Publications

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

• Heinzel, C., Baumdicker, F., Pfaffelhuber, P.. Revealing the range of equally likely estimates in the admixture model. 15 , G3. 2025.
• Heinzel, C., Purucker, L., Hutter, F., Pfaffelhuber, P.. Advancing Biogeographical Ancestry Predictions Through Machine Learning. 79 , Forensic Science International: Genetics. 2025.
• Maurer, T., Purucker, L., Hutter, F., Pfaffelhuber, P., Heinzel, C.. Enhancing Intra-Continental Biogeographical Ancestry Prediction Through a Machine Learning Marker Selection Method. , submitted. 2025.
• Depperschmidt, A., Greven, A., Pfaffelhuber, P.. Duality and the well-posedness of a martingale problem. 159 59--73 , Theoretical Population Biology. 2024.
• Smyser, T., Pfaffelhuber, P., Giglio, R., DeSaix, M., Davis, A., Bowden, C., Tabak, M., Manunza, A., B{\^a}lteanu, V., Amills, M., others, . Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa). 15 e4774 , Ecosphere. 2024.
• Criens, D., Pfaffelhuber, P., Schmidt, T.. The martingale problem method revisited. 28 1--46 , Electronic Journal of Probability. 2023.
• Enger, T., Pfaffelhuber, P.. A unified framework for limit results in chemical reaction networks on multiple time-scales. 28 1--33 , Electronic Journal of Probability. 2023.
• Pfaffelhuber, P., Wakolbinger, A.. A diploid population model for copy number variation of genetic elements. 28 1--15 , Electronic Journal of Probability. 2023.
• Burger, K., Pfaffelhuber, P., Baumdicker, F.. Neural networks for self-adjusting mutation rate estimation when the recombination rate is unknown. 18 e1010407 , PLOS Computational Biology. 2022.
• Pfaffelhuber, P., Rohde, A.. A central limit theorem concerning uncertainty in estimates of individual admixture. 148 28--39 , Theoretical Population Biology. 2022.
• Pfaffelhuber, P., Rotter, S., Stiefel, J.. Mean-field limits for non-linear Hawkes processes with excitation and inhibition. 153 57--78 , Stochastic Processes and their Applications. 2022.
• Pfaffelhuber, P., Sester-Huss, E., Baumdicker, F., Naue, J., Lutz-Bonengel, S., Staubach, F.. Inference of recent admixture using genotype data. 56 102593 , Forensic Science International: Genetics. 2022.
• Hermann, F., Pfaffelhuber, P.. The partial duplication random graph with edge deletion. 18 325--347 , ALEA. 2021.
• Lipphardt, V., Surdu, M., Ellebrecht, N., Pfaffelhuber, P., Wienroth, M., Rappold, G.. Europe’s {R}oma people are vulnerable to poor practice in genetics. 599 368--371 , Nature. 2021.
• Pfaffelhuber, P., Stiefel, J.. The range of once-reinforced random walk in one dimension. 58 164--175 , Random Structures \& Algorithms. 2021.
• Scherer, N., Sekula, P., Pfaffelhuber, P., Koettgen, A., Schlosser, P.. Pgainsim: A Method to Assess the Mode of Inheritance for Quantitative Trait Loci in Genome-Wide Association Studies. 85 91--92 , . 2021.
• Baumdicker, F., Sester-Huss, E., Pfaffelhuber, P.. Modifiers of mutation rate in selectively fluctuating environments. 130 6843--6862 , Stochastic Processes and their Applications. 2020.
• Hermann, F., Pfaffelhuber, P.. Markov branching processes with disasters: extinction, survival and duality to p-jump processes. 130 2488--2518 , Stochastic Processes and their Applications. 2020.
• Huss, E., Pfaffelhuber, P.. Genealogical distances under low levels of selection. 131 2--11 , Theoretical Population Biology. 2020.
• Lynch, M., Haubold, B., Pfaffelhuber, P., Maruki, T.. Inference of historical population-size changes with allele-frequency data. 10 211--223 , G3: Genes, Genomes, Genetics. 2020.
