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Lenhard B and Sternberg MJE. (2020). Computational Resources for Molecular Biology: Special Issue 2020. Journal of Molecular Biology, 431(13), 2395.

Bonetti A, Agostini F, Suzuki AM, Hashimoto K, Pascarella G, Gimenez J, Roos L, Nash AJ, Ghilotti M, Cameron CJF, Valentine M, Medvedeva YA, Nogucki S, Agirre E, Kashi K, Luginbuhl J, Cazzoli R, Agrawal S, Luscombe NM, Blanchette M, Kasukawa T, De Hoon M, Arner E, Lenhard B, Plessy C, Castelo-Branco G, Orlando V, Carninci P. (2020). RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions. Nature Communications, doi.org/10.1038/s41467-020-14337-6.

Nepal C, Hadzhiev Y, Balwierz P, Tarifeno-Saldivia E, Cardenas R, Wragg JW, Suzuki A-M, Carninci P, Peers B, Lenhard B, Andersen JB, Muller F. (2020). Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing. Nature Communications, 11(168).

Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Baranasic D, Santana-Garcia W, Tan G, Cheneby J, Ballester B, Parcy F, Sandelin A, Lenhard B, Wasserman WW, Mathelier A. (2020). JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acid Research, doi.org/10.1093/nar/gkz1001.

Baresic A, Nash AJ, Dahoun T, Howes O and Lenhard B. (2020). Understanding the genetics of neuropsychiatric disorders: the potential role of genomic regulatory blocks. Nature Molecular Psychiatry 25, 6–18.

Nash AJ and Lenhard B. (2019). A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates. Bioinformatics 35 (14), 2354–2361.

Newton MD, Taylor BJ, Driessen RPC, Roos L, Cvetesic N, Allyjaun S, Lenhard B, Cuomo ME & Rueda DS. (2019). DNA stretching induces Cas9 off-target activity. Nature Structural & Molecular Biology, doi: 10.1038/s41594-019-0188-z

Börlin CS, Cvetesic N, Holland P, Bergenholm D, Siewers V, Lenhard B, Nielsen J. (2018). Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions. FEMS Yeast Research, doi.org/10.1093/femsyr/foy128

Nash AJ and Lenhard B. (2018). A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates. Bioinformatics, doi: 10.1093/bioinformatics/bty1014

Cvetesic N, Leitch HG, Borkowska M, Muller F, Carninci P, Hajkova P, Lenhard B. (2018). SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA. Genome Research, doi:10.1101/gr.235937.118

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A. (2017). JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic acids research 46(D1), D260-D266.

Harmston N, Ing-Simmons E, Tan G, Perry M, Merkenschlager M, Lenhard B. (2017). Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation. Nature communications 8(1), 441.

Polychronopoulos D, King JWD, Nash AJ, Tan G, Lenhard B. (2017). Conserved non-coding elements: developmental gene regulation meets genome organization. Nucleic acids research 45(22), 12611-12624.

Cvetesic N, Lenhard B. (2017). Core promoters across the genome. Nature biotechnology 35(2), 123.

Haberle V, Forrest AR, Hayashizaki Y, Carninci P, Lenhard B. (2015). CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Nucleic Acids Res pii: gkv054. [Epub ahead of print].

Ing-Simmons E, Seitan VC, Faure AJ, Flicek P, Carroll T, Dekker J, Fisher AG, Lenhard B, Merkenschlager M. (2015). Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin. Genome Res [Epub ahead of print].

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Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C, Gehrig J, Dong X, Akalin A, Suzuki AM, van IJcken WFJ, Armant O, Ferg M, Strähle U, Carninci P, Müller F, Lenhard B. (2014). Two independent transcription initiation codes overlap on vertebrate core promoters. Nature 507(7492), 381–385.