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Liens UNIL

Faculty of Biology and Medicine

Department of Computational Biology

Publications

You can find here the publications list with the links to publications of my group. You can also check this on my google scholar account.

Publications | Masters and Phd thesis

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Publications

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In Press | 2024 | 2023 | 2022 | 2021 | 2020 | ...

In Press

An evolutionary perspective of C4 photosynthesis in maize

Christin PA Besnard G dans Avances in maize, Prioul JL.

[serval:BIB_FCF024CBEBBB]

Exploring the Macroevolutionary Signature of Asymmetric Inheritance at Speciation.

Gaboriau T., Tobias J.A., Silvestro D., Salamin N. Systematic biology. Peer-reviewed.

[DOI][Pmid][serval:BIB_04FF91A74ECB]

Detecting diversifying selection for a trait from within and between-species genotypes and phenotypes.

Latrille T., Bastian M., Gaboriau T., Salamin N. Journal of evolutionary biology. Peer-reviewed.

[DOI][Pmid][serval:BIB_0EF18EA23CFD]

2024

preview resource BIB_15E89A0A809D.P001

Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation.

Silvestro D., Latrille T., Salamin N., 2024/10/30. Systematic biology, 73 (5) pp. 789-806. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_15E89A0A809D]

preview resource BIB_62B3CDA8C5C0.P001

Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish.

Schmid S., Bachmann Salvy M., Garcia Jimenez A., Bertrand JAM, Cortesi F., Heim S., Huyghe F., Litsios G., Marcionetti A., O'Donnell J.L. et al., 2024/07. Molecular ecology, 33 (14) pp. e17436. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_62B3CDA8C5C0]

preview resource BIB_6E177F953F6F.P001

Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex.

Marcionetti A., Bertrand JAM, Cortesi F., Donati GFA, Heim S., Huyghe F., Kochzius M., Pellissier L., Salamin N., 2024/06. Molecular ecology, 33 (11) pp. e17347. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_6E177F953F6F]

Hyper-Cryptic radiation of a tropical montane plant lineage.

Olivares I., Tusso S., José Sanín M., de La Harpe M., Loiseau O., Rolland J., Salamin N., Kessler M., Shimizu K.K., Paris M., 2024/01. Molecular phylogenetics and evolution, 190 p. 107954. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_33075489A124]

2023

Conceptual and empirical bridges between micro- and macroevolution.

Rolland J., Henao-Diaz L.F., Doebeli M., Germain R., Harmon L.J., Knowles L.L., Liow L.H., Mank J.E., Machac A., Otto S.P. et al., 2023/08. Nature ecology & evolution, 7 (8) pp. 1181-1193. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_8AB15E512733]

preview resource BIB_35025EC7D7BF.P001

Insights into the Genomics of Clownfish Adaptive Radiation: The Genomic Substrate of the Diversification.

Marcionetti A., Salamin N., 2023/07/03. Genome biology and evolution, 15 (7). Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_35025EC7D7BF]

preview resource BIB_6E38BFCA1196.P001

Divergence in metabolomic profile in clownfish and damselfish skin mucus

Heim S., Teav T., Gallart-Ayala H., Ivanisevic J., Salamin N., 2023/02/07. Frontiers in Ecology and Evolution, 11.

[URN][DOI][WoS][serval:BIB_6E38BFCA1196]

2022

Geogenomics of montane palms points to Miocene-Pliocene Andean segmentation related to strike-slip tectonics.

Sanín María José, Mejía-Franco Fabián Gregorio, Paris Margot, Valencia-Montoya Wendy A., Salamin Nicolas, Kessler Michael, Olivares Ingrid, Jaramillo Juan Sebastián, Cardona Agustín, 2022/09. Journal of Biogeography, 49 (9) pp. 1711-1725.

[DOI][WoS][serval:BIB_EC27D475E4DD]

2021

preview resource BIB_C1BA117F09FD.P001

Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae).

Zhang Q., Ree R.H., Salamin N., Xing Y., Silvestro D., 2021/12/16. Systematic biology, 71 (1) pp. 242-258. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_C1BA117F09FD]

Evolution of life cycles and reproductive traits: Insights from the brown algae.

Heesch S., Serrano-Serrano M., Barrera-Redondo J., Luthringer R., Peters A.F., Destombe C., Cock J.M., Valero M., Roze D., Salamin N. et al., 2021/07. Journal of evolutionary biology, 34 (7) pp. 992-1009. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_9FC279E4C2BC]

preview resource BIB_961363B69EFE.P001

Large-scale whole-genome resequencing unravels the domestication history of Cannabis sativa.

Ren G., Zhang X., Li Y., Ridout K., Serrano-Serrano M.L., Yang Y., Liu A., Ravikanth G., Nawaz M.A., Mumtaz A.S. et al., 2021/07. Science Advances, 7 (29) pp. eabg2286. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_961363B69EFE]

preview resource BIB_BE78FE659A7E.P001

A Cautionary Note on the Use of Genotype Callers in Phylogenomics.

Duchen P., Salamin N., 2021/06/16. Systematic biology, 70 (4) pp. 844-854. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_BE78FE659A7E]

Thyroid hormones regulate the formation and environmental plasticity of white bars in clownfishes.

Salis P., Roux N., Huang D., Marcionetti A., Mouginot P., Reynaud M., Salles O., Salamin N., Pujol B., Parichy D.M. et al., 2021/06/08. Proceedings of the National Academy of Sciences of the United States of America, 118 (23). Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_3175D86F9AC6]

preview resource BIB_0102B1359D1E.P001

Phylogenomics of Gesneriaceae using targeted capture of nuclear genes.

