Publications

pre-print

Abdullaev, E.; Haridoss, D. A.; Arndt, P. F.: Predicting the methylation status of CpG islands from read distribution biases. BMC Genomics 26, 973 (2025)

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Alberge, J.-B.; Dutta, A.; Poletti, A.; Coorens, T. H. H.; Lightbody, E.; Toenges, R.; Loinaz, X.; Wallin, S.; Dunford, A.; Priebe, O. et al.; Dagan, J.; Boehner, C. J.; Horowitz, E.; Su, N. K.; Barr, H.; Hevenor, L.; Towle, K.; Beesam, R.; Beckwith, J. B.; Perry, .; Cordas dos Santos, D. M.; Bertamini, L.; Greipp , . T.; Kübler, K.; Arndt, P. F.; Terragna, C.; Zamagni, E.; Boyle, E.; Yong, K.; Morgan, G.; Walker, B. A.; Dimopoulos, M.; Kastritis, E.; Hess, J.; Sklavenitis-Pistofidis, R.; Stewart, C.; Getz, G.; Ghobrial, I. M.: Genomic landscape of multiple myeloma and its precursor conditions. Nature Genetics (2025)

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Abdullaev, E. T.; Haridoss, D. A.; Arndt, P. F.: Reconstruction of Segmental Duplication Rates and Associated Genomic Features by Network Analysis. Genome Biology and Evolution 17 (3), Article evaf011 (2025)

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2024

Ulicevic, J.; Shao, Z.; Jasnovidova, O.; Bressin, A.; Gajos, M.; Ng, A. H.; Annaldasula, S.; Meierhofer, D.; Church, G. M.; Busskamp, V. et al.; Mayer, A.: Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Molecular Systems Biology 20 (7), pp. 767 - 798 (2024)

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Rosebrock, D.; Vingron, M.; Arndt, P. F.: Modeling gene expression cascades during cell state transitions. iScience 27 (4), Article 109386 (2024)

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Sheinman, M.; Arndt, P. F.; Massip, F.: Modeling the mosaic structure of bacterial genomes to infer their evolutionary history. PNAS 121 (13), Article e2313367121 (2024)

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2023

Rosebrock, D.: Dissecting regional heterogeneity and modeling transcriptional cascades in brain organoids. Dissertation, vii, 129 pp. (2023)

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2022

Kleinert, P.: Computational interpretation of disease-causing, structural, and non-coding human genetic variants. Dissertation, 118 pp. (2022)

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Abdullaev, E.: Dynamical Aspects of the Evolution of Segmental Duplications in the Human Genome. Dissertation, xiii, 129 pp. (2022)

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Rosebrock, D.; Arora, S.; Mutukula, N.; Volkman, R.; Gralinska, E.; Balaskas, A.; Aragonés Hernández, A.; Buschow, R.; Brändl, B.; Müller, F.-J. et al.; Arndt, P. F.; Vingron, M.; Elkabetz, Y.: Enhanced cortical neural stem cell identity through short SMAD and WNT inhibition in human cerebral organoids facilitates emergence of outer radial glial cells. Nature Cell Biology 24 (6), pp. 981 - 995 (2022)

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2021

Abdullaev, E.; Umarova, I. R.; Arndt, P. F.: Modelling segmental duplications in the human genome. BMC Genomics 22 (1), Article 496 (2021)

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Sheinman, M.; Arkhipova, K.; Arndt, P. F.; Dutilh, B. E. ..; Hermsen, R.; Massip, F.: Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain. eLife 10, Article e62719 (2021)

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2019

Arndt, P. F.: Sequential and continuous time stick-breaking. Journal of Statistical Mechanics: Theory and Experiment 6 (6), Article 064003 (2019)

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2018

Smith, T. C. A.; Arndt, P. F.; Eyre-Walker, A.: Large scale variation in the rate of germ-line de novo mutation, base composition, divergence and diversity in humans. PLoS Genetics 14 (3), e1007254 (2018)

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2017

Kuruoglu, E. E.; Arndt, P. F.: The information capacity of the genetic code: Is the natural code optimal? Journal of Theoretical Biology 419, pp. 227 - 237 (2017)

