Argumentative Feedback: A Linguistically-Motivated Term Expansion for Information Retrieval. - Patrick Ruch; Imad Tbahriti; Julien Gobeill; Alan R. Aronson (ACL, 2006)

Translation by Text Categorisation: Medical Image Retrieval in ImageCLEFmed 2006. - Julien Gobeill; Henning Müller; Patrick Ruch (CLEF, 2006)

Query and Document Translation by Automatic Text Categorization: A Simple Approach to Establish a Strong Textual Baseline for ImageCLEFmed 2006. - Julien Gobeill; Henning Müller; Patrick Ruch (CLEF (Working Notes), 2006)

Report on the TREC 2006 Experiment: Genomics Track. - Patrick Ruch; Frédéric Ehrler; Julien Gobeill; Imad Tbahriti; Antonio Jimeno-Yepes (TREC, 2006)

University and Hospitals of Geneva Participating at ImageCLEF 2007. - Xin Zhou 002; Julien Gobeill; Patrick Ruch; Henning Müller (CLEF, 2007)

University and Hospitals of Geneva at ImageCLEF 2007. - Xin Zhou 002; Julien Gobeill; Patrick Ruch; Henning Müller (CLEF (Working Notes), 2007)

Recherche d'information et analyse bibliographique appliquées à la mise à jour automatique de Swiss-Prot. - Imad Tbahriti; Anne-Lise Veuthey; Patrick Ruch; Julien Gobeill (CORIA, 2007)

Using Discourse Analysis to Improve Text Categorization in MEDLINE. - Patrick Ruch; Antoine Geissbühler; Julien Gobeill; Frédéric Lisacek; Imad Tbahriti; Anne-Lise Veuthey; Alan R. Aronson (MedInfo, 2007)

Vocabulary-Driven Passage Retrieval for Question-Answering in Genomics. - Julien Gobeill; Imad Tbahriti; Frédéric Ehrler; Patrick Ruch (TREC, 2007)

Using argumentation to extract key sentences from biomedical abstracts. - Patrick Ruch; Célia Boyer; Christine Chichester; Imad Tbahriti; Antoine Geissbühler; Paul Fabry; Julien Gobeill; Violaine Pillet; Dietrich Rebholz-Schuhmann; Christian Lovis; Anne-Lise Veuthey (Int. J. Medical Informatics, 2007)

From Episodes of Care to Diagnosis Codes: Automatic Text Categorization for Medico-Economic Encoding. - Patrick Ruch; Julien Gobeill; Imad Tbahriti; Antoine Geissbühler (AMIA, 2008)

First Participation of University and Hospitals of Geneva to Domain-Specific Track in CLEF 2008. - Julien Gobeill; Patrick Ruch (CLEF (Working Notes), 2008)

Query and Document Expansion with Medical Subject Headings Terms at Medical Imageclef 2008. - Julien Gobeill; Patrick Ruch; Xin Zhou 002 (CLEF, 2008)

Text-only Cross-language Image Search at Medical ImageCLEF 2008. - Julien Gobeill; Patrick Ruch; Xin Zhou 002 (CLEF (Working Notes), 2008)

The MedGIFT Group at ImageCLEF 2008. - Xin Zhou 002; Julien Gobeill; Henning Müller (CLEF, 2008)

MedGIFT at ImageCLEF 2008. - Xin Zhou 002; Julien Gobeill; Henning Müller (CLEF (Working Notes), 2008)

Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction. - Julien Gobeill; Imad Tbahriti; Frédéric Ehrler; Anaïs Mottaz; Anne-Lise Veuthey; Patrick Ruch (BMC Bioinform., 2008)

Automatic medical encoding with SNOMED categories. - Patrick Ruch; Julien Gobeill; Christian Lovis; Antoine Geissbühler (BMC Medical Informatics Decis. Mak., 2008)

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)

Exploring a Wide Range of Simple Pre and Post Processing Strategies for Patent Searching in CLEF IP 2009. - Julien Gobeill; Douglas Theodoro; 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)

Comparing a rule-based versus statistical system for automatic categorization of MEDLINE documents according to biomedical specialty. - Susanne M. Humphrey; Aurélie Névéol; Allen C. Browne; Julien Gobeill; Patrick Ruch; Stéfan Jacques Darmoni (J. Assoc. Inf. Sci. Technol., 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)

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)

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)

BiTeM Site Report for the Claims to Passage Task in CLEF-IP 2012. - Julien Gobeill; Patrick Ruch (CLEF (Online Working Notes/Labs/Workshop), 2012)

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)

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 a Question-Answering Approach in Machine Reading Task of Biomedical Texts about the Alzheimer Disease. - Dina Vishnyakova; Julien Gobeill; Patrick Ruch (CLEF (Working Notes), 2013)

