MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. - Anthony Mathelier; Alessandra Carbone (Bioinform., 2010)

The Next Generation of Transcription Factor Binding Site Prediction. - Anthony Mathelier; Wyeth W. Wasserman (PLoS Comput. Biol., 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)

NAR Breakthrough Article: TFBSshape: a motif database for DNA shape features of transcription factor binding sites. - Lin Yang; Tianyin Zhou; Iris Dror; Anthony Mathelier; Wyeth W. Wasserman; Raluca Gordân; Remo Rohs (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)

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. - David J. Arenillas; Alistair R. R. Forrest; Hideya Kawaji; Timo Lassmann; Wyeth W. Wasserman; Anthony Mathelier (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)

Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. - Aziz Khan 001; Anthony Mathelier (BMC Bioinform., 2017)

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. - Marina Lizio; Jayson Harshbarger; Imad Abugessaisa; Shuei Noguchi; Atsushi Kondo; Jessica Severin; Chris Mungall; David J. Arenillas; Anthony Mathelier; Yulia A. Medvedeva; Andreas Lennartsson; Finn Drabløs; et al. (Nucleic Acids Res., 2017)

JASPAR RESTful API: accessing JASPAR data from any programming language. - Aziz Khan 001; Anthony Mathelier (Bioinform., 2018)

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. - Jeanne Chèneby; Marius Gheorghe; Marie Artufel; Anthony Mathelier; Benoît Ballester (Nucleic Acids Res., 2018)

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)

Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis. - Stefania Salvatore; Knut Dagestad Rand; Ivar Grytten; Egil Ferkingstad; Diana Domanska; Lars Holden; Marius Gheorghe; Anthony Mathelier; Ingrid Kristine Glad; Geir Kjetil Sandve (Briefings Bioinform., 2020)

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)

MirGeneDB 2.0: the metazoan microRNA complement. - Bastian Fromm; Diana Domanska; Eirik Høye; Vladimir Ovchinnikov; Wenjing Kang; Ernesto Aparicio-Puerta; Morten Johansen; Kjersti Flatmark; Anthony Mathelier; Eivind Hovig; Michael Hackenberg; Marc R. Friedländer; et al. (Nucleic Acids Res., 2020)

BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences. - Aziz Khan 001; Rafael Riudavets Puig; Paul Boddie; Anthony Mathelier (Bioinform., 2021)

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)

OnTarget: in silico design of MiniPromoters for targeted delivery of expression. - Oriol Fornes; Tamar Vered Av-Shalom; Andrea J. Korecki; Rachelle A. Farkas; David J. Arenillas; Anthony Mathelier; Elizabeth M. Simpson; Wyeth W. Wasserman (Nucleic Acids Res., 2023)

CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data. - Ping-Han Hsieh; Ru-Xiu Hsiao; Katalin Ferenc; Anthony Mathelier; Rebekka Burkholz; Chien-Yu Chen 001; Geir Kjetil Sandve; Tatiana Belova; Marieke L. Kuijjer (CoRR, 2024)

Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation. - Jørgen Ankill; Zhi Zhao; Xavier Tekpli; Elin H. Kure; Vessela N. Kristensen; Anthony Mathelier; Thomas Fleischer (PLoS Comput. Biol., 2024)

Gene regulatory network integration with multi-omics data enhances survival predictions in cancer. - Romana T. Pop; Ping-Han Hsieh; Tatiana Belova; Anthony Mathelier; Marieke L. Kuijjer (Briefings Bioinform., 2025)