Large Scale Protein Modeling and Model Repository. - Manuel C. Peitsch (ISMB, 1997)

MDB: a database system utilizing automatic construction of modules and STAR-derived universal language. - Eugenia Migliavacca; Alexei A. Adzhubei; Manuel C. Peitsch (Bioinform., 2001)

About the use of protein models. - Manuel C. Peitsch (Bioinform., 2002)

SWISS-MODEL: an automated protein homology-modeling server. - Torsten Schwede; Jürgen Kopp; Nicolas Guex; Manuel C. Peitsch (Nucleic Acids Res., 2003)

Genome Size and Numbers of Biological Functions. - Ernest Feytmans; Denis Noble; Manuel C. Peitsch (Trans. Comp. Sys. Biology, 2005)

Grid Computing in Drug Discovery. - Manuel C. Peitsch (CCGRID, 2006)

The SwissBioGrid Project: Objectivse, Preliminary Results and Lessons Learned. - Michael Podvinec; Sergio Maffioletti; Peter Z. Kunszt; Konstantin Arnold; Lorenzo Cerutti; Bruno Nyffeler; Ralph Schlapbach; Can Türker; Heinz Stockinger; Arthur J. Thomas; Manuel C. Peitsch; Torsten Schwede (e-Science, 2006)

Tandem Mass Spectrometry Protein Identification on a PC Grid. - Dominique Zosso; Michael Podvinec; Markus Müller; Ruedi Aebersold; Manuel C. Peitsch; Torsten Schwede (HealthGrid, 2007)

A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue. - Walter K. Schlage; Jurjen Willem Westra; Stephan Gebel; Natalie L. Catlett; Carole Mathis; Brian P. Frushour; Arnd Hengstermann; Aaron A. Van Hooser; Carine Poussin; Ben Wong; Michael Lietz; Jennifer Park; et al. (BMC Syst. Biol., 2011)

Construction of a computable cell proliferation network focused on non-diseased lung cells. - Jurjen Willem Westra; Walter K. Schlage; Brian P. Frushour; Stephan Gebel; Natalie L. Catlett; Wan-Jiang Han; Sean F. Eddy; Arnd Hengstermann; Andrea L. Matthews; Carole Mathis; Rosemarie B. Lichtner; Carine Poussin; et al. (BMC Syst. Biol., 2011)

Industrial methodology for process verification in research (IMPROVER): toward systems biology verification. - Pablo Meyer 001; Julia Hoeng; John Jeremy Rice; Raquel Norel; Jörg Sprengel; Katrin Stolle; Thomas Bonk; Stephanie Corthesy; Ajay K. Royyuru; Manuel C. Peitsch; Gustavo Stolovitzky (Bioinform., 2012)

Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks. - Florian Martin 002; Ty M. Thomson; Alain Sewer; David A. Drubin; Carole Mathis; Dirk Weisensee; Dexter Pratt; Julia Hoeng; Manuel C. Peitsch (BMC Syst. Biol., 2012)

Building an R&D chemical registration system. - Elyette Martin; Aurélien Monge; Jacques-Antoine Duret; Federico Gualandi; Manuel C. Peitsch; Pavel Pospisil (J. Cheminformatics, 2012)

BEL Networks Derived from Qualitative Translations of BioNLP Shared Task Annotations. - Juliane Fluck; Alexander Klenner; Sumit Madan; Sam Ansari; Tamara Bobic; Julia Hoeng; Martin Hofmann-Apitius; Manuel C. Peitsch (BioNLP@ACL, 2013)

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge. - Adi L. Tarca; Mario Lauria; Michael Unger; Erhan Bilal; Stéphanie Boué; Kushal Kumar Dey; Julia Hoeng; Heinz Koeppl; Florian Martin 002; Pablo Meyer 001; Preetam Nandy; Raquel Norel; et al. (Bioinform., 2013)

CSEO - the Cigarette Smoke Exposure Ontology. - Erfan Younesi; Sam Ansari; Michaela Gündel; Shiva Ahmadi; Chris Coggins; Julia Hoeng; Martin Hofmann-Apitius; Manuel C. Peitsch (J. Biomed. Semant., 2014)

Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models. - Florian Martin 002; Alain Sewer; Marja Talikka; Yang Xiang; Julia Hoeng; Manuel C. Peitsch (BMC Bioinform., 2014)

