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1. Durai DA, Schulz MH: Improving in-silico Normalization using Read Weights. Scientific Reports 2019, 9.
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@article{Durai2019, TITLE = {Improving in-silico Normalization using Read Weights}, AUTHOR = {Durai, Dilip Ariyur and Schulz, Marcel Holger}, LANGUAGE = {eng}, ISSN = {2045-2322}, DOI = {10.1038/s41598-019-41502-9}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London, UK}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Scientific Reports}, VOLUME = {9}, EID = {5133}, }
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%0 Journal Article %A Durai, Dilip Ariyur %A Schulz, Marcel Holger %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Improving in-silico Normalization using Read Weights : %G eng %U http://hdl.handle.net/21.11116/0000-0003-5F5F-A %R 10.1038/s41598-019-41502-9 %7 2019 %D 2019 %J Scientific Reports %O Sci. Rep. %V 9 %Z sequence number: 5133 %I Nature Publishing Group %C London, UK %@ false %U https://doi.org/10.1038/s41598-019-41502-9
2. Gérard D, Schmidt F, Ginolhac A, Schmitz M, Halder R, Ebert P, Schulz MH, Sauter T, Sinkkonen L: Temporal Enhancer Profiling of Parallel Lineages Identifies AHR and GLIS1 as Regulators of Mesenchymal Multipotency. Nucleic Acids Research 2019, 47.
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@article{Gerard2019, TITLE = {Temporal enhancer profiling of parallel lineages identifies {AHR} and {GLIS1} as regulators of mesenchymal multipotency}, AUTHOR = {G{\'e}rard, Deborah and Schmidt, Florian and Ginolhac, Aur{\'e}lien and Schmitz, Martine and Halder, Rashi and Ebert, Peter and Schulz, Marcel Holger and Sauter, Thomas and Sinkkonen, Lasse}, LANGUAGE = {eng}, ISSN = {0305-1048}, DOI = {10.1093/nar/gky1240}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Nucleic Acids Research}, VOLUME = {47}, NUMBER = {3}, PAGES = {1141--1163}, }
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%0 Journal Article %A Gérard, Deborah %A Schmidt, Florian %A Ginolhac, Aurélien %A Schmitz, Martine %A Halder, Rashi %A Ebert, Peter %A Schulz, Marcel Holger %A Sauter, Thomas %A Sinkkonen, Lasse %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Temporal Enhancer Profiling of Parallel Lineages Identifies AHR and GLIS1 as Regulators of Mesenchymal Multipotency : %G eng %U http://hdl.handle.net/21.11116/0000-0003-1AFD-4 %R 10.1093/nar/gky1240 %7 2018 %D 2019 %J Nucleic Acids Research %O Nucleic Acids Res %V 47 %N 3 %& 1141 %P 1141 - 1163 %I Oxford University Press %C Oxford %@ false
3. Kosack L, Wingelhofer B, Popa A, Orlova A, Agerer B, Vilagos B, Majek P, Parapatics K, Lercher A, Ringler A, Klughammer J, Smyth M, Khamina K, Baazim H, de Araujo ED, Rosa DA, Park J, Tin G, Ahmar S, Gunning PT, Bock C, Siddle HV, Woods GM, Kubicek S, Murchison EP, Bennett KL, Moriggl R, Bergthaler A: The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease. Cancer Cell 2019, 35.
