Julien Gobeill

78 papers A* 1Misc 3Journal 24Unranked 50

Year	Rank	Type	Title / Venue / Authors
2024	—	`conf`	Comparing Sequence-Based and Literature-Based Pathogenicity Scoring Methods for Human Variants. MIE Luc Mottin, Nona Naderi, Anaïs Mottaz, Pierre-André Michel, Lennart F. Johansson, Morris A. Swertz, Andrew Stubbs, Emilie Pasche, Julien Gobeill, Patrick Ruch
2024	—	`conf`	SIB Text-Mining at TREC PLABA 2024. TREC Luc Mottin, Anaïs Mottaz, Julien Knafou, Alexandre Flament, Julien Gobeill, Patrick Ruch
2023	J	`jnl`	Assessing the use of supplementary materials to improve genomic variant discovery. Database J. Biol. Databases Curation Emilie Pasche, Anaïs Mottaz, Julien Gobeill, Pierre-André Michel, Déborah Caucheteur, Nona Naderi, Patrick Ruch
2023	J	`jnl`	COVoc and COVTriage: novel resources to support literature triage. Bioinform. Déborah Caucheteur, Zoë May Pendlington, Paola Roncaglia, Julien Gobeill, Luc Mottin, Nicolas Matentzoglu, Donat Agosti, David Osumi-Sutherland, Helen E. Parkinson, Patrick Ruch
2023	J	`jnl`	Multilingual RECIST classification of radiology reports using supervised learning. Frontiers Digit. Health 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, Christian Lovis, Alexander B. Leichtle, Michael Kiessling, Olivier Michielin, Sylvain Pradervand, Vasiliki Foufi, Patrick Ruch
2022	—	`conf`	Classification of Oncology Treatment Responses from French Radiology Reports with Supervised Machine Learning. MIE Jean-Philippe Goldman, Luc Mottin, Jamil Zaghir, Daniel Keszthelyi, Belinda Lokaj, Hugues Turbé, Julien Gobeill, Patrick Ruch, Julien Ehrsam, Christian Lovis
2022	Misc	`conf`	Classification of oncology treatment responses from radiology reports with supervised machine learning. AMIA 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, Christian Lovis, Alexander B. Leichtle, Michael Kiessling, Olivier Michielin, Sylvain Pradervand, Vasiliki Foufi, Patrick Ruch
2022	J	`jnl`	Variomes: a high recall search engine to support the curation of genomic variants. Bioinform. Emilie Pasche, Anaïs Mottaz, Déborah Caucheteur, Julien Gobeill, Pierre-André Michel, Patrick Ruch
2021	—	`conf`	SIB Text Mining at TREC Clinical Trials 2021. TREC Déborah Caucheteur, Emilie Pasche, Luc Mottin, Anaïs Mottaz, Julien Gobeill, Patrick Ruch
2020	J	`jnl`	DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res. 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
2020	—	`conf`	Machine Learning for Automatic Encoding of French Electronic Medical Records: Is More Data Better? MIE Julien Gobeill, Patrick Ruch, Rodolphe Meyer
2020	J	`jnl`	SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. Nucleic Acids Res. Julien Gobeill, Déborah Caucheteur, Pierre-André Michel, Luc Mottin, Emilie Pasche, Patrick Ruch
2020	—	`conf`	SIB Text Mining at TREC Precision Medicine 2020. TREC Emilie Pasche, Déborah Caucheteur, Luc Mottin, Anaïs Mottaz, Julien Gobeill, Patrick Ruch
2020	—	`conf`	Text-Mining Services of the Swiss Variant Interpretation Platform for Oncology. MIE Déborah Caucheteur, Julien Gobeill, Anaïs Mottaz, Emilie Pasche, Pierre-André Michel, Luc Mottin, Daniel J. Stekhoven, Valérie Barbié, Patrick Ruch
