Signal search analysis: a new method to localize and characterize functionally important DNA sequences. - Philipp Bucher; B. Bryan (Nucleic Acids Res., 1984)

A Generalized Profile Syntax for Biomolecular Sequence Motifs and its Function in Automatic Sequence Interpretation. - Philipp Bucher; Amos Bairoch (ISMB, 1994)

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

Computational analysis of transcriptional regulatory elements: a field in flux. - Philipp Bucher; James W. Fickett; Artemis G. Hatzigeorgiou (Comput. Appl. Biosci., 1996)

A Flexible Motif Search Technique Based on Generalized Profiles. - Philipp Bucher; Kevin Karplus; Nicolas Moeri; Kay Hofmann (Comput. Chem., 1996)

The PROSITE database, its status in 1995. - Amos Bairoch; Philipp Bucher; Kay Hofmann (Nucleic Acids Res., 1996)

The PROSITE database, its status in 1997. - Amos Bairoch; Philipp Bucher; Kay Hofmann (Nucleic Acids Res., 1997)

SEView: a Java applet for browsing molecular sequence data. - Thomas Junier; Philipp Bucher (Silico Biol., 1998)

Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA. - Emmanuelle Roulet; Igor Fisch; Thomas Junier; Philipp Bucher; Nicolas Mermod (Silico Biol., 1998)

The Eukaryotic Promoter Database EPD. - Rouaïda Périer; Thomas Junier; Philipp Bucher (Nucleic Acids Res., 1998)

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

The PROSITE database, its status in 1999. - Kay Hofmann; Philipp Bucher; Laurent Falquet; Amos Bairoch (Nucleic Acids Res., 1999)

The Eukaryotic Promoter Database (EPD): recent developments. - Rouaïda Périer; Thomas Junier; Claude Bonnard; Philipp Bucher (Nucleic Acids Res., 1999)

InterPro-an integrated documentation resource for protein families, domains and functional sites. - 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; et al. (Bioinform., 2000)

The Eukaryotic Promoter Database (EPD). - Rouaïda Cavin Périer; Viviane Praz; Thomas Junier; Claude Bonnard; Philipp Bucher (Nucleic Acids Res., 2000)

mmsearch: a motif arrangement language and search program. - Thomas Junier; Marco Pagni; Philipp Bucher (Bioinform., 2001)

The InterPro database, an integrated documentation resource for protein families, domains and functional sites. - 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; et al. (Nucleic Acids Res., 2001)

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

InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites - 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; et al. (Briefings Bioinform., 2002)

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

The PROSITE database, its status in 2002. - Laurent Falquet; Marco Pagni; Philipp Bucher; Nicolas Hulo; Christian J. A. Sigrist; Kay Hofmann; Amos Bairoch (Nucleic Acids Res., 2002)

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

Modeling sequencing errors by combining Hidden Markov models. - Claudio Lottaz; Christian Iseli; C. Victor Jongeneel; Philipp Bucher (ECCB, 2003)

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

Signal search analysis server. - Giovanna Ambrosini; Viviane Praz; Vidhya Jagannathan; Philipp Bucher (Nucleic Acids Res., 2003)

The InterPro Database, 2003 brings increased coverage and new features. - 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; et al. (Nucleic Acids Res., 2003)

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

CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature. - Viviane Praz; Vidhya Jagannathan; Philipp Bucher (Nucleic Acids Res., 2004)

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

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

Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge. - Florence Armand; Philipp Bucher; C. Victor Jongeneel; Edward E. Farmer (Bioinform., 2005)

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

HTPSELEX - a database of high-throughput SELEX libraries for transcription factor binding sites. - Vidhya Jagannathan; Emmanuelle Roulet; Mauro Delorenzi; Philipp Bucher (Nucleic Acids Res., 2006)

EPD in its twentieth year: towards complete promoter coverage of selected model organisms. - Christoph D. Schmid; Rouaïda Périer; Viviane Praz; Philipp Bucher (Nucleic Acids Res., 2006)

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

MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data. - Christoph D. Schmid; Thierry Sengstag; Philipp Bucher; Mauro Delorenzi (Nucleic Acids Res., 2007)

CleanEx: new data extraction and merging tools based on MeSH term annotation. - Viviane Praz; Philipp Bucher (Nucleic Acids Res., 2009)

