Publications by authors named "Robin Andersson"

54Publications

Determinants of enhancer and promoter activities of regulatory elements.

Nat Rev Genet 2020 02 11;21(2):71-87. Epub 2019 Oct 11.

Department of Biology, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1038/s41576-019-0173-8DOI Listing
February 2020

CAGEfightR: analysis of 5'-end data using R/Bioconductor.

BMC Bioinformatics 2019 Oct 4;20(1):487. Epub 2019 Oct 4.

Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark.

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http://dx.doi.org/10.1186/s12859-019-3029-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6778389PMC
October 2019

PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells.

Elife 2019 01 23;8. Epub 2019 Jan 23.

Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.7554/eLife.40364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344081PMC
January 2019

MCM2 promotes symmetric inheritance of modified histones during DNA replication.

Science 2018 09 16;361(6409):1389-1392. Epub 2018 Aug 16.

Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.

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http://dx.doi.org/10.1126/science.aau0294DOI Listing
September 2018

Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions.

Nat Commun 2018 02 5;9(1):487. Epub 2018 Feb 5.

The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Copenhagen, Denmark.

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http://dx.doi.org/10.1038/s41467-017-02798-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5799294PMC
February 2018

Histone acetylation of glucose-induced thioredoxin-interacting protein gene expression in pancreatic islets.

Int J Biochem Cell Biol 2016 12 29;81(Pt A):82-91. Epub 2016 Oct 29.

Diabetes and Endocrinology, Department of Clinical Sciences, Lund University, Malmö, SE-20502, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.biocel.2016.10.022DOI Listing
December 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

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers.

Cancer Res 2016 Jan 9;76(2):216-26. Epub 2015 Nov 9.

RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan. Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia.

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http://dx.doi.org/10.1158/0008-5472.CAN-15-0484DOI Listing
January 2016

Human Gene Promoters Are Intrinsically Bidirectional.

Mol Cell 2015 Nov;60(3):346-7

Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, C.F. Møllers Alle 3, Building 1130, 8000 Aarhus, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.10.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5485825PMC
November 2015

The frequent evolutionary birth and death of functional promoters in mouse and human.

Genome Res 2015 Oct 30;25(10):1546-57. Epub 2015 Jul 30.

MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom;

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http://dx.doi.org/10.1101/gr.190546.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579340PMC
October 2015

A unified architecture of transcriptional regulatory elements.

Trends Genet 2015 Aug 11;31(8):426-33. Epub 2015 Jun 11.

Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA; Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S01689525150010
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http://dx.doi.org/10.1016/j.tig.2015.05.007DOI Listing
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

Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model.

Authors:
Robin Andersson

Bioessays 2015 Mar 2;37(3):314-23. Epub 2014 Dec 2.

The Bioinformatics Centre, Section for Computational and RNA Biology, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Denmark.

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http://dx.doi.org/10.1002/bies.201400162DOI Listing
March 2015

Nuclear stability and transcriptional directionality separate functionally distinct RNA species.

Nat Commun 2014 Nov 12;5:5336. Epub 2014 Nov 12.

The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark.

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http://www.nature.com/articles/ncomms6336
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http://dx.doi.org/10.1038/ncomms6336DOI Listing
November 2014

Identification of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2.

DNA Res 2014 Dec 2;21(6):569-83. Epub 2014 Jul 2.

The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, Copenhagen DK-2200, Denmark

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http://dx.doi.org/10.1093/dnares/dsu022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263293PMC
December 2014

Nucleosome regulatory dynamics in response to TGFβ.

Nucleic Acids Res 2014 Jun 25;42(11):6921-34. Epub 2014 Apr 25.

Science for Life Laboratory, Department of Immunology, Genetics and Pathology, BMC, Box 815, Uppsala University, SE-75108 Uppsala, Sweden

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gku326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066760PMC
June 2014

Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions.

Mol Genet Metab 2014 May 16;112(1):73-83. Epub 2013 Dec 16.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK; The University of Queensland Northside Clinical School, Prince Charles Hospital, Chermside 4032, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.ymgme.2013.12.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4019825PMC
May 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

Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality.

Nat Struct Mol Biol 2013 Aug 14;20(8):923-8. Epub 2013 Jul 14.

Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.

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http://dx.doi.org/10.1038/nsmb.2640DOI Listing
August 2013

A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements.

Algorithms Mol Biol 2012 Jan 16;7(1). Epub 2012 Jan 16.

The Linnaeus Centre for Bioinformatics, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Center, Uppsala University, Box 598, SE-75124 Uppsala, Sweden.

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http://almob.biomedcentral.com/articles/10.1186/1748-7188-7-
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http://dx.doi.org/10.1186/1748-7188-7-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371767PMC
January 2012

Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa.

BMC Cancer 2011 Oct 19;11:450. Epub 2011 Oct 19.

The Linnaeus Centre for Bioinformatics, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden.

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http://dx.doi.org/10.1186/1471-2407-11-450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216894PMC
October 2011

SICTIN: Rapid footprinting of massively parallel sequencing data.

BioData Min 2010 Aug 13;3(1). Epub 2010 Aug 13.

Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE-75124 Uppsala, Sweden.

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http://dx.doi.org/10.1186/1756-0381-3-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928217PMC
August 2010

Integrative epigenomic and genomic analysis of malignant pheochromocytoma.

Exp Mol Med 2010 Jul;42(7):484-502

Department of Surgical Sciences, Uppsala University, Uppsala University Hospital, SE-75185 Uppsala, Sweden.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912476PMC
http://dx.doi.org/10.3858/emm.2010.42.7.050DOI Listing
July 2010

Nucleosomes are well positioned in exons and carry characteristic histone modifications.

Genome Res 2009 Oct 17;19(10):1732-41. Epub 2009 Aug 17.

The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden.

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http://dx.doi.org/10.1101/gr.092353.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765275PMC
October 2009

Histone H3 lysine 27 trimethylation in adult differentiated colon associated to cancer DNA hypermethylation.

Epigenetics 2009 Feb 1;4(2):107-13. Epub 2009 Mar 1.

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

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http://dx.doi.org/10.4161/epi.4.2.8038DOI Listing
February 2009

A segmental maximum a posteriori approach to genome-wide copy number profiling.

Bioinformatics 2008 Mar 19;24(6):751-8. Epub 2008 Jan 19.

The Linnaeus Centre for Bioinformatics, Uppsala University, 751 24 Uppsala, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btn003DOI Listing
March 2008

A previously unrecognized microdeletion syndrome on chromosome 22 band q11.2 encompassing the BCR gene.

Am J Med Genet A 2007 Sep;143A(18):2178-84

Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.

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http://dx.doi.org/10.1002/ajmg.a.31882DOI Listing
September 2007