Professional Experience

Assistant Professor, University of Vienna

Since August 2021

Group leader of the Computational Admixture Genomics lab at the Department for Evolutionary Anthropology, with funding from WWTF.

LaCaixa JuniorLeader, UPF

April 2019 – July 2021

Postdoctoral fellow at the Universitat Pompeu Fabra, Barcelona

Postdoctoral researcher, Universitat Pompeu Fabra

October 2015 – March 2019

Postdoctoral researcher at the Institute for Evolutionary Biology, Universitat Pompeu Fabra, Barcelona
Oct 2015 – Oct 2018 with a fellowship from Deutsche Forschungsgemeinschaft (DFG)
Supervisor: Tomas Marques-Bonet

Max-Planck-Institute for Evolutionary Anthropology

June 2010 – October 2015

PhD student at MPI-EVA/University of Leipzig, Germany
Supervisor: Svante Pääbo
Grade: Magna cum laude

University of Halle-Wittenberg

2004 – 2010

German Diplom studies in Biology at the University of Halle-Wittenberg, Germany
Thesis supervisor: Gunter Reuter

Publications as main author

Links lead to publisher website. I will happily share PDFs in case you cannot access them there.

Harnessing deep learning for population genetic inference

2023, Nature Reviews Genetics

X. Huang, A. Rymbekova, O. Dolgova, O. Lao, M. Kuhlwilm

Ghost admixture in eastern gorillas

2023, Nature Ecology & Evolution

H. Pawar, A. Rymbekova, S. Cuadros-Espinoza, X. Huang, M. de Manuel, T. van der Valk, I. Lobon, M. Alvarez-Estape, M. Haber, O. Dolgova, S. Han, P. Esteller-Cucala, D. Juan, Q. Ayub, R. Bautista, J.L. Kelley, O.E. Cornejo, O. Lao, A.M. Andrés, K. Guschanski, B. Ssebide, M. Cranfield, C. Tyler-Smith, Y. Xue, J. Prado-Martinez, T. Marques-Bonet*, and M. Kuhlwilm*

sstar: A Python package for detecting archaic introgression from population genetic data with S*

2022, Molecular Biology & Evolution

X. Huang, P. Kruisz, M. Kuhlwilm

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

2021, BMC Genomics

C. Fontsere, P. Frandsen, J. Hernandez-Rodriguez, J. Niemann, C.H. Scharff-Olsen, D. Vallet, P. Le Gouar, N. Ménard, A. Navarro, H.R. Siegismund, C. Hvilsom, M.T.P. Gilbert, M. Kuhlwilm*, D. Hughes*, and T. Marques-Bonet*

HuConTest: Testing human contamination in great ape samples

2021, Genome Biology & Evolution

M. Kuhlwilm, C. Fontsere, S. Han, M. Alvarez-Estape, and T. Marques-Bonet

Admixture in mammals and how to understand its functional implications

2019, BioEssays

C. Fontsere*, M. de Manuel*, T. Marques-Bonet, M. Kuhlwilm

A catalog of single nucleotide changes distinguishing modern humans from archaic hominins

2019, Scientific Reports

M. Kuhlwilm and C. Boeckx

Ancient admixture from an extinct ape lineage into bonobos

2019, Nature Ecology & Evolution

M. Kuhlwilm, S. Han, V. C. Sousa, L. Excoffier, T. Marques-Bonet

Genetic variation in Pan species is shaped by demographic history and harbors lineage-specific functions

