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2020 – today
- 2023
[j12]Emilie Pasche
, Anaïs Mottaz, Julien Gobeill, Pierre-André Michel, Déborah Caucheteur, Nona Naderi, Patrick Ruch:
Assessing the use of supplementary materials to improve genomic variant discovery. Database J. Biol. Databases Curation 2023 (2023)- 2022
- [c33]Anaïs Mottaz, Emilie Pasche, Pierre-André Michel, Luc Mottin, Douglas Teodoro, Patrick Ruch:
Designing an Optimal Expansion Method to Improve the Recall of a Genomic Variant Curation-Support Service. MIE 2022: 839-843 - 2021
- [c32]Déborah Caucheteur, Emilie Pasche, Luc Mottin, Anaïs Mottaz, Julien Gobeill, Patrick Ruch:
SIB Text Mining at TREC Clinical Trials 2021. TREC 2021 - 2020
- [j11]Douglas Teodoro, Julien Knafou, Nona Naderi, Emilie Pasche, Julien Gobeill, Cecilia N. Arighi, Patrick Ruch:
UPCLASS: a deep learning-based classifier for UniProtKB entry publications. Database J. Biol. Databases Curation 2020 (2020) - [j10]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, Radoslav Davidovic, A. Keith Dunker, Arne Elofsson, Julien Gobeill, Nicolás S. González Foutel, Govindarajan Sudha, Mainak Guharoy, Tamás Horváth, Valentin Iglesias, Andrey V. Kajava, Orsolya P. Kovács, John Lamb, Matteo Lambrughi, Tamas Lazar, Jeremy Y. Leclercq, Emanuela Leonardi, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Emiliano Maiani, José A. Manso, Cristina Marino Buslje, Elizabeth Martínez-Pérez, Bálint Mészáros, Ivan Micetic, Giovanni Minervini, Nikoletta Murvai, Marco Necci, Christos A. Ouzounis, Mátyás Pajkos, Lisanna Paladin, Rita Pancsa, Elena Papaleo, Gustavo D. Parisi, Emilie Pasche, Pedro J. Barbosa Pereira, Vasilis J. Promponas, Jordi Pujols, Federica Quaglia, Patrick Ruch, Marco Salvatore, Éva Schád, Beáta Szabó, Tamás Szaniszló, Stella Tamana, Ágnes Tantos, Nevena Veljkovic, Salvador Ventura, Wim F. Vranken, Zsuzsanna Dosztányi, Peter Tompa, Silvio C. E. Tosatto, Damiano Piovesan:
DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res. 48(Database-Issue): D269-D276 (2020) - [j9]Julien Gobeill, Déborah Caucheteur, Pierre-André Michel, Luc Mottin, Emilie Pasche, Patrick Ruch:
SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. Nucleic Acids Res. 48(Webserver-Issue): W12-W16 (2020) - [c31]Déborah Caucheteur, Julien Gobeill, Anaïs Mottaz, Emilie Pasche, Pierre-André Michel, Luc Mottin, Daniel J. Stekhoven, Valérie Barbié, Patrick Ruch:
Text-Mining Services of the Swiss Variant Interpretation Platform for Oncology. MIE 2020: 884-888 - [c30]Emilie Pasche, Déborah Caucheteur, Luc Mottin, Anaïs Mottaz, Julien Gobeill, Patrick Ruch:
SIB Text Mining at TREC Precision Medicine 2020. TREC 2020
2010 – 2019
- 2019
- [c29]Julien Gobeill, Emilie Pasche, Patrick Ruch:
Retrieving the Evidence of a Free Text Annotation in a Scientific Article: A Data Free Approach. CICLing (1) 2019: 233-246 - [c28]Nona Naderi, Julien Gobeill, Douglas Teodoro, Emilie Pasche, Patrick Ruch:
A Baseline Approach for Early Detection of Signs of Anorexia and Self-harm in Reddit Posts. CLEF (Working Notes) 2019 - [c27]Déborah Caucheteur, Emilie Pasche, Julien Gobeill, Anaïs Mottaz, Luc Mottin, Patrick Ruch:
Designing retrieval models to contrast precision-driven ad hoc search vs. recall-driven treatment extraction in Precision Medicine. TREC 2019 - 2018
- [j8]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:
Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt. Database J. Biol. Databases Curation 2018: bay129 (2018) - 2017
