Publications

Publications with contributions of the Genomics Facility Basel:

2016

• Trebosc V, Gartenmann S, Royet K, Manfredi P, Tötzl M, Schellhorn B, Pieren M, Tigges M, Lociuro S, Sennhenn PC, Gitzinger M, Bumann D, Kemmer C. external pageA Novel Genome-Editing Platform for Drug-Resistant Acinetobacter baumannii Reveals an AdeR-Unrelated Tigecycline Resistance Mechanismcall_made. Antimicrob Agents Chemother. 2016 Nov 21;60(12):7263-7271.
• Stewart EL, Croll D, Lendenmann MH, Sanchez-Vallet A, Hartmann FE, Palma-Guerrero J, Ma X, McDonald BA. external pageQTL mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria triticicall_made. Mol Plant Pathol. 2016 Nov 21. doi: 10.1111/mpp.12515.
• Mohd-Assaad N, McDonald BA, Croll D. external pageMultilocus resistance evolution to azole fungicides in fungal plant pathogen populationscall_made. Mol Ecol. 2016 Nov 14. doi: 10.1111/mec.13916.
• Zemp N, Tavares R, Muyle A, Charlesworth D, Marais GA, Widmer A. external pageEvolution of sex-biased gene expression in a dioecious plantcall_made. Nat Plants. 2016 Nov 3;2(11):16168. doi: 10.1038/nplants.2016.168.
• Hauri S, Comoglio F, Seimiya M, Gerstung M, Glatter T, Hansen K, Aebersold R, Paro R, Gstaiger M, Beisel C. external pageA High-Density Map for Navigating the Human Polycomb Complexomecall_made. Cell Rep. 2016 Oct 4;17(2):583-595. doi: 10.1016/j.celrep.2016.08.096.
• Rodrigues M, Ostermann T, Kremeser L, Lindner H, Beisel C, Berezikov E, Hobmayer B, Ladurner P. external pageProfiling of adhesive-related genes in the freshwater cnidarian Hydra magnipapillata by transcriptomics and proteomicscall_made. Biofouling. 2016 Oct;32(9):1115-1129.
• Novikova PY, Hohmann N, Nizhynska V, Tsuchimatsu T, Ali J, Muir G, Guggisberg A, Paape T, Schmid K, Fedorenko OM, Holm S, Säll T, Schlötterer C, Marhold K, Widmer A, Sese J, Shimizu KK, Weigel D, Krämer U, Koch MA, Nordborg M. external pageSequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphismcall_made. Nat Genet. 2016 Sep;48(9):1077-82. doi: 10.1038/ng.3617.
  
• Muyle A, Käfer J, Zemp N, Mousset S, Picard F, Marais GA. external pageSEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organismscall_made. Genome Biol Evol. 2016 Aug 29;8(8):2530-43. doi: 10.1093/gbe/evw172.
• Shimizu T, Kubovcakova L, Nienhold R, Zmajkovic J, Meyer SC, Hao-Shen H, Geier F, Dirnhofer S, Guglielmelli P, Vannucchi AM, Feenstra JD, Kralovics R, Orkin SH6, Skoda RC. external pageLoss of Ezh2 synergizes with JAK2-V617F in initiating myeloproliferative neoplasms and promoting myelofibrosiscall_made. J Exp Med. 2016 Jul 25;213(8):1479-96. doi: 10.1084/jem.20151136.
• Traunmüller L, Gomez AM, Nguyen TM, Scheiffele P. external pageControl of neuronal synapse specification by a highly dedicated alternative splicing programcall_made. Science. 2016 May 20;352(6288):982-6. doi: 10.1126/science.aaf2397.
• Junkin M, Kaestli AJ, Cheng Z, Jordi C, Albayrak C, Hoffmann A, Tay S. external pageHigh-Content Quantification of Single-Cell Immune Dynamicscall_made.Cell Rep. 2016 Apr 12;15(2):411-22. doi: 10.1016/j.celrep.2016.03.033.
• Degrauwe N, Schlumpf TB, Janiszewska M, Martin P, Cauderay A, Provero P, Riggi N, Suvà Mario-L, Paro R and Stamenkovic I.
  external pageThe RNA Binding Protein IMP2 Preserves Glioblastoma Stem Cells by Preventing let-7 Target Gene Silencingcall_made
  Cell Reports (2016) doi:10.1016/j.celrep.2016.04.086.
• Jeschek M, Gerngross D, Panke S. external pageRationally reduced libraries for combinatorial pathway optimization minimizing experimental effortcall_made. Nat Commun. 2016 Mar 31;7:11163. doi: 10.1038/ncomms11163.
• Albayrak C, Jordi CA, Zechner C, Lin J, Bichsel CA, Khammash M, Tay S. external pageDigital Quantification of Proteins and mRNA in Single Mammalian Cellscall_made. Mol Cell. 2016 Mar 17;61(6):914-24. doi: 10.1016/j.molcel.2016.02.030.
• Khan TA, Friedensohn S, Gorter de Vries AR, Straszewski J, Ruscheweyh HJ, Reddy ST. external pageAccurate and predictive antibody repertoire profiling by molecular amplification fingerprintingcall_made. Sci Adv. 2016 Mar 11;2(3):e1501371. doi: 10.1126/sciadv.1501371.

