Works by Bork, Peer

Results: 294

A Holistic Approach to Marine Eco-Systems Biology.

Published in:

PLoS Biology, 2011, v. 9, n. 10, p. 1, doi. 10.1371/journal.pbio.1001177

By:

Karsenti, Eric;
Acinas, Silvia G.;
Bork, Peer;
Bowler, Chris;
De Vargas, Colomban;
Raes, Jeroen;
Sullivan, Matthew;
Arendt, Detlev;
Benzoni, Francesca;
Claverie, Jean-Michel;
Follows, Mick;
Gorsky, Gaby;
Hingamp, Pascal;
Iudicone, Daniele;
Jaillon, Olivier;
Kandels-Lewis, Stefanie;
Krzic, Uros;
Not, Fabrice;
Ogata, Hiroyuki;
Pesant, Stéphane

Publication type:

Article

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

Published in:

PLoS Biology, 2010, v. 8, n. 5, p. 1, doi. 10.1371/journal.pbio.1000374

By:

Jensen, Lars J.;
Bork, Peer

Publication type:

Article

NAIL--Network Analysis Interface for Linking HMMER results.

Published in:

Bioinformatics, 2000, v. 16, n. 7, p. 656, doi. 10.1093/bioinformatics/16.7.656

By:

Sánchez-Pulido, Luis;
Yuan, Yan P.;
Andrade, Miguel A.;
Bork, Peer

Publication type:

Article

Associative database of protein sequences.

Published in:

Bioinformatics, 1999, v. 15, n. 9, p. 741, doi. 10.1093/bioinformatics/15.9.741

By:

Hanke, Jens;
Lehmann, Gerrit;
Bork, Peer;
Reich, Jens G.

Publication type:

Article

valuation of human‐readable annotation in biomolecular sequence databases with biological rule libraries.

Published in:

Bioinformatics, 1999, v. 15, n. 7, p. 528, doi. 10.1093/bioinformatics/15.7.528

By:

Eisenhaber, Frank;
Bork, Peer

Publication type:

Article

Towards detection of orthologues in sequence databases.

Published in:

Bioinformatics, 1998, v. 14, n. 3, p. 285, doi. 10.1093/bioinformatics/14.3.285

By:

Yuan, Yan P.;
Eulenstein, Oliver;
Vingron, Martin;
Bork, Peer

Publication type:

Article

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

Published in:

Bioinformatics, 1998, v. 14, n. 3, p. 271, doi. 10.1093/bioinformatics/14.3.271

By:

Dandekar, Thomas;
Beyer, Katrin;
Bork, Peer;
Kenealy, Mary-Rose;
Pantopoulos, Kostas;
Hentze, Mathias;
Sonntag-Buck, Vera;
Flouriot, Gilles;
Gannon, Frank;
Schreiber, Sonja

Publication type:

Article

Frame: detection of genomic sequencing errors.

Published in:

Bioinformatics, 1998, v. 14, n. 4, p. 367, doi. 10.1093/bioinformatics/14.4.367

By:

Brown, Nigel P.;
Sander, Chris;
Bork, Peer

Publication type:

Article

Efficient Recovery of Complete Gut Viral Genomes by Combined Short‐ and Long‐Read Sequencing.

Published in:

Advanced Science, 2024, v. 11, n. 13, p. 1, doi. 10.1002/advs.202305818

By:

Chen, Jingchao;
Sun, Chuqing;
Dong, Yanqi;
Jin, Menglu;
Lai, Senying;
Jia, Longhao;
Zhao, Xueyang;
Wang, Huarui;
Gao, Na L.;
Bork, Peer;
Liu, Zhi;
Chen, Wei‐Hua;
Zhao, Xing‐Ming

Publication type:

Article

Long‐Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage‐Encoded Methyltransferases.

Published in:

Advanced Science, 2023, v. 10, n. 25, p. 1, doi. 10.1002/advs.202302159

By:

Sun, Chuqing;
Chen, Jingchao;
Jin, Menglu;
Zhao, Xueyang;
Li, Yun;
Dong, Yanqi;
Gao, Na;
Liu, Zhi;
Bork, Peer;
Zhao, Xing‐Ming;
Chen, Wei‐Hua

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2010, v. 38, p. D552, doi. 10.1093/nar/gkp937

By:

Kuhn, Michael;
Szklarczyk, Damian;
Franceschini, Andrea;
Campillos, Monica;
von Mering, Christian;
Jensen, Lars Juhl;
Beyer, Andreas;
Bork, Peer

Publication type:

Article

SelTarbase, a database of human mononucleotidemicrosatellite mutations and their potential impact to tumorigenesis and immunology.

