Publications

2018

Barghi, Neda; Tobler, Raymond; Nolte, Viola; Jaksic, Ana Marija; Mallard, Francois; Otte, Kathrin; Dolezal, Marlies; Taus, Thomas; Kofler, Robert; Schlötterer, Christian

Polygenic adaptation fuels genetic redundancy in Drosophila Artikel

bioRxiv, S. 332122, 2018.

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Kofler, Robert; Nolte, Viola; Tobler, Ray; Schlötterer, Christian

Molecular dissection of a natural transposable element invasion Artikel

Genome Research, 2018.

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2017

Kofler, Robert

SimulaTE: simulating complex landscapes of transposable elements of populations Artikel

Bioinformatics, (November 2017), S. 1–2, 2017, ISSN: 1367-4803.

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Oppold, Ann Marie; Schmidt, Hanno; Rose, Marcel; Hellmann, Sören Lukas; Dolze, Florian; Ripp, Fabian; Weich, Bettina; Schmidt-Ott, Urs; Schmidt, Erwin; Kofler, Robert; Hankeln, Thomas; Pfenninger, Markus

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

Molecular Ecology, 26 (12), S. 3256–3275, 2017, ISSN: 1365294X.

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Jaksic, Ana Marija; Kofler, Robert; Schlötterer, Christian

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

Molecular Ecology, (May), 2017, ISSN: 09621083.

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2016

Kofler, Robert; Langm, Anna Maria; Nouhaud, Pierre; Otte, Anna; Schlötterer, Christian

Suitability of different mapping algorithms for genome-wide polymorphism scans with Pool-Seq data Artikel

Submitted, 6 (November), S. 1–20, 2016, ISSN: 2160-1836.

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Kofler, Robert; Gómez-Sánchez, Daniel; Schlötterer, Christian

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

Molecular Biology and Evolution, 33 (10), S. 2759–2764, 2016, ISSN: 15371719.

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Franssen, Susanne U; Kofler, Robert; Schlötterer, Christian

Uncovering the genetic signature of quantitative trait evolution with replicated time series data Keywords Artikel

(August), S. 1–10, 2016, ISSN: 0018-067X.

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Kofler, Robert; Nolte, Viola; Schlötterer, Christian

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

Molecular ecology resources, 16 (1), S. 118–122, 2016, ISSN: 1755-0998.

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2015

Kofler, Robert; Nolte, Viola; Schlötterer, Christian

Tempo and Mode of Transposable Element Activity in Drosophila. Artikel

PLoS genetics, 11 (7), S. e1005406, 2015, ISSN: 1553-7404.

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Schlötterer, C; Kofler, R; Versace, E; Tobler, R; Franssen, S U

Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation. Artikel

Heredity, 114 (5), S. 431–40, 2015, ISSN: 1365-2540.

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Kofler, Robert; Hill, Tom; Nolte, Viola; Betancourt, Andrea J; Schlötterer, Christian

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

Proceedings of the National Academy of Sciences of the United States of America, 112 (21), S. 6659–63, 2015, ISSN: 1091-6490.

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Topa, Hande; Jónás, Ágnes; Kofler, Robert; Kosiol, Carolin; Honkela, Antti

Gaussian process test for high-throughput sequencing time series: Application to experimental evolution Artikel

Bioinformatics, 31 (11), S. 1762–1770, 2015, ISSN: 14602059.

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2014

Schlötterer, Christian; Tobler, Raymond; Kofler, Robert; Nolte, Viola

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

Nature Reviews Genetics, 15 (11), S. 749–763, 2014, ISSN: 14710064.

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Tobler, Ray; Franssen, Susanne U; Kofler, Robert; Orozco-Terwengel, Pablo; Nolte, Viola; Hermisson, Joachim; Schlötterer, Christian

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

Molecular Biology and Evolution, 31 (2), S. 364–375, 2014, ISSN: 07374038.

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2013

Kofler, Robert; Schlötterer, Christian

A Guide for the Design of Evolve and Resequencing Studies. Artikel

Molecular biology and evolution, 31 (2), S. 474–483, 2013, ISSN: 1537-1719.

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Llorens, Franc; Hummel, Manuela; Pantano, Lorena; Pastor, Xavier; Vivancos, Ana; Castillo, Ester; Matllin, Heidi; Ferrer, Anna; Ingham, Matthew; Noguera, Marc; Kofler, Robert; Dohm, Juliane C; Pluvinet, Raquel; ò, M; Himmelbauer, Heinz; del Rio, José Antonio; à, Eul; Sumoy, Lauro

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

BMC Genomics, 14 (1), S. 371, 2013, ISSN: 1471-2164.

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Boitard, Simon; Kofler, Robert; ç, Pierre Fran; Robelin, David; Schlötterer, Christian; Futschik, Andreas

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

Molecular Ecology Resources, S. n/a–n/a, 2013, ISSN: 1755098X.