- [j7]Luc Mottin, Emilie Pasche, Julien Gobeill, Valentine Rech de Laval, Anne Gleizes, Pierre-André Michel, Amos Bairoch, Pascale Gaudet, Patrick Ruch:
Triage by ranking to support the curation of protein interactions. Database J. Biol. Databases Curation 2017: bax040 (2017) - [c26]Emilie Pasche, Julien Gobeill, Luc Mottin, Anaïs Mottaz, Douglas Teodoro, Paul Van Rijen, Patrick Ruch:
Customizing a Variant Annotation-Support Tool: an Inquiry into Probability Ranking Principles for TREC Precision Medicine. TREC 2017 - 2016
- [j6]Luc Mottin, Julien Gobeill, Emilie Pasche, Pierre-André Michel, Isabelle Cusin, Pascale Gaudet, Patrick Ruch:
neXtA5: accelerating annotation of articles via automated approaches in neXtProt. Database J. Biol. Databases Curation 2016 (2016) - [c25]Luc Mottin, Julien Gobeill, Anaïs Mottaz, Emilie Pasche, Arnaud Gaudinat, Patrick Ruch:
BiTeM at CLEF eHealth Evaluation Lab 2016 Task 2: Multilingual Information Extraction. CLEF (Working Notes) 2016: 94-102 - 2015
- [j5]Julien Gobeill, Arnaud Gaudinat, Emilie Pasche, Dina Vishnyakova, Pascale Gaudet, Amos Bairoch, Patrick Ruch:
Deep Question Answering for protein annotation. Database J. Biol. Databases Curation 2015 (2015) - 2014
- [j4]Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch:
Closing the loop: from paper to protein annotation using supervised Gene Ontology classification. Database J. Biol. Databases Curation 2014 (2014) - [j3]Emilie Pasche, Julien Gobeill, Olivier Kreim, Fatma Oezdemir-Zaech, Thérèse Vachon, Christian Lovis, Patrick Ruch:
Development and tuning of an original search engine for patent libraries in medicinal chemistry. BMC Bioinform. 15(S-1): S15 (2014) - [c24]Daniel Schober, Rémy Choquet, Kristof Depraetere, Frank Enders, Philipp Daumke, Marie-Christine Jaulent, Douglas Teodoro, Emilie Pasche, Christian Lovis, Martin Boeker:
DebugIT: Ontology-mediated Layered Data Integration for Real-time Antibiotics Resistance Surveillance. SWAT4LS 2014 - [c23]Julien Gobeill, Arnaud Gaudinat, Emilie Pasche, Patrick Ruch:
Full-texts representation with Medical Subject Headings, and co-citations network rerank- ing strategies for TREC 2014 Clinical Decision Support Track. TREC 2014 - 2013
- [j2]Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch:
Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases. Database J. Biol. Databases Curation 2013 (2013) - [c22]Dina Vishnyakova, Emilie Pasche, Christian Lovis, Patrick Ruch:
Utilization of Ontology Look-Up Services in Information Retrieval for Biomedical Literature. EFMI-STC 2013: 155-159 - [c21]Emilie Pasche, Julien Gobeill, Dina Vishnyakova, Patrick Ruch, Christian Lovis:
Use of Controlled Vocabularies to Improve Biomedical Information Retrieval Tasks. MedInfo 2013: 1068 - 2012
- [j1]Dina Vishnyakova, Emilie Pasche, Patrick Ruch:
Using binary classification to prioritize and curate articles for the Comparative Toxicogenomics Database. Database J. Biol. Databases Curation 2012 (2012) - [c20]Dina Vishnyakova, Emilie Pasche, Douglas Teodoro, Christian Lovis, Patrick Ruch:
Pathogens and Gene Product Normalization in the Biomedical Literature. EFMI-STC 2012: 89-93 - [c19]Emilie Pasche, Julien Gobeill, Douglas Teodoro, Arnaud Gaudinat, Dina Vishnyakova, Christian Lovis, Patrick Ruch:
A User-Friendly Tool for Medical-Related Patent Retrieval. EFMI-STC 2012: 121-125 - [c18]Emilie Pasche, Julien Gobeill, Douglas Teodoro, Arnaud Gaudinat, Dina Vishnyakova, Christian Lovis, Patrick Ruch:
