| 2008 |
|---|
| 60 | EE | Yannick Haudry,
Chuang Kee Ong,
Laurence Ettwiller,
Hugo Berube,
Ivica Letunic,
Misha Kapushesky,
Paul-Daniel Weeber,
Xi Wang,
Julien Gagneur,
Charles Girardot,
Detlev Arendt,
Peer Bork,
Alvis Brazma,
Eileen E. M. Furlong,
Joachim Wittbrodt,
Thorsten Henrich:
Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress.
APBC 2008: 373-382 |
| 59 | EE | Eoghan D. Harrington,
Peer Bork:
Sircah: a tool for the detection and visualization of alternative transcripts.
Bioinformatics 24(17): 1959-1960 (2008) |
| 58 | EE | Lars Juhl Jensen,
Philippe Julien,
Michael Kuhn,
Christian von Mering,
Jean Muller,
Tobias Doerks,
Peer Bork:
eggNOG: automated construction and annotation of orthologous groups of genes.
Nucleic Acids Research 36(Database-Issue): 250-254 (2008) |
| 57 | EE | Michael Kuhn,
Christian von Mering,
Monica Campillos,
Lars Juhl Jensen,
Peer Bork:
STITCH: interaction networks of chemicals and proteins.
Nucleic Acids Research 36(Database-Issue): 684-688 (2008) |
| 56 | EE | Rune Linding,
Lars Juhl Jensen,
Adrian Pasculescu,
Marina Olhovsky,
Karen Colwill,
Peer Bork,
Michael B. Yaffe,
Tony Pawson:
NetworKIN: a resource for exploring cellular phosphorylation networks.
Nucleic Acids Research 36(Database-Issue): 695-699 (2008) |
| 55 | EE | Yannick Haudry,
Hugo Berube,
Ivica Letunic,
Paul-Daniel Weeber,
Julien Gagneur,
Charles Girardot,
Misha Kapushesky,
Detlev Arendt,
Peer Bork,
Alvis Brazma,
Eileen E. M. Furlong,
Joachim Wittbrodt,
Thorsten Henrich:
4DXpress: a database for cross-species expression pattern comparisons.
Nucleic Acids Research 36(Database-Issue): 847-853 (2008) |
| 54 | EE | Stefan Günther,
Michael Kuhn,
Mathias Dunkel,
Monica Campillos,
Christian Senger,
Evangelia Petsalaki,
Jessica Ahmed,
Eduardo Garcia Urdiales,
Andreas Gewiess,
Lars Juhl Jensen,
Reinhard Schneider,
Roman Skoblo,
Robert B. Russell,
Philip E. Bourne,
Peer Bork,
Robert Preissner:
SuperTarget and Matador: resources for exploring drug-target relationships.
Nucleic Acids Research 36(Database-Issue): 919-922 (2008) |
| 2007 |
|---|
| 53 | EE | Ivica Letunic,
Peer Bork:
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
Bioinformatics 23(1): 127-128 (2007) |
| 52 | EE | Nicola J. Mulder,
Rolf Apweiler,
Teresa K. Attwood,
Amos Bairoch,
Alex Bateman,
David Binns,
Peer Bork,
Virginie Buillard,
Lorenzo Cerutti,
Richard R. Copley,
Emmanuel Courcelle,
Ujjwal Das,
Louise Daugherty,
Mark Dibley,
Robert D. Finn,
Wolfgang Fleischmann,
Julian Gough,
Daniel H. Haft,
Nicolas Hulo,
Sarah Hunter,
Daniel Kahn,
Alexander Kanapin,
Anish Kejariwal,
Alberto Labarga,
Petra S. Langendijk-Genevaux,
David Lonsdale,
Rodrigo Lopez,
Ivica Letunic,
Martin Madera,
John Maslen,
Craig McAnulla,
Jennifer McDowall,
Jaina Mistry,
Alex Mitchell,
Anastasia N. Nikolskaya,
Sandra E. Orchard,
Christine A. Orengo,
Robert Petryszak,
Jeremy D. Selengut,
Christian J. A. Sigrist,
Paul D. Thomas,
Franck Valentin,
Derek Wilson,
Cathy H. Wu,
Corin Yeats:
New developments in the InterPro database.
