• K Labun, TG Montague, JA Gagnon, SB Thyme and E Valen. CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. Nucleic Acids Research
  • SB Thyme, L Akhmetova, TG Montague, E Valen & AF Schier. Internal guide RNA interactions interfere with Cas9-mediated cleavage. Nature Communications


  • F Merkle et al. Efficient CRISPR-Cas9-Mediated Generation of Knockin Human Pluripotent Stem Cells Lacking Undesired Mutations at the Targeted Locus. Cell Reports
  • A Pauli, E Valen and AF Schier.  Identifying (non‐) coding RNAs and small peptides: Challenges and opportunities. Bioessays


  • TG Montague, JM Cruz, JA Gagnon, GM Church and E Valen. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Research
  • R. Andersson et al. Nuclear stability and transcriptional directionality separate functionally distinct RNA species. Nature Communications
  • JA Gagnon, E Valen et al. Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS ONE
  • A Pauli, ML Norris, E Valen et al. Toddler: an embryonic signal that promotes cell movement via apelin receptors. Science
  • The Fantom Consortium. A promoter-level mammalian expression atlas. Nature
  • R Andersson et al. An atlas of active enhancers across human cell types and tissues. Nature
  • JS Pedersen, E Valen et al. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Research
  • A Gorbatenko et al. ErbB2 upregulates the Na+, HCO3−-cotransporter NBCn1/SLC4A7 in human breast cancer cells via Akt, ERK, Src, and Krüppel-like factor 4. The FASEB Journal


  • E Ntini et al. Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality. Nature Structural & Molecular Biology
  • GL Chew, A Pauli, JL Rinn, A Regev, AF Schier and E Valen. Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs. Development
  • A Gorbatenko, C Olesen, E Valen and SF Pedersen. Regulation of the Na+, HCO3-cotransporter NBCn1 (SLC4A7) by a constitutively active ErbB2 receptor in MCF-7 breast cancer cells. The FASEB Journal


  • A Pauli, E Valen et al. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Research


  • E Valen and A Sandelin. Genomic and chromatin signals underlying transcription start-site selection. Trends in Genetics
  • Y Chen et al. Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data. BMC Genomics
  • P Preker et al. PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters.  Nucleic Acids Research
  • E Valen et al. Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes. Nature Structural & Molecular Biology
  • X Zhao, E Valen, BJ Parker, A Sandelin. Systematic clustering of transcription start site landscapes. PLoS ONE


  •  D Motti et al. Gene expression analysis of the emergence of epileptiform activity after focal injection of kainic acid into mouse hippocampus. European Journal of Neuroscience
  • A Pansoy et al. 3-methylcholanthrene induces differential recruitment of aryl hydrocarbon receptor to human promoters. Toxicological Sciences


  •  E Valen, A Sandelin, O Winther and A Krogh. Discovery of regulatory elements is improved by a discriminatory approach. PLoS Computational Biology
  • E Portales-Casamar et al. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Research
  • H Suzuki. et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics
  • E Valen et al. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Research
  • S Ahmed, E Valen, A Sandelin and J Matthews. Dioxin increases the interaction between aryl hydrocarbon receptor and estrogen receptor alpha at human promoters. Toxicological Sciences


  •  TT Marstrand et al. Asap: a framework for over-representation statistics for transcription factor binding sites. PLoS ONE
  • Y Liu et al. The genome landscape of ERα-and ERβ-binding DNA regions. PNAS
  • MC Frith, E Valen, A Krogh, Y Hayashizaki, P Carninci, A Sandelin. A code for transcription initiation in mammalian genomes. Genome Research
  • JC Bryne and E Valen et al. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Research