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Publications

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

Here is the list from MathSciNet
Here is the list from google scholar

  • P. Pfaffelhuber, A. Wakolbinger. A diploid population model for copy number variation of genetic elements. arxiv.org/pdf/2204.11140 Electron. J. Probab. 28, 1-15, 2023.
  • P. Pfaffelhuber, A. Rohde. A central Limit Theorem Concerning Uncertainty in estimates of individual admixture. arxiv.org/pdf/2110.08348 Theo. Pop. Biol., 148, 28-39, 2022. 
  • T. Enger, P. Pfaffelhuber. A unified framework for limit results in Chemical Reaction Networks on multiple time-scales. arxiv.org/pdf/2111.15396 Electron. J. Probab. 28, 1-33, 2023.
  • D. Criens, P. Pfaffelhuber, T. Schmidt. The Martingale Problem Method Revisited arxiv.org/pdf/2108.11930 Electron. J. Probab. 28, 1-46, 2023.
  • P. Pfaffelhuber, S. Rotter, J. Stiefel. Mean-field limits for non-linear Hawkes processes with excitation and inhibition. arxiv.org/pdf/2102.01052 153, 57-78, 2022.
  • P. Pfaffelhuber, E. Sester-Huss, F. Baumdicker, J. Naue, S. Lutz-Bonengel, F. Staubach. Inference of recent admixture using genotype data. Forensic Sci. Int. Genet. 56:102593, 2022. www.biorxiv.org/content/10.1101/2020.09.16.300640v2
  • M. Hutzenthaler, P. Pfaffelhuber. Diffusion limits of genealogies under various modes of selection. EMS Series of Congress Reports Vol. 17,. Editors Ellen Baake and Anton Wakolbinger, European Mathematical Society, 409-426, 2021.
  • R. Backofen, P. Pfaffelhuber. The population genetics of the CRISPR-Cas system in bacteria. EMS Series of Congress Reports Vol. 17,. Editors Ellen Baake and Anton Wakolbinger, European Mathematical Society, 69-84, 2021.
  • N. Scherer, P. Sekula, P. Pfaffelhuber, P. Schlosser. pgainsim: an R-package to assess the mode of inheritance. Bioinformatics, 37(18), 3061-3063, 2021
  • F. Baumdicker, E. Sester-Huss, P. Pfaffelhuber. Modifiers of mutation rate in selectively fluctuating environments, [arxiv math.PR/1909.06241]  Stochastic Processes and their Applications, 130, 6843-6862, 2020
  • P. Pfaffelhuber, F. Grundner-Culemann, V. Lipphardt, F. Baumdicker. How to choose sets of ancestry informative markers: A supervised feature selection approach, [biorxiv], Forensic Science International: Genetics, 46, 102259, 2020
  • M. Lynch, B. Haubold, P. Pfaffelhuber, T. Maruki. Inference of Historical Population-size Changes with Allele-frequency data. G3, 10, 211–223, 2020
  • F. Hermann, P. Pfaffelhuber. The partial duplication random graph with edge deletion, [arxiv math.PR/1904.00718]  Submitted, 2019
  • P. Pfaffelhuber, J. Stiefel. The range of once-reinforced random walk in one dimension. , [arxiv math.PR/1903.05234]  Random Structures and Algotithms, 58: 164–175, 2021
  • E. Huss, P. Pfaffelhuber. Genealogical distances under low levels of selection. [biorxiv] Theo. Pop. Biol., 131, 2–11, 2020
  • F. Hermann, P. Pfaffelhuber. Markov branching processes with disasters: extinction, survival and duality to p-jump processes, [arxiv math.PR/1808.00073]  accepted in Stoch. Proc. Appl., 2020
  • A. Pirogov, P. Pfaffelhuber, A. Börsch-Haubold and B. Haubold. High-Complexity Regions in Mammalian Genomes are Enriched for Developmental Genes. Bioinformatics, doi: 10.1093/bioinformatics/bty922, 2018
  • P. Pfaffelhuber, A. Wakolbinger. Fixation probabilities and hitting times under small frequency-dependent selection,[Arxiv.org/abs/1801.01584] Theo. Pop. Biol., 124, 61–69, 2018
  • P. Czuppon, P. Pfaffelhuber. Limits of noise for autoregulated gene expression, [biorxiv], J. Math. Biol., 77, 1153–1191, 2018
  • N. Buchanan, F. Staubach, M. Wienroth, P. Pfaffelhuber, M. Surdu, A. Lipphardt, A. Köttgen, D. Syndercombe-Court, V. Lipphardt. Forensic DNA phenotyping legislation cannot be based on “Ideal FDP”—A response to Caliebe, Krawczak and Kayser. FSI Genetics, 34, e13–e14, 2018
  • S. Bossert, P. Pfaffelhuber. The fixation probability and time for a doubly beneficial mutant, [Arxiv math.PR/1610.06633]. Stoch. Proc. Appl. 128, 4018–4050, 2018
  • F. Baumdicker, A.M.I. Huebner, P. Pfaffelhuber. The independent loss model with ordered insertions for the evolution of CRISPR spacers. Theo. Pop. Biol. 119, 72-82, 2017

