Marc Robinson-Rechavi

46 papers B 1Misc 1Journal 40Unranked 4

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	The BeeBiome data portal provides easy access to bee microbiome information. BMC Bioinform. Valentine Rech de Laval, Benjamin Dainat, Philippe Engel, Marc Robinson-Rechavi
2023	J	`jnl`	Boosting interoperability: towards an increasingly reusable bioinformatics knowledge base. CoRR Tarcisio Mendes de Farias, Julien Wollbrett, Marc Robinson-Rechavi, Frederic B. Bastian
2022	J	`jnl`	Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation. Distributed Parallel Databases Ana Claudia Sima, Tarcisio Mendes de Farias, Maria Anisimova, Christophe Dessimoz, Marc Robinson-Rechavi, Erich Zbinden, Kurt Stockinger
2022	J	`jnl`	Rhythmicity is linked to expression cost at the protein level but to expression precision at the mRNA level. PLoS Comput. Biol. David Laloum, Marc Robinson-Rechavi
2021	B	`conf`	Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data. SSDBM Ana Claudia Sima, Tarcisio Mendes de Farias, Maria Anisimova, Christophe Dessimoz, Marc Robinson-Rechavi, Erich Zbinden, Kurt Stockinger
2021	J	`jnl`	Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data. CoRR Ana Claudia Sima, Tarcisio Mendes de Farias, Maria Anisimova, Christophe Dessimoz, Marc Robinson-Rechavi, Erich Zbinden, Kurt Stockinger
2021	J	`jnl`	OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. Bioinform. Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz
2021	J	`jnl`	The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. Nucleic Acids Res. Frederic B. Bastian, Julien Roux, Anne Niknejad, Aurélie Comte, Sara S. Fonseca Costa, Tarcisio Mendes de Farias, Sébastien Moretti, Gilles Parmentier, Valentine Rech de Laval, Marta Rosikiewicz, Julien Wollbrett, Amina Echchiki, Angélique Escoriza, Walid H. Gharib, Mar Gonzales-Porta, Yohan Jarosz, Balazs Laurenczy, Philippe Moret, Emilie Person, Patrick Roelli, Komal Sanjeev, Mathieu Seppey, Marc Robinson-Rechavi
2020	J	`jnl`	Methods detecting rhythmic gene expression are biologically relevant only for strong signal. PLoS Comput. Biol. David Laloum, Marc Robinson-Rechavi
2020	J	`jnl`	Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. Genom. Proteom. Bioinform. Qingyu Chen, Ramona Britto, Ivan Erill, Constance J. Jeffery, Arthur Liberzon, Michele Magrane, Jun-ichi Onami, Marc Robinson-Rechavi, Jana Sponarova, Justin Zobel, Karin Verspoor
2019	J	`jnl`	Cross-species functional modules link proteostasis to human normal aging. PLoS Comput. Biol. Andrea Komljenovic, Hao Li, Vincenzo Sorrentino, Zoltán Kutalik, Johan Auwerx, Marc Robinson-Rechavi
2019	J	`jnl`	Enabling semantic queries across federated bioinformatics databases. Database J. Biol. Databases Curation Ana Claudia Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz
2019	Misc	`conf`	OncoMX: an Integrated Cancer Mutation and Expression Knowledgebase for Biomarker Evaluation and Discovery. AMIA Amanda Bell, Raja Mazumder, Daniel J. Crichton, Vijay K. Shanker, Frédéric B. Bastian, Hayley Dingerdissen, Samir Gupta, Evan Holmes, Robel Y. Kahsay, Heather L. Kincaid, A. S. M. Ashique Mahmood, Marc Robinson-Rechavi, Stephanie S. Singleton
2017	J	`jnl`	A benchmark of gene expression tissue-specificity metrics. Briefings Bioinform. Nadezda Kryuchkova-Mostacci, Marc Robinson-Rechavi
