Publications by authors named "Eivind Valen"

41Publications

Assessment of tumor suppressor promoter methylation in healthy individuals.

Clin Epigenetics 2020 Aug 28;12(1):131. Epub 2020 Aug 28.

K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.

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http://dx.doi.org/10.1186/s13148-020-00920-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7455917PMC
August 2020

Profiling of Small Ribosomal Subunits Reveals Modes and Regulation of Translation Initiation.

Cell Rep 2020 Apr;31(3):107534

Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway; Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5008, Norway. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.107534DOI Listing
April 2020

Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation.

PLoS Genet 2020 01 15;16(1):e1008546. Epub 2020 Jan 15.

Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.

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http://dx.doi.org/10.1371/journal.pgen.1008546DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986763PMC
January 2020

Intellectual Disability in K Channel Neonatal Diabetes.

Diabetes Care 2020 03 13;43(3):526-533. Epub 2020 Jan 13.

Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway

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http://dx.doi.org/10.2337/dc19-1013DOI Listing
March 2020

Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR.

BMC Genomics 2019 Nov 29;20(1):908. Epub 2019 Nov 29.

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

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http://dx.doi.org/10.1186/s12864-019-6277-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883708PMC
November 2019

: alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing.

RNA 2019 10 2;25(10):1229-1241. Epub 2019 Jul 2.

Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway.

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http://dx.doi.org/10.1261/rna.071332.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800471PMC
October 2019

CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing.

Nucleic Acids Res 2019 07;47(W1):W171-W174

Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway.

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http://dx.doi.org/10.1093/nar/gkz365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602426PMC
July 2019

Accurate analysis of genuine CRISPR editing events with ampliCan.

Genome Res 2019 05 8;29(5):843-847. Epub 2019 Mar 8.

Department of Informatics/Computational Biology Unit, University of Bergen, Bergen 5008, Norway.

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http://dx.doi.org/10.1101/gr.244293.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499316PMC
May 2019

Shoelaces: an interactive tool for ribosome profiling processing and visualization.

BMC Genomics 2018 Jul 18;19(1):543. Epub 2018 Jul 18.

Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, 5008, Norway.

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http://dx.doi.org/10.1186/s12864-018-4912-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6052522PMC
July 2018

REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes.

Nucleic Acids Res 2017 Nov;45(20):e168

VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium.

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http://dx.doi.org/10.1093/nar/gkx758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714196PMC
November 2017

Ribosome signatures aid bacterial translation initiation site identification.

BMC Biol 2017 08 30;15(1):76. Epub 2017 Aug 30.

Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, 5020, Norway.

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http://dx.doi.org/10.1186/s12915-017-0416-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5576327PMC
August 2017

Internal guide RNA interactions interfere with Cas9-mediated cleavage.

Nat Commun 2016 06 10;7:11750. Epub 2016 Jun 10.

Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1038/ncomms11750DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4906408PMC
June 2016

CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering.

Nucleic Acids Res 2016 07 16;44(W1):W272-6. Epub 2016 May 16.

Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway

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http://dx.doi.org/10.1093/nar/gkw398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987937PMC
July 2016

Efficient CRISPR-Cas9-mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus.

Cell Rep 2015 May 30;11(6):875-883. Epub 2015 Apr 30.

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; The Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.04.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5533178PMC
May 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

Identifying (non-)coding RNAs and small peptides: challenges and opportunities.

Bioessays 2015 Jan 24;37(1):103-12. Epub 2014 Oct 24.

Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.

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http://dx.doi.org/10.1002/bies.201400103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4433033PMC
January 2015

Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs.

PLoS One 2014 29;9(5):e98186. Epub 2014 May 29.

Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America; Center for Brain Science, Harvard University, Cambridge, Massachusetts, United States of America; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America; Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0098186PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4038517PMC
January 2015

CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing.

Nucleic Acids Res 2014 Jul 26;42(Web Server issue):W401-7. Epub 2014 May 26.

Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA

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http://dx.doi.org/10.1093/nar/gku410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086086PMC
July 2014

ErbB2 upregulates the Na+,HCO3(-)-cotransporter NBCn1/SLC4A7 in human breast cancer cells via Akt, ERK, Src, and Kruppel-like factor 4.

FASEB J 2014 Jan 2;28(1):350-63. Epub 2013 Oct 2.

1Department of Biology, University of Copenhagen, 13, Universitetsparken, DK-2100 Copenhagen, Denmark.

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http://dx.doi.org/10.1096/fj.13-233288DOI Listing
January 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

Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs.

Development 2013 Jul 22;140(13):2828-34. Epub 2013 May 22.

Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1242/dev.098343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3678345PMC
July 2013

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.

Genome Res 2012 Mar 22;22(3):577-91. Epub 2011 Nov 22.

Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1101/gr.133009.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3290793PMC
March 2012

Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data.

BMC Genomics 2011 Nov 3;12:544. Epub 2011 Nov 3.

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

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http://dx.doi.org/10.1186/1471-2164-12-544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228824PMC
November 2011

Genomic and chromatin signals underlying transcription start-site selection.

Trends Genet 2011 Nov 15;27(11):475-85. Epub 2011 Sep 15.

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

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http://dx.doi.org/10.1016/j.tig.2011.08.001DOI Listing
November 2011

Systematic clustering of transcription start site landscapes.

PLoS One 2011 24;6(8):e23409. Epub 2011 Aug 24.

Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, Copenhagen University, Copenhagen, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0023409PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160847PMC
January 2012

Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes.

Nat Struct Mol Biol 2011 Aug 7;18(9):1075-82. Epub 2011 Aug 7.

The Bioinformatics Centre, Department of Biology and the Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1038/nsmb.2091DOI Listing
August 2011

PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters.

Nucleic Acids Res 2011 Sep 19;39(16):7179-93. Epub 2011 May 19.

Department of Molecular Biology, Centre for mRNP Biogenesis and Metabolism, Aarhus University, C.F. Møllers Allé, Building 1130, 8000 Aarhus, Denmark.

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http://dx.doi.org/10.1093/nar/gkr370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167610PMC
September 2011

3-methylcholanthrene induces differential recruitment of aryl hydrocarbon receptor to human promoters.

Toxicol Sci 2010 Sep 26;117(1):90-100. Epub 2010 Mar 26.

Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/toxsci/kfq096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5148624PMC
September 2010

Discovery of regulatory elements is improved by a discriminatory approach.

PLoS Comput Biol 2009 Nov 13;5(11):e1000562. Epub 2009 Nov 13.

The Bioinformatics Centre, Department of Biology and the Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1371/journal.pcbi.1000562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770120PMC
November 2009

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

Dioxin increases the interaction between aryl hydrocarbon receptor and estrogen receptor alpha at human promoters.

Toxicol Sci 2009 Oct 2;111(2):254-66. Epub 2009 Jul 2.

Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.

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http://dx.doi.org/10.1093/toxsci/kfp144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2999625PMC
October 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

Asap: a framework for over-representation statistics for transcription factor binding sites.

PLoS One 2008 Feb 20;3(2):e1623. Epub 2008 Feb 20.

Bioinformatics Centre, Department of Molecular Biology and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001623PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2229843PMC
February 2008

The genome landscape of ERalpha- and ERbeta-binding DNA regions.

Proc Natl Acad Sci U S A 2008 Feb 13;105(7):2604-9. Epub 2008 Feb 13.

Department of Biosciences and Nutrition, Karolinska Institutet, Novum, SE-14157 Huddinge, Sweden.

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http://dx.doi.org/10.1073/pnas.0712085105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2268183PMC
February 2008

A code for transcription initiation in mammalian genomes.

Genome Res 2008 Jan 21;18(1):1-12. Epub 2007 Nov 21.

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

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http://dx.doi.org/10.1101/gr.6831208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134772PMC
January 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