Publications

2011

• Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes.
  Brian P Cusack, Peter F Arndt, Laurent Duret, Hugues Roest Crollius
  PLoS Genetics 7 (2011) e1002276
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• Substitution patterns are under different influences in primates and rodents.
  Yves Clement, Peter F Arndt
  Genome Biology and Evolution 3 (2011) 236-245
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• CpG deamination creates transcription factor binding sites with high efficiency.
  Tomasz Zemojtel, Szymon M Kielbasa, Peter F Arndt, Sarah Behrens, Guillaume Bourque, Martin Vingron
  Genome Biology and Evolution (2011)
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2010

• A calibrated diversity assay for nucleic acid libraries using DiStRO--a Diversity Standard of Random Oligonucleotides.
  Tatjana Schütze, Peter F Arndt, Marcus Menger, Aniela Wochner, Martin Vingron, Volker A Erdmann, Hans Lehrach, Christian Kaps, Jörn Glökler
  Nucleic Acids Research 38 (2010) e23
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• The evolution of transcription-associated biases of mutations across vertebrates.
  Paz Polak, Robert Querfurth, Peter F Arndt
  BMC Evolutionary Biology 10 (2010) 187
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2009

• Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila.
  Nadia D Singh, Peter F Arndt, Andrew G Clark, Charles F Aquadro
  Molecular Biology and Evolution 26 (2009) 1591-1605
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• Methylation and deamination of CpGs generate p53-binding sites on a genomic scale.
  Tomasz Zemojtel, Szymon M Kielbasa, Peter F Arndt, Ho-Ryun Chung, Martin Vingron
  Trends in Genetics : TIG 25 (2009) 63-66
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• Long-range bidirectional strand asymmetries originate at CpG islands in the human genome.
  Paz Polak, Peter F Arndt
  Genome Biology and Evolution 1 (2009) 189-197
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2008

• The impact of recombination on nucleotide substitutions in the human genome.
  Laurent Duret, Peter F Arndt
  PLoS Genetics 4 (2008) e1000071
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• Transcription induces strand-specific mutations at the 5' end of human genes.
  Paz Polak, Peter F Arndt
  Genome Research 18 (2008) 1216-1223
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• Quantifying the stationarity and time reversibility of the nucleotide substitution process.
  Federico Squartini, Peter F Arndt
  Molecular Biology and Evolution 25 (2008) 2525-2535
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• Genetic alterations of HLA-class II in ovarian cancer.
  Kirsten Kübler, Peter F Arndt, Eva Wardelmann, Christina Landwehr, Dieter Krebs, Walther Kuhn, Katrin van der Ven
  International Journal of Cancer 123 (2008) 1350-1356
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2007

• The majority of recent short DNA insertions in the human genome are tandem duplications.
  Philipp W Messer, Peter F Arndt
  Molecular Biology and Evolution 24 (2007) 1190-1197
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• Reconstruction of ancestral nucleotide sequences and estimation of substitution frequencies in a star phylogeny.
  Peter F Arndt
  Gene 390 (2007) 75-83
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• Effects of long-range correlations in DNA on sequence alignment score statistics.
  Philipp W Messer, Ralf Bundschuh, Martin Vingron, Peter F Arndt
  Journal of Computational Biology : a Journal of Computational Molecular Cell Biology 14 (2007) 655-668
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• DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage.
  Nicole de la Chaux, Philipp W Messer, Peter F Arndt
  BMC Evolutionary Biology 7 (2007) 191
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• The Otto Warburg International Summer School and Workshop on Networks and Regulation
  Peter F Arndt, Martin Vingron
  BMC Bioinformatics 8 (2007) S1
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2006

• Alignment Statistics for Long-Range Correlated Genomic Sequences
  Philipp W Messer, Ralf Bundschuh, Martin Vingron, Peter F Arndt
  Lecture Notes in Computer Science 3909 (2006) 426-440
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• Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters.
  Stefan Roepcke, Degui Zhi, Martin Vingron, Peter F Arndt
  Gene 365 (2006) 48-56
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• CorGen--measuring and generating long-range correlations for DNA sequence analysis.
  Philipp W Messer, Peter F Arndt
  Nucleic Acids Research 34 (2006) W692-5
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• Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences.
  Nadia D Singh, Peter F Arndt, Dmitri A Petrov
  BMC Biology 4 (2006) 37
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• A novel method distinguishes between mutation rates and fixation biases in patterns of single-nucleotide substitution.
  Mikhail Lipatov, Peter F Arndt, Terence Hwa, Dmitri A Petrov
  Journal of Molecular Evolution 62 (2006) 168-175
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• HLA-class II haplotype associations with ovarian cancer.
  Kirsten Kübler, Peter F Arndt, Eva Wardelmann, Dieter Krebs, Walther Kuhn, Katrin van der Ven
  International Journal of Cancer 119 (2006) 2980-2985
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2005

