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LAMTOR/Ragulator regulates lipid metabolism in macrophages and foam cell differentiation.

Lamberti G, De Smet CH, Angelova M, Kremser L, Taub N, Herrmann C, Hess MW, Rainer J, Tancevski I, Schweigreiter R, Kofler R, Schmiedinger T, Vietor I, Trajanoski Z, Ejsing CS, Lindner HH, Huber LA, Stasyk T.

FEBS Lett. 2019 Aug 19. doi: 10.1002/1873-3468.13579. [Epub ahead of print]


Benchmarking software tools for detecting and quantifying selection in evolve and resequencing studies.

Vlachos C, Burny C, Pelizzola M, Borges R, Futschik A, Kofler R, Schlötterer C.

Genome Biol. 2019 Aug 15;20(1):169. doi: 10.1186/s13059-019-1770-8.


Optimizing the power to identify the genetic basis of complex traits with Evolve and Resequence studies.

Vlachos C, Kofler R.

Mol Biol Evol. 2019 Aug 10. pii: msz183. doi: 10.1093/molbev/msz183. [Epub ahead of print]


DeviaTE: Assembly-free analysis and visualization of mobile genetic element composition.

Weilguny L, Kofler R.

Mol Ecol Resour. 2019 Sep;19(5):1346-1354. doi: 10.1111/1755-0998.13030. Epub 2019 Jul 3.


Dynamics of Transposable Element Invasions with piRNA Clusters.

Kofler R.

Mol Biol Evol. 2019 Jul 1;36(7):1457-1472. doi: 10.1093/molbev/msz079.


Genetic redundancy fuels polygenic adaptation in Drosophila.

Barghi N, Tobler R, Nolte V, Jakšić AM, Mallard F, Otte KA, Dolezal M, Taus T, Kofler R, Schlötterer C.

PLoS Biol. 2019 Feb 4;17(2):e3000128. doi: 10.1371/journal.pbio.3000128. eCollection 2019 Feb.


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.


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.


3D-cultivation of NSCLC cell lines induce gene expression alterations of key cancer-associated pathways and mimic in-vivo conditions.

Gamerith G, Rainer J, Huber JM, Hackl H, Trajanoski Z, Koeck S, Lorenz E, Kern J, Kofler R, Kelm JM, Zwierzina H, Amann A.

Oncotarget. 2017 Nov 6;8(68):112647-112661. doi: 10.18632/oncotarget.22636. eCollection 2017 Dec 22.


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.


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.


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.


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.


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

Franssen SU, Kofler R, Schlötterer C.

Heredity (Edinb). 2017 Jan;118(1):42-51. doi: 10.1038/hdy.2016.98. Epub 2016 Nov 16.


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.


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.


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

Schlötterer C, Kofler R, Versace E, Tobler R, Franssen SU.

Heredity (Edinb). 2016 Feb;116(2):248. doi: 10.1038/hdy.2015.85. No abstract available.


Performance evaluation of the PelvoCheck CT/NG test kit for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae.

Meyer T, Klos C, Kofler R, Kilic A, Hänel K.

BMJ Open. 2016 Jan 4;6(1):e009894. doi: 10.1136/bmjopen-2015-009894.


Quantitative proteomic analysis reveals maturation as a mechanism underlying glucocorticoid resistance in B lineage ALL and re-sensitization by JNK inhibition.

Nicholson L, Evans CA, Matheson E, Minto L, Keilty C, Sanichar M, Case M, Schwab C, Williamson D, Rainer J, Harrison CJ, Kofler R, Hall AG, Redfern CP, Whetton AD, Irving JA.

Br J Haematol. 2015 Nov;171(4):595-605. doi: 10.1111/bjh.13647. Epub 2015 Aug 27.


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.


The p53 binding protein PDCD5 is not rate-limiting in DNA damage induced cell death.

Bock FJ, Tanzer MC, Haschka MD, Krumschnabel G, Sohm B, Goetsch K, Kofler R, Villunger A.

Sci Rep. 2015 Jun 11;5:11268. doi: 10.1038/srep11268.


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.


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.


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.


The role of the Janus-faced transcription factor PAX5-JAK2 in acute lymphoblastic leukemia.

Schinnerl D, Fortschegger K, Kauer M, Marchante JR, Kofler R, Den Boer ML, Strehl S.

Blood. 2015 Feb 19;125(8):1282-91. doi: 10.1182/blood-2014-04-570960. Epub 2014 Dec 16.


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

Schlötterer C, Kofler R, Versace E, Tobler R, Franssen SU.

Heredity (Edinb). 2015 May;114(5):431-40. doi: 10.1038/hdy.2014.86. Epub 2014 Oct 1. Review. Erratum in: Heredity (Edinb). 2016 Feb;116(2):248.


C10ORF10/DEPP, a transcriptional target of FOXO3, regulates ROS-sensitivity in human neuroblastoma.

Salcher S, Hagenbuchner J, Geiger K, Seiter MA, Rainer J, Kofler R, Hermann M, Kiechl-Kohlendorfer U, Ausserlechner MJ, Obexer P.

Mol Cancer. 2014 Sep 28;13:224. doi: 10.1186/1476-4598-13-224.


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.


The synthetic glucocorticoids prednisolone and dexamethasone regulate the same genes in acute lymphoblastic leukemia cells.

Bindreither D, Ecker S, Gschirr B, Kofler A, Kofler R, Rainer J.

