensen, Parantu K. Shah, 2005, PLoS Comput. Biol..

Extensive impact of non-antibiotic drugs on human gut bacteria

Peer Bork, Kiran Raosaheb Patil, Michael Kuhn, 2018, Nature.

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

Peer Bork, Ivica Letunic, P. Bork, 2011, Nucleic Acids Res..

SmashCommunity: a metagenomic annotation and analysis tool

Peer Bork, Konrad U. Förstner, Jeroen Raes, 2010, Bioinform..

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

Damian Szklarczyk, Christian von Mering, Peer Bork, 2009, Nucleic Acids Res..

Systematic genomic screening and analysis of mRNA in the 5' and 3' untranslated region

Katrin Beyer, Peer Bork, Thomas Dandekar, 1997, German Conference on Bioinformatics.

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

Damian Szklarczyk, Christian von Mering, John H. Morris, 2018, Nucleic Acids Res..

Entschlüsselung von Proteinfunktionen mit Hilfe des Computers: Erkennung und Interpretation entfernter Sequenzähnlichkeiten

Peer Bork, Peer Bork, 1993, Informatik in den Biowissenschaften.

CART—a chemical annotation retrieval toolkit

Peer Bork, Georg Zeller, Murat Iskar, 2016, Bioinform..

STITCH 2: an interaction network database for small molecules and proteins

Damian Szklarczyk, Christian von Mering, Andrea Franceschini, 2009, Nucleic Acids Res..

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

Jun Wang, Peer Bork, Junhua Li, 2015, Nature.

Information extraction from full text scientific articles: Where are the keywords?

Miguel A. Andrade-Navarro, Peer Bork, Carolina Perez-Iratxeta, 2003, BMC Bioinformatics.

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

Damian Szklarczyk, Christian von Mering, John H. Morris, 2016, Nucleic Acids Res..

SMART: identification and annotation of domains from signalling and extracellular protein sequences

Peer Bork, Chris P. Ponting, Jörg Schultz, 1999, Nucleic Acids Res..

The InterPro protein families database: the classification resource after 15 years

Huaiyu Mi, Robert D. Finn, Matthew Fraser, 2014, Nucleic Acids Res..

Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology

Thomas Lengauer, Peer Bork, Douglas L. Brutlag, 1998, ISMB 1999.

Bioinformatics: Bits and Bytes

Peer Bork, Jens G. Reich, Shamil R. Sunyaev, 1999 .

MOCAT2: a metagenomic assembly, annotation and profiling framework

Peer Bork, Jaime Huerta-Cepas, Shinichi Sunagawa, 2016, Bioinform..

STITCH 3: zooming in on protein–chemical interactions

Damian Szklarczyk, Christian von Mering, Andrea Franceschini, 2011, Nucleic Acids Res..

STRING: a database of predicted functional associations between proteins

Christian von Mering, Peer Bork, Berend Snel, 2003, Nucleic Acids Res..

SMART: a web-based tool for the study of genetically mobile domains

Peer Bork, Chris P. Ponting, Jörg Schultz, 2000, Nucleic Acids Res..

The Functional Composition of Living Machines as a Design Principle for Artificial Organisms

Chris Sander, Alfonso Valencia, Peer Bork, 1995, ECAL.

InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites

Alex Bateman, Rolf Apweiler, Henning Hermjakob, 2002, Briefings Bioinform..

MVP: a microbe–phage interaction database

Xing-Ming Zhao, Zhi Liu, Peer Bork, 2017, Nucleic Acids Res..

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

Damian Szklarczyk, Christian von Mering, Peer Bork, 2011, Nucleic Acids Res..

OGEE: an online gene essentiality database

Peer Bork, Pablo Minguez, Martin J. Lercher, 2011, Nucleic Acids Res..

SMART 4.0: towards genomic data integration

Peer Bork, Francesca D. Ciccarelli, Ivica Letunic, 2004, Nucleic Acids Res..

STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

Damian Szklarczyk, Christian von Mering, Peer Bork, 2015, Nucleic Acids Res..

SMART 5: domains in the context of genomes and networks

Peer Bork, Ivica Letunic, Jörg Schultz, 2005, Nucleic Acids Res..

OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines

Xing-Ming Zhao, Xiao Chen, Peer Bork, 2016, Nucleic Acids Res..

eggNOG: automated construction and annotation of orthologous groups of genes

Christian von Mering, Peer Bork, Jean Muller, 2007, Nucleic Acids Res..

The WHy domain mediates the response to desiccation in plants and bacteria

Peer Bork, Francesca D. Ciccarelli, P. Bork, 2005, Bioinform..

STRING 8—a global view on proteins and their functional interactions in 630 organisms

Christian von Mering, Peer Bork, Jean Muller, 2008, Nucleic Acids Res..

Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries

Peer Bork, Frank Eisenhaber, P. Bork, 1999, Bioinform..

STITCH 4: integration of protein–chemical interactions with user data

Damian Szklarczyk, Christian von Mering, Thomas Blicher, 2013, Nucleic Acids Res..

Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches

Katrin Beyer, Peer Bork, Thomas Dandekar, 1998, Bioinform..

Associative database of protein sequences

Peer Bork, Jens G. Reich, Jens Hanke, 1999, Bioinform..

KEGG Atlas mapping for global analysis of metabolic pathways

Peer Bork, Susumu Goto, Minoru Kanehisa, 2008, Nucleic Acids Res..

Comparison of computational methods for the identification of cell cycle-regulated genes

Peer Bork, Søren Brunak, Lars Juhl Jensen, 2005, Bioinform..

4DXpress: a database for cross-species expression pattern comparisons

Thorsten Henrich, Joachim Wittbrodt, Peer Bork, 2007, Nucleic Acids Res..

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

Silvio C. E. Tosatto, Neil D. Rawlings, Robert D. Finn, 2018, Nucleic Acids Res..

Sircah: a tool for the detection and visualization of alternative transcripts

Peer Bork, Eoghan D. Harrington, P. Bork, 2008, Bioinform..

Von Genomsequenzen zu Proteinfunktionen

Peer Bork, 1996, Informationstechnik Tech. Inform..

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features

Peer Bork, Yuanyue Li, Michael Kuhn, 2020, Bioinform..

Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, August 6-10, 1999, Heidelberg, Germany

Thomas Lengauer, Reinhard Schneider, Peer Bork, 1999, Intelligent Systems in Molecular Biology.

Addendum: Enterotypes of the human gut microbiome

Jun Wang, Tetsuya Hayashi, Peer Bork, 2014, Nature.

NAIL-Network Analysis Interface for Linking HMMER results

Miguel A. Andrade-Navarro, Yan P. Yuan, Peer Bork, 2000, Bioinform..

The InterPro Database, 2003 brings increased coverage and new features

Alex Bateman, Rolf Apweiler, Nicola J. Mulder, 2003, Nucleic Acids Res..

The STRING database in 2017

Damian Szklarczyk, Peer Bork, Michael Kuhn, 2017 .

InterPro in 2011: new developments in the family and domain prediction database

Robert D. Finn, Matthew Fraser, Cathy H. Wu, 2011, Nucleic acids research.

iPath2.0: interactive pathway explorer

Peer Bork, Minoru Kanehisa, Shujiro Okuda, 2011, Nucleic Acids Res..

Systematic identification of phosphorylation-mediated protein interaction switches

Matthew J. Betts, Robert B. Russell, Peer Bork, 2017, PLoS Comput. Biol..

Update on XplorMed: a web server for exploring scientific literature

Miguel A. Andrade-Navarro, Peer Bork, Carolina Perez-Iratxeta, 2003, Nucleic Acids Res..

Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress

Xi Wang, Thorsten Henrich, Joachim Wittbrodt, 2008, APBC.

SMART: recent updates, new developments and status in 2020

Peer Bork, Ivica Letunic, Supriya Khedkar, 2020, Nucleic Acids Res..

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines

Xing-Ming Zhao, Peer Bork, Robin B. Gasser, 2020, Nucleic Acids Res..

A complex prediction: three‐dimensional model of the yeast exosome

Peer Bork, Patrick Aloy, Giulio Superti‐Furga, 2002, EMBO reports.

Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer

Peer Bork, Rotem Sorek, P. Bork, 2007, Science.

children with inflammatory bowel disease and healthy siblings in taxonomic and functional composition : a metagenomic analysis

Peer Bork, Shinichi Sunagawa, Kristoffer Forslund, 2018 .

