Carsten Daub

Carsten Daub

UNVERIFIED PROFILE

Are you Carsten Daub?   Register this Author

Register author
Carsten Daub

Carsten Daub

Publications by authors named "Carsten Daub"

Are you Carsten Daub?   Register this Author

78Publications

2127Reads

35Profile Views

Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis.

BMC Genomics 2019 Sep 18;20(1):718. Epub 2019 Sep 18.

Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-6063-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6751898PMC
September 2019

Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1β.

Sci Rep 2018 09 3;8(1):13164. Epub 2018 Sep 3.

Vascular Biology and Translational Research, School of Medical Sciences, University of New South Wales, Sydney, 2052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-30702-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120868PMC
September 2018

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection.

Cerebellum 2018 Jun;17(3):308-325

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12311-017-0912-3DOI Listing
June 2018

Long-Term Improvement in Aortic Pulse Wave Velocity After Weight Loss Can Be Predicted by White Adipose Tissue Factors.

Am J Hypertens 2018 03;31(4):450-457

Department of Medicine (H7), Karolinska Institutet, C2-94, Karolinska University Hospital, Huddinge, Stockholm, Sweden.

View Article

Download full-text PDF

Source
https://academic.oup.com/ajh/article/31/4/450/4644826
Publisher Site
http://dx.doi.org/10.1093/ajh/hpx201DOI Listing
March 2018

Correction to: Relatively frequent switching of transcription start sites during cerebellar development.

BMC Genomics 2018 01 11;19(1):39. Epub 2018 Jan 11.

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-017-4291-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5763542PMC
January 2018

Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes.

EBioMedicine 2017 Oct 12;24:257-266. Epub 2017 Sep 12.

Micro-Signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies, Wako, Saitama 3510198, Japan; Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo 1058461, Japan. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ebiom.2017.09.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5652006PMC
October 2017

FANTOM5 CAGE profiles of human and mouse samples.

Authors:
Shuhei Noguchi Takahiro Arakawa Shiro Fukuda Masaaki Furuno Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Kaoru Kaida Ai Kaiho Mutsumi Kanamori-Katayama Tsugumi Kawashima Miki Kojima Atsutaka Kubosaki Ri-Ichiroh Manabe Mitsuyoshi Murata Sayaka Nagao-Sato Kenichi Nakazato Noriko Ninomiya Hiromi Nishiyori-Sueki Shohei Noma Eri Saijyo Akiko Saka Mizuho Sakai Christophe Simon Naoko Suzuki Michihira Tagami Shoko Watanabe Shigehiro Yoshida Peter Arner Richard A Axton Magda Babina J Kenneth Baillie Timothy C Barnett Anthony G Beckhouse Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher Ailsa J Carlisle Hans C Clevers Carrie A Davis Michael Detmar Taeko Dohi Albert S B Edge Matthias Edinger Anna Ehrlund Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Mary C Farach-Carson Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley M Forrester Rie Fujita Jun-Ichi Furusawa Teunis B Geijtenbeek Thomas Gingeras Daniel Goldowitz Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Yuki Hasegawa Meenhard Herlyn Peter Heutink Kelly J Hitchens David A Hume Tomokatsu Ikawa Yuri Ishizu Chieko Kai Hiroshi Kawamoto Yuki I Kawamura Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura Sarah Klein S Peter Klinken Alan J Knox Soichi Kojima Haruhiko Koseki Shigeo Koyasu Weonju Lee Andreas Lennartsson Alan Mackay-Sim Niklas Mejhert Yosuke Mizuno Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Kelly J Morris Hozumi Motohashi Christine L Mummery Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Tadasuke Nozaki Soichi Ogishima Naganari Ohkura Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Swati Pradhan-Bhatt Xian-Yang Qin Michael Rehli Patrizia Rizzu Sugata Roy Antti Sajantila Shimon Sakaguchi Hiroki Sato Hironori Satoh Suzana Savvi Alka Saxena Christian Schmidl Claudio Schneider Gundula G Schulze-Tanzil Anita Schwegmann Guojun Sheng Jay W Shin Daisuke Sugiyama Takaaki Sugiyama Kim M Summers Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Andru Tomoiu Hiroo Toyoda Marc van de Wetering Linda M van den Berg Roberto Verardo Dipti Vijayan Christine A Wells Louise N Winteringham Ernst Wolvetang Yoko Yamaguchi Masayuki Yamamoto Chiyo Yanagi-Mizuochi Misako Yoneda Yohei Yonekura Peter G Zhang Silvia Zucchelli Imad Abugessaisa Erik Arner Jayson Harshbarger Atsushi Kondo Timo Lassmann Marina Lizio Serkan Sahin Thierry Sengstag Jessica Severin Hisashi Shimoji Masanori Suzuki Harukazu Suzuki Jun Kawai Naoto Kondo Masayoshi Itoh Carsten O Daub Takeya Kasukawa Hideya Kawaji Piero Carninci Alistair R R Forrest Yoshihide Hayashizaki

