Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, Fan L, Sandelin A, Rinn JL, Regev A. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Research. 2012;22:577–591.Abstract

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. Nature Structural & Molecular Biology. 2011;18:1075–1082.Abstract

Valen E, Sandelin A. Genomic and chromatin signals underlying transcription start-site selection. Trends in Genetics. 2011.Abstract

Chen Y, Jorgensen 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. 2011;12:544.Abstract

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 research. 2011;39:7179–7193.Abstract

Zhao X, Valen E, Parker BJ, Sandelin A. Systematic clustering of transcription start site landscapes. PloS one. 2011;6:e23409.Abstract

Pansoy A, Ahmed S, Valen E, Sandelin A, Matthews J. 3-methylcholanthrene induces differential recruitment of aryl hydrocarbon receptor to human promoters. Toxicological Sciences. 2010;117:90–100.Abstract

Motti D, Le Duigou C, Eugène E, Chemaly N, Wittner L, Lazarevic D, Krmac H, Marstrand T, Valen E, Sanges R. Gene expression analysis of the emergence of epileptiform activity after focal injection of kainic acid into mouse hippocampus. European Journal of Neuroscience. 2010;32:1364–1379.Abstract

Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Research. 2010;38:D105.Abstract

Ahmed S, Valen E, Sandelin A, Matthews J. Dioxin increases the interaction between aryl hydrocarbon receptor and estrogen receptor alpha at human promoters. Toxicological Sciences. 2009;111:254.Abstract

Valen E, Sandelin A, Winther O, Krogh A. Discovery of regulatory elements is improved by a discriminatory approach. PLoS computational biology. 2009;5:e1000562.Abstract

Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome research. 2009;19:255–265.Abstract

Suzuki H, Forrest ARR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJL. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature genetics. 2009;41:553–562.Abstract

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. 2008;3:e1623.Abstract

Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, Sandelin A. A code for transcription initiation in mammalian genomes. Genome research. 2008;18:1–12.Abstract

Liu Y, Gao H, Marstrand TT, Ström A, Valen E, Sandelin A, Gustafsson J{\AA}., Dahlman-Wright K. The genome landscape of ER$\alpha$-and ER$\beta$-binding DNA regions. Proceedings of the National Academy of Sciences. 2008;105:2604.Abstract

Bryne JC, Valen E, Tang MHE, Marstrand T, Winther O, Da Piedade I, Krogh A, Lenhard B, Sandelin A. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic acids research. 2008;36:D102–D106.Abstract