  • F. Staubach, V. Lipphardt, N. Buchanan, A. Köttgen, A. Lipphardt, A.C. Mupepele, P. Pfaffelhuber, M. Surdu, M. Wienroth. Note limitations of DNA legislation. Nature, 2017; 545: 30-30. : http://doi:10.1038/545030c (download: Paper link)

  • P. Czuppon,  P. Pfaffelhuber. A spatial model for selection and cooperation, [Arxiv math.PR/1603.00645], Journal of Applied Probability 54 (2), 522-539, 2017.
  • A. Greven, P. Pfaffelhuber, C. Pokalyuk and A. Wakolbinger. The fixation time of a strongly beneficial allele in a structured population, [Arxiv math.PR/1402.1769], Elec. J. Probab., 21 (61), 2016

  • M. Hutzenthaler, P. Pfaffelhuber. Stochastic averaging for multiscale Markov processes with an application to branching random walk in random environment, [Arxiv math.PR/1504.01508], submitted, 2015

  • F. Hermann, P. Pfaffelhuber. Large-scale behavior of the partial duplication random graph, [Arxiv math.PR/1408.0904], ALEA, Lat. Am. J. Probab. Math. Stat. 13, 687–710, 2016

  • M. Jansen, P. Pfaffelhuber, M. Hoffmann, G. Puetz, K. Winkler. In silico modeling of the dynamics of low density lipoprotein composition by a single plasma sample. http://dx.doi.org/10.1194/jlr.M058446, J. Lipid. Res., 57 (5): 882–893, 2016

  • A. Depperschmidt, E. Pardoux, P. Pfaffelhuber. A mixing tree-valued process arising under neutral evolution with recombination. [Arxiv math.PR/1505.01165], Elec. J. Probab., 20(94), 1–22, 2015

  • J. Schlüter, P. Czuppon, O. Schauer, P. Pfaffelhuber, M. McIntosh, A. Becker. Classification of phenotypic subpopulations in isogenic bacterial cultures by triple promoter probing at single cell level, J. Biotechnol., 198, 3–14, 2015

  • P. Pfaffelhuber, L. Popovic. How spatial heterogeneity shapes multiscale biochemical reaction network dynamics. J. Roy. Soc. Interface, 12(104), 2015

  • B. Melykuti and P. Pfaffelhuber. The stationary distribution of a Markov jump process on a state space glued together from two state spaces at two vertices, [Arxiv math.PR/1401.6400], Stochastic Models, 31(4), 525–553, 2015

  • A. Depperschmidt, P. Pfaffelhuber and A. Scheuringer. Some large deviation results for Kingman's coalescent, [Arxiv math.PR/1311.0649], Elec. Comm. Probab., 20(7), 1–14, 2015

  • M. Jansen and P. Pfaffelhuber. Stochastic Gene Expression with Delay, [Arxiv math.PR/1305.6635], J. Theo. Biology, 364, 355–363, 2015

  • P. Pfaffelhuber and L. Popovic. Scaling limits of spatial chemical reaction networks, [Arxiv math.PR/1302.0774], Ann. Appl. Probab., 25(6), 3162--3208, 2015

