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Peer Bork

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Chemicals & Drugs

Proteins

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Publications

TOP 3
Yamada Takuji; Bork Peer
Evolution of biomolecular networks: lessons from metabolic and protein interactions.
Koscielny Gautier; Le Texier Vincent; Gopalakrishnan Chellappa; Kumanduri Vasudev; Riethoven Jean-Jack; Nardone Francesco; Stanley Eleanor; Fallsehr Christine; Hofmann Oliver; Kull Meelis; Harrington Eoghan; Boué Stéphanie; Eyras Eduardo; Plass Mireya; Lopez Fabrice; Ritchie William; Moucadel Virginie; Ara Takeshi; Pospisil Heike; Herrmann Alexander; G Reich Jens; Guigó Roderic; Bork Peer; Doeberitz Magnus von Knebel; Vilo Jaak; Hide Winston; Apweiler Rolf; Thanaraj Thangavel Alphonse; Gautheret Daniel
ASTD: The Alternative Splicing and Transcript Diversity database.
Gianoulis Tara A; Raes Jeroen; Patel Prianka V; Bjornson Robert; Korbel Jan O; Letunic Ivica; Yamada Takuji; Paccanaro Alberto; Jensen Lars J; Snyder Michael; Bork Peer; Gerstein Mark B
Quantifying environmental adaptation of metabolic pathways in metagenomics.

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All Publications

2009: Yamada Takuji; Bork Peer
Evolution of biomolecular networks: lessons from metabolic and protein interactions.
Nature reviews. Molecular cell biology 2009;10(11):791-803.
2009: Koscielny Gautier; Le Texier Vincent; Gopalakrishnan Chellappa; Kumanduri Vasudev; Riethoven Jean-Jack; Nardone Francesco; Stanley Eleanor; Fallsehr Christine; Hofmann Oliver; Kull Meelis; Harrington Eoghan; Boué Stéphanie; Eyras Eduardo; Plass Mireya; Lopez Fabrice; Ritchie William; Moucadel Virginie; Ara Takeshi; Pospisil Heike; Herrmann Alexander; G Reich Jens; Guigó Roderic; Bork Peer; Doeberitz Magnus von Knebel; Vilo Jaak; Hide Winston; Apweiler Rolf; Thanaraj Thangavel Alphonse; Gautheret Daniel
ASTD: The Alternative Splicing and Transcript Diversity database.
Genomics 2009;93(3):213-20.
2009: Gianoulis Tara A; Raes Jeroen; Patel Prianka V; Bjornson Robert; Korbel Jan O; Letunic Ivica; Yamada Takuji; Paccanaro Alberto; Jensen Lars J; Snyder Michael; Bork Peer; Gerstein Mark B
Quantifying environmental adaptation of metabolic pathways in metagenomics.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(5):1374-9.
2008: Jensen Lars Juhl; Bork Peer
Biochemistry. Not comparable, but complementary.
Science (New York, N.Y.) 2008;322(5898):56-7.
2008: Harrington Eoghan D; Bork Peer
Sircah: a tool for the detection and visualization of alternative transcripts.
Bioinformatics (Oxford, England) 2008;24(17):1959-60.
2008: Raes Jeroen; Bork Peer
Molecular eco-systems biology: towards an understanding of community function.
Nature reviews. Microbiology 2008;6(9):693-9.
2008: Campillos Monica; Kuhn Michael; Gavin Anne-Claude; Jensen Lars Juhl; Bork Peer
Drug target identification using side-effect similarity.
Science (New York, N.Y.) 2008;321(5886):263-6.
2008: Pincus David; Letunic Ivica; Bork Peer; Lim Wendell A
Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(28):9680-4.
2008: Okuda Shujiro; Yamada Takuji; Hamajima Masami; Itoh Masumi; Katayama Toshiaki; Bork Peer; Goto Susumu; Kanehisa Minoru
KEGG Atlas mapping for global analysis of metabolic pathways.
Nucleic acids research 2008;36(Web Server issue):W423-6.
2008: Harrington Eoghan D; Jensen Lars J; Bork Peer
Predicting biological networks from genomic data.
FEBS letters 2008;582(8):1251-8.
2008: Kuhn Michael; Campillos Mónica; González Paula; Jensen Lars Juhl; Bork Peer
Large-scale prediction of drug-target relationships.
FEBS letters 2008;582(8):1283-90.
2008: Letunic Ivica; Yamada Takuji; Kanehisa Minoru; Bork Peer
iPath: interactive exploration of biochemical pathways and networks.
Trends in biochemical sciences 2008;33(3):101-3.
2008: Kuhn Michael; von Mering Christian; Campillos Monica; Jensen Lars Juhl; Bork Peer
STITCH: interaction networks of chemicals and proteins.
Nucleic acids research 2008;36(Database issue):D684-8.
2008: Shah Parantu K; Tripathi Lokesh P; Jensen Lars Juhl; Gahnim Murad; Mason Christopher; Furlong Eileen E; Rodrigues Veronica; White Kevin P; Bork Peer; Sowdhamini R
Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families.
Gene 2008;407(1-2):199-215.
2008: Linding Rune; Jensen Lars Juhl; Pasculescu Adrian; Olhovsky Marina; Colwill Karen; Bork Peer; Yaffe Michael B; Pawson Tony
NetworKIN: a resource for exploring cellular phosphorylation networks.
Nucleic acids research 2008;36(Database issue):D695-9.
2008: Günther Stefan; Kuhn Michael; Dunkel Mathias; Campillos Monica; Senger Christian; Petsalaki Evangelia; Ahmed Jessica; Urdiales Eduardo Garcia; Gewiess Andreas; Jensen Lars Juhl; Schneider Reinhard; Skoblo Roman; Russell Robert B; Bourne Philip E; Bork Peer; Preissner Robert
SuperTarget and Matador: resources for exploring drug-target relationships.
Nucleic acids research 2008;36(Database issue):D919-22.
2008: Jensen Lars Juhl; Julien Philippe; Kuhn Michael; von Mering Christian; Muller Jean; Doerks Tobias; Bork Peer
eggNOG: automated construction and annotation of orthologous groups of genes.
Nucleic acids research 2008;36(Database issue):D250-4.
2008: Haudry Yannick; Berube Hugo; Letunic Ivica; Weeber Paul-Daniel; Gagneur Julien; Girardot Charles; Kapushesky Misha; Arendt Detlev; Bork Peer; Brazma Alvis; Furlong Eileen E M; Wittbrodt Joachim; Henrich Thorsten
4DXpress: a database for cross-species expression pattern comparisons.
Nucleic acids research 2008;36(Database issue):D847-53.