2015

• Talas F, McDonald BA. external pageGenome-wide analysis of Fusarium graminearum field populations reveals hotspots of recombinationcall_made. BMC Genomics. 2015 Nov 24;16:996. doi: 10.1186/s12864-015-2166-0.
• Croll D, Lendenmann MH, Stewart E, McDonald BA. external pageThe Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogencall_made. Genetics. 2015 Nov;201(3):1213-28. doi: 10.1534/genetics.115.180968.
• Yilmaz A, Engeler R, Constantinescu S, Kokkaliaris KD, Dimitrakopoulos C, Schroeder T, Beerenwinkel N and Paro R. external pageEctopic expression of Msx2 in mammalian myotubes recapitulates aspects of amphibian muscle dedifferentiation.call_made Stem Cell Res. 2015 Nov;15(3):542-53. doi: 10.1016/j.scr.2015.09.012.
  
• Kellogg RA, Tian C, Lipniacki T, Quake SR, Tay S. external pageDigital signaling decouples activation probability and population heterogeneitycall_made. Elife. 2015 Oct 21;4:e08931. doi: 10.7554/eLife.08931.
• Fracassetti M, Griffin PC, Willi Y. external pageValidation of Pooled Whole-Genome Re-Sequencing in Arabidopsis lyratacall_made. PLoS One. 2015 Oct 13;10(10):e0140462. doi: 10.1371/journal.pone.0140462.
  
• Zemp N, Tavares R, Widmer A. external pageFungal Infection Induces Sex-Specific Transcriptional Changes and Alters Sexual Dimorphism in the Dioecious Plant Silene latifoliacall_made. PLoS Genet. 2015 Oct 8;11(10):e1005536. doi: 10.1371/journal.pgen.1005536.
• Lendenmann MH, Croll D, McDonald BA. external pageQTL mapping of fungicide sensitivity reveals novel genes and pleiotropy with melanization in the pathogen Zymoseptoria triticicall_made. Fungal Genet Biol. 2015 Jul;80:53-67. doi: 10.1016/j.fgb.2015.05.001.
• Arbore R, Sekii K, Beisel C, Ladurner P, Berezikov E, Schärer L. external pagePositional RNA-Seq identifies candidate genes for phenotypic engineering of sexual traitscall_made. Front Zool. 2015 Jul 3;12:14. doi: 10.1186/s12983-015-0106-0.
• Greiff V, Bhat P, Cook SC, Menzel U, Kang W, Reddy ST. external pageA bioinformatic framework for immune repertoire diversity profiling enables detection of immunological statuscall_made. Genome Med. 2015 May 28;7(1):49. doi: 10.1186/s13073-015-0169-8.
  
• Comoglio F, Schlumpf T, Schmid V, Rohs R, Beisel C and Paro R. external pageHigh-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Originscall_made Cell Reports  (2015) April 23, DOI: http://dx.doi.org/10.1016/j.celrep.2015.03.070.
• Mehling M, Frank T, Albayrak C, Tay S. external pageReal-time tracking, retrieval and gene expression analysis of migrating human T cellscall_made. Lab Chip. 2015 Mar 7;15(5):1276-83. doi: 10.1039/c4lc01038h.
• Kellogg RA, Tay S. external pageNoise facilitates transcriptional control under dynamic inputscall_made. Cell. 2015 Jan 29;160(3):381-92. doi: 10.1016/j.cell.2015.01.013.
• Krönig M, Walter M, Drendel V, Werner M, Jilg CA, Richter AS, Backofen R, McGarry D, Follo M, Schultze-Seemann W, Schüle R. external pageCell type specific gene expression analysis of prostate needle biopsies resolves tumor tissue heterogeneitycall_made. Oncotarget. 2015 Jan 20;6(2):1302-14.
  