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2016

Massip, F.; Sheinman, M.; Schbath, S.; Arndt, P.: Comparing the Statistical Fate of Paralogous and Orthologous Sequences. Genetics 204 (2), pp. 475 - 482 (2016)

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Moorjani, P.; Amorim, C. E.; Arndt, P. F.; Przeworski, M.: Variation in the molecular clock of primates. Proceedings of the National Academy of Sciences of the United States of America 113 (38), pp. 10607 - 10612 (2016)

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Sheinman, M.; Ramisch, A.; Massip, F.; Arndt, P. F.: Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences. Scientific Reports 6, 30851 (2016)

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2015

Glémin, S.; Arndt, P. F.; Messer, P. W.; Petrov, D.; Galtier, N.; Duret, L.: Quantification of GC-biased gene conversion in the human genome. Genome Research 25 (8), pp. 1215 - 1228 (2015)

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Francioli, L. C.; Polak, P. P.; Koren, A.; Menelaou, A.; Chun, S.; Renkens, I.; Genome of the Netherlands, C.; van Duijn, C. M.; Swertz, M.; Wijmenga, C. et al.; van Ommen, G.; Slagboom, P. E.; Boomsma, D. I.; Ye, K.; Guryev, V.; Arndt, P. F.; Kloosterman, W. P.; de Bakker, P. I.; Sunyaev, S. R.: Genome-wide patterns and properties of de novo mutations in humans. Nature Genetics 47 (7), pp. 822 - 826 (2015)

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Sheinman, M.; Massip, F.; Arndt, P. F.: Statistical properties of pairwise distances between leaves on a random Yule tree. PLoS One 10 (3), e0120206 (2015)

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Massip, F.; Sheinman, M.; Schbath, S.; Arndt, P. F.: How evolution of genomes is reflected in exact DNA sequence match statistics. Mol Biol Evol 32 (2), pp. 524 - 535 (2015)

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Mugal, C. F.; Arndt, P. F.; Holm, L.; Ellegren, H.: Evolutionary consequences of DNA methylation on the GC content in vertebrate genomes. G3: Genes, Genomes, Genetics 5 (3), pp. 441 - 447 (2015)

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Sheinman, M.; Sharma, A.; Alvarado, J.; Koenderink, G. H.; MacKintosh, F. C.: Anomalous discontinuity at the percolation critical point of active gels. Phys Rev Lett 114 (9), 098104 (2015)

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2014

Berglund, J.; Quilez, J.; Arndt, P. F.; Webster, M. T.: Germ line Methylation Patterns Determine the Distribution of Recombination Events in the Dog Genome. Genome biology and evolution 7 (2), pp. 522 - 530 (2014)

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Almirantis, Y.; Arndt, P.; Li, W.; Provata, A.: Editorial: Complexity in genomes. Computational Biology and Chemistry 53, pp. 1 - 4 (2014)

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Muino, J. M.; Kuruoglu, E. E.; Arndt, P. F.: Evidence of a cancer type-specific distribution for consecutive somatic mutation distances. Computational Biology and Chemistry 53, Pt A, pp. 79 - 83 (2014)

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Busse, C. E.; Czogiel, I.; Braun, P.; Arndt, P. F.; Wardemann, H.: Single-cell based high-throughput sequencing of full-length immunoglobulin heavy and light chain genes. European Journal of Immunology 44 (2), pp. 597 - 603 (2014)

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Ebert, G.; Steininger, A.; Weissmann, R.; Boldt, V.; Lind-Thomsen, A.; Grune, J.; Badelt, S.; Hessler, M.; Peiser, M.; Hitzler, M. et al.; Jensen, L. R.; Müller, I.; Hu, H.; Arndt, P. F.; Kuss, A. W.; Tebel, K.; Ullmann, R.: Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7. BMC Genomics 15, p. 15:537 - 15:537 (2014)

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2013

Mugal, C. F.; Arndt, P. F.; Ellegren, H.: Twisted signatures of GC-biased gene conversion embedded in an evolutionary stable karyotype. Molecular Biology and Evolution 30 (7), pp. 1700 - 1712 (2013)

