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Items: 1 to 50 of 52

1.

Targeting miR-34a/Pdgfra interactions partially corrects alveologenesis in experimental bronchopulmonary dysplasia.

Ruiz-Camp J, Quantius J, Lignelli E, Arndt PF, Palumbo F, Nardiello C, Surate Solaligue DE, Sakkas E, Mižíková I, Rodríguez-Castillo JA, Vadász I, Richardson WD, Ahlbrecht K, Herold S, Seeger W, Morty RE.

EMBO Mol Med. 2019 Mar;11(3). pii: e9448. doi: 10.15252/emmm.201809448.

2.

Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma.

Gopal RK, Kübler K, Calvo SE, Polak P, Livitz D, Rosebrock D, Sadow PM, Campbell B, Donovan SE, Amin S, Gigliotti BJ, Grabarek Z, Hess JM, Stewart C, Braunstein LZ, Arndt PF, Mordecai S, Shih AR, Chaves F, Zhan T, Lubitz CC, Kim J, Iafrate AJ, Wirth L, Parangi S, Leshchiner I, Daniels GH, Mootha VK, Dias-Santagata D, Getz G, McFadden DG.

Cancer Cell. 2018 Aug 13;34(2):242-255.e5. doi: 10.1016/j.ccell.2018.06.013.

3.

Large scale variation in the rate of germ-line de novo mutation, base composition, divergence and diversity in humans.

Smith TCA, Arndt PF, Eyre-Walker A.

PLoS Genet. 2018 Mar 28;14(3):e1007254. doi: 10.1371/journal.pgen.1007254. eCollection 2018 Mar.

4.

The information capacity of the genetic code: Is the natural code optimal?

Kuruoglu EE, Arndt PF.

J Theor Biol. 2017 Apr 21;419:227-237. doi: 10.1016/j.jtbi.2017.01.046. Epub 2017 Feb 3.

PMID:
28163008
5.

Variation in the molecular clock of primates.

Moorjani P, Amorim CE, Arndt PF, Przeworski M.

Proc Natl Acad Sci U S A. 2016 Sep 20;113(38):10607-12. doi: 10.1073/pnas.1600374113. Epub 2016 Sep 6.

6.

Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences.

Sheinman M, Ramisch A, Massip F, Arndt PF.

Sci Rep. 2016 Aug 4;6:30851. doi: 10.1038/srep30851.

7.

Comparing the Statistical Fate of Paralogous and Orthologous Sequences.

Massip F, Sheinman M, Schbath S, Arndt PF.

Genetics. 2016 Oct;204(2):475-482. Epub 2016 Jul 29.

8.

sciReptor: analysis of single-cell level immunoglobulin repertoires.

Imkeller K, Arndt PF, Wardemann H, Busse CE.

BMC Bioinformatics. 2016 Feb 4;17:67. doi: 10.1186/s12859-016-0920-1.

9.

Quantification of GC-biased gene conversion in the human genome.

Glémin S, Arndt PF, Messer PW, Petrov D, Galtier N, Duret L.

Genome Res. 2015 Aug;25(8):1215-28. doi: 10.1101/gr.185488.114. Epub 2015 May 20.

10.

Genome-wide patterns and properties of de novo mutations in humans.

Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I; Genome of the Netherlands Consortium, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, Boomsma DI, Ye K, Guryev V, Arndt PF, Kloosterman WP, de Bakker PIW, Sunyaev SR.

Nat Genet. 2015 Jul;47(7):822-826. doi: 10.1038/ng.3292. Epub 2015 May 18.

11.

Statistical properties of pairwise distances between leaves on a random Yule tree.

Sheinman M, Massip F, Arndt PF.

PLoS One. 2015 Mar 31;10(3):e0120206. doi: 10.1371/journal.pone.0120206. eCollection 2015.

12.

Evolutionary consequences of DNA methylation on the GC content in vertebrate genomes.

Mugal CF, Arndt PF, Holm L, Ellegren H.

G3 (Bethesda). 2015 Jan 15;5(3):441-7. doi: 10.1534/g3.114.015545.

13.

Germline methylation patterns determine the distribution of recombination events in the dog genome.

Berglund J, Quilez J, Arndt PF, Webster MT.

Genome Biol Evol. 2014 Dec 19;7(2):522-30. doi: 10.1093/gbe/evu282.

14.

How evolution of genomes is reflected in exact DNA sequence match statistics.