2008: Quijano Carlos; Tomancak Pavel; Lopez-Marti Jesus; Suyama Mikita; Bork Peer; Milan Marco; Torrents David; Manzanares Miguel
Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution.
Genome biology 2008;9(12):R176.
2008: Perotti Christian; Liu Ruixuan; Parusel Christine T; Böcher Nadine; Schultz Jörg; Bork Peer; Pfitzner Edith; Groner Bernd; Shemanko Carrie S
Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation.
Breast cancer research : BCR 2008;10(6):R94.
2008: Korff Sebastian; Woerner Stefan M; Yuan Yan P; Bork Peer; von Knebel Doeberitz Magnus; Gebert Johannes
Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability.
BMC cancer 2008;8():329.
2008: Foerstner Konrad U; Doerks Tobias; Creevey Christopher J; Doerks Anja; Bork Peer
A computational screen for type I polyketide synthases in metagenomics shotgun data.
PloS one 2008;3(10):e3515.
2008: Miller Martin Lee; Jensen Lars Juhl; Diella Francesca; Jørgensen Claus; Tinti Michele; Li Lei; Hsiung Marilyn; Parker Sirlester A; Bordeaux Jennifer; Sicheritz-Ponten Thomas; Olhovsky Marina; Pasculescu Adrian; Alexander Jes; Knapp Stefan; Blom Nikolaj; Bork Peer; Li Shawn; Cesareni Gianni; Pawson Tony; Turk Benjamin E; Yaffe Michael B; Brunak Søren; Linding Rune
Linear motif atlas for phosphorylation-dependent signaling.
Science signaling 2008;1(35):ra2.
2008: Pallejà Albert; Harrington Eoghan D; Bork Peer
Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?
BMC genomics 2008;9():335.
2008: Hooper Sean D; Raes Jeroen; Foerstner Konrad U; Harrington Eoghan D; Dalevi Daniel; Bork Peer
A molecular study of microbe transfer between distant environments.
PloS one 2008;3(7):e2607.
2008: Jensen Lars Juhl; de Lichtenberg Ulrik; Jensen Thomas Skøt; Brunak Søren; Bork Peer
Circular reasoning rather than cyclic expression.
Genome biology 2008;9(6):403.
2008: Kunin Victor; Raes Jeroen; Harris J Kirk; Spear John R; Walker Jeffrey J; Ivanova Natalia; von Mering Christian; Bebout Brad M; Pace Norman R; Bork Peer; Hugenholtz Philip
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.
Molecular systems biology 2008;4():198.
2008: Soldà Giulia; Suyama Mikita; Pelucchi Paride; Boi Silvia; Guffanti Alessandro; Rizzi Ermanno; Bork Peer; Tenchini Maria Luisa; Ciccarelli Francesca D
Non-random retention of protein-coding overlapping genes in Metazoa.
BMC genomics 2008;9():174.
2007: Sorek Rotem; Zhu Yiwen; Creevey Christopher J; Francino M Pilar; Bork Peer; Rubin Edward M
Genome-wide experimental determination of barriers to horizontal gene transfer.
Science (New York, N.Y.) 2007;318(5855):1449-52.
2007: Raes Jeroen; Foerstner Konrad Ulrich; Bork Peer
Get the most out of your metagenome: computational analysis of environmental sequence data.
Current opinion in microbiology 2007;10(5):490-8.
2007: Eulalio Ana; Rehwinkel Jan; Stricker Mona; Huntzinger Eric; Yang Schu-Fee; Doerks Tobias; Dorner Silke; Bork Peer; Boutros Michael; Izaurralde Elisa
Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing.
Genes & development 2007;21(20):2558-70.
2007: Harrington E D; Singh A H; Doerks T; Letunic I; von Mering C; Jensen L J; Raes J; Bork P
Quantitative assessment of protein function prediction from metagenomics shotgun sequences.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(35):13913-8.
2007: de Lichtenberg Ulrik; Jensen Thomas Skøt; Brunak Søren; Bork Peer; Jensen Lars Juhl
Evolution of cell cycle control: same molecular machines, different regulation.
Cell cycle (Georgetown, Tex.) 2007;6(15):1819-25.
2007: Perez-Iratxeta Carolina; Bork Peer; Andrade-Navarro Miguel A
Update of the G2D tool for prioritization of gene candidates to inherited diseases.
Nucleic acids research 2007;35(Web Server issue):W212-6.
2007: Pachkov Mikhail; Dandekar Thomas; Korbel Jan; Bork Peer; Schuster Stefan
Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism.
Gene 2007;396(2):215-25.
2007: Raes Jeroen; Harrington Eoghan Donal; Singh Amoolya Hardev; Bork Peer
Protein function space: viewing the limits or limited by our view?
Current opinion in structural biology 2007;17(3):362-9.
2007: Linding Rune; Jensen Lars Juhl; Ostheimer Gerard J; van Vugt Marcel A T M; Jørgensen Claus; Miron Ioana M; Diella Francesca; Colwill Karen; Taylor Lorne; Elder Kelly; Metalnikov Pavel; Nguyen Vivian; Pasculescu Adrian; Jin Jing; Park Jin Gyoon; Samson Leona D; Woodgett James R; Russell Robert B; Bork Peer; Yaffe Michael B; Pawson Tony
Systematic discovery of in vivo phosphorylation networks.
Cell 2007;129(7):1415-26.
2007: Danckwardt Sven; Kaufmann Isabelle; Gentzel Marc; Foerstner Konrad U; Gantzert Anne-Susan; Gehring Niels H; Neu-Yilik Gabriele; Bork Peer; Keller Walter; Wilm Matthias; Hentze Matthias W; Kulozik Andreas E
Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals.
The EMBO journal 2007;26(11):2658-69.
2007: Boettner Mewes; Steffens Christina; von Mering Christian; Bork Peer; Stahl Ulf; Lang Christine
Sequence-based factors influencing the expression of heterologous genes in the yeast Pichia pastoris--A comparative view on 79 human genes.
Journal of biotechnology 2007;130(1):1-10.
2007: von Mering C; Hugenholtz P; Raes J; Tringe S G; Doerks T; Jensen L J; Ward N; Bork P
Quantitative phylogenetic assessment of microbial communities in diverse environments.
Science (New York, N.Y.) 2007;315(5815):1126-30.
2007: von Mering Christian; Jensen Lars J; Kuhn Michael; Chaffron Samuel; Doerks Tobias; Krüger Beate; Snel Berend; Bork Peer
STRING 7--recent developments in the integration and prediction of protein interactions.
Nucleic acids research 2007;35(Database issue):D358-62.