BMC Genomics. 2014 Aug 7;15:662. doi: 10.1186/1471-2164-15-662.


Development of a multipurpose GATEWAY-based lentiviral tetracycline-regulated conditional RNAi system (GLTR).

Sigl R, Ploner C, Shivalingaiah G, Kofler R, Geley S.

PLoS One. 2014 May 19;9(5):e97764. doi: 10.1371/journal.pone.0097764. eCollection 2014.


Differential neuronal targeting of a new and two known calcium channel β4 subunit splice variants correlates with their regulation of gene expression.

Etemad S, Obermair GJ, Bindreither D, Benedetti A, Stanika R, Di Biase V, Burtscher V, Koschak A, Kofler R, Geley S, Wille A, Lusser A, Flockerzi V, Flucher BE.

J Neurosci. 2014 Jan 22;34(4):1446-61. doi: 10.1523/JNEUROSCI.3935-13.2014.


Translational profiling in childhood acute lymphoblastic leukemia: no evidence for glucocorticoid regulation of mRNA translation.

Aneichyk T, Bindreither D, Mantinger C, Grazio D, Goetsch K, Kofler R, Rainer J.

BMC Genomics. 2013 Dec 1;14:844. doi: 10.1186/1471-2164-14-844.


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.


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.


Variability in functional p53 reactivation by PRIMA-1(Met)/APR-246 in Ewing sarcoma.

Aryee DN, Niedan S, Ban J, Schwentner R, Muehlbacher K, Kauer M, Kofler R, Kovar H.

Br J Cancer. 2013 Nov 12;109(10):2696-704. doi: 10.1038/bjc.2013.635. Epub 2013 Oct 15.


Suppression of FOXO1 is responsible for a growth regulatory repressive transcriptional sub-signature of EWS-FLI1 in Ewing sarcoma.

Niedan S, Kauer M, Aryee DN, Kofler R, Schwentner R, Meier A, Pötschger U, Kontny U, Kovar H.

Oncogene. 2014 Jul 24;33(30):3927-38. doi: 10.1038/onc.2013.361. Epub 2013 Sep 2.


Chinese hamster genome sequenced from sorted chromosomes.

Brinkrolf K, Rupp O, Laux H, Kollin F, Ernst W, Linke B, Kofler R, Romand S, Hesse F, Budach WE, Galosy S, Müller D, Noll T, Wienberg J, Jostock T, Leonard M, Grillari J, Tauch A, Goesmann A, Helk B, Mott JE, Pühler A, Borth N.

Nat Biotechnol. 2013 Aug;31(8):694-5. doi: 10.1038/nbt.2645. No abstract available.


The p27-Skp2 axis mediates glucocorticoid-induced cell cycle arrest in T-lymphoma cells.

Kullmann MK, Grubbauer C, Goetsch K, Jäkel H, Podmirseg SR, Trockenbacher A, Ploner C, Cato AC, Weiss C, Kofler R, Hengst L.

Cell Cycle. 2013 Aug 15;12(16):2625-35. doi: 10.4161/cc.25622. Epub 2013 Jul 9.


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.


CLP1 links tRNA metabolism to progressive motor-neuron loss.

Hanada T, Weitzer S, Mair B, Bernreuther C, Wainger BJ, Ichida J, Hanada R, Orthofer M, Cronin SJ, Komnenovic V, Minis A, Sato F, Mimata H, Yoshimura A, Tamir I, Rainer J, Kofler R, Yaron A, Eggan KC, Woolf CJ, Glatzel M, Herbst R, Martinez J, Penninger JM.

Nature. 2013 Mar 28;495(7442):474-80. doi: 10.1038/nature11923. Epub 2013 Mar 10.


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.


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.


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.


"Bam," a novel glucocorticoid-induced BH3-only transcript from the BCL2L11/Bim locus, does not appear to be translated.

Mansha M, Hussain A, Kofler A, Grubbauer C, Goetsch K, Ploner C, Kofler R.

Leuk Lymphoma. 2013 Feb;54(2):353-8. doi: 10.3109/10428194.2012.708928. Epub 2012 Sep 6.


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.


Promyelocytic leukemia zinc finger protein (PLZF) enhances glucocorticoid-induced apoptosis in leukemic cell line NALM6.

Wasim M, Mansha M, Kofler A, Awan AR, Babar ME, Kofler R.

Pak J Pharm Sci. 2012 Jul;25(3):617-21.


Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies.

Kofler R, Schlötterer C.

Bioinformatics. 2012 Aug 1;28(15):2084-5. doi: 10.1093/bioinformatics/bts315. Epub 2012 May 26.


Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster.

Kofler R, Betancourt AJ, Schlötterer C.

PLoS Genet. 2012 Jan;8(1):e1002487. doi: 10.1371/journal.pgen.1002487. Epub 2012 Jan 26.


Research resource: transcriptional response to glucocorticoids in childhood acute lymphoblastic leukemia.

Rainer J, Lelong J, Bindreither D, Mantinger C, Ploner C, Geley S, Kofler R.

Mol Endocrinol. 2012 Jan;26(1):178-93. doi: 10.1210/me.2011-1213. Epub 2011 Nov 10.


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

Esteve-Codina A, Kofler R, Palmieri N, Bussotti G, Notredame C, Pérez-Enciso M.

BMC Genomics. 2011 Nov 8;12:552. doi: 10.1186/1471-2164-12-552.

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