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@article{Kosack2019, TITLE = {The {ERBB}-{STAT3} Axis Drives {T}asmanian Devil Facial Tumor Disease}, AUTHOR = {Kosack, Lindsay and Wingelhofer, Bettina and Popa, Alexandra and Orlova, Anna and Agerer, Benedikt and Vilagos, Bojan and Majek, Peter and Parapatics, Katja and Lercher, Alexander and Ringler, Anna and Klughammer, Johanna and Smyth, Mark and Khamina, Kseniya and Baazim, Hatoon and de Araujo, Elvin D. and Rosa, David A. and Park, Jisung and Tin, Gary and Ahmar, Siawash and Gunning, Patrick T. and Bock, Christoph and Siddle, Hannah V. and Woods, Gregory M. and Kubicek, Stefan and Murchison, Elizabeth P. and Bennett, Keiryn L. and Moriggl, Richard and Bergthaler, Andreas}, LANGUAGE = {eng}, ISSN = {1535-6108}, DOI = {10.1016/j.ccell.2018.11.018}, PUBLISHER = {Cell Press}, ADDRESS = {Cambridge, Mass.}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Cancer Cell}, VOLUME = {35}, NUMBER = {1}, PAGES = {125--139}, EID = {e9}, }
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%0 Journal Article %A Kosack, Lindsay %A Wingelhofer, Bettina %A Popa, Alexandra %A Orlova, Anna %A Agerer, Benedikt %A Vilagos, Bojan %A Majek, Peter %A Parapatics, Katja %A Lercher, Alexander %A Ringler, Anna %A Klughammer, Johanna %A Smyth, Mark %A Khamina, Kseniya %A Baazim, Hatoon %A de Araujo, Elvin D. %A Rosa, David A. %A Park, Jisung %A Tin, Gary %A Ahmar, Siawash %A Gunning, Patrick T. %A Bock, Christoph %A Siddle, Hannah V. %A Woods, Gregory M. %A Kubicek, Stefan %A Murchison, Elizabeth P. %A Bennett, Keiryn L. %A Moriggl, Richard %A Bergthaler, Andreas %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease : %G eng %U http://hdl.handle.net/21.11116/0000-0002-F715-0 %R 10.1016/j.ccell.2018.11.018 %7 2019 %D 2019 %J Cancer Cell %O Cancer Cell %V 35 %N 1 %& 125 %P 125 - 139 %Z sequence number: e9 %I Cell Press %C Cambridge, Mass. %@ false
4. Li Z, Schulz MH, Look T, Begemann M, Zenke M, Costa IG: Identification of Transcription Factor Binding Sites using ATAC-seq. Genome Research 2019, 20.
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@article{Li2019, TITLE = {Identification of transcription factor binding sites using {ATAC}-seq}, AUTHOR = {Li, Zhijian and Schulz, Marcel Holger and Look, Thomas and Begemann, Matthias and Zenke, Martin and Costa, Ivan G.}, LANGUAGE = {eng}, ISSN = {1088-9051}, DOI = {10.1186/s13059-019-1642-2}, PUBLISHER = {Cold Spring Harbor Laboratory Press}, ADDRESS = {Cold Spring Harbor, N.Y.}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Genome Research}, VOLUME = {20}, EID = {45}, }
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%0 Journal Article %A Li, Zhijian %A Schulz, Marcel Holger %A Look, Thomas %A Begemann, Matthias %A Zenke, Martin %A Costa, Ivan G. %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T Identification of Transcription Factor Binding Sites using ATAC-seq : %G eng %U http://hdl.handle.net/21.11116/0000-0003-2AF1-E %R 10.1186/s13059-019-1642-2 %7 2019 %D 2019 %J Genome Research %V 20 %Z sequence number: 45 %I Cold Spring Harbor Laboratory Press %C Cold Spring Harbor, N.Y. %@ false
5. Müller F, Scherer M, Assenov Y, Lutsik P, Walter J, Lengauer T, Bock C: RnBeads 2.0: Comprehensive Analysis of DNA Methylation Data. Genome Biology 2019, 20.
