Department of Ecology and Evolution

Groupe Bertelsmeier | Groupe Chapuisat | Groupe Christe | Groupe Fumagalli | Groupe Goudet | Groupe Guisan | Groupe Kawecki | Groupe Lehmann | Groupe Mullon | Groupe Pannell | Groupe Robinson-Rechavi | Groupe Roulin | Groupe Sanders | Groupe Schwander | Groupe Van de Waal | Groupe Wedekind
Publications | Phd and Masters theses

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173 publications

2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 |
2024
Pseudocryptic diversity and species boundaries in the sea cucumber Stichopus cf. horrens (Echinodermata: Stichopodidae) revealed by mitochondrial and microsatellite markers.
Lizano AMD, Kim K.M., Juinio-Meñez M.A., Ravago-Gotanco R., 2024/02/28. Scientific reports, 14 (1) p. 4886. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_9C3A50F95C0E]
 
The SIB Swiss Institute of Bioinformatics Semantic Web of data.
SIB Swiss Institute of Bioinformatics RDF Group Members, Mendes de Farias T., 2024/01/05. Nucleic acids research, 52 (D1) pp. D44-D51. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A29FECE3B301]
2023
On the Potential of Artificial Intelligence Chatbots for Data Exploration of Federated Bioinformatics Knowledge Graphs
Sima Ana-Claudia, Mendes de Farias Tarcisio, 2023/08/29. dans SeWebMeDa’23: 6th Workshop on Semantic Web solutions for large-scale biomedical data analytics, CEUR Workshop Proceedings (CEUR-WS.org).
[URN][serval:BIB_85E3858D9118]
Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience.
Mendes de Farias T., Wollbrett J., Robinson-Rechavi M., Bastian F., 2023/08/17. GigaScience, 12 pp. giad058. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_D4A608774943]
Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets
Mendes de Farias Tarcisio, Kushida Tatsuya, Sima Ana-Claudia, Dessimoz Christophe, Chiba Hirokazu, Bastian Frédéric, Masuya Hiroshi, 2023/06/22. dans SWAT4HCLS 2023: The 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences.
[URN][serval:BIB_818CA7FA57C2]
 
Towards predicting essential proteins via federated SPARQL queries
Liakopoulos Petros, Banfalvi Borbala, Wang Xinyi, Majidian Sina, Mendes de Farias Tarcisio, Dessimoz Christophe, Sima Ana Claudia, 2023/06/22. dans SWAT4HCLS 2023: The 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences.
[serval:BIB_5DBECBB5FD4F]
Genome structures resolve the early diversification of teleost fishes.
Parey E., Louis A., Montfort J., Bouchez O., Roques C., Iampietro C., Lluch J., Castinel A., Donnadieu C., Desvignes T. et al., 2023/02/10. Science, 379 (6632) pp. 572-575. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_7F288BABFB22]
2022
X chromosomes show relaxed selection and complete somatic dosage compensation across Timema stick insect species.
Parker D.J., Jaron K.S., Dumas Z., Robinson-Rechavi M., Schwander T., 2022/12. Journal of evolutionary biology, 35 (12) pp. 1734-1750. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_08C40767A03A]
Rhythmicity is linked to expression cost at the protein level but to expression precision at the mRNA level
Laloum David, Robinson-Rechavi Marc, 2022/09/12. PLOS Computational Biology, 18 (9) pp. e1010399. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_8DA78A121767]
Federating and querying heterogeneous and distributed Web APIs and triple stores
Mendes de Farias Tarcisio, Dessimoz Christophe, Ayllon Benitez Aaron, Yang Chen, Long Jiao, Sima Ana-Claudia, 2022/08/02. dans 2022 ISMB Bio-Ontologies Community of Special Interest. Peer-reviewed.
[URN][DOI][serval:BIB_6A2C0BEAD983]
An ancient truncated duplication of the anti-Müllerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family.
Wen M., Pan Q., Jouanno E., Montfort J., Zahm M., Cabau C., Klopp C., Iampietro C., Roques C., Bouchez O. et al., 2022/08. Molecular ecology resources, 22 (6) pp. 2411-2428. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_72F2B4092924]
Dynamics of sex-biased gene expression during development in the stick insect Timema californicum.
Djordjevic J., Dumas Z., Robinson-Rechavi M., Schwander T., Parker D.J., 2022/08. Heredity, 129 (2) pp. 113-122. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A0C665A95881]
Modern venomics-Current insights, novel methods, and future perspectives in biological and applied animal venom research.
von Reumont B.M., Anderluh G., Antunes A., Ayvazyan N., Beis D., Caliskan F., Crnković A., Damm M., Dutertre S., Ellgaard L. et al., 2022/05/18. GigaScience, 11. Peer-reviewed.
[URN][Pmid][serval:BIB_D7CBD21B54E6]
Taxonbridge: an R package to create custom taxonomies based on the NCBI and GBIF taxonomies
Veldsman Werner P., Campli Giulia, Dind Sagane, Rech de Laval Valentine, Drage Harriet B., Waterhouse Robert M., Robinson-Rechavi Marc, 2022/05/04..
[URN][DOI][serval:BIB_16185728F41B]
 
Phylogeny and taxonomy of the African frog genus Strongylopus (Anura: Pyxicephalidae)
Channing Alan, Schmitz Andreas, Zancolli Giulia, Conradie Werner, Rödel Mark-Oliver, 2022/04/21. Revue suisse de Zoologie, 129 (1).
[DOI][WoS][serval:BIB_7FFD2F8E0DF6]
Convergent consequences of parthenogenesis on stick insect genomes.
Jaron K.S., Parker D.J., Anselmetti Y., Tran Van P., Bast J., Dumas Z., Figuet E., François C.M., Hayward K., Rossier V. et al., 2022/02/25. Science advances, 8 (8) pp. eabg3842. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_F7578E44D8BF]
 
INODE : Building an End-to-End Data Exploration System in Practice
Amer-Yahia Sihem, Koutrika Georgia, Braschler Martin, Calvanese Diego, Lanti Davide, Lücke-Tieke Hendrik, Mosca Alessandro, Mendes de Farias Tarcisio, Papadopoulos Dimitris, Patil Yogendra et al., 2022/01/31. ACM SIGMOD Record, 50 (4) pp. 23-29.
[DOI][serval:BIB_E16BD277810E]
Convergent evolution of venom gland transcriptomes across Metazoa.
Zancolli G., Reijnders M., Waterhouse R.M., Robinson-Rechavi M., 2022/01/04. Proceedings of the National Academy of Sciences of the United States of America, 119 (1) pp. e2111392119. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_1D15F06B4071]
Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation.
Sima A.C., Mendes de Farias T., Anisimova M., Dessimoz C., Robinson-Rechavi M., Zbinden E., Stockinger K., 2022. Distributed and parallel databases, 40 (2-3) pp. 409-440. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_EE90AD3795B0]
 
