Samuel Neuenschwander

Publications | Phd and Masters theses

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35 publications

En préparation
 
Indigenous peoples in eastern Brazil: insights from 19<sup>th</sup> century genomes and metagenomes
Cruz Dávalos Diana Ivette, Arizmendi Cárdenas Yami Ommar, Bravo-Lopez Miriam Jetzabel, Neuenschwander Samuel, Reis Silvia, Bastos Murilo Q. R., Stenderup Jesper, Yediay Fulya Eylem, Villa-Islas Viridiana, Reyna-Blanco Carlos S. et al..
[DOI][serval:BIB_47F5B2CAEC7C]
2024
 
Towards predicting the geographical origin of ancient samples with metagenomic data.
Bozzi D., Neuenschwander S., Cruz Dávalos D.I., Sousa da Mota B., Schroeder H., Moreno-Mayar J.V., Allentoft M.E., Malaspinas A.S., 2024/09/18. Scientific reports, 14 (1) p. 21794. Peer-reviewed.
[DOI][Pmid][serval:BIB_4C67F4828BA4]
2023
 
Mapache: a flexible pipeline to map ancient DNA.
Neuenschwander S., Cruz Dávalos D.I., Anchieri L., Sousa da Mota B., Bozzi D., Rubinacci S., Delaneau O., Rasmussen S., Malaspinas A.S., 2023/02/03. Bioinformatics, 39 (2) pp. btad028. Peer-reviewed.
[DOI][Pmid][serval:BIB_B6D821D0E6BE]
2022
Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study.
Arizmendi Cárdenas Y.O., Neuenschwander S., Malaspinas A.S., 2022. PeerJ, 10 pp. e12784. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_F63ADE26A585]
2021
The genomic history of the Aegean palatial civilizations.
Clemente F., Unterländer M., Dolgova O., Amorim CEG, Coroado-Santos F., Neuenschwander S., Ganiatsou E., Cruz Dávalos D.I., Anchieri L., Michaud F. et al., 2021/05/13. Cell, 184 (10) pp. 2565-2586.e21. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_114B1DCAE1B5]
2020
Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland.
Gauthier J., Pajkovic M., Neuenschwander S., Kaila L., Schmid S., Orlando L., Alvarez N., 2020/09. Molecular ecology resources, 20 (5) pp. 1191-1205. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9AFAA5147BB2]
New genome assembly of the barn owl (Tyto alba alba).
Ducrest A.L., Neuenschwander S., Schmid-Siegert E., Pagni M., Train C., Dylus D., Nevers Y., Warwick Vesztrocy A., San-Jose L.M., Dupasquier M. et al., 2020/03. Ecology and evolution, 10 (5) pp. 2284-2298. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_83891497D9E8]
Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release.
Duroy P.O., Bosshard S., Schmid-Siegert E., Neuenschwander S., Arib G., Lemercier P., Masternak J., Roesch L., Buron F., Girod P.A. et al., 2020/02. Biotechnology and bioengineering, 117 (2) pp. 466-485. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3F6D075DCCE1]
2019
 
Impact of deleterious mutations, sexually antagonistic selection, and mode of recombination suppression on transitions between male and female heterogamety.
Saunders P.A., Neuenschwander S., Perrin N., 2019/09. Heredity, 123 (3) pp. 419-428. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_4C83D16AEB79]
QuantiNemo 2: a Swiss knife to simulate complex demographic and genetic scenarios, forward and backward in time.
Neuenschwander S., Michaud F., Goudet J., 2019/03/01. Bioinformatics, 35 (5) pp. 886-888. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_6D2F79671E91]
2018
 
Sex-antagonistic genes, XY recombination and feminized Y chromosomes.
Cavoto E., Neuenschwander S., Goudet J., Perrin N., 2018/03. Journal of evolutionary biology, 31 (3) pp. 416-427. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F6C923B3D9F4]
Spatial and temporal genetic dynamics of the grasshopper <i>Oedaleus decorus</i> revealed by museum genomics.
Schmid S., Neuenschwander S., Pitteloud C., Heckel G., Pajkovic M., Arlettaz R., Alvarez N., 2018/02. Ecology and evolution, 8 (3) pp. 1480-1495. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_7E8FE095D4D3]
Complex genetic patterns in human arise from a simple range-expansion model over continental landmasses.
Kanitz R., Guillot E.G., Antoniazza S., Neuenschwander S., Goudet J., 2018. PLoS One, 13 (2) pp. e0192460. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_77ADA568BCF2]
Sex chromosome turnovers and genetic drift: a simulation study.
Saunders P.A., Neuenschwander S., Perrin N., 2018. Journal of Evolutionary Biology, 31 (9) pp. 1413-1419. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_81445E80C6C9]
2017
MAR-Mediated transgene integration into permissive chromatin and increased expression by recombination pathway engineering.
Kostyrko K., Neuenschwander S., Junier T., Regamey A., Iseli C., Schmid-Siegert E., Bosshard S., Majocchi S., Le Fourn V., Girod P.A. et al., 2017. Biotechnology and Bioengineering, 114 (2) pp. 384-396. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_322831BD76E3]
2016
Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations.
Rougemont Q., Roux C., Neuenschwander S., Goudet J., Launey S., Evanno G., 2016. PeerJ, 4 pp. e1910.
[URN][DOI][WoS][Pmid][serval:BIB_B3842DC657B0]
2014
Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine.
Fodor A., Segura V., Denis M., Neuenschwander S., Fournier-Level A., Chatelet P., Homa F.A., Lacombe T., This P., Le Cunff L., 2014. PLoS One, 9 (11) pp. e110436. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_7AB7E9EC65F1]
 