• Pfaffelhuber, P., Grundner-Culemann, F., Lipphardt, V., Baumdicker, F.. How to choose sets of ancestry informative markers: A supervised feature selection approach. 46 102259 , Forensic Science International: Genetics. 2020.
• Lipphardt, V., Buchanan, N., Pfaffelhuber, P., Staubach, F., Wienroth, M.. Interdisziplin{\"a}re {Ü}berlegungen zu Erweiterten {DNA}-Analysen. 24 119--154 , Jahrbuch f{\"u}r Wissenschaft und Ethik. 2019.
• Pirogov, A., Pfaffelhuber, P., B{\"o}rsch-Haubold, A., Haubold, B.. High-complexity regions in mammalian genomes are enriched for developmental genes. 35 1813--1819 , Bioinformatics. 2019.
• Baumdicker, F., Huebner, A., Pfaffelhuber, P.. The independent loss model with ordered insertions for the evolution of {CRISPR} spacers. 119 72--82 , Theoretical Population Biology. 2018.
• Bossert, S., Pfaffelhuber, P.. The fixation probability and time for a doubly beneficial mutant. 128 4018--4050 , Stochastic Processes and their Applications. 2018.
• Buchanan, N., Staubach, F., Wienroth, M., Pfaffelhuber, P., Surdu, M., Lipphardt, A., K{\"o}ttgen, A., Lipphardt, V., others, . Forensic DNA phenotyping legislation cannot be based on “Ideal {FDP}”—A response to {C}aliebe, {K}rawczak and {K}ayser (2017). 34 e13--e14 , Forensic Science International: Genetics. 2018.
• Czuppon, P., Pfaffelhuber, P.. Limits of noise for autoregulated gene expression. 77 1153--1191 , Journal of mathematical biology. 2018.
• Pfaffelhuber, P., Wakolbinger, A.. Fixation probabilities and hitting times for low levels of frequency-dependent selection. 124 61--69 , Theoretical Population Biology. 2018.
• Czuppon, P., Pfaffelhuber, P.. A spatial model for selection and cooperation. 54 522--539 , Journal of Applied Probability. 2017.
• Greven, A., Pfaffelhuber, P., Pokalyuk, C., Wakolbinger, A.. The fixation time of a strongly beneficial allele in a structured population. 21 1--42 , Electron. J. Probab. 2016.
• Hermann, F., Pfaffelhuber, P.. Large-scale behavior of the partial duplication random graph. 13 687--710 , ALEA. Latin American Journal of Probability \& Mathematical Statistics. 2016.
• Jansen, M., Pfaffelhuber, P., Hoffmann, M., Puetz, G., Winkler, K.. In silico modeling of the dynamics of low density lipoprotein composition via a single plasma sample [S]. 57 882--893 , Journal of lipid research. 2016.
• Depperschmidt, A., Pardoux, {., Pfaffelhuber, P.. A mixing tree-valued process arising under neutral evolution with recombination. 20 1--22 , Electronic Journal of Probability. 2015.
• Haubold, B., Kl{\"o}tzl, F., Pfaffelhuber, P.. andi: Fast and accurate estimation of evolutionary distances between closely related genomes. 31 1169--1175 , Bioinformatics. 2015.
• Jansen, M., Pfaffelhuber, P.. Stochastic gene expression with delay. 364 355--363 , Journal of theoretical biology. 2015.
• M{\'e}lyk{\'u}ti, B., Pfaffelhuber, P.. The stationary distribution of a markov jump process glued together from two state spaces at two vertices. 31 525--553 , Stochastic Models. 2015.
• Pfaffelhuber, P., Popovic, L.. Scaling limits of spatial compartment models for chemical reaction networks. 25 3162--3208 , The Annals of Applied Probability. 2015.
• Pfaffelhuber, P., Popovic, L.. How spatial heterogeneity shapes multiscale biochemical reaction network dynamics. 12 20141106 , Journal of the Royal Society Interface. 2015.