Corrigendum: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

Falk Hildebrand, Peer Bork, Søren Brunak, 2017, Nature.

Genome and protein evolution in eukaryotes.

Peer Bork, Ivica Letunic, Richard R Copley, 2002, Current opinion in chemical biology.

Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology

Peer Bork, Chris Sander, Georg Casari, 1995, Molecular microbiology.

Environmental characteristics of Agulhas rings affect interocean plankton transport

Peer Bork, Shinichi Sunagawa, Stéphane Audic, 2015, Science.

Consistency of genome‐based methods in measuring Metazoan evolution

Peer Bork, Ivica Letunic, Christian von Mering, 2005, FEBS letters.

The draft sequences: Filling in the gaps

Peer Bork, P. Bork, R. Copley, 2001, Nature.

Bioinformatics Analysis of Functional Associations of PTMs.

Peer Bork, Pablo Minguez, P. Bork, 2017, Methods in molecular biology.

Sequence and Structure of Proteins

Peer Bork, Frank Eisenhaber, P. Bork, 2001 .

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages.

Peer Bork, Pavel A Pevzner, Glenn Tesler, 2005, Genome research.

Impact of selection, mutation rate and genetic drift on human genetic variation.

Peer Bork, Vasily Ramensky, Shamil Sunyaev, 2003, Human molecular genetics.

What's in a genome?

Chris Sander, Peer Bork, Christos Ouzounis, 1992, Nature.

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Peer Bork, Bas E. Dutilh, Shinichi Sunagawa, 2016, Nature.

Divergent evolution of a β/α‐barrel subclass: Detection of numerous phosphate‐binding sites by motif search

Peer Bork, Rob W. W. Hooft, P. Bork, 1995 .

Homology‐based functional proteomics by mass spectrometry: Application to the Xenopus microtubule‐associated proteome

Peer Bork, Bianca Habermann, Eric Karsenti, 2004, Proteomics.

The cytidylyltransferase superfamily: Identification of the nucleotide‐binding site and fold prediction

Chris Sander, Liisa Holm, Peer Bork, 1995, Proteins.

Comparative Genome and Proteome Analysis of Anopheles gambiae and Drosophila melanogaster

Peer Bork, Ewan Birney, Ivica Letunic, 2002, Science.

Exploring MEDLINE abstracts with XplorMed.

Peer Bork, Carolina Perez-Iratxeta, Miguel A Andrade, 2002, Drugs of today.

Discovery and validation of the antimetastatic activity of citalopram in colorectal cancer

Peer Bork, Murat Iskar, P. Bork, 2015, Molecular & cellular oncology.

Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species

Erich Bornberg-Bauer, Peer Bork, Alexandre Souvorov, 2010, Science.

Systematic Association of Genes to Phenotypes by Genome and Literature Mining

Peer Bork, Carolina Perez-Iratxeta, Lars J Jensen, 2005, PLoS biology.

Microbial Cell Factories Structural Genomics of Human Proteins – Target Selection and Generation of a Public Catalogue of Expression Clones

Peer Bork, Konrad Büssow, Hans Lehrach, 2022 .

Molecular modelling of the Norrie disease protein predicts a cystine knot growth factor tertiary structure

Chris Sander, Thomas Meitinger, Peer Bork, 1993, Nature Genetics.

The way we write

Peer Bork, Carolina Perez-Iratxeta, Miguel A. Andrade, 2003, EMBO Reports.

A lipid-binding domain in Wnt: a case of mistaken identity?

Robert B. Russell, Peer Bork, Chris P. Ponting, 1999, Current Biology.

Protein function space: viewing the limits or limited by our view?

Peer Bork, Jeroen Raes, P. Bork, 2007, Current opinion in structural biology.

Classification and quantification of bacteriophage taxa in human gut metagenomes

Peer Bork, Shinichi Sunagawa, Eugene V Koonin, 2014, The ISME Journal.

A superfamily of conserved domains in DNA damage‐ responsive cell cycle checkpoint proteins

Peer Bork, Philipp Bucher, S. Altschul, 1997, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Computational eco-systems biology in Tara Oceans: translating data into knowledge

Peer Bork, Shinichi Sunagawa, Eric Karsenti, 2015, Molecular systems biology.