2020	J	`jnl`	UPCLASS: a deep learning-based classifier for UniProtKB entry publications. Database J. Biol. Databases Curation Douglas Teodoro, Julien Knafou, Nona Naderi, Emilie Pasche, Julien Gobeill, Cecilia N. Arighi, Patrick Ruch
2019	—	`conf`	A Baseline Approach for Early Detection of Signs of Anorexia and Self-harm in Reddit Posts. CLEF (Working Notes) Nona Naderi, Julien Gobeill, Douglas Teodoro, Emilie Pasche, Patrick Ruch
2019	—	`conf`	Designing retrieval models to contrast precision-driven ad hoc search vs. recall-driven treatment extraction in Precision Medicine. TREC Déborah Caucheteur, Emilie Pasche, Julien Gobeill, Anaïs Mottaz, Luc Mottin, Patrick Ruch
2019	—	`conf`	Retrieving the Evidence of a Free Text Annotation in a Scientific Article: A Data Free Approach. CICLing (1) Julien Gobeill, Emilie Pasche, Patrick Ruch
2018	J	`jnl`	Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt. Database J. Biol. Databases Curation 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
2018	—	`conf`	Instance-based Learning for ICD10 Categorization. CLEF (Working Notes) Julien Gobeill, Patrick Ruch
2018	J	`jnl`	Overview of the BioCreative VI text-mining services for Kinome Curation Track. Database J. Biol. Databases Curation Julien Gobeill, Pascale Gaudet, Daniel Dopp, Adam Morrone, Indika Kahanda, Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu, Patrick Ruch
2017	—	`conf`	Customizing a Variant Annotation-Support Tool: an Inquiry into Probability Ranking Principles for TREC Precision Medicine. TREC Emilie Pasche, Julien Gobeill, Luc Mottin, Anaïs Mottaz, Douglas Teodoro, Paul Van Rijen, Patrick Ruch
2017	J	`jnl`	Global picture of OAI-PMH repositories through the analysis of 6 key open archive meta-catalogs. CoRR Arnaud Gaudinat, Jonas Beausire, Megan Fuss, Elisa Banfi, Julien Gobeill, Patrick Ruch
2017	J	`jnl`	Improving average ranking precision in user searches for biomedical research datasets. Database J. Biol. Databases Curation Douglas Teodoro, Luc Mottin, Julien Gobeill, Arnaud Gaudinat, Thérèse Vachon, Patrick Ruch
2017	J	`jnl`	Improving average ranking precision in user searches for biomedical research datasets. CoRR Douglas Teodoro, Luc Mottin, Julien Gobeill, Arnaud Gaudinat, Thérèse Vachon, Patrick Ruch
2017	J	`jnl`	Triage by ranking to support the curation of protein interactions. Database J. Biol. Databases Curation Luc Mottin, Emilie Pasche, Julien Gobeill, Valentine Rech de Laval, Anne Gleizes, Pierre-André Michel, Amos Bairoch, Pascale Gaudet, Patrick Ruch
2016	—	`conf`	BiTeM at CLEF eHealth Evaluation Lab 2016 Task 2: Multilingual Information Extraction. CLEF (Working Notes) Luc Mottin, Julien Gobeill, Anaïs Mottaz, Emilie Pasche, Arnaud Gaudinat, Patrick Ruch
2016	J	`jnl`	neXtA Database J. Biol. Databases Curation Luc Mottin, Julien Gobeill, Emilie Pasche, Pierre-André Michel, Isabelle Cusin, Pascale Gaudet, Patrick Ruch
2015	J	`jnl`	Deep Question Answering for protein annotation. Database J. Biol. Databases Curation Julien Gobeill, Arnaud Gaudinat, Emilie Pasche, Dina Vishnyakova, Pascale Gaudet, Amos Bairoch, Patrick Ruch
2015	—	`conf`	Exploiting incoming and outgoing citations for improving Information Retrieval in the TREC 2015 Clinical Decision Support Track. TREC Julien Gobeill, Arnaud Gaudinat, Patrick Ruch
