Valen Group | Publications

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Publications 2016

Labun K, Montague TG, Gagnon JA, Thyme SB, Valen E (2016)
CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering
Nucleic Acids Res, 44 (W1), W272-6
PubMed 27185894

Seale AC, Koech AC, Sheppard AE, Barsosio HC, Langat J, Anyango E, Mwakio S, Mwarumba S, Morpeth SC, Anampiu K, Vaughan A, Giess A, Mogeni P, Walusuna L, Mwangudzah H, Mwanzui D, Salim M, Kemp B, Jones C, Mturi N, Tsofa B, Mumbo E, Mulewa D, Bandika V, Soita M et al. (2016)
Maternal colonization with Streptococcus agalactiae and associated stillbirth and neonatal disease in coastal Kenya
Nat Microbiol, 1 (7), 16067
PubMed 27572968

Stokowy T, Garbulowski M, Fiskerstrand T, Holdhus R, Labun K, Sztromwasser P, Gilissen C, Hoischen A, Houge G, Petersen K, Jonassen I, Steen VM (2016)
RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data
Bioinformatics, 32 (19), 3018-20
PubMed 27288501

Thyme SB, Akhmetova L, Montague TG, Valen E, Schier AF (2016)
Internal guide RNA interactions interfere with Cas9-mediated cleavage
Nat Commun, 7, 11750
PubMed 27282953

Publications 2015

Merkle FT, Neuhausser WM, Santos D, Valen E, Gagnon JA, Maas K, Sandoe J, Schier AF, Eggan K (2015)
Efficient CRISPR-Cas9-mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus
Cell Rep, 11 (6), 875-83
PubMed 25937281

Publications 2014

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM et al. (2014)
An atlas of active enhancers across human cell types and tissues
Nature, 507 (7493), 455-61
PubMed 24670763

Andersson R, Refsing Andersen P, Valen E, Core LJ, Bornholdt J, Boyd M, Heick Jensen T, Sandelin A (2014)
Nuclear stability and transcriptional directionality separate functionally distinct RNA species
Nat Commun, 5, 5336
PubMed 25387874

Gagnon JA, Valen E, Thyme SB, Huang P, Akhmetova L, Pauli A, Montague TG, Zimmerman S, Richter C, Schier AF (2014)
Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs
PLoS One, 9 (5), e98186
PubMed 24873830

Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E (2014)
CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing
Nucleic Acids Res, 42 (Web Server issue), W401-7
PubMed 24861617

Pauli A, Norris ML, Valen E, Chew GL, Gagnon JA, Zimmerman S, Mitchell A, Ma J, Dubrulle J, Reyon D, Tsai SQ, Joung JK, Saghatelian A, Schier AF (2014)
Toddler: an embryonic signal that promotes cell movement via Apelin receptors
Science, 343 (6172), 1248636
PubMed 24407481

Pauli A, Valen E, Schier AF (2014)
Identifying (non-)coding RNAs and small peptides: challenges and opportunities
Bioessays, 37 (1), 103-12
PubMed 25345765

Publications 2013

Chew GL, Pauli A, Rinn JL, Regev A, Schier AF, Valen E (2013)
Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs
Development, 140 (13), 2828-34
PubMed 23698349

Gorbatenko A, Olesen CW, Mørup N, Thiel G, Kallunki T, Valen E, Pedersen SF (2013)
ErbB2 upregulates the Na+,HCO3(-)-cotransporter NBCn1/SLC4A7 in human breast cancer cells via Akt, ERK, Src, and Kruppel-like factor 4
FASEB J, 28 (1), 350-63
PubMed 24088818

Ntini E, Järvelin AI, Bornholdt J, Chen Y, Boyd M, Jørgensen M, Andersson R, Hoof I, Schein A, Andersen PR, Andersen PK, Preker P, Valen E, Zhao X, Pelechano V, Steinmetz LM, Sandelin A, Jensen TH(2013)
Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality
Nat Struct Mol Biol, 20 (8), 923-8
PubMed 23851456

