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ORCIDMarc Robinson-Rechavi
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- affiliation: University of Lausanne, Department of Ecology and Evolution, Switzerland
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Journal Articles
- 2022
[j35]Ana Claudia Sima, Tarcisio Mendes de Farias, Maria Anisimova
, Christophe Dessimoz, Marc Robinson-Rechavi, Erich Zbinden, Kurt Stockinger:
Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation. Distributed Parallel Databases 40(2-3): 409-440 (2022)- [j34]David Laloum, Marc Robinson-Rechavi:
Rhythmicity is linked to expression cost at the protein level but to expression precision at the mRNA level. PLoS Comput. Biol. 18(9): 1010399 (2022) - 2021
- [j33]Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz:
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. Bioinform. 37(18): 2866-2873 (2021) - [j32]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:
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. Nucleic Acids Res. 49(Database-Issue): D831-D847 (2021) - 2020
- [j31]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:
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. Genom. Proteom. Bioinform. 18(2): 91-103 (2020) - [j30]David Laloum, Marc Robinson-Rechavi:
Methods detecting rhythmic gene expression are biologically relevant only for strong signal. PLoS Comput. Biol. 16(3) (2020) - 2019
- [j29]Ana Claudia Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz:
Enabling semantic queries across federated bioinformatics databases. Database J. Biol. Databases Curation 2019: baz106 (2019) - [j28]Andrea Komljenovic, Hao Li, Vincenzo Sorrentino, Zoltán Kutalik, Johan Auwerx, Marc Robinson-Rechavi:
Cross-species functional modules link proteostasis to human normal aging. PLoS Comput. Biol. 15(7) (2019) - 2017
- [j27]Nadezda Kryuchkova-Mostacci, Marc Robinson-Rechavi:
A benchmark of gene expression tissue-specificity metrics. Briefings Bioinform. 18(2): 205-214 (2017) - [j26]Iakov I. Davydov, Marc Robinson-Rechavi, Nicolas Salamin:
State aggregation for fast likelihood computations in molecular evolution. Bioinform. 33(3): 354-362 (2017) - 2016
- [j25]Marta Rosikiewicz, Marc Robinson-Rechavi:
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. Bioinform. 32(16): 2565 (2016) - [j24]Nadezda Kryuchkova-Mostacci, Marc Robinson-Rechavi:
Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs. PLoS Comput. Biol. 12(12) (2016) - 2015
- [j23]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:
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database J. Biol. Databases Curation 2015 (2015) - 2014
- [j22]Mario Valle, Hannes Schabauer, Christoph Pacher, Heinz Stockinger, Alexandros Stamatakis, Marc Robinson-Rechavi, Nicolas Salamin:
Optimization strategies for fast detection of positive selection on phylogenetic trees. Bioinform. 30(8): 1129-1137 (2014) - [j21]Marta Rosikiewicz, Marc Robinson-Rechavi:
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. Bioinform. 30(10): 1392-1399 (2014) - [j20]Erik L. L. Sonnhammer, Toni Gabaldón, Alan W. Sousa da Silva, Maria Jesus Martin, Marc Robinson-Rechavi, Brigitte Boeckmann, Paul D. Thomas, Christophe Dessimoz, The Quest for Orthologs Consortium:
Big data and other challenges in the quest for orthologs. Bioinform. 30(21): 2993-2998 (2014) - [j19]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:
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J. Biomed. Semant. 5: 21 (2014) - [j18]Nadezda Kryuchkova, Marc Robinson-Rechavi:
Determinants of protein evolutionary rates in light of ENCODE functional genomics. BMC Bioinform. 15(S-3): A9 (2014) - [j17]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:
Selectome update: quality control and computational improvements to a database of positive selection. Nucleic Acids Res. 42(Database-Issue): 917-921 (2014) - 2013
- [j16]Pascale Gaudet, Monica C. Munoz-Torres, Marc Robinson-Rechavi, Teresa K. Attwood, Alex Bateman, J. Michael Cherry, Renate Kania, Claire O'Donovan, Chisato Yamasaki:
DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration. Database J. Biol. Databases Curation 2013 (2013) - [j15]Marta Rosikiewicz, Aurélie Comte, Anne Niknejad, Marc Robinson-Rechavi, Frederic B. Bastian:
Uncovering hidden duplicated content in public transcriptomics data. Database J. Biol. Databases Curation 2013 (2013) - 2012
- [j14]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:
Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. Database J. Biol. Databases Curation 2012 (2012) - [j13]Anne Niknejad, Aurélie Comte, Gilles Parmentier, Julien Roux, Frederic B. Bastian, Marc Robinson-Rechavi:
