Boris Lenhard

Boris Lenhard

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Boris Lenhard

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CNEr: A toolkit for exploring extreme noncoding conservation.

PLoS Comput Biol 2019 Aug 26;15(8):e1006940. Epub 2019 Aug 26.

Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1006940DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6730951PMC
August 2019

A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates.

Bioinformatics 2019 Jul;35(14):2354-2361

Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences.

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http://dx.doi.org/10.1093/bioinformatics/bty1014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612856PMC
July 2019

Computation Resources for Molecular Biology: Special Issue 2019.

J Mol Biol 2019 Jun 30;431(13):2395-2397. Epub 2019 May 30.

Structural Bioinformatics Group, Centre for Integrative systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.05.034DOI Listing
June 2019

Transcription Start Site Mapping Using Super-low Input Carrier-CAGE.

J Vis Exp 2019 Jun 26(148). Epub 2019 Jun 26.

Institute of Clinical Sciences, Faculty of Medicine, Imperial College London; MRC London Institute of Medical Sciences; Sars International Centre for Marine Molecular Biology, University of Bergen;

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http://dx.doi.org/10.3791/59805DOI Listing
June 2019

Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions.

FEMS Yeast Res 2019 03;19(2)

Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden.

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http://dx.doi.org/10.1093/femsyr/foy128DOI Listing
March 2019

DNA stretching induces Cas9 off-target activity.

Nat Struct Mol Biol 2019 Mar 25;26(3):185-192. Epub 2019 Feb 25.

Molecular Virology, Department of Medicine, Imperial College London, London, UK.

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http://www.nature.com/articles/s41594-019-0188-z
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http://dx.doi.org/10.1038/s41594-019-0188-zDOI Listing
March 2019

SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA.

Genome Res 2018 12 7;28(12):1943-1956. Epub 2018 Nov 7.

Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.235937.118
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http://dx.doi.org/10.1101/gr.235937.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6280763PMC
December 2018

Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome.

Genome Res 2018 05 4;28(5):676-688. Epub 2018 Apr 4.

The Francis Crick Institute, London NW1 1AT, United Kingdom.

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http://dx.doi.org/10.1101/gr.231449.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5932608PMC
May 2018

Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate.

BMC Genomics 2018 02 26;19(1):164. Epub 2018 Feb 26.

Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5006, Norway.

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http://dx.doi.org/10.1186/s12864-018-4504-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389100PMC
February 2018

Conserved non-coding elements: developmental gene regulation meets genome organization.

Nucleic Acids Res 2017 Dec;45(22):12611-12624

Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.

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http://dx.doi.org/10.1093/nar/gkx1074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5728398PMC
December 2017

Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation.

Nat Commun 2017 09 5;8(1):441. Epub 2017 Sep 5.

Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, W12 0NN, UK.

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http://dx.doi.org/10.1038/s41467-017-00524-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5585340PMC
September 2017

Core promoters across the genome.

Nat Biotechnol 2017 02;35(2):123-124

Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK, and the MRC London Institute of Medical Sciences, London, UK.

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http://dx.doi.org/10.1038/nbt.3788DOI Listing
February 2017

Allele-specific analysis of cell fusion-mediated pluripotent reprograming reveals distinct and predictive susceptibilities of human X-linked genes to reactivation.

Genome Biol 2017 01 25;18(1). Epub 2017 Jan 25.

Lymphocyte Development Group, MRC London Institute of Medical Sciences, Hammersmith Campus, Imperial College London, Du Cane Road, London, W12 0NN, UK.

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http://dx.doi.org/10.1186/s13059-016-1136-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5264468PMC
January 2017

Promoter architectures and developmental gene regulation.

Semin Cell Dev Biol 2016 09 16;57:11-23. Epub 2016 Jan 16.

Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK. Electronic address:

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http://dx.doi.org/10.1016/j.semcdb.2016.01.014DOI Listing
September 2016

TFBSTools: an R/bioconductor package for transcription factor binding site analysis.

Bioinformatics 2016 05 21;32(10):1555-6. Epub 2016 Jan 21.

Computational Regulatory Genomics, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK.

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http://dx.doi.org/10.1093/bioinformatics/btw024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866524PMC
May 2016

Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs.

Nucleic Acids Res 2016 Apr 15;44(7):3070-81. Epub 2015 Dec 15.

Institute of Clinical Sciences MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK Department of Informatics, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway

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http://dx.doi.org/10.1093/nar/gkv1354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838339PMC
April 2016

Naturally Occurring Isoleucyl-tRNA Synthetase without tRNA-dependent Pre-transfer Editing.