Sci Data 2017 08 29;4:170112. Epub 2017 Aug 29.

RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/sdata.2017.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574368PMC
August 2017

The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity.

Cell Rep 2016 08 18;16(9):2317-26. Epub 2016 Aug 18.

Department of Medicine, Karolinska University Hospital Huddinge, Karolinska Institutet, 141 86 Stockholm, Sweden. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2016.07.070DOI Listing
August 2016

Transcriptome analysis of controlled and therapy-resistant childhood asthma reveals distinct gene expression profiles.

J Allergy Clin Immunol 2015 Sep 9;136(3):638-48. Epub 2015 Apr 9.

Department of Biosciences and Nutrition and Center for Innovative Medicine (CIMED), Karolinska Institutet, Stockholm, Sweden; Omics Science Center,§ RIKEN Yokohama Institute, Yokohama, Japan; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S00916749150032
Publisher Site
http://dx.doi.org/10.1016/j.jaci.2015.02.026DOI Listing
September 2015

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.

Nucleic Acids Res 2015 Aug 27;43(14):6787-98. Epub 2015 Jun 27.

Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, 14183, Sweden Science for Life Laboratory, Karolinska Institute, Solna, 17121, Sweden RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan

View Article

Download full-text PDF

Source
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
Publisher Site
http://dx.doi.org/10.1093/nar/gkv608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538815PMC
August 2015

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Authors:
Erik Arner Carsten O Daub Kristoffer Vitting-Seerup Robin Andersson Berit Lilje Finn Drabløs Andreas Lennartsson Michelle Rönnerblad Olga Hrydziuszko Morana Vitezic Tom C Freeman Ahmad M N Alhendi Peter Arner Richard Axton J Kenneth Baillie Anthony Beckhouse Beatrice Bodega James Briggs Frank Brombacher Margaret Davis Michael Detmar Anna Ehrlund Mitsuhiro Endoh Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley Forrester Daniel Goldowitz Reto Guler Thomas Ha Mitsuko Hara Meenhard Herlyn Tomokatsu Ikawa Chieko Kai Hiroshi Kawamoto Levon M Khachigian S Peter Klinken Soichi Kojima Haruhiko Koseki Sarah Klein Niklas Mejhert Ken Miyaguchi Yosuke Mizuno Mitsuru Morimoto Kelly J Morris Christine Mummery Yutaka Nakachi Soichi Ogishima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Xian-Yang Qin Sugata Roy Hiroki Sato Suzana Savvi Alka Saxena Anita Schwegmann Daisuke Sugiyama Rolf Swoboda Hiroshi Tanaka Andru Tomoiu Louise N Winteringham Ernst Wolvetang Chiyo Yanagi-Mizuochi Misako Yoneda Susan Zabierowski Peter Zhang Imad Abugessaisa Nicolas Bertin Alexander D Diehl Shiro Fukuda Masaaki Furuno Jayson Harshbarger Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Yuri Ishizu Masayoshi Itoh Tsugumi Kawashima Miki Kojima Naoto Kondo Marina Lizio Terrence F Meehan Christopher J Mungall Mitsuyoshi Murata Hiromi Nishiyori-Sueki Serkan Sahin Sayaka Nagao-Sato Jessica Severin Michiel J L de Hoon Jun Kawai Takeya Kasukawa Timo Lassmann Harukazu Suzuki Hideya Kawaji Kim M Summers Christine Wells David A Hume Alistair R R Forrest Albin Sandelin Piero Carninci Yoshihide Hayashizaki

Science 2015 Feb 12;347(6225):1010-4. Epub 2015 Feb 12.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1259418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681433PMC
February 2015

Telomerase reverse transcriptase regulates microRNAs.