An advanced search engine for patent analytics in medicinal chemistry. MIE 2012: 204-209 - [c17]Dina Vishnyakova, Emilie Pasche, Julien Gobeill, Arnaud Gaudinat, Christian Lovis, Patrick Ruch:
Classification and Prioritization of Biomedical Literature for the Comparative Toxicogenomics Database. MIE 2012: 210-214 - 2011
- [c16]Douglas Teodoro, Rémy Choquet, Daniel Schober, Giovanni Mels, Emilie Pasche, Patrick Ruch, Christian Lovis:
Interoperability Driven Integration of Biomedical Data Sources. MIE 2011: 185-189 - [c15]Emilie Pasche, Julien Gobeill, Douglas Teodoro, Dina Vishnyakova, Arnaud Gaudinat, Patrick Ruch, Christian Lovis:
Using Multimodal Mining to Drive Clinical Guidelines Development. MIE 2011: 477-481 - [c14]Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova:
BiTeM Group Report for TREC Chemical IR Track 2011. TREC 2011 - [c13]Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova:
BiTeM Group Report for TREC Medical Records Track 2011. TREC 2011 - 2010
- [c12]Douglas Teodoro, Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch, Christian Lovis:
Automatic Prior Art Searching and Patent Encoding at CLEF-IP '10. CLEF (Notebook Papers/LABs/Workshops) 2010 - [c11]Rémy Choquet, Douglas Teodoro, Giovanni Mels, Ariane Assélé Kama, Emilie Pasche, Patrick Ruch, Christian Lovis, Marie-Christine Jaulent:
Partage de Données Biomédicales sur le Web Sémantique. WSM@IC 2010: 3-12 - [c10]Rémy Choquet, Samiha Qouiyd, Emilie Pasche, Christel Daniel, Omar Boussaïd, Marie-Christine Jaulent:
Un modèle de connaissances pour mesurer la qualité d'une source d'information. IC 2010: 93-104 - [c9]Rémy Choquet, Samiha Qouiyd, David Ouagne, Emilie Pasche, Christel Daniel, Omar Boussaïd, Marie-Christine Jaulent:
The Information Quality Triangle: A methodology to assess Clinical Information quality. MedInfo 2010: 699-703 - [c8]Douglas Teodoro, Emilie Pasche, Dina Vishnyakova, Julien Gobeill, Patrick Ruch, Christian Lovis:
Automatic IPC Encoding and Novelty Tracking for Effective Patent Mining. NTCIR 2010: 309-317 - [c7]Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova:
BiTeM site Report for TREC Chemistry 2010: Impact of Citations Feeback for Patent Prior Art Search and Chemical Compounds Expansion for Ad Hoc Retrieval. TREC 2010
2000 – 2009
- 2009
- [c6]Emilie Pasche, Douglas Teodoro, Julien Gobeill, Patrick Ruch, Christian Lovis:
QA-driven Guidelines Generation for Bacteriotherapy. AMIA 2009 - [c5]Julien Gobeill, Emilie Pasche, Douglas Teodoro, Patrick Ruch:
Simple Pre and Post Processing Strategies for Patent Searching in CLEF Intellectual Property Track 2009. CLEF (1) 2009: 444-451 - [c4]Julien Gobeill, Douglas Theodoro, Emilie Pasche, Patrick Ruch:
Taking Benefit of Query and Document Expansion using MeSH Descriptors in Medical ImageCLEF 2009. CLEF (Working Notes) 2009 - [c3]Douglas Teodoro, Rémy Choquet, Emilie Pasche, Julien Gobeill, Christel Daniel, Patrick Ruch, Christian Lovis:
Biomedical Data Management: A Proposal Framework. MIE 2009: 175-179 - [c2]Emilie Pasche, Douglas Teodoro, Julien Gobeill, Patrick Ruch, Christian Lovis:
Automatic Medical Knowledge Acquisition Using Question-Answering. MIE 2009: 569-573 - [c1]Julien Gobeill, Douglas Teodoro, Emilie Pasche, Patrick Ruch:
Report on the TREC 2009 Experiments: Chemical IR Track. TREC 2009
Coauthor Index
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