C
Carsten O. Daub
Researcher at Karolinska Institutet
Publications - 102
Citations - 16438
Carsten O. Daub is an academic researcher from Karolinska Institutet. The author has contributed to research in topics: Cap analysis gene expression & Regulation of gene expression. The author has an hindex of 47, co-authored 97 publications receiving 14374 citations. Previous affiliations of Carsten O. Daub include April & Max Planck Society.
Papers
More filters
Journal ArticleDOI
An atlas of active enhancers across human cell types and tissues
Robin Andersson,Claudia Gebhard,Irene Miguel-Escalada,Ilka Hoof,Jette Bornholdt,Mette Boyd,Yun Chen,Xiaobei Zhao,Xiaobei Zhao,Christian Schmidl,Takahiro Suzuki,Evgenia Ntini,Erik Arner,Eivind Valen,Eivind Valen,Kang Li,Lucia Schwarzfischer,Dagmar Glatz,Johanna Raithel,Berit Lilje,Nicolas Rapin,Frederik Otzen Bagger,Mette Rose Jørgensen,Peter Refsing Andersen,Nicolas Bertin,Owen J. L. Rackham,A. Maxwell Burroughs,J Kenneth Baillie,Yuri Ishizu,Yuri Shimizu,Erina Furuhata,Shiori Maeda,Yutaka Negishi,Christopher J. Mungall,Terrence F. Meehan,Timo Lassmann,Masayoshi Itoh,Hideya Kawaji,Naoto Kondo,Jun Kawai,Andreas Lennartsson,Carsten O. Daub,Peter Heutink,David A. Hume,Torben Heick Jensen,Harukazu Suzuki,Yoshihide Hayashizaki,Ferenc Müller,Alistair R. R. Forrest,Piero Carninci,Michael Rehli,Albin Sandelin +51 more
TL;DR: It is shown that enhancers share properties with CpG-poor messenger RNA promoters but produce bidirectional, exosome-sensitive, relatively short unspliced RNAs, the generation of which is strongly related to enhancer activity.
Journal ArticleDOI
A promoter-level mammalian expression atlas
Alistair R. R. Forrest,Hideya Kawaji,Michael Rehli,J Kenneth Baillie,Michiel J. L. de Hoon,Vanja Haberle,Vanja Haberle,Timo Lassmann,Ivan V. Kulakovskiy,Ivan V. Kulakovskiy,Marina Lizio,Masayoshi Itoh,Robin Andersson,Christopher J. Mungall,Terrence F. Meehan,Sebastian Schmeier,Sebastian Schmeier,Nicolas Bertin,Mette C. Jørgensen,Emmanuel Dimont,Erik Arner,Christian Schmidl,Christian Schmidl,Ulf Schaefer,Yulia A. Medvedeva,Yulia A. Medvedeva,Charles Plessy,Morana Vitezic,Jessica Severin,Colin A. Semple,Yuri Ishizu,Robert Young,Margherita Francescatto,Margherita Francescatto,Intikhab Alam Altschuler,Davide Albanese,Gabriel M. Altschule,Takahiro Arakawa,John A.C. Archer,Peter Arner,Magda Babina,Sarah Rennie,Piotr J. Balwierz,Anthony G Beckhouse,Swati Pradhan-Bhatt,Judith A. Blake,Antje Blumenthal,Beatrice Bodega,Alessandro Bonetti,James Briggs,James Briggs,Frank Brombacher,Frank Brombacher,A. Maxwell Burroughs,Andrea Califano,Carlo Vittorio Cannistraci,Carlo Vittorio Cannistraci,Daniel Carbajo,Yun Chen,Marco Chierici,Yari Ciani,Hans Clevers,Hans Clevers,Emiliano Dalla,Carrie A. Davis,Michael Detmar,Alexander D. Diehl,Taeko Dohi,Finn