Nucleic Acids Research 35(Database-Issue): 224-228 (2007) |
| 51 | EE | Christian von Mering,
Lars Juhl Jensen,
Michael Kuhn,
Samuel Chaffron,
Tobias Doerks,
Beate Krüger,
Berend Snel,
Peer Bork:
STRING 7 - recent developments in the integration and prediction of protein interactions.
Nucleic Acids Research 35(Database-Issue): 358-362 (2007) |
| 50 | EE | Carolina Perez-Iratxeta,
Peer Bork,
Miguel A. Andrade-Navarro:
Update of the G2D tool for prioritization of gene candidates to inherited diseases.
Nucleic Acids Research 35(Web-Server-Issue): 212-216 (2007) |
| 2006 |
|---|
| 49 | EE | Jasmin Saric,
Lars Juhl Jensen,
Rossitza Ouzounova,
Isabel Rojas,
Peer Bork:
Extraction of regulatory gene/protein networks from Medline.
Bioinformatics 22(6): 645-650 (2006) |
| 48 | EE | Parantu K. Shah,
Peer Bork:
LSAT: learning about alternative transcripts in MEDLINE.
Bioinformatics 22(7): 857-865 (2006) |
| 47 | EE | Ivica Letunic,
Richard R. Copley,
Birgit Pils,
Stefan Pinkert,
Jörg Schultz,
Peer Bork:
SMART 5: domains in the context of genomes and networks.
Nucleic Acids Research 34(Database-Issue): 257-260 (2006) |
| 46 | EE | Mikita Suyama,
David Torrents,
Peer Bork:
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
Nucleic Acids Research 34(Web-Server-Issue): 609-612 (2006) |
| 2005 |
|---|
| 45 | EE | Raimund Tenhaken,
Tobias Doerks,
Peer Bork:
DCD - a novel plant specific domain in proteins involved in development and programmed cell death.
BMC Bioinformatics 6: 169 (2005) |
| 44 | EE | Sean D. Hooper,
Peer Bork:
Medusa: a simple tool for interaction graph analysis.
Bioinformatics 21(24): 4432-4433 (2005) |
| 43 | EE | Ulrik de Lichtenberg,
Lars Juhl Jensen,
Anders Fausbøll,
Thomas Skøt Jensen,
Peer Bork,
Søren Brunak:
Comparison of computational methods for the identification of cell cycle-regulated genes.
Bioinformatics 21(7): 1164-1171 (2005) |
| 42 | EE | Francesca Ciccarelli,
Peer Bork:
The WHy domain mediates the response to desiccation in plants and bacteria.
Bioinformatics 21(8): 1304-1307 (2005) |
| 41 | EE | Nicola J. Mulder,
Rolf Apweiler,
Teresa K. Attwood,
Amos Bairoch,
Alex Bateman,
David Binns,
Paul Bradley,
Peer Bork,
Phillip Bucher,
Lorenzo Cerutti,
Richard R. Copley,
Emmanuel Courcelle,
Ujjwal Das,
Richard Durbin,
Wolfgang Fleischmann,
Julian Gough,
Daniel H. Haft,
Nicola Harte,
Nicolas Hulo,
Daniel Kahn,
Alexander Kanapin,
Maria Krestyaninova,
David Lonsdale,
Rodrigo Lopez,
Ivica Letunic,
Martin Madera,
John Maslen,
Jennifer McDowall,
Alex Mitchell,
Anastasia N. Nikolskaya,
Sandra E. Orchard,
Marco Pagni,
Chris P. Ponting,
Emmanuel Quevillon,
Jeremy D. Selengut,
Christian J. A. Sigrist,
Ville Silventoinen,
David J. Studholme,
Robert Vaughan,
Cathy H. Wu:
InterPro, progress and status in 2005.
Nucleic Acids Research 33(Database-Issue): 201-205 (2005) |
| 40 | EE | Christian von Mering,
Lars Juhl Jensen,
Berend Snel,
Sean D. Hooper,
Markus Krupp,
Mathilde Foglierini,
Nelly Jouffre,
Martijn A. Huynen,
Peer Bork:
STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
Nucleic Acids Research 33(Database-Issue): 433-437 (2005) |
| 2004 |
|---|
| 39 | EE | Jasmin Saric,
Lars Juhl Jensen,
Peer Bork,
Rossitza Ouzounova,
Isabel Rojas:
Extracting Regulatory Gene Expression Networks From Pubmed.
