Publications

Our research is published in both, mathematical and biological journals. Only peer-reviewed papers are listed.

• Carola Sophia Heinzel, Lennart Purucker, Frank Hutter, and Peter Pfaffelhuber. Advancing Biogeographical Ancestry Predictions Through Machine Learning. Forensic Science International: Genetics, forthcoming, , 2025.
• Timothy J Smyser, Peter Pfaffelhuber, Rachael M Giglio, Matthew G DeSaix, Amy J Davis, Courtney F Bowden, Michael A Tabak, Arianna Manunza, Valentin Adrian B{\^a}lteanu, Marcel Amills, and others. Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa). Ecosphere 15(2), 15 (2), e4774 , 2024.
• David Criens, Peter Pfaffelhuber, and Thorsten Schmidt. The martingale problem method revisited. Electronic Journal of Probability, 28, 1--46 , 2023.
• Peter Pfaffelhuber and Anton Wakolbinger. A diploid population model for copy number variation of genetic elements. Electronic Journal of Probability, 28, 1--15 , 2023.
• Timo Enger and Peter Pfaffelhuber. A unified framework for limit results in chemical reaction networks on multiple time-scales. Electronic Journal of Probability, 28, 1--33 , 2023.
• Peter Pfaffelhuber, Stefan Rotter, and Jakob Stiefel. Mean-field limits for non-linear Hawkes processes with excitation and inhibition. Stochastic Processes and their Applications, 153, 57--78 , 2022.
• Peter Pfaffelhuber, Elisabeth Sester-Huss, Franz Baumdicker, Jana Naue, Sabine Lutz-Bonengel, and Fabian Staubach. Inference of recent admixture using genotype data. Forensic Science International: Genetics, 56, 102593 , 2022.
• Klara Elisabeth Burger, Peter Pfaffelhuber, and Franz Baumdicker. Neural networks for self-adjusting mutation rate estimation when the recombination rate is unknown. PLOS Computational Biology 18(8), 18 (8), e1010407 , 2022.
• Peter Pfaffelhuber and Angelika Rohde. A central limit theorem concerning uncertainty in estimates of individual admixture. Theoretical Population Biology, 148, 28--39 , 2022.
• Veronika Lipphardt, Mihai Surdu, Nils Ellebrecht, Peter Pfaffelhuber, Matthias Wienroth, and Gudrun A Rappold. Europe’s Roma people are vulnerable to poor practice in genetics. Nature 599(7885), 599 (7885), 368--371 , 2021.
• Peter Pfaffelhuber and Jakob Stiefel. The range of once-reinforced random walk in one dimension. Random Structures \& Algorithms 58(1), 58 (1), 164--175 , 2021.
• Felix Hermann and Peter Pfaffelhuber. The partial duplication random graph with edge deletion. ALEA, 18, 325--347 , 2021.
• Nora Scherer, Peggy Sekula, Peter Pfaffelhuber, Anna Koettgen, and Pascal Schlosser. Pgainsim: A Method to Assess the Mode of Inheritance for Quantitative Trait Loci in Genome-Wide Association Studies. Human Heredity, 85 (2), 91--92 , 2021.
• Peter Pfaffelhuber, Franziska Grundner-Culemann, Veronika Lipphardt, and Franz Baumdicker. How to choose sets of ancestry informative markers: A supervised feature selection approach. Forensic Science International: Genetics, 46, 102259 , 2020.
• Michael Lynch, Bernhard Haubold, Peter Pfaffelhuber, and Takahiro Maruki. Inference of historical population-size changes with allele-frequency data. G3: Genes, Genomes, Genetics 10(1), 10 (1), 211--223 , 2020.
• Felix Hermann and Peter Pfaffelhuber. Markov branching processes with disasters: extinction, survival and duality to p-jump processes. Stochastic Processes and their Applications 130(4), 130 (4), 2488--2518 , 2020.
• Franz Baumdicker, Elisabeth Sester-Huss, and Peter Pfaffelhuber. Modifiers of mutation rate in selectively fluctuating environments. Stochastic Processes and their Applications 130(11), 130 (11), 6843--6862 , 2020.
• Elisabeth Huss and Peter Pfaffelhuber. Genealogical distances under low levels of selection. Theoretical Population Biology, 131, 2--11 , 2020.