The systems toxicology challenge: how to leverage omics data to predict mechanisms of toxicity? - Nikolai V. Ivanov; Carine Poussin; Stéphanie Boué; Florian Martin 002; Alain Sewer; Bjoern Titz; Manuel C. Peitsch; Julia Hoeng (BCB, 2015)

Reputation-Based Collaborative Network Biology. - Jean Binder; Stéphanie Boué; Anselmo Di Fabio; Brett Fields; William Hayes; Julia Hoeng; Jennifer Park; Manuel C. Peitsch (Pacific Symposium on Biocomputing, 2015)

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems. - Stéphanie Boué; Marja Talikka; Jurjen Willem Westra; William Hayes; Anselmo Di Fabio; Jennifer Park; Walter K. Schlage; Alain Sewer; Brett Fields; Sam Ansari; Florian Martin 002; Emilija Veljkovic; et al. (Database J. Biol. Databases Curation, 2015)

Construction of biological networks from unstructured information based on a semi-automated curation workflow. - Justyna Szostak; Sam Ansari; Sumit Madan; Juliane Fluck; Marja Talikka; Anita Iskandar; Hector De Leon; Martin Hofmann-Apitius; Manuel C. Peitsch; Julia Hoeng (Database J. Biol. Databases Curation, 2015)

A crowd-sourcing approach for the construction of species-specific cell signaling networks. - Erhan Bilal; Theodore Sakellaropoulos; Challenge Participants; Ioannis N. Melas; Dimitris E. Messinis; Vincenzo Belcastro; Kahn Rhrissorrakrai; Pablo Meyer 001; Raquel Norel; Anita Iskandar; Elise Blaese; John Jeremy Rice; et al. (Bioinform., 2015)

Where are we at regarding species translation? A review of the sbv IMPROVER challenge. - Julia Hoeng; Manuel C. Peitsch; Pablo Meyer 001; Igor Jurisica (Bioinform., 2015)

Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge. - Kahn Rhrissorrakrai; Vincenzo Belcastro; Erhan Bilal; Raquel Norel; Carine Poussin; Carole Mathis; Rémi H. J. Dulize; Nikolai V. Ivanov; Leonidas G. Alexopoulos; John Jeremy Rice; Manuel C. Peitsch; Gustavo Stolovitzky; et al. (Bioinform., 2015)

Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL). - Juliane Fluck; Sumit Madan; Sam Ansari; Alpha Tom Kodamullil; Reagon Karki; Majid Rastegar-Mojarad; Natalie L. Catlett; William Hayes; Justyna Szostak; Julia Hoeng; Manuel C. Peitsch (Database J. Biol. Databases Curation, 2016)

The BEL information extraction workflow (BELIEF): evaluation in the BioCreative V BEL and IAT track. - Sumit Madan; Sven Hodapp; Philipp Senger; Sam Ansari; Justyna Szostak; Julia Hoeng; Manuel C. Peitsch; Juliane Fluck (Database J. Biol. Databases Curation, 2016)

Supporting evidence-based analysis for modified risk tobacco products through a toxicology data-sharing infrastructure. - Stéphanie Boué; Thomas E. Exner; Samik Ghosh; Vincenzo Belcastro; Joh Dokler; David Page; Akash R. Boda; Filipe Bonjour; Barry J. Hardy; Patrick Vanscheeuwijck; Julia Hoeng; Manuel C. Peitsch (F1000Research, 2017)

Systems Toxicology Approach to Unravel Early Indicators of Squamous Cell Carcinoma Rate in Rat Nasal Epithelium Induced by Formaldehyde Exposure. - Florian Martin 002; Marja Talikka; Julia Hoeng; Manuel C. Peitsch (PACBB, 2019)

GladiaTOX: GLobal Assessment of Dose-IndicAtor in TOXicology. - Vincenzo Belcastro; Stephane Cano; Diego Marescotti; Stefano Acali; Carine Poussin; Ignacio Gonzalez-Suarez; Florian Martin 002; Filipe Bonjour; Nikolai V. Ivanov; Manuel C. Peitsch; Julia Hoeng (Bioinform., 2019)

NPA: an R package for computing network perturbation amplitudes using gene expression data and two-layer networks. - Florian Martin 002; Sylvain Gubian; Marja Talikka; Julia Hoeng; Manuel C. Peitsch (BMC Bioinform., 2019)