ACL 2004: 191-198 |
| 38 | EE | Mikita Suyama,
David Torrents,
Peer Bork:
BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments.
Bioinformatics 20(12): 1968-1970 (2004) |
| 37 | EE | Antonio Jesús Pérez,
Carolina Perez-Iratxeta,
Peer Bork,
Guillermo Thode,
Miguel A. Andrade:
Gene annotation from scientific literature using mappings between keyword systems.
Bioinformatics 20(13): 2084-2091 (2004) |
| 36 | EE | Torsten Crass,
Iris Antes,
Rico Basekow,
Peer Bork,
Christian Buning,
Maik Christensen,
Holger Claussen,
Christian Ebeling,
Peter Ernst,
Valérie Gailus-Durner,
Karl-Heinz Glatting,
Rolf Gohla,
Frank Gößling,
Korbinian Grote,
Karsten R. Heidtke,
Alexander Herrmann,
Sean O'Keeffe,
O. Kießlich,
Sven Kolibal,
Jan O. Korbel,
Thomas Lengauer,
Ines Liebich,
Mark van der Linden,
Hannes Luz,
Kathrin Meissner,
Christian von Mering,
Heinz-Theodor Mevissen,
Hans-Werner Mewes,
Holger Michael,
Martin Mokrejs,
Tobias Müller,
Heike Pospisil,
Matthias Rarey,
Jens G. Reich,
Ralf Schneider,
Dietmar Schomburg,
Steffen Schulze-Kremer,
Knut Schwarzer,
Ingolf Sommer,
Stephan Springstubbe,
Sándor Suhai,
Gnanasekaran Thoppae,
Martin Vingron,
Jens Warfsmann,
Thomas Werner,
Daniel Wetzler,
Edgar Wingender,
Ralf Zimmer:
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.
Bioinformatics 20(2): 268-270 (2004) |
| 35 | | Ivica Letunic,
Richard R. Copley,
Steffen Schmidt,
Francesca Ciccarelli,
Tobias Doerks,
Jörg Schultz,
Chris P. Ponting,
Peer Bork:
SMART 4.0: towards genomic data integration.
Nucleic Acids Research 32(Database-Issue): 142-144 (2004) |
| 34 | | Lars Juhl Jensen,
Julien Lagarde,
Christian von Mering,
Peer Bork:
ArrayProspector: a web resource of functional associations inferred from microarray expression data.
Nucleic Acids Research 32(Web-Server-Issue): 445-448 (2004) |
| 2003 |
|---|
| 33 | EE | Parantu K. Shah,
Carolina Perez-Iratxeta,
Peer Bork,
Miguel A. Andrade:
Information extraction from full text scientific articles: Where are the keywords?
BMC Bioinformatics 4: 20 (2003) |
| 32 | EE | Francesca Ciccarelli,
Elisa Izaurralde,
Peer Bork:
The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold.
BMC Bioinformatics 4: 64 (2003) |
| 31 | | Roland Krause,
Christian von Mering,
Peer Bork:
A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens.
Bioinformatics 19(15): 1901-1908 (2003) |
| 30 | | Christian von Mering,
Martijn A. Huynen,
Daniel Jaeggi,
Steffen Schmidt,
Peer Bork,
Berend Snel:
STRING: a database of predicted functional associations between proteins.
Nucleic Acids Research 31(1): 258-261 (2003) |
| 29 | | Nicola J. Mulder,
Rolf Apweiler,
Terri K. Attwood,
Amos Bairoch,
Daniel Barrell,
Alex Bateman,
David Binns,
Margaret Biswas,
Paul Bradley,
Peer Bork,
Philipp Bucher,
Richard R. Copley,
Emmanuel Courcelle,
Ujjwal Das,
Richard Durbin,
Laurent Falquet,
Wolfgang Fleischmann,
Sam Griffiths-Jones,
Daniel H. Haft,
Nicola Harte,
Nicolas Hulo,
Daniel Kahn,
Alexander Kanapin,
Maria Krestyaninova,
Rodrigo Lopez,
Ivica Letunic,
David Lonsdale,
Ville Silventoinen,
Sandra E. Orchard,
Marco Pagni,
David Peyruc,
Chris P. Ponting,
Jeremy D. Selengut,
Florence Servant,
Christian J. A. Sigrist,
Robert Vaughan,
Evgeni M. Zdobnov:
The InterPro Database, 2003 brings increased coverage and new features.