Massip F, Sheinman M, Schbath S, Arndt PF.

Mol Biol Evol. 2015 Feb;32(2):524-35. doi: 10.1093/molbev/msu313. Epub 2014 Nov 13.

15.

Evidence of a cancer type-specific distribution for consecutive somatic mutation distances.

Muiño JM, Kuruoğlu EE, Arndt PF.

Comput Biol Chem. 2014 Dec;53 Pt A:79-83. doi: 10.1016/j.compbiolchem.2014.08.012. Epub 2014 Aug 23.

PMID:
25179009
16.

Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7.

Ebert G, Steininger A, Weißmann R, Boldt V, Lind-Thomsen A, Grune J, Badelt S, Heßler M, Peiser M, Hitzler M, Jensen LR, Müller I, Hu H, Arndt PF, Kuss AW, Tebel K, Ullmann R.

BMC Genomics. 2014 Jun 29;15:537. doi: 10.1186/1471-2164-15-537.

17.

Single-cell based high-throughput sequencing of full-length immunoglobulin heavy and light chain genes.

Busse CE, Czogiel I, Braun P, Arndt PF, Wardemann H.

Eur J Immunol. 2014 Feb;44(2):597-603. doi: 10.1002/eji.201343917. Epub 2013 Oct 22.

18.

Meiotic recombination strongly influences GC-content evolution in short regions in the mouse genome.

Clément Y, Arndt PF.

Mol Biol Evol. 2013 Dec;30(12):2612-8. doi: 10.1093/molbev/mst154. Epub 2013 Sep 11.

PMID:
24030552
19.

Twisted signatures of GC-biased gene conversion embedded in an evolutionary stable karyotype.

Mugal CF, Arndt PF, Ellegren H.

Mol Biol Evol. 2013 Jul;30(7):1700-12. doi: 10.1093/molbev/mst067. Epub 2013 Apr 5.

20.

Neutral evolution of duplicated DNA: an evolutionary stick-breaking process causes scale-invariant behavior.

Massip F, Arndt PF.

Phys Rev Lett. 2013 Apr 5;110(14):148101. Epub 2013 Apr 2.

PMID:
25167038
21.

Probing the SELEX process with next-generation sequencing.

Schütze T, Wilhelm B, Greiner N, Braun H, Peter F, Mörl M, Erdmann VA, Lehrach H, Konthur Z, Menger M, Arndt PF, Glökler J.

PLoS One. 2011;6(12):e29604. doi: 10.1371/journal.pone.0029604. Epub 2011 Dec 29.

22.

Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes.

Cusack BP, Arndt PF, Duret L, Roest Crollius H.

PLoS Genet. 2011 Oct;7(10):e1002276. doi: 10.1371/journal.pgen.1002276. Epub 2011 Oct 13.

23.

CpG deamination creates transcription factor-binding sites with high efficiency.

Zemojtel T, Kielbasa SM, Arndt PF, Behrens S, Bourque G, Vingron M.

Genome Biol Evol. 2011;3:1304-11. doi: 10.1093/gbe/evr107. Epub 2011 Oct 19.

24.

Substitution patterns are under different influences in primates and rodents.

Clément Y, Arndt PF.

Genome Biol Evol. 2011;3:236-45. doi: 10.1093/gbe/evr011. Epub 2011 Feb 21.

25.

The evolution of transcription-associated biases of mutations across vertebrates.

Polak P, Querfurth R, Arndt PF.

BMC Evol Biol. 2010 Jun 18;10:187. doi: 10.1186/1471-2148-10-187.

26.

A calibrated diversity assay for nucleic acid libraries using DiStRO--a Diversity Standard of Random Oligonucleotides.

Schütze T, Arndt PF, Menger M, Wochner A, Vingron M, Erdmann VA, Lehrach H, Kaps C, Glökler J.

Nucleic Acids Res. 2010 Mar;38(4):e23. doi: 10.1093/nar/gkp1108. Epub 2009 Dec 3.

27.

Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila.

Singh ND, Arndt PF, Clark AG, Aquadro CF.

Mol Biol Evol. 2009 Jul;26(7):1591-605. doi: 10.1093/molbev/msp071. Epub 2009 Apr 7.

28.

Long-range bidirectional strand asymmetries originate at CpG islands in the human genome.

Polak P, Arndt PF.

Genome Biol Evol. 2009 Aug 3;1:189-97. doi: 10.1093/gbe/evp024.