2007: Zdobnov Evgeny M; Bork Peer
Quantification of insect genome divergence.
Trends in genetics : TIG 2007;23(1):16-20.
2007: Letunic Ivica; Bork Peer
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
Bioinformatics (Oxford, England) 2007;23(1):127-8.
2007: Hooper Sean D; Boué Stephanie; Krause Roland; Jensen Lars J; Mason Christopher E; Ghanim Murad; White Kevin P; Furlong Eileen E M; Bork Peer
Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis.
Molecular systems biology 2007;3():72.
2007: Raes Jeroen; Korbel Jan O; Lercher Martin J; von Mering Christian; Bork Peer
Prediction of effective genome size in metagenomic samples.
Genome biology 2007;8(1):R10.
2006: Raible Florian; Tessmar-Raible Kristin; Arboleda Enrique; Kaller Tobias; Bork Peer; Arendt Detlev; Arnone Maria I
Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome.
Developmental biology 2006;300(1):461-75.
2006: Campillos Mónica; Doerks Tobias; Shah Parantu K; Bork Peer
Computational characterization of multiple Gag-like human proteins.
Trends in genetics : TIG 2006;22(11):585-9.
2006: Perocchi Fabiana; Jensen Lars J; Gagneur Julien; Ahting Uwe; von Mering Christian; Bork Peer; Prokisch Holger; Steinmetz Lars M
Assessing systems properties of yeast mitochondria through an interaction map of the organelle.
PLoS genetics 2006;2(10):e170.
2006: Jensen Lars Juhl; Jensen Thomas Skøt; de Lichtenberg Ulrik; Brunak Søren; Bork Peer
Co-evolution of transcriptional and post-translational cell-cycle regulation.
Nature 2006;443(7111):594-7.
2006: Suyama Mikita; Torrents David; Bork Peer
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
Nucleic acids research 2006;34(Web Server issue):W609-12.
2006: Behm-Ansmant Isabelle; Rehwinkel Jan; Doerks Tobias; Stark Alexander; Bork Peer; Izaurralde Elisa
mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes.
Genes & development 2006;20(14):1885-98.
2006: Suyama Mikita; Harrington Eoghan; Bork Peer; Torrents David
Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes.
PLoS computational biology 2006;2(6):e76.
2006: Sandmann Thomas; Jensen Lars J; Jakobsen Janus S; Karzynski Michal M; Eichenlaub Michael P; Bork Peer; Furlong Eileen E M
A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development.
Developmental cell 2006;10(6):797-807.
2006: Shah Parantu K; Bork Peer
LSAT: learning about alternative transcripts in MEDLINE.
Bioinformatics (Oxford, England) 2006;22(7):857-65.
2006: Foerstner Konrad U; von Mering Christian; Bork Peer
Comparative analysis of environmental sequences: potential and challenges.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2006;361(1467):519-23.
2006: Ciccarelli Francesca D; Doerks Tobias; von Mering Christian; Creevey Christopher J; Snel Berend; Bork Peer
Toward automatic reconstruction of a highly resolved tree of life.
Science (New York, N.Y.) 2006;311(5765):1283-7.
2006: Yanai Itai; Korbel Jan O; Boue Stephanie; McWeeney Shannon K; Bork Peer; Lercher Martin J
Similar gene expression profiles do not imply similar tissue functions.
Trends in genetics : TIG 2006;22(3):132-8.
2006: Campillos Mónica; von Mering Christian; Jensen Lars Juhl; Bork Peer
Identification and analysis of evolutionarily cohesive functional modules in protein networks.
Genome research 2006;16(3):374-82.
2006: Saric Jasmin; Jensen Lars Juhl; Ouzounova Rossitza; Rojas Isabel; Bork Peer
Extraction of regulatory gene/protein networks from Medline.
Bioinformatics (Oxford, England) 2006;22(6):645-50.
2006: Jensen Lars Juhl; Saric Jasmin; Bork Peer
Literature mining for the biologist: from information retrieval to biological discovery.
Nature reviews. Genetics 2006;7(2):119-29.
2006: Letunic Ivica; Copley Richard R; Pils Birgit; Pinkert Stefan; Schultz Jörg; Bork Peer
SMART 5: domains in the context of genomes and networks.
Nucleic acids research 2006;34(Database issue):D257-60.
2005: Foerstner Konrad U; von Mering Christian; Hooper Sean D; Bork Peer
Environments shape the nucleotide composition of genomes.
EMBO reports 2005;6(12):1208-13.
2005: Hooper Sean D; Bork Peer
Medusa: a simple tool for interaction graph analysis.
Bioinformatics (Oxford, England) 2005;21(24):4432-3.
2005: Mees Anaid; Rock Rebecca; Ciccarelli Francesca D; Leberfinger Cornelia B; Borawski Johanna M; Bork Peer; Wiese Stefan; Gessler Manfred; Kerkhoff Eugen
Very-KIND is a novel nervous system specific guanine nucleotide exchange factor for Ras GTPases.
Gene expression patterns : GEP 2005;6(1):79-85.
2005: Raible Florian; Tessmar-Raible Kristin; Osoegawa Kazutoyo; Wincker Patrick; Jubin Claire; Balavoine Guillaume; Ferrier David; Benes Vladimir; de Jong Pieter; Weissenbach Jean; Bork Peer; Arendt Detlev
Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii.
Science (New York, N.Y.) 2005;310(5752):1325-6.
2005: Taxis Christof; Keller Philipp; Kavagiou Zaharoula; Jensen Lars Juhl; Colombelli Julien; Bork Peer; Stelzer Ernst H K; Knop Michael
Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system.
The Journal of cell biology 2005;171(4):627-40.
2005: Rehwinkel Jan; Letunic Ivica; Raes Jeroen; Bork Peer; Izaurralde Elisa
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets.
RNA (New York, N.Y.) 2005;11(10):1530-44.
2005: Suyama Mikita; Lathe Warren C; Bork Peer
Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii.
FEBS letters 2005;579(24):5281-6.
2005: Büssow Konrad; Scheich Christoph; Sievert Volker; Harttig Ulrich; Schultz Jörg; Simon Bernd; Bork Peer; Lehrach Hans; Heinemann Udo
Structural genomics of human proteins--target selection and generation of a public catalogue of expression clones.
Microbial cell factories 2005;4():21.
2005: Shah Parantu K; Jensen Lars J; Boué Stéphanie; Bork Peer
Extraction of transcript diversity from scientific literature.
PLoS computational biology 2005;1(1):e10.
2005: Zdobnov Evgeny M; von Mering Christian; Letunic Ivica; Bork Peer
Consistency of genome-based methods in measuring Metazoan evolution.
