Philipp Bucher

Slavica Dimitrieva, Philipp Bucher: UCNEbase - a database of ultraconserved non-coding elements and genomic regulatory blocks. Nucleic Acids Research 41(Database-Issue): 101-109 (2013)

René Dreos, Giovanna Ambrosini, Rouaïda Cavin Périer, Philipp Bucher: EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. Nucleic Acids Research 41(Database-Issue): 157-164 (2013)

Slavica Dimitrieva, Philipp Bucher: Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements. Bioinformatics 28(18): 395-401 (2012)

Slavica Dimitrieva, Philipp Bucher: Practicality and Time Complexity of a Sparsified RNA Folding Algorithm. J. Bioinformatics and Computational Biology 10(2) (2012)

Thomas J. Cradick, Giovanna Ambrosini, Christian Iseli, Philipp Bucher, Anton P. McCaffrey: ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites. BMC Bioinformatics 12: 152 (2011)

Viviane Praz, Philipp Bucher: CleanEx: new data extraction and merging tools based on MeSH term annotation. Nucleic Acids Research 37(Database-Issue): 880-884 (2009)

Davide Rambaldi, Barbara Felice, Viviane Praz, Philipp Bucher, Davide Cittaro, Alessandro Guffanti: Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data. BMC Bioinformatics 8(S-1) (2007)

Christoph D. Schmid, Thierry Sengstag, Philipp Bucher, Mauro Delorenzi: MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data. Nucleic Acids Research 35(Web-Server-Issue): 201-205 (2007)

Christoph D. Schmid, Rouaïda Périer, Viviane Praz, Philipp Bucher: EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic Acids Research 34(Database-Issue): 82-85 (2006)

Vidhya Jagannathan, Emmanuelle Roulet, Mauro Delorenzi, Philipp Bucher: HTPSELEX - a database of high-throughput SELEX libraries for transcription factor binding sites. Nucleic Acids Research 34(Database-Issue): 90-94 (2006)

Philipp Bucher, Bernard M. E. Moret (Eds.): Algorithms in Bioinformatics, 6th International Workshop, WABI 2006, Zurich, Switzerland, September 11-13, 2006, Proceedings. Lecture Notes in Computer Science 4175, Springer 2006, isbn 3-540-39583-0

Florence Armand, Philipp Bucher, C. Victor Jongeneel, Edward E. Farmer: Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge. Bioinformatics 21(12): 2906-2908 (2005)

Peter Sperisen, Christoph D. Schmid, Philipp Bucher, Olav Zilian: Stealth Proteins: In Silico Identification of a Novel Protein Family Rendering Bacterial Pathogens Invisible to Host Immune Defense. PLoS Computational Biology 1(6) (2005)

Christoph D. Schmid, Viviane Praz, Mauro Delorenzi, Rouaïda Périer, Philipp Bucher: The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Nucleic Acids Research 32(Database-Issue): 82-85 (2004)

Nicolas Hulo, Christian J. A. Sigrist, Virginie Le Saux, Petra S. Langendijk-Genevaux, Lorenza Bordoli, Alexandre Gattiker, Edouard De Castro, Philipp Bucher, Amos Bairoch: Recent improvements to the PROSITE database. Nucleic Acids Research 32(Database-Issue): 134-137 (2004)

Peter Sperisen, Christian Iseli, Marco Pagni, Brian J. Stevenson, Philipp Bucher, C. Victor Jongeneel: trome, trEST and trGEN: databases of predicted protein sequences. Nucleic Acids Research 32(Database-Issue): 509-511 (2004)

Viviane Praz, Vidhya Jagannathan, Philipp Bucher: CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature. Nucleic Acids Research 32(Database-Issue): 542-547 (2004)

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)

Giovanna Ambrosini, Viviane Praz, Vidhya Jagannathan, Philipp Bucher: Signal search analysis server. Nucleic Acids Research 31(13): 3618-3620 (2003)

Claudio Lottaz, Christian Iseli, C. Victor Jongeneel, Philipp Bucher: Modeling sequencing errors by combining Hidden Markov models. ECCB 2003: 103-112