  • P. Czuppon, P. Pfaffelhuber. Some limit results for Markov chains indexed by trees, [Arxiv math.PR/1406.3768], Elec. Comm. Probab., 19(77), 1–11, 2014

  • F. Baumdicker and P. Pfaffelhuber. The infinitely many genes model with horizontal gene transfer, [Arxiv math.PR/1301.6547], Elec. J. Probab., 19(115), 1–27, 2014

  • M. Lynch, S. Xu, T. Maruki, X. Jiang, P. Pfaffelhuber, B. Haubold. Genome-Wide Linkage-Disequilibrium Profiles from Single Individuals. Genetics, 198(1), 269–281, 2014

  • S. Bossert, P. Pfaffelhuber. The Yule Approximation for the Site Frequency Spectrum after a Selective Sweep, PLoS One, 8(21), e81738, 2013

  • C. Pokalyuk, P. Pfaffelhuber. The ancestral selection graph under strong directional selection, Theoretical Population Biology, 87, 25–33, 2013

  • M. McIntosh, P. Czuppon, K. Best, A. Becker, P. Pfaffelhuber. Modeling Quorum Sensing in Sinorhizobium meliloti, Indian  J. Biochemistry & Biophysics (IJBB), 2(1), 59–74, 2013

  • B. Haubold, L. Krause, T. Horn and P. Pfaffelhuber. An Alignment-free Test for Recombination. Bioinformatics, 29(24), 3121–3127, 2013

  • A. Depperschmidt, A. Greven and P. Pfaffelhuber. Path-properties of the tree-valued Fleming-Viot process, [Arxiv math.PR/1212.5386], Elec. J. Probab., 18(84): 1–47, 2013

  • C. Pokalyuk, L. Mathew, D. Metzler, P. Pfaffelhuber. Competing islands limit the rate of adaptation in structured populations, Theoretical Population Biology, 90, 1–11, 2013

  • A. Greven, P. Pfaffelhuber and A. Winter. Tree-valued resampling dynamics Martingale problems and applications, [Arxiv math.PR/0806.2224], Prob. Theo. Rel. Fields, 155: 789–838, 2013

  • F. Baumdicker, P. Pfaffelhuber, W. Hess. The infinitely many genes model for the distributed genome of bacteria, Genome Biology and Evolution, 4, 443–456, 2012

  • A. Depperschmidt, N. Ketterer and P. Pfaffelhuber. A Brownian ratchet for protein translocation including dissociation of ratcheting sites, [Arxiv math.PR/1107.5219], J. Math. Biol., 66, 505–534, 2013

  • B. Haubold, P. Pfaffelhuber. Alignment-Free Population Genomics: An Efficient Estimator of Sequence Diversity. Genes, Genomes, Genetics, 2:883–889, 2012

  • P. Pfaffelhuber, P. R. Staab and A. Wakolbinger. Muller's ratchet with compensatory mutations, [Arxiv math.PR/1108.4059], Ann. Appl. Probab., 22(5), 2108–2132, 2012

  • F. H. Biehler, P. Pfaffelhuber. Compact metric measure spaces and Lambda-coalescents coming down from infinity, [Arxiv math.PR/1105.2409], ALEA, 9, 269–278, 2012

  • A. Depperschmidt, A. Greven and P. Pfaffelhuber. Tree-valued Fleming-Viot dynamics with mutation and selection, [Arxiv math.PR/1101.0759], Ann. Appl. Probab., 22(6), 2560–2615, 2012

  • P. Pfaffelhuber, H. Weisshaupt. Sensitivity analysis of one parameter semigroups exemplified by the Wright-Fisher diffusion, [Arxiv math.PR/1104.1876], Intern. J. Funct. Anal., Oper. Th. Appl., 3(2), 109–128, 2011

  • A. Tellier, P. Pfaffelhuber, B. Haubold, L. Naduvilezhath, L. Rose, T. Städler, W. Stephan, D. Metzler. Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum, PLoS One, 6, e18155, 2011

  • A. Depperschmidt, A. Greven, P. Pfaffelhuber. Marked metric measure spaces, [Arxiv math.PR/1101.4213], Elec. Comm. Probab., 16: 174–188, 2011