FEBS letters 2005;579(15):3355-61.
2005: Bork Peer; Serrano Luis
Towards cellular systems in 4D.
Cell 2005;121(4):507-9.
2005: Shah Parantu K; Aloy Patrick; Bork Peer; Russell Robert B
Structural similarity to bridge sequence space: finding new families on the bridges.
Protein science : a publication of the Protein Society 2005;14(5):1305-14.
2005: Korbel Jan O; Doerks Tobias; Jensen Lars J; Perez-Iratxeta Carolina; Kaczanowski Szymon; Hooper Sean D; Andrade Miguel A; Bork Peer
Systematic association of genes to phenotypes by genome and literature mining.
PLoS biology 2005;3(5):e134.
2005: Tringe Susannah Green; von Mering Christian; Kobayashi Arthur; Salamov Asaf A; Chen Kevin; Chang Hwai W; Podar Mircea; Short Jay M; Mathur Eric J; Detter John C; Bork Peer; Hugenholtz Philip; Rubin Edward M
Comparative metagenomics of microbial communities.
Science (New York, N.Y.) 2005;308(5721):554-7.
2005: Ciccarelli Francesca D; Bork Peer
The WHy domain mediates the response to desiccation in plants and bacteria.
Bioinformatics (Oxford, England) 2005;21(8):1304-7.
2005: de Lichtenberg Ulrik; Jensen Lars Juhl; Fausbøll Anders; Jensen Thomas S; Bork Peer; Brunak Søren
Comparison of computational methods for the identification of cell cycle-regulated genes.
Bioinformatics (Oxford, England) 2005;21(7):1164-71.
2005: Ciccarelli Francesca D; von Mering Christian; Suyama Mikita; Harrington Eoghan D; Izaurralde Elisa; Bork Peer
Complex genomic rearrangements lead to novel primate gene function.
Genome research 2005;15(3):343-51.
2005: de Lichtenberg Ulrik; Jensen Lars Juhl; Brunak Søren; Bork Peer
Dynamic complex formation during the yeast cell cycle.
Science (New York, N.Y.) 2005;307(5710):724-7.
2005: von Mering Christian; Jensen Lars J; Snel Berend; Hooper Sean D; Krupp Markus; Foglierini Mathilde; Jouffre Nelly; Huynen Martijn A; Bork Peer
STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
Nucleic acids research 2005;33(Database issue):D433-7.
2005: Bourque Guillaume; Zdobnov Evgeny M; Bork Peer; Pevzner Pavel A; Tesler Glenn
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages.
Genome research 2005;15(1):98-110.
2005: Bork Peer
Is there biological research beyond Systems Biology? A comparative analysis of terms.
Molecular systems biology 2005;1():2005.0012.
2005: Perez-Iratxeta Carolina; Wjst Matthias; Bork Peer; Andrade Miguel A
G2D: a tool for mining genes associated with disease.
BMC genetics 2005;6():45.
2005: Tenhaken Raimund; Doerks Tobias; Bork Peer
DCD - a novel plant specific domain in proteins involved in development and programmed cell death.
BMC bioinformatics 2005;6():169.
2005: Zdobnov Evgeny M; Campillos Mónica; Harrington Eoghan D; Torrents David; Bork Peer
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.
Nucleic acids research 2005;33(3):946-54.
2004: Koehl Alexander; Schmidt Nicole; Rieger Anne; Pilgram Sara M; Letunic Ivica; Bork Peer; Soto Florentina; Friauf Eckhard; Nothwang Hans Gerd
Gene expression profiling of the rat superior olivary complex using serial analysis of gene expression.
The European journal of neuroscience 2004;20(12):3244-58.
2004: Krause Roland; von Mering Christian; Bork Peer; Dandekar Thomas
Shared components of protein complexes--versatile building blocks or biochemical artefacts?
BioEssays : news and reviews in molecular, cellular and developmental biology 2004;26(12):1333-43.
2004: Liska Adam J; Popov Andrei V; Sunyaev Shamil; Coughlin Peg; Habermann Bianca; Shevchenko Anna; Bork Peer; Karsenti Eric; Shevchenko Andrej
Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome.
Proteomics 2004;4(9):2707-21.
2004: Pérez Antonio J; Perez-Iratxeta Carolina; Bork Peer; Thode Guillermo; Andrade Miguel A
Gene annotation from scientific literature using mappings between keyword systems.
Bioinformatics (Oxford, England) 2004;20(13):2084-91.
2004: Suyama Mikita; Torrents David; Bork Peer
BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments.
Bioinformatics (Oxford, England) 2004;20(12):1968-70.
2004: Korbel Jan O; Jensen Lars J; von Mering Christian; Bork Peer
Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs.
Nature biotechnology 2004;22(7):911-7.
2004: Jensen Lars Juhl; Lagarde Julien; von Mering Christian; Bork Peer
ArrayProspector: a web resource of functional associations inferred from microarray expression data.
Nucleic acids research 2004;32(Web Server issue):W445-8.
2004: Bork Peer; Jensen Lars J; von Mering Christian; Ramani Arun K; Lee Insuk; Marcotte Edward M
Protein interaction networks from yeast to human.
Current opinion in structural biology 2004;14(3):292-9.
2004: Doerks Tobias; Andrade Miguel A; Lathe Warren; von Mering Christian; Bork Peer
Global analysis of bacterial transcription factors to predict cellular target processes.
Trends in genetics : TIG 2004;20(3):126-31.
2004: Aloy Patrick; Böttcher Bettina; Ceulemans Hugo; Leutwein Christina; Mellwig Christian; Fischer Susanne; Gavin Anne-Claude; Bork Peer; Superti-Furga Giulio; Serrano Luis; Russell Robert B
Structure-based assembly of protein complexes in yeast.
Science (New York, N.Y.) 2004;303(5666):2026-9.
2004: Forler Daniel; Rabut Gwénaël; Ciccarelli Francesca D; Herold Andrea; Köcher Thomas; Niggeweg Ricarda; Bork Peer; Ellenberg Jan; Izaurralde Elisa
RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the nuclear pore complex and functions in nuclear mRNA export.
Molecular and cellular biology 2004;24(3):1155-67.
2004: Letunic Ivica; Copley Richard R; Schmidt Steffen; Ciccarelli Francesca D; Doerks Tobias; Schultz Jörg; Ponting Chris P; Bork Peer
SMART 4.0: towards genomic data integration.
Nucleic acids research 2004;32(Database issue):D142-4.
2004: Doerks Tobias; von Mering Christian; Bork Peer
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes.
Nucleic acids research 2004;32(21):6321-6.
2003: Ciccarelli Francesca D; Izaurralde Elisa; Bork Peer
The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold.
