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Page 1
Landscape of transcription in human cells.
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR. Djebali S, et al. Among authors: merkel a. Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233. Nature. 2012. PMID: 22955620 Free PMC article.
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R. Derrien T, et al. Among authors: merkel a. Genome Res. 2012 Sep;22(9):1775-89. doi: 10.1101/gr.132159.111. Genome Res. 2012. PMID: 22955988 Free PMC article.
Grape RNA-Seq analysis pipeline environment.
Knowles DG, Röder M, Merkel A, Guigó R. Knowles DG, et al. Among authors: merkel a. Bioinformatics. 2013 Mar 1;29(5):614-21. doi: 10.1093/bioinformatics/btt016. Epub 2013 Jan 17. Bioinformatics. 2013. PMID: 23329413 Free PMC article.
The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia.
Beekman R, Chapaprieta V, Russiñol N, Vilarrasa-Blasi R, Verdaguer-Dot N, Martens JHA, Duran-Ferrer M, Kulis M, Serra F, Javierre BM, Wingett SW, Clot G, Queirós AC, Castellano G, Blanc J, Gut M, Merkel A, Heath S, Vlasova A, Ullrich S, Palumbo E, Enjuanes A, Martín-García D, Beà S, Pinyol M, Aymerich M, Royo R, Puiggros M, Torrents D, Datta A, Lowy E, Kostadima M, Roller M, Clarke L, Flicek P, Agirre X, Prosper F, Baumann T, Delgado J, López-Guillermo A, Fraser P, Yaspo ML, Guigó R, Siebert R, Martí-Renom MA, Puente XS, López-Otín C, Gut I, Stunnenberg HG, Campo E, Martin-Subero JI. Beekman R, et al. Among authors: merkel a. Nat Med. 2018 Jun;24(6):868-880. doi: 10.1038/s41591-018-0028-4. Epub 2018 May 21. Nat Med. 2018. PMID: 29785028 Free PMC article.
Epigenetic regulation of gene expression in Chinese Hamster Ovary cells in response to the changing environment of a batch culture.
Hernandez I, Dhiman H, Klanert G, Jadhav V, Auer N, Hanscho M, Baumann M, Esteve-Codina A, Dabad M, Gómez J, Alioto T, Merkel A, Raineri E, Heath S, Rico D, Borth N. Hernandez I, et al. Among authors: merkel a. Biotechnol Bioeng. 2019 Mar;116(3):677-692. doi: 10.1002/bit.26891. Epub 2019 Jan 4. Biotechnol Bioeng. 2019. PMID: 30512195 Free PMC article.
Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.
Ecker S, Chen L, Pancaldi V, Bagger FO, Fernández JM, Carrillo de Santa Pau E, Juan D, Mann AL, Watt S, Casale FP, Sidiropoulos N, Rapin N, Merkel A; BLUEPRINT Consortium; Stunnenberg HG, Stegle O, Frontini M, Downes K, Pastinen T, Kuijpers TW, Rico D, Valencia A, Beck S, Soranzo N, Paul DS. Ecker S, et al. Among authors: merkel a. Genome Biol. 2017 Jan 26;18(1):18. doi: 10.1186/s13059-017-1156-8. Genome Biol. 2017. PMID: 28126036 Free PMC article.
Whole-genome fingerprint of the DNA methylome during human B cell differentiation.
Kulis M, Merkel A, Heath S, Queirós AC, Schuyler RP, Castellano G, Beekman R, Raineri E, Esteve A, Clot G, Verdaguer-Dot N, Duran-Ferrer M, Russiñol N, Vilarrasa-Blasi R, Ecker S, Pancaldi V, Rico D, Agueda L, Blanc J, Richardson D, Clarke L, Datta A, Pascual M, Agirre X, Prosper F, Alignani D, Paiva B, Caron G, Fest T, Muench MO, Fomin ME, Lee ST, Wiemels JL, Valencia A, Gut M, Flicek P, Stunnenberg HG, Siebert R, Küppers R, Gut IG, Campo E, Martín-Subero JI. Kulis M, et al. Among authors: merkel a. Nat Genet. 2015 Jul;47(7):746-56. doi: 10.1038/ng.3291. Epub 2015 Jun 8. Nat Genet. 2015. PMID: 26053498 Free PMC article.
Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils.
Grassi L, Pourfarzad F, Ullrich S, Merkel A, Were F, Carrillo-de-Santa-Pau E, Yi G, Hiemstra IH, Tool ATJ, Mul E, Perner J, Janssen-Megens E, Berentsen K, Kerstens H, Habibi E, Gut M, Yaspo ML, Linser M, Lowy E, Datta A, Clarke L, Flicek P, Vingron M, Roos D, van den Berg TK, Heath S, Rico D, Frontini M, Kostadima M, Gut I, Valencia A, Ouwehand WH, Stunnenberg HG, Martens JHA, Kuijpers TW. Grassi L, et al. Among authors: merkel a. Cell Rep. 2018 Sep 4;24(10):2784-2794. doi: 10.1016/j.celrep.2018.08.018. Cell Rep. 2018. PMID: 30184510 Free PMC article.
Genome analysis of the platypus reveals unique signatures of evolution.
Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK. Warren WC, et al. Among authors: merkel a. Nature. 2008 May 8;453(7192):175-83. doi: 10.1038/nature06936. Nature. 2008. PMID: 18464734 Free PMC article.
232 results