• Veronika Lipphardt, Nicholas Buchanan, Peter Pfaffelhuber, Fabian Staubach, and Matthias Wienroth. Interdisziplin\"are Überlegungen zu Erweiterten DNA-Analysen. Jahrbuch f\"ur Wissenschaft und Ethik 24(1), 24 (1), 119--154 , 2019.
• Anton Pirogov, Peter Pfaffelhuber, Angelika B{\"o}rsch-Haubold, and Bernhard Haubold. High-complexity regions in mammalian genomes are enriched for developmental genes. Bioinformatics 35(11), 35 (11), 1813--1819 , 2019.
• Nicholas Buchanan, Fabian Staubach, Matthias Wienroth, Peter Pfaffelhuber, Mihai Surdu, Anna Lipphardt, Anna K{\"o}ttgen, Veronika Lipphardt, and others. Forensic DNA phenotyping legislation cannot be based on “Ideal FDP”—A response to Caliebe, Krawczak and Kayser (2017). Forensic Science International: Genetics, 34, e13--e14 , 2018.
• Peter Czuppon and Peter Pfaffelhuber. Limits of noise for autoregulated gene expression. Journal of mathematical biology 77(4), 77 (4), 1153--1191 , 2018.
• Sebastian Bossert and Peter Pfaffelhuber. The fixation probability and time for a doubly beneficial mutant. Stochastic Processes and their Applications 128(12), 128 (12), 4018--4050 , 2018.
• Franz Baumdicker, Ariana MI Huebner, and Peter Pfaffelhuber. The independent loss model with ordered insertions for the evolution of CRISPR spacers. Theoretical Population Biology, 119, 72--82 , 2018.
• P Pfaffelhuber and A Wakolbinger. Fixation probabilities and hitting times for low levels of frequency-dependent selection. Theoretical Population Biology, 124, 61--69 , 2018.
• Peter Czuppon and Peter Pfaffelhuber. A spatial model for selection and cooperation. Journal of Applied Probability 54(2), 54 (2), 522--539 , 2017.
• Felix Hermann and Peter Pfaffelhuber. Large-scale behavior of the partial duplication random graph. ALEA. Latin American Journal of Probability \& Mathematical Statistics, 13, 687--710 , 2016.
• Andreas Greven, Peter Pfaffelhuber, Cornelia Pokalyuk, and Anton Wakolbinger. The fixation time of a strongly beneficial allele in a structured population. Electron. J. Probab 21(61), 21 (61), 1--42 , 2016.
• Martin Jansen, Peter Pfaffelhuber, Michael M Hoffmann, Gerhard Puetz, and Karl Winkler. In silico modeling of the dynamics of low density lipoprotein composition via a single plasma sample [S]. Journal of lipid research 57(5), 57 (5), 882--893 , 2016.
• Bernhard Haubold, Fabian Kl{\"o}tzl, and Peter Pfaffelhuber. andi: Fast and accurate estimation of evolutionary distances between closely related genomes. Bioinformatics 31(8), 31 (8), 1169--1175 , 2015.
• Jan-Philip Schl{\"u}ter, Peter Czuppon, Oliver Schauer, Peter Pfaffelhuber, Matthew McIntosh, and Anke Becker. Classification of phenotypic subpopulations in isogenic bacterial cultures by triple promoter probing at single cell level. Journal of Biotechnology, 198, 3--14 , 2015.
• Martin Jansen and Peter Pfaffelhuber. Stochastic gene expression with delay. Journal of theoretical biology, 364, 355--363 , 2015.
• Peter Pfaffelhuber and Lea Popovic. Scaling limits of spatial compartment models for chemical reaction networks. The Annals of Applied Probability 25(6), 25 (6), 3162--3208 , 2015.
• Bence M{\'e}lyk{\'u}ti and Peter Pfaffelhuber. The stationary distribution of a markov jump process glued together from two state spaces at two vertices. Stochastic Models 31(4), 31 (4), 525--553 , 2015.
• Peter Pfaffelhuber and Lea Popovic. How spatial heterogeneity shapes multiscale biochemical reaction network dynamics. Journal of the Royal Society Interface 12(104), 12 (104), 20141106 , 2015.
• Andrej Depperschmidt, {\'E}tienne Pardoux, and Peter Pfaffelhuber. A mixing tree-valued process arising under neutral evolution with recombination. Electronic Journal of Probability, 20, 1--22 , 2015.