BMC bioinformatics 2003;4():64.
2003: von Mering Christian; Zdobnov Evgeny M; Tsoka Sophia; Ciccarelli Francesca D; Pereira-Leal Jose B; Ouzounis Christos A; Bork Peer
Genome evolution reveals biochemical networks and functional modules.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(26):15428-33.
2003: Torrents David; Suyama Mikita; Zdobnov Evgeny; Bork Peer
A genome-wide survey of human pseudogenes.
Genome research 2003;13(12):2559-67.
2003: Sunyaev Shamil; Kondrashov Fyodor A; Bork Peer; Ramensky Vasily
Impact of selection, mutation rate and genetic drift on human genetic variation.
Human molecular genetics 2003;12(24):3325-30.
2003: Linding Rune; Jensen Lars Juhl; Diella Francesca; Bork Peer; Gibson Toby J; Russell Robert B
Protein disorder prediction: implications for structural proteomics.
Structure (London, England : 1993) 2003;11(11):1453-9.
2003: Boue Stephanie; Letunic Ivica; Bork Peer
Alternative splicing and evolution.
BioEssays : news and reviews in molecular, cellular and developmental biology 2003;25(11):1031-4.
2003: Krause Roland; von Mering Christian; Bork Peer
A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens.
Bioinformatics (Oxford, England) 2003;19(15):1901-8.
2003: Gatfield David; Unterholzner Leonie; Ciccarelli Francesca D; Bork Peer; Izaurralde Elisa
Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways.
The EMBO journal 2003;22(15):3960-70.
2003: Ciccarelli Francesca D; Bork Peer; Kerkhoff Eugen
The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold.
Trends in biochemical sciences 2003;28(7):349-52.
2003: Perez-Iratxeta Carolina; Pérez Antonio J; Bork Peer; Andrade Miguel A
Update on XplorMed: A web server for exploring scientific literature.
Nucleic acids research 2003;31(13):3866-8.
2003: Puntervoll Pål; Linding Rune; Gemünd Christine; Chabanis-Davidson Sophie; Mattingsdal Morten; Cameron Scott; Martin David M A; Ausiello Gabriele; Brannetti Barbara; Costantini Anna; Ferrè Fabrizio; Maselli Vincenza; Via Allegra; Cesareni Gianni; Diella Francesca; Superti-Furga Giulio; Wyrwicz Lucjan; Ramu Chenna; McGuigan Caroline; Gudavalli Rambabu; Letunic Ivica; Bork Peer; Rychlewski Leszek; Küster Bernhard; Helmer-Citterich Manuela; Hunter William N; Aasland Rein; Gibson Toby J
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.
Nucleic acids research 2003;31(13):3625-30.
2003: Morett Enrique; Korbel Jan O; Rajan Emmanuvel; Saab-Rincon Gloria; Olvera Leticia; Olvera Maricela; Schmidt Steffen; Snel Berend; Bork Peer
Systematic discovery of analogous enzymes in thiamin biosynthesis.
Nature biotechnology 2003;21(7):790-5.
2003: Schmidt Steffen; Sunyaev Shamil; Bork Peer; Dandekar Thomas
Metabolites: a helping hand for pathway evolution?
Trends in biochemical sciences 2003;28(6):336-41.
2003: Shah Parantu K; Perez-Iratxeta Carolina; Bork Peer; Andrade Miguel A
Information extraction from full text scientific articles: where are the keywords?
BMC bioinformatics 2003;4():20.
2003: Netzel Rebecca; Perez-Iratxeta Carolina; Bork Peer; Andrade Miguel A
The way we write.
EMBO reports 2003;4(5):446-51.
2003: Woerner Stefan M; Benner Axel; Sutter Christian; Schiller Marian; Yuan Yan P; Keller Gisela; Bork Peer; Doeberitz Magnus von Knebel; Gebert Johannes F
Pathogenesis of DNA repair-deficient cancers: a statistical meta-analysis of putative Real Common Target genes.
Oncogene 2003;22(15):2226-35.
2003: Ciccarelli Francesca D; Proukakis Christos; Patel Heema; Cross Harold; Azam Shakil; Patton Michael A; Bork Peer; Crosby Andrew H
The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia.
Genomics 2003;81(4):437-41.
2003: Huynen Martijn A; Snel Berend; von Mering Christian; Bork Peer
Function prediction and protein networks.
Current opinion in cell biology 2003;15(2):191-8.
2003: Kriventseva Evgenia V; Koch Ina; Apweiler Rolf; Vingron Martin; Bork Peer; Gelfand Mikhail S; Sunyaev Shamil
Increase of functional diversity by alternative splicing.
Trends in genetics : TIG 2003;19(3):124-8.
2003: Kanehisa Minoru; Bork Peer
Bioinformatics in the post-sequence era.
Nature genetics 2003;33 Suppl():305-10.
2003: von Mering Christian; Huynen Martijn; Jaeggi Daniel; Schmidt Steffen; Bork Peer; Snel Berend
STRING: a database of predicted functional associations between proteins.
Nucleic acids research 2003;31(1):258-61.
2003: Waterston R H; Hillier L W; Fulton L A; Fulton R S; Graves T A; Pepin K H; Bork P; Suyama M; Torrents D; Chinwalla A T; Mardis E R; McPherson J D; Wilson R K
The human genome: genes, pseudogenes, and variation on chromosome 7.
Cold Spring Harbor symposia on quantitative biology 2003;68():13-22.
2003: Perez-Iratxeta Carolina; Astola Nagore; Ciccarelli Francesca D; Sha Parantu K; Bork Peer; Andrade Miguel A
A protocol for the update of references to scientific literature in biological databases.
Applied bioinformatics 2003;2(3):189-91.
2003: Shevchenko Anna; Sunyaev Shamil; Liska Adam; Bork Peer; Shevchenko Andrej
Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes.
Methods in molecular biology (Clifton, N.J.) 2003;211():221-34.
2002: Kloor Matthias; Bork Peer; Duwe Alexander; Klaes Ruediger; von Knebel Doeberitz Magnus; Ridder Ruediger
Identification and characterization of UEV3, a human cDNA with similarities to inactive E2 ubiquitin-conjugating enzymes.
Biochimica et biophysica acta 2002;1579(2-3):219-24.
2002: Schell Mark A; Karmirantzou Maria; Snel Berend; Vilanova David; Berger Bernard; Pessi Gabriella; Zwahlen Marie-Camille; Desiere Frank; Bork Peer; Delley Michele; Pridmore R David; Arigoni Fabrizio
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(22):14422-7.