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

Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements. - Slavica Dimitrieva; Philipp Bucher (Bioinform., 2012)

Practicality and Time Complexity of a Sparsified RNA Folding Algorithm. - Slavica Dimitrieva; Philipp Bucher (J. Bioinform. Comput. Biol., 2012)

Phylogenetic Analysis of Cell Types Using Histone Modifications. - Nishanth Ulhas Nair; Yu Lin 001; Philipp Bucher; Bernard M. E. Moret (WABI, 2013)

UCNEbase - a database of ultraconserved non-coding elements and genomic regulatory blocks. - Slavica Dimitrieva; Philipp Bucher (Nucleic Acids Res., 2013)

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. - René Dreos; Giovanna Ambrosini; Rouaïda Cavin Périer; Philipp Bucher (Nucleic Acids Res., 2013)

Principles of ChIP-seq Data Analysis Illustrated with Examples. - Giovanna Ambrosini; René Dreos; Philipp Bucher (IWBBIO, 2014)

Transcription factor binding and nucleosome positioning are alternative pathways for transcription start site selection in eukaryotic promoters. - René Dreos; Giovanna Ambrosini; Philipp Bucher (IWBBIO, 2014)

Probabilistic partitioning methods to find significant patterns in ChIP-Seq data. - Nishanth Ulhas Nair; Sunil Kumar; Bernard M. E. Moret; Philipp Bucher (Bioinform., 2014)

Study of cell differentiation by phylogenetic analysis using histone modification data. - Nishanth Ulhas Nair; Yu Lin 001; Ana Manasovska; Jelena Antic; Paulina Grnarova; Avinash Das Sahu; Philipp Bucher; Bernard M. E. Moret (BMC Bioinform., 2014)

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. - Heinz Stockinger; Adrian M. Altenhoff; Konstantin Arnold; Amos Bairoch; Frederic B. Bastian; Sven Bergmann; Lydie Bougueleret; Philipp Bucher; Mauro Delorenzi; Lydie Lane; Philippe Le Mercier; Frédérique Lisacek; et al. (Nucleic Acids Res., 2014)

The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools. - René Dreos; Giovanna Ambrosini; Rouaïda Cavin Périer; Philipp Bucher (Nucleic Acids Res., 2015)

Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features. - Sunil Kumar; Philipp Bucher (BMC Bioinform., 2016)

A maximum-likelihood approach for building cell-type trees by lifting. - Nishanth Ulhas Nair; Laura Hunter; Mingfu Shao; Paulina Grnarova; Yu Lin 001; Philipp Bucher; Bernard M. E. Moret (BMC Genom., 2016)

Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters. - René Dreos; Giovanna Ambrosini; Philipp Bucher (PLoS Comput. Biol., 2016)

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms. - René Dreos; Giovanna Ambrosini; Romain Groux; Rouaïda Cavin Périer; Philipp Bucher (Nucleic Acids Res., 2017)

SNP2TFBS - a database of regulatory SNPs affecting predicted transcription factor binding site affinity. - Sunil Kumar; Giovanna Ambrosini; Philipp Bucher (Nucleic Acids Res., 2017)

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix. - Giovanna Ambrosini; Romain Groux; Philipp Bucher (Bioinform., 2018)

MGA repository: a curated data resource for ChIP-seq and other genome annotated data. - René Dreos; Giovanna Ambrosini; Romain Groux; Rouaïda Cavin Périer; Philipp Bucher (Nucleic Acids Res., 2018)

SPar-K: a method to partition NGS signal data. - Romain Groux; Philipp Bucher (Bioinform., 2019)

EPD in 2020: enhanced data visualization and extension to ncRNA promoters. - Patrick Meylan; René Dreos; Giovanna Ambrosini; Romain Groux; Philipp Bucher (Nucleic Acids Res., 2020)

Computational identification and experimental characterization of preferred downstream positions in human core promoters. - René Dreos; Anna Sloutskin; Nati Malachi; Diana Ideses; Philipp Bucher; Tamar Juven-Gershon (PLoS Comput. Biol., 2021)

Codes across (life)sciences. - Robert Prinz; Philipp Bucher; Ádám Kun; Omar Paredes; Anna Aragno; Candice Shelby; Markus Gumbel; Elena Fimmel; Lutz Strüngmann (Biosyst., 2025)