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Massip, F.; Arndt, P. F.: Neutral Evolution of Duplicated DNA: An Evolutionary Stick-Breaking Process Causes Scale-Invariant Behavior. Physical Review Letters 110 (14), p. 148101 - 148101 (2013)

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2012

Clément, Y.: The evolution of base composition in mammalian genomes. Dissertation (2012)

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Habermann, K.; Mirgorodskaya, E.; Gobom, J.; Lehmann, V.; Müller, H.; Blümlein, K.; Deery, M. J.; Czogiel, I.; Erdmann, C.; Ralser, M. et al.; von Kries, J. P.; Lange, B. M. H.: Functional analysis of centrosomal kinase substrates in Drosophila melanogaster reveals a new function of the nuclear envelope component otefin in cell cycle progression. Molecular and Cellular Biology (Washington, DC) 32 (17), pp. 3554 - 3569 (2012)

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2011

Schütze, T.; Wilhelm, B.; Greiner, N.; Braun, H.; Peter, F.; Mörl, M.; Erdmann, V. A.; Lehrach, H.; Konthur, Z.; Menger, M. et al.; Arndt, P. F.; Glökler, J.: Probing the SELEX Process with Next-Generation Sequencing. PLoS ONE 6 (12), e29604 (2011)

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Clement, Y.; Arndt, P. F.: Substitution patterns are under different influences in primates and rodents. Genome Biol Evol 3, pp. 236 - 45 (2011)

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Cusack, B. P.; Arndt, P. F.; Duret, L.; Roest Crollius, H.: Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes. PLoS Genet 7 (10), p. e1002276 (2011)

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Dohm, J. C.; Lange, C.; Holtgrawe, D.; Rosleff Sorensen, T.; Borchardt, D.; Schulz, B.; Lehrach, H.; Weisshaar, B.; Himmelbauer, H.: Palaeohexaploid Ancestry for Caryophyllales Inferred from Extensive Gene-Based Physical and Genetic Mapping of the Sugar Beet Genome (Beta vulgaris). The Plant Journal: for Cell and Molecular Biology (2011)

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Zemojtel, T.; Kielbasa, S. M.; Arndt, P. F.; Behrens, S.; Bourque, G.; Vingron, M.: CpG deamination creates transcription factor-binding sites with high efficiency. Genome Biol Evol 3, pp. 1304 - 11 (2011)

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2010

Schütze, T.; Arndt, P. F.; Menger, M.; Wochner, A.; Vingron, M.; Erdmann, V. A.; Lehrach, H.; Kaps, C.; Glökler, J.: A calibrated diversity assay for nucleic acid libraries using DiStRO-a Diversity Standard of Random Oligonucleotides. Nucleic Acids Research 38 (4), p. e23 - e23 (2010)

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Polak, P.: Discovering mutational patterns in mammals using comparative genomics. Dissertation, IV, 117 pp., Freie Universität, Berlin (2010)

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Polak, P.; Querfurth, R.; Arndt, P. F.: The evolution of transcription-associated biases of mutations across vertebrates. BMC Evolutionary Biology 10, p. 10:187 - 10:187 (2010)

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Squartini, F.; von Haeseler, A.: Stationarity and reversibility in the nucleotide evolutionary process. Dissertation, 72 pp., Freie Universität, Berlin (2010)

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2009

Zemojtel, T.; Kielbasa, S. M.; Arndt, P. F.; Chung, H.-R.; Vingron, M.: Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. Trends in Genetics 25 (2), pp. 63 - 66 (2009)

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2008

Squartini, F.; Arndt, P. F.: Quantifying the stationarity and time reversibility of the nucleotide substitution process. Molecular Biology and Evolution 25 (12), pp. 2525 - 2535 (2008)

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Duret, L.; Arndt, P. F.: The Impact of Recombination on Nucleotide Substitutions in the Human Genome e1000071 (2008). PLoS Genetics 4 (5), p. e1000071 - e1000071 (2008)

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Polak, P.; Arndt, P. F.: Transcription induces strand-specific mutations at the 5? end of human genes. Genome Research 18 (8), pp. 1216 - 1223 (2008)