Creation and unification of development and life stage ontologies for animals
Niknejad Anne, Mungall Christopher J., Osumi-Sutherland David, Robinson-Rechavi Marc, Bastian Frederic B., 2022..
[DOI][serval:BIB_A85E6647A76E]
Robust inference of expression state in bulk and single-cell RNA-Seq using curated intergenic regions
Fonseca Costa Sara S., Rosikiewicz Marta, Roux Julien, Wollbrett Julien, Bastian Frederic B., Robinson-Rechavi Marc, 2022..
[URN][DOI][serval:BIB_0D18349C923C]
2021
Accessing scientific data through knowledge graphs with Ontop.
Calvanese D., Lanti D., Mendes De Farias T., Mosca A., Xiao G., 2021/10/08. Patterns, 2 (10) p. 100346. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_962C4367A194]
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches.
Rossier V., Warwick Vesztrocy A., Robinson-Rechavi M., Dessimoz C., 2021/09/29. Bioinformatics, 37 (18) pp. 2866-2873. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E9D32F404F19]
Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova.
Brandt A., Tran Van P., Bluhm C., Anselmetti Y., Dumas Z., Figuet E., François C.M., Galtier N., Heimburger B., Jaron K.S. et al., 2021/09/21. Proceedings of the National Academy of Sciences of the United States of America, 118 (38) pp. e2101485118. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_A92AB05DA145]
The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection.
Liu J., Viales R.R., Khoueiry P., Reddington J.P., Girardot C., Furlong EEM, Robinson-Rechavi M., 2021/09. Genome research, 31 (9) pp. 1573-1581. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_7EF03DE26E06]
First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes.
Tran Van P., Anselmetti Y., Bast J., Dumas Z., Galtier N., Jaron K.S., Martens K., Parker D.J., Robinson-Rechavi M., Schwander T. et al., 2021/04/15. G3, 11 (4) pp. jkab043. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_19612ACE0AC4]
Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes.
Begum T., Robinson-Rechavi M., 2021/04/13. Molecular biology and evolution, 38 (4) pp. 1614-1626. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C4CAC6CE8CD6]
 
Sex-specific responses to cold in a very cold-tolerant, northern Drosophila species.
Parker D.J., Envall T., Ritchie M.G., Kankare M., 2021/04. Heredity, 126 (4) pp. 695-705. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_646B55DBD682]
The new COST Action European Venom Network (EUVEN)-synergy and future perspectives of modern venomics.
Modica M.V., Ahmad R., Ainsworth S., Anderluh G., Antunes A., Beis D., Caliskan F., Serra M.D., Dutertre S., Moran Y. et al., 2021/03/25. GigaScience, 10 (3) pp. giab019. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_18C45BC8A28B]
 
Genomic Features of Parthenogenetic Animals.
Jaron K.S., Bast J., Nowell R.W., Ranallo-Benavidez T.R., Robinson-Rechavi M., Schwander T., 2021/03/12. The Journal of heredity, 112 (1) pp. 19-33. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_E1A133CAFF7A]
 
A genome-wide investigation of adaptive signatures in protein-coding genes related to tool behaviour in New Caledonian and Hawaiian crows.
Dussex N., Kutschera V.E., Wiberg RAW, Parker D.J., Hunt G.R., Gray R.D., Rutherford K., Abe H., Fleischer R.C., Ritchie M.G. et al., 2021/02. Molecular ecology, 30 (4) pp. 973-986. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_970EA2875929]
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals.
Bastian F.B., Roux J., Niknejad A., Comte A., Fonseca Costa S.S., de Farias T.M., Moretti S., Parmentier G., Rech de Laval V., Rosikiewicz M. et al., 2021/01/08. Nucleic acids research, 49 (D1) pp. D831-D847. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_FD0CF4F734E7]
 
Chromatin Immunoprecipitation (ChIP) from Mouse Liver Nuclei
Fonseca Costa SS, Ripperger JA, 2021. pp. 115-125 dans Brown Steven A. (eds.) Circadian Clocks: Methods and Protocols, Springer US.
[DOI][serval:BIB_B8CFCE544378]
 
Performance of a phylogenetic independent contrast method and an improved pairwise comparison under different scenarios of trait evolution after speciation and duplication
Begum Tina, Serrano-Serrano Martha Liliana, Robinson-Rechavi Marc, 2021. Methods Ecol Evol, 12 pp. 1875-1887. Peer-reviewed.
[DOI][serval:BIB_E6A0AF8DC9DE]
Querying knowledge graphs in natural language.
Liang S., Stockinger K., de Farias T.M., Anisimova M., Gil M., 2021. Journal of big data, 8 (3) pp. 1-23. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_673D6C6C570E]
2020
Single-cell transcriptomics allows novel insights into aging and circadian processes.
Fonseca Costa S.S., Robinson-Rechavi M., Ripperger J.A., 2020/12/04. Briefings in functional genomics, 19 (5-6) pp. 343-349. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_0223DAE8F649]
Robust inference of positive selection on regulatory sequences in the human brain.
Liu J., Robinson-Rechavi M., 2020/11. Science advances, 6 (48) pp. eabc9863. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_805F3C22323C]
Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo.
Liu J., Frochaux M., Gardeux V., Deplancke B., Robinson-Rechavi M., 2020/09/19. BMC biology, 18 (1) p. 129. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_076B6D0800A4]
 
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals
Bastian FB, Roux J, Niknejad A, Comte A, Fonseca Costa SS, Mendes de Farias T, Moretti S, Parmentier G, Rech de Laval V, Rosikiewicz M et al., 2020/05/29..
[DOI][serval:BIB_65A649E27A82]
 
