Preprints
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
biorxiv
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