Publications
Entries are generated from verified bibliographic records. Author order follows the published version. Peer-reviewed journal articles are listed separately from preprints and manuscripts.
2024
Extending the IICR to multiple genomes and identification of limitations of some demographic inferential methods
Lounès Chikhi, , Cyriel Paris, Marine Ha-Shan, Alexane Jouniaux, Armando Arredondo, Camille Noûs, Simona Grusea, Josué Corujo, Inês Lourenço, Simon Boitard, Olivier Mazet
bioRxiv, 2024
DOI ·
BibTeX
@article{chikhi2024extending, title = {Extending the IICR to multiple genomes and identification of limitations of some demographic inferential methods}, author = {Chikhi, Loun{\`e}s and Rodr{\'i}guez, Willy and Paris, Cyriel and Ha-Shan, Marine and Jouniaux, Alexane and Arredondo, Armando and No{\^u}s, Camille and Grusea, Simona and Corujo, Josu{\'e} and Louren{\c{c}}o, In{\^e}s and Boitard, Simon and Mazet, Olivier}, journal = {bioRxiv}, year = {2024}, doi = {10.1101/2024.08.16.608273} }2024
On the demographic history of chimpanzees and some consequences of integrating population structure in chimpanzees and other great apes
Camille Steux, Clément Couloigner, Armando Arredondo, , Olivier Mazet, Rémi Tournebize, Lounès Chikhi
bioRxiv, 2024
DOI ·
BibTeX
@article{steux2024chimpanzees, title = {On the demographic history of chimpanzees and some consequences of integrating population structure in chimpanzees and other great apes}, author = {Steux, Camille and Couloigner, Cl{\'e}ment and Arredondo, Armando and Rodr{\'i}guez, Willy and Mazet, Olivier and Tournebize, R{\'e}mi and Chikhi, Loun{\`e}s}, journal = {bioRxiv}, year = {2024}, doi = {10.1101/2024.06.14.599042} }2022
SeSAM: software for automatic construction of order-robust linkage maps
Adrien Vidal, Franck Gauthier, , Nadège Guiglielmoni, Damien Leroux, Nicolas Chevrolier, Sylvain Jasson, Elise Tourrette, Olivier C. Martin, Matthieu Falque
BMC Bioinformatics, 23, article 499, 2022
BibTeX
@article{vidal2022sesam, title = {SeSAM: software for automatic construction of order-robust linkage maps}, author = {Vidal, Adrien and Gauthier, Franck and Rodrigez, Willy and Guiglielmoni, Nad{\`e}ge and Leroux, Damien and Chevrolier, Nicolas and Jasson, Sylvain and Tourrette, Elise and Martin, Olivier C. and Falque, Matthieu}, journal = {BMC Bioinformatics}, volume = {23}, pages = {499}, year = {2022}, doi = {10.1186/s12859-022-05045-7} }2021
Inferring number of populations and changes in connectivity under the n-island model
Armando Arredondo, Beatriz Mourato, Khoa Nguyen, Simon Boitard, , Olivier Mazet, Lounès Chikhi
Heredity, 126(6), 896-912, 2021
BibTeX
@article{arredondo2021nisland, title = {Inferring number of populations and changes in connectivity under the n-island model}, author = {Arredondo, Armando and Mourato, Beatriz and Nguyen, Khoa and Boitard, Simon and Rodr{\'i}guez, Willy and Mazet, Olivier and Chikhi, Loun{\`e}s}, journal = {Heredity}, volume = {126}, number = {6}, pages = {896--912}, year = {2021}, doi = {10.1038/s41437-021-00426-9} }2020
Epidemic Dynamics via Wavelet Theory and Machine Learning with Applications to Covid-19
Tô Tat Dat, Frédéric Protin, Nguyen T. T. Hang, Jules Martel, Nguyen Duc Thang, Charles Piffault, , Susely Figueroa, Hông Vân Lê, Wilderich Tuschmann, Tien Zung Nguyen
Biology, 9(12), article 477, 2020
DOI ·
BibTeX
@article{to2020epidemic, title = {Epidemic Dynamics via Wavelet Theory and Machine Learning with Applications to Covid-19}, author = {T{\^o}, Tat Dat and Protin, Fr{\'e}d{\'e}ric and Hang, Nguyen T. T. and Martel, Jules and Nguyen, Duc Thang and Piffault, Charles and Rodr{\'i}guez, Willy and Figueroa, Susely and L{\^e}, H{\^o}ng V{\^a}n and Tuschmann, Wilderich and Nguyen, Tien Zung}, journal = {Biology}, volume = {9}, number = {12}, pages = {477}, year = {2020}, doi = {10.3390/biology9120477} }2019