Drabløs,Albert S.B. Edge,Matthias Edinger,Karl Ekwall,Mitsuhiro Endoh,Hideki Enomoto,Michela Fagiolini,Lynsey Fairbairn,Hai Fang,Mary C. Farach-Carson,Geoffrey J. Faulkner,Alexander V. Favorov,Alexander V. Favorov,Alexander V. Favorov,Malcolm E. Fisher,Martin C. Frith,Rie Fujita,Shiro Fukuda,Cesare Furlanello,Masaaki Furuno,Jun Ichi Furusawa,Teunis B. H. Geijtenbeek,Andrew P. Gibson,Thomas R. Gingeras,Dan Goldowitz,Julian Gough,Sven Guhl,Reto Guler,Reto Guler,Stefano Gustincich,Thomas J. Ha,Masahide Hamaguchi,Mitsuko Hara,Matthias Harbers,Jayson Harshbarger,Akira Hasegawa,Yuki Hasegawa,Takehiro Hashimoto,Meenhard Herlyn,Kelly J Hitchens,Shannan J. Ho Sui,Oliver Hofmann,Ilka Hoof,Fumi Hori,Lukasz Huminiecki,Kei Iida,Tomokatsu Ikawa,Boris R. Jankovic,Hui Jia,Anagha Joshi,Giuseppe Jurman,Bogumil Kaczkowski,Chieko Kai,Kaoru Kaida,Ai Kaiho,Kazuhiro Kajiyama,Mutsumi Kanamori-Katayama,Artem S. Kasianov,Takeya Kasukawa,Shintaro Katayama,Sachi Kato,Shuji Kawaguchi,Hiroshi Kawamoto,Yuki I. Kawamura,Tsugumi Kawashima,Judith S. Kempfle,Tony J. Kenna,Juha Kere,Juha Kere,Levon M. Khachigian,Toshio Kitamura,S. Peter Klinken,Alan J. Knox,Miki Kojima,Soichi Kojima,Naoto Kondo,Haruhiko Koseki,Shigeo Koyasu,Sarah Krampitz,Atsutaka Kubosaki,Andrew T. Kwon,Jeroen F. J. Laros,Weon Ju Lee,Andreas Lennartsson,Kang Li,Berit Lilje,Leonard Lipovich,Alan Mackay-Sim,Ri Ichiroh Manabe,Jessica C. Mar,Benoit Marchand,Anthony Mathelier,Niklas Mejhert,Alison M. Meynert,Yosuke Mizuno,David A. de Lima Morais,Hiromasa Morikawa,Mitsuru Morimoto,Kazuyo Moro,Efthymios Motakis,Hozumi Motohashi,Christine L. Mummery,Mitsuyoshi Murata,Sayaka Nagao-Sato,Yutaka Nakachi,Fumio Nakahara,Toshiyuki Nakamura,Yukio Nakamura,Kenichi Nakazato,Erik van Nimwegen,Noriko Ninomiya,Hiromi Nishiyori,Shohei Noma,Tadasuke Nozaki,Soichi Ogishima,Soichi Ogishima,Naganari Ohkura,Hiroko Ohmiya,Hiroshi Ohno,Mitsuhiro Ohshima,Mariko Okada-Hatakeyama,Yasushi Okazaki,Valerio Orlando,Dmitry A. Ovchinnikov,Arnab Pain,Robert Passier,Margaret Patrikakis,Helena Persson,Silvano Piazza,James Prendergast,Owen J. L. Rackham,Jordan A. Ramilowski,Mamoon Rashid,Timothy Ravasi,Patrizia Rizzu,Marco Roncador,Sugata Roy,Morten Beck Rye,Eri Saijyo,Antti Sajantila,Akiko Saka,Shimon Sakaguchi,Mizuho Sakai,Hiroki Sato,Hironori Satoh,Suzana Savvi,Suzana Savvi,Alka Saxena,Claudio Schneider,Erik Anthony Schultes,Gundula G. Schulze-Tanzil,Anita Schwegmann,Anita Schwegmann,Thierry Sengstag,Guojun Sheng,Hisashi Shimoji,Yishai Shimoni,Jay W. Shin,Christophe Simon,Daisuke Sugiyama,Takaaki Sugiyama,Masanori Suzuki,Naoko Suzuki,Rolf Swoboda,Peter A C 't Hoen,Michihira Tagami,Naoko Takahashi Tagami,Jun Takai,Hiroshi Tanaka,Hideki Tatsukawa,Zuotian Tatum,Mark Thompson,Hiroo Toyoda,Tetsuro Toyoda,Eivind Valen,Marc van de Wetering,Linda M. van den Berg,Roberto Verardo,Dipti