QA-driven Guidelines Generation for Bacteriotherapy. - Emilie Pasche; Douglas Teodoro; Julien Gobeill; Patrick Ruch; Christian Lovis (AMIA, 2009)

Simple Pre and Post Processing Strategies for Patent Searching in CLEF Intellectual Property Track 2009. - Julien Gobeill; Emilie Pasche; Douglas Teodoro; Patrick Ruch (CLEF (1), 2009)

Taking Benefit of Query and Document Expansion using MeSH Descriptors in Medical ImageCLEF 2009. - Julien Gobeill; Douglas Theodoro; Emilie Pasche; Patrick Ruch (CLEF (Working Notes), 2009)

Automatic Medical Knowledge Acquisition Using Question-Answering. - Emilie Pasche; Douglas Teodoro; Julien Gobeill; Patrick Ruch; Christian Lovis (MIE, 2009)

Biomedical Data Management: A Proposal Framework. - Douglas Teodoro; Rémy Choquet; Emilie Pasche; Julien Gobeill; Christel Daniel; Patrick Ruch; Christian Lovis (MIE, 2009)

Report on the TREC 2009 Experiments: Chemical IR Track. - Julien Gobeill; Douglas Teodoro; Emilie Pasche; Patrick Ruch (TREC, 2009)

Automatic Prior Art Searching and Patent Encoding at CLEF-IP '10. - Douglas Teodoro; Julien Gobeill; Emilie Pasche; Dina Vishnyakova; Patrick Ruch; Christian Lovis (CLEF (Notebook Papers/LABs/Workshops), 2010)

Un modèle de connaissances pour mesurer la qualité d'une source d'information. - Rémy Choquet; Samiha Qouiyd; Emilie Pasche; Christel Daniel; Omar Boussaïd; Marie-Christine Jaulent (IC, 2010)

Partage de Données Biomédicales sur le Web Sémantique. - Rémy Choquet; Douglas Teodoro; Giovanni Mels; Ariane Assélé Kama; Emilie Pasche; Patrick Ruch; Christian Lovis; Marie-Christine Jaulent (WSM@IC, 2010)

The Information Quality Triangle: A methodology to assess Clinical Information quality. - Rémy Choquet; Samiha Qouiyd; David Ouagne; Emilie Pasche; Christel Daniel; Omar Boussaïd; Marie-Christine Jaulent (MedInfo, 2010)

Automatic IPC Encoding and Novelty Tracking for Effective Patent Mining. - Douglas Teodoro; Emilie Pasche; Dina Vishnyakova; Julien Gobeill; Patrick Ruch; Christian Lovis (NTCIR, 2010)

BiTeM site Report for TREC Chemistry 2010: Impact of Citations Feeback for Patent Prior Art Search and Chemical Compounds Expansion for Ad Hoc Retrieval. - Julien Gobeill; Arnaud Gaudinat; Patrick Ruch; Emilie Pasche; Douglas Teodoro; Dina Vishnyakova (TREC, 2010)

Using Multimodal Mining to Drive Clinical Guidelines Development. - Emilie Pasche; Julien Gobeill; Douglas Teodoro; Dina Vishnyakova; Arnaud Gaudinat; Patrick Ruch; Christian Lovis (MIE, 2011)

Interoperability Driven Integration of Biomedical Data Sources. - Douglas Teodoro; Rémy Choquet; Daniel Schober; Giovanni Mels; Emilie Pasche; Patrick Ruch; Christian Lovis (MIE, 2011)

BiTeM Group Report for TREC Chemical IR Track 2011. - Julien Gobeill; Arnaud Gaudinat; Patrick Ruch; Emilie Pasche; Douglas Teodoro; Dina Vishnyakova (TREC, 2011)

BiTeM Group Report for TREC Medical Records Track 2011. - Julien Gobeill; Arnaud Gaudinat; Patrick Ruch; Emilie Pasche; Douglas Teodoro; Dina Vishnyakova (TREC, 2011)

A User-Friendly Tool for Medical-Related Patent Retrieval. - Emilie Pasche; Julien Gobeill; Douglas Teodoro; Arnaud Gaudinat; Dina Vishnyakova; Christian Lovis; Patrick Ruch (EFMI-STC, 2012)