Microbial abundance, activity and population genomic profiling with mOTUs2

Peer Bork, Shinichi Sunagawa, Pascal Hingamp, 2019, Nature Communications.

Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families.

Peer Bork, Lokesh P. Tripathi, Lars Juhl Jensen, 2008, Gene.

Extensive transmission of microbes along the gastrointestinal tract

Peer Bork, Shinichi Sunagawa, Paul Wilmes, 2019, eLife.

Younger Genes Are Less Likely to Be Essential than Older Genes, and Duplicates Are Less Likely to Be Essential than Singletons of the Same Age

Peer Bork, Martin J. Lercher, Kalliopi Trachana, 2012, Molecular biology and evolution.

Country-specific antibiotic use practices impact the human gut resistome

Peer Bork, Shinichi Sunagawa, Manimozhiyan Arumugam, 2013, Genome research.

Classification and quantification of bacteriophage taxa in human gut metagenomes

Peer Bork, Shinichi Sunagawa, Eugene V Koonin, 2014, The ISME Journal.

Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

Peer Bork, Jeroen Raes, Christopher J. Creevey, 2011, PloS one.

The exploration of network motifs as potential drug targets from post-translational regulatory networks

Xing-Ming Zhao, Jiangning Song, Peer Bork, 2016, Scientific Reports.

Insight into Structure and Assembly of the Nuclear Pore Complex by Utilizing the Genome of a Eukaryotic Thermophile

Peer Bork, Vera van Noort, Manimozhiyan Arumugam, 2011, Cell.

Insights into social insects from the genome of the honeybee Apis mellifera

Ying Wang, Michal Linial, Andrew G. Clark, 2006, Nature.

Spatiotemporal variation of mammalian protein complex stoichiometries

Peer Bork, Martin Beck, Murat Iskar, 2016, Genome Biology.

Common exon duplication in animals and its role in alternative splicing.

Peer Bork, Ivica Letunic, Richard R Copley, 2002, Human molecular genetics.

Transcriptional interactions suggest niche segregation among microorganisms in the human gut

Peer Bork, Søren Brunak, Torben Hansen, 2016, Nature Microbiology.

HEAT repeats in the Huntington's disease protein

Peer Bork, Miguel A. Andrade, P. Bork, 1995, Nature Genetics.

The Genome Sequence of the Malaria Mosquito Anopheles gambiae

Jian Wang, Eugene W. Myers, Andrew G. Clark, 2002, Science.

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

Peer Bork, Natalia Ivanova, Jeroen Raes, 2008, Molecular systems biology.

A fair comparison

Peer Bork, Shinichi Sunagawa, Georg Zeller, 2014, Nature Methods.

Lateral Gene Transfer, Genome Surveys, and the Phylogeny of Prokaryotes

Peer Bork, Berend Snel, Martijn A. Huynen, 1999 .

Deciphering a global network of functionally associated post-translational modifications

Peer Bork, Manuela Helmer-Citterich, Pablo Minguez, 2012, Molecular systems biology.

Computing fuzzy associations for the analysis of biological literature.

Peer Bork, Carolina Perez-Iratxeta, Miguel A Andrade, 2002, BioTechniques.

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

Peer Bork, Jun Wang, Daniel R. Mende, 2012, PloS one.

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Terrence S. Furey, Sean R. Eddy, Li Ding, 2005, Nature.

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

Peer Bork, Arcady R. Mushegian, Eugene V. Koonin, 2012, Journal of bacteriology.

Exploitation of gene context to infer evolution and to predict function

Peer Bork, Berend Snel, Martijn A. Huynen, 2000 .

High-resolution transcription atlas of the mitotic cell cycle in budding yeast

Matthew E Ritchie, Peer Bork, Wolfgang Huber, 2010, Genome Biology.

Quantifying compartment‐associated variations of protein abundance in proteomics data

Peer Bork, Martin Beck, Luca Parca, 2018, Molecular systems biology.

Self‐organizing hierarchic networks for pattern recognition in protein sequence

Peer Bork, Jens Hanke, P. Bork, 1996, Protein science : a publication of the Protein Society.