Venom Systems as Models for Studying the Origin and Regulation of Evolutionary Novelties.
Zancolli G., Casewell N.R., 2020/05/27. Molecular biology and evolution, 37 (10) pp. 2777-2790. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_216418A5928B]
Correction to: Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae)
Selmoni Oliver M., Maitre Diane, Roux Julien, Wilkins Laetitia G. E., Marques da Cunha Lucas, Vermeirssen Etienne L. M., Knörr Susanne, Robinson-Rechavi Marc, Wedekind Claus, 2020/05/20. BMC Genomics, 21 (1) p. 371.
[URN][DOI][Pmid][serval:BIB_B83E6BB3F5EE]
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases
Chen Qingyu, Britto Ramona, Erill Ivan, Jeffery Constance J., Liberzon Arthur, Magrane Michele, Onami Jun-ichi, Robinson-Rechavi Marc, Sponarova Jana, Zobel Justin et al., 2020/04/01. Genomics, Proteomics & Bioinformatics, 18 pp. 91-103. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_688EF9445320]
Methods detecting rhythmic gene expression are biologically relevant only for strong signal
Laloum David, Robinson-Rechavi Marc, 2020/03. PLOS Computational Biology, 16 (3) pp. 1-23.
[URN][DOI][serval:BIB_C090B1967D37]
Molecular Evolution and Gene Function
Robinson-Rechavi Marc, 2020. dans Phylogenetics in the Genomic Era, hal.inria.fr.
[URN][serval:BIB_BB2B81C3E623]
The Expression Comparison Tool in Bgee
Robinson-Rechavi Marc, Rech de Laval Valentine, Bastian Frédéric B., Wollbrett Julien, Bgee Team, 2020. dans Phylogenetics in the Genomic Era, hal.inria.fr.
[URN][serval:BIB_D44AAAA828A2]
2019
Identifying gene function and module connections by the integration of multispecies expression compendia
Li Hao, Rukina Daria, David Fabrice P.A., Li Terytty Yang, Oh Chang-Myung, Gao Arwen W., Katsyuba Elena, Bou Sleiman Maroun, Komljenovic Andrea, Huang Qingyao et al., 2019/12. Genome Research, 29 (12) pp. 2034-2045. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_7B783B226A9E]
Sex-biased gene expression is repeatedly masculinized in asexual females.
Parker D.J., Bast J., Jalvingh K., Dumas Z., Robinson-Rechavi M., Schwander T., 2019/10/11. Nature communications, 10 (1) p. 4638. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_BBF4929EFCF6]
 
Validating the Demethylating Effects of 5-aza-2′-deoxycytidine in Insects Requires a Whole-Genome Approach : (A Reply to Ellers et al.)
Cook Nicola, Parker Darren J., Tauber Eran, Pannebakker Bart A., Shuker David M., 2019/09. The American Naturalist, 194 (3) pp. 432-438.
[DOI][WoS][Pmid][serval:BIB_8FB64E91DB0D]
Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae).
Selmoni O.M., Maitre D., Roux J., Wilkins LGE, Marques da Cunha L., Vermeirssen ELM, Knörr S., Robinson-Rechavi M., Wedekind C., 2019/07/15. BMC Genomics, 20 (1) p. 583. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_146003703B65]
Cross-species functional modules link proteostasis to human normal aging.
Komljenovic A., Li H., Sorrentino V., Kutalik Z., Auwerx J., Robinson-Rechavi M., 2019/07. PLoS computational biology, 15 (7) pp. e1007162. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_DB3E6C72F674]
Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection.
Davydov I.I., Salamin N., Robinson-Rechavi M., 2019/06/01. Molecular biology and evolution, 36 (6) pp. 1316-1332. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FF45CD1C1260]
Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles.
Seppey M., Ioannidis P., Emerson B.C., Pitteloud C., Robinson-Rechavi M., Roux J., Escalona H.E., McKenna D.D., Misof B., Shin S. et al., 2019/05/17. Genome biology, 20 (1) p. 98. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_4EC401109BAD]
 
Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5.
Ellegaard K.M., Brochet S., Bonilla-Rosso G., Emery O., Glover N., Hadadi N., Jaron K.S., van der Meer J.R., Robinson-Rechavi M., Sentchilo V. et al., 2019/05. Molecular ecology, 28 (9) pp. 2224-2237. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_37C4AFA6D4D6]
 
When one phenotype is not enough: divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species.
Zancolli G., Calvete J.J., Cardwell M.D., Greene H.W., Hayes W.K., Hegarty M.J., Herrmann H.W., Holycross A.T., Lannutti D.I., Mulley J.F. et al., 2019/03/13. Proceedings. Biological sciences, 286 (1898) p. 20182735. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_430ECBB141F9]
Repeated Evolution of Asexuality Involves Convergent Gene Expression Changes.
Parker D.J., Bast J., Jalvingh K., Dumas Z., Robinson-Rechavi M., Schwander T., 2019/02/01. Molecular biology and evolution, 36 (2) pp. 350-364. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_50533A2E2A2E]
Enabling semantic queries across federated bioinformatics databases.
Sima A.C., Mendes de Farias T., Zbinden E., Anisimova M., Gil M., Stockinger H., Stockinger K., Robinson-Rechavi M., Dessimoz C., 2019/01/01. Database, 2019. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_ED991CD0F569]
Olfactory Proteins in Timema Stick Insects
Parker D.J., Djordjevic J., Schwander T., 2019. Frontiers in Ecology and Evolution, 7 p. 101. Peer-reviewed.
[URN][DOI][WoS][serval:BIB_B92A4650771D]
 
Semantic Integration and Enrichment of Heterogeneous Biological Databases.
Sima A.C., Stockinger K., de Farias T.M., Gil M., 2019. Methods in molecular biology, 1910 pp. 655-690. Peer-reviewed.
[DOI][Pmid][serval:BIB_3D396F44C44D]
 
Snake venom can vary in a single species - and it’s not just about adaptation to their prey
Wüster W, Zancolli Giulia, 2019. The Conversation.
[serval:BIB_67CB138E734E]
 