Coalescence times for three genes provide sufficient information to distinguish population structure from population size changes
Simona Grusea, , Didier Pinchon, Lounès Chikhi, Simon Boitard, Olivier Mazet
Journal of Mathematical Biology, 78(1), 189-224, 2019
BibTeX
@article{grusea2019coalescence, title = {Coalescence times for three genes provide sufficient information to distinguish population structure from population size changes}, author = {Grusea, Simona and Rodr{\'i}guez, Willy and Pinchon, Didier and Chikhi, Loun{\`e}s and Boitard, Simon and Mazet, Olivier}, journal = {Journal of Mathematical Biology}, volume = {78}, number = {1}, pages = {189--224}, year = {2019}, doi = {10.1007/s00285-018-1272-4} }2018
The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure
, Olivier Mazet, Simona Grusea, Armando Arredondo, Josué M. Corujo, Simon Boitard, Lounès Chikhi
Heredity, 121(6), 663-678, 2018
BibTeX
@article{rodriguez2018nssc, title = {The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure}, author = {Rodr{\'i}guez, Willy and Mazet, Olivier and Grusea, Simona and Arredondo, Armando and Corujo, Josu{\'e} M. and Boitard, Simon and Chikhi, Loun{\`e}s}, journal = {Heredity}, volume = {121}, number = {6}, pages = {663--678}, year = {2018}, doi = {10.1038/s41437-018-0148-0} }2018
The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice
Lounès Chikhi, , Simona Grusea, Patrícia Santos, Simon Boitard, Olivier Mazet
Heredity, 120(1), 13-24, 2018
BibTeX
@article{chikhi2018iicr, title = {The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice}, author = {Chikhi, Loun{\`e}s and Rodr{\'i}guez, Willy and Grusea, Simona and Santos, Patr{\'i}cia and Boitard, Simon and Mazet, Olivier}, journal = {Heredity}, volume = {120}, number = {1}, pages = {13--24}, year = {2018}, doi = {10.1038/s41437-017-0005-6} }2016
On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?
Olivier Mazet, , Simona Grusea, Simon Boitard, Lounès Chikhi
Heredity, 116, 362-371, 2016
DOI ·
BibTeX
@article{mazet2016structured, title = {On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?}, author = {Mazet, Olivier and Rodr{\'i}guez, Willy and Grusea, Simona and Boitard, Simon and Chikhi, Loun{\`e}s}, journal = {Heredity}, volume = {116}, pages = {362--371}, year = {2016}, doi = {10.1038/hdy.2015.104} }2016
Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach
Simon Boitard, , Flora Jay, Stefano Mona, Frédéric Austerlitz
PLOS Genetics, 12(3), article e1005877, 2016
DOI ·
BibTeX
@article{boitard2016popsize, title = {Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach}, author = {Boitard, Simon and Rodr{\'i}guez, Willy and Jay, Flora and Mona, Stefano and Austerlitz, Fr{\'e}d{\'e}ric}, journal = {PLOS Genetics}, volume = {12}, number = {3}, pages = {e1005877}, year = {2016}, doi = {10.1371/journal.pgen.1005877} }2015
Demographic inference using genetic data from a single individual: Separating population size variation from population structure
Olivier Mazet, , Lounès Chikhi
Theoretical Population Biology, 104, 46-58, 2015
DOI ·
BibTeX
@article{mazet2015demographic, title = {Demographic inference using genetic data from a single individual: Separating population size variation from population structure}, author = {Mazet, Olivier and Rodr{\'i}guez, Willy and Chikhi, Loun{\`e}s}, journal = {Theoretical Population Biology}, volume = {104}, pages = {46--58}, year = {2015}, doi = {10.1016/j.tpb.2015.06.003} }