Int J Mol Sci 2015 Jan 6;16(1):1192-208. Epub 2015 Jan 6.

Cancer Stem Cell Project, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms16011192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4307298PMC
January 2015

MOIRAI: a compact workflow system for CAGE analysis.

BMC Bioinformatics 2014 May 16;15:144. Epub 2014 May 16.

RIKEN Center for Life Science Technologies (CLST), Riken Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Kanagawa, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-15-144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033680PMC
May 2014

Additive effects of microRNAs and transcription factors on CCL2 production in human white adipose tissue.

Diabetes 2014 Apr 30;63(4):1248-58. Epub 2013 Dec 30.

Department of Medicine, Huddinge, Lipid Laboratory, Karolinska Institutet, Stockholm, Sweden.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2337/db13-0702DOI Listing
April 2014

High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis.

Blood 2014 Apr 26;123(17):e46-57. Epub 2014 Mar 26.

Department of Bioscience and Nutrition, Center for Biosciences, NOVUM, Karolinska Institutet, Stockholm, Sweden;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1182/blood-2013-02-483537DOI Listing
April 2014

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh Robin Andersson Christopher J Mungall Terrence F Meehan Sebastian Schmeier Nicolas Bertin Mette Jørgensen Emmanuel Dimont Erik Arner Christian Schmidl Ulf Schaefer Yulia A Medvedeva Charles Plessy Morana Vitezic Jessica Severin Colin A Semple Yuri Ishizu Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler 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 Frank Brombacher A Maxwell Burroughs Andrea Califano Carlo V Cannistraci Daniel Carbajo Yun Chen Marco Chierici Yari Ciani Hans C 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 Malcolm E Fisher Martin C Frith Rie Fujita Shiro Fukuda Cesare Furlanello Masaaki Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas Gingeras Daniel Goldowitz Julian Gough Sven Guhl 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 M Hofmann Ilka Hoof Furni 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 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 Weonju 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 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 Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya 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 G D Prendergast Owen J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato Suzana Savvi Alka Saxena Claudio Schneider Erik A Schultes Gundula G Schulze-Tanzil Anita Schwegmann Thierry Sengstag Guojun Sheng Hisashi Shimoji Yishai Shimoni Jay W Shin Christophe Simon Daisuke Sugiyama Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado Dipti Vijayan Ilya E Vorontsov Wyeth W Wasserman Shoko Watanabe Christine A Wells Louise N Winteringham Ernst 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 Vladimir B Bajic Martin S Taylor Vsevolod J Makeev Albin Sandelin David A Hume Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU.

Nat Biotechnol 2014 Mar;32(3):217-9

1] RIKEN Center for Life Science Technologies (Division of Genomic Technologies), Suehiro-cho, Tsurumi-ku, Yokohama, Japan. [2] RIKEN Omics Science Center (OSC), Yokohama, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt.2840DOI Listing
March 2014

Regional differences in gene expression and promoter usage in aged human brains.

Neurobiol Aging 2013 Jul 19;34(7):1825-36. Epub 2013 Feb 19.

Section Medical Genomics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.neurobiolaging.2013.01.005DOI Listing
July 2013

Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals.

Plant Cell Physiol 2013 May 14;54(5):697-710. Epub 2013 Apr 14.

RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045 Japan.

View Article

Download full-text PDF

Source
https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/
Publisher Site
http://dx.doi.org/10.1093/pcp/pct057DOI Listing
May 2013

Molecular networks of DYX1C1 gene show connection to neuronal migration genes and cytoskeletal proteins.

Biol Psychiatry 2013 Mar 1;73(6):583-90. Epub 2012 Oct 1.