J Biol Chem 2016 Apr 26;291(16):8618-31. Epub 2016 Feb 26.

From the Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia and

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http://dx.doi.org/10.1074/jbc.M115.698225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4861432PMC
April 2016

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.

Nucleic Acids Res 2016 Jan 3;44(D1):D110-5. Epub 2015 Nov 3.

Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, BC, Canada

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http://dx.doi.org/10.1093/nar/gkv1176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702842PMC
January 2016

Targeting Aberrant Epigenetic Networks Mediated by PRMT1 and KDM4C in Acute Myeloid Leukemia.

Cancer Cell 2016 Jan;29(1):32-48

Leukemia and Stem Cell Biology Group, Division of Cancer Studies, Department of Haematological Medicine, King's College London, Denmark Hill Campus, London SE5 9NU, UK. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2015.12.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4712026PMC
January 2016

GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data.

BMC Genomics 2015 Nov 17;16:963. Epub 2015 Nov 17.

Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, W12 0NN, UK.

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http://dx.doi.org/10.1186/s12864-015-2140-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650858PMC
November 2015

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses.

Nucleic Acids Res 2015 Apr 4;43(8):e51. Epub 2015 Feb 4.

Department of Molecular Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London and MRC Clinical Sciences Centre, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK Department of Informatics, University of Bergen, Høyteknologisenteret, Thormøhlensgate 55, N-5008 Bergen, Norway

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http://dx.doi.org/10.1093/nar/gkv054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417143PMC
April 2015

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin.

Genome Res 2015 Apr 12;25(4):504-13. Epub 2015 Feb 12.

Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom;

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http://dx.doi.org/10.1101/gr.184986.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381522PMC
April 2015

Trans-splicing and operons in metazoans: translational control in maternally regulated development and recovery from growth arrest.

Mol Biol Evol 2015 Mar 17;32(3):585-99. Epub 2014 Dec 17.

Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway Department of Biology, University of Bergen, Bergen, Norway

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http://dx.doi.org/10.1093/molbev/msu336DOI Listing
March 2015

Computational characterization of modes of transcriptional regulation of nuclear receptor genes.

PLoS One 2014 13;9(2):e88880. Epub 2014 Feb 13.

Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, and MRC Clinical Sciences Centre, London, United Kingdom ; Department of Informatics, University of Bergen, Bergen, Norway.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0088880PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3923872PMC
October 2014

Two independent transcription initiation codes overlap on vertebrate core promoters.

Nature 2014 Mar 16;507(7492):381-385. Epub 2014 Feb 16.

Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, United Kingdom.

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http://dx.doi.org/10.1038/nature12974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820030PMC
March 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

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.

Nucleic Acids Res 2014 Jan 4;42(Database issue):D142-7. Epub 2013 Nov 4.

Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada, Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, Copenhagen University, Ole Maaloes Vej 5, DK-2200, Denmark, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA, Laboratoire Physiologie Cellulaire & Végétale, Université Grenoble Alpes, CNRS, CEA, iRTSV, INRA, 38054 Grenoble, France, Computational Regulatory Genomics, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK, and Department of Informatics, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway.

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http://dx.doi.org/10.1093/nar/gkt997DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965086PMC
January 2014

The mystery of extreme non-coding conservation.

Philos Trans R Soc Lond B Biol Sci 2013 Dec 11;368(1632):20130021. Epub 2013 Nov 11.

Institute of Clinical Sciences, Faculty of Medicine, Imperial College London and MRC Clinical Sciences Centre, , Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.

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http://dx.doi.org/10.1098/rstb.2013.0021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3826495PMC
December 2013

The aurora B kinase and the polycomb protein ring1B combine to regulate active promoters in quiescent lymphocytes.

Mol Cell 2013 Sep;51(5):647-61

Gene Regulation and Chromatin Group, MRC Clinical Sciences Centre, Imperial College, Hammersmith Campus, London W12 0NN, UK.

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http://dx.doi.org/10.1016/j.molcel.2013.08.022DOI Listing
September 2013

Chromatin and epigenetic features of long-range gene regulation.

Nucleic Acids Res 2013 Aug 13;41(15):7185-99. Epub 2013 Jun 13.

MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London W12 0NN, UK, Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London W12 0NN, UK and Department of Informatics, University of Bergen, Thromøhlensgate 55, N-5008 Bergen, Norway.

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http://dx.doi.org/10.1093/nar/gkt499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753629PMC
August 2013

Dissecting genomic regulatory elements in vivo.