2017	J	`jnl`	State aggregation for fast likelihood computations in molecular evolution. Bioinform. Iakov I. Davydov, Marc Robinson-Rechavi, Nicolas Salamin
2016	J	`jnl`	BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests. F1000Research Andrea Komljenovic, Julien Roux, Marc Robinson-Rechavi, Frederic B. Bastian
2016	J	`jnl`	IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. Bioinform. Marta Rosikiewicz, Marc Robinson-Rechavi
2016	J	`jnl`	Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs. PLoS Comput. Biol. Nadezda Kryuchkova-Mostacci, Marc Robinson-Rechavi
2015	J	`jnl`	The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database J. Biol. Databases Curation Frederic B. Bastian, Marcus C. Chibucos, Pascale Gaudet, Michelle G. Giglio, Gemma L. Holliday, Hong Huang, Suzanna E. Lewis, Anne Niknejad, Sandra E. Orchard, Sylvain Poux, Nives Skunca, Marc Robinson-Rechavi
2014	J	`jnl`	Big data and other challenges in the quest for orthologs. Bioinform. Erik L. L. Sonnhammer, Toni Gabaldón, Alan W. Sousa da Silva, Maria Jesus Martin, Marc Robinson-Rechavi, Brigitte Boeckmann, Paul D. Thomas, Christophe Dessimoz, Quest for Orthologs Consortium
2014	J	`jnl`	Determinants of protein evolutionary rates in light of ENCODE functional genomics. BMC Bioinform. Nadezda Kryuchkova, Marc Robinson-Rechavi
2014	J	`jnl`	IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. Bioinform. Marta Rosikiewicz, Marc Robinson-Rechavi
2014	J	`jnl`	Optimization strategies for fast detection of positive selection on phylogenetic trees. Bioinform. Mario Valle, Hannes Schabauer, Christoph Pacher, Heinz Stockinger, Alexandros Stamatakis, Marc Robinson-Rechavi, Nicolas Salamin
2014	J	`jnl`	Selectome update: quality control and computational improvements to a database of positive selection. Nucleic Acids Res. Sébastien Moretti, Balazs Laurenczy, Walid H. Gharib, Briséïs Castella, Arnold Kuzniar, Hannes Schabauer, Romain A. Studer, Mario Valle, Nicolas Salamin, Heinz Stockinger, Marc Robinson-Rechavi
2014	J	`jnl`	Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J. Biomed. Semant. Melissa A. Haendel, James P. Balhoff, Frederic B. Bastian, David C. Blackburn, Judith A. Blake, Yvonne M. Bradford, Aurélie Comte, Wasila M. Dahdul, Thomas Dececchi, Robert E. Druzinsky, Terry F. Hayamizu, Nizar Ibrahim, Suzanna E. Lewis, Paula M. Mabee, Anne Niknejad, Marc Robinson-Rechavi, Paul C. Sereno, Christopher J. Mungall
2013	J	`jnl`	DATABASE, Database J. Biol. Databases Curation Pascale Gaudet, Monica C. Munoz-Torres, Marc Robinson-Rechavi, Teresa K. Attwood, Alex Bateman, J. Michael Cherry, Renate Kania, Claire O'Donovan, Chisato Yamasaki
2013	J	`jnl`	Uncovering hidden duplicated content in public transcriptomics data. Database J. Biol. Databases Curation Marta Rosikiewicz, Aurélie Comte, Anne Niknejad, Marc Robinson-Rechavi, Frederic B. Bastian
2012	J	`jnl`	Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human. Bioinform. Barbara Piasecka, Marc Robinson-Rechavi, Sven Bergmann
2012	J	`jnl`	Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. Database J. Biol. Databases Curation Pascale Gaudet, Cecilia N. Arighi, Frederic B. Bastian, Alex Bateman, Judith A. Blake, J. Michael Cherry, Peter D'Eustachio, Robert D. Finn, Michelle G. Giglio, Lynette Hirschman, Renate Kania, William Klimke, Maria Jesus Martin, Ilene Karsch-Mizrachi, Monica C. Munoz-Torres, Darren A. Natale, Claire O'Donovan, B. F. Francis Ouellette, Kim D. Pruitt, Marc Robinson-Rechavi, Susanna-Assunta Sansone, Paul N. Schofield, Granger G. Sutton, Kimberly Van Auken, Sona Vasudevan, Cathy H. Wu, Jasmine Young, Raja Mazumder
