preprints

• Fine, A.; Steinrücken, M.: A novel expectation-maximization approach to infer general diploid selection from time-series genetic data. [Preprint at bioRχiv]

published papers

2025

• Wences, A. H., Peñaloza, L., Steinrücken, M., Siri-Jégousse, A.: The TMRCA of general genealogies in populations of variable size. Theor. Popul. Biol. 165, pp. 1-9 (2025) [Preprint at bioRχiv]
• Urban Aragon, J. A., Bandyopadhyay, E., Fernando, A. S., de la Fuente Castro, C., Welikala, A. H. J., Biddanda, A., Witonsky, D., Sander, N., Kotelawala, J. T. Pasupuleti, N., Steinrücken, M., Adikari, G., Tennekoon, K., Ragsdale, A. P., Terhorst, J., Ranasinghe, R., Rai, N., Raghavan, M.: Population histories of the Indigenous Adivasi and Sinhalese from Sri Lanka using whole genomes. Curr. Biol. 35(11), pp. 2554-2566.e7 (2025)
• Cheng, X.; Steinrücken, M.: diplo-locus: A lightweight toolkit for inference and simulation of time-series genetic data under general diploid selection. G3 Genes|Genomes|Genetics, jkaf123 (2025) [Preprint at bioRχiv]
• Klunk, J., Vilgalys, T. P., Demeure, C. E., Cheng, X., Shiratori, M., Madej, J., Beau, R., Elli, D., Patino, M. I., Redfern, R., DeWitte, S. N., Gamble, J. A., Boldsen, J. L., Carmichael, A., Varlik, N., Eaton, K., Grenier, J., Golding, G. B., Devault, A., Rouillard, J., Yotova, V., Sindeaux, R., Ye, C. J., Bikaran, M., Dumaine, A., Brinkworth, J. F., Missiakas, D., Rouleau, G. A., Steinrücken, M., Pizarro-Cerdá, J., Poinar, H. N., and Barreiro, L. B.: Reply to: Insufficient evidence for natural selection associated with the Black Death. Nature 638, E23–E29 (2025)

2024

• Cheng, X.; Steinrücken, M.: Population Genomic Scans for Natural Selection and Demography. Annu. Rev. Genet. 58, pp. 319-339 (2024)

2022

• Klunk, J., Vilgalys, T. P., Demeure, C. E., Cheng, X., Shiratori, M., Madej, J., Beau, R., Elli, D., Patino, M. I., Redfern, R., DeWitte, S. N., Gamble, J. A., Boldsen, J. L., Carmichael, A., Varlik, N., Eaton, K., Grenier, J., Golding, G. B., Devault, A., Rouillard, J., Yotova, V., Sindeaux, R., Ye, C. J., Bikaran, M., Dumaine, A., Brinkworth, J. F., Missiakas, D., Rouleau, G. A., Steinrücken, M., Pizarro-Cerdá, J., Poinar, H. N., and Barreiro, L. B.: Evolution of immune genes is associated with the Black Death. Nature 611, pp. 312–319 (2022)
• Upadhya, G.R.; Steinrücken, M.: Robust inference of population size histories from genomic sequencing data. PLoS Comput. Biol. 18(9), e1010419 (2022) [Preprint at bioRχiv]
• Carlson, M.O.; Rice, D.P.; Berg, J.J.; Steinrücken, M.: Polygenic score accuracy in ancient samples: quantifying the effects of allelic turnover. PLoS Genet.18(5), e1010170 (2022) [Preprint at bioRχiv]
• Porubsky, D., Höps, W., Ashraf, H., Hsieh, P., Rodriguez- Martin, B., Yilmaz, F., Ebler, J., Hallast, P., Maggiolini, F.A.M., Harvey, W.T., Henning, B., Audano, P.A., Gordon, D. S., Ebert, P., Hasenfeld, P., Benito, E., Zhu, Q., Human Genome Structural Variation Consortium (HGSVC), Lee, C., Antonacci, F., Steinrücken, M., Beck, C.R., Sanders, A.D., Marschall, T., Eichler, E.E., Korbel, J.O.: Haplotype-resolved inversion landscape reveals hotspots of mutational recurrence associated with genomic disorders. Cell 185, pp. 1–20, (2022) [Preprint at bioRχiv]
• Biddanda, A.; Steinrücken, M.; Novembre, J.: Properties of Two-Locus Genealogies and Linkage Disequilibrium in Temporally Structured Samples. Genetics 221(1), iyac038 (2022) [Preprint at bioRχiv]
• Friedlander, E.; Steinrücken, M.: A numerical framework for genetic hitchhiking in populations of variable size. Genetics 220(3), iyac012 (2022) [Preprint at bioRχiv]

2021

• Ringbauer, H.; Novembre, J.; Steinrücken, M.: Parental relatedness through time revealed by runs of homozygosity in ancient DNA. Nat. Commun. 12, 5425 (2021) [Preprint at bioRχiv (previous version)]

2020

• Ringbauer, H.; Steinrücken, M.; Fehren-Schmitz, L.; Reich, D.: Increased rate of close-kin unions in the central Andes in the half millennium before European contact. Curr. Biol. 30(17), pp. PR980-R981 (2020)