Pedersen JS, Valen E, Velazquez AM, Parker BJ, Rasmussen M, Lindgreen S, Lilje B, Tobin DJ, Kelly TK, Vang S, Andersson R, Jones PA, Hoover CA, Tikhonov A, Prokhortchouk E, Rubin EM, Sandelin A, Gilbert MT, Krogh A, Willerslev E, Orlando L (2013)
Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
Genome Res, 24 (3), 454-66
PubMed 24299735

Publications 2011

Chen Y, Jørgensen M, Kolde R, Zhao X, Parker B, Valen E, Wen J, Sandelin A (2011)
Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data
BMC Genomics, 12, 544
PubMed 22047616

Clemente-Blanco A, Sen N, Mayan-Santos M, Sacristán MP, Graham B, Jarmuz A, Giess A, Webb E, Game L, Eick D, Bueno A, Merkenschlager M, Aragón L (2011)
Cdc14 phosphatase promotes segregation of telomeres through repression of RNA polymerase II transcription
Nat Cell Biol, 13 (12), 1450-6
PubMed 22020438

Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, Fan L, Sandelin A, Rinn JL, Regev A, Schier AF (2011)
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
Genome Res, 22 (3), 577-91
PubMed 22110045

Preker P, Almvig K, Christensen MS, Valen E, Mapendano CK, Sandelin A, Jensen TH (2011)
PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters
Nucleic Acids Res, 39 (16), 7179-93
PubMed 21596787

Valen E, Preker P, Andersen PR, Zhao X, Chen Y, Ender C, Dueck A, Meister G, Sandelin A, Jensen TH (2011)
Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes
Nat Struct Mol Biol, 18 (9), 1075-82
PubMed 21822281

Valen E, Sandelin A (2011)
Genomic and chromatin signals underlying transcription start-site selection
Trends Genet, 27 (11), 475-85
PubMed 21924514

Zhao X, Valen E, Parker BJ, Sandelin A (2011)
Systematic clustering of transcription start site landscapes
PLoS One, 6 (8), e23409
PubMed 21887249

Publications 2010

Motti D, Le Duigou C, Eugène E, Chemaly N, Wittner L, Lazarevic D, Krmac H, Marstrand T, Valen E, Sanges R, Stupka E, Sandelin A, Cherubini E, Gustincich S, Miles R (2010)
Gene expression analysis of the emergence of epileptiform activity after focal injection of kainic acid into mouse hippocampus
Eur J Neurosci, 32 (8), 1364-79
PubMed 20950280

Pansoy A, Ahmed S, Valen E, Sandelin A, Matthews J (2010)
3-methylcholanthrene induces differential recruitment of aryl hydrocarbon receptor to human promoters
Toxicol Sci, 117 (1), 90-100
PubMed 20348232

Publications 2009

Ahmed S, Valen E, Sandelin A, Matthews J (2009)
Dioxin increases the interaction between aryl hydrocarbon receptor and estrogen receptor alpha at human promoters
Toxicol Sci, 111 (2), 254-66
PubMed 19574409

FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D et al. (2009)
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
Nat Genet, 41 (5), 553-62
PubMed 19377474

Valen E, Sandelin A, Winther O, Krogh A (2009)
Discovery of regulatory elements is improved by a discriminatory approach
PLoS Comput Biol, 5 (11), e1000562
PubMed 19911049

Publications 2008

Liu Y, Gao H, Marstrand TT, Ström A, Valen E, Sandelin A, Gustafsson JA, Dahlman-Wright K (2008)
The genome landscape of ERalpha- and ERbeta-binding DNA regions
Proc Natl Acad Sci U S A, 105 (7), 2604-9
PubMed 18272478

Marstrand TT, Frellsen J, Moltke I, Thiim M, Valen E, Retelska D, Krogh A (2008)
Asap: a framework for over-representation statistics for transcription factor binding sites
PLoS One, 3 (2), e1623
PubMed 18286180

Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, Marstrand TT, Tang MH, Zhao X, Krogh A, Winther O, Arakawa T, Kawai J, Wells C, Daub C, Harbers M, Hayashizaki Y, Gustincich S, Sandelin A, Carninci P (2008)
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
Genome Res, 19 (2), 255-65
PubMed 19074369

Publications 2007

Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, Sandelin A (2007)
A code for transcription initiation in mammalian genomes
Genome Res, 18 (1), 1-12
PubMed 18032727