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1.

Harnessing deep learning for population genetic inference.

Huang, Xin; Rymbekova, Aigerim; Dolgova, Olga; Lao, Oscar; Kuhlwilm, Martin.

Nat Rev Genet ; 25(1): 61-78, 2024 Jan.

Artículo en Inglés | MEDLINE | ID: mdl-37666948

2.

Identification of constrained sequence elements across 239 primate genomes.

Kuderna, Lukas F K; Ulirsch, Jacob C; Rashid, Sabrina; Ameen, Mohamed; Sundaram, Laksshman; Hickey, Glenn; Cox, Anthony J; Gao, Hong; Kumar, Arvind; Aguet, Francois; Christmas, Matthew J; Clawson, Hiram; Haeussler, Maximilian; Janiak, Mareike C; Kuhlwilm, Martin; Orkin, Joseph D; Bataillon, Thomas; Manu, Shivakumara; Valenzuela, Alejandro; Bergman, Juraj; Rouselle, Marjolaine; Silva, Felipe Ennes; Agueda, Lidia; Blanc, Julie; Gut, Marta; de Vries, Dorien; Goodhead, Ian; Harris, R Alan; Raveendran, Muthuswamy; Jensen, Axel; Chuma, Idriss S; Horvath, Julie E; Hvilsom, Christina; Juan, David; Frandsen, Peter; Schraiber, Joshua G; de Melo, Fabiano R; Bertuol, Fabrício; Byrne, Hazel; Sampaio, Iracilda; Farias, Izeni; Valsecchi, João; Messias, Malu; da Silva, Maria N F; Trivedi, Mihir; Rossi, Rogerio; Hrbek, Tomas; Andriaholinirina, Nicole; Rabarivola, Clément J; Zaramody, Alphonse.

Nature ; 625(7996): 735-742, 2024 Jan.

Artículo en Inglés | MEDLINE | ID: mdl-38030727

3.

The dental proteome of Homo antecessor.

Welker, Frido; Ramos-Madrigal, Jazmín; Gutenbrunner, Petra; Mackie, Meaghan; Tiwary, Shivani; Rakownikow Jersie-Christensen, Rosa; Chiva, Cristina; Dickinson, Marc R; Kuhlwilm, Martin; de Manuel, Marc; Gelabert, Pere; Martinón-Torres, María; Margvelashvili, Ann; Arsuaga, Juan Luis; Carbonell, Eudald; Marques-Bonet, Tomas; Penkman, Kirsty; Sabidó, Eduard; Cox, Jürgen; Olsen, Jesper V; Lordkipanidze, David; Racimo, Fernando; Lalueza-Fox, Carles; Bermúdez de Castro, José María; Willerslev, Eske; Cappellini, Enrico.

Nature ; 580(7802): 235-238, 2020 04.

Artículo en Inglés | MEDLINE | ID: mdl-32269345

4.

Author Correction: The dental proteome of Homo antecessor.

Welker, Frido; Ramos-Madrigal, Jazmín; Gutenbrunner, Petra; Mackie, Meaghan; Tiwary, Shivani; Jersie-Christensen, Rosa Rakownikow; Chiva, Cristina; Dickinson, Marc R; Kuhlwilm, Martin; de Manuel, Marc; Gelabert, Pere; Martinón-Torres, María; Margvelashvili, Ann; Arsuaga, Juan Luis; Carbonell, Eudald; Marques-Bonet, Tomas; Penkman, Kirsty; Sabidó, Eduard; Cox, Jürgen; Olsen, Jesper V; Lordkipanidze, David; Racimo, Fernando; Lalueza-Fox, Carles; de Castro, José María Bermúdez; Willerslev, Eske; Cappellini, Enrico.

Nature ; 584(7820): E19, 2020 Aug.

Artículo en Inglés | MEDLINE | ID: mdl-32724207

5.

Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories.

Bentley, Blair P; Carrasco-Valenzuela, Tomás; Ramos, Elisa K S; Pawar, Harvinder; Souza Arantes, Larissa; Alexander, Alana; Banerjee, Shreya M; Masterson, Patrick; Kuhlwilm, Martin; Pippel, Martin; Mountcastle, Jacquelyn; Haase, Bettina; Uliano-Silva, Marcela; Formenti, Giulio; Howe, Kerstin; Chow, William; Tracey, Alan; Sims, Ying; Pelan, Sarah; Wood, Jonathan; Yetsko, Kelsey; Perrault, Justin R; Stewart, Kelly; Benson, Scott R; Levy, Yaniv; Todd, Erica V; Shaffer, H Bradley; Scott, Peter; Henen, Brian T; Murphy, Robert W; Mohr, David W; Scott, Alan F; Duffy, David J; Gemmell, Neil J; Suh, Alexander; Winkler, Sylke; Thibaud-Nissen, Françoise; Nery, Mariana F; Marques-Bonet, Tomas; Antunes, Agostinho; Tikochinski, Yaron; Dutton, Peter H; Fedrigo, Olivier; Myers, Eugene W; Jarvis, Erich D; Mazzoni, Camila J; Komoroske, Lisa M.