  
  

2014

• Routtu J, Hall MD, Albere B, Beisel C, Bergeron RD, Chaturvedi A, Choi JH, Colbourne J, De Meester L, Stephens MT, Stelzer CP, Solorzano E, Thomas WK, Pfrender ME, Ebert D. external pageAn SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traitscall_made. BMC Genomics. 2014 Nov 27;15:1033. doi: 10.1186/1471-2164-15-1033.
• Osterwalder M, Speziale D, Shoukry M, Mohan R, Ivanek R, Kohler M, Beisel C, Wen X, Scales SJ, Christoffels VM, Visel A, Lopez-Rios J, Zeller R. external pageHAND2 targets define a network of transcriptional regulators that compartmentalize the early limb bud mesenchymecall_made. Dev Cell. 2014 Nov 10;31(3):345-57. doi: 10.1016/j.devcel.2014.09.018.
• Lendenmann MH, Croll D, Stewart EL, McDonald BA. external pageQuantitative trait locus mapping of melanization in the plant pathogenic fungus Zymoseptoria triticicall_made. G3 (Bethesda). 2014 Oct 29;4(12):2519-33. doi: 10.1534/g3.114.015289.
  
• Schreiner D, Nguyen TM, Russo G, Heber S, Patrignani A, Ahrné E, Scheiffele P. external pageTargeted combinatorial alternative splicing generates brain region-specific repertoires of neurexinscall_made. Neuron. 2014 Oct 22;84(2):386-98. doi: 10.1016/j.neuron.2014.09.011.
• Lundberg P, Takizawa H, Kubovcakova L, Guo G, Hao-Shen H, Dirnhofer S, Orkin SH, Manz MG, Skoda RC. external pageMyeloproliferative neoplasms can be initiated from a single hematopoietic stem cell expressing JAK2-V617Fcall_made. J Exp Med. 2014 Oct 20;211(11):2213-30. doi: 10.1084/jem.20131371.
• Lalevée S, Lapaire O, Bühler M. external pagemiR455 is linked to hypoxia signaling and is deregulated in preeclampsiacall_made. Cell Death Dis. 2014 Sep 4;5:e1408. doi: 10.1038/cddis.2014.368.
• Giallonardo FD, Töpfer A, Rey M, Prabhakaran S, Duport Y, Leemann C, Schmutz S, Campbell NK1, Joos B, Lecca MR, Patrignani A, Däumer M, Beisel C, Rusert P, Trkola A, Günthard HF, Roth V, Beerenwinkel N, Metzner KJ. external pageFull-length haplotype reconstruction to infer the structure of heterogeneous virus populationscall_made. Nucleic Acids Res. 2014 Aug;42(14):e115. doi: 10.1093/nar/gku537.
• Baresic M, Salatino S, Kupr B, van Nimwegen E, Handschin C. external pageTranscriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene programcall_made. Mol Cell Biol. 2014 Aug;34(16):2996-3012. doi: 10.1128/MCB.01710-13.
  
• Kellogg RA, Gómez-Sjöberg R, Leyrat AA, Tay S. external pageHigh-throughput microfluidic single-cell analysis pipeline for studies of signaling dynamicscall_made. Nat Protoc. 2014 Jul;9(7):1713-26. doi: 10.1038/nprot.2014.120.
• Lopez-Rios J, Duchesne A, Speziale D, Andrey G, Peterson KA, Germann P, Unal E, Liu J, Floriot S, Barbey S, Gallard Y, Müller-Gerbl M, Courtney AD, Klopp C, Rodriguez S, Ivanek R14, Beisel C, Wicking C, Iber D, Robert B, McMahon AP, Duboule D, Zeller R. external pageAttenuated sensing of SHH by Ptch1 underlies evolution of bovine limbscall_made. Nature. 2014 Jul 3;511(7507):46-51. doi: 10.1038/nature13289.
• Menzel U, Greiff V, Khan TA, Haessler U, Hellmann I, Friedensohn S, Cook SC, Pogson M, Reddy ST. external pageComprehensive evaluation and optimization of amplicon library preparation methods for high-throughput antibody sequencingcall_made. PLoS One. 2014 May 8;9(5):e96727. doi: 10.1371/journal.pone.0096727.
  