Predicting protein cellular localization using a domain projection method.

Peer Bork, Jörg Schultz, Chris P Ponting, 2002, Genome research.

Systematic identification of novel protein domain families associated with nuclear functions.

Peer Bork, Tobias Doerks, Richard R Copley, 2002, Genome research.

Determinants of community structure in the global plankton interactome

Peer Bork, Pablo Sánchez, Shinichi Sunagawa, 2015, Science.

Conservation of gene co-regulation in prokaryotes and eukaryotes

Peer Bork, Berend Snel, Martijn A. Huynen, 2002 .

Correction: LotuS: an efficient and user-friendly OTU processing pipeline

Falk Hildebrand, Peer Bork, Jeroen Raes, 2014, Microbiome.

Mobile modules and motifs

Peer Bork, P. Bork, 1992, Current Biology.

Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing.

Peer Bork, Elisa Izaurralde, Tobias Doerks, 2007, Genes & development.

The rhodanese/Cdc25 phosphatase superfamily

Peer Bork, P. Bork, D. Bordo, 2002, EMBO reports.

Discovering Functional Novelty in Metagenomes: Examples from Light-Mediated Processes

Peer Bork, Ivica Letunic, Jeroen Raes, 2008, Journal of bacteriology.

The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract

Peer Bork, Berend Snel, Frank Desiere, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Pelin Yilmaz, Folker Meyer, Shibu Yooseph, 2018, Nature Biotechnology.

Inter-individual differences in the gene content of human gut bacterial species

Peer Bork, Shinichi Sunagawa, Daniel R Mende, 2015, Genome Biology.

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Jean-Michel Claverie, Hervé Moreau, Peer Bork, 2013, The ISME Journal.

Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes.

Peer Bork, Tobias Doerks, Christian von Mering, 2004, Nucleic acids research.

Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats

Peer Bork, Martin Beck, Murat Iskar, 2015, Cell systems.

Increase of functional diversity by alternative splicing.

Martin Vingron, Rolf Apweiler, Peer Bork, 2003, Trends in genetics : TIG.

A Computational Screen for Type I Polyketide Synthases in Metagenomics Shotgun Data

Peer Bork, Christopher J. Creevey, Tobias Doerks, 2008, PloS one.

Metabolic dependencies drive species co-occurrence in diverse microbial communities

Peer Bork, Kiran Raosaheb Patil, Aleksej Zelezniak, 2015, Proceedings of the National Academy of Sciences.

Structure and function of the global topsoil microbiome

Falk Hildebrand, Peer Bork, Sofia K. Forslund, 2018, Nature.

ASTD: The Alternative Splicing and Transcript Diversity database.

Oliver Hofmann, Gautier Koscielny, William Ritchie, 2009, Genomics.

Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

Peer Bork, Bas E. Dutilh, Shinichi Sunagawa, 2016, bioRxiv.

Genome organization: Teamed up for transcription

Christian von Mering, Peer Bork, P. Bork, 2002, Nature.

Structural analysis of protein‐ligand interactions: the binding of endogenous compounds and of synthetic drugs

Peer Bork, P. Bork, D. Bordo, 2014, Journal of molecular recognition : JMR.

Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment

Alexander Sczyrba, Andreas Keller, Christian Drosten, 2020, Cell.

Erratum to: LotuS: an efficient and user-friendly OTU processing pipeline

Falk Hildebrand, Peer Bork, Jeroen Raes, 2014, Microbiome.

AUTOMATED PAIR-WISE COMPARISONS OF MICROBIAL GENOMES

Peter J. Stuckey, Peer Bork, Arvind K. Bansal, 1998 .

A network of conserved co-occurring motifs for the regulation of alternative splicing

Peer Bork, Eoghan D. Harrington, Mikita Suyama, 2010, Nucleic acids research.

A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation

Peer Bork, Tobias Doerks, Tomas Larsson, 2014, PloS one.

Quantifying environmental adaptation of metabolic pathways in metagenomics

Jan O. Korbel, Peer Bork, Ivica Letunic, 2009, Proceedings of the National Academy of Sciences.

SAM as a protein interaction domain involved in developmental regulation

Peer Bork, Kay Hofmann, Jörg Schultz, 1997, Protein science : a publication of the Protein Society.

