preprints

• Cheng, X.; Steinrücken, M.: diplo-locus: A lightweight toolkit for inference and simulation of time-series genetic data under general diploid selection. [Preprint at bioRχiv]

published papers

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)