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@article{Mueller_GenomeBiology2019, TITLE = {{RnBeads} 2.0: {C}omprehensive analysis of {DNA} methylation data}, AUTHOR = {M{\"u}ller, Fabian and Scherer, Michael and Assenov, Yassen and Lutsik, Pavlo and Walter, J{\"o}rn and Lengauer, Thomas and Bock, Christoph}, LANGUAGE = {eng}, ISSN = {1465-6906}, DOI = {10.1186/s13059-019-1664-9}, PUBLISHER = {BioMed Central Ltd.}, ADDRESS = {London}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Genome Biology}, VOLUME = {20}, EID = {55}, }
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%0 Journal Article %A Müller, Fabian %A Scherer, Michael %A Assenov, Yassen %A Lutsik, Pavlo %A Walter, Jörn %A Lengauer, Thomas %A Bock, Christoph %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T RnBeads 2.0: Comprehensive Analysis of DNA Methylation Data : %G eng %U http://hdl.handle.net/21.11116/0000-0003-2DF3-9 %R 10.1186/s13059-019-1664-9 %7 2019 %D 2019 %J Genome Biology %V 20 %Z sequence number: 55 %I BioMed Central Ltd. %C London %@ false
6. Schmidl C, Vladimer GI, Rendeiro AF, Schnabl S, Krausgruber T, Taubert C, Krall N, Pemovska T, Araghi M, Snijder B, Hubmann R, Ringler A, Runggatscher K, Demirtas D, Lopez de la Fuente O, Hilgarth M, Skrabs C, Porpaczy E, Gruber M, Hoermann G, Kubicek S, Staber PB, Shehata M, Superti-Furga G, Jaeger U, Bock C: Combined Chemosensitivity and Chromatin Profiling Prioritizes Drug Combinations in CLL. Nature Chemical Biology 2019, 15.
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@article{Schmidl2019, TITLE = {Combined Chemosensitivity and Chromatin Profiling Prioritizes Drug Combinations in {CLL}}, AUTHOR = {Schmidl, Christian and Vladimer, Gregory I. and Rendeiro, Andre F. and Schnabl, Susanne and Krausgruber, Thomas and Taubert, Christina and Krall, Nikolaus and Pemovska, Tea and Araghi, Mohammad and Snijder, Berend and Hubmann, Rainer and Ringler, Anna and Runggatscher, Kathrin and Demirtas, Dita and Lopez de la Fuente, Oscar and Hilgarth, Martin and Skrabs, Cathrin and Porpaczy, Edit and Gruber, Michaela and Hoermann, Gregor and Kubicek, Stefan and Staber, Philipp B. and Shehata, Medhat and Superti-Furga, Giulio and Jaeger, Ulrich and Bock, Christoph}, LANGUAGE = {eng}, ISSN = {1552-4450}, DOI = {10.1038/s41589-018-0205-2}, PUBLISHER = {Nature Pub. Group}, ADDRESS = {New York, NY}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Nature Chemical Biology}, VOLUME = {15}, NUMBER = {3}, PAGES = {232--240}, }
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%0 Journal Article %A Schmidl, Christian %A Vladimer, Gregory I. %A Rendeiro, Andre F. %A Schnabl, Susanne %A Krausgruber, Thomas %A Taubert, Christina %A Krall, Nikolaus %A Pemovska, Tea %A Araghi, Mohammad %A Snijder, Berend %A Hubmann, Rainer %A Ringler, Anna %A Runggatscher, Kathrin %A Demirtas, Dita %A Lopez de la Fuente, Oscar %A Hilgarth, Martin %A Skrabs, Cathrin %A Porpaczy, Edit %A Gruber, Michaela %A Hoermann, Gregor %A Kubicek, Stefan %A Staber, Philipp B. %A Shehata, Medhat %A Superti-Furga, Giulio %A Jaeger, Ulrich %A Bock, Christoph %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Combined Chemosensitivity and Chromatin Profiling Prioritizes Drug Combinations in CLL : %G eng %U http://hdl.handle.net/21.11116/0000-0003-1434-C %R 10.1038/s41589-018-0205-2 %7 2019 %D 2019 %J Nature Chemical Biology %O Nat. Chem. Biol. %V 15 %N 3 %& 232 %P 232 - 240 %I Nature Pub. Group %C New York, NY %@ false