2015	—	`conf`	Instance-Based Learning for Tweet Monitoring and Categorization. CLEF Julien Gobeill, Arnaud Gaudinat, Patrick Ruch
2014	J	`jnl`	Closing the loop: from paper to protein annotation using supervised Gene Ontology classification. Database J. Biol. Databases Curation Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch
2014	J	`jnl`	Development and tuning of an original search engine for patent libraries in medicinal chemistry. BMC Bioinform. Emilie Pasche, Julien Gobeill, Olivier Kreim, Fatma Oezdemir-Zaech, Thérèse Vachon, Christian Lovis, Patrick Ruch
2014	—	`conf`	Electronic Processing of Informed Consents in a Global Pharmaceutical Company Environment. MIE Dina Vishnyakova, Julien Gobeill, Fatma Oezdemir-Zaech, Olivier Kreim, Thérèse Vachon, Thierry Cladé, Xavier Haenning, Dmitri Mikhailov, Patrick Ruch
2014	—	`conf`	Full-texts representation with Medical Subject Headings, and co-citations network rerank- ing strategies for TREC 2014 Clinical Decision Support Track. TREC Julien Gobeill, Arnaud Gaudinat, Emilie Pasche, Patrick Ruch
2014	—	`conf`	Instance-based Learning for Tweet Categorization in CLEF RepLab 2014. CLEF (Working Notes) Julien Gobeill, Arnaud Gaudinat, Patrick Ruch
2014	J	`jnl`	Overview of the gene ontology task at BioCreative IV. Database J. Biol. Databases Curation 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, Anh Tuan Luu, Jung-Jae Kim, Jung-Hsien Chiang, Yu-De Chen, Chia-Jung Yang, Hongfang Liu, Dongqing Zhu, Yanpeng Li, Hong Yu, Ehsan Emadzadeh, Graciela Gonzalez, Jian-Ming Chen, Hong-Jie Dai, Zhiyong Lu
2013	J	`jnl`	Application of text-mining for updating protein post-translational modification annotation in UniProtKB. BMC Bioinform. Anne-Lise Veuthey, Alan J. Bridge, Julien Gobeill, Patrick Ruch, Johanna R. McEntyre, Lydie Bougueleret, Ioannis Xenarios
2013	—	`conf`	Khresmoi - Multilingual Semantic Search of Medical Text and Images. MedInfo Niraj Aswani, Thomas Beckers, Erich Birngruber, Célia Boyer, Andreas Burner, Jakub Bystron, Khalid Choukri, Sarah Cruchet, Hamish Cunningham, Jan Dedek, Ljiljana Dolamic, René Donner, Sebastian Dungs, Ivan Eggel, Antonio Foncubierta-Rodríguez, Norbert Fuhr, Adam Funk, Alba Garcia Seco de Herrera, Arnaud Gaudinat, Georgi Georgiev, Julien Gobeill, Lorraine Goeuriot, Paz Gomez, Robert Mark Greenwood, Manfred Gschwandtner, Allan Hanbury, Jan Hajic, Jaroslava Hlavácová, Markus Holzer, Gareth J. F. Jones, Blanca Jordan, Matthias Jordan, Klemens Kaderk, Franz Kainberger, Liadh Kelly, Sascha Kriewel, Marlene Kritz, Georg Langs, Nolan Lawson, Dimitrios Markonis, Iván Martínez, Vassil Momtchev, Alexandre Masselot, Hélène Mazo, Henning Müller, João R. M. Palotti, Pavel Pecina, Konstantin Pentchev, Deyan Peychev, Natalia Pletneva, Diana Pottecher, Angus Roberts, Patrick Ruch, Alexander Sachs, Matthias Samwald, Priscille Schneller, Veronika Stefanov, Miguel Angel Tinte, Zdenka Uresová, Alejandro Vargas, Dina Vishnyakova
2013	J	`jnl`	Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases. Database J. Biol. Databases Curation Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch
2013	—	`conf`	Use of Controlled Vocabularies to Improve Biomedical Information Retrieval Tasks. MedInfo Emilie Pasche, Julien Gobeill, Dina Vishnyakova, Patrick Ruch, Christian Lovis