• Identification and measurement of neighbor-dependent nucleotide substitution processes.
  Peter F Arndt, Terence Hwa
  Bioinformatics (Oxford, England) 21 (2005) 2322-2328
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• Solvable sequence evolution models and genomic correlations.
  Philipp W Messer, Peter F Arndt, Michael Lässig
  Physical Review Letters 94 (2005) 138103
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• Universality of long-range correlations in expansion-randomization systems
  Philipp W Messer, Michael Lässig, Peter F Arndt
  Journal of Statistical Mechanics: Theory and Experiment 2005 (2005) P10004--P10004
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• Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster.
  Nadia D Singh, Peter F Arndt, Dmitri A Petrov
  Genetics 169 (2005) 709-722
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• Comparative promoter region analysis powered by CORG.
  Christoph Dieterich, Steffen Grossmann, Andrea Tanzer, Stefan Röpcke, Peter F Arndt, Peter F Stadler, Martin Vingron
  BMC Genomics 6 (2005) 24
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• Male-driven biased gene conversion governs the evolution of base composition in human alu repeats.
  Matthew T Webster, Nick G C Smith, Lina Hultin-Rosenberg, Peter F Arndt, Hans Ellegren
  Molecular Biology and Evolution 22 (2005) 1468-1474
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• Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects.
  Peter F Arndt, Terence Hwa, Dmitri A Petrov
  Journal of Molecular Evolution 60 (2005) 748-763
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2004

• Regional and time-resolved mutation patterns of the human genome.
  Peter F Arndt, Terence Hwa
  Bioinformatics (Oxford, England) 20 (2004) 1482-1485
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• Identification and Measurement of Neighbor Dependent Nucleotide Substitution Processes
  Peter F Arndt
  Lecture Notes in Informatics P-53 (2004) 227-234
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2003

• DNA sequence evolution with neighbor-dependent mutation.
  Peter F Arndt, Christopher B Burge, Terence Hwa
  Journal of Computational Biology : a Journal of Computational Molecular Cell Biology 10 (2003) 313-322
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• Distinct changes of genomic biases in nucleotide substitution at the time of Mammalian radiation.
  Peter F Arndt, Dmitri A Petrov, Terence Hwa
  Molecular Biology and Evolution 20 (2003) 1887-1896
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• The History of Nucleotide Substitution Pattern in Human
  Peter F Arndt
  Biophysics 48 (2003) 585-589
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2002

• DNA Sequence Evolution with Neighbor-Dependent Mutation
  Peter F Arndt, Christopher B Burge, Terence Hwa
  RECOMB 2002, Proceedings of the 6th Annual International Conference on Computational Biology (2002) 32-38
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• Spontaneous Breaking of Translational Invariance and Spatial Condensation in Stationary States on a Ring. II. The Charged System and the Two-Component Burgers Equations
  Peter F Arndt, Vladimir Rittenberg
  Journal of Statistical Physics 107 (2002) 989-1013
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2001

• Criterion for crack formation in disordered materials
  Peter F Arndt, Thomas Nattermann
  Physical Review B 63 (2001) 134204
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• Directed percolation, fractal roots and the Lee-Yang theorem
  Peter F Arndt, Silvio Renato Dahmen, Haye Hinrichsen
  Physica A: Statistical Mechanics and its Applications 295 (2001) 128-131
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1999

• Spontaneous breaking of translational invariance and spatial condensation in stationary states on a ring. I. The neutral system
  Peter F Arndt, Thomas Heinzel, Vladimir Rittenberg
  Journal of Statistical Physics 97 (1999) 1-65
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1998

• Spontaneous breaking of translational invariance in one-dimensional stationary states on a ring
  Peter F Arndt, Thomas Heinzel, Vladimir Rittenberg
  Journal of Physics A: Mathematical and Theoretical 31 (1998) L45--L51
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• Metastability and Spinodal Points for a Random Walker on a Triangle
  Peter F Arndt, Thomas Heinzel
  Journal of Statistical Physics 92 (1998) 837-864
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• First-order phase transitions in one-dimensional steady states
  Peter F Arndt, Thomas Heinzel, Vladimir Rittenberg
  Journal of Statistical Physics 90 (1998) 783-815
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• Stochastic models on a ring and quadratic algebras. The three-species diffusion problem
  Peter F Arndt, Thomas Heinzel, Vladimir Rittenberg
  Journal of Physics A: Mathematical and Theoretical 31 (1998) 833-844
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1995

• Temperley-Lieb words as valence-bond ground states
  Peter F Arndt, Thomas Heinzel, C M Yung
  Journal of Physics A: Mathematical and Theoretical 28 (1995) L323--L329
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• Numerical investigation of correlation functions for the UqSU(2) invariant spin-1/2 Heisenberg chain
  Peter F Arndt, Thomas Heinzel
  Journal of Physics A: Mathematical and Theoretical 28 (1995) 3567-3578
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1992

• Third-order spin-wave theory for the Heisenberg antiferromagnet
  Chris J Hamer, Zheng Weihong, Peter F Arndt
  Physical Review B 46 (1992) 6276-6292
  [Abstract] [Journal] [Fulltext]