Current large-scale projects the group is involved with:

  • FANTOM6: Functional annotation of lncRNAs using CAGE and perturbation experiments.
  • ZENCODE: Marie-Curie HO20 initial training program to understand genome regulation in Zebrafish.
  • DANIOCODE: An international collaboration that aims to annotate the functional elements of the zebrafish genome.

Resources developed by the group:

  • ANCORA: Genome-wide visualisation of highly conserved noncoding element densities.
  • Synorth: Web resource for exploring genomic regulatory blocks.
  • JASPAR: Open database of high quality transcription factor binding profiles.
  • TFBS: Perl modules for transcription factor binding site detection and analysis.
  • Lenhard group Genome Browser (access restricted to collaborators)

R/bioconductor packages developed by the group:

  • r3Cseq: 3C-seq analysis in R.
  • CAGEr: Analysis of cap analysis of gene expression data.
  • TFBStools: Analysis and manipulation of TFBS and TF profile matrices.
  • CNEr: Detection and analysis of Conserved Noncoding Elements.
  • TFMPvalue: Efficient and accurate P-value computation for Position Weight Matrices
  • GenomicInteractions: Bioconductor package for exploring chromatin interaction data.

Recent publications:

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

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 2020Journal 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 transCell iScience

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 interactionsNature 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 processingNature 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 profilesNucleic 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 blocksNature Molecular Psychiatry 25, 6–18.

Nash AJ and Lenhard B. (2019). A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primatesBioinformatics 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 activityNature 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 conditionsFEMS 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 frameworkNucleic 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 conservationNature communications 8(1), 441.

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

Cvetesic N, Lenhard B. (2017). Core promoters across the genomeNature 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 cohesinGenome Research

FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva, ……..  Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y. (2014). A promoter-level mammalian expression atlas. Nature 507(7493), 462–470. doi: 10.1038/nature13182.

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 promotersNature 507(7492), 381–385.

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