Vijayan,Ilya E. Vorontsov,Wyeth W. Wasserman,Shoko Watanabe,Christine A. Wells,Louise N. Winteringham,Ernst J. Wolvetang,Emily J. Wood,Yoko Yamaguchi,Masayuki Yamamoto,Misako Yoneda,Yohei Yonekura,Shigehiro Yoshida,Susan E. Zabierowski,Peter G. Zhang,Xiaobei Zhao,Silvia Zucchelli,Kim M. Summers,Harukazu Suzuki,Carsten O. Daub,Jun Kawai,Peter Heutink,Winston Hide,Tom C. Freeman,Boris Lenhard,Boris Lenhard,Lenhard Vladimir B. Bajic,Martin S. Taylor,Vsevolod J. Makeev,Vsevolod J. Makeev,Vsevolod J. Makeev,Albin Sandelin,David A. Hume,Piero Carninci,Yoshihide Hayashizaki +280 more
TL;DR: For example, the authors mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body.
Journal ArticleDOI
An atlas of human long non-coding RNAs with accurate 5′ ends
Chung-Chau Hon,Jordan A. Ramilowski,Jayson Harshbarger,Nicolas Bertin,Nicolas Bertin,Owen J. L. Rackham,Owen J. L. Rackham,Julian Gough,Elena Denisenko,Sebastian Schmeier,Thomas M. Poulsen,Jessica Severin,Marina Lizio,Hideya Kawaji,Takeya Kasukawa,Masayoshi Itoh,A. Maxwell Burroughs,Shohei Noma,Sarah Djebali,Sarah Djebali,Tanvir Alam,Yulia A. Medvedeva,Alison C. Testa,Leonard Lipovich,Chi Wai Yip,Imad Abugessaisa,Mickal Mendez,Akira Hasegawa,Dave Tang,Timo Lassmann,Peter Heutink,Magda Babina,Christine A. Wells,Christine A. Wells,Soichi Kojima,Yukio Nakamura,Harukazu Suzuki,Carsten O. Daub,Michiel J. L. de Hoon,Erik Arner,Yoshihide Hayashizaki,Piero Carninci,Alistair R. R. Forrest +42 more
TL;DR: This work integrates multiple transcript collections to generate a comprehensive atlas of 27,919 human lncRNA genes with high-confidence 5′ ends and expression profiles across 1,829 samples from the major human primary cell types and tissues, identifying 19,175 potentially functional lncRNAs in the human genome.
Journal ArticleDOI
The mutual information: detecting and evaluating dependencies between variables.
TL;DR: The findings show that the algorithms used so far may be quite substantially improved upon when dealing with small datasets, finite sample effects and other sources of potentially misleading results have to be taken into account.
Journal ArticleDOI
The regulated retrotransposon transcriptome of mammalian cells.
Geoffrey J. Faulkner,Yasumasa Kimura,Carsten O. Daub,Shivangi Wani,Charles Plessy,Katharine M. Irvine,Kate Schroder,Nicole Cloonan,Anita L Steptoe,Timo Lassmann,Kazunori Waki,Nadine Hornig,Takahiro Arakawa,Hazuki Takahashi,Jun Kawai,Alistair R. R. Forrest,Harukazu Suzuki,Yoshihide Hayashizaki,David A. Hume,Valerio Orlando,Sean M. Grimmond,Piero Carninci +21 more
TL;DR: It is reported that 6–30% of cap-selected mouse and human RNA transcripts initiate within repetitive elements, and it is concluded that retrotransposon transcription has a key influence upon the transcriptional output of the mammalian genome.