Published in:

Nucleic Acids Research, 2010, v. 38, p. D682, doi. 10.1093/nar/gkp839

By:

Woerner, Stefan M.;
Yuan, Yan P.;
Benner, Axel;
Korff, Sebastian;
von Knebel Doeberitz, Magnus;
Bork, Peer

Publication type:

Article

SMART 6: recent updates and new developments.

Published in:

Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D229, doi. 10.1093/nar/gkn808

By:

Letunic, Ivica;
Doerks, Tobias;
Bork, Peer

Publication type:

Article

InterPro: the integrative protein signature database.

Published in:

Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D211, doi. 10.1093/nar/gkn785

By:

Hunter, Sarah;
Apweiler, Rolf;
Attwood, Teresa K.;
Bairoch, Amos;
Bateman, Alex;
Binns, David;
Bork, Peer;
Das, Ujjwal;
Daugherty, Louise;
Duquenne, Lauranne;
Finn, Robert D.;
Gough, Julian;
Haft, Daniel;
Hulo, Nicolas;
Kahn, Daniel;
Kelly, Elizabeth;
Laugraud, Aurélie;
Letunic, Ivica;
Lonsdale, David;
Lopez, Rodrigo

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D412, doi. 10.1093/nar/gkn760

By:

Jensen, Lars J.;
Kuhn, Michael;
Stark, Manuel;
Chaffron, Samuel;
Creevey, Chris;
Muller, Jean;
Doerks, Tobias;
Julien, Philippe;
Roth, Alexander;
Simonovic, Milan;
Bork, Peer;
von Mering, Christian

Publication type:

Article

KEGG Atlas mapping for global analysis of metabolic pathways.

Published in:

Nucleic Acids Research, 2008, v. 36, n. suppl_2, p. W423, doi. 10.1093/nar/gkn282

By:

Okuda, Shujiro;
Yamada, Takuji;
Hamajima, Masami;
Itoh, Masumi;
Katayama, Toshiaki;
Bork, Peer;
Goto, Susumu;
Kanehisa, Minoru

Publication type:

Article

SuperTarget and Matador: resources for exploring drug-target relationships.

Published in:

Nucleic Acids Research, 2008, v. 36, p. D919

By:

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

Publication type:

Article

eggNOG: automated construction and annotation of orthologous groups of genes.

Published in:

Nucleic Acids Research, 2008, v. 36, p. D250

By:

Jensen, Lars Juhl;
Julien, Philippe;
Kuhn, Michael;
von Mering, Christian;
Muller, Jean;
Doerks, Tobias;
Bork, Peer

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2008, v. 36, p. D847

By:

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

Publication type:

Article

NetworKIN: a resource for exploring cellular phosphorylation networks.

Published in:

Nucleic Acids Research, 2008, v. 36, p. D695

By:

Linding, Rune;
Jensen, Lars Juhl;
Pasculescu, Adrian;
Olhovsky, Marina;
Colwill, Karen;
Bork, Peer;
Yaffe, Michael B.;
Pawson, Tony

Publication type:

Article

STITCH: interaction networks of chemicals and proteins.

Published in:

Nucleic Acids Research, 2008, v. 36, p. D684

By:

Kuhn, Michael;
von Mering, Christian;
Campillos, Monica;
Jensen, Lars Juhl;
Bork, Peer

Publication type:

Article

Update of the G2D tool for prioritization of gene candidates to inherited diseases.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W212, doi. 10.1093/nar/gkm223

By:

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

Publication type:

Article

New developments in the InterPro database.

Published in:

Nucleic Acids Research, 2007, v. 35, p. d224, doi. 10.1093/nar/gkl841

By:

Mulder, Nicola J.;
Apweiler, Rolf;
Attwood, Teresa K.;
Bairoch, Amos;
Bateman, Alex;
Binns, David;
Bork, Peer;
Buillard, Virginie;
Cerutti, Lorenzo;
Copley, Richard;
Courcelle, Emmanuel;
Das, Ujjwal;
Daugherty, Louise;
Dibley, Mark;
Finn, Robert;
Fleischmann, Wolfgang;
Gough, Julian;
Haft, Daniel;
Hulo, Nicolas;
Hunter, Sarah

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2007, v. 35, p. d358, doi. 10.1093/nar/gkl825

By:

von Mering, Christian;
Jensen, Lars J.;
Kuhn, Michael;
Chaffron, Samuel;
Doerks, Tobias;
Krüger, Beate;
Snel, Berend;
Bork, Peer

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2006, v. 34, n. 11, p. w609, doi. 10.1093/nar/gkl315

By:

Suyama, Mikita;
Torrents, David;
Bork, Peer

Publication type:

Article

SMART 5: domains in the context of genomes and networks.

