TFBS: Computational framework for transcription factor binding site analysis. - Boris Lenhard; Wyeth W. Wasserman (Bioinform., 2002)

HGVbase: a curated resource describing human DNA variation and phenotype relationships. - D. Fredman; G. Munns; Daniel Rios; F. Sjöholm; Marianne Siegfried; Boris Lenhard; Heikki Lehväslaiho; Anthony J. Brookes (Nucleic Acids Res., 2004)

JASPAR: an open-access database for eukaryotic transcription factor binding profiles. - Albin Sandelin; Wynand Alkema; Pär G. Engström; Wyeth W. Wasserman; Boris Lenhard (Nucleic Acids Res., 2004)

ConSite: web-based prediction of regulatory elements using cross-species comparison. - Albin Sandelin; Wyeth W. Wasserman; Boris Lenhard (Nucleic Acids Res., 2004)

Grid Computing For The Analysis Of Regulatory Elements In Co-Regulated Sets Of Genes. - Johan Geijer; Boris Lenhard; Roxana Merino-Martinez; Gunnar Norstedt; Amilcar Flores-Morales (Parallel Process. Lett., 2004)

RNAdb - a comprehensive mammalian noncoding RNA database. - Ken C. Pang; Stuart Stephen; Pär G. Engström; Khairina Tajul-Arifin; Weisan Chen; Claes Wahlestedt; Boris Lenhard; Yoshihide Hayashizaki; John S. Mattick (Nucleic Acids Res., 2005)

A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. - Dominique Vlieghe; Albin Sandelin; Pieter J. De Bleser; Kris Vleminckx; Wyeth W. Wasserman; Frans van Roy; Boris Lenhard (Nucleic Acids Res., 2006)

RNAdb 2.0 - an expanded database of mammalian non-coding RNAs. - Ken C. Pang; Stuart Stephen; Marcel E. Dinger; Pär G. Engström; Boris Lenhard; John S. Mattick (Nucleic Acids Res., 2007)

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. - Jan Christian Bryne; Eivind Valen; Man-Hung Eric Tang; Troels Torben Marstrand; Ole Winther; Isabelle da Piedade; Anders Krogh; Boris Lenhard; Albin Sandelin (Nucleic Acids Res., 2008)

In Silico Detection of Sequence Variations Modifying Transcriptional Regulation. - Malin C. Andersen; Pär G. Engström; Stuart Lithwick; David J. Arenillas; Per Eriksson; Boris Lenhard; Wyeth W. Wasserman; Jacob Odeberg (PLoS Comput. Biol., 2008)

Translog, a web browser for studying the expression divergence of homologous genes. - Xianjun Dong; Altuna Akalin; Yogita Sharma; Boris Lenhard (BMC Bioinform., 2010)

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. - Elodie Portales-Casamar; Supat Thongjuea; Andrew T. Kwon; David J. Arenillas; Xiaobei Zhao; Eivind Valen; Dimas Yusuf; Boris Lenhard; Wyeth W. Wasserman; Albin Sandelin (Nucleic Acids Res., 2010)

OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica. - Gemma B. Danks; Coen Campsteijn; Mrutyunjaya Parida; Stephen Butcher; Harsha Doddapaneni; Bolei Fu; Raul Petrin; Raghu Metpally; Boris Lenhard; Patrick Wincker; Daniel Chourrout; Eric M. Thompson; et al. (Nucleic Acids Res., 2013)

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. - Anthony Mathelier; Xiaobei Zhao; Allen W. Zhang; François Parcy; Rebecca Worsley-Hunt; David J. Arenillas; Sorana Buchman; Chih-Yu Chen; Alice Yi Chou; Hans Ienasescu; Jonathan S. Lim; Casper Shyr; et al. (Nucleic Acids Res., 2014)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)

Two independent transcription initiation codes overlap on vertebrate core promoters. - Vanja Haberle; Nan Li; Yavor Hadzhiev; Charles Plessy; Christopher Previti; Chirag Nepal; Jochen Gehrig; Xianjun Dong; Altuna Akalin; Ana Maria Suzuki; Wilfred F. J. van IJcken; Olivier Armant; et al. (Nat., 2014)

TFBSTools: an R/bioconductor package for transcription factor binding site analysis. - Ge Tan; Boris Lenhard (Bioinform., 2016)

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. - Anthony Mathelier; Oriol Fornes; David J. Arenillas; Chih-Yu Chen; Grégoire Denay; Jessica J. Y. Lee; Wenqiang Shi; Casper Shyr; Ge Tan; Rebecca Worsley-Hunt; Allen W. Zhang; François Parcy; et al. (Nucleic Acids Res., 2016)

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. - Aziz Khan 001; Oriol Fornes; Arnaud Stigliani; Marius Gheorghe; Jaime Abraham Castro-Mondragón; Robin van der Lee; Adrien Bessy; Jeanne Chèneby; Shubhada R. Kulkarni; Ge Tan; Damir Baranasic; David J. Arenillas; et al. (Nucleic Acids Res., 2018)

A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates. - Alexander J. Nash; Boris Lenhard (Bioinform., 2019)

CNEr: A toolkit for exploring extreme noncoding conservation. - Ge Tan; Dimitris Polychronopoulos; Boris Lenhard (PLoS Comput. Biol., 2019)

JASPAR 2020: update of the open-access database of transcription factor binding profiles. - Oriol Fornes; Jaime Abraham Castro-Mondragón; Aziz Khan 001; Robin van der Lee; Xi Zhang; Phillip Andrew Richmond; Bhavi P. Modi; Solenne Correard; Marius Gheorghe; Damir Baranasic; Walter Santana-Garcia; Ge Tan; et al. (Nucleic Acids Res., 2020)

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. - Jaime Abraham Castro-Mondragón; Rafael Riudavets Puig; Ieva Rauluseviciute; Roza Berhanu lemma; Laura Turchi; Romain Blanc-Mathieu; Jeremy Lucas; Paul Boddie; Aziz Khan 001; Nicolás Manosalva Pérez; Oriol Fornes; Tiffany Y. Leung; et al. (Nucleic Acids Res., 2022)

Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation. - Sarvesh Nikumbh; Boris Lenhard (PLoS Comput. Biol., 2023)