• Miki TS, Rüegger S, Gaidatzis D, Stadler MB, Großhans H.
  external pageEngineering of a conditional allele reveals multiple roles of XRN2 in Caenorhabditis elegans development and substrate specificity in microRNA turnover.call_made Nucleic Acids Res. 2014 Apr;42(6):4056-67.
• Lundberg P, Karow A, Nienhold R, Looser R, Hao-Shen H, Nissen I, Girsberger S, Lehmann T, Passweg J, Stern M, Beisel C, Kralovics R, Skoda RC. external pageClonal evolution and clinical correlates of somatic mutations in myeloproliferative neoplasmscall_made. Blood. 2014 Apr 3;123(14):2220-8. doi: 10.1182/blood-2013-11-537167.
• Diepenbruck M, Waldmeier L, Ivanek R, Berninger P, Arnold P, van Nimwegen E, Christofori G. external pageTead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transitioncall_made. J Cell Sci. 2014 Apr 1;127(Pt 7):1523-36. doi: 10.1242/jcs.139865.
• Roesti M, Gavrilets S, Hendry AP, Salzburger W, Berner D. external pageThe genomic signature of parallel adaptation from shared genetic variation.call_made Mol Ecol. 2014 Mar 18.
• Berner D, Moser D, Roesti M, Buescher H, Salzburger W. external pageGenetic architecture of skeletal evolution in european lake and stream stickleback.call_made Evolution. 2014 Feb 26.
• Diepenbruck M, Waldmeier L, Ivanek R, Berninger P, Arnold P, van Nimwegen E, Christofori G. external pageTead2 expression levels control Yap/Taz subcellular distribution, zyxin expression, and epithelial-mesenchymal transition.call_made J Cell Sci. 2014 Feb 19.
• Sievers C, Comoglio F, Seimiya M, Merdes G, Paro R. external pageA Deterministic Analysis of Genome Integrity during Neoplastic Growth in Drosophila.call_made PLoS One. 2014 Feb 6;9(2):e87090.
• Hendriks GJ, Gaidatzis D, Aeschimann F, Großhans H. external pageExtensive oscillatory gene expression during C. elegans larval development.call_made Mol Cell. 2014 Feb 6;53(3):380-92.
  

2013

• Vigano MA1, Ivanek R, Balwierz P, Berninger P, van Nimwegen E, Karjalainen K, Rolink A. external pageAn epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendantscall_made. Eur J Immunol. 2013 Dec 27.
• Feldmann A, Ivanek R, Murr R, Gaidatzis D, Burger L, Schübeler D. external pageTranscription factor occupancy can mediate active turnover of DNA methylation at regulatory regions.call_made PLoS Genet. 2013 Dec;9(12):e1003994.
• Kishore S, Gruber AR, Jedlinski DJ, Syed AP, Jorjani H, Zavolan M. external pageInsights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing.call_made Genome Biol. 2013 Sep 9;14(5):R45.
• Keller C, Kulasegaran-Shylini R, Shimada Y, Hotz HR, Bühler M. external pageNoncoding RNAs prevent spreading of a repressive histone markcall_made. Nat Struct Mol Biol. 2013 Aug;20(8):994-1000. doi: 10.1038/nsmb.2619.
  
• Mateus CS, Stange M, Berner D, Roesti M, Quintella BR, Alves MJ, Almeida PR, Salzburger W. external pageStrong genome-wide divergence between sympatric European river and brook lampreys.call_made Curr Biol. 2013 Aug 5;23(15):R649-R650.
• Tiwari N, Meyer-Schaller N, Arnold P, Antoniadis H, Pachkov M, van Nimwegen E, Christofori G. external pageKlf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8)call_made. PLoS One. 2013;8(2):e57329. doi: 10.1371/journal.pone.0057329.
• Tiwari N, Tiwari VK, Waldmeier L, Balwierz PJ, Arnold P, Pachkov M, Meyer-Schaller N, Schübeler D, van Nimwegen E, Christofori G. external pageSox4 is a master regulator of epithelial-mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming.call_made Cancer Cell. 2013 Jun 10;23(6):768-83.
• Baubec T, Ivánek R, Lienert F, Schübeler D. external pageMethylation-dependent and -independent genomic targeting principles of the MBD protein family.call_made Cell. 2013 Apr 11;153(2):480-92.
• Erkek S, Hisano M, Liang CY, Gill M, Murr R, Dieker J, Schübeler D, van der Vlag J, Stadler MB, Peters AH. external pageMolecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa.call_made Nat Struct Mol Biol. 2013 Jul;20(7):868-75.
• Thakurela S, Garding A, Jung J, Schübeler D, Burger L, Tiwari VK. external pageGene regulation and priming by topoisomerase IIα in embryonic stem cells.call_made Nat Commun. 2013;4:2478.
• Roesti M, Moser D, Berner D. external pageRecombination in the threespine stickleback genome-patterns and consequences.call_made Mol Ecol. 2013 Apr 22.
• Yokobayashi S, Liang CY, Kohler H, Nestorov P, Liu Z, Vidal M, van Lohuizen M, Roloff TC, Peters AH. external pagePRC1 coordinates timing of sexual differentiation of female primordial germ cells.call_made Nature. 2013 Mar 14;495(7440):236-40.
• Kockmann T, Gerstung M, Schlumpf T, Xhinzhou Z, Hess D, Beerenwinkel N, Beisel C, Paro R. external pageThe BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophilacall_made. Genome Biol. 2013 Feb 25;14(2):R18. doi: 10.1186/gb-2013-14-2-r18.