Published in:

Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d257, doi. 10.1093/nar/gkj079

By:

Letunic, Ivica;
Copley, Richard R.;
Pils, Birgit;
Pinkert, Stefan;
Schultz, Jörg;
Bork, Peer

Publication type:

Article

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 3, p. 946, doi. 10.1093/nar/gki236

By:

Zdobnov, Evgeny M.;
Campillos, Mónica;
Harrington, Eoghan D.;
Torrents, David;
Bork, Peer

Publication type:

Article

InterPro, progress and status in 2005.

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d201

By:

Mulder, Nicola J.;
Apweiler, Rolf;
Attwood, Teresa K.;
Bairoch, Amos;
Bateman, Alex;
Binns, David;
Bradley, Paul;
Bork, Peer;
Bucher, Phillip;
Cerutti, Lorenzo;
Copley, Richard;
Courcelle, Emmanuel;
Das, Ujjwal;
Durbin, Richard;
Fleischmann, Wolfgang;
Gough, Julian;
Haft, Daniel;
Harte, Nicola;
Hulo, Nicolas;
Kahn, Daniel

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d433

By:

von Mering, Christian;
Jensen, Lars J.;
Snel, Berend;
Hooper, Sean D.;
Krupp, Markus;
Foglierini, Mathilde;
Jouffre, Nelly;
Huynen, Martijn A.;
Bork, Peer

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2004, v. 32, n. 21, p. 6321, doi. 10.1093/nar/gkh973

By:

Doerks, Tobias;
von Mering, Christian;
Bork, Peer

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w445, doi. 10.1093/nar/gkh407

By:

Jensen, Lars Juhl;
Lagarde, Julien;
von Mering, Christian;
Bork, Peer

Publication type:

Article

SMART 4.0: towards genomic data integration.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d142

By:

Letunic, Ivica;
Copley, Richard R.;
Schmidt, Steffen;
Ciccarelli, Francesca D.;
Doerks, Tobias;
Schultz, Jörg;
Ponting, Chris P.;
Bork, Peer

Publication type:

Article

Update on XplorMed: a web server for exploring scientific literature.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 13, p. 3866, doi. 10.1093/nar/gkg538

By:

Perez-Iratxeta, Carolina;
Pérez, Antonio J.;
Bork, Peer;
Andrade, Miguel A.

Publication type:

Article

The InterPro Database, 2003 brings increased coverage and new features.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 1, p. 315, doi. 10.1093/nar/gkg046

By:

Mulder, Nicola J.;
Apweiler, Rolf;
Attwood, Teresa K.;
Bairoch, Amos;
Barrell, Daniel;
Bateman, Alex;
Binns, David;
Biswas, Margaret;
Bradley, Paul;
Bork, Peer;
Bucher, Phillip;
Copley, Richard R.;
Courcelle, Emmanuel;
Das, Ujjwal;
Durbin, Richard;
Falquet, Laurent;
Fleischmann, Wolfgang;
Griffiths-Jones, Sam;
Haft, Daniel;
Harte, Nicola

Publication type:

Article

STRING: a database of predicted functional associations between proteins.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 1, p. 258, doi. 10.1093/nar/gkg034

By:

Mering, Christian von;
Huynen, Martijn;
Jaeggi, Daniel;
Schmidt, Steffen;
Bork, Peer;
Snel, Berend

Publication type:

Article

Human non‐synonymous SNPs: server and survey.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 17, p. 3894, doi. 10.1093/nar/gkf493

By:

Ramensky, Vasily;
Bork, Peer;
Sunyaev, Shamil

Publication type:

Article

Recent improvements to the SMART domain-based sequence annotation resource.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 1, p. 242, doi. 10.1093/nar/30.1.242

By:

Letunic, Ivica;
Goodstadt, Leo;
Dickens, Nicholas J.;
Doerks, Tobias;
Schultz, Joerg;
Mott, Richard;
Ciccarelli, Francesca;
Copley, Richard R.;
Ponting, Chris P.;
Bork, Peer

Publication type:

Article

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.

Published in:

Nucleic Acids Research, 2000, v. 28, n. 17, p. 3278, doi. 10.1093/nar/28.17.3278

By:

Dandekar, Thomas;
Huynen, Martijn;
Regula, Jörg Thomas;
Ueberle, Barbara;
Zimmermann, Carl Ulrich;
Andrade, Miguel A.;
Doerks, Tobias;
Sánchez-Pulido, Luis;
Snel, Berend;
Suyama, Mikita;
Yuan, Yan P.;
Herrmann, Richard;
Bork, Peer

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2000, v. 28, n. 1, p. 356, doi. 10.1093/nar/28.1.356

By:

Brookes, Anthony J.;
Lehväslaiho, Heikki;
Siegfried, Marianne;
Boehm, Jana G.;
Yuan, Yan P.;
Sarkar, Chandra M.;
Bork, Peer;
Ortigao, Flavio

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2000, v. 28, n. 1, p. 231, doi. 10.1093/nar/28.1.231

By:

Schultz, Jörg;
Copley, Richard R.;
Doerks, Tobias;
Ponting, Chris P.;
Bork, Peer

Publication type:

Article

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

Published in:

Nucleic Acids Research, 1999, v. 27, n. 1, p. 229, doi. 10.1093/nar/27.1.229

By:

Ponting, Chris P.;
Schultz, Jörg;
Milpetz, Frank;
Bork, Peer

Publication type:

Article

Linear Motif Atlas for Phosphorylation-Dependent Signaling.