2019, Genome Biology & Evolution

S. Han, A. M. Andrés, T. Marques-Bonet, and M. Kuhlwilm

The evolution of FOXP2 in the light of admixture

2018, Current Opinion in Behavioral Sciences

M. Kuhlwilm

Chimpanzee genomic diversity reveals ancient admixture with bonobos

2016, Science

M. de Manuel*, M. Kuhlwilm*, P. Frandsen*, V. C. Sousa, T. Desai, J. Prado-Martinez, J. Hernandez-Rodriguez, I. Dupanloup, O. Lao, P. Hallast, J. M. Schmidt, J. M. Heredia-Genestar, A. Benazzo, G. Barbujani, B. M. Peter, L. F. K. Kuderna, F. Casals, S. Angedakin, M. Arandjelovic, C. Boesch, H. Kühl, L. Vigilant, K. Langergraber, J. Novembre, M. Gut, I. Gut, A. Navarro, F. Carlsen, A. M. Andrés, H. R. Siegismund, A. Scally, L. Excoffier, C. Tyler-Smith, S. Castellano, Y. Xue, C. Hvilsom, and T. Marques-Bonet

Ancient Gene Flow from Early Modern Humans into Eastern Neanderthals

2016, Nature

M. Kuhlwilm*, I. Gronau*, M. J. Hubisz, C. de Filippo, J. Prado-Martinez, M. Kircher, Q. Fu, H. A. Burbano, C. Lalueza-Fox, M. de la Rasilla, A. Rosas, P. Rudan, D. Brajkovic, Z. Kucan, I. Gusic, T. Marques-Bonet, A. M. Andres, B. Viola, S. Pääbo, M. Meyer, A. Siepel, and S. Castellano

Identification of Putative Target Genes of the Transcription Factor Runx2

2013, PLOS One

M. Kuhlwilm, A. Davierwala, and S. Pääbo

Other publications

Identification of constrained sequence elements across 239 primate genomes

2023, Nature

L. F. K. Kuderna, J. C. Ulirsch, S. Rashid, M. Ameen, L. Sundaram, G. Hickey, A. J. Cox, H. Gao, A. Kumar, F. Aguet, M. J. Christmas, H. Clawson, M. Haeussler, M. C. Janiak, M. Kuhlwilm, J. D. Orkin, T. Bataillon, S. Manu, A. Valenzuela, J. Bergman, M. Rouselle, F.E. Silva, L. Agueda, J. Blanc, M. Gut, D. de Vries, J. Goodhead, R. A. Harris, M. Raveendran, A. Jensen, I. S. Chuma, J. E. Horvath, C. Hvilsom, D. Juan, P. Frandsen, J. G. Schraiber, F. R. de Melo, F. Bertuol, H. Byrne, I. Sampaio, I. Farias, J. Valsecchi, M. Messias, M. N. F. da Silva, M. Trivedi, R. Rossi, T. Hrbek, N. Andriaholinirina, C. J. Rabarivola, A. Zaramody, C. J. Jolly, J. Phillips-Conroy, G. Wilkerson, C. Abee, J. H. Simmons, E. Fernandez-Duque, S. Kanthaswamy, F. Shiferaw, D. Wu, L. Zhou, Y. Shao, G. Zhang, J. D. Keyyu, S. Knauf, M. D. Le, E. Lizano, S. Merker, A. Navarro, T. Nadler, C. C. Khor, J. Lee, P. Tan, W. K. Lim, A. C. Kitchener, D. Zinner, I. Gut, A.D. Melin, K. Guschanski, M. H. Schierup, R. M. D. Beck, I. Karakikes, K. C. Wang, G. Umapathy, C. Roos, J. P. Boubli, A. Siepel, A. Kundaje, B. Paten, K. Lindblad-Toh, J. Rogers, T. Marques Bonet, and K. K.-H. Farh