7. Schmidt F, Schulz MH: On the Problem of Confounders in Modeling Gene Expression. Bioinformatics 2019, 35.
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@article{Schmidt2019, TITLE = {On the Problem of Confounders in Modeling Gene Expression}, AUTHOR = {Schmidt, Florian and Schulz, Marcel Holger}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/bty674}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Bioinformatics}, VOLUME = {35}, NUMBER = {4}, PAGES = {711--719}, }
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%0 Journal Article %A Schmidt, Florian %A Schulz, Marcel Holger %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T On the Problem of Confounders in Modeling Gene Expression : %G eng %U http://hdl.handle.net/21.11116/0000-0003-2094-1 %R 10.1093/bioinformatics/bty674 %7 2018 %D 2019 %J Bioinformatics %V 35 %N 4 %& 711 %P 711 - 719 %I Oxford University Press %C Oxford %@ false
8. Yi G, Wierenga ATJ, Petraglia F, Narang P, Janssen-Megens EM, Mandoli A, Merkel A, Berentsen K, Kim B, Matarese F, Singh AA, Habibi E, Prange KHM, Mulder AB, Jansen JH, Clarke L, Heath S, van der Reijden BA, Flicek P, Yaspo M-L, Gut I, Bock C, Schuringa JJ, Altucci L, Vellenga E, Stunnenberg HG, Martens J, H. A: Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes. Cell Reports 2019, 26.
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@article{Yi2019, TITLE = {Chromatin-Based Classification of Genetically Heterogeneous {AMLs} into Two Distinct Subtypes with Diverse Stemness Phenotypes}, AUTHOR = {Yi, Guoqiang and Wierenga, Albertus T. J. and Petraglia, Francesca and Narang, Pankaj and Janssen-Megens, Eva M. and Mandoli, Amit and Merkel, Angelika and Berentsen, Kim and Kim, Bowon and Matarese, Filomena and Singh, Abhishek A. and Habibi, Ehsan and Prange, Koen H. M. and Mulder, Andre B. and Jansen, Joop H. and Clarke, Laura and Heath, Simon and van der Reijden, Bert A. and Flicek, Paul and Yaspo, Marie-Laure and Gut, Ivo and Bock, Christoph and Schuringa, Jan Jacob and Altucci, Lucia and Vellenga, Edo and Stunnenberg, Hendrik G. and Martens, Joost and H., A.}, LANGUAGE = {eng}, ISSN = {2211-1247}, DOI = {10.1016/j.celrep.2018.12.098}, PUBLISHER = {Cell Press}, ADDRESS = {Maryland Heights, MO}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Cell Reports}, VOLUME = {26}, NUMBER = {4}, PAGES = {1059--1069}, EID = {e6}, }
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%0 Journal Article %A Yi, Guoqiang %A Wierenga, Albertus T. J. %A Petraglia, Francesca %A Narang, Pankaj %A Janssen-Megens, Eva M. %A Mandoli, Amit %A Merkel, Angelika %A Berentsen, Kim %A Kim, Bowon %A Matarese, Filomena %A Singh, Abhishek A. %A Habibi, Ehsan %A Prange, Koen H. M. %A Mulder, Andre B. %A Jansen, Joop H. %A Clarke, Laura %A Heath, Simon %A van der Reijden, Bert A. %A Flicek, Paul %A Yaspo, Marie-Laure %A Gut, Ivo %A Bock, Christoph %A Schuringa, Jan Jacob %A Altucci, Lucia %A Vellenga, Edo %A Stunnenberg, Hendrik G. %A Martens, Joost %A H., A. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes : %G eng %U http://hdl.handle.net/21.11116/0000-0002-F6CB-4 %R 10.1016/j.celrep.2018.12.098 %7 2019 %D 2019 %J Cell Reports %V 26 %N 4 %& 1059 %P 1059 - 1069 %Z sequence number: e6 %I Cell Press %C Maryland Heights, MO %@ false