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 page A Novel Genome-Editing Platform for Drug-Resistant Acinetobacter baumannii Reveals an AdeR-Unrelated Tigecycline Resistance Mechanism. 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 page QTL mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici. Mol Plant Pathol. 2016 Nov 21. doi: 10.1111/mpp.12515.
• Mohd-Assaad N, McDonald BA, Croll D. external page Multilocus resistance evolution to azole fungicides in fungal plant pathogen populations. Mol Ecol. 2016 Nov 14. doi: 10.1111/mec.13916.
• Zemp N, Tavares R, Muyle A, Charlesworth D, Marais GA, Widmer A. external page Evolution of sex-biased gene expression in a dioecious plant. 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 page A High-Density Map for Navigating the Human Polycomb Complexome. 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 page Profiling of adhesive-related genes in the freshwater cnidarian Hydra magnipapillata by transcriptomics and proteomics. 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 page Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. 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 page SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms. 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 page Loss of Ezh2 synergizes with JAK2-V617F in initiating myeloproliferative neoplasms and promoting myelofibrosis. J Exp Med. 2016 Jul 25;213(8):1479-96. doi: 10.1084/jem.20151136.
• Traunmüller L, Gomez AM, Nguyen TM, Scheiffele P. external page Control of neuronal synapse specification by a highly dedicated alternative splicing program. 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 page High-Content Quantification of Single-Cell Immune Dynamics.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 page The RNA Binding Protein IMP2 Preserves Glioblastoma Stem Cells by Preventing let-7 Target Gene Silencing
  Cell Reports (2016) doi:10.1016/j.celrep.2016.04.086.
• Jeschek M, Gerngross D, Panke S. external page Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort. 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 page Digital Quantification of Proteins and mRNA in Single Mammalian Cells. 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 page Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting. Sci Adv. 2016 Mar 11;2(3):e1501371. doi: 10.1126/sciadv.1501371.

2015

• Talas F, McDonald BA. external page Genome-wide analysis of Fusarium graminearum field populations reveals hotspots of recombination. BMC Genomics. 2015 Nov 24;16:996. doi: 10.1186/s12864-015-2166-0.
• Croll D, Lendenmann MH, Stewart E, McDonald BA. external page The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen. 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 page Ectopic expression of Msx2 in mammalian myotubes recapitulates aspects of amphibian muscle dedifferentiation. 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 page Digital signaling decouples activation probability and population heterogeneity. Elife. 2015 Oct 21;4:e08931. doi: 10.7554/eLife.08931.
• Fracassetti M, Griffin PC, Willi Y. external page Validation of Pooled Whole-Genome Re-Sequencing in Arabidopsis lyrata. PLoS One. 2015 Oct 13;10(10):e0140462. doi: 10.1371/journal.pone.0140462.
  
• Zemp N, Tavares R, Widmer A. external page Fungal Infection Induces Sex-Specific Transcriptional Changes and Alters Sexual Dimorphism in the Dioecious Plant Silene latifolia. PLoS Genet. 2015 Oct 8;11(10):e1005536. doi: 10.1371/journal.pgen.1005536.
• Lendenmann MH, Croll D, McDonald BA. external page QTL mapping of fungicide sensitivity reveals novel genes and pleiotropy with melanization in the pathogen Zymoseptoria tritici. 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 page Positional RNA-Seq identifies candidate genes for phenotypic engineering of sexual traits. 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 page A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status. 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 page High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins 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 page Real-time tracking, retrieval and gene expression analysis of migrating human T cells. Lab Chip. 2015 Mar 7;15(5):1276-83. doi: 10.1039/c4lc01038h.
• Kellogg RA, Tay S. external page Noise facilitates transcriptional control under dynamic inputs. 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 page Cell type specific gene expression analysis of prostate needle biopsies resolves tumor tissue heterogeneity. 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 page An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits. 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 page HAND2 targets define a network of transcriptional regulators that compartmentalize the early limb bud mesenchyme. 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 page Quantitative trait locus mapping of melanization in the plant pathogenic fungus Zymoseptoria tritici. 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 page Targeted combinatorial alternative splicing generates brain region-specific repertoires of neurexins. 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 page Myeloproliferative neoplasms can be initiated from a single hematopoietic stem cell expressing JAK2-V617F. J Exp Med. 2014 Oct 20;211(11):2213-30. doi: 10.1084/jem.20131371.
• Lalevée S, Lapaire O, Bühler M. external page miR455 is linked to hypoxia signaling and is deregulated in preeclampsia. 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 page Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations. 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 page Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program. 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 page High-throughput microfluidic single-cell analysis pipeline for studies of signaling dynamics. 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 page Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs. 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 page Comprehensive evaluation and optimization of amplicon library preparation methods for high-throughput antibody sequencing. 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 page Engineering of a conditional allele reveals multiple roles of XRN2 in Caenorhabditis elegans development and substrate specificity in microRNA turnover. 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 page Clonal evolution and clinical correlates of somatic mutations in myeloproliferative neoplasms. 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 page Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transition. 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 page The genomic signature of parallel adaptation from shared genetic variation. Mol Ecol. 2014 Mar 18.
• Berner D, Moser D, Roesti M, Buescher H, Salzburger W. external page Genetic architecture of skeletal evolution in european lake and stream stickleback. Evolution. 2014 Feb 26.
• Diepenbruck M, Waldmeier L, Ivanek R, Berninger P, Arnold P, van Nimwegen E, Christofori G. external page Tead2 expression levels control Yap/Taz subcellular distribution, zyxin expression, and epithelial-mesenchymal transition. J Cell Sci. 2014 Feb 19.
• Sievers C, Comoglio F, Seimiya M, Merdes G, Paro R. external page A Deterministic Analysis of Genome Integrity during Neoplastic Growth in Drosophila. PLoS One. 2014 Feb 6;9(2):e87090.
• Hendriks GJ, Gaidatzis D, Aeschimann F, Großhans H. external page Extensive oscillatory gene expression during C. elegans larval development. 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 page An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants. Eur J Immunol. 2013 Dec 27.
• Feldmann A, Ivanek R, Murr R, Gaidatzis D, Burger L, Schübeler D. external page Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions. PLoS Genet. 2013 Dec;9(12):e1003994.
• Kishore S, Gruber AR, Jedlinski DJ, Syed AP, Jorjani H, Zavolan M. external page Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing. Genome Biol. 2013 Sep 9;14(5):R45.
• Keller C, Kulasegaran-Shylini R, Shimada Y, Hotz HR, Bühler M. external page Noncoding RNAs prevent spreading of a repressive histone mark. 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 page Strong genome-wide divergence between sympatric European river and brook lampreys. 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 page Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8). 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 page Sox4 is a master regulator of epithelial-mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming. Cancer Cell. 2013 Jun 10;23(6):768-83.
• Baubec T, Ivánek R, Lienert F, Schübeler D. external page Methylation-dependent and -independent genomic targeting principles of the MBD protein family. 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 page Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa. Nat Struct Mol Biol. 2013 Jul;20(7):868-75.
• Thakurela S, Garding A, Jung J, Schübeler D, Burger L, Tiwari VK. external page Gene regulation and priming by topoisomerase IIα in embryonic stem cells. Nat Commun. 2013;4:2478.
• Roesti M, Moser D, Berner D. external page Recombination in the threespine stickleback genome-patterns and consequences. 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 page PRC1 coordinates timing of sexual differentiation of female primordial germ cells. 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 page The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila. 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 page Cleavage factor Im is a key regulator of 3' UTR length. RNA Biol. 2012 Dec 1;9(12):1405-12.
  