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

2023, Science

L. F. K. Kuderna, H. Gao, M. C. Janiak, M. Kuhlwilm, J. D. Orkin, T. Bataillon, S. Manu, A. Valenzuela, J. Bergman, M. Rousselle, F. E. Silva, L. Agueda, J. Blanc, M. Gut, D. de Vries, I. Goodhead, R. A. Harris, M. Raveendran, A. Jensen, I. S. Chuma, J. E. Horvath, C. Hvilsom, D. Juan, P. Frandsen, J. G. Schraiber, F. R. de Melo, F. Bertuol, H. Byrne, I. Sampaio, I. Farias, J. Valsecchi, M. Messias, M. N. F. da Silva, M. Trivedi, R. Rossi, T. Hrbek, N. Andriaholinirina, C. J. Rabarivola, A. Zaramody, C. J. Jolly, J. Phillips-Conroy, G. Wilkerson, C. Abee, J. H. Simmons, E. Fernandez-Duque, S. Kanthaswamy, F. Shiferaw, D. Wu, L. Zhou, Y. Shao, G. Zhang, J. D. Keyyu, S. Knauf, M. D. Le, E. Lizano, S. Merker, A. Navarro, T. Nadler, C. C. Khor, J. Lee, P. Tan, W. K. Lim, A. C. Kitchener, D. Zinner, I. Gut, A. D. Melin, K. Guschanski, M. H. Schierup, R. M. D. Beck, G. Umapathy, C. Roos, J. P. Boubli, J. Rogers, K. K.-H. Farh, and T. Marques Bonet

The landscape of tolerated genetic variation in humans and primates

2023, Science

H. Gao, T. Hamp, J. Ede, J. G. Schraiber, J. McRae, M. Singer-Berk, Y. Yang, A. S. D. Dietrich, P. P. Fiziev, L. F. K. Kuderna, L. Sundaram, Y. Wu, A. Adhikari, Y. Field, C. Chen, S. Batzoglou, F. Aguet, G. Lemire, R. Reimers, D. Balick, M. C. Janiak, M. Kuhlwilm, J. D. Orkin, S. Manu, A. Valenzuela, J. Bergman, M. Rousselle, F. E. Silva, L. Agueda, J. Blanc, M. Gut, D. de Vries, I. Goodhead, R. A. Harris, M. Raveendran, A. Jensen, I. S. Chuma, J. E. Horvath, C. Hvilsom, D. Juan, P. Frandsen, F. R. de Melo, F. Bertuol, H. Byrne, I. Sampaio, I. Farias, J. V. do Amaral, M. Messias, M. N. F. da Silva, M. Trivedi, R. Rossi, T. Hrbek, N. Andriaholinirina, C. J. Rabarivola, A. Zaramody, C. J. Jolly, J. Phillips-Conroy, G. Wilkerson, C. Abee, J. H. Simmons, E. Fernandez-Duque, S. Kanthaswamy, F. Shiferaw, D. Wu, L. Zhou, Y. Shao, G. Zhang, J. D. Keyyu, S. Knauf, M. D. Le, E. Lizano, S. Merker, A. Navarro, T. Bataillon, T. Nadler, C. C. Khor, J. Lee, P. Tan, W. K. Lim, A. C. Kitchener, D. Zinner, I. Gut, A. Melin, K. Guschanski, M. H. Schierup, R. M. D. Beck, G. Umapathy, C. Roos, J. P. Boubli, M. Lek, S. Sunyaev, A. O’Donnell-Luria, H. L. Rehm, J. Xu, J. Rogers, T. Marques-Bonet, and K. K.-H. Farh

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

2023, Science

E. F. Sørensen, R. A. Harris, L. Zhang, M. Raveendran, L. F. K. Kuderna, J. A. Walker, J. M. Storer, M. Kuhlwilm, C. Fontsere, L. Seshadri, C. M. Bergey, A. S. Burrell, J. Bergman, J. E. Phillips-Conroy, F. Shiferaw, K. L. Chiou, I. S. Chuma, J. D. Keyyu, J. Fischer, M.-C. Gingras, S. Salvi, H. Doddapaneni, M. H. Schierup, M. A. Batzer, C. J. Jolly, S. Knauf, D. Zinner, K. K.-H. Farh, T. Marques-Bonet, K. Munch, C. Roos, and J. Rogers