Enterotypes in the landscape of gut microbial community composition

Falk Hildebrand, Peer Bork, Rob Knight, 2017, Nature Microbiology.

Shared components of protein complexes--versatile building blocks or biochemical artefacts?

Peer Bork, Christian von Mering, Roland Krause, 2004, BioEssays : news and reviews in molecular, cellular and developmental biology.

Peer Bork, Itai Yanai, Shannon K McWeeney, 2006, Trends in genetics : TIG.

Is there biological research beyond Systems Biology? A comparative analysis of terms

Peer Bork, P. Bork, 2005, Molecular systems biology.

Ontologies in Quantitative Biology: A Basis for Comparison, Integration, and Discovery

Peer Bork, Lars J. Jensen, P. Bork, 2010, PLoS biology.

Peer Bork, Luis Pedro Coelho, Jens Roat Kultima, 2018, Microbiome.

Global analysis of bacterial transcription factors to predict cellular target processes.

Peer Bork, Tobias Doerks, Christian von Mering, 2004, Trends in genetics : TIG.

Enterotypes of the human gut microbiome

Peer Bork, Søren Brunak, Daniel R. Mende, 2011, Nature.

Luminal signalling links cell communication to tissue architecture during organogenesis

Peer Bork, Murat Iskar, Yannick Schwab, 2014, Nature.

SMART, a simple modular architecture research tool

Peer Bork, Chris P. Ponting, Jörg Schultz, 1998 .

A phosphotyrosine interaction domain

Peer Bork, P. Bork, B. Margolis, 1995, Cell.

Annotation of the M. tuberculosis Hypothetical Orfeome: Adding Functional Information to More than Half of the Uncharacterized Proteins

Peer Bork, Pablo Minguez, Tobias Doerks, 2012, PloS one.

Comparative analysis of environmental sequences: potential and challenges

Christian von Mering, Peer Bork, P. Bork, 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

Ancient animal microRNAs and the evolution of tissue identity

Peer Bork, Oleg Simakov, Raju Tomer, 2010, Nature.

Analysis of amino acid sequences

Peer Bork, 2000 .

Enterotypes of the human gut microbiome

Peer Bork, Daniel R. Mende, David Torrents, 2011, Nature.

Mobile modules and motifs

Peer Bork, P. Bork, 1992, Current Biology.

Sequences and topology Deriving biological knowledge from genomic sequences

Peer Bork, David Eisenberg, P. Bork, 1998 .

The Genome of the Model Beetle and Pest Tribolium Castaneum Vertebrate-specific Orthologues Insect-specific Orthologues Homology Undetectable Similarity

Peer Bork, Alexandre Souvorov, Liangjiang Wang, 2022 .

Alternative splicing and evolution.

Peer Bork, Ivica Letunic, Stephanie Boue, 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

More than 1,000 putative new human signalling proteins revealed by EST data mining

Peer Bork, Chris P. Ponting, Tobias Doerks, 2000, Nature Genetics.

Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism.

Peer Bork, Stefan Schuster, Mikhail Pachkov, 2007, Gene.

Towards Cellular Systems in 4D

Peer Bork, Luis Serrano, P. Bork, 2005, Cell.

Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases

Peer Bork, Thomas Dandekar, Martijn Huynen, 1998, Journal of Molecular Medicine.

Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle

Peer Bork, Lars M Steinmetz, Lars J Jensen, 2006, PLoS genetics.

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

Peer Bork, Michiel Kleerebezem, Jeroen Raes, 2012, The ISME Journal.

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Andreas Wilke, Renzo Kottmann, Pelin Yilmaz, 2010 .

Not Comparable, But Complementary

Peer Bork, Lars Juhl Jensen, P. Bork, 2008, Science.

Pervasive Protein Thermal Stability Variation during the Cell Cycle

Peer Bork, Martin Beck, Nils Kurzawa, 2018, Cell.

Metagenomic species profiling using universal phylogenetic marker genes

Alexandros Stamatakis, Peer Bork, Søren Brunak, 2013, Nature Methods.

George MW, Gene ER. Insights into social insects from the genome of the honeybee Apis mellifera. Nature

Ying Wang, Michal Linial, Peer Bork, 2006 .