Orla O'Sullivan, Mark Zehnder, Desmond G. Higgins, Philipp Bucher, Aurélien Grosdidier, Cédric Notredame: APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. ISMB (Supplement of Bioinformatics) 2003: 215-221

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)

Christian J. A. Sigrist, Lorenzo Cerutti, Nicolas Hulo, Alexandre Gattiker, Laurent Falquet, Marco Pagni, Amos Bairoch, Philipp Bucher: PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors. Briefings in Bioinformatics 3(3): 265-274 (2002)

Laurent Falquet, Marco Pagni, Philipp Bucher, Nicolas Hulo, Christian J. A. Sigrist, Kay Hofmann, Amos Bairoch: The PROSITE database, its status in 2002. Nucleic Acids Research 30(1): 235-238 (2002)

Viviane Praz, Rouaïda Périer, Claude Bonnard, Philipp Bucher: The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucleic Acids Research 30(1): 322-324 (2002)

Thomas Junier, Marco Pagni, Philipp Bucher: mmsearch: a motif arrangement language and search program. Bioinformatics 17(12): 1234-1235 (2001)

Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov: The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Research 29(1): 37-40 (2001)

Marco Pagni, Christian Iseli, Thomas Junier, Laurent Falquet, C. Victor Jongeneel, Philipp Bucher: trEST, trGEN and Hits: access to databases of predicted protein sequences. Nucleic Acids Research 29(1): 148-151 (2001)

Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov: InterPro-an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16(12): 1145-1150 (2000)

Rouaïda Cavin Périer, Viviane Praz, Thomas Junier, Claude Bonnard, Philipp Bucher: The Eukaryotic Promoter Database (EPD). Nucleic Acids Research 28(1): 302-303 (2000)

Kay Hofmann, Philipp Bucher, Laurent Falquet, Amos Bairoch: The PROSITE database, its status in 1999. Nucleic Acids Research 27(1): 215-219 (1999)

Rouaïda Périer, Thomas Junier, Claude Bonnard, Philipp Bucher: The Eukaryotic Promoter Database (EPD): recent developments. Nucleic Acids Research 27(1): 307-309 (1999)

Christian Iseli, C. Victor Jongeneel, Philipp Bucher: ESTScan: A Program for Detecting, Evaluating, and Reconstructing Potential Coding Regions in EST Sequences. ISMB 1999: 138-148

Thomas Junier, Philipp Bucher: SEView: a Java applet for browsing molecular sequence data. In Silico Biology 1: 3 (1998)

Emmanuelle Roulet, Igor Fisch, Thomas Junier, Philipp Bucher, Nicolas Mermod: Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA. In Silico Biology 1: 4 (1998)

Rouaïda Périer, Thomas Junier, Philipp Bucher: The Eukaryotic Promoter Database EPD. Nucleic Acids Research 26(1): 353-357 (1998)

Amos Bairoch, Philipp Bucher, Kay Hofmann: The PROSITE database, its status in 1997. Nucleic Acids Research 25(1): 217-221 (1997)

Philipp Bucher, James W. Fickett, Artemis G. Hatzigeorgiou: Computational analysis of transcriptional regulatory elements: a field in flux. Computer Applications in the Biosciences 12(5): 361-362 (1996)

Philipp Bucher, Kevin Karplus, Nicolas Moeri, Kay Hofmann: A Flexible Motif Search Technique Based on Generalized Profiles. Computers & Chemistry 20(1): 3-23 (1996)

Amos Bairoch, Philipp Bucher, Kay Hofmann: The PROSITE database, its status in 1995. Nucleic Acids Research 24(1): 189-196 (1996)

Philipp Bucher, Kay Hofmann: A Sequence Similarity Search Algorithm Based on a Probabilistic Interpretation of an Alignment Scoring System. ISMB 1996: 44-51

Philipp Bucher, Amos Bairoch: A Generalized Profile Syntax for Biomolecular Sequence Motifs and its Function in Automatic Sequence Interpretation. ISMB 1994: 53-61

Philipp Bucher, B. Bryan: Signal search analysis: a new method to localize and characterize functionally important DNA sequences. Nucleic Acids Research 12(1): 287-305 (1984)