VoIDext: Vocabulary and Patterns for Enhancing Interoperable Datasets with Virtual Links
Mendes de Farias Tarcisio, Stockinger Kurt, Dessimoz Christophe, 2019. Lecture Notes in Computer Science pp. 607-625. Peer-reviewed.
[DOI][serval:BIB_B5FCAC161AA9]
2018
Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.
Bochkareva O.O., Moroz E.V., Davydov I.I., Gelfand M.S., 2018/12/27. BMC genomics, 19 (1) p. 965. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_6472B5BCD4D2]
Evolutionary and developmental dynamics of sex-biased gene expression in common frogs with proto-Y chromosomes.
Ma W.J., Veltsos P., Sermier R., Parker D.J., Perrin N., 2018/10/05. Genome biology, 19 (1) p. 156. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3979DBC2E6AC]
Developmental Constraints on Genome Evolution in Four Bilaterian Model Species.
Liu J., Robinson-Rechavi M., 2018/09/01. Genome biology and evolution, 10 (9) pp. 2266-2277. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F61F6F919170]
Inter and Intraspecific Genomic Divergence in Drosophila montana Shows Evidence for Cold Adaptation.
Parker D.J., Wiberg RAW, Trivedi U., Tyukmaeva V.I., Gharbi K., Butlin R.K., Hoikkala A., Kankare M., Ritchie M.G., 2018/08/01. Genome Biology and Evolution, 10 (8) pp. 2086-2101. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_2BF47F2414C9]
 
Erratum to: Widespread vulnerability of Malagasy predators to the toxins of an introduced toad.
Marshall B.M., Casewell N.R., Vences M., Glaw F., Andreone F., Rakotoarison A., Zancolli G., Woog F., Wüster W., 2018/07/09. Current biology, 28 (13) p. 2194. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_23CB752E8DA1]
Consequences of Asexuality in Natural Populations: Insights from Stick Insects.
Bast J., Parker D.J., Dumas Z., Jalvingh K.M., Tran Van P., Jaron K.S., Figuet E., Brandt A., Galtier N., Schwander T., 2018/07/01. Molecular biology and evolution, 35 (7) pp. 1668-1677. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_00D517ACA82A]
 
Widespread vulnerability of Malagasy predators to the toxins of an introduced toad.
Marshall B.M., Casewell N.R., Vences M., Glaw F., Andreone F., Rakotoarison A., Zancolli G., Woog F., Wüster W., 2018/06/04. Current biology, 28 (11) pp. R654-R655. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_DBC687926ACD]
myTAI: evolutionary transcriptomics with R.
Drost H.G., Gabel A., Liu J., Quint M., Grosse I., 2018/05/01. Bioinformatics, 34 (9) pp. 1589-1590. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_11FF54BB96E1]
Photosensitive Alternative Splicing of the Circadian Clock Gene <i>timeless</i> Is Population Specific in a Cold-Adapted Fly, <i>Drosophila montana</i>.
Tapanainen R., Parker D.J., Kankare M., 2018/03/28. G3, 8 (4) pp. 1291-1297. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_BB77B76435C1]
 
Evaluation of tools for long read RNA-seq splice-aware alignment.
Križanovic K., Echchiki A., Roux J., Šikic M., 2018/03/01. Bioinformatics, 34 (5) pp. 748-754. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_2AD9D09B9A6F]
 
Amphibian diversity on Mt Kilimanjaro
Zancolli Giulia, 2018. dans The KiLi Project: Kilimanjaro ecosystems under global change: Linking biodiversity, biotic interactions and biogeochemical ecosystem processes, Senckenberg Gesellschaft für Naturforschung.
[serval:BIB_CF2A39A31847]
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests.
Komljenovic A., Roux J., Wollbrett J., Robinson-Rechavi M., Bastian F.B., 2018. F1000Research, 5 p. 2748. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_0AA1ED033ECE]
Fundamental and realized feeding niche breadths of sexual and asexual stick insects.
Larose C., Parker D.J., Schwander T., 2018. Proceedings of the Royal Society. B Biological sciences, 285 (1892) p. 20181805. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_69B6EEF0F15E]
2017
Sustainable computational science: the ReScience initiative
Rougier Nicolas P., Hinsen Konrad, Alexandre Frédéric, Arildsen Thomas, Barba Lorena A., Benureau Fabien C.Y., Brown C. Titus, de Buyl Pierre, Caglayan Ozan, Davison Andrew P. et al., 2017/12/18. PeerJ Computer Science, 3 pp. e142. Peer-reviewed.
[URN][DOI][WoS][serval:BIB_135A94DD70C5]
Leveraging logical rules for efficacious representation of large orthology datasets
Mendes de Farias Tarcisio, Chiba Hirokazu, Fernández-Breis Jesualdo T. (eds.), 2017/12/01..
[URN][serval:BIB_8D8E82340A71]
 
Low number of fixed somatic mutations in a long-lived oak tree.
Schmid-Siegert E., Sarkar N., Iseli C., Calderon S., Gouhier-Darimont C., Chrast J., Cattaneo P., Schütz F., Farinelli L., Pagni M. et al., 2017/12. Nature plants, 3 (12) pp. 926-929. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_66296D0251EE]
Sex differentiation in grayling (Salmonidae) goes through an all-male stage and is delayed in genetic males who instead grow faster.
Maitre D., Selmoni O.M., Uppal A., Marques da Cunha L., Wilkins LGE, Roux J., Mobley K.B., Castro I., Knörr S., Robinson-Rechavi M. et al., 2017/11/03. Scientific reports, 7 (1) p. 15024. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F6A409506084]
 
A performance benchmark over semantic rule checking approaches in construction industry
Pauwels P., de Farias T.M., Zhang C., Roxin A., Beetz J., De Roo J., Nicolle C., 2017/08. Advanced Engineering Informatics, 33 pp. 68-88. Peer-reviewed.
[DOI][WoS][serval:BIB_97A6B1A2B677]
Bayesian association scan reveals loci associated with human lifespan and linked biomarkers.
McDaid A.F., Joshi P.K., Porcu E., Komljenovic A., Li H., Sorrentino V., Litovchenko M., Bevers RPJ, Rüeger S., Reymond A. et al., 2017/07/27. Nature communications, 8 p. 15842. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C06E0694F6CC]
 
Venom On-a-Chip: A Fast and Efficient Method for Comparative Venomics.
Zancolli G., Sanz L., Calvete J.J., Wüster W., 2017/05/28. Toxins, 9 (6). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_7882BC14C879]
Sex-specific changes in gene expression and delayed sex differentiation in response to estrogen pollution in grayling (Salmonidae)
Selmoni O. M., Maitre D., Roux J., Wilkins L. G. E., Marques da Cunha L., Vermeirssen E. L. M., Knörr S., Robinson-Rechavi M., Wedekind C., 2017/05/09..
[URN][DOI][serval:BIB_8B3A5682EAF5]
Updates in Rhea - an expert curated resource of biochemical reactions.
Morgat A., Lombardot T., Axelsen K.B., Aimo L., Niknejad A., Hyka-Nouspikel N., Coudert E., Pozzato M., Pagni M., Moretti S. et al., 2017/01/04. Nucleic acids research, 45 (D1) pp. D415-D418. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_D4F55C24D893]
 