Pathogens and Gene Product Normalization in the Biomedical Literature. - Dina Vishnyakova; Emilie Pasche; Douglas Teodoro; Christian Lovis; Patrick Ruch (EFMI-STC, 2012)

An advanced search engine for patent analytics in medicinal chemistry. - Emilie Pasche; Julien Gobeill; Douglas Teodoro; Arnaud Gaudinat; Dina Vishnyakova; Christian Lovis; Patrick Ruch (MIE, 2012)

Classification and Prioritization of Biomedical Literature for the Comparative Toxicogenomics Database. - Dina Vishnyakova; Emilie Pasche; Julien Gobeill; Arnaud Gaudinat; Christian Lovis; Patrick Ruch (MIE, 2012)

Using binary classification to prioritize and curate articles for the Comparative Toxicogenomics Database. - Dina Vishnyakova; Emilie Pasche; Patrick Ruch (Database J. Biol. Databases Curation, 2012)

Utilization of Ontology Look-Up Services in Information Retrieval for Biomedical Literature. - Dina Vishnyakova; Emilie Pasche; Christian Lovis; Patrick Ruch (EFMI-STC, 2013)

Use of Controlled Vocabularies to Improve Biomedical Information Retrieval Tasks. - Emilie Pasche; Julien Gobeill; Dina Vishnyakova; Patrick Ruch; Christian Lovis (MedInfo, 2013)

Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases. - Julien Gobeill; Emilie Pasche; Dina Vishnyakova; Patrick Ruch (Database J. Biol. Databases Curation, 2013)

DebugIT: Ontology-mediated Layered Data Integration for Real-time Antibiotics Resistance Surveillance. - Daniel Schober; Rémy Choquet; Kristof Depraetere; Frank Enders; Philipp Daumke; Marie-Christine Jaulent; Douglas Teodoro; Emilie Pasche; Christian Lovis; Martin Boeker (SWAT4LS, 2014)

Full-texts representation with Medical Subject Headings, and co-citations network rerank- ing strategies for TREC 2014 Clinical Decision Support Track. - Julien Gobeill; Arnaud Gaudinat; Emilie Pasche; Patrick Ruch (TREC, 2014)

Closing the loop: from paper to protein annotation using supervised Gene Ontology classification. - Julien Gobeill; Emilie Pasche; Dina Vishnyakova; Patrick Ruch (Database J. Biol. Databases Curation, 2014)

Development and tuning of an original search engine for patent libraries in medicinal chemistry. - Emilie Pasche; Julien Gobeill; Olivier Kreim; Fatma Oezdemir-Zaech; Thérèse Vachon; Christian Lovis; Patrick Ruch (BMC Bioinform., 2014)

Deep Question Answering for protein annotation. - Julien Gobeill; Arnaud Gaudinat; Emilie Pasche; Dina Vishnyakova; Pascale Gaudet; Amos Bairoch; Patrick Ruch (Database J. Biol. Databases Curation, 2015)

BiTeM at CLEF eHealth Evaluation Lab 2016 Task 2: Multilingual Information Extraction. - Luc Mottin; Julien Gobeill; Anaïs Mottaz; Emilie Pasche; Arnaud Gaudinat; Patrick Ruch (CLEF (Working Notes), 2016)

neXtA5: accelerating annotation of articles via automated approaches in neXtProt. - Luc Mottin; Julien Gobeill; Emilie Pasche; Pierre-André Michel; Isabelle Cusin; Pascale Gaudet; Patrick Ruch (Database J. Biol. Databases Curation, 2016)

Customizing a Variant Annotation-Support Tool: an Inquiry into Probability Ranking Principles for TREC Precision Medicine. - Emilie Pasche; Julien Gobeill; Luc Mottin; Anaïs Mottaz; Douglas Teodoro; Paul Van Rijen; Patrick Ruch (TREC, 2017)

