Publications

2009

• Long-Range Bidirectional Strand Asymmetries Originate at CpG Islands in the Human Genome
  Paz Polak, Peter F Arndt
  Genome Biology and Evolution 2009 (2009) 189
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• 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) 1591-605
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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) 63-6
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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) 1216-23
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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) 2525-35
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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) 1350-6
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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) 1190-7
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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) 655-68
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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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• 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) 168-75
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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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• 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) 2980-5
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2005

• Identification and measurement of neighbor-dependent nucleotide substitution processes
  Peter F Arndt, Terence Hwa
  Bioinformatics (Oxford; England) 21 (2005) 2322-8
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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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• Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster
  Nadia D Singh, Peter F Arndt, Dmitri A Petrov
  Genetics 169 (2005) 709-22
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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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• 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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• 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) 748-63
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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) 1468-74
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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) 1482-5
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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

• 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) 1887-96
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• 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) 313-22
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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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2000

• Yang-Lee theory for a nonequilibrium phase transition
  Peter F Arndt
  Physical Review Letters 84 (2000) 814-7
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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
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