29.

Methylation and deamination of CpGs generate p53-binding sites on a genomic scale.

Zemojtel T, Kielbasa SM, Arndt PF, Chung HR, Vingron M.

Trends Genet. 2009 Feb;25(2):63-6. doi: 10.1016/j.tig.2008.11.005. Epub 2008 Dec 26.

PMID:
19101055
30.

Quantifying the stationarity and time reversibility of the nucleotide substitution process.

Squartini F, Arndt PF.

Mol Biol Evol. 2008 Dec;25(12):2525-35. doi: 10.1093/molbev/msn169. Epub 2008 Aug 5.

PMID:
18682605
31.

Genetic alterations of HLA-class II in ovarian cancer.

Kübler K, Arndt PF, Wardelmann E, Landwehr C, Krebs D, Kuhn W, van der Ven K.

Int J Cancer. 2008 Sep 15;123(6):1350-6. doi: 10.1002/ijc.23624.

32.

The impact of recombination on nucleotide substitutions in the human genome.

Duret L, Arndt PF.

PLoS Genet. 2008 May 9;4(5):e1000071. doi: 10.1371/journal.pgen.1000071.

33.

Transcription induces strand-specific mutations at the 5' end of human genes.

Polak P, Arndt PF.

Genome Res. 2008 Aug;18(8):1216-23. doi: 10.1101/gr.076570.108. Epub 2008 May 7.

34.
35.

Effects of long-range correlations in DNA on sequence alignment score statistics.

Messer PW, Bundschuh R, Vingron M, Arndt PF.

J Comput Biol. 2007 Jun;14(5):655-68. Review.

PMID:
17683266
36.

The majority of recent short DNA insertions in the human genome are tandem duplications.

Messer PW, Arndt PF.

Mol Biol Evol. 2007 May;24(5):1190-7. Epub 2007 Feb 24.

PMID:
17322553
37.
39.

HLA-class II haplotype associations with ovarian cancer.

Kübler K, Arndt PF, Wardelmann E, Krebs D, Kuhn W, van der Ven K.

Int J Cancer. 2006 Dec 15;119(12):2980-5.

40.

CorGen--measuring and generating long-range correlations for DNA sequence analysis.

Messer PW, Arndt PF.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W692-5.

41.

A novel method distinguishes between mutation rates and fixation biases in patterns of single-nucleotide substitution.

Lipatov M, Arndt PF, Hwa T, Petrov DA.

J Mol Evol. 2006 Feb;62(2):168-75. Epub 2005 Dec 14. Erratum in: J Mol Evol. 2006 Feb;62(2):245.

PMID:
16362483
42.

Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters.

Roepcke S, Zhi D, Vingron M, Arndt PF.

Gene. 2006 Jan 3;365:48-56. Epub 2005 Dec 15.

PMID:
16343812
43.
44.

Solvable sequence evolution models and genomic correlations.

Messer PW, Arndt PF, Lässig M.

Phys Rev Lett. 2005 Apr 8;94(13):138103. Epub 2005 Apr 8.

PMID:
15904043
45.

Male-driven biased gene conversion governs the evolution of base composition in human alu repeats.

Webster MT, Smith NG, Hultin-Rosenberg L, Arndt PF, Ellegren H.

Mol Biol Evol. 2005 Jun;22(6):1468-74. Epub 2005 Mar 16.

PMID:
15772377
46.

Identification and measurement of neighbor-dependent nucleotide substitution processes.

Arndt PF, Hwa T.

Bioinformatics. 2005 May 15;21(10):2322-8. Epub 2005 Mar 15.

PMID:
15769841
47.

Comparative promoter region analysis powered by CORG.

Dieterich C, Grossmann S, Tanzer A, Röpcke S, Arndt PF, Stadler PF, Vingron M.

BMC Genomics. 2005 Feb 21;6:24.

48.

Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster.

Singh ND, Arndt PF, Petrov DA.

Genetics. 2005 Feb;169(2):709-22. Epub 2004 Nov 1.

49.

Regional and time-resolved mutation patterns of the human genome.

Arndt PF, Hwa T.

Bioinformatics. 2004 Jul 10;20(10):1482-5.

PMID:
15231538
50.

DNA sequence evolution with neighbor-dependent mutation.

Arndt PF, Burge CB, Hwa T.

J Comput Biol. 2003;10(3-4):313-22.

PMID:
12935330

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