• Schl{\"u}ter, J., Czuppon, P., Schauer, O., Pfaffelhuber, P., McIntosh, M., Becker, A.. Classification of phenotypic subpopulations in isogenic bacterial cultures by triple promoter probing at single cell level. 198 3--14 , Journal of Biotechnology. 2015.
• Baumdicker, F., Pfaffelhuber, P.. The infinitely many genes model with horizontal gene transfer. 19 1--27 , Electron. J. Probab. 2014.
• Bossert, S., Pfaffelhuber, P.. Correction: The Yule Approximation for the Site Frequency Spectrum after a Selective Sweep. 9 , Plos one. 2014.
• Czuppon, P., Pfaffelhuber, P.. Some limit results for {M}arkov chains indexed by trees. 19 1--11 , Elect. Comm. in Probab.. 2014.
• Depperschmidt, A., Pfaffelhuber, P., Scheuringer, A.. Some large deviations in {K}ingman's coalescent. 20 1--14 , Elec. Comm. Probab.. 2014.
• Lynch, M., Xu, S., Maruki, T., Jiang, X., Pfaffelhuber, P., Haubold, B.. Genome-wide linkage-disequilibrium profiles from single individuals. 198 269--281 , Genetics. 2014.
• Bossert, S., Pfaffelhuber, P.. The yule approximation for the site frequency spectrum after a selective sweep. 8 e81738 , PLoS One. 2013.
• Depperschmidt, A., Greven, A., Pfaffelhuber, P.. Path-properties of the tree-valued Fleming--Viot process. 18 1--47 , Electron. J. Probab. 2013.
• Depperschmidt, A., Ketterer, N., Pfaffelhuber, P.. A Brownian ratchet for protein translocation including dissociation of ratcheting sites. 66 505--534 , Journal of mathematical biology. 2013.
• Greven, A., Pfaffelhuber, P., Winter, A.. Tree-valued resampling dynamics martingale problems and applications. 155 789--838 , Probability Theory and Related Fields. 2013.
• Haubold, B., Krause, L., Horn, T., Pfaffelhuber, P.. An alignment-free test for recombination. 29 3121--3127 , Bioinformatics. 2013.
• McIntosh, M., Czuppon, P., Best, K., Becker, A., Pfaffelhuber, P.. Modeling quorum sensing in Sinorhizobium meliloti. 2 59--74 , International Journal of Biomathematics and Biostatistics. 2013.
• Pokalyuk, C., Mathew, L., Metzler, D., Pfaffelhuber, P.. Competing islands limit the rate of adaptation in structured populations. 90 1--11 , Theoretical population biology. 2013.
• Pokalyuk, C., Pfaffelhuber, P.. The ancestral selection graph under strong directional selection. 87 25--33 , Theoretical population biology. 2013.
• Baumdicker, F., Hess, W., Pfaffelhuber, P.. The infinitely many genes model for the distributed genome of bacteria. 4 443--456 , Genome biology and evolution. 2012.
• Biehler, H., Pfaffelhuber, P.. Compact metric measure spaces and $\Lambda$-coalescents coming down from infinity. 9 269--278 , ALEA. 2012.
• Depperschmidt, A., Greven, A., Pfaffelhuber, P.. Tree-valued {F}leming-{V}iot dynamics with mutation and selection. 22 2560--2615 , Annals of applied probability. 2012.
• Haubold, B., Pfaffelhuber, P.. Alignment-free population genomics: an efficient estimator of sequence diversity. 2 883--889 , G3: Genes| Genomes| Genetics. 2012.
• Pfaffelhuber, P., Staab, P., Wakolbinger, A.. Muller's ratchet with compensatory mutations. 22 2108--2132 , Annals of applied probability. 2012.
• Depperschmidt, A., Greven, A., Pfaffelhuber, P.. Marked metric measure spaces. 16 174--188 , Elect. Comm. in Probab.. 2011.
• Ewing, G., Hermisson, J., Pfaffelhuber, P., Rudolf, J.. Selective sweeps for recessive alleles and for other modes of dominance. 63 399--431 , Journal of mathematical biology. 2011.