Published in:

Science Signaling, 2008, v. 1, n. 35, p. 1, doi. 10.1126/scisignal.1159433

By:

Miller, Martin Lee;
Jensen, Lars Juhl;
Diella, Francesca;
Jørgensen, Claus;
Tinti, Michele;
Lei Li;
Hsiung, Marilyn;
Parker, Sirlester A.;
Bordeaux, Jennifer;
Sicheritz-Ponten, Thomas;
Olhovsky, Marina;
Pasculescu, Adrian;
Alexander, Jes;
Knapp, Stefan;
Blom, Nikolaj;
Bork, Peer;
Shawn Li;
Cesareni, Gianni;
Pawson, Tony;
Turk, Benjamin E.

Publication type:

Article

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

Published in:

Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/S13059-015-0646-9

By:

Zhu, Ana;
Shinichi Sunagawa;
Mende, Daniel R.;
Bork, Peer

Publication type:

Article

Temporal and technical variability of human gut metagenomes.

Published in:

Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/S13059-015-0639-8

By:

Voigt, Anita Y.;
Costea, Paul I.;
Kultima, Jens Roat;
Li, Simone S.;
Zeller, Georg;
Sunagawa, Shinichi;
Bork, Peer

Publication type:

Article

Experimental characterization of the human nonsequence- specific nucleic acid interactome.

Published in:

Genome Biology, 2013, v. 14, n. 7, p. 1, doi. 10.1186/gb-2013-14-7-r81

By:

Dürnberger, Gerhard;
Bürckstümmer, Tilmann;
Huber, Kilian;
Giambruno, Roberto;
Doerks, Tobias;
Karayel, Evren;
Burkard, Thomas R.;
Kaupe, Ines;
Müller, André C.;
Schönegger, Andreas;
Ecker, Gerhard F.;
Lohninger, Hans;
Bork, Peer;
Bennett, Keiryn L.;
Superti-Furga, Giulio;
Colinge, Jacques

Publication type:

Article

High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities.

Published in:

Nature Protocols, 2024, v. 19, n. 3, p. 668, doi. 10.1038/s41596-023-00926-4

By:

Müller, Patrick;
de la Cuesta-Zuluaga, Jacobo;
Kuhn, Michael;
Baghai Arassi, Maral;
Treis, Tim;
Blasche, Sonja;
Zimmermann, Michael;
Bork, Peer;
Patil, Kiran Raosaheb;
Typas, Athanasios;
Garcia-Santamarina, Sarela;
Maier, Lisa

Publication type:

Article

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

Published in:

Nature Protocols, 2018, v. 13, n. 12, p. 2781, doi. 10.1038/s41596-018-0064-z

By:

Pedersen, Helle Krogh;
Forslund, Sofia K.;
Gudmundsdottir, Valborg;
Petersen, Anders Østergaard;
Hildebrand, Falk;
Hyötyläinen, Tuulia;
Nielsen, Trine;
Hansen, Torben;
Bork, Peer;
Ehrlich, S. Dusko;
Brunak, Søren;
Oresic, Matej;
Pedersen, Oluf;
Nielsen, Henrik Bjørn

Publication type:

Article

Splicing factors stimulate polyadenylation via USEs at non-canonical 3′ end formation signals.

Published in:

EMBO Journal, 2007, v. 26, n. 11, p. 2658, doi. 10.1038/sj.emboj.7601699

By:

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.

Publication type:

Article

Nonsense-mediated mRNA decay in Drosophila:at the intersection of the yeast and mammalian pathways.

Published in:

EMBO Journal, 2003, v. 22, n. 15, p. 3960, doi. 10.1093/emboj/cdg371

By:

Gatfield, David;
Unterholzner, Leonie;
Ciccarelli, Francesca D.;
Bork, Peer;
Izaurralde, Elisa

Publication type:

Article

Quantifying compartment‐associated variations of protein abundance in proteomics data.

Published in:

Molecular Systems Biology, 2018, v. 14, n. 7, p. 1, doi. 10.15252/msb.20178131

By:

Parca, Luca;
Beck, Martin;
Bork, Peer;
Ori, Alessandro

Publication type:

Article