2002: Ramensky Vasily; Bork Peer; Sunyaev Shamil
Human non-synonymous SNPs: server and survey.
Nucleic acids research 2002;30(17):3894-900.
2002: Andrade Miguel A; Ciccarelli Francesca D; Perez-Iratxeta Carolina; Bork Peer
NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria.
Genome biology 2002;3(9):RESEARCH0047.
2002: Mott Richard; Schultz Jörg; Bork Peer; Ponting Chris P
Predicting protein cellular localization using a domain projection method.
Genome research 2002;12(8):1168-74.
2002: Bordo Domenico; Bork Peer
The rhodanese/Cdc25 phosphatase superfamily. Sequence-structure-function relations.
EMBO reports 2002;3(8):741-6.
2002: Patel Heema; Cross Harold; Proukakis Christos; Hershberger Ruth; Bork Peer; Ciccarelli Francesca D; Patton Michael A; McKusick Victor A; Crosby Andrew H
SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia.
Nature genetics 2002;31(4):347-8.
2002: Aloy Patrick; Ciccarelli Francesca D; Leutwein Christina; Gavin Anne-Claude; Superti-Furga Giulio; Bork Peer; Bottcher Bettina; Russell Robert B
A complex prediction: three-dimensional model of the yeast exosome.
EMBO reports 2002;3(7):628-35.
2002: Perez-Iratxeta Carolina; Bork Peer; Andrade Miguel A
Association of genes to genetically inherited diseases using data mining.
Nature genetics 2002;31(3):316-9.
2002: Perez-Iratxeta Carolina; Bork Peer; Andrade Miguel A
Exploring MEDLINE abstracts with XplorMed.
Drugs of today (Barcelona, Spain : 1998) 2002;38(6):381-9.
2002: von Mering Christian; Bork Peer
Teamed up for transcription.
Nature 2002;417(6891):797-8.
2002: Perez-Iratxeta Carolina; Keer Harindar S; Bork Peer; Andrade Miguel A
Computing fuzzy associations for the analysis of biological literature.
BioTechniques 2002;32(6):1380-2, 1384-5.
2002: Thomasova Dana; Ton Lucas Q; Copley Richard R; Zdobnov Evgeny M; Wang Xuelan; Hong Young S; Sim Cheolho; Bork Peer; Kafatos Fotis C; Collins Frank H
Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(12):8179-84.
2002: Letunic Ivica; Copley Richard R; Bork Peer
Common exon duplication in animals and its role in alternative splicing.
Human molecular genetics 2002;11(13):1561-7.
2002: von Mering Christian; Krause Roland; Snel Berend; Cornell Michael; Oliver Stephen G; Fields Stanley; Bork Peer
Comparative assessment of large-scale data sets of protein-protein interactions.
Nature 2002;417(6887):399-403.
2002: Snel Berend; Bork Peer; Huynen Martijn A
The identification of functional modules from the genomic association of genes.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(9):5890-5.
2002: Doerks Tobias; Huber Saskia; Buchner Erich; Bork Peer
BSD: a novel domain in transcription factors and synapse-associated proteins.
Trends in biochemical sciences 2002;27(4):168-70.
2002: Schmidt Steffen; Bork Peer; Dandekar Thomas
A versatile structural domain analysis server using profile weight matrices.
Journal of chemical information and computer sciences 2002;42(2):405-7.
2002: Ciccarelli Francesca D; Doerks Tobias; Bork Peer
AMOP, a protein module alternatively spliced in cancer cells.
Trends in biochemical sciences 2002;27(3):113-5.
2002: Korbel Jan O; Snel Berend; Huynen Martijn A; Bork Peer
SHOT: a web server for the construction of genome phylogenies.
Trends in genetics : TIG 2002;18(3):158-62.
2002: Copley Richard R; Doerks Tobias; Letunic Ivica; Bork Peer
Protein domain analysis in the era of complete genomes.
FEBS letters 2002;513(1):129-34.
2002: Ciccarelli Francesca D; Copley Richard R; Doerks Tobias; Russell Robert B; Bork Peer
CASH--a beta-helix domain widespread among carbohydrate-binding proteins.
Trends in biochemical sciences 2002;27(2):59-62.
2002: Copley Richard R; Letunic Ivica; Bork Peer
Genome and protein evolution in eukaryotes.
Current opinion in chemical biology 2002;6(1):39-45.
2002: Doerks Tobias; Copley Richard R; Schultz Jörg; Ponting Chris P; Bork Peer
Systematic identification of novel protein domain families associated with nuclear functions.
Genome research 2002;12(1):47-56.
2002: Snel Berend; Bork Peer; Huynen Martijn A
Genomes in flux: the evolution of archaeal and proteobacterial gene content.
Genome research 2002;12(1):17-25.
2002: Letunic Ivica; Goodstadt Leo; Dickens Nicholas J; Doerks Tobias; Schultz Joerg; Mott Richard; Ciccarelli Francesca; Copley Richard R; Ponting Chris P; Bork Peer
Recent improvements to the SMART domain-based sequence annotation resource.
Nucleic acids research 2002;30(1):242-4.
2002: Brett David; Pospisil Heike; Valcárcel Juan; Reich Jens; Bork Peer
Alternative splicing and genome complexity.
Nature genetics 2002;30(1):29-30.
2002: Copley Richard R; Ponting Chris P; Schultz Jörg; Bork Peer
Sequence analysis of multidomain proteins: past perspectives and future directions.
Advances in protein chemistry 2002;61():75-98.
2002: Bork Peer
Comparative analysis of protein interaction networks.
Bioinformatics (Oxford, England) 2002;18 Suppl 2():S64.
2001: Kerkhoff E; Simpson J C; Leberfinger C B; Otto I M; Doerks T; Bork P; Rapp U R; Raabe T; Pepperkok R
The Spir actin organizers are involved in vesicle transport processes.
Current biology : CB 2001;11(24):1963-8.
2001: Perez-Iratxeta C; Bork P; Andrade M A
XplorMed: a tool for exploring MEDLINE abstracts.
Trends in biochemical sciences 2001;26(9):573-5.
2001: Woerner S M; Gebert J; Yuan Y P; Sutter C; Ridder R; Bork P; von Knebel Doeberitz M
Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells.
International journal of cancer. Journal international du cancer 2001;93(1):12-9.
2001: Linnebacher M; Gebert J; Rudy W; Woerner S; Yuan Y P; Bork P; von Knebel Doeberitz M
Frameshift peptide-derived T-cell epitopes: a source of novel tumor-specific antigens.
International journal of cancer. Journal international du cancer 2001;93(1):6-11.