  • G. Ewing, J. Hermisson, P. Pfaffelhuber, J. Rudolf. Selective sweeps for recessive alleles and for other modes of dominance, [Arxiv math.PR/1005.5536], J. Math. Biol., 63: 399–431, 2011

  • B. Haubold, F. Reed, P. Pfaffelhuber. Alignment-free estimation of nucleotide diversity identifies a novel genomic outlier of unusually low genetic diversity in Drosophila melanogaster, Bioinformatics, 27: 449–455, 2011

  • P. Pfaffelhuber, A. Wakolbinger, H. Weisshaupt. The tree length of an evolving coalescent, [Arxiv math.PR/0908.2444], Prob. Theo. Rel. Fields, 151, 529–557, 2011

  • K. Best, P. Pfaffelhuber. The Aldous-Shields model revisited (with application to cellular ageing), [Arxiv math.PR/1004.1581], Elec. Comm. Probab., 15, 475–488, 2010

  • B. Haubold, P. Pfaffelhuber, M. Lynch. mlRho – A program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes, Mol. Ecol., 19 (Supp 1): 274–284, 2010

  • F. Baumdicker, W. R. Hess, P. Pfaffelhuber. The diversity of a distributed genome in bacterial populations, [Arxiv math.PR/0907.2572], [Mathematica Notebook], Ann. Appl. Probab., 20(5), 1567–1606, 2010

  • A. Depperschmidt, P. Pfaffelhuber. Asymptotics of a Brownian ratchet for Protein Translocation, [Arxiv math.PR/0904.2276], Stoch. Proc. Appl., 120: 901–925, 2010

  • T. Städler, B. Haubold, C. Merino, W. Stephan and P. Pfaffelhuber. The impact of sampling schemes on the site frequency spectrum in non-equilibrium subdivided populations. Genetics, 182: 205–216, 2009

  • B. Haubold, P. Pfaffelhuber, M. Domazet-Loso and T. Wiehe. Estimating Mutation Distances from Unaligned Genomes, J. Comp. Biol., 16(10): 1487–1500, 2009

  • A. Greven, P. Pfaffelhuber and A. Winter, Convergence in distribution of random metric measure spaces: (Lambda-coalescent measure trees), [ArXiv math.PR/0609801], Prob. Theo. Rel. Fields, 145(1): 285–322, 2009

  • J. Hermisson and P. Pfaffelhuber. The pattern of genetic hitchhiking under recurrent mutation, Elec. J. Probab., 13(68): 2069–2106, 2008

  • P. Pfaffelhuber, A. Lehnert and W. Stephan. Linkage disequilibrium under genetic hitchhiking in finite populations, Genetics, 179: 527–537, 2008

  • A. Etheridge, P. Pfaffelhuber and A. Wakolbinger. How often does the ratchet click? Facts, heuristics, asymptotics. In Trends in Stochastic Analysis (J. Blath, P. Mörters, M. Scheutzow eds.), LMS 353, Cambridge University Press, Lecture Notes Series 353, [Arxiv math.PR/0709.2775], pp. 365–390, 2009

  • P. Pfaffelhuber and A. Studeny, Approximating genealogies for partially linked neutral loci under a selective sweep [ArXiv q-bio.PE/0611029], J. Math. Biol., 55: 299–330, 2007

  • P. Pfaffelhuber and A. Wakolbinger. The process of most recent common ancestors in an evolving coalescent, [ArXiv math.PR/0511743], Stoch. Proc. Appl., 116: 1836–1859, 2006

  • P. Pfaffelhuber, B. Haubold and A. Wakolbinger. Approximate genealogies under genetic hitchhiking, Genetics, 174: 1995–2008, 2006 

  • A. Etheridge, P. Pfaffelhuber and A. Wakolbinger. An approximate sampling formula under genetic hitchhiking, [ArXiv math.PR/0503485], Ann. Appl. Probab., 16(2), 685–729, 2006

  • P. Pfaffelhuber. The Finite System Scheme  for State-dependent interacting multitype Branching Systems, ALEA, 2: 1-66, (pdf), 2006