2013	—	`conf`	Using a Question-Answering Approach in Machine Reading Task of Biomedical Texts about the Alzheimer Disease. CLEF (Working Notes) Dina Vishnyakova, Julien Gobeill, Patrick Ruch
2012	—	`conf`	A User-Friendly Tool for Medical-Related Patent Retrieval. EFMI-STC Emilie Pasche, Julien Gobeill, Douglas Teodoro, Arnaud Gaudinat, Dina Vishnyakova, Christian Lovis, Patrick Ruch
2012	—	`conf`	An advanced search engine for patent analytics in medicinal chemistry. MIE Emilie Pasche, Julien Gobeill, Douglas Teodoro, Arnaud Gaudinat, Dina Vishnyakova, Christian Lovis, Patrick Ruch
2012	—	`conf`	BiTeM Site Report for the Claims to Passage Task in CLEF-IP 2012. CLEF (Online Working Notes/Labs/Workshop) Julien Gobeill, Patrick Ruch
2012	—	`conf`	Classification and Prioritization of Biomedical Literature for the Comparative Toxicogenomics Database. MIE Dina Vishnyakova, Emilie Pasche, Julien Gobeill, Arnaud Gaudinat, Christian Lovis, Patrick Ruch
2011	—	`conf`	BiTeM Group Report for TREC Chemical IR Track 2011. TREC Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova
2011	—	`conf`	BiTeM Group Report for TREC Medical Records Track 2011. TREC Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova
2011	—	`conf`	Using Multimodal Mining to Drive Clinical Guidelines Development. MIE Emilie Pasche, Julien Gobeill, Douglas Teodoro, Dina Vishnyakova, Arnaud Gaudinat, Patrick Ruch, Christian Lovis
2010	—	`conf`	Automatic IPC Encoding and Novelty Tracking for Effective Patent Mining. NTCIR Douglas Teodoro, Emilie Pasche, Dina Vishnyakova, Julien Gobeill, Patrick Ruch, Christian Lovis
2010	—	`conf`	Automatic Prior Art Searching and Patent Encoding at CLEF-IP '10. CLEF (Notebook Papers/LABs/Workshops) Douglas Teodoro, Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch, Christian Lovis
2010	—	`conf`	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 Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova
2009	—	`conf`	Automatic Medical Knowledge Acquisition Using Question-Answering. MIE Emilie Pasche, Douglas Teodoro, Julien Gobeill, Patrick Ruch, Christian Lovis
2009	—	`conf`	Biomedical Data Management: A Proposal Framework. MIE Douglas Teodoro, Rémy Choquet, Emilie Pasche, Julien Gobeill, Christel Daniel, Patrick Ruch, Christian Lovis
2009	J	`jnl`	Comparing a rule-based versus statistical system for automatic categorization of MEDLINE documents according to biomedical specialty. J. Assoc. Inf. Sci. Technol. Susanne M. Humphrey, Aurélie Névéol, Allen C. Browne, Julien Gobeill, Patrick Ruch, Stéfan Jacques Darmoni
2009	—	`conf`	Exploring a Wide Range of Simple Pre and Post Processing Strategies for Patent Searching in CLEF IP 2009. CLEF (Working Notes) Julien Gobeill, Douglas Theodoro, Patrick Ruch
2009	Misc	`conf`	QA-driven Guidelines Generation for Bacteriotherapy. AMIA Emilie Pasche, Douglas Teodoro, Julien Gobeill, Patrick Ruch, Christian Lovis
2009	—	`conf`	Report on the TREC 2009 Experiments: Chemical IR Track. TREC Julien Gobeill, Douglas Teodoro, Emilie Pasche, Patrick Ruch
2009	—	`conf`	Simple Pre and Post Processing Strategies for Patent Searching in CLEF Intellectual Property Track 2009. CLEF (1) Julien Gobeill, Emilie Pasche, Douglas Teodoro, Patrick Ruch
