Peer Bork - researchr alias

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2011

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scoredDamian Szklarczyk, Andrea Franceschini, Michael Kuhn, Milan Simonovic, Alexander Roth, Pablo Minguez, Tobias Doerks, Manuel Stark, Jean Muller, Peer Bork, Lars J. Jensen, Christian von Mering. nar, 39(Database-Issue):561-568, 2011. [doi]

2010

STITCH 2: an interaction network database for small molecules and proteinsMichael Kuhn 0004, Damian Szklarczyk, Andrea Franceschini, Monica Campillos, Christian von Mering, Lars Juhl Jensen, Andreas Beyer, Peer Bork. nar, 38(Database-Issue):552-556, 2010. [doi]

SmashCommunity: a metagenomic annotation and analysis toolManimozhiyan Arumugam, Eoghan D. Harrington, Konrad U. Foerstner, Jeroen Raes, Peer Bork. bioinformatics, 26(23):2977-2978, 2010. [doi]

SmashCell: a software framework for the analysis of single-cell amplified genome sequencesEoghan D. Harrington, Manimozhiyan Arumugam, Jeroen Raes, Peer Bork, David A. Relman. bioinformatics, 26(23):2979-2980, 2010. [doi]

AQUA: automated quality improvement for multiple sequence alignmentsJean Muller, Christopher J. Creevey, Julie D. Thompson, Detlev Arendt, Peer Bork. bioinformatics, 26(2):263-265, 2010. [doi]

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotationsJean Muller, Damian Szklarczyk, Philippe Julien, Ivica Letunic, Alexander Roth, Michael Kuhn, S. Powell, Christian von Mering, Tobias Doerks, Lars Juhl Jensen, Peer Bork. nar, 38(Database-Issue):190-195, 2010. [doi]

SelTar::::base::::, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunologyStefan M. Woerner, Yan P. Yuan, Axel Benner, Sebastian Korff, Magnus von Knebel Doeberitz, Peer Bork. nar, 38(Database-Issue):682-689, 2010. [doi]

2009

STRING 8 - a global view on proteins and their functional interactions in 630 organismsLars Juhl Jensen, Michael Kuhn 0004, Manuel Stark, Samuel Chaffron, Chris Creevey, Jean Muller, Tobias Doerks, Philippe Julien, Alexander Roth, Milan Simonovic, Peer Bork, Christian von Mering. nar, 37(Database-Issue):412-416, 2009. [doi]

SMART 6: recent updates and new developmentsIvica Letunic, Tobias Doerks, Peer Bork. nar, 37(Database-Issue):229-232, 2009. [doi]

2008

STITCH: interaction networks of chemicals and proteinsMichael Kuhn 0004, Christian von Mering, Monica Campillos, Lars Juhl Jensen, Peer Bork. nar, 36(Database-Issue):684-688, 2008. [doi]

SuperTarget and Matador: resources for exploring drug-target relationshipsStefan Günther, Michael Kuhn 0004, 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. nar, 36(Database-Issue):919-922, 2008. [doi]

Sircah: a tool for the detection and visualization of alternative transcriptsEoghan D. Harrington, Peer Bork. bioinformatics, 24(17):1959-1960, 2008. [doi]

4D::::Xpress::::: a database for cross-species expression pattern comparisonsYannick 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. nar, 36(Database-Issue):847-853, 2008. [doi]

Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpressYannick 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. apbc 2008: 373-382 [doi]

eggNOG: automated construction and annotation of orthologous groups of genesLars Juhl Jensen, Philippe Julien, Michael Kuhn 0004, Christian von Mering, Jean Muller, Tobias Doerks, Peer Bork. nar, 36(Database-Issue):250-254, 2008. [doi]

NetworKIN: a resource for exploring cellular phosphorylation networksRune Linding, Lars Juhl Jensen, Adrian Pasculescu, Marina Olhovsky, Karen Colwill, Peer Bork, Michael B. Yaffe, Tony Pawson. nar, 36(Database-Issue):695-699, 2008. [doi]

