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Items: 1 to 20 of 32

1.

MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies.

Vlachos C, Kofler R.

PLoS Comput Biol. 2018 Aug 16;14(8):e1006413. doi: 10.1371/journal.pcbi.1006413. eCollection 2018 Aug.

2.

Molecular dissection of a natural transposable element invasion.

Kofler R, Senti KA, Nolte V, Tobler R, Schlötterer C.

Genome Res. 2018 Jun;28(6):824-835. doi: 10.1101/gr.228627.117. Epub 2018 Apr 30.

3.

SimulaTE: simulating complex landscapes of transposable elements of populations.

Kofler R.

Bioinformatics. 2018 Apr 15;34(8):1439. doi: 10.1093/bioinformatics/btx832. No abstract available.

4.

SimulaTE: simulating complex landscapes of transposable elements of populations.

Kofler R.

Bioinformatics. 2018 Apr 15;34(8):1419-1420. doi: 10.1093/bioinformatics/btx772. Erratum in: Bioinformatics. 2018 Apr 15;34(8):1439.

5.

Regulation of transposable elements: Interplay between TE-encoded regulatory sequences and host-specific trans-acting factors in Drosophila melanogaster.

Jakšić AM, Kofler R, Schlötterer C.

Mol Ecol. 2017 Oct;26(19):5149-5159. doi: 10.1111/mec.14259. Epub 2017 Aug 16.

PMID:
28742942
6.

Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence.

Oppold AM, Schmidt H, Rose M, Hellmann SL, Dolze F, Ripp F, Weich B, Schmidt-Ott U, Schmidt E, Kofler R, Hankeln T, Pfenninger M.

Mol Ecol. 2017 Jun;26(12):3256-3275. doi: 10.1111/mec.14111. Epub 2017 Apr 12.

PMID:
28316106
7.

Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data.

Kofler R, Langmüller AM, Nouhaud P, Otte KA, Schlötterer C.

G3 (Bethesda). 2016 Nov 8;6(11):3507-3515. doi: 10.1534/g3.116.034488.

8.

PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq.

Kofler R, Gómez-Sánchez D, Schlötterer C.

Mol Biol Evol. 2016 Oct;33(10):2759-64. doi: 10.1093/molbev/msw137. Epub 2016 Aug 2.

9.

Tempo and Mode of Transposable Element Activity in Drosophila.

Kofler R, Nolte V, Schlötterer C.

PLoS Genet. 2015 Jul 17;11(7):e1005406. doi: 10.1371/journal.pgen.1005406. eCollection 2015 Jul.

10.

The impact of library preparation protocols on the consistency of allele frequency estimates in Pool-Seq data.

Kofler R, Nolte V, Schlötterer C.

Mol Ecol Resour. 2016 Jan;16(1):118-22. doi: 10.1111/1755-0998.12432. Epub 2015 Jun 9.

11.

The recent invasion of natural Drosophila simulans populations by the P-element.

Kofler R, Hill T, Nolte V, Betancourt AJ, Schlötterer C.

Proc Natl Acad Sci U S A. 2015 May 26;112(21):6659-63. doi: 10.1073/pnas.1500758112. Epub 2015 May 11.

12.

Gaussian process test for high-throughput sequencing time series: application to experimental evolution.

Topa H, Jónás Á, Kofler R, Kosiol C, Honkela A.

Bioinformatics. 2015 Jun 1;31(11):1762-70. doi: 10.1093/bioinformatics/btv014. Epub 2015 Jan 21.

13.

Sequencing pools of individuals - mining genome-wide polymorphism data without big funding.

Schlötterer C, Tobler R, Kofler R, Nolte V.

Nat Rev Genet. 2014 Nov;15(11):749-63. doi: 10.1038/nrg3803. Epub 2014 Sep 23. Review.

PMID:
25246196
14.

A guide for the design of evolve and resequencing studies.

Kofler R, Schlötterer C.

Mol Biol Evol. 2014 Feb;31(2):474-83. doi: 10.1093/molbev/mst221. Epub 2013 Nov 9.

15.

Massive habitat-specific genomic response in D. melanogaster populations during experimental evolution in hot and cold environments.

Tobler R, Franssen SU, Kofler R, Orozco-Terwengel P, Nolte V, Hermisson J, Schlötterer C.

Mol Biol Evol. 2014 Feb;31(2):364-75. doi: 10.1093/molbev/mst205. Epub 2013 Oct 22.

16.

Microarray and deep sequencing cross-platform analysis of the mirRNome and isomiR variation in response to epidermal growth factor.

Llorens F, Hummel M, Pantano L, Pastor X, Vivancos A, Castillo E, Mattlin H, Ferrer A, Ingham M, Noguera M, Kofler R, Dohm JC, Pluvinet R, Bayés M, Himmelbauer H, del Rio JA, Martí E, Sumoy L.

BMC Genomics. 2013 Jun 1;14:371. doi: 10.1186/1471-2164-14-371.

17.

Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples.

Boitard S, Kofler R, Françoise P, Robelin D, Schlötterer C, Futschik A.

Mol Ecol Resour. 2013 Mar;13(2):337-40. doi: 10.1111/1755-0998.12063. Epub 2013 Jan 11.

18.

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana.

Nolte V, Pandey RV, Kofler R, Schlötterer C.

Genome Res. 2013 Jan;23(1):99-110. doi: 10.1101/gr.139873.112. Epub 2012 Oct 10.

19.

Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America.

Fabian DK, Kapun M, Nolte V, Kofler R, Schmidt PS, Schlötterer C, Flatt T.

Mol Ecol. 2012 Oct;21(19):4748-69. doi: 10.1111/j.1365-294X.2012.05731.x. Epub 2012 Aug 22.

20.

Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles.

Orozco-terWengel P, Kapun M, Nolte V, Kofler R, Flatt T, Schlötterer C.

Mol Ecol. 2012 Oct;21(20):4931-41. doi: 10.1111/j.1365-294X.2012.05673.x. Epub 2012 Jun 21.

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