Valen Group | Publications


O Begik, G Diensthuber, H Liu, A Delgado-Tejedor, C Kontur, AM Niazi, E Valen, AJ Giraldez, J-D Beaudoin, JS Mattick, EM Novoa
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing


Publications 2022

TT Bizuayehu, K Labun, M Jakubec, K Jefimov, A Niazi, E Valen
Long-read Single-Molecule RNA Structure Sequencing using nanopore
Nucleic Acids Research
Pubmed 36166000


Publications 2021

Reint G. et al.
Rapid genome editing by CRISPR-Cas9-POLD3 fusion
eLife 10
Pubmed 34898428

H Tjeldnes, K Labun, YNT Cleuren, K Chyżyńyska, M Świrski, E Valen
ORFik: a comprehensive R toolkit for the analysis of translation
BMC Bioinformatics 22
Pubmed 34147079

K Labun, M Krause, Y Torres Cleuren, E Valen
CRISPR Genome Editing Made Easy Through the CHOPCHOP Website
Current Protocols 1 (4), e46
Pubmed 33905612

AM Niazi, M Krause, E Valen
Transcript Isoform-Specific Estimation of Poly (A) Tail Length by Nanopore Sequencing of Native RNA.
Methods in Molecular Biology 2284, 543-567
Pubmed 33835463

K Chyżyńska, K Labun, C Jones, SN Grellscheid, E Valen
Deep conservation of ribosome stall sites across RNA processing genes
NAR genomics and bioinformatics 3 (2)
Pubmed 34056595


Publications 2020

DB Poduval, E Ognedal, Z Sichmanova, E Valen, et al.
Assessment of tumor suppressor promoter methylation in healthy individuals
Clinical epigenetics 12 (1), 1-15
Pubmed 32859265

Giess A, Torres Cleuren YN, Tjeldnes H, Krause M, Bizuayehu TT, Hiensch S, Okon A, Wagner CR, Valen E
Profiling of Small Ribosomal Subunits Reveals Modes and Regulation of Translation Initiation
Cell Reports 31 (3)
Pubmed 32320657

Pálfy M, Schulze G, Valen E, Vastenhouw NL
Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation
PLoS Genetics 16 (1), e1008546
Pubmed 31940339

Svalastoga P, Sulen Å, Fehn JR, Aukland SM, Irgens H, Sirnes E, Fevang SKE, Valen E, Elgen IB, Njølstad PR
Intellectual Disability in KATP Channel Neonatal Diabetes
Diabetes Care
Pubmed 31932458


Publications 2019

Danks GB, Galbiati H, Raasholm M, Torres Cleuren YN, Valen E, Navratilova P, Thompson EM
Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR.
BMC Genomics 20, Article number: 908
Pubmed 31783727

Labun K, Montague TG, Krause M, Torres Cleuren YN, Tjeldnes H, Valen E
CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing
Nucleic Acids Research, W171-174
Pubmed 31106371

Labun K, Guo X, Chavez A, Church G, Gagnon JA, Valen E
Accurate analysis of genuine CRISPR editing events with ampliCan
Genome research, gr. 244293.118
PubMed 30850374

Krause M, Niazi AM, Labun K, Torres Cleuren YN, Müller FS, Valen E
tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing
RNA, 1229-1241
PubMed 31266821


Publications 2018

Birkeland Å, ChyŻyńska K, Valen E
Shoelaces: an interactive tool for ribosome profiling processing and visualization
BMC Genomics, 19:543
PubMed 30021517


Publications 2017

Giess A, Jonckheere V, Ndah E, Chyżyńska K, Van Damme P, Valen E
Ribosome signatures aid bacterial translation initiation site identification
BMC Biol, 15 (1), 76
PubMed 28854918

Ndah E,  Jonckheere V, Giess A, Valen E, Menschaert G, Van Damme P
REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes
Nucleic Acids Research, Volume 45, Issue 20,
PubMed 28977509


Publications 2016

Labun K, Montague TG, Gagnon JA, Thyme SB, Valen E
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.
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
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
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
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.
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
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
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
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
Toddler: an embryonic signal that promotes cell movement via Apelin receptors
Science, 343 (6172), 1248636
PubMed 24407481

Pauli A, Valen E, Schier AF
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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.
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
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
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
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
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
A code for transcription initiation in mammalian genomes
Genome Res, 18 (1), 1-12
PubMed 18032727