A benchmark of gene expression tissue-specificity metrics.
Kryuchkova-Mostacci N., Robinson-Rechavi M., 2017. Briefings in Bioinformatics, 18 (2) pp. 205-214. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_87132E302513]
 
Assessing lamprey populations in Scottish rivers using eDNA: proof of concept.
Zancolli Giulia, Foote A., Seymour M., Creer S., 2017., Bangor University.
[serval:BIB_9F97CE5BB8B3]
Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans.
Daub J.T., Moretti S., Davydov I.I., Excoffier L., Robinson-Rechavi M., 2017. Molecular Biology and Evolution, 34 (6) pp. 1391-1402. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E977192342AB]
No evidence for the radiation time lag model after whole genome duplications in Teleostei.
Laurent S., Salamin N., Robinson-Rechavi M., 2017. PLoS One, 12 (4) pp. e0176384. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_6A5C276B250D]
 
Paternity analysis of wild-caught females shows that sperm package size and placement influence fertilization success in the bushcricket Pholidoptera griseoaptera.
Parker D.J., Zaborowska J., Ritchie M.G., Vahed K., 2017. Molecular Ecology, 26 (11) pp. 3050-3061. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_8D73B5044DE6]
Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates.
Roux J., Liu J., Robinson-Rechavi M., 2017. Molecular Biology and Evolution, 34 (11) pp. 2773-2791. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C757F185D6C7]
2016
Predictors of elevational biodiversity gradients change from single taxa to the multi-taxa community level.
Peters M.K., Hemp A., Appelhans T., Behler C., Classen A., Detsch F., Ensslin A., Ferger S.W., Frederiksen S.B., Gebert F. et al., 2016/12/22. Nature communications, 7 p. 13736. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F82170DF55C1]
Is Hybridization a Source of Adaptive Venom Variation in Rattlesnakes? A Test, Using a Crotalus scutulatus × viridis Hybrid Zone in Southwestern New Mexico.
Zancolli G., Baker T.G., Barlow A., Bradley R.K., Calvete J.J., Carter K.C., de Jager K., Owens J.B., Price J.F., Sanz L. et al., 2016/06/16. Toxins, 8 (6). Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_BD5BD485BC4B]
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.
SIB Swiss Institute of Bioinformatics Members, Bultet L.A., 2016/01/04. Nucleic acids research, 44 (D1) pp. D27-37. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_71EF45D9A3D9]
Selectoscope: A Modern Web-App for Positive Selection Analysis of Genomic Data
Zaika A.V., Davydov I.I., Gelfand M.S., 2016. Bioinformatics Research and Applications, 9683 pp. 253-257. Peer-reviewed.
[URN][DOI][WoS][serval:BIB_AA1D1FFA391C]
State aggregation for fast likelihood computations in molecular evolution.
Davydov I.I., Robinson-Rechavi M., Salamin N., 2016. Bioinformatics, 33 pp. 354-362. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_54224013033C]
Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs.
Kryuchkova-Mostacci N., Robinson-Rechavi M., 2016. PLoS Computational Biology, 12 (12) pp. e1005274. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F27D450F2B07]
Tools and data services registry: a community effort to document bioinformatics resources.
Ison J., Rapacki K., Ménager H., Kalaš M., Rydza E., Chmura P., Anthon C., Beard N., Berka K., Bolser D. et al., 2016. Nucleic Acids Research, 44 (D1) pp. D38-D47.
[URN][DOI][WoS][Pmid][serval:BIB_B3F966DA99C6]
2015
 
Reptiles as Reservoirs of Bacterial Infections: Real Threat or Methodological Bias?
Zancolli G., Mahsberg D., Sickel W., Keller A., 2015/10. Microbial ecology, 70 (3) pp. 579-584. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_7EB016B44DAC]
 
Cell-based computational modeling of vascular morphogenesis using Tissue Simulation Toolkit.
Daub J.T., Merks R.M., 2015. Methods in Molecular Biology, 1214 pp. 67-127.
[DOI][WoS][Pmid][serval:BIB_0E9ECBD6E606]
Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.
Miyazaki R., Bertelli C., Benaglio P., Canton J., De Coi N., Gharib W.H., Gjoksi B., Goesmann A., Greub G., Harshman K. et al., 2015. Environmental Microbiology, 17 (1) pp. 91-104.
[URN][DOI][WoS][Pmid][serval:BIB_EBE76C19261B]
Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions.
Laurent S., Robinson-Rechavi M., Salamin N., 2015. BMC Evolutionary Biology, 15 p. 157. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_01FF6A3D8DC9]
 
Genomics is changing Evo-Devo.
Robinson-Rechavi M., 2015. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution, 324 (4) p. 315.
[DOI][WoS][Pmid][serval:BIB_E8ACA475D130]
High Frequency Haplotypes are Expected Events, not Historical Figures.
Guillot E.G., Cox M.P., 2015. F1000Research, 4 p. 666.
[URN][DOI][Pmid][serval:BIB_8516AEED5D71]
Inference of Evolutionary Forces Acting on Human Biological Pathways.
Daub J.T., Dupanloup I., Robinson-Rechavi M., Excoffier L., 2015. Genome Biology and Evolution, 7 (6) pp. 1546-1558. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F1C43009CD42]
Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.
Bertelli C., Aeby S., Chassot B., Clulow J., Hilfiker O., Rappo S., Ritzmann S., Schumacher P., Terrettaz C., Benaglio P. et al., 2015. Frontiers in Microbiology, 6 (101) p. 101. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5BB2A564D83D]
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.
Bastian F.B., Chibucos M.C., Gaudet P., Giglio M., Holliday G.L., Huang H., Lewis S.E., Niknejad A., Orchard S., Poux S. et al., 2015. Database, 2015 pp. bav043. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_60CACFAC405E]
Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse.
Kryuchkova-Mostacci N., Robinson-Rechavi M., 2015. Plos One, 10 (6) pp. e0131673. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B6BE63795D1F]
What to compare and how: Comparative transcriptomics for Evo-Devo.
Roux J., Rosikiewicz M., Robinson-Rechavi M., 2015. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution, 324 (4) pp. 372-382. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E322E5E2A13A]
2014
 