2019

• Steinrücken, M.; Kamm, J.A.; Spence, J.P.; Song, Y.S.: Inference of complex population histories using whole-genome sequences from multiple populations. Proc. Natl. Acad. Sci. U.S.A. 116(34), pp. 17115-17120 (2019) [Preprint at bioRχiv (previous version)]

2018

• Spence, J.P.; Steinrücken, M.; Terhorst, J.; Song, Y.S.: Inference of population history using coalescent HMMs: review and outlook. Curr. Opin. Genetics. Dev. 53, pp. 70-76 (2018) [Preprint at arXiv:1807.02763]
• Steinrücken, M.; Spence, J.P.; Kamm, J.A.; Wieczorek, E.; Song, Y.S.: Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans. Mol. Ecol. 27(19), pp. 3873-3888 (2018)
• Moreno-Mayar, J.V.; Potter, B.A.; Vinner, L.; Steinrücken, M.; Rasmussen, S.; Terhorst, J.; Kamm, J.A.; Albrechtsen, A.; Malaspinas, A.; Sikora, M.; Reuther, J.D.; Irish, J.D.; Malhi, R.S; Orlando, L.; Song, Y.S.; Nielsen, R.; Meltzer, D.J.; Willerslev E.: Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature 553, pp. 203-207 (2018)
  

2017

• Miroshnikov, A.; Steinrücken, M.: Computing the joint distribution of the total tree length across loci in populations with variable size. Theor. Popul. Biol. 118, pp. 1-19 (2017) [Preprint at arXiv:1609.08880]

2016

• Jewett, E. M.; Steinrücken, M.; Song, Y.S.: The effects of population size histories on estimates of selection coefficients from time-series genetic data. Mol. Biol. Evol. 33(11), pp. 3002–3027 (2016) [Preprint at bioRχiv]
• Steinrücken, M.; Jewett, E. M.; Song, Y.S.: SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates and effective population sizes. Bioinformatics 32(5), pp. 795-797 (2016)

2015

• Raghavan, M.; Steinrücken, M.; Harris, K.; Schiffels, S.; Rasmussen, S.; DeGiorgio, M.; Albrechtsen, A.; Valdiosera, C.; Ávila-Arcos, M.C.; Malaspinas, A.; … (88 authors) …; Song, Y.S.; Nielsen, R.; Willerslev, E.: Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 349(6250), aab3884 (2015)
• Živković, D.; Steinrücken, M.; Song, Y.S.; Stephan W.: Transition densities and sample frequency spectra of diffusion processes with selection and variable population size. Genetics 200(2), pp. 601-617 (2015) [Preprint at bioRχiv]

2014

• Steinrücken, M.; Bhaskar, A.; Song, Y.S.: A novel spectral method for inferring general selection from time series genetic data. Ann. Appl. Stat. 8, pp. 2203-2222 (2014) [Preprint at arXiv:1310.1068]

2013

• Steinrücken, M.; Paul, J.S.; Song, Y.S.: A sequentially Markov conditional sampling distribution for structured populations with migration and recombination. Theor. Popul. Biol. 87, pp. 51-61 (2013) [Preprint at arXiv:1208.5086]
• Steinrücken, M.; Birkner, M.; Blath, J.: Analysis of DNA sequence variation within marine species using Beta-coalescents. Theor. Popul. Biol. 87, pp. 15-24 (2013) [Preprint at arXiv:1209.0813]
• Steinrücken, M.; Wang, Y. X. R.; Song, Y.S.: An explicit transition density expansion for a multi-allelic Wright-Fisher diffusion with general diploid selection. Theor. Popul. Biol. 83, pp. 1-14 (2013) [Preprint at arXiv:1208.5087]

2012

• Song, Y.S.; Steinrücken, M.: A Simple Method for Finding Explicit Analytic Transition Densities of Diffusion Processes with General Diploid Selection. Genetics 190(3), pp. 1117-1129 (2012)

2011

• Birkner, M.; Blath, J.; Steinrücken, M.: Importance sampling for Lambda-coalescents in the infinitely many sites model. Theor. Popul. Biol. 79(4), pp. 155-173 (2011)[Preprint at arXiv:1105.1836]
• Paul, J.S.; Steinrücken, M.; Song, Y.S.: An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination. Genetics 187(4), pp. 1115-1128 (2011)

2009

• Birkner, M.; Blath, J.;Möhle, M.; Steinrücken, M.; Tams, J.: A modified lookdown construction for the Xi-Fleming-Viot process with mutation and populations with recurrent bottlenecks, ALEA Lat. Am. J. Probab. Math. Stat. 6, pp. 25-61 (2009) [Preprint at arXiv:0808.0412]

2006

• Plötz, T.; Fink, G.; Husemann, P.; Kanies, S.; Lienemann, K.; Marschall, T.; Martin, M.; Schillingmann, L.; Steinrücken, M.; Sudek, H.: Automatic Detection of Song Changes in Music Mixes Using Stochastic Models. 18th International Conference on Pattern Recognition (ICPR’06), pp. 665-668 (2006)

Theses

• Steinrücken, M.: Multiple Merger Coalescents and Population Genetic Inference. PhD thesis, (2009)
• Steinrücken, M.: Deterministische Rekombinationsdynamik mit Selektion. Diplomarbeit, (2006)