Proc Natl Acad Sci U S A ; 120(7): e2201076120, 2023 02 14.

Artículo en Inglés | MEDLINE | ID: mdl-36749728

6.

Enamel proteome shows that Gigantopithecus was an early diverging pongine.

Welker, Frido; Ramos-Madrigal, Jazmín; Kuhlwilm, Martin; Liao, Wei; Gutenbrunner, Petra; de Manuel, Marc; Samodova, Diana; Mackie, Meaghan; Allentoft, Morten E; Bacon, Anne-Marie; Collins, Matthew J; Cox, Jürgen; Lalueza-Fox, Carles; Olsen, Jesper V; Demeter, Fabrice; Wang, Wei; Marques-Bonet, Tomas; Cappellini, Enrico.

Nature ; 576(7786): 262-265, 2019 12.

Artículo en Inglés | MEDLINE | ID: mdl-31723270

7.

Link between Monkeypox Virus Genomes from Museum Specimens and 1965 Zoo Outbreak.

Hämmerle, Michelle; Rymbekova, Aigerim; Gelabert, Pere; Sawyer, Susanna; Cheronet, Olivia; Bernardi, Paolo; Calvignac-Spencer, Sébastien; Kuhlwilm, Martin; Guellil, Meriam; Pinhasi, Ron.

Emerg Infect Dis ; 30(4): 816-818, 2024 Apr.

Artículo en Inglés | MEDLINE | ID: mdl-38526306

8.

sstar: A Python Package for Detecting Archaic Introgression from Population Genetic Data with S.

Huang, Xin; Kruisz, Patricia; Kuhlwilm, Martin.

Mol Biol Evol ; 39(11)2022 11 03.

Artículo en Inglés | MEDLINE | ID: mdl-36181428

9.

Ancient gene flow from early modern humans into Eastern Neanderthals.

Kuhlwilm, Martin; Gronau, Ilan; Hubisz, Melissa J; de Filippo, Cesare; Prado-Martinez, Javier; Kircher, Martin; Fu, Qiaomei; Burbano, Hernán A; Lalueza-Fox, Carles; de la Rasilla, Marco; Rosas, Antonio; Rudan, Pavao; Brajkovic, Dejana; Kucan, Zeljko; Gusic, Ivan; Marques-Bonet, Tomas; Andrés, Aida M; Viola, Bence; Pääbo, Svante; Meyer, Matthias; Siepel, Adam; Castellano, Sergi.

Nature ; 530(7591): 429-33, 2016 Feb 25.

Artículo en Inglés | MEDLINE | ID: mdl-26886800

10.

The genetic impact of an Ebola outbreak on a wild gorilla population.

Fontsere, Claudia; Frandsen, Peter; Hernandez-Rodriguez, Jessica; Niemann, Jonas; Scharff-Olsen, Camilla Hjorth; Vallet, Dominique; Le Gouar, Pascaline; Ménard, Nelly; Navarro, Arcadi; Siegismund, Hans R; Hvilsom, Christina; Gilbert, M Thomas P; Kuhlwilm, Martin; Hughes, David; Marques-Bonet, Tomas.

BMC Genomics ; 22(1): 735, 2021 Oct 11.

Artículo en Inglés | MEDLINE | ID: mdl-34635054

11.

Admixture in Mammals and How to Understand Its Functional Implications: On the Abundance of Gene Flow in Mammalian Species, Its Impact on the Genome, and Roads into a Functional Understanding.

Fontsere, Claudia; de Manuel, Marc; Marques-Bonet, Tomas; Kuhlwilm, Martin.

Bioessays ; 41(12): e1900123, 2019 12.

Artículo en Inglés | MEDLINE | ID: mdl-31664727

12.

The complete genome sequence of a Neanderthal from the Altai Mountains.