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

2023, Proceedings of the National Academy of Sciences

B.P. Bentley, T. Carrasco-Valenzuela, E.K.S. Ramos, H. Pawar, L. Souza Arantes, A. Alexander, S.M. Banerjee, P. Masterson, M. Kuhlwilm, M. Pippel, J. Mountcastle, B. Haase, M. Uliano-Silva, G. Formenti, K. Howe, W. Chow, A. Tracey, Y. Sims, S. Pelan, J. Wood, K. Yetsko, J.R. Perrault, K. Stewart, S.R. Benson, Y. Levy, E.V. Toddt , H.B. Shaffer, P. Scott, B.T. Henen, R.W. Murphy, D.W. Mohr, A.F. Scott, DJ. Duffy, N.J. Gemmell, A.Suh, S. Winkler, F. Thibaud-Nissen, M.F. Nery, T. Marques-Bonet, A.Antunes, Y. Tikochinski, P.H. Dutton, O. Fedrigo, E.W. Myers, E.D. Jarvis, C.J. Mazzoni, L.M. Komoroske

Temporal mapping of derived high-frequency gene variants supports the mosaic nature of the evolution of Homo sapiens

2022, Scientific Reports

A. Andirkó, J. Moriano, A. Vitriolo, M. Kuhlwilm, G. Testa, and C. Boeckx

Population dynamics and genetic connectivity in recent chimpanzee history

2022, Cell Genomics

C. Fontsere, M. Kuhlwilm, C. Morcillo-Suarez, M. Alvarez-Estape, J.D. Lester, P. Gratton, J.M. Schmidt, P. Dieguez, T. Aebischer, P. Álvarez-Varona, A. Agbor, S. Angedakin, A.K. Assumang, E.A. Ayimisin, E. Bailey, D. Barubiyo, M. Bessone, A. Carretero-Alonso, R. Chancellor, H. Cohen, E. Danquah, T. Deschner, A. Dunn, J. Dupain, V.E. Egbe, O. Feliu, A. Goedmakers, A. Granjon, J. Head, D. Hedwig, V. Hermans, R.A. Hernandez-Aguilar, I. Imong, S. Jones, J. Junker, P. Kadam, M. Kaiser, M. Kambere, M.V. Kambale, A.K. Kalan, I. Kienast, D. Kujirakwinja, K. Langergraber, J. Lapuente, B. Larson, A. Laudisoit, K. Lee, M. Llana, M. Llorente, S. Marrocoli, D. Morgan, F. Mulindahabi, M. Murai, E. Neil, S. Nicholl, S. Nixon, E. Normand, C. Orbell, L.J. Ormsby, L. Pacheco, A. Piel, L. Riera, M.M. Robbins, A. Rundus, C. Sanz, L. Sciaky, V. Sommer, F.A. Stewart, N. Tagg, L.R. Tedonzong, E. Ton, J. van Schijndel, V. Vergnes, E.G. Wessling, J. Willie, R.M. Wittig, Y.G. Yuh, K. Yurkiw, K. Zuberbuehler, J. Hecht, L. Vigilant, C. Boesch, A.M. Andres, D.A. Hughes, H.S. Kühl, E. Lizano, M. Arandjelovic, and T. Marques-Bonet

Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures

2021, Nature Communcations

R. García-Pérez, P. Esteller-Cucala, G. Mas, I. Lobón, V. Di Carlo, M. Riera, M. Kuhlwilm, A. Navarro, A. Blancher, L. Di Croce, J. L. Gómez-Skarmeta, D. Juan, and T. Marquès-Bonet

Maximizing the acquisition of unique reads in non-invasive capture sequencing experiments

2020, Molecular Ecology Resources

C. Fontsere, M. Alvarez-Estape, J. Lester, M. Arandjelovic, M. Kuhlwilm, P. Dieguez, A. Agbor, S. Angedakin, E. A. Ayimisin, M. Bessone, G. Brazzola, T. Deschner, M. Eno-Nku, A.-C. Granjon, J. Head, P. Kadam, A. K. Kalan, M. Kambi, K. Langergraber, J. Lapuente, G. Maretti, L. J. Ormsby, A. Piel, M. M. Robbins, F. Stewart, V. Vergnes, R. M. Wittig, H. S. Kühl, T. Marques-Bonet, D. A. Hughes, and E. Lizano

Resurrection of the ghosts (Comment on DOI 10.1002/bies.202000012)