KEGG Atlas mapping for global analysis of metabolic pathwaysShujiro Okuda, Takuji Yamada, Masami Hamajima, Masumi Itoh, Toshiaki Katayama, Peer Bork, Susumu Goto, Minoru Kanehisa. nar, 36(Web-Server-Issue):423-426, 2008. [doi]

2007

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotationIvica Letunic, Peer Bork. bioinformatics, 23(1):127-128, 2007. [doi]

New developments in the InterPro databaseNicola 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. nar, 35(Database-Issue):224-228, 2007. [doi]

Update of the G2D tool for prioritization of gene candidates to inherited diseasesCarolina Perez-Iratxeta, Peer Bork, Miguel A. Andrade-Navarro. nar, 35(Web-Server-Issue):212-216, 2007. [doi]

STRING 7 - recent developments in the integration and prediction of protein interactionsChristian von Mering, Lars Juhl Jensen, Michael Kuhn 0004, Samuel Chaffron, Tobias Doerks, Beate Krüger, Berend Snel, Peer Bork. nar, 35(Database-Issue):358-362, 2007. [doi]

2006

SMART 5: domains in the context of genomes and networksIvica Letunic, Richard R. Copley, Birgit Pils, Stefan Pinkert, Jörg Schultz, Peer Bork. nar, 34(Database-Issue):257-260, 2006. [doi]

Extraction of regulatory gene/protein networks from MedlineJasmin Saric, Lars Juhl Jensen, Rossitza Ouzounova, Isabel Rojas, Peer Bork. bioinformatics, 22(6):645-650, 2006. [doi]

LSAT: learning about alternative transcripts in MEDLINEParantu K. Shah, Peer Bork. bioinformatics, 22(7):857-865, 2006. [doi]

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignmentsMikita Suyama, David Torrents, Peer Bork. nar, 34(Web-Server-Issue):609-612, 2006. [doi]

2005

The WHy domain mediates the response to desiccation in plants and bacteriaFrancesca Ciccarelli, Peer Bork. bioinformatics, 21(8):1304-1307, 2005. [doi]

Comparison of computational methods for the identification of cell cycle-regulated genesUlrik de Lichtenberg, Lars Juhl Jensen, Anders Fausbøll, Thomas Skøt Jensen, Peer Bork, Søren Brunak. bioinformatics, 21(7):1164-1171, 2005. [doi]

Medusa: a simple tool for interaction graph analysisSean D. Hooper, Peer Bork. bioinformatics, 21(24):4432-4433, 2005. [doi]

DCD - a novel plant specific domain in proteins involved in development and programmed cell deathRaimund Tenhaken, Tobias Doerks, Peer Bork. bmcbi, 6:169, 2005. [doi]

STRING: known and predicted protein-protein associations, integrated and transferred across organismsChristian von Mering, Lars Juhl Jensen, Berend Snel, Sean D. Hooper, Markus Krupp, Mathilde Foglierini, Nelly Jouffre, Martijn A. Huynen, Peer Bork. nar, 33(Database-Issue):433-437, 2005. [doi]

2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resourcesTorsten 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. bioinformatics, 20(2):268-270, 2004. [doi]

ArrayProspector: a web resource of functional associations inferred from microarray expression dataLars Juhl Jensen, Julien Lagarde, Christian von Mering, Peer Bork. nar, 32(Web-Server-Issue):445-448, 2004.

SMART 4.0: towards genomic data integrationIvica Letunic, Richard R. Copley, Steffen Schmidt, Francesca Ciccarelli, Tobias Doerks, Jörg Schultz, Chris P. Ponting, Peer Bork. nar, 32(Database-Issue):142-144, 2004.