Comparative landscape genetics of two river frog species occurring at different elevations on Mount Kilimanjaro.
Zancolli G., Rödel M.O., Steffan-Dewenter I., Storfer A., 2014/10. Molecular ecology, 23 (20) pp. 4989-5002. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_8D32208FF08F]
 
Amphibian diversity on the roof of Africa: unveiling the effects of habitat degradation, altitude and biogeography
Zancolli Giulia, Steffan-Dewenter Ingolf, Rödel Mark-Oliver, 2014/03. Diversity and Distributions, 20 (3) pp. 297-308.
[DOI][WoS][serval:BIB_F7B3F38D13AF]
Big data and other challenges in the quest for orthologs.
Sonnhammer E.L., Gabaldón T., Sousa da Silva A.W., Martin M., Robinson-Rechavi M., Boeckmann B., Thomas P.D., Dessimoz C., Quest for Orthologs consortium, 2014. Bioinformatics, 30 (21) pp. 2993-2998. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_172DE4708266]
 
Determinants of protein evolutionary rates in light of ENCODE functional genomics
Kryuchkova Nadezda, Robinson-Rechavi Marc, 2014. pp. A9 dans BMC Bioinformatics.
[DOI][serval:BIB_603F1CF898E3]
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.
Stockinger H., Altenhoff A.M., Arnold K., Bairoch A., Bastian F., Bergmann S., Bougueleret L., Bucher P., Delorenzi M., Lane L. et al., 2014. Nucleic Acids Research, 42 (Web Server issue) pp. W436-W441. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_28A5775B7C38]
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics.
Rosikiewicz M., Robinson-Rechavi M., 2014. Bioinformatics, 30 (10) pp. 1392-1399. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_0E5C20608CA6]
Optimization strategies for fast detection of positive selection on phylogenetic trees.
Valle M., Schabauer H., Pacher C., Stockinger H., Stamatakis A., Robinson-Rechavi M., Salamin N., 2014. Bioinformatics, 30 (8) pp. 1129-1137. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_EE03C80A1584]
Patterns of positive selection in seven ant genomes.
Roux J., Privman E., Moretti S., Daub J.T., Robinson-Rechavi M., Keller L., 2014. Molecular Biology and Evolution, 31 (7) pp. 1661-1685. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_95722591AAD3]
Selectome update: quality control and computational improvements to a database of positive selection.
Moretti S., Laurenczy B., Gharib W.H., Castella B., Kuzniar A., Schabauer H., Studer R.A., Valle M., Salamin N., Stockinger H. et al., 2014. Nucleic Acids Research, 42 (1) pp. D917-D921. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_BD16E97A0D18]
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.
Haendel M.A., Balhoff J.P., Bastian F.B., Blackburn D.C., Blake J.A., Bradford Y., Comte A., Dahdul W.M., Dececchi T.A., Druzinsky R.E. et al., 2014. Journal of Biomedical Semantics, 5 p. 21. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F76940F670C4]
2013
A cell-based model of extracellular-matrix-guided endothelial cell migration during angiogenesis.
Daub J.T., Merks R.M., 2013. Bulletin of Mathematical Biology, 75 (8) pp. 1377-1399. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_0F557EB2332C]
Community-wide plasmid gene mobilization and selection.
Sentchilo V., Mayer A.P., Guy L., Miyazaki R., Green Tringe S., Barry K., Malfatti S., Goessmann A., Robinson-Rechavi M., van der Meer J.R., 2013. ISME Journal, 7 (6) pp. 1173-1186.
[URN][DOI][WoS][Pmid][serval:BIB_B5128FCC3FB5]
 
Detection of Batrachochytrium dendrobatidis in river frogs (genus Amietia) on Mount Kilimanjaro, Tanzania
Zancolli G., Storfer A., Rödel M.-O., 2013. Herpetological Review, 44 (4) pp. 611-614.
[serval:BIB_5A930BDE59AC]
Developmental and Environmental Regulation of Aquaporin Gene Expression across Populus Species: Divergence or Redundancy?
Cohen D., Bogeat-Triboulot M.B., Vialet-Chabrand S., Merret R., Courty P.E., Moretti S., Bizet F., Guilliot A., Hummel I., 2013. PLoS One, 8 (2) pp. e55506. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_87FBFC197FE8]
Enhanced EGFP Fluorescence Emission in Presence of PEG Aqueous Solutions and PIB1000-PEG6000-PIB1000 Copolymer Vesicles.
Muhammad N., Kryuchkova N., Dworeck T., Rodríguez-Ropero F., Fioroni M., 2013. Biomed Research International, 2013 p. 329087.
[URN][DOI][WoS][Pmid][serval:BIB_90DEE3A67B27]
 