vHOG, a multispecies vertebrate ontology of homologous organs groups. Bioinform. 28(7): 1017-1020 (2012) - [j12]Barbara Piasecka, Marc Robinson-Rechavi, Sven Bergmann:
Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human. Bioinform. 28(14): 1865-1872 (2012) - [j11]Adrian M. Altenhoff, Romain A. Studer, Marc Robinson-Rechavi, Christophe Dessimoz:
Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs. PLoS Comput. Biol. 8(5) (2012) - 2011
- [j10]Brigitte Boeckmann, Marc Robinson-Rechavi, Ioannis Xenarios, Christophe Dessimoz:
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. Briefings Bioinform. 12(5): 423-435 (2011) - [j9]Walid H. Gharib, Marc Robinson-Rechavi:
When orthologs diverge between human and mouse. Briefings Bioinform. 12(5): 436-441 (2011) - [j8]Vidhya Jagannathan, Marc Robinson-Rechavi:
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. 5: 138 (2011) - 2010
- [j7]Gilles Parmentier, Frederic B. Bastian, Marc Robinson-Rechavi:
Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy. Bioinform. 26(14): 1766-1771 (2010) - 2009
- [j6]Estelle Proux-Wéra, Romain A. Studer, Sébastien Moretti, Marc Robinson-Rechavi:
Selectome: a database of positive selection. Nucleic Acids Res. 37(Database-Issue): 404-407 (2009) - 2007
- [j5]Grigoris D. Amoutzias, Elgar Pichler, Nina Mian, David De Graaf, Anastasia Imsiridou, Marc Robinson-Rechavi, Erich Bornberg-Bauer, David L. Robertson, Stephen G. Oliver:
A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. BMC Syst. Biol. 1: 34 (2007) - 2004
- [j4]David Ruau, Jorge Duarte, Tarik Ourjdal, Guy Perrière, Vincent Laudet, Marc Robinson-Rechavi:
Update of NUREBASE: nuclear hormone receptor functional genomics. Nucleic Acids Res. 32(Database-Issue): 165-167 (2004) - 2002
- [j3]Jorge Duarte, Guy Perrière, Vincent Laudet, Marc Robinson-Rechavi:
NUREBASE: database of nuclear hormone receptors. Nucleic Acids Res. 30(1): 364-368 (2002) - 2000
- [j2]Marc Robinson-Rechavi, Dorothée Huchon:
RRTree: Relative-Rate Tests between groups of sequences on a phylogenetic tree. Bioinform. 16(3): 296-297 (2000) - 1999
- [j1]Isabelle Gonçalves, Marc Robinson-Rechavi, Guy Perrière, Dominique Mouchiroud:
JaDis: computing distances between nucleic acid sequences. Bioinform. 15(5): 424-425 (1999)
Conference and Workshop Papers
- 2021
- [c6]Ana Claudia Sima, Tarcisio Mendes de Farias, Maria Anisimova, Christophe Dessimoz, Marc Robinson-Rechavi, Erich Zbinden, Kurt Stockinger:
Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data. SSDBM 2021: 61-72 - 2019
- [c5]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:
OncoMX: an Integrated Cancer Mutation and Expression Knowledgebase for Biomarker Evaluation and Discovery. AMIA 2019 - 2012
- [c4]Sébastien Moretti, Riccardo Murri, Sergio Maffioletti, Arnold Kuzniar, Briséïs Castella, Nicolas Salamin, Marc Robinson-Rechavi, Heinz Stockinger:
gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution. HealthGrid 2012: 59-68 - [c3]Hannes Schabauer, Mario Valle, Christoph Pacher, Heinz Stockinger, Alexandros Stamatakis, Marc Robinson-Rechavi, Ziheng Yang, Nicolas Salamin:
SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model. IPDPS Workshops 2012: 706-714 - 2010
- [c2]Adam Kraut, Sébastien Moretti, Marc Robinson-Rechavi, Heinz Stockinger, Dean Flanders:
Phylogenetic Code in the Cloud - Can it Meet the Expectations? HealthGrid 2010: 55-63 - 2008
- [c1]Frederic B. Bastian, Gilles Parmentier, Julien Roux, Sébastien Moretti, Vincent Laudet, Marc Robinson-Rechavi:
Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species. DILS 2008: 124-131
Informal and Other Publications
- 2023
- [i4]Tarcisio Mendes de Farias, Julien Wollbrett, Marc Robinson-Rechavi, Frederic B. Bastian:
Boosting interoperability: towards an increasingly reusable bioinformatics knowledge base. CoRR abs/2303.12329 (2023) - 2021
- [i3]Ana Claudia Sima, Tarcisio Mendes de Farias, Maria Anisimova, Christophe Dessimoz, Marc Robinson-Rechavi, Erich Zbinden, Kurt Stockinger:
Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data. CoRR abs/2104.13744 (2021) - 2016
- [i2]Andrea Komljenovic, Julien Roux, Marc Robinson-Rechavi, Frederic B. Bastian:
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests. F1000Research 5: 2748 (2016) - 2012
- [i1]Sébastien Moretti, Riccardo Murri, Sergio Maffioletti, Arnold Kuzniar, Briséïs Castella, Nicolas Salamin, Marc Robinson-Rechavi, Heinz Stockinger:
gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution. CoRR abs/1203.3092 (2012)
Coauthor Index
aka: Frédéric B. Bastian
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