Ogutcen Ezgi, Christe Camille, Nishii Kanae, Salamin Nicolas, Möller Michael, Perret Mathieu, 2021/04. Molecular phylogenetics and evolution, 157 p. 107068. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_0102B1359D1E]

preview resource BIB_FDE71488549F.P001

On the Effect of Asymmetrical Trait Inheritance on Models of Trait Evolution.

Duchen P., Alfaro M.L., Rolland J., Salamin N., Silvestro D., 2021/02/10. Systematic biology, 70 (2) pp. 376-388. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_FDE71488549F]

2020

Genomic footprints of repeated evolution of CAM photosynthesis in a Neotropical species radiation.

De La Harpe M., Paris M., Hess J., Barfuss MHJ, Serrano-Serrano M.L., Ghatak A., Chaturvedi P., Weckwerth W., Till W., Salamin N. et al., 2020/12. Plant, cell & environment, 43 (12) pp. 2987-3001. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_AF228E1EBF7B]

preview resource BIB_1D26146BBFF5.P001

Rapid climate change results in long-lasting spatial homogenization of phylogenetic diversity

Saladin Bianca, Pellissier Loïc, Graham Catherine H., Nobis Michael P., Salamin Nicolas, Zimmermann Niklaus E., 2020/12. Nature Communications, 11 (1). Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_1D26146BBFF5]

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Phd thesis

Publications (15)

preview resource BIB_4378AC7E7774.P001

The impact of mutualistic interactions on the ecology and evolution of clownfishes

García Jiménez Alberto J., 2024., Université de Lausanne, Faculté de biologie et médecine, Salamin Nicolas (dir.).

[URN][serval:BIB_4378AC7E7774]

preview resource BIB_247B252C9293.P001

Machine learning to infer the process of coevolution under the light of evolution

RAMA BALLESTEROS Rocío, 2022., Université de Lausanne, Faculté de biologie et médecine, Salamin Nicolas (dir.).

[URN][serval:BIB_247B252C9293]

preview resource BIB_26D5A182653A.P001

Evolutionary-functional genomics for an enhanced resolution of arthropod gene function

RUZZANTE Livio, 2022., Université de Lausanne, Faculté de biologie et médecine, Waterhouse Robert (dir.).

[URN][serval:BIB_26D5A182653A]

preview resource BIB_EB509CF38FFB.P001

How hybridisation and gene flow shaped the clownfishes’ evolutionary history

SCHMID Sarah, 2022., Université de Lausanne, Faculté de biologie et médecine, Salamin Nicolas (dir.).

[URN][serval:BIB_EB509CF38FFB]

preview resource BIB_7360DFA238AF.P001

Genomics of clownfish adaptive radiation

MARCIONETTI Anna, 2021., Université de Lausanne, Faculté de biologie et médecine, Salamin Nicolas (dir.).

[URN][serval:BIB_7360DFA238AF]

Plant diversification in Neotropical rainforests

Loiseau Oriane, 2019/04/12., Université de Lausanne, Faculté de biologie et médecine, Salamin Nicolas (dir.).

[serval:BIB_17938308CDAE]

preview resource BIB_D24577D3A885.P001

Progressive Multiple Sequence Alignment with Indel Evolution

Maiolo Massimo, 2019., Université de Lausanne, Faculté de biologie et médecine, Dessimoz Christophe (dir.).

[URN][serval:BIB_D24577D3A885]

preview resource BIB_D71D8857D8D8.P001

Molecular évolution of RuBisCO subunits

Yamada Kana, 2019., Université de Lausanne, Faculté de biologie et médecine, Salamin Nicolas (dir.).

[URN][serval:BIB_D71D8857D8D8]

preview resource BIB_123B86126BB5.P001

Genetic conséquences of historically geological and climatic events in Qinghai-Tibet Plateau : the Primula section Armerina as a case study

Ren Guangpeng, 2017., Université de Lausanne, Faculté de biologie et médecine, Salamin Nicolas (dir.).

[URN][serval:BIB_123B86126BB5]

preview resource BIB_D4955919051E.P002

CORRELATES AND GENETIC BASIS OF PLANT DIVERSIFICATION IN THE NEOTROPICS: THE GESNERIACEAE AS A CASE STUDY

SERRANO SERRANO Martha Liliana, 2016/09. 116, Université de Lausanne, Faculté de biologie et médecine, Nicolas Salamin (dir.).

[URN][serval:BIB_D4955919051E]

preview resource BIB_8E5536BAC604.P001

Long term evolutionary responses to whole genome duplication

Laurent S., 2016/08. 134, Université de Lausanne, Faculté de biologie et médecine, Robinson-Rechavi M. (dir.).

[URN][serval:BIB_8E5536BAC604]

Evolution of intraspecific variation : a comparative phylogenetic approach

Kostikova A., 2014. 219, Université de Lausanne, Faculté de biologie et médecine, Salamin N. (dir.).

[serval:BIB_732A4972EC08]

La spéciation écologique racontée au travers de l'étude de l'évolution des poissons-clowns et de quelques autres

Litsios G., 2014. 197, Université de Lausanne, Faculté de biologie et médecine, Salamin N. (dir.).

[serval:BIB_EFB3B1DF729C]

KCM, a general framework for codon-based model of evolution

Zaheri M., 2014. 118, Université de Lausanne, Faculté de biologie et médecine, Salamin N., Goudet J. (dir.).

[serval:BIB_A1A258358443]

The role of phylogeny in the spatial distributions and assembly of mountain plant communities.

Ndiribe C., 2013/09. 517, Université de Lausanne, Faculté de biologie et médecine, Guisan A. (dir.).

[serval:BIB_7DCA97328A7E]

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