2020, BioEssays

M. Kuhlwilm

The dental proteome of Homo antecessor

2020, Nature

F. Welker, J. Ramos-Madrigal, P. Gutenbrunner, M. Mackie, S. Tiwary, R. Rakownikow Jersie-Christensen, C. Chiva, M. R. Dickinson, M. Kuhlwilm, M. de Manuel, P. Gelabert, M. Martinón-Torres, A. Margvelashvili, J. L. Arsuaga, E. Carbonell, T. Marques-Bonet, K. Penkman, E. Sabidó, J. Cox, J. V. Olsen, D. Lordkipanidze, F. Racimo, C. Lalueza-Fox, J. M. Bermúdez de Castro, E. Willerslev, E. Cappellini

Dental enamel proteome sequencing reveals Gigantopithecus as an early diverging pongine

2019, Nature

F. Welker, J. Ramos-Madrigal, M. Kuhlwilm, W. Liao, P. Gutenbrunner, M. de Manuel, D. Samodova, M. Mackie, M. E. Allentoft, A.-M. Bacon, J. Cox, C. Lalueza-Fox, J. V. Olsen, F. Demeter , W. Wang, T. Marques-Bonet, E. Cappellini

The Genomic Footprints of the Fall and Recovery of the Crested Ibis

2019, Current Biology

S. Feng, Q. Fang, R. Barnett, C. Li, S. Han, M. Kuhlwilm, L. Zhou, H. Pan, Y. Deng, G. Chen, A. Gamauf, F. Woog, R. Prys-Jones, T. Marques-Bonet, M. T. P. Gilbert, and G. Zhang

Selective single molecule sequencing and assembly of a human Y chromosome of African origin

2019, Nature Communications

L. F. K. Kuderna, E. Lizano, E. Julià, J. Gomez-Garrido, A. Serres-Armero, M. Kuhlwilm, R. A. Alandes, M. Alvarez-Estape, D. Juan, S. Heath, T. Alioto, M. Gut, I. Gut, M. H. Schierup, O. Fornas, and T. Marques-Bonet

Selection in the Introgressed Regions of the Chimpanzee Genome

2018, Genome Biology & Evolution

J. Nye, H. Laayouni, M. Kuhlwilm, M. Mondal, T. Marques-Bonet, and J. Bertranpetit

Evolution and demography of the great apes

2016, Current Opinion in Genetics & Development

M. Kuhlwilm*, M. de Manuel*, A. Nater*, M. P. Greminger*, M. Krützen, and T. Marques-Bonet

A Test for Ancient Selective Sweeps and an Application to Candidate Sites in Modern Humans

2014, Molecular Biology & Evolution

F. Racimo, M. Kuhlwilm, and M. Slatkin

Analysis of Candidate Genes for Lineage-Specific Expression Changes in Humans and Primates

2014, Journal of Proteome Research

C. Lindskog, M. Kuhlwilm, A. Davierwala, N. Fu, G. Hegde, M. Uhlen, S. Navani, S. Paabo, and F. Ponten

Patterns of Coding Variation in the Complete Exomes of Three Neandertals

2014, Proceedings of the National Academy of Sciences of the USA

S. Castellano, G. Parra*, F. A. Sanchez-Quinto*, F. Racimo*, M. Kuhlwilm*, M. Kircher, S. Sawyer, Q. Fu, A. Heinze, B. Nickel, J. Dabney, M. Siebauer, L. White, H. A. Burbano, G. Renaud, U. Stenzel, C. Lalueza-Fox, M. de la Rasilla, A. Rosas, P. Rudan, D. Brajkovic, Z. Kucan, I. Gusic, M. V. Shunkov, A. P. Derevianko, B. Viola, M. Meyer, J. Kelso, A. M. Andres, and S. Pääbo