Gene annotation from scientific literature using mappings between keyword systemsAntonio Jesús Pérez, Carolina Perez-Iratxeta, Peer Bork, Guillermo Thode, Miguel A. Andrade. bioinformatics, 20(13):2084-2091, 2004. [doi]

Extracting Regulatory Gene Expression Networks From PubmedJasmin Saric, Lars Juhl Jensen, Peer Bork, Rossitza Ouzounova, Isabel Rojas. acl 2004: 191-198 [doi]

BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragmentsMikita Suyama, David Torrents, Peer Bork. bioinformatics, 20(12):1968-1970, 2004. [doi]

2003

The PAM domain, a multi-protein complex-associated module with an all-alpha-helix foldFrancesca Ciccarelli, Elisa Izaurralde, Peer Bork. bmcbi, 4:64, 2003. [doi]

A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screensRoland Krause, Christian von Mering, Peer Bork. bioinformatics, 19(15):1901-1908, 2003.

Update on XplorMed: a web server for exploring scientific literatureCarolina Perez-Iratxeta, Antonio Jesús Pérez, Peer Bork, Miguel A. Andrade. nar, 31(13):3866-3868, 2003.

Information extraction from full text scientific articles: Where are the keywords?Parantu K. Shah, Carolina Perez-Iratxeta, Peer Bork, Miguel A. Andrade. bmcbi, 4:20, 2003. [doi]

STRING: a database of predicted functional associations between proteinsChristian von Mering, Martijn A. Huynen, Daniel Jaeggi, Steffen Schmidt, Peer Bork, Berend Snel. nar, 31(1):258-261, 2003.

2002

Comparative analysis of protein interaction networksPeer Bork. eccb 2002: 64-64

HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sourcesD. Fredman, Marianne Siegfried, Yan P. Yuan, Peer Bork, Heikki Lehväslaiho, Anthony J. Brookes. nar, 30(1):387-391, 2002.

Recent improvements to the SMART domain-based sequence annotation resourceIvica Letunic, Leo Goodstadt, Nicholas J. Dickens, Tobias Doerks, Jörg Schultz, Richard Mott, Francesca Ciccarelli, Richard R. Copley, Chris P. Ponting, Peer Bork. nar, 30(1):242-244, 2002.

A Versatile Structural Domain Analysis Server Using Profile Weight MatricesSteffen Schmidt, Peer Bork, Thomas Dandekar. jcisd, 42(2):405-407, 2002. [doi]

2000

1999

Applying Logic Programming to Derive Novel Functional Information of GenomesArvind K. Bansal, Peer Bork. padl 1998: 275-289 [doi]

Comparing genes and genomes (abstract): from polymorphism to phylogenyPeer Bork. recomb 1999: 69-76 [doi]

Evaluation of human-readable annotation in biomolecular sequence databases with biological rule librariesFrank Eisenhaber, Peer Bork. bioinformatics, 15(7):528-535, 1999.

Associative database of protein sequencesJens Hanke, Gerrit Lehmann, Peer Bork, Jens G. Reich. bioinformatics, 15(9):741-748, 1999.

Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, August 6-10, 1999, Heidelberg, GermanyThomas Lengauer, Reinhard Schneider, Peer Bork, Douglas L. Brutlag, Janice I. Glasgow, Hans-Werner Mewes, Ralf Zimmer, editors, AAAI, 1999.

SMART: identification and annotation of domains from signalling and extracellular protein sequencesChris P. Ponting, Jörg Schultz, Frank Milpetz, Peer Bork. nar, 27(1):229-232, 1999.

1998

1997

1995

The Functional Composition of Living Machines as a Design Principle for Artificial OrganismsChristos A. Ouzounis, Alfonso Valencia, Javier Tamames, Peer Bork, Chris Sander. ecal 1995: 843-851

1994

GeneQuiz: A Workbench for Sequence AnalysisMichael Scharf, Reinhard Schneider, Georg Casari, Peer Bork, Alfonso Valencia, Christos A. Ouzounis, Chris Sander. ismb 1994: 348-353

1993

Entschlüsselung von Proteinfunktionen mit Hilfe des Computers: Erkennung und Interpretation entfernter SequenzähnlichkeitenPeer Bork. biow 1993: 67-78

A fast, sensitive pattern-matching approach for protein sequencesK. Rohde, Peer Bork. bioinformatics, 9(2):183-189, 1993.