• Michael Lynch, Sen Xu, Takahiro Maruki, Xiaoqian Jiang, Peter Pfaffelhuber, and Bernhard Haubold. Genome-wide linkage-disequilibrium profiles from single individuals. Genetics 198(1), 198 (1), 269--281 , 2014.
• Franz Baumdicker and Peter Pfaffelhuber. The infinitely many genes model with horizontal gene transfer. Electron. J. Probab 19(115), 19 (115), 1--27 , 2014.
• A. Depperschmidt, P. Pfaffelhuber, and A. Scheuringer. Some large deviations in Kingman's coalescent. Elec. Comm. Probab. 20(7), 20 (7), 1--14 , 2014.
• P. Czuppon and P. Pfaffelhuber. Some limit results for Markov chains indexed by trees. Elect. Comm. in Probab. 19(77), 19 (77), 1--11 , 2014.
• Sebastian Bossert and Peter Pfaffelhuber. Correction: The Yule Approximation for the Site Frequency Spectrum after a Selective Sweep. Plos one 9(1), 9 (1), , 2014.
• Andreas Greven, Peter Pfaffelhuber, and Anita Winter. Tree-valued resampling dynamics martingale problems and applications. Probability Theory and Related Fields 155(3-4), 155 (3-4), 789--838 , 2013.
• Cornelia Pokalyuk and Peter Pfaffelhuber. The ancestral selection graph under strong directional selection. Theoretical population biology, 87, 25--33 , 2013.
• Bernhard Haubold, Linda Krause, Thomas Horn, and Peter Pfaffelhuber. An alignment-free test for recombination. Bioinformatics 29(24), 29 (24), 3121--3127 , 2013.
• Andrej Depperschmidt, Andreas Greven, and Peter Pfaffelhuber. Path-properties of the tree-valued Fleming--Viot process. Electron. J. Probab 18(84), 18 (84), 1--47 , 2013.
• A Depperschmidt, N Ketterer, and P Pfaffelhuber. A Brownian ratchet for protein translocation including dissociation of ratcheting sites. Journal of mathematical biology 66(3), 66 (3), 505--534 , 2013.
• Cornelia Pokalyuk, Lisha A Mathew, Dirk Metzler, and Peter Pfaffelhuber. Competing islands limit the rate of adaptation in structured populations. Theoretical population biology, 90, 1--11 , 2013.
• M McIntosh, P Czuppon, K Best, A Becker, and P Pfaffelhuber. Modeling quorum sensing in Sinorhizobium meliloti. International Journal of Biomathematics and Biostatistics, 2, 59--74 , 2013.
• Sebastian Bossert and Peter Pfaffelhuber. The yule approximation for the site frequency spectrum after a selective sweep. PLoS One 8(12), 8 (12), e81738 , 2013.
• Franz Baumdicker, Wolfgang R Hess, and Peter Pfaffelhuber. The infinitely many genes model for the distributed genome of bacteria. Genome biology and evolution 4(4), 4 (4), 443--456 , 2012.
• Andrej Depperschmidt, Andreas Greven, and Peter Pfaffelhuber. Tree-valued Fleming-Viot dynamics with mutation and selection. Annals of applied probability 22(6), 22 (6), 2560--2615 , 2012.
• P Pfaffelhuber, PR Staab, and A Wakolbinger. Muller's ratchet with compensatory mutations. Annals of applied probability 22(5), 22 (5), 2108--2132 , 2012.
• Bernhard Haubold and Peter Pfaffelhuber. Alignment-free population genomics: an efficient estimator of sequence diversity. G3: Genes| Genomes| Genetics 2(8), 2 (8), 883--889 , 2012.
• Holger F Biehler and Peter Pfaffelhuber. Compact metric measure spaces and $\Lambda$-coalescents coming down from infinity. ALEA, 9, 269--278 , 2012.
• A. Depperschmidt, A. Greven, and P. Pfaffelhuber. Marked metric measure spaces. Elect. Comm. in Probab., 16, 174--188 , 2011.
• Peter Pfaffelhuber, Anton Wakolbinger, and Heinz Weisshaupt. The tree length of an evolving coalescent. Probability theory and related fields, 151, 529--557 , 2011.
• Bernhard Haubold, Floyd A Reed, and Peter Pfaffelhuber. Alignment-free estimation of nucleotide diversity. Bioinformatics 27(4), 27 (4), 449--455 , 2011.