Evidence for polygenic adaptation to pathogens in the human genome.
Daub J.T., Hofer T., Cutivet E., Dupanloup I., Quintana-Murci L., Robinson-Rechavi M., Excoffier L., 2013. Molecular Biology and Evolution, 30 (7) pp. 1544-1558. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5B46808B83ED]
The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC.
Gharib W.H., Robinson-Rechavi M., 2013. Molecular Biology and Evolution, 30 (7) pp. 1675-1686. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E31E37CD7B01]
The hourglass and the early conservation models--co-existing patterns of developmental constraints in vertebrates.
Piasecka B., Lichocki P., Moretti S., Bergmann S., Robinson-Rechavi M., 2013. Plos Genetics, 9 (4) pp. e1003476. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B03DCB0498A7]
Uncovering hidden duplicated content in public transcriptomics data.
Rosikiewicz M., Comte A., Niknejad A., Robinson-Rechavi M., Bastian F.B., 2013. Database, 2013 pp. bat010. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_230AE9FE1902]
2012
Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs.
Roux J., Gonzàlez-Porta M., Robinson-Rechavi M., 2012. Nucleic Acids Research, 40 (13) pp. 5890-5900. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_062426040422]
Comparative modular analysis of gene expression in vertebrate organs.
Piasecka B., Kutalik Z., Roux J., Bergmann S., Robinson-Rechavi M., 2012. Bmc Genomics, 13 p. 124. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_94FEE072331D]
Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human.
Piasecka B., Robinson-Rechavi M., Bergmann S., 2012. Bioinformatics, 28 (14) pp. 1865-1872. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FFE8D8F98971]
ExPASy: SIB bioinformatics resource portal.
Artimo P., Jonnalagedda M., Arnold K., Baratin D., Csardi G., de Castro E., Duvaud S., Flegel V., Fortier A., Gasteiger E. et al., 2012. Nucleic Acids Research, 40 pp. W597-W603.
[URN][DOI][WoS][Pmid][serval:BIB_60D126CF045C]
gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution
Moretti S., Murri R., Maffioletti S., Kuzniar A., Castella B, Salamin N., Robinson-Rechavi M., Stockinger H., 2012. pp. 59-68 dans Glatard T, Silverstein J (eds.) HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences, IOS Press Books online.
[URN][DOI][serval:BIB_542C5BE6E2B7]
How much does the amphioxus genome represent the ancestor of chordates?
Louis A., Roest Crollius H., Robinson-Rechavi M., 2012. Briefings in Functional Genomics, 11 (2) pp. 89-95. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_093626E06B3F]
Recent advances in biocuration: meeting report from the fifth International Biocuration Conference.
Gaudet P., Arighi C., Bastian F., Bateman A., Blake J.A., Cherry M.J., D'Eustachio P., Finn R., Giglio M., Hirschman L. et al., 2012. Database, 2012 pp. bas036. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_C16E4B98CEB3]
Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs.
Altenhoff A.M., Studer R.A., Robinson-Rechavi M., Dessimoz C., 2012. PLoS Computational Biology, 8 (5) pp. e1002514. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_89CB0AF6A1E2]
SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model
Schabauer H., Valle M., Pacher C., Stockinger H., Stamatakis A., Robinson-Rechavi M., Yang Z., Salamin N., 2012. pp. 700-708 dans Aluru S., Bader D.A. (eds.) HiCOMB (11th IEEE International Workshop on High Performance Computational Biology). Peer-reviewed, IEEE.
[URN][DOI][serval:BIB_5F7B13551FF8]
vHOG, a multispecies vertebrate ontology of homologous organs groups.
Niknejad A., Comte A., Parmentier G., Roux J., Bastian F.B., Robinson-Rechavi M., 2012. Bioinformatics, 28 (7) pp. 1017-1020. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5605BDB61FC5]
2011
Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication.
Roux J., Robinson-Rechavi M., 2011. Genome Research, 21 (3) pp. 357-363. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_21E4AE52DF8C]
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees.
Boeckmann B., Robinson-Rechavi M., Xenarios I., Dessimoz C., 2011. Briefings in Bioinformatics, 12 (5) pp. 423-435. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3EF9A7BDC38C]
 
Evolution of the epithelial sodium channel and the sodium pump as limiting factors of aldosterone action on sodium transport.
Studer R.A., Person E., Robinson-Rechavi M., Rossier B.C., 2011. Physiological Genomics, 43 (13) pp. 844-854. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_FAC3750250F9]
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.
Jagannathan V., Robinson-Rechavi M., 2011. BMC Systems Biology, 5 (1) p. 138. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_8CDBA887EAAA]
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.
Di Tommaso P., Moretti S., Xenarios I., Orobitg M., Montanyola A., Chang J.M., Taly J.F., Notredame C., 2011. Nucleic Acids Research, 39 (Web Server issue) pp. W13-W17.
[URN][DOI][Pmid][serval:BIB_EE8EDC0ACBE8]
 
The challenge of modeling nuclear receptor regulatory networks in mammalian cells.
Jagannathan V., Robinson-Rechavi M., 2011. Molecular and Cellular Endocrinology, 334 (1-2) pp. 91-97. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_64B60EC69445]
When orthologs diverge between human and mouse.
Gharib W.H., Robinson-Rechavi M., 2011. Briefings in Bioinformatics, 12 (5) pp. 436-441. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_006579177FCC]
2010
 
Adaptive divergence of ancient gene duplicates in the avian MHC class II beta.
Burri R., Salamin N., Studer R.A., Roulin A., Fumagalli L., 2010. Molecular Biology and Evolution, 27 (10) pp. 2360-2374. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_58E9592A045F]
An ontology to clarify homology-related concepts.
Roux J., Robinson-Rechavi M., 2010. Trends in Genetics, 26 (3) pp. 99-102. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_611EAEEC4DD5]
 
Evolution moléculaire
Duret L., Bataillon T., Bierne N., Daubin V., Dutheil J., Gautier C., Glemin S., Gouy M., Heyer E., Marais G. et al., 2010. pp. 123-182 dans Thomas F., Lefevre T., Raymond M. (eds.) Biologie évolutive chap. 5, de Boeck.
[serval:BIB_F2FDBFECBF3D]
Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy.
Parmentier G., Bastian F.B., Robinson-Rechavi M., 2010. Bioinformatics, 26 (14) pp. 1766-1771. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_1DA8753017CD]
 
Interactome mapping of the phosphatidylinositol 3-kinase-mammalian target of rapamycin pathway identifies deformed epidermal autoregulatory factor-1 as a new glycogen synthase kinase-3 interactor.
Pilot-Storck F., Chopin E., Rual J.F., Baudot A., Dobrokhotov P., Robinson-Rechavi M., Brun C., Cusick M.E., Hill D.E., Schaeffer L. et al., 2010. Molecular and Cellular Proteomics, 9 (7) pp. 1578-1593. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_99B5C8832AB6]
Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution.
Studer R.A., Robinson-Rechavi M., 2010. Molecular Biology and Evolution, 27 (11) pp. 2618-2627. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_47EE94487936]
Molecular evidence for a functional ecdysone signaling system in Brugia malayi.
Tzertzinis G., Egaña A.L., Palli S.R., Robinson-Rechavi M., Gissendanner C.R., Liu C., Unnasch T.R., Maina C.V., 2010. PLoS Neglected Tropical Diseases, 4 (3) pp. e625. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3EC23B792936]
Molecular signaling in zebrafish development and the vertebrate phylotypic period
Comte A., Roux J., Robinson-Rechavi M., 2010. Evolution and Development, 12 (2) pp. 144-156. Peer-reviewed.
[URN][DOI][WoS][serval:BIB_AD3A9D7540C9]
 
Phylogenetic Code in the Cloud - Can it Meet the Expectations?
Kraut A., Moretti S., Robinson-Rechavi M., Stockinger H., Flanders D., 2010. Studies in Health Technology and Informatics, 159 pp. 55-63. Peer-reviewed.
[DOI][Pmid][serval:BIB_1F5A96C03D27]
2009
Bioinformatics for evolutionary developmental biology
Robinson-Rechavi M., 2009. pp. 355-378 dans Appel R.D., Feytmans E. (eds.) Bioinformatics: A Swiss Perspective chap. 13, World Scientific Publishing Company.
[URN][serval:BIB_55CE3435659A]
 