2001: Andrade M A; Petosa C; O'Donoghue S I; Müller C W; Bork P
Comparison of ARM and HEAT protein repeats.
Journal of molecular biology 2001;309(1):1-18.
2001: Shevchenko A; Sunyaev S; Loboda A; Shevchenko A; Bork P; Ens W; Standing K G
Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching.
Analytical chemistry 2001;73(9):1917-26.
2001: Doerks T; Copley R; Bork P
DDT -- a novel domain in different transcription and chromosome remodeling factors.
Trends in biochemical sciences 2001;26(3):145-6.
2001: Sunyaev S; Ramensky V; Koch I; Lathe W; Kondrashov A S; Bork P
Prediction of deleterious human alleles.
Human molecular genetics 2001;10(6):591-7.
2001: Sunyaev S; Lathe W; Bork P
Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms.
Current opinion in structural biology 2001;11(1):125-30.
2001: Eisenhaber B; Bork P; Eisenhaber F
Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes.
Protein engineering 2001;14(1):17-25.
2000: Herold A; Suyama M; Rodrigues J P; Braun I C; Kutay U; Carmo-Fonseca M; Bork P; Izaurralde E
TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture.
Molecular and cellular biology 2000;20(23):8996-9008.
2000: Copley R R; Bork P
Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways.
Journal of molecular biology 2000;303(4):627-41.
2000: Lathe W C; Snel B; Bork P
Gene context conservation of a higher order than operons.
Trends in biochemical sciences 2000;25(10):474-9.
2000: Snel B; Lehmann G; Bork P; Huynen M A
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.
Nucleic acids research 2000;28(18):3442-4.
2000: Brett D; Lehmann G; Hanke J; Gross S; Reich J; Bork P
EST analysis online: WWW tools for detection of SNPs and alternative splice forms.
Trends in genetics : TIG 2000;16(9):416-8.
2000: Dandekar T; Huynen M; Regula J T; Ueberle B; Zimmermann C U; Andrade M A; Doerks T; Sánchez-Pulido L; Snel B; Suyama M; Yuan Y P; Herrmann R; Bork P
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.
Nucleic acids research 2000;28(17):3278-88.
2000: Huynen M; Snel B; Lathe W; Bork P
Predicting protein function by genomic context: quantitative evaluation and qualitative inferences.
Genome research 2000;10(8):1204-10.
2000: Sunyaev S R; Lathe W C; Ramensky V E; Bork P
SNP frequencies in human genes an excess of rare alleles and differing modes of selection.
Trends in genetics : TIG 2000;16(8):335-7.
2000: Suyama M; Doerks T; Braun I C; Sattler M; Izaurralde E; Bork P
Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins.
EMBO reports 2000;1(1):53-8.
2000: Sánchez-Pulido L; Yuan Y P; Andrade M A; Bork P
NAIL-Network Analysis Interface for Linking HMMER results.
Bioinformatics (Oxford, England) 2000;16(7):656-7.
2000: Eisenhaber B; Bork P; Yuan Y; Löffler G; Eisenhaber F
Automated annotation of GPI anchor sites: case study C. elegans.
Trends in biochemical sciences 2000;25(7):340-1.
2000: Andrade M A; Bork P
Automated extraction of information in molecular biology.
FEBS letters 2000;476(1-2):12-7.
2000: Huynen M; Snel B; Lathe W; Bork P
Exploitation of gene context.
Current opinion in structural biology 2000;10(3):366-70.
2000: Dimopoulos G; Casavant T L; Chang S; Scheetz T; Roberts C; Donohue M; Schultz J; Benes V; Bork P; Ansorge W; Soares M B; Kafatos F C
Anopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(12):6619-24.
2000: Brett D; Hanke J; Lehmann G; Haase S; Delbrück S; Krueger S; Reich J; Bork P
EST comparison indicates 38% of human mRNAs contain possible alternative splice forms.
FEBS letters 2000;474(1):83-6.
2000: Sunyaev S; Ramensky V; Bork P
Towards a structural basis of human non-synonymous single nucleotide polymorphisms.
Trends in genetics : TIG 2000;16(5):198-200.
2000: Andrade M A; Ponting C P; Gibson T J; Bork P
Homology-based method for identification of protein repeats using statistical significance estimates.
Journal of molecular biology 2000;298(3):521-37.
2000: Stutz F; Bachi A; Doerks T; Braun I C; Séraphin B; Wilm M; Bork P; Izaurralde E
REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export.
RNA (New York, N.Y.) 2000;6(4):638-50.
2000: Otto I M; Raabe T; Rennefahrt U E; Bork P; Rapp U R; Kerkhoff E
The p150-Spir protein provides a link between c-Jun N-terminal kinase function and actin reorganization.
Current biology : CB 2000;10(6):345-8.
2000: Snel B; Bork P; Huynen M
Genome evolution. Gene fusion versus gene fission.
Trends in genetics : TIG 2000;16(1):9-11.
2000: Sunyaev S; Hanke J; Brett D; Aydin A; Zastrow I; Lathe W; Bork P; Reich J
Individual variation in protein-coding sequences of human genome.
Advances in protein chemistry 2000;54():409-37.
1999: Liu Z; Macias M J; Bottomley M J; Stier G; Linge J P; Nilges M; Bork P; Sattler M
The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins.
Structure (London, England : 1993) 1999;7(12):1557-66.
1999: Sunyaev S; Hanke J; Aydin A; Wirkner U; Zastrow I; Reich J; Bork P
Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes.
Journal of molecular medicine (Berlin, Germany) 1999;77(11):754-60.
1999: Hanke J; Brett D; Zastrow I; Aydin A; Delbrück S; Lehmann G; Luft F; Reich J; Bork P
Alternative splicing of human genes: more the rule than the exception?
Trends in genetics : TIG 1999;15(10):389-90.
1999: Hanke J; Lehmann G; Bork P; Reich J G
Associative database of protein sequences.
Bioinformatics (Oxford, England) 1999;15(9):741-8.
1999: Eisenhaber B; Bork P; Eisenhaber F
Prediction of potential GPI-modification sites in proprotein sequences.
Journal of molecular biology 1999;292(3):741-58.
1999: Eisenhaber F; Bork P
Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries.
Bioinformatics (Oxford, England) 1999;15(7-8):528-35.
1999: Huynen M A; Dandekar T; Bork P
Variation and evolution of the citric-acid cycle: a genomic perspective.
Trends in microbiology 1999;7(7):281-91.
1999: Copley R R; Schultz J; Ponting C P; Bork P
Protein families in multicellular organisms.
Current opinion in structural biology 1999;9(3):408-15.
1999: Snel B; Bork P; Huynen M A
Genome phylogeny based on gene content.