Triage by ranking to support the curation of protein interactions. - Luc Mottin; Emilie Pasche; Julien Gobeill; Valentine Rech de Laval; Anne Gleizes; Pierre-André Michel; Amos Bairoch; Pascale Gaudet; Patrick Ruch (Database J. Biol. Databases Curation, 2017)

Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt. - Aurore Britan; Isabelle Cusin; Valérie Hinard; Luc Mottin; Emilie Pasche; Julien Gobeill; Valentine Rech de Laval; Anne Gleizes; Daniel Dinis Teixeira; Pierre-André Michel; Patrick Ruch; Pascale Gaudet (Database J. Biol. Databases Curation, 2018)

Retrieving the Evidence of a Free Text Annotation in a Scientific Article: A Data Free Approach. - Julien Gobeill; Emilie Pasche; Patrick Ruch (CICLing (1), 2019)

A Baseline Approach for Early Detection of Signs of Anorexia and Self-harm in Reddit Posts. - Nona Naderi; Julien Gobeill; Douglas Teodoro; Emilie Pasche; Patrick Ruch (CLEF (Working Notes), 2019)

Designing retrieval models to contrast precision-driven ad hoc search vs. recall-driven treatment extraction in Precision Medicine. - Déborah Caucheteur; Emilie Pasche; Julien Gobeill; Anaïs Mottaz; Luc Mottin; Patrick Ruch (TREC, 2019)

Text-Mining Services of the Swiss Variant Interpretation Platform for Oncology. - Déborah Caucheteur; Julien Gobeill; Anaïs Mottaz; Emilie Pasche; Pierre-André Michel; Luc Mottin; Daniel J. Stekhoven; Valérie Barbié; Patrick Ruch (MIE, 2020)

SIB Text Mining at TREC Precision Medicine 2020. - Emilie Pasche; Déborah Caucheteur; Luc Mottin; Anaïs Mottaz; Julien Gobeill; Patrick Ruch (TREC, 2020)

UPCLASS: a deep learning-based classifier for UniProtKB entry publications. - Douglas Teodoro; Julien Knafou; Nona Naderi; Emilie Pasche; Julien Gobeill; Cecilia N. Arighi; Patrick Ruch (Database J. Biol. Databases Curation, 2020)

SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. - Julien Gobeill; Déborah Caucheteur; Pierre-André Michel; Luc Mottin; Emilie Pasche; Patrick Ruch (Nucleic Acids Res., 2020)

DisProt: intrinsic protein disorder annotation in 2020. - András Hatos; Borbála Hajdu-Soltész; Alexander Miguel Monzon; Nicolas Palopoli; Lucía Álvarez; Burcu Aykaç Fas; Claudio Bassot; Guillermo I. Benítez; Martina Bevilacqua; Anastasia Chasapi; Lucía B. Chemes; Norman E. Davey; et al. (Nucleic Acids Res., 2020)

SIB Text Mining at TREC Clinical Trials 2021. - Déborah Caucheteur; Emilie Pasche; Luc Mottin; Anaïs Mottaz; Julien Gobeill; Patrick Ruch (TREC, 2021)

Designing an Optimal Expansion Method to Improve the Recall of a Genomic Variant Curation-Support Service. - Anaïs Mottaz; Emilie Pasche; Pierre-André Michel; Luc Mottin; Douglas Teodoro; Patrick Ruch (MIE, 2022)

Variomes: a high recall search engine to support the curation of genomic variants. - Emilie Pasche; Anaïs Mottaz; Déborah Caucheteur; Julien Gobeill; Pierre-André Michel; Patrick Ruch (Bioinform., 2022)

Assessing the use of supplementary materials to improve genomic variant discovery. - Emilie Pasche; Anaïs Mottaz; Julien Gobeill; Pierre-André Michel; Déborah Caucheteur; Nona Naderi; Patrick Ruch (Database J. Biol. Databases Curation, 2023)

Comparing Sequence-Based and Literature-Based Pathogenicity Scoring Methods for Human Variants. - Luc Mottin; Nona Naderi; Anaïs Mottaz; Pierre-André Michel; Lennart F. Johansson; Morris A. Swertz; Andrew Stubbs; Emilie Pasche; Julien Gobeill; Patrick Ruch (MIE, 2024)