Nat Biotechnol 2012 Jun 7;30(6):504-6. Epub 2012 Jun 7.

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http://www.nature.com/articles/nbt.2266
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http://dx.doi.org/10.1038/nbt.2266DOI Listing
June 2012

Metazoan promoters: emerging characteristics and insights into transcriptional regulation.

Nat Rev Genet 2012 Mar 6;13(4):233-45. Epub 2012 Mar 6.

Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.

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http://dx.doi.org/10.1038/nrg3163DOI Listing
March 2012

Making enhancers from spare parts of the genome.

Genome Biol 2011 Dec 29;12(12):138. Epub 2011 Dec 29.

Institute of Clinical Sciences, Imperial College London and MRC Clinical Sciences Centre, Hammersmith Hospital Campus, Du Cane Road, London, UK.

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http://dx.doi.org/10.1186/gb-2011-12-12-138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334608PMC
December 2011

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

Nucleic Acids Res 2010 Mar 6;38(4):1071-85. Epub 2009 Dec 6.

Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway.

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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/gkp1124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2831330PMC
March 2010

Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish.

Mol Genet Genomics 2010 Feb 29;283(2):171-84. Epub 2009 Dec 29.

Sars Centre for Marine Molecular Biology, University of Bergen, 5008, Bergen, Norway.

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http://dx.doi.org/10.1007/s00438-009-0503-1DOI Listing
February 2010

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles.

Nucleic Acids Res 2010 Jan 11;38(Database issue):D105-10. Epub 2009 Nov 11.

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

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http://dx.doi.org/10.1093/nar/gkp950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808906PMC
January 2010

Translog, a web browser for studying the expression divergence of homologous genes.

BMC Bioinformatics 2010 Jan 18;11 Suppl 1:S59. Epub 2010 Jan 18.

Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-11-S1-S59DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009532PMC
January 2010

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes.

Genome Biol 2009 21;10(8):R86. Epub 2009 Aug 21.

Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway.

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http://dx.doi.org/10.1186/gb-2009-10-8-r86DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745767PMC
October 2009

CpG-depleted promoters harbor tissue-specific transcription factor binding signals--implications for motif overrepresentation analyses.

Nucleic Acids Res 2009 Oct 6;37(19):6305-15. Epub 2009 Sep 6.

Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin.

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http://dx.doi.org/10.1093/nar/gkp682DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770660PMC
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.

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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

Web-based tools and approaches to study long-range gene regulation in Metazoa.

Brief Funct Genomic Proteomic 2009 Jul 15;8(4):231-42. Epub 2009 Jul 15.

University of Vienna.

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http://dx.doi.org/10.1093/bfgp/elp023DOI Listing
July 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

Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes.

Dev Biol 2009 Mar 12;327(2):526-40. Epub 2008 Nov 12.

Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway.

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http://dx.doi.org/10.1016/j.ydbio.2008.10.044DOI Listing
March 2009

Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes.

Genome Biol 2008 15;9(2):R34. Epub 2008 Feb 15.

Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate, N-5008 Bergen, Norway.

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http://dx.doi.org/10.1186/gb-2008-9-2-r34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2374709PMC
May 2008

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.

Nucleic Acids Res 2008 Jan 15;36(Database issue):D102-6. Epub 2007 Nov 15.

Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway.

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http://dx.doi.org/10.1093/nar/gkm955DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238834PMC
January 2008