Nature genetics 1999;21(1):108-10.
1998: Eisenhaber B; Bork P; Eisenhaber F
Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase.
Protein engineering 1998;11(12):1155-61.
1998: Bork P; Dandekar T; Diaz-Lazcoz Y; Eisenhaber F; Huynen M; Yuan Y
Predicting function: from genes to genomes and back.
Journal of molecular biology 1998;283(4):707-25.
1998: Dandekar T; Snel B; Huynen M; Bork P
Conservation of gene order: a fingerprint of proteins that physically interact.
Trends in biochemical sciences 1998;23(9):324-8.
1998: Morett E; Bork P
Evolution of new protein function: recombinational enhancer Fis originated by horizontal gene transfer from the transcriptional regulator NtrC.
FEBS letters 1998;433(1-2):108-12.
1998: Schultz J; Milpetz F; Bork P; Ponting C P
SMART, a simple modular architecture research tool: identification of signaling domains.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(11):5857-64.
1998: Huynen M A; Bork P
Measuring genome evolution.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(11):5849-56.
1998: Eisenhaber F; Bork P
Wanted: subcellular localization of proteins based on sequence.
Trends in cell biology 1998;8(4):169-70.
1998: Huynen M; Dandekar T; Bork P
Differential genome analysis applied to the species-specific features of Helicobacter pylori.
FEBS letters 1998;426(1):1-5.
1998: Bork P; Dandekar T; Eisenhaber F; Huynen M
Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases.
Journal of molecular medicine (Berlin, Germany) 1998;76(2):77-9.
1998: Beckmann G; Hanke J; Bork P; Reich J G
Merging extracellular domains: fold prediction for laminin G-like and amino-terminal thrombospondin-like modules based on homology to pentraxins.
Journal of molecular biology 1998;275(5):725-30.
1998: Yuan Y P; Eulenstein O; Vingron M; Bork P
Towards detection of orthologues in sequence databases.
Bioinformatics (Oxford, England) 1998;14(3):285-9.
1998: Dandekar T; Beyer K; Bork P; Kenealy M R; Pantopoulos K; Hentze M; Sonntag-Buck V; Flouriot G; Gannon F; Schreiber S
Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches.
Bioinformatics (Oxford, England) 1998;14(3):271-8.
1997: Huynen M A; Diaz-Lazcoz Y; Bork P
Differential genome display.
Trends in genetics : TIG 1997;13(10):389-90.
1997: Bork P; Schultz J; Ponting C P
Cytoplasmic signalling domains: the next generation.
Trends in biochemical sciences 1997;22(8):296-8.
1997: Schultz J; Ponting C P; Hofmann K; Bork P
SAM as a protein interaction domain involved in developmental regulation.
Protein science : a publication of the Protein Society 1997;6(1):249-53.
1996: Bork P; Brown N P; Hegyi H; Schultz J
The protein phosphatase 2C (PP2C) superfamily: detection of bacterial homologues.
Protein science : a publication of the Protein Society 1996;5(7):1421-5.
1996: Hanke J; Beckmann G; Bork P; Reich J G
Self-organizing hierarchic networks for pattern recognition in protein sequence.
Protein science : a publication of the Protein Society 1996;5(1):72-82.
1995: Ouzounis C; Bork P; Casari G; Sander C
New protein functions in yeast chromosome VIII.
Protein science : a publication of the Protein Society 1995;4(11):2424-8.
1995: Casari G; Andrade M A; Bork P; Boyle J; Daruvar A; Ouzounis C; Schneider R; Tamames J; Valencia A; Sander C
Challenging times for bioinformatics.
Nature 1995;376(6542):647-8.
1995: Bork P; Patthy L
The SEA module: a new extracellular domain associated with O-glycosylation.
Protein science : a publication of the Protein Society 1995;4(7):1421-5.
1995: Bork P; Ouzounis C; Casari G; Schneider R; Sander C; Dolan M; Gilbert W; Gillevet P M
Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology.
Molecular microbiology 1995;16(5):955-67.
1995: Bork P; Ouzounis C; McEntyre J
Ready for a motif submission? A proposed checklist.
Trends in biochemical sciences 1995;20(3):104.
1995: Bork P; Gellerich J; Groth H; Hooft R; Martin F
Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search.
Protein science : a publication of the Protein Society 1995;4(2):268-74.
1994: Bork P; Sudol M
The WW domain: a signalling site in dystrophin?
Trends in biochemical sciences 1994;19(12):531-3.
1994: Bork P; Holm L; Sander C
The immunoglobulin fold. Structural classification, sequence patterns and common core.
Journal of molecular biology 1994;242(4):309-20.
1994: Bork P; Koonin E V
A new family of carbon-nitrogen hydrolases.
Protein science : a publication of the Protein Society 1994;3(8):1344-6.
1994: Ouzounis C; Bork P; Sander C
The modular structure of NifU proteins.
Trends in biochemical sciences 1994;19(5):199-200.
1994: Scharf M; Schneider R; Casari G; Bork P; Valencia A; Ouzounis C; Sander C
GeneQuiz: a workbench for sequence analysis.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1994;2():348-53.
1993: Bork P; Sander C
A hybrid protein kinase-RNase in an interferon-induced pathway?
FEBS letters 1993;334(2):149-52.
1993: Bork P; Doolittle R F
Fibronectin type III modules in the receptor phosphatase CD45 and tapeworm antigens.
Protein science : a publication of the Protein Society 1993;2(7):1185-7.
1993: Bork P
The modular architecture of a new family of growth regulators related to connective tissue growth factor.
FEBS letters 1993;327(2):125-30.
1993: Bork P; Beckmann G
The CUB domain. A widespread module in developmentally regulated proteins.
Journal of molecular biology 1993;231(2):539-45.
1993: Bork P; Sander C; Valencia A
Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases.
Protein science : a publication of the Protein Society 1993;2(1):31-40.
1992: Bork P; Ouzounis C; Sander C; Scharf M; Schneider R; Sonnhammer E
Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III.
Protein science : a publication of the Protein Society 1992;1(12):1677-90.
1992: Bork P; Doolittle R F
Proposed acquisition of an animal protein domain by bacteria.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(19):8990-4.
1992: Bork P; Sander C; Valencia A
An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(16):7290-4.
1992: Bork P
The modular architecture of vertebrate collagens.
FEBS letters 1992;307(1):49-54.
1992: Bork P; Sander C; Valencia A; Bukau B
A module of the DnaJ heat shock proteins found in malaria parasites.
Trends in biochemical sciences 1992;17(4):129.
1992: Bork P; Sander C
A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor.
FEBS letters 1992;300(3):237-40.

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