• Haubold, B., Reed, F., Pfaffelhuber, P.. Alignment-free estimation of nucleotide diversity. 27 449--455 , Bioinformatics. 2011.
• Jansen, M., Winkler, K., Puetz, G., Pfaffelhuber, P., Mann, M.. In silico modelling of human lipoprotein metabolism. 12 22--23 , . 2011.
• Pfaffelhuber, P., Wakolbinger, A., Weisshaupt, H.. The tree length of an evolving coalescent. 151 529--557 , Probability theory and related fields. 2011.
• Pfaffelhuber, P., Weisshaupt, H.. Sensitivity analysis of one parameter semigroups exemplified by the {W}right--{F}isher diffusion. 3 109--128 , Intern. J. Funct. Anal., Oper. Th. Appl.. 2011.
• Tellier, A., Pfaffelhuber, P., Haubold, B., Naduvilezhath, L., Rose, L., St{\"a}dler, T., Stephan, W., Metzler, D.. Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum. 6 e18155 , PLoS One. 2011.
• Baumdicker, F., Hess, W., Pfaffelhuber, P.. The diversity of a distributed genome in bacterial populations. 1567--1606 , The Annals of Applied Probability. 2010.
• Best, K., Pfaffelhuber, P.. The {A}ldous--{S}hields model revisited (with application to cellular ageing). 15 475--488 , Elec. Comm. Probab.. 2010.
• Depperschmidt, A., Pfaffelhuber, P.. Asymptotics of a Brownian ratchet for protein translocation. 120 901--925 , Stochastic processes and their applications. 2010.
• Haubold, B., Pfaffelhuber, P.. Experimentelle und theoretische Biologie: getrennte Welten?. 40 12--12 , Biologie in unserer Zeit. 2010.
• Haubold, B., Pfaffelhuber, P., Lynch, M.. mlRho--a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes. 19 277--284 , Molecular ecology. 2010.
• Etheridge, A., Pfaffelhuber, P., Wakolbinger, A.. How often does the ratchet click? Facts, heuristics, asymptotics. 353 365--390 , Trends in stochastic analysis. 2009.
• Greven, A., Pfaffelhuber, P., Winter, A.. Convergence in distribution of random metric measure spaces ($\Lambda$-coalescent measure trees). 145 285--322 , Probability Theory and Related Fields. 2009.
• Haubold, B., Pfaffelhuber, P., Domazet-Los˘ o, M., Wiehe, T.. Estimating mutation distances from unaligned genomes. 16 1487--1500 , Journal of Computational Biology. 2009.
• Städler, T., Haubold, B., Merino, C., Stephan, W., Pfaffelhuber, P.. The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. 182 205--216 , Genetics. 2009.
• Hermisson, J., Pfaffelhuber, P.. The pattern of genetic hitchhiking under recurrent mutation. 13 2069--2106 , Elec. J. Probab.. 2008.
• Pfaffelhuber, P., Lehnert, A., Stephan, W.. Linkage disequilibrium under genetic hitchhiking in finite populations. 179 527--537 , Genetics. 2008.
• Pfaffelhuber, P., Studeny, A.. Approximating genealogies for partially linked neutral loci under a selective sweep. 55 299--330 , Journal of mathematical biology. 2007.
• Etheridge, A., Pfaffelhuber, P., Wakolbinger, A.. An approximate sampling formula under genetic hitchhiking. 16 , Annals of Applied Probability. 2006.
• Pfaffelhuber, P.. The Finite System Scheme for State-dependent interacting multitype Branching Systems. 2 1--66 , ALEA. 2006.
• Pfaffelhuber, P., Haubold, B., Wakolbinger, A.. Approximate genealogies under genetic hitchhiking. 174 1995--2008 , Genetics. 2006.
• Pfaffelhuber, P., Wakolbinger, A.. The process of most recent common ancestors in an evolving coalescent. 116 1836--1859 , Stochastic Processes and their Applications. 2006.