2009	—	`conf`	Taking Benefit of Query and Document Expansion using MeSH Descriptors in Medical ImageCLEF 2009. CLEF (Working Notes) Julien Gobeill, Douglas Theodoro, Emilie Pasche, Patrick Ruch
2008	J	`jnl`	Automatic medical encoding with SNOMED categories. BMC Medical Informatics Decis. Mak. Patrick Ruch, Julien Gobeill, Christian Lovis, Antoine Geissbühler
2008	—	`conf`	First Participation of University and Hospitals of Geneva to Domain-Specific Track in CLEF 2008. CLEF (Working Notes) Julien Gobeill, Patrick Ruch
2008	Misc	`conf`	From Episodes of Care to Diagnosis Codes: Automatic Text Categorization for Medico-Economic Encoding. AMIA Patrick Ruch, Julien Gobeill, Imad Tbahriti, Antoine Geissbühler
2008	J	`jnl`	Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction. BMC Bioinform. Julien Gobeill, Imad Tbahriti, Frédéric Ehrler, Anaïs Mottaz, Anne-Lise Veuthey, Patrick Ruch
2008	—	`conf`	MedGIFT at ImageCLEF 2008. CLEF (Working Notes) Xin Zhou, Julien Gobeill, Henning Müller
2008	—	`conf`	Query and Document Expansion with Medical Subject Headings Terms at Medical Imageclef 2008. CLEF Julien Gobeill, Patrick Ruch, Xin Zhou
2008	—	`conf`	Text-only Cross-language Image Search at Medical ImageCLEF 2008. CLEF (Working Notes) Julien Gobeill, Patrick Ruch, Xin Zhou
2008	—	`conf`	The MedGIFT Group at ImageCLEF 2008. CLEF Xin Zhou, Julien Gobeill, Henning Müller
2007	—	`conf`	Recherche d'information et analyse bibliographique appliquées à la mise à jour automatique de Swiss-Prot. CORIA Imad Tbahriti, Anne-Lise Veuthey, Patrick Ruch, Julien Gobeill
2007	—	`conf`	University and Hospitals of Geneva Participating at ImageCLEF 2007. CLEF Xin Zhou, Julien Gobeill, Patrick Ruch, Henning Müller
2007	—	`conf`	University and Hospitals of Geneva at ImageCLEF 2007. CLEF (Working Notes) Xin Zhou, Julien Gobeill, Patrick Ruch, Henning Müller
2007	—	`conf`	Using Discourse Analysis to Improve Text Categorization in MEDLINE. MedInfo Patrick Ruch, Antoine Geissbühler, Julien Gobeill, Frédéric Lisacek, Imad Tbahriti, Anne-Lise Veuthey, Alan R. Aronson
2007	J	`jnl`	Using argumentation to extract key sentences from biomedical abstracts. Int. J. Medical Informatics Patrick Ruch, Célia Boyer, Christine Chichester, Imad Tbahriti, Antoine Geissbühler, Paul Fabry, Julien Gobeill, Violaine Pillet, Dietrich Rebholz-Schuhmann, Christian Lovis, Anne-Lise Veuthey
2007	—	`conf`	Vocabulary-Driven Passage Retrieval for Question-Answering in Genomics. TREC Julien Gobeill, Imad Tbahriti, Frédéric Ehrler, Patrick Ruch
2006	A*	`conf`	Argumentative Feedback: A Linguistically-Motivated Term Expansion for Information Retrieval. ACL Patrick Ruch, Imad Tbahriti, Julien Gobeill, Alan R. Aronson
2006	—	`conf`	Query and Document Translation by Automatic Text Categorization: A Simple Approach to Establish a Strong Textual Baseline for ImageCLEFmed 2006. CLEF (Working Notes) Julien Gobeill, Henning Müller, Patrick Ruch
2006	—	`conf`	Report on the TREC 2006 Experiment: Genomics Track. TREC Patrick Ruch, Frédéric Ehrler, Julien Gobeill, Imad Tbahriti, Antonio Jimeno-Yepes
2006	—	`conf`	Translation by Text Categorisation: Medical Image Retrieval in ImageCLEFmed 2006. CLEF Julien Gobeill, Henning Müller, Patrick Ruch