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Messer, P. W.: Tandem Duplications in the Human Genome. Dissertation, IV, 106 pp., Freie Universität Berlin, Berlin (2008)

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ZIP

2007

Arndt, P. F.; Vingron, M.: The Otto Warburg International Summer School and Workshop on Networks and Regulation. BMC Bioinformatics 8 (Suppl) (6), p. S1 - S1 (2007)

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de la Chaux, N.; Messer, P. W.; Arndt, P.: DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage. BMC Evolutionary Biology 7, pp. 191 - 102 (2007)

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Messer, P. W.; Bundschuh, R.; Vingron, M.; Arndt, P. F.: Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics. Journal of Computational Biology: A Journal of Computational Molecular Cell Biology 14 (5), pp. 655 - 668 (2007)

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Messer, P. W.; Arndt, P. F.: The Majority of Recent Short DNA Insertions in the Human Genome Are Tandem Duplications. Molecular Biology and Evolution: MBE 24 (5), pp. 1190 - 1197 (2007)

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2006

Alignment Statistics for Long-Range Correlated Genomic Sequences (Lecture Notes in Computer Science, 3909/2006). 10th Annual International Conference, RECOMB 2006, Venice, Italy, April 02, 2006 - April 05, 2006. Springer, Berlin/Heidelberg (2006), 612 pp.

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Messer, P. W.; Arndt, P. F.: CorGen-measuring and generating long-range correlations for DNA sequence analysis. Nucleic Acids Research 34, pp. W692 - W695 (2006)

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Lipatov1, M.; Arndt, P. F.; Hwa, T.; Petrov, D. A.: A novel method distinguishes between mutation rates and fixation biases in patterns of single-nucleotide substitution. Journal of Molecular Evolution: the Journal of the International Society of Molecular Evolution 62 (2), pp. 168 - 175 (2006)

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Roepcke, S.; Zhi, D.; Vingron, M.; Arndt, P. F.: Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters. Gene 365, pp. 48 - 56 (2006)

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2005

Messer, P.; Lässig, M.; Arndt, P. F.: Universality of long-range correlations in expansion-randomization systems. Journal of Statistical Mechanics: Theory and Experiment (10), p. P10004 - P10004 (2005)

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Arndt, P. F.; Hwa, T.; Petrov, D. A.: Substantial Regional Variation in Substitution Rates in the Human Genome: Importance of GC Content, Gene Density, and Telomere-Specific Effects. Journal of Molecular Evolution: the Journal of the International Society of Molecular Evolution 60 (6), pp. 748 - 763 (2005)

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Messer, P. W.; Arndt, P. F.; Lässig, M.: Solvable Sequence Evolution Models and Genomic Correlations. Physical Review Letters 94, pp. 138103-1 - 138103-4 (2005)

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Webster, M. T.; Smith, N. G. C.; Hultin-Rosenberg, L.; Arndt, P. F.; Ellegren, H.: Male-Driven Biased Gene Conversion Governs the Evolution of Base Composition in Human Alu Repeats. Molecular Biology and Evolution 22 (6), pp. 1468 - 1474 (2005)

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Arndt, P. F.; Hwa, T.: Identification and measurement of neighbor-dependent nucleotide substitution processes. Bioinformatics 21 (10), pp. 3222 - 2328 (2005)

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Singh, N. D.; Arndt, P. F.; Petrov, D. A.: Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster. Genetics 169 (2), pp. 709 - 722 (2005)

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2004

Arndt, P. F.; Hwa, T.: Regional and time-resolved mutation patterns of the human genome. 18th GERMAN CONFERENCE ON BIOINFORMATICS 2003 (GCB’03), Technische Universitaet Muenchen, October 12, 2003 - October 14, 2003. Bioinformatics 20 (10), pp. 1482 - 1485 (2004)

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2003

Arndt, P. F.; Petrov, D. A.; Hwa, T.: Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation. Molecular Biology and Evolution 20 (11), pp. 1887 - 1896 (2003)

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Arndt, P. F.; Burge, C. B.; Hwa, T.: DNA sequence evolution with neighbor-dependent mutation. Journal of Computational Biology 10 (3-4), pp. 313 - 322 (2003)

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