2012	J	`jnl`	Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs. PLoS Comput. Biol. Adrian M. Altenhoff, Romain A. Studer, Marc Robinson-Rechavi, Christophe Dessimoz
2012	—	`conf`	SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model. IPDPS Workshops Hannes Schabauer, Mario Valle, Christoph Pacher, Heinz Stockinger, Alexandros Stamatakis, Marc Robinson-Rechavi, Ziheng Yang, Nicolas Salamin
2012	J	`jnl`	gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution CoRR Sébastien Moretti, Riccardo Murri, Sergio Maffioletti, Arnold Kuzniar, Briséïs Castella, Nicolas Salamin, Marc Robinson-Rechavi, Heinz Stockinger
2012	—	`conf`	gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution. HealthGrid Sébastien Moretti, Riccardo Murri, Sergio Maffioletti, Arnold Kuzniar, Briséïs Castella, Nicolas Salamin, Marc Robinson-Rechavi, Heinz Stockinger
2012	J	`jnl`	vHOG, a multispecies vertebrate ontology of homologous organs groups. Bioinform. Anne Niknejad, Aurélie Comte, Gilles Parmentier, Julien Roux, Frederic B. Bastian, Marc Robinson-Rechavi
2011	J	`jnl`	Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. Briefings Bioinform. Brigitte Boeckmann, Marc Robinson-Rechavi, Ioannis Xenarios, Christophe Dessimoz
2011	J	`jnl`	Meta-analysis of estrogen response in MCF-7 distinguishes early target genes involved in signaling and cell proliferation from later target genes involved in cell cycle and DNA repair. BMC Syst. Biol. Vidhya Jagannathan, Marc Robinson-Rechavi
2011	J	`jnl`	When orthologs diverge between human and mouse. Briefings Bioinform. Walid H. Gharib, Marc Robinson-Rechavi
2010	J	`jnl`	Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy. Bioinform. Gilles Parmentier, Frederic B. Bastian, Marc Robinson-Rechavi
2010	—	`conf`	Phylogenetic Code in the Cloud - Can it Meet the Expectations? HealthGrid Adam Kraut, Sébastien Moretti, Marc Robinson-Rechavi, Heinz Stockinger, Dean Flanders
2009	J	`jnl`	Selectome: a database of positive selection. Nucleic Acids Res. Estelle Proux-Wéra, Romain A. Studer, Sébastien Moretti, Marc Robinson-Rechavi
2008	—	`conf`	Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species. DILS Frederic B. Bastian, Gilles Parmentier, Julien Roux, Sébastien Moretti, Vincent Laudet, Marc Robinson-Rechavi
2007	J	`jnl`	A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. BMC Syst. Biol. Grigoris D. Amoutzias, Elgar Pichler, Nina Mian, David De Graaf, Anastasia Imsiridou, Marc Robinson-Rechavi, Erich Bornberg-Bauer, David L. Robertson, Stephen G. Oliver
2004	J	`jnl`	Update of NUREBASE: nuclear hormone receptor functional genomics. Nucleic Acids Res. David Ruau, Jorge Duarte, Tarik Ourjdal, Guy Perrière, Vincent Laudet, Marc Robinson-Rechavi
2002	J	`jnl`	NUREBASE: database of nuclear hormone receptors. Nucleic Acids Res. Jorge Duarte, Guy Perrière, Vincent Laudet, Marc Robinson-Rechavi
2000	J	`jnl`	RRTree: Relative-Rate Tests between groups of sequences on a phylogenetic tree. Bioinform. Marc Robinson-Rechavi, Dorothée Huchon
1999	J	`jnl`	JaDis: computing distances between nucleic acid sequences. Bioinform. Isabelle Gonçalves, Marc Robinson-Rechavi, Guy Perrière, Dominique Mouchiroud