The Complete Genome Sequence of a Neanderthal from the Altai Mountains

2014, Nature

K. Prüfer, F. Racimo, N. Patterson, F. Jay, S. Sankararaman, S. Sawyer, A. Heinze, G. Renaud, P. H. Sudmant, C. de Filippo, H. Li, S. Mallick, M. Dannemann, Q. Fu, M. Kircher, M. Kuhlwilm, M. Lachmann, M. Meyer, M. Ongyerth, M. Siebauer, C. Theunert, A. Tandon, P. Moorjani, J. Pickrell, J. C. Mullikin, S. H. Vohr, R. E. Green, I. Hellmann, P. L. Johnson, H. Blanche, H. Cann, J. O. Kitzman, J. Shendure, E. E. Eichler, E. S. Lein, T. E. Bakken, L. V. Golovanova, V. B. Doronichev, M. V. Shunkov, A. P. Derevianko, B. Viola, M. Slatkin, D. Reich, J. Kelso, and S. Pääbo


Teaching

UniVie Winter semester:
Computational genomics approaches to evolution and human history

Applications of admixture genomics

UniVie Summer semester:
Evolutionary Genomics and admixture in humans and primates


July 2022/September 2023: iNEAL network Training school workshops at University of Vienna

2017-2018: Teaching Mentorship Programme of Universitat Pompeu Fabra
2017|2018|2019|2020: Course Genomes & Systems (with Prof. Marques-Bonet), UPF
2015-2019: Lectures at MPI-EVA, UPF, Autonomous University of Barcelona

Experience & Achievements

Conferences & Talks

2023: 2nd Münster Evolution Meeting, Münster

2019: EMBO|EMBL Symposium “Reconstructing the Human Past”, Heidelberg

2018: 1st AsiaEvo Conference, Shenzhen (Invited speaker)

2017: 15th RECOMB Comparative Genomics Satellite Conference, Barcelona

2017: Protolang 5, Barcelona (Keynote speaker)

2016: XXI Population Genetics and Evolution Seminar, Sitges

Invited talks at University of Buffalo (2023), VetMedUni Vienna (2023), Free University of Berlin (2022), University of Zürich (2022, 2023), The Norwegian University of Life Sciences (2022, online), Al-Khwarizmi Engineering College Baghdad (2021, online), Aarhus University (2019), University of Barcelona (2016), Ewha Womens University (2015)

Poster presentations at EMBO|EMBL Symposium “Reconstructing the Human Past” (2022), Evolution II (2019), CSHL Biology of Genomes (2017), SMBE (2014, 2023), EMBO Evolution Conference (2014)

Grants & Networks

Networks

HEAS: Human Evolution & Archaeological Sciences

iNEAL: Integrating Neanderthal Legacy

Grants

FWF 1000 ideas grant 2021

WWTF Vienna Research Groups for Young Investigators 2020

SMBE Young Investigator Travel Award 2020

LaCaixa JuniorLeader postdoctoral fellowship 2019-2022

DFG (German Research Society) postdoctoral fellowship 2016-2018

PhD Stipend 2010-2014 awarded by the Max Planck Society

Rejected grant proposals: MSCA postdoctoral fellowship, EMBO postdoctoral fellowship; DFG Emmy Noether programme, ERC Starting Grant, Volkswagen Foundation Freigeist fellowship

Outreach

Lecture on human evolution (in German) at the NHM, January 2023

Article in University of Vienna magazine (in German), May 2022

Reviewing activity

Reviewing activity for scientific journals: Science, Nature Ecology & Evolution, Molecular Biology & Evolution, Plos Genetics, Cell Genomics, Genetics, Cell Reports, Communications Biology, Systematic Biology, Genome Biology & Evolution, BioEssays, Frontiers in Genetics, RSOS, Genes, Diversity, Evolutionary Bioinformatics, Journal of Archaeological Method and Theory, Plos One, Zoological Research, The Leakey Foundation, National Science Center Poland

Other

Wet lab: Molecular biology, cell culture, sequencing technologies
Dry lab: Programming in R and other languages, data analysis and visualization
Secondary: Grant writing, visual design with Inkscape etc.
Language: German (native), English (proficient), French (medium), Spanish (basic)