Evidence for an episodic model of protein sequence evolution.
Studer R.A., Robinson-Rechavi M., 2009. Biochemical Society transactions, 37 (Pt 4) pp. 783-786. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_43CBA0DC9689]
How confident can we be that orthologs are similar, but paralogs differ?
Studer R.A., Robinson-Rechavi M., 2009. Trends in Genetics, 25 (5) pp. 210-216. Peer-reviewed.
[URN][DOI][WoS][serval:BIB_39F8106EE698]
Large-Scale Analyses of Positive Selection Using Codon Models
Studer R.A., Robinson-Rechavi M., 2009. pp. 217-236 dans Pontarotti P. (eds.) Evolutionary Biology: Concept, Modeling, and Application chap. 13, Springer‐Verlag.
[URN][DOI][serval:BIB_69764375A158]
Selectome: a database of positive selection.
Proux E., Studer R.A., Moretti S., Robinson-Rechavi M., 2009. Nucleic Acids Research, 37 (Database issue) pp. D404-D407. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_92B1AFBBA077]
 
Structural and evolutionary innovation of the heterodimerization interface between USP and the ecdysone receptor ECR in insects.
Iwema T., Chaumot A., Studer R.A., Robinson-Rechavi M., Billas I.M., Moras D., Laudet V., Bonneton F., 2009. Molecular Biology and Evolution, 26 (4) pp. 753-768. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6C84793F923C]
The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes.
Cruz F., Roux J., Robinson-Rechavi M., 2009. BMC Genomics, 10 (1) p. 619. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_AE3C1C5E6707]
2008
 
Analisi della dieta di Euproctus platycephalus (“Diet analysis of Euproctus platycephalus”)
Sotgiu A, Zancolli Giulia, Bovero S, Angelini C, Giacoma C, 2008. dans Herpetologia Sardiniae.
[serval:BIB_9573EDD9B716]
Bgee: integrating and comparing heterogeneous transcriptome data among species
Bastian F., Parmentier G., Roux J., Moretti S., Laudet V., Robinson-Rechavi M., 2008. pp. 124-131 dans Istrail S., Pevzner P., Waterman M. (eds.) Data Integration in Life Sciences, Lecture Notes in Computer Science. Peer-reviewed, Springer.
[URN][DOI][serval:BIB_5A6F9D63F92D]
Developmental constraints on vertebrate genome evolution.
Roux J., Robinson-Rechavi M., 2008. PLoS Genetics, 4 (12) pp. e1000311. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F11302BD61EC]
 
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.
Abad P., Gouzy J., Aury J.M., Castagnone-Sereno P., Danchin E.G., Deleury E., Perfus-Barbeoch L., Anthouard V., Artiguenave F., Blok V.C. et al., 2008. Nature Biotechnology, 26 (8) pp. 909-915. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0FED258C5533]
 
Orthologues of the Drosophila melanogaster E75 molting control gene in the filarial parasites Brugia malayi and Dirofilaria immitis.
Crossgrove K., Maina C.V., Robinson-Rechavi M., Lochner M.C., 2008. Molecular and Biochemical Parasitology, 157 (1) pp. 92-97. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_3BBFB417BF02]
Perspective: from molecular endocrinology of mouse to genomic endocrinology of animals.
Robinson-Rechavi M., 2008. Molecular and Cellular Endocrinology, 293 (1-2) pp. 2-4.
[URN][DOI][WoS][Pmid][serval:BIB_C469EC983655]
 
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes.
Studer R.A., Penel S., Duret L., Robinson-Rechavi M., 2008. Genome Research, 18 (9) pp. 1393-1402. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_08713507D4D6]
 
The amphioxus genome and the evolution of the chordate karyotype.
Putnam N.H., Butts T., Ferrier D.E., Furlong R.F., Hellsten U., Kawashima T., Robinson-Rechavi M., Shoguchi E., Terry A., Yu J.K. et al., 2008. Nature, 453 (7198) pp. 1064-1071. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_335B81A678B3]
 
The amphioxus genome illuminates vertebrate origins and cephalochordate biology.
Holland L.Z., Albalat R., Azumi K., Benito-Gutiérrez E., Blow M.J., Bronner-Fraser M., Brunet F., Butts T., Candiani S., Dishaw L.J. et al., 2008. Genome Research, 18 (7) pp. 1100-1111. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_987DB6FE8B4B]
 
The legacy of domestication: accumulation of deleterious mutations in the dog genome.
Cruz F., Vilà C., Webster M.T., 2008. Molecular Biology and Evolution, 25 (11) pp. 2331-2336. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_EC8C84DC5332]
2007
A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network.
Amoutzias G.D., Pichler E.E., Mian N., De Graaf D., Imsiridou A., Robinson-Rechavi M., Bornberg-Bauer E., Robertson D.L., Oliver S.G., 2007. BMC Systems Biology, 1 p. 34. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_8C6B61D79078]
 
One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity.
Amoutzias G.D., Veron A.S., Weiner J., Robinson-Rechavi M., Bornberg-Bauer E., Oliver S.G., Robertson D.L., 2007. Molecular Biology and Evolution, 24 (3) pp. 827-835.
[DOI][WoS][Pmid][serval:BIB_A168E290C027]
2006
Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima.
Robinson-Rechavi M., Alibés A., Godzik A., 2006. Journal of Molecular Biology, 356 (2) pp. 547-557. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_DE7A148B9A94]
 
Gene loss and evolutionary rates following whole-genome duplication in teleost fishes.
Brunet F.G., Roest Crollius H., Paris M., Aury J.M., Gibert P., Jaillon O., Laudet V., Robinson-Rechavi M., 2006. Molecular Biology and Evolution, 23 (9) pp. 1808-1816. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_90789EA4F9CB]
Neofunctionalization in vertebrates: the example of retinoic acid receptors.
Escriva H., Bertrand S., Germain P., Robinson-Rechavi M., Umbhauer M., Cartry J., Duffraisse M., Holland L., Gronemeyer H., Laudet V., 2006. PLoS Genetics, 2 (7) pp. e102. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9B994D87AC3D]
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