• Greg Ewing, Joachim Hermisson, Peter Pfaffelhuber, and Johannes Rudolf. Selective sweeps for recessive alleles and for other modes of dominance. Journal of mathematical biology 63(3), 63 (3), 399--431 , 2011.
• Aur{\'e}lien Tellier, Peter Pfaffelhuber, Bernhard Haubold, Lisha Naduvilezhath, Laura E Rose, Thomas St{\"a}dler, Wolfgang Stephan, and Dirk Metzler. Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum. PLoS One 6(5), 6 (5), e18155 , 2011.
• M Jansen, K Winkler, G Puetz, P Pfaffelhuber, and M Mann. In silico modelling of human lipoprotein metabolism. Atherosclerosis Supplements, 12 (1), 22--23 , 2011.
• P. Pfaffelhuber and H. Weisshaupt. Sensitivity analysis of one parameter semigroups exemplified by the Wright--Fisher diffusion. Intern. J. Funct. Anal., Oper. Th. Appl. 3(2), 3 (2), 109--128 , 2011.
• Bernhard Haubold, Peter Pfaffelhuber, and Michael Lynch. mlRho--a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes. Molecular ecology, 19, 277--284 , 2010.
• F Baumdicker, WR Hess, and P Pfaffelhuber. The diversity of a distributed genome in bacterial populations. The Annals of Applied Probability, 1567--1606 , 2010.
• K. Best and P. Pfaffelhuber. The Aldous--Shields model revisited (with application to cellular ageing). Elec. Comm. Probab., 15, 475--488 , 2010.
• Andrej Depperschmidt and Peter Pfaffelhuber. Asymptotics of a Brownian ratchet for protein translocation. Stochastic processes and their applications 120(6), 120 (6), 901--925 , 2010.
• Bernhard Haubold and Peter Pfaffelhuber. Experimentelle und theoretische Biologie: getrennte Welten?. Biologie in unserer Zeit 40(1), 40 (1), 12--12 , 2010.
• Thomas Städler, Bernhard Haubold, Carlos Merino, Wolfgang Stephan, and Peter Pfaffelhuber. The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics 182(1), 182 (1), 205--216 , 2009.
• Andreas Greven, Peter Pfaffelhuber, and Anita Winter. Convergence in distribution of random metric measure spaces ($\Lambda$-coalescent measure trees). Probability Theory and Related Fields 145(1-2), 145 (1-2), 285--322 , 2009.
• Bernhard Haubold, Peter Pfaffelhuber, Mirjana Domazet-Los˘ o, and Thomas Wiehe. Estimating mutation distances from unaligned genomes. Journal of Computational Biology 16(10), 16 (10), 1487--1500 , 2009.
• Alison Etheridge, Peter Pfaffelhuber, and Anton Wakolbinger. How often does the ratchet click? Facts, heuristics, asymptotics. Trends in stochastic analysis, 353, 365--390 , 2009.
• Peter Pfaffelhuber, Andreas Lehnert, and Wolfgang Stephan. Linkage disequilibrium under genetic hitchhiking in finite populations. Genetics 179(1), 179 (1), 527--537 , 2008.
• J. Hermisson and P. Pfaffelhuber. The pattern of genetic hitchhiking under recurrent mutation. Elec. J. Probab. 13(68), 13 (68), 2069--2106 , 2008.
• P Pfaffelhuber and A Studeny. Approximating genealogies for partially linked neutral loci under a selective sweep. Journal of mathematical biology 55(3), 55 (3), 299--330 , 2007.
• A Etheridge, P Pfaffelhuber, and A Wakolbinger. An approximate sampling formula under genetic hitchhiking. Annals of Applied Probability 16(2), 16 (2), , 2006.
• Peter Pfaffelhuber and Anton Wakolbinger. The process of most recent common ancestors in an evolving coalescent. Stochastic Processes and their Applications 116(12), 116 (12), 1836--1859 , 2006.
• Peter Pfaffelhuber, B Haubold, and A Wakolbinger. Approximate genealogies under genetic hitchhiking. Genetics 174(4), 174 (4), 1995--2008 , 2006.
• Peter Pfaffelhuber. The Finite System Scheme for State-dependent interacting multitype Branching Systems. ALEA, 2, 1--66 , 2006.