Khresmoi - Multilingual Semantic Search of Medical Text and Images. - Niraj Aswani; Thomas Beckers 002; Erich Birngruber; Célia Boyer; Andreas Burner; Jakub Bystron; Khalid Choukri; Sarah Cruchet; Hamish Cunningham; Jan Dedek; Ljiljana Dolamic; René Donner; et al. (MedInfo, 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)

Application of text-mining for updating protein post-translational modification annotation in UniProtKB. - Anne-Lise Veuthey; Alan J. Bridge; Julien Gobeill; Patrick Ruch; Johanna R. McEntyre; Lydie Bougueleret; Ioannis Xenarios (BMC Bioinform., 2013)

Instance-based Learning for Tweet Categorization in CLEF RepLab 2014. - Julien Gobeill; Arnaud Gaudinat; Patrick Ruch (CLEF (Working Notes), 2014)

Electronic Processing of Informed Consents in a Global Pharmaceutical Company Environment. - Dina Vishnyakova; Julien Gobeill; Fatma Oezdemir-Zaech; Olivier Kreim; Thérèse Vachon; Thierry Cladé; Xavier Haenning; Dmitri Mikhailov; Patrick Ruch (MIE, 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)

Overview of the gene ontology task at BioCreative IV. - Yuqing Mao; Kimberly Van Auken; Donghui Li; Cecilia N. Arighi; Peter McQuilton; G. Thomas Hayman; Susan Tweedie; Mary L. Schaeffer; Stanley J. F. Laulederkind; Shur-Jen Wang; Julien Gobeill; Patrick Ruch; et al. (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)

Instance-Based Learning for Tweet Monitoring and Categorization. - Julien Gobeill; Arnaud Gaudinat; Patrick Ruch (CLEF, 2015)

Exploiting incoming and outgoing citations for improving Information Retrieval in the TREC 2015 Clinical Decision Support Track. - Julien Gobeill; Arnaud Gaudinat; Patrick Ruch (TREC, 2015)

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)

Improving average ranking precision in user searches for biomedical research datasets. - Douglas Teodoro; Luc Mottin; Julien Gobeill; Arnaud Gaudinat; Thérèse Vachon; Patrick Ruch (Database J. Biol. Databases Curation, 2017)

Global picture of OAI-PMH repositories through the analysis of 6 key open archive meta-catalogs. - Arnaud Gaudinat; Jonas Beausire; Megan Fuss; Elisa Banfi; Julien Gobeill; Patrick Ruch (CoRR, 2017)

Instance-based Learning for ICD10 Categorization. - Julien Gobeill; Patrick Ruch (CLEF (Working Notes), 2018)

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)

Overview of the BioCreative VI text-mining services for Kinome Curation Track. - Julien Gobeill; Pascale Gaudet; Daniel Dopp; Adam Morrone; Indika Kahanda; Yi-Yu Hsu; Chih-Hsuan Wei; Zhiyong Lu; Patrick Ruch (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)

Machine Learning for Automatic Encoding of French Electronic Medical Records: Is More Data Better? - Julien Gobeill; Patrick Ruch; Rodolphe Meyer (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)

Classification of oncology treatment responses from radiology reports with supervised machine learning. - Luc Mottin; Jean-Philippe Goldman; Christoph Jäggli; Rita Achermann; Julien Gobeill; Julien Knafou; Julien Ehrsam; Alexandre Wicky; Camille L. Gerard; Tanja Schwenk; Mélinda Charrier; Petros Tsantoulis; et al. (AMIA, 2022)

Classification of Oncology Treatment Responses from French Radiology Reports with Supervised Machine Learning. - Jean-Philippe Goldman; Luc Mottin; Jamil Zaghir; Daniel Keszthelyi; Belinda Lokaj; Hugues Turbé; Julien Gobeill; Patrick Ruch; Julien Ehrsam; Christian Lovis (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)

COVoc and COVTriage: novel resources to support literature triage. - Déborah Caucheteur; Zoë May Pendlington; Paola Roncaglia; Julien Gobeill; Luc Mottin; Nicolas Matentzoglu; Donat Agosti; David Osumi-Sutherland; Helen E. Parkinson; Patrick Ruch (Bioinform., 2023)

Multilingual RECIST classification of radiology reports using supervised learning. - Luc Mottin; Jean-Philippe Goldman; Christoph Jäggli; Rita Achermann; Julien Gobeill; Julien Knafou; Julien Ehrsam; Alexandre Wicky; Camille L. Gerard; Tanja Schwenk; Mélinda Charrier; Petros Tsantoulis; et al. (Frontiers Digit. Health, 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)