Nucleic Acids Research 31(1): 315-318 (2003) |
| 28 | | Pål Puntervoll,
Rune Linding,
Christine Gemünd,
Sophie Chabanis-Davidson,
Morten Mattingsdal,
Scott Cameron,
David M. A. Martin,
Gabriele Ausiello,
Barbara Brannetti,
Anna Costantini,
Fabrizio Ferrè,
Vincenza Maselli,
Allegra Via,
Gianni Cesareni,
Francesca Diella,
Giulio Superti-Furga,
Lucjan Stanislaw Wyrwicz,
Chenna Ramu,
Caroline McGuigan,
Rambabu Gudavalli,
Ivica Letunic,
Peer Bork,
Leszek Rychlewski,
Bernhard Küster,
Manuela Helmer-Citterich,
William N. Hunter,
Rein Aasland,
Toby J. Gibson:
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins.
Nucleic Acids Research 31(13): 3625-3630 (2003) |
| 27 | | Carolina Perez-Iratxeta,
Antonio Jesús Pérez,
Peer Bork,
Miguel A. Andrade:
Update on XplorMed: a web server for exploring scientific literature.
Nucleic Acids Research 31(13): 3866-3868 (2003) |
| 2002 |
|---|
| 26 | | Peer Bork:
Comparative analysis of protein interaction networks.
ECCB 2002: 64-64 |
| 25 | | Nicola J. Mulder,
Rolf Apweiler,
Terri K. Attwood,
Amos Bairoch,
Alex Bateman,
David Binns,
Margaret Biswas,
Paul Bradley,
Peer Bork,
Philipp Bucher,
Richard R. Copley,
Emmanuel Courcelle,
Richard Durbin,
Laurent Falquet,
Wolfgang Fleischmann,
Jérôme Gouzy,
Sam Griffiths-Jones,
Daniel H. Haft,
Henning Hermjakob,
Nicolas Hulo,
Daniel Kahn,
Alexander Kanapin,
Maria Krestyaninova,
Rodrigo Lopez,
Ivica Letunic,
Sue Orchard,
Marco Pagni,
David Peyruc,
Chris P. Ponting,
Florence Servant,
Christian J. A. Sigrist:
InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites
Briefings in Bioinformatics 3(3): 225-235 (2002) |
| 24 | EE | Steffen Schmidt,
Peer Bork,
Thomas Dandekar:
A Versatile Structural Domain Analysis Server Using Profile Weight Matrices.
Journal of Chemical Information and Computer Sciences 42(2): 405-407 (2002) |
| 23 | | Ivica Letunic,
Leo Goodstadt,
Nicholas J. Dickens,
Tobias Doerks,
Jörg Schultz,
Richard Mott,
Francesca Ciccarelli,
Richard R. Copley,
Chris P. Ponting,
Peer Bork:
Recent improvements to the SMART domain-based sequence annotation resource.
Nucleic Acids Research 30(1): 242-244 (2002) |
| 22 | | D. Fredman,
Marianne Siegfried,
Yan P. Yuan,
Peer Bork,
Heikki Lehväslaiho,
Anthony J. Brookes:
HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources.
Nucleic Acids Research 30(1): 387-391 (2002) |
| 2000 |
|---|
| 21 | | Luis Sánchez-Pulido,
Yan P. Yuan,
Miguel A. Andrade,
Peer Bork:
NAIL-Network Analysis Interface for Linking HMMER results.
Bioinformatics 16(7): 656-657 (2000) |
| 20 | | Jörg Schultz,
Richard R. Copley,
Tobias Doerks,
Chris P. Ponting,
Peer Bork:
SMART: a web-based tool for the study of genetically mobile domains.
Nucleic Acids Research 28(1): 231-234 (2000) |
| 19 | | Anthony J. Brookes,
Heikki Lehväslaiho,
Marianne Siegfried,
Jana G. Boehm,
Yan P. Yuan,
Chandra M. Sarkar,
Peer Bork,
J. Flavio R. Ortigao:
HGBASE: a database of SNPs and other variations in and around human genes.