Center for Biosciences, Department of Biosciences and Nutrition, Novum, Karolinska Institutet, Huddinge, Sweden.

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S00063223120072
Publisher Site
http://dx.doi.org/10.1016/j.biopsych.2012.08.012DOI Listing
March 2013

pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5'/3' arm variation including concomitant cleavage and polyuridylation patterns.

Nucleic Acids Res 2012 Feb 3;40(4):1424-37. Epub 2011 Nov 3.

Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkr903DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287202PMC
February 2012

The short non-coding transcriptome of the protozoan parasite Trypanosoma cruzi.

PLoS Negl Trop Dis 2011 Aug 30;5(8):e1283. Epub 2011 Aug 30.

Science for Life Laboratory, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pntd.0001283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166047PMC
August 2011

SAMStat: monitoring biases in next generation sequencing data.

Bioinformatics 2011 Jan 18;27(1):130-1. Epub 2010 Nov 18.

Omics Science Center, Riken Yokohama Institute, Tsurumi-ku, Yokohama, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btq614DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008642PMC
January 2011

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.

Genome Biol 2009 22;10(7):R79. Epub 2009 Jul 22.

Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, 4056-CH, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2009-10-7-r79DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728533PMC
January 2010

NGSView: an extensible open source editor for next-generation sequencing data.

Bioinformatics 2010 Jan 24;26(1):125-6. Epub 2009 Oct 24.

RIKEN Omics Science Center, RIKEN Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btp611DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796816PMC
January 2010

TagDust--a program to eliminate artifacts from next generation sequencing data.

Bioinformatics 2009 Nov 7;25(21):2839-40. Epub 2009 Sep 7.

Omics Science Center, Riken Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

View Article

Download full-text PDF

Source
https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btp527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781754PMC
November 2009

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite.

Bioinformatics 2009 Oct 15;25(19):2613-4. Epub 2009 Jul 15.

Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

View Article

Download full-text PDF

Source
https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btp438DOI Listing
October 2009

Transcriptional features of genomic regulatory blocks.

Genome Biol 2009 19;10(4):R38. Epub 2009 Apr 19.

Computational Biology Unit, Bergen Center for Computational Science, and Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2009-10-4-r38DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688929PMC
September 2009

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Authors:
Harukazu Suzuki Alistair R R Forrest Erik van Nimwegen Carsten O Daub Piotr J Balwierz Katharine M Irvine Timo Lassmann Timothy Ravasi Yuki Hasegawa Michiel J L de Hoon Shintaro Katayama Kate Schroder Piero Carninci Yasuhiro Tomaru Mutsumi Kanamori-Katayama Atsutaka Kubosaki Altuna Akalin Yoshinari Ando Erik Arner Maki Asada Hiroshi Asahara Timothy Bailey Vladimir B Bajic Denis Bauer Anthony G Beckhouse Nicolas Bertin Johan Björkegren Frank Brombacher Erika Bulger Alistair M Chalk Joe Chiba Nicole Cloonan Adam Dawe Josee Dostie Pär G Engström Magbubah Essack Geoffrey J Faulkner J Lynn Fink David Fredman Ko Fujimori Masaaki Furuno Takashi Gojobori Julian Gough Sean M Grimmond Mika Gustafsson Megumi Hashimoto Takehiro Hashimoto Mariko Hatakeyama Susanne Heinzel Winston Hide Oliver Hofmann Michael Hörnquist Lukasz Huminiecki Kazuho Ikeo Naoko Imamoto Satoshi Inoue Yusuke Inoue Ryoko Ishihara Takao Iwayanagi Anders Jacobsen Mandeep Kaur Hideya Kawaji Markus C Kerr Ryuichiro Kimura Syuhei Kimura Yasumasa Kimura Hiroaki Kitano Hisashi Koga Toshio Kojima Shinji Kondo Takeshi Konno Anders Krogh Adele Kruger Ajit Kumar Boris Lenhard Andreas Lennartsson Morten Lindow Marina Lizio Cameron Macpherson Norihiro Maeda Christopher A Maher Monique Maqungo Jessica Mar Nicholas A Matigian Hideo Matsuda John S Mattick Stuart Meier Sei Miyamoto Etsuko Miyamoto-Sato Kazuhiko Nakabayashi Yutaka Nakachi Mika Nakano Sanne Nygaard Toshitsugu Okayama Yasushi Okazaki Haruka Okuda-Yabukami Valerio Orlando Jun Otomo Mikhail Pachkov Nikolai Petrovsky Charles Plessy John Quackenbush Aleksandar Radovanovic Michael Rehli Rintaro Saito Albin Sandelin Sebastian Schmeier Christian Schönbach Ariel S Schwartz Colin A Semple Miho Sera Jessica Severin Katsuhiko Shirahige Cas Simons George St Laurent Masanori Suzuki Takahiro Suzuki Matthew J Sweet Ryan J Taft Shizu Takeda Yoichi Takenaka Kai Tan Martin S Taylor Rohan D Teasdale Jesper Tegnér Sarah Teichmann Eivind Valen Claes Wahlestedt Kazunori Waki Andrew Waterhouse Christine A Wells Ole Winther Linda Wu Kazumi Yamaguchi Hiroshi Yanagawa Jun Yasuda Mihaela Zavolan David A Hume Takahiro Arakawa Shiro Fukuda Kengo Imamura Chikatoshi Kai Ai Kaiho Tsugumi Kawashima Chika Kawazu Yayoi Kitazume Miki Kojima Hisashi Miura Kayoko Murakami Mitsuyoshi Murata Noriko Ninomiya Hiromi Nishiyori Shohei Noma Chihiro Ogawa Takuma Sano Christophe Simon Michihira Tagami Yukari Takahashi Jun Kawai Yoshihide Hayashizaki