Prüfer, Kay; Racimo, Fernando; Patterson, Nick; Jay, Flora; Sankararaman, Sriram; Sawyer, Susanna; Heinze, Anja; Renaud, Gabriel; Sudmant, Peter H; de Filippo, Cesare; Li, Heng; Mallick, Swapan; Dannemann, Michael; Fu, Qiaomei; Kircher, Martin; Kuhlwilm, Martin; Lachmann, Michael; Meyer, Matthias; Ongyerth, Matthias; Siebauer, Michael; Theunert, Christoph; Tandon, Arti; Moorjani, Priya; Pickrell, Joseph; Mullikin, James C; Vohr, Samuel H; Green, Richard E; Hellmann, Ines; Johnson, Philip L F; Blanche, Hélène; Cann, Howard; Kitzman, Jacob O; Shendure, Jay; Eichler, Evan E; Lein, Ed S; Bakken, Trygve E; Golovanova, Liubov V; Doronichev, Vladimir B; Shunkov, Michael V; Derevianko, Anatoli P; Viola, Bence; Slatkin, Montgomery; Reich, David; Kelso, Janet; Pääbo, Svante.

Nature ; 505(7481): 43-9, 2014 Jan 02.

Artículo en Inglés | MEDLINE | ID: mdl-24352235

13.

Resurrection of the Ghosts.

Kuhlwilm, Martin.

Bioessays ; 42(6): e2000057, 2020 06.

Artículo en Inglés | MEDLINE | ID: mdl-32364279

14.

Patterns of coding variation in the complete exomes of three Neandertals.

Castellano, Sergi; Parra, Genís; Sánchez-Quinto, Federico A; Racimo, Fernando; Kuhlwilm, Martin; Kircher, Martin; Sawyer, Susanna; Fu, Qiaomei; Heinze, Anja; Nickel, Birgit; Dabney, Jesse; Siebauer, Michael; White, Louise; Burbano, Hernán A; Renaud, Gabriel; Stenzel, Udo; Lalueza-Fox, Carles; de la Rasilla, Marco; Rosas, Antonio; Rudan, Pavao; Brajkovic, Dejana; Kucan, Zeljko; Gusic, Ivan; Shunkov, Michael V; Derevianko, Anatoli P; Viola, Bence; Meyer, Matthias; Kelso, Janet; Andrés, Aida M; Pääbo, Svante.

Proc Natl Acad Sci U S A ; 111(18): 6666-71, 2014 May 06.

Artículo en Inglés | MEDLINE | ID: mdl-24753607

15.

A test for ancient selective sweeps and an application to candidate sites in modern humans.

Racimo, Fernando; Kuhlwilm, Martin; Slatkin, Montgomery.

Mol Biol Evol ; 31(12): 3344-58, 2014 Dec.

Artículo en Inglés | MEDLINE | ID: mdl-25172957

16.

Analysis of candidate genes for lineage-specific expression changes in humans and primates.

Lindskog, Cecilia; Kuhlwilm, Martin; Davierwala, Armaity; Fu, Ning; Hegde, Geeta; Uhlén, Mathias; Navani, Sanjay; Pääbo, Svante; Pontén, Fredrik.

J Proteome Res ; 13(8): 3596-606, 2014 Aug 01.

Artículo en Inglés | MEDLINE | ID: mdl-24911366

17.

Ghost admixture in eastern gorillas.

Pawar, Harvinder; Rymbekova, Aigerim; Cuadros-Espinoza, Sebastian; Huang, Xin; de Manuel, Marc; van der Valk, Tom; Lobon, Irene; Alvarez-Estape, Marina; Haber, Marc; Dolgova, Olga; Han, Sojung; Esteller-Cucala, Paula; Juan, David; Ayub, Qasim; Bautista, Ruben; Kelley, Joanna L; Cornejo, Omar E; Lao, Oscar; Andrés, Aida M; Guschanski, Katerina; Ssebide, Benard; Cranfield, Mike; Tyler-Smith, Chris; Xue, Yali; Prado-Martinez, Javier; Marques-Bonet, Tomas; Kuhlwilm, Martin.

Nat Ecol Evol ; 7(9): 1503-1514, 2023 09.

Artículo en Inglés | MEDLINE | ID: mdl-37500909

18.

Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons.