Natural selection in a postglacial range expansion: the case of the colour cline in the European barn owl.
Antoniazza S., Kanitz R., Neuenschwander S., Burri R., Gaigher A., Roulin A., Goudet J., 2014. Molecular Ecology, 23 (22) pp. 5508-5523. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A02C8265EEBB]
 
Regulation of 11β-hydroxysteroid dehydrogenase type 2 by microRNA.
Rezaei M., Andrieu T., Neuenschwander S., Bruggmann R., Mordasini D., Frey F.J., Vogt B., Frey B.M., 2014. Hypertension, 64 (4) pp. 860-866.
[DOI][WoS][Pmid][serval:BIB_9AFEA2A232DA]
 
Sex-chromosome turnovers: the hot-potato model.
Blaser O., Neuenschwander S., Perrin N., 2014. American Naturalist, 183 (1) pp. 140-146. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C2F255A0AE23]
 
Wheat alleles introgress into selfing wild relatives: empirical estimates from approximate Bayesian computation in Aegilops triuncialis.
Pajkovic M., Lappe S., Barman R., Parisod C., Neuenschwander S., Goudet J., Alvarez N., Guadagnuolo R., Felber F., Arrigo N., 2014. Molecular Ecology, 23 (20) pp. 5089-5101. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F38A9A03E51F]
2013
 
Evolutionary history of almond tree domestication in the Mediterranean basin.
Delplancke M., Alvarez N., Benoit L., Espíndola A., I Joly H., Neuenschwander S., Arrigo N., 2013. Molecular Ecology, 22 (4) pp. 1092-1104. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_518F08C4D8E8]
 
Sex-chromosome turnovers induced by deleterious mutation load.
Blaser O., Grossen C., Neuenschwander S., Perrin N., 2013. Evolution, 67 (3) pp. 635-645. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_E41CACA16176]
2012
 
The balanced lethal system of crested newts: a ghost of sex chromosomes past?
Grossen C., Neuenschwander S., Perrin N., 2012. American Naturalist, 180 (6) pp. E174-E183. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_38CA0C260197]
 
The evolution of XY recombination: sexually antagonistic selection versus deleterious mutation load.
Grossen C., Neuenschwander S., Perrin N., 2012. Evolution, 66 (10) pp. 3155-3166. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5C77F2084812]
2011
 
On the maintenance of sex-chromosome polymorphism by sex-antagonistic selection
Blaser O., Neuenschwander S., Perrin N., 2011. American Naturalist, 178 (4) pp. 515-524. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_16087D661A53]
 
Temperature-dependent turnovers in sex-determination mechanisms: a quantitative model.
Grossen C., Neuenschwander S., Perrin N., 2011. Evolution, 65 (1) pp. 64-78. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B977C469C445]
2010
ABCtoolbox: a versatile toolkit for approximate Bayesian computations.
Wegmann D., Leuenberger C., Neuenschwander S., Excoffier L., 2010. BMC Bioinformatics, 11 (1) p. 116.
[URN][DOI][WoS][Pmid][serval:BIB_C966F74A3943]
2008
 
Colonization history of the Swiss Rhine basin by the bullhead (Cottus gobio): Inference under a Bayesian spatially explicit framework.
Neuenschwander S Largiadèr CR Ray N Currat M Vonlanthen P Excoffier Laurent, 2008. Molecular Ecology, 17 (3) pp. 757-772.
[DOI][WoS][serval:BIB_F50210AA184F]
quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation.
Neuenschwander S., Hospital F., Guillaume F., Goudet J., 2008. Bioinformatics, 24 (13) pp. 1552-1553. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_DD30BF02D4FC]
 
Reply: Reply to Garrigan and Hammer: Ancient lineages and assimilation
Fagundes N J R, Ray N, Beaumont M, Neuenschwander S, Salzano F M, Bonatto S L & Excoffier L , 2008. Proceedings of the National Academy of Sciences USA, 105 pp. E4. Peer-reviewed.
[serval:BIB_3E25B8F43F9E]
2007
 
Genetic analysis of potential postglacial watershed crossings in Central Europe by the bullhead (Cottus gobio L.).
Vonlanthen P., Excoffier L., Bittner D., Persat H., Neuenschwander S., Largiadèr C.R., 2007. Molecular Ecology, 16 (21) pp. 4572-4584. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_1A8A5BC8CFC3]
 
Statistical evaluation of alternative models of human evolution.
Fagundes N.J., Ray N., Beaumont M., Neuenschwander S., Salzano F.M., Bonatto S.L., Excoffier L., 2007. Proceedings of the National Academy of Sciences of the United States of America, 104 (45) pp. 17614-17619. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_131A12AF1402]
2006
 
AQUASPLATCHE: A program to simulate genetic diversity in populations living in linear habitats.
Neuenschwander S., 2006. Molecular Ecology Notes, 6 (3) pp. 583-585. Peer-reviewed.
[WoS][serval:BIB_2C277E37E7FB]
2003
 
Brood size, sibling competition, and the cost of begging in great tits (Parus major).
Neuenschwander S., Brinkhof Martin W. G., Kölliker M., Richner H., 2003. Behavioral Ecology, 14 (4) pp. 457-462.
[WoS][serval:BIB_0A6473C757B3]
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