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

Authors:
Chisato Yamasaki Katsuhiko Murakami Yasuyuki Fujii Yoshiharu Sato Erimi Harada Jun-ichi Takeda Takayuki Taniya Ryuichi Sakate Shingo Kikugawa Makoto Shimada Motohiko Tanino Kanako O Koyanagi Roberto A Barrero Craig Gough Hong-Woo Chun Takuya Habara Hideki Hanaoka Yosuke Hayakawa Phillip B Hilton Yayoi Kaneko Masako Kanno Yoshihiro Kawahara Toshiyuki Kawamura Akihiro Matsuya Naoki Nagata Kensaku Nishikata Akiko Ogura Noda Shin Nurimoto Naomi Saichi Hiroaki Sakai Ryoko Sanbonmatsu Rie Shiba Mami Suzuki Kazuhiko Takabayashi Aiko Takahashi Takuro Tamura Masayuki Tanaka Susumu Tanaka Fusano Todokoro Kaori Yamaguchi Naoyuki Yamamoto Toshihisa Okido Jun Mashima Aki Hashizume Lihua Jin Kyung-Bum Lee Yi-Chueh Lin Asami Nozaki Katsunaga Sakai Masahito Tada Satoru Miyazaki Takashi Makino Hajime Ohyanagi Naoki Osato Nobuhiko Tanaka Yoshiyuki Suzuki Kazuho Ikeo Naruya Saitou Hideaki Sugawara Claire O'Donovan Tamara Kulikova Eleanor Whitfield Brian Halligan Mary Shimoyama Simon Twigger Kei Yura Kouichi Kimura Tomohiro Yasuda Tetsuo Nishikawa Yutaka Akiyama Chie Motono Yuri Mukai Hideki Nagasaki Makiko Suwa Paul Horton Reiko Kikuno Osamu Ohara Doron Lancet Eric Eveno Esther Graudens Sandrine Imbeaud Marie Anne Debily Yoshihide Hayashizaki Clara Amid Michael Han Andreas Osanger Toshinori Endo Michael A Thomas Mika Hirakawa Wojciech Makalowski Mitsuteru Nakao Nam-Soon Kim Hyang-Sook Yoo Sandro J De Souza Maria de Fatima Bonaldo Yoshihito Niimura Vladimir Kuryshev Ingo Schupp Stefan Wiemann Matthew Bellgard Masafumi Shionyu Libin Jia Danielle Thierry-Mieg Jean Thierry-Mieg Lukas Wagner Qinghua Zhang Mitiko Go Shinsei Minoshima Masafumi Ohtsubo Kousuke Hanada Peter Tonellato Takao Isogai Ji Zhang Boris Lenhard Sangsoo Kim Zhu Chen Ursula Hinz Anne Estreicher Kenta Nakai Izabela Makalowska Winston Hide Nicola Tiffin Laurens Wilming Ranajit Chakraborty Marcelo Bento Soares Maria Luisa Chiusano Yutaka Suzuki Charles Auffray Yumi Yamaguchi-Kabata Takeshi Itoh Teruyoshi Hishiki Satoshi Fukuchi Ken Nishikawa Sumio Sugano Nobuo Nomura Yoshio Tateno Tadashi Imanishi Takashi Gojobori

Nucleic Acids Res 2008 Jan 18;36(Database issue):D793-9. Epub 2007 Dec 18.

Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan.

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http://dx.doi.org/10.1093/nar/gkm999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238988PMC
January 2008

In silico detection of sequence variations modifying transcriptional regulation.

PLoS Comput Biol 2008 Jan 27;4(1):e5. Epub 2007 Nov 27.

Department of Gene Technology, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), Stockholm, Sweden.

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http://dx.doi.org/10.1371/journal.pcbi.0040005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2211530PMC
January 2008

Genomic regulatory blocks underlie extensive microsynteny conservation in insects.

Genome Res 2007 Dec 7;17(12):1898-908. Epub 2007 Nov 7.

Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen 5008, Norway.

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http://www.genome.org/cgi/doi/10.1101/gr.6669607
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http://dx.doi.org/10.1101/gr.6669607DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099597PMC
December 2007

The random versus fragile breakage models of chromosome evolution: a matter of resolution.

Mol Genet Genomics 2007 Nov 13;278(5):487-91. Epub 2007 Sep 13.

Sars Centre, University of Bergen, Bergen, Norway.

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http://link.springer.com/10.1007/s00438-007-0287-0
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http://dx.doi.org/10.1007/s00438-007-0287-0DOI Listing
November 2007

Mammalian microRNA prediction through a support vector machine model of sequence and structure.

PLoS One 2007 Sep 26;2(9):e946. Epub 2007 Sep 26.

Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000946PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1978525PMC
September 2007

Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters.

Genome Biol 2006 17;7(8):R78. Epub 2006 Aug 17.

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1186/gb-2006-7-8-R78DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779604PMC
June 2007

Mammalian RNA polymerase II core promoters: insights from genome-wide studies.

Nat Rev Genet 2007 Jun 8;8(6):424-36. Epub 2007 May 8.

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://www.nature.com/articles/nrg2026
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http://dx.doi.org/10.1038/nrg2026DOI Listing
June 2007

RNAdb 2.0--an expanded database of mammalian non-coding RNAs.

Nucleic Acids Res 2007 Jan 1;35(Database issue):D178-82. Epub 2006 Dec 1.

ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia.

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http://dx.doi.org/10.1093/nar/gkl926DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1751534PMC
January 2007

A global genomic transcriptional code associated with CNS-expressed genes.

Exp Cell Res 2006 Oct 21;312(16):3108-19. Epub 2006 Jun 21.

Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institute, S-171, 77 Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.yexcr.2006.06.017DOI Listing
October 2006