2012

• Gruber AR, Martin G, Keller W, Zavolan M. external pageCleavage factor Im is a key regulator of 3' UTR length.call_made RNA Biol. 2012 Dec 1;9(12):1405-12.
  
• Zagordi O, Däumer M, Beisel C, Beerenwinkel N. external pageRead length versus depth of coverage for viral quasispecies reconstructioncall_made. PLoS One. 2012;7(10):e47046. doi: 10.1371/journal.pone.0047046.
• Arnold P, Schöler A, Pachkov M, Balwierz P, Jørgensen H, Stadler MB, van Nimwegen E, Schübeler D. external pageModeling of epigenome dynamics identifies transcription factors that mediate Polycomb targetingcall_made. Genome Res. 2012 Sep 10.  
• Tippmann SC, Ivanek R, Gaidatzis D, Schöler A, Hoerner L, van Nimwegen E, Stadler PF, Stadler MB, Schübeler D. external pageChromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levelscall_made. Mol Syst Biol. 2012 Jul 17;8:593.
• Sievers C, Schlumpf T, Sawarkar R, Comoglio F, Paro R. external pageMixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP datacall_made. Nucleic Acids Res. 2012 Jul 28.  
• Roesti M, Salzburger W, Berner D. external pageUninformative polymorphisms bias genome scans for signatures of selectioncall_made. BMC Evol Biol. 2012 Jun 22;12:94.
• Martin G, Gruber AR, Keller W, Zavolan M. external pageGenome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR lengthcall_made. Cell Rep. 2012 Jun 28;1(6):753-63. Epub 2012 Jun 7.
• Sawarkar R, Sievers C, Paro R. external pageHsp90 globally targets paused RNA polymerase to regulate gene expression in response to environmental stimulicall_made. Cell. 2012 May 11;149(4):807-18.
• Gerstung M, Beisel C, Rechsteiner M, Wild P, Schraml P, Moch H, Beerenwinkel N. external pageReliable detection of subclonal single-nucleotide variants in tumour cell populationscall_made. Nat Commun. 2012 May 1;3:811. doi: 10.1038/ncomms1814.
• Tiwari VK, Burger L, Nikoletopoulou V, Deogracias R, Thakurela S, Wirbelauer C, Kaut J, Terranova R, Hoerner L, Mielke C, Boege F, Murr R, Peters AH, Barde YA, Schübeler D. external pageTarget genes of Topoisomerase IIβ regulate neuronal survival and are defined by their chromatin statecall_made. Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):E934-43.  
• Roesti M, Hendry AP, Salzburger W, Berner D. external pageGenome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairscall_made. Mol Ecol. 2012 Jun;21(12):2852-62.
  
• Sakoparnig T, Kockmann T, Paro R, Beisel C, Beerenwinkel N. external pageBinding profiles of chromatin-modifying proteins are predictive for transcriptional activity and promoter-proximal pausingcall_made. J Comput Biol. 2012 Feb;19(2):126-38. doi: 10.1089/cmb.2011.0258.
  

