Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva Rauluseviciute, …, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, Anthony Mathelier. (2021). JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Research 50 (D1), D165-D173

Ana R López-Pérez, Piotr J Balwierz, Boris Lenhard, Ferenc Muller, Fiona C Wardle, Isabelle Manfroid, Marianne L Voz, Bernard Peers. (2021). Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics. Nature Scientific Reports 11 (1), 1-16

Bernd B Zeisig, Tsz Kan Fung, Magdalena Zarowiecki, …, Boris Lenhard, Suming Huang, Ghulam J Mufti, Chi Wai Eric So. (2021). Functional reconstruction of human AML reveals stem cell origin and vulnerability of treatment-resistant MLL-rearranged leukemia. Science Translational Medicine 13 (582), eabc4822

José M Martín-Durán, Bruno C Vellutini, Ferdinand Marlétaz, …, Daniel Chourrout, Jose Luis Gómez-Skarmeta, Manuel Irimia, Boris Lenhard, Katrine Worsaae, Andreas Hejnol. (2021). Conservative route to genome compaction in a miniature annelid. Nature Ecology & Evolution 5 (2), 231-242

Mohammad M Karimi, Ya Guo, Xiaokai Cui, …, Boris Lenhard, Holger Heyn, Amanda G Fisher, Ondřej Štěpánek, Matthias Merkenschlager. (2021). The order and logic of CD4 versus CD8 lineage choice and differentiation in mouse thymus. Nature Communications 12 (1), 1-14

Fabio M. D’Orazio, Piotr J. Balwierz, Ada Jimenez González, Yixuan Guo, Benjamín Hernández-Rodríguez, Lucy Wheatley, Aleksandra Jasiulewicz, Yavor Hadzhiev, Juan M. Vaquerizas, Bradley Cairns, Boris Lenhard and Ferenc Müller (2021). Germ cell differentiation requires Tdrd7-dependent chromatin and transcriptome reprogramming marked by germ plasm relocalization. Developmental Cell

Antoni Beltran Marqués, Elena Pahita, Subhanita Ghosh, Boris Lenhard, Peter Sarkies. (2021). Integrator is recruited to promoter-proximally paused RNA Pol II to generate Caenorhabditis elegans piRNA precursors. The EMBO Journal 40, e105564

Liam McAllan, Damir Baranasic, Sergio Villicana, …, Boris Lenhard, Rachel L Batterham, Jordana Bell, John Chambers, Jaspal Kooner, William Robert Scott. (2021) Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes. medRxiv

Livia Lopez-Noriega, Rebecca Callingham, Aida Martinez-Sánchez, Grazia Pizza, Nejc Haberman, Nevena Cvetesic, Marie-Sophie Nguyen-Tu, Boris Lenhard, Piero Marchetti, Lorenzo Piemonti, Eelco de Koning, AM James Shapiro, Paul R Johnson, Isabelle Leclerc, Timothy J Pullen, Guy A Rutter. (2021) The long non-coding RNA Pax6os1/PAX6-AS1 modulates pancreatic β-cell identity and function. bioRxiv

Changwei Yu, Nevena Cvetesic, Vincent Hisler, Kapil Gupta, Tao Ye, Emese Gazdag, Luc Negroni, Petra Hajkova, Imre Berger, Boris Lenhard, Ferenc Müller, Stéphane D Vincent, László Tora. (2020). TBPL2/TFIIA complex establishes the maternal transcriptome through oocyte-specific promoter usage. Nature Communications 11 (1), 1-13

Changwei Yu, Nevena Cvetesic, Kapil Gupta, Tao Ye, Emese Gazdag, Vincent Hisler, Luc Negroni, Petra Hajkova, Boris Lenhard, Ferenc Müller, Imre Berger, Stéphane Vincent, Làszlo Tora. (2020). TBPL2/TFIIA complex overhauls oocyte transcriptome during oocyte growth. HAL open science

Wragg JW, Roos L, Vucenovic D, Cvetesic N, Lenhard B and Müller F. (2020). Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-associated core promoter regulation. Nucleic Acids Research

Jordan A. Ramilowski, Chi Wai Yip, Saumya Agrawal, … ,Boris Lenhard, Claudio Schneider, Harukazu Suzuki, Ken Yagi, Michiel J.L. de Hoon, Jay W. Shin and Piero Carninci (2020). Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Research

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

Chirag Nepal, Andrzej Taranta, Yavor Hadzhiev, Sachin Pundhir, Piotr Mydel, Boris Lenhard, FerencMüller, Jesper B.Andersen. (2020). Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans. Cell iScience

Samuel H Lewis, Laura Ross, Stevie A Bain, Eleni Pahita, Stephen A Smith, Richard Cordaux, Eric A Miska, Boris Lenhard, Francis M Jiggins, Peter Sarkies. (2020) Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods. PLOS Genetics 16 (6), e1008864

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 Research 

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 Research

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.