Sørensen, Erik F; Harris, R Alan; Zhang, Liye; Raveendran, Muthuswamy; Kuderna, Lukas F K; Walker, Jerilyn A; Storer, Jessica M; Kuhlwilm, Martin; Fontsere, Claudia; Seshadri, Lakshmi; Bergey, Christina M; Burrell, Andrew S; Bergman, Juraj; Phillips-Conroy, Jane E; Shiferaw, Fekadu; Chiou, Kenneth L; Chuma, Idrissa S; Keyyu, Julius D; Fischer, Julia; Gingras, Marie-Claude; Salvi, Sejal; Doddapaneni, Harshavardhan; Schierup, Mikkel H; Batzer, Mark A; Jolly, Clifford J; Knauf, Sascha; Zinner, Dietmar; Farh, Kyle K-H; Marques-Bonet, Tomas; Munch, Kasper; Roos, Christian; Rogers, Jeffrey.

Science ; 380(6648): eabn8153, 2023 06 02.

Artículo en Inglés | MEDLINE | ID: mdl-37262153

19.

Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons.

Sørensen, Erik F; Harris, R Alan; Zhang, Liye; Raveendran, Muthuswamy; Kuderna, Lukas F K; Walker, Jerilyn A; Storer, Jessica M; Kuhlwilm, Martin; Fontsere, Claudia; Seshadri, Lakshmi; Bergey, Christina M; Burrell, Andrew S; Bergmann, Juraj; Phillips-Conroy, Jane E; Shiferaw, Fekadu; Chiou, Kenneth L; Chuma, Idrissa S; Keyyu, Julius D; Fischer, Julia; Gingras, Marie-Claude; Salvi, Sejal; Doddapaneni, Harshavardhan; Schierup, Mikkel H; Batzer, Mark A; Jolly, Clifford J; Knauf, Sascha; Zinner, Dietmar; Farh, Kyle K-H; Marques-Bonet, Tomas; Munch, Kasper; Roos, Christian; Rogers, Jeffrey.

bioRxiv ; 2023 May 02.

Artículo en Inglés | MEDLINE | ID: mdl-37205419

20.

A global catalog of whole-genome diversity from 233 primate species.

Kuderna, Lukas F K; Gao, Hong; Janiak, Mareike C; Kuhlwilm, Martin; Orkin, Joseph D; Bataillon, Thomas; Manu, Shivakumara; Valenzuela, Alejandro; Bergman, Juraj; Rousselle, Marjolaine; Silva, Felipe Ennes; Agueda, Lidia; Blanc, Julie; Gut, Marta; de Vries, Dorien; Goodhead, Ian; Harris, R Alan; Raveendran, Muthuswamy; Jensen, Axel; Chuma, Idrissa S; Horvath, Julie E; Hvilsom, Christina; Juan, David; Frandsen, Peter; Schraiber, Joshua G; de Melo, Fabiano R; Bertuol, Fabrício; Byrne, Hazel; Sampaio, Iracilda; Farias, Izeni; Valsecchi, João; Messias, Malu; da Silva, Maria N F; Trivedi, Mihir; Rossi, Rogerio; Hrbek, Tomas; Andriaholinirina, Nicole; Rabarivola, Clément J; Zaramody, Alphonse; Jolly, Clifford J; Phillips-Conroy, Jane; Wilkerson, Gregory; Abee, Christian; Simmons, Joe H; Fernandez-Duque, Eduardo; Kanthaswamy, Sree; Shiferaw, Fekadu; Wu, Dongdong; Zhou, Long; Shao, Yong.

Science ; 380(6648): 906-913, 2023 06 02.

Artículo en Inglés | MEDLINE | ID: mdl-37262161

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Harnessing deep learning for population genetic inference.

Identification of constrained sequence elements across 239 primate genomes.

The dental proteome of Homo antecessor.

Author Correction: The dental proteome of Homo antecessor.

Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories.

Enamel proteome shows that Gigantopithecus was an early diverging pongine.

Link between Monkeypox Virus Genomes from Museum Specimens and 1965 Zoo Outbreak.

sstar: A Python Package for Detecting Archaic Introgression from Population Genetic Data with S.

Ancient gene flow from early modern humans into Eastern Neanderthals.

The genetic impact of an Ebola outbreak on a wild gorilla population.

Admixture in Mammals and How to Understand Its Functional Implications: On the Abundance of Gene Flow in Mammalian Species, Its Impact on the Genome, and Roads into a Functional Understanding.

The complete genome sequence of a Neanderthal from the Altai Mountains.

Resurrection of the Ghosts.

Patterns of coding variation in the complete exomes of three Neandertals.

A test for ancient selective sweeps and an application to candidate sites in modern humans.

Analysis of candidate genes for lineage-specific expression changes in humans and primates.

Ghost admixture in eastern gorillas.

Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons.

Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons.

A global catalog of whole-genome diversity from 233 primate species.