2011

• Tiwari VK, Stadler MB, Wirbelauer C, Paro R, Schübeler D, Beisel C. external pageA chromatin-modifying function of JNK during stem cell differentiationcall_made. Nat Genet. 2011 Dec 18;44(1):94-100. doi: 10.1038/ng.1036.
• Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, van Nimwegen E, Wirbelauer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schübeler D. external pageDNA-binding factors shape the mouse methylome at distal regulatory regionscall_made. Nature. 2011 Dec 14;480(7378):490-5.
• Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, Beisel C, Malmström L, Aebersold R, Rinn B. external pageopenBIS: a flexible framework for managing and analyzing complex data in biology researchcall_made. BMC Bioinformatics. 2011 Dec 8;12:468. doi: 10.1186/1471-2105-12-468.
• Rammelt C, Bilen B, Zavolan M, Keller W. external pagePAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif. RNAcall_made. 2011 Sep;17(9):1737-46.
• Barraud P, Emmerth S, Shimada Y, Hotz HR, Allain FH, Bühler M. external pageAn extended dsRBD with a novel zinc-binding motif mediates nuclear retention of fission yeast Dicercall_made. EMBO J. 2011 Aug 16;30(20):4223-35. doi: 10.1038/emboj.2011.300.
  
• Wolff P, Weinhofer I, Seguin J, Roszak P, Beisel C, Donoghue MT, Spillane C, Nordborg M, Rehmsmeier M, Köhler C. external pageHigh-resolution analysis of parent-of-origin allelic expression in the Arabidopsis Endospermcall_made. PLoS Genet. 2011 Jun;7(6):e1002126. doi: 10.1371/journal.pgen.1002126.
• Lienert F, Mohn F, Tiwari VK, Baubec T, Roloff TC, Gaidatzis D, Stadler MB, Schübeler D. external pageGenomic prevalence of heterochromatic H3K9me2 and transcription do not discriminate pluripotent from terminally differentiated cellscall_made. PLoS Genet. 2011 Jun;7(6):e1002090.
• Kishore S, Jaskiewicz L, Burger L, Hausser J, Khorshid M, Zavolan M. external pageA quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteinscall_made. Nat Methods. 2011 May 15;8(7):559-64.
• Enderle D, Beisel C, Stadler MB, Gerstung M, Athri P, Paro R. external pagePolycomb preferentially targets stalled promoters of coding and noncoding transcriptscall_made. Genome Res. 2011 Feb;21(2):216-26. doi: 10.1101/gr.114348.110.
• Berninger P, Jaskiewicz L, Khorshid M, Zavolan M. external pageConserved generation of short products at piRNA locicall_made. BMC Genomics. 2011 Jan 19;12:46.
• Buller F, Steiner M, Frey K, Mircsof D, Scheuermann J, Kalisch M, Buhlmann P, Supuran CT, Neri D. external pageSelection of Carbonic Anhydrase IX Inhibitors from One Million DNA-Encoded Compoundscall_made. ACS Chem Biol. 2011 Apr 15;6(4):336-44.
  

2010

• Bell O, Schwaiger M, Oakeley EJ, Lienert F, Beisel C, Stadler MB, Schübeler D. external pageAccessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing.call_made Nat Struct Mol Biol. 2010 Jul;17(7):894-900. doi: 10.1038/nsmb.1825.
• Buller F, Steiner M, Scheuermann J, Mannocci L, Nissen I, Kohler M, Beisel C, Neri D. external pageHigh-throughput sequencing for the identification of binding molecules from DNA-encoded chemical librariescall_made. Bioorg Med Chem Lett. 2010 Jul 15;20(14):4188-92. doi: 10.1016/j.bmcl.2010.05.053.
• Brykczynska U, Hisano M, Erkek S, Ramos L, Oakeley EJ, Roloff TC, Beisel C, Schübeler D, Stadler MB, Peters AH. external pageRepressive and active histone methylation mark distinct promoters in human and mouse spermatozoacall_made. Nat Struct Mol Biol. 2010 Jun;17(6):679-87. doi: 10.1038/nsmb.1821.
• Krol J, Busskamp V, Markiewicz I, Stadler MB, Ribi S, Richter J, Duebel J, Bicker S, Fehling HJ, Schübeler D, Oertner TG, Schratt G, Bibel M, Roska B, Filipowicz W. external pageCharacterizing light-regulated retinal microRNAs reveals rapid turnover as a common property of neuronal microRNAscall_made. Cell. 2010 May 14;141(4):618-31.
• Emmerth S, Schober H, Gaidatzis D, Roloff T, Jacobeit K, Bühler M. external pageNuclear retention of fission yeast dicer is a prerequisite for RNAi-mediated heterochromatin assemblycall_made. Dev Cell. 2010 Jan 19;18(1):102-13.
  

2009

• Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E. external pageMethods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE datacall_made. Genome Biol. 2009;10(7):R79. doi: 10.1186/gb-2009-10-7-r79.