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2012

Nolte, V; Pandey, R V; Kofler, R; Schlotterer, C

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

Genome Research, 23 (1), S. 99–110, 2012, ISSN: 1088-9051.

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Fabian, Daniel K; Kapun, Martin; Nolte, Viola; Kofler, Robert; Schmidt, Paul S; Schlötterer, Christian; Flatt, Thomas

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

Molecular Ecology, S. n/a–n/a, 2012, ISSN: 09621083.

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Orozco-Terwengel, Pablo; Kapun, Martin; Nolte, Viola; Kofler, Robert; Flatt, Thomas; ã, Christian Schl

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

Molecular Ecology, 21 (20), S. 4931–4941, 2012, ISSN: 09621083.

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Kofler, Robert; Schlötterer, Christian

Gowinda: unbiased analysis of gene set enrichment for Genome Wide Association Studies. Artikel

Bioinformatics (Oxford, England), 2012, ISSN: 1367-4811.

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Kofler, Robert; Betancourt, Andrea J; Schlötterer, Christian

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster. Artikel

PLoS genetics, 8 (1), S. e1002487, 2012, ISSN: 1553-7404.

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2011

Kofler, Robert; Pandey, Ram Vinay; Schlötterer, Christian

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Artikel

Bioinformatics (Oxford, England), 27 (24), S. 3435–6, 2011, ISSN: 1367-4811.

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Esteve-Codina, A; Kofler, R; Himmelbauer, H; Ferretti, L; Vivancos, A P; Groenen, M A M; Folch, J M; Rodríguez, M C; Pérez-Enciso, M

Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof. Artikel

Heredity, 107 (3), S. 256–64, 2011, ISSN: 1365-2540.

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Kofler, Robert; Orozco-terWengel, Pablo; De Maio, Nicola ; Pandey, Ram Vinay; Nolte, Viola; Futschik, Andreas; Kosiol, Carolin; Schlötterer, Christian

PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals. Artikel

PloS one, 6 (1), S. e15925, 2011, ISSN: 1932-6203.

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Pandey, Ram Vinay; Kofler, Robert; Orozco-terWengel, Pablo; Nolte, Viola; Schlötterer, Christian

PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila. Artikel

BMC genetics, 12 , S. 27, 2011, ISSN: 1471-2156.

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Llorens, Franc; Hummel, Manuela; Pastor, Xavier; Ferrer, Anna; Pluvinet, Raquel; Vivancos, Ana; Castillo, Ester; Iraola, Susana; Mosquera, Ana M; González, Eva; Lozano, Juanjo; Ingham, Matthew; Dohm, Juliane C; Noguera, Marc; Kofler, Robert; del Río, Jose Antonio; ò, M; Himmelbauer, Heinz; Sumoy, Lauro

Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis. Artikel

BMC genomics, 12 , S. 326, 2011, ISSN: 1471-2164.

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Esteve-Codina, Anna; Kofler, Robert; Palmieri, Nicola; Bussotti, Giovanni; Notredame, Cedric; Pérez-Enciso, Miguel

Exploring the gonad transcriptome of two extreme male pigs with RNA-seq. Artikel

BMC genomics, 12 , S. 552, 2011, ISSN: 1471-2164.

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2009

Kofler, Robert; Teixeira Torres, Tatiana ; Lelley, Tamas; Schlötterer, Christian

PanGEA: identification of allele specific gene expression using the 454 technology. Artikel

BMC bioinformatics, 10 , S. 143, 2009, ISSN: 1471-2105.

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2008

Kofler, Robert; Bartos, Jan; Gong, Li; Stift, Gertraud; Suchánková, Pavla; Simková, Hana; Berenyi, Maria; Burg, Kornel; Dolezel, Jaroslav; Lelley, Tamas

Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1. Artikel

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 117 (6), S. 915–26, 2008, ISSN: 0040-5752.

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Gong, L; Stift, G; Kofler, R; Pachner, M; Lelley, T

Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L. Artikel

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 117 (1), S. 37–48, 2008, ISSN: 0040-5752.

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Bartos, Jan; Paux, Etienne; Kofler, Robert; Havránková, Miroslava; ý, David Kopeck; Suchánková, Pavla; Safár, Jan; Simková, Hana; Town, Christopher D; Lelley, Tamas; Feuillet, Catherine; Dolezel, Jaroslav

A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R. Artikel

BMC plant biology, 8 , S. 95, 2008, ISSN: 1471-2229.

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Kofler, Robert; Schlötterer, Christian; Luschützky, Evita; Lelley, Tamas

Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites. Artikel

BMC genomics, 9 , S. 612, 2008, ISSN: 1471-2164.

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2007

Kofler, Robert; Schlötterer, Christian; Lelley, Tamas

SciRoKo: a new tool for whole genome microsatellite search and investigation. Artikel

Bioinformatics (Oxford, England), 23 (13), S. 1683–5, 2007, ISSN: 1367-4811.

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