• Zagordi O, Däumer M, Beisel C, Beerenwinkel N. external page Read length versus depth of coverage for viral quasispecies reconstruction. 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 page Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. 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 page Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels. Mol Syst Biol. 2012 Jul 17;8:593.
• Sievers C, Schlumpf T, Sawarkar R, Comoglio F, Paro R. external page Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data. Nucleic Acids Res. 2012 Jul 28.  
• Roesti M, Salzburger W, Berner D. external page Uninformative polymorphisms bias genome scans for signatures of selection. BMC Evol Biol. 2012 Jun 22;12:94.
• Martin G, Gruber AR, Keller W, Zavolan M. external page Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length. Cell Rep. 2012 Jun 28;1(6):753-63. Epub 2012 Jun 7.
• Sawarkar R, Sievers C, Paro R. external page Hsp90 globally targets paused RNA polymerase to regulate gene expression in response to environmental stimuli. Cell. 2012 May 11;149(4):807-18.
• Gerstung M, Beisel C, Rechsteiner M, Wild P, Schraml P, Moch H, Beerenwinkel N. external page Reliable detection of subclonal single-nucleotide variants in tumour cell populations. 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 page Target genes of Topoisomerase IIβ regulate neuronal survival and are defined by their chromatin state. Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):E934-43.  
• Roesti M, Hendry AP, Salzburger W, Berner D. external page Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs. Mol Ecol. 2012 Jun;21(12):2852-62.
  
• Sakoparnig T, Kockmann T, Paro R, Beisel C, Beerenwinkel N. external page Binding profiles of chromatin-modifying proteins are predictive for transcriptional activity and promoter-proximal pausing. 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 page A chromatin-modifying function of JNK during stem cell differentiation. 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 page DNA-binding factors shape the mouse methylome at distal regulatory regions. 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 page openBIS: a flexible framework for managing and analyzing complex data in biology research. BMC Bioinformatics. 2011 Dec 8;12:468. doi: 10.1186/1471-2105-12-468.
• Rammelt C, Bilen B, Zavolan M, Keller W. external page PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif. RNA. 2011 Sep;17(9):1737-46.
• Barraud P, Emmerth S, Shimada Y, Hotz HR, Allain FH, Bühler M. external page An extended dsRBD with a novel zinc-binding motif mediates nuclear retention of fission yeast Dicer. 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 page High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis Endosperm. 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 page Genomic prevalence of heterochromatic H3K9me2 and transcription do not discriminate pluripotent from terminally differentiated cells. PLoS Genet. 2011 Jun;7(6):e1002090.
• Kishore S, Jaskiewicz L, Burger L, Hausser J, Khorshid M, Zavolan M. external page A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nat Methods. 2011 May 15;8(7):559-64.
• Enderle D, Beisel C, Stadler MB, Gerstung M, Athri P, Paro R. external page Polycomb preferentially targets stalled promoters of coding and noncoding transcripts. Genome Res. 2011 Feb;21(2):216-26. doi: 10.1101/gr.114348.110.
• Berninger P, Jaskiewicz L, Khorshid M, Zavolan M. external page Conserved generation of short products at piRNA loci. 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 page Selection of Carbonic Anhydrase IX Inhibitors from One Million DNA-Encoded Compounds. 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 page Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing. 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 page High-throughput sequencing for the identification of binding molecules from DNA-encoded chemical libraries. 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 page Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa. 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 page Characterizing light-regulated retinal microRNAs reveals rapid turnover as a common property of neuronal microRNAs. Cell. 2010 May 14;141(4):618-31.
• Emmerth S, Schober H, Gaidatzis D, Roloff T, Jacobeit K, Bühler M. external page Nuclear retention of fission yeast dicer is a prerequisite for RNAi-mediated heterochromatin assembly. 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 page Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol. 2009;10(7):R79. doi: 10.1186/gb-2009-10-7-r79.