Erik Arner

Erik Arner

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Erik Arner

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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.

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

MicroRNA-27a/b-3p and PPARG regulate SCAMP3 through a feed-forward loop during adipogenesis.

Sci Rep 2019 Sep 25;9(1):13891. Epub 2019 Sep 25.

RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1038/s41598-019-50210-3DOI Listing
September 2019

Detailed Functional Characterization of a Waist-Hip Ratio Locus in 7p15.2 Defines an Enhancer Controlling Adipocyte Differentiation.

iScience 2019 Sep 10;20:42-59. Epub 2019 Sep 10.

Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2019.09.006DOI Listing
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.

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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.

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

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

Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment.

Bioinformatics 2017 Dec;33(23):3696-3700

Molecular Network Control Genomics Unit, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btx503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860321PMC
December 2017

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:

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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.

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

Discriminative identification of transcriptional responses of promoters and enhancers after stimulus.

Nucleic Acids Res 2017 02;45(4):e25

Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1093/nar/gkw1015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389464PMC
February 2017

Expression of FBN1 during adipogenesis: Relevance to the lipodystrophy phenotype in Marfan syndrome and related conditions.

Mol Genet Metab 2016 09 23;119(1-2):174-85. Epub 2016 Jun 23.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5044862PMC
http://dx.doi.org/10.1016/j.ymgme.2016.06.009DOI Listing
September 2016

Datasets of genes coexpressed with FBN1 in mouse adipose tissue and during human adipogenesis.

Data Brief 2016 Sep 5;8:851-7. Epub 2016 Jul 5.

The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK.

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http://dx.doi.org/10.1016/j.dib.2016.06.055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959917PMC
September 2016

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

Nucleic Acids Res 2016 Apr 21;44(7):3233-52. Epub 2016 Mar 21.

Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021, China St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA

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http://dx.doi.org/10.1093/nar/gkw162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838384PMC
April 2016

Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors.

Epigenetics Chromatin 2015 14;8:55. Epub 2015 Dec 14.

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

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http://dx.doi.org/10.1186/s13072-015-0043-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4678690PMC
December 2015

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics.

Nucleic Acids Res 2015 Aug 27;43(14):6969-82. Epub 2015 Jun 27.

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan Riken Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan

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http://dx.doi.org/10.1093/nar/gkv646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538831PMC
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.

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

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.

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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;

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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

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

Health and obesity: not just skin deep.

Science 2013 Nov;342(6158):558-9

Department of Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, SE-141 86 Huddinge, Sweden.

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http://dx.doi.org/10.1126/science.342.6158.558-bDOI Listing
November 2013

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.

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

Genetic predisposition for Type 2 diabetes, but not for overweight/obesity, is associated with a restricted adipogenesis.

PLoS One 2011 Apr 12;6(4):e18284. Epub 2011 Apr 12.

Department of Medicine, Karolinska Institute at Karolinska Hospital, Huddinge, Stockholm, Sweden.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018284PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3075240PMC
April 2011

Adipocyte turnover: relevance to human adipose tissue morphology.

Diabetes 2010 Jan 21;59(1):105-9. Epub 2009 Oct 21.

Department of Medicine, Karolinska Institutet at Karolinska University Hospital, Stockholm, Sweden.

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http://dx.doi.org/10.2337/db09-0942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2797910PMC
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.

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

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.

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

Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation.

Genome Biol 2009 19;10(4):R41. Epub 2009 Apr 19.

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

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http://dx.doi.org/10.1186/gb-2009-10-4-r41DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688932PMC
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.

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

Database of Trypanosoma cruzi repeated genes: 20,000 additional gene variants.

BMC Genomics 2007 Oct 26;8:391. Epub 2007 Oct 26.

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

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http://dx.doi.org/10.1186/1471-2164-8-391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2204015PMC
October 2007

GRAT--genome-scale rapid alignment tool.

Comput Methods Programs Biomed 2007 Apr 9;86(1):87-92. Epub 2007 Feb 9.

Department of Cell and Molecular Biology, Karolinska Institutet, Berzelius Väg 35, S-17177 Stockholm, Sweden.

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http://linkinghub.elsevier.com/retrieve/pii/S016926070700006
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http://dx.doi.org/10.1016/j.cmpb.2007.01.002DOI Listing
April 2007

DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions.

BMC Bioinformatics 2006 Mar 20;7:155. Epub 2006 Mar 20.

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

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http://dx.doi.org/10.1186/1471-2105-7-155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1459207PMC
March 2006

Adipocyte lipases and defect of lipolysis in human obesity.

Diabetes 2005 Nov;54(11):3190-7

Obesity Research Unit, Institut National de la Santé et de la Recherche Médicale, Université Paul Sabatier (UPS) U586, Louis Bugnard Institute, Toulouse University Hospitals, Toulouse, France.

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http://dx.doi.org/10.2337/diabetes.54.11.3190DOI Listing
November 2005

The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease.

Science 2005 Jul;309(5733):409-15

Department of Parasite Genomics, Institute for Genomic Research, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1126/science.1112631DOI Listing
July 2005

ReDiT: Repeat Discrepancy Tagger--a shotgun assembly finishing aid.

Bioinformatics 2004 Mar 29;20(5):803-4. Epub 2004 Jan 29.

Karolinska Institutet, Center for Genomics and Bioinformatics (CGB), Berzelius Väg 35, S-171 77 Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/bth004DOI Listing
March 2004

Correcting errors in shotgun sequences.

Nucleic Acids Res 2003 Aug;31(15):4663-72

Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius väg 35, 171 77 Stockholm, Sweden.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC169956PMC
http://dx.doi.org/10.1093/nar/gkg653;DOI Listing
August 2003

TRAP: Tandem Repeat Assembly Program produces improved shotgun assemblies of repetitive sequences.

Comput Methods Programs Biomed 2003 Jan;70(1):47-59

Department of Genetics and Pathology, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden.

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http://dx.doi.org/10.1016/s0169-2607(01)00194-8DOI Listing
January 2003

Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs.

Bioinformatics 2002 Mar;18(3):379-88

Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/18.3.379DOI Listing
March 2002