Nucleic Acids Research 28(1): 356-360 (2000) |
| 1999 |
|---|
| 18 | | Thomas Lengauer,
Reinhard Schneider,
Peer Bork,
Douglas L. Brutlag,
Janice I. Glasgow,
Hans-Werner Mewes,
Ralf Zimmer:
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, August 6-10, 1999, Heidelberg, Germany
AAAI 1999 |
| 17 | EE | Arvind K. Bansal,
Peer Bork:
Applying Logic Programming to Derive Novel Functional Information of Genomes.
PADL 1999: 275-289 |
| 16 | EE | Peer Bork:
Comparing genes and genomes (abstract): from polymorphism to phylogeny.
RECOMB 1999: 69-76 |
| 15 | | Frank Eisenhaber,
Peer Bork:
Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries.
Bioinformatics 15(7): 528-535 (1999) |
| 14 | | Jens Hanke,
Gerrit Lehmann,
Peer Bork,
Jens G. Reich:
Associative database of protein sequences.
Bioinformatics 15(9): 741-748 (1999) |
| 13 | | Chris P. Ponting,
Jörg Schultz,
Frank Milpetz,
Peer Bork:
SMART: identification and annotation of domains from signalling and extracellular protein sequences.
Nucleic Acids Research 27(1): 229-232 (1999) |
| 1998 |
|---|
| 12 | | Thomas Dandekar,
Stefan Schuster,
Martijn A. Huynen,
Peer Bork:
Pathway alignment: Application in the comparative analysis of glycolysis.
German Conference on Bioinformatics 1998 |
| 11 | | Thomas Dandekar,
Katrin Beyer,
Peer Bork,
Mary-Rose Kenealy,
Kostas Pantopoulos,
Mathias Hentze,
Vera Sonntag-Buck,
Gilles Flouriot,
Frank Gannon,
Sonja Schreiber:
Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches.
Bioinformatics 14(3): 271-278 (1998) |
| 10 | | Yan P. Yuan,
Oliver Eulenstein,
Martin Vingron,
Peer Bork:
Towards detection of orthologues in sequence databases.
Bioinformatics 14(3): 285-289 (1998) |
| 9 | | N. P. Brown,
Chris Sander,
Peer Bork:
Frame: detection of genomic sequencing errors.
Bioinformatics 14(4): 367-371 (1998) |
| 1997 |
|---|
| 8 | | Jens Hanke,
Peer Bork,
Jens G. Reich:
Associative Data Base of Biomolecuiar Sequences.
German Conference on Bioinformatics 1997: 149 |
| 7 | | Yan P. Yuan,
Oliver Eulenstein,
Martin Vingron,
Peer Bork:
Towards detection of sequence orthologs.
German Conference on Bioinformatics 1997: 25-30 |
| 6 | | Thomas Dandekar,
Katrin Beyer,
Peer Bork,
Vera Sonntag-Buck,
Gilles Flouriot,
Frank Gannon,
W. Keller,
Sonja Schreiber:
Systematic genomic screening and analysis of mRNA in the 5' and 3` untranslated region.
German Conference on Bioinformatics 1997: 31-32 |
| 5 | | Hedvig Hegyi,
J. M. Lai,
Peer Bork:
The Sequence Alerting Server - a new WEB server.
Computer Applications in the Biosciences 13(6): 619-620 (1997) |
| 1995 |
|---|
| 4 | | Christos A. Ouzounis,
Alfonso Valencia,
Javier Tamames,
Peer Bork,
Chris Sander:
The Functional Composition of Living Machines as a Design Principle for Artificial Organisms.
ECAL 1995: 843-851 |
| 1994 |
|---|
| 3 | | Michael Scharf,
Reinhard Schneider,
Georg Casari,
Peer Bork,
Alfonso Valencia,
Christos A. Ouzounis,
Chris Sander:
GeneQuiz: A Workbench for Sequence Analysis.
ISMB 1994: 348-353 |
| 1993 |
|---|
| 2 | | Peer Bork:
Entschlüsselung von Proteinfunktionen mit Hilfe des Computers: Erkennung und Interpretation entfernter Sequenzähnlichkeiten.
Informatik in den Biowissenschaften 1993: 67-78 |
| 1 | | K. Rohde,
Peer Bork:
A fast, sensitive pattern-matching approach for protein sequences.
Computer Applications in the Biosciences 9(2): 183-189 (1993) |