Nat Genet 2009 May 19;41(5):553-62. Epub 2009 Apr 19.

RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ng.375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711855PMC
May 2009

SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processes.

BMC Bioinformatics 2009 May 7;10:133. Epub 2009 May 7.

RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan.

View Article

Download full-text PDF

Source
https://bmcbioinformatics.biomedcentral.com/articles/10.1186
Publisher Site
http://dx.doi.org/10.1186/1471-2105-10-133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689195PMC
May 2009

Employing conservation of co-expression to improve functional inference.

BMC Syst Biol 2008 Sep 22;2:81. Epub 2008 Sep 22.

Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.

View Article

Download full-text PDF

Source
http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
Publisher Site
http://dx.doi.org/10.1186/1752-0509-2-81DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2561017PMC
September 2008

Hidden layers of human small RNAs.

BMC Genomics 2008 Apr 10;9:157. Epub 2008 Apr 10.

Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-9-157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2359750PMC
April 2008

Prediction of function divergence in protein families using the substitution rate variation parameter alpha.

Mol Biol Evol 2006 Jul 3;23(7):1406-13. Epub 2006 May 3.

Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden.

View Article

Download full-text PDF

Source
http://academic.oup.com/mbe/article/23/7/1406/1065102/Predic
Publisher Site
http://dx.doi.org/10.1093/molbev/msl002DOI Listing
July 2006

Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response.

J Exp Bot 2005 Jul 23;56(417):1887-96. Epub 2005 May 23.

Max Planck Institute of Molecular Plant Physiology, Department of Molecular Physiology, Am Mühlenberg 1, D-14476 Golm, Germany.

View Article

Download full-text PDF

Source
http://academic.oup.com/jxb/article/56/417/1887/484342/Integ
Publisher Site
http://dx.doi.org/10.1093/jxb/eri179DOI Listing
July 2005

Estimating mutual information using B-spline functions--an improved similarity measure for analysing gene expression data.

BMC Bioinformatics 2004 Aug 31;5:118. Epub 2004 Aug 31.

Max Planck Institute of Molecular Plant Physiology, Potsdam, 14424, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-5-118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC516800PMC
August 2004

MetaGeneAlyse: analysis of integrated transcriptional and metabolite data.

Bioinformatics 2003 Nov;19(17):2332-3

Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btg321DOI Listing
November 2003