Anthony Mathelier

23 papers Journal 23
YearRankTypeTitle / Venue / Authors
2026 J jnl
inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences.
Bioinform.
Katalin Ferenc, Lorenzo Martini, Ieva Rauluseviciute, Geir Kjetil Ferkingstad Sandve, Anthony Mathelier
2025 J jnl
Gene regulatory network integration with multi-omics data enhances survival predictions in cancer.
Briefings Bioinform.
Romana T. Pop, Ping-Han Hsieh, Tatiana Belova, Anthony Mathelier, Marieke L. Kuijjer
2024 J jnl
CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data.
CoRR
Ping-Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien-Yu Chen, Geir Kjetil Sandve, Tatiana Belova, Marieke L. Kuijjer
2024 J jnl
Improving bioinformatics software quality through teamwork.
Bioinform.
Katalin Ferenc, Ieva Rauluseviciute, Ladislav Hovan, Vipin Kumar, Marieke L. Kuijjer, Anthony Mathelier
2024 J jnl
Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation.
PLoS Comput. Biol.
Jørgen Ankill, Zhi Zhao, Xavier Tekpli, Elin H. Kure, Vessela N. Kristensen, Anthony Mathelier, Thomas Fleischer
2023 J jnl
OnTarget:
Nucleic Acids Res.
Oriol Fornes, Tamar Vered Av-Shalom, Andrea J. Korecki, Rachelle A. Farkas, David J. Arenillas, Anthony Mathelier, Elizabeth M. Simpson, Wyeth W. Wasserman
2022 J jnl
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles.
Nucleic Acids Res.
Jaime Abraham Castro-Mondragón, Rafael Riudavets Puig, Ieva Rauluseviciute, Roza Berhanu lemma, Laura Turchi, Romain Blanc-Mathieu, Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol Fornes, Tiffany Y. Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel Schmelter, Damir Baranasic, Benoît Ballester, Albin Sandelin, Boris Lenhard, Klaas Vandepoele, Wyeth W. Wasserman, François Parcy, Anthony Mathelier
2021 J jnl
BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences.
Bioinform.
Aziz Khan, Rafael Riudavets Puig, Paul Boddie, Anthony Mathelier
2020 J jnl
Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis.
Briefings Bioinform.
Stefania Salvatore, Knut Dagestad Rand, Ivar Grytten, Egil Ferkingstad, Diana Domanska, Lars Holden, Marius Gheorghe, Anthony Mathelier, Ingrid Kristine Glad, Geir Kjetil Sandve
2020 J jnl
JASPAR 2020: update of the open-access database of transcription factor binding profiles.
Nucleic Acids Res.
Oriol Fornes, Jaime Abraham Castro-Mondragón, Aziz Khan, Robin van der Lee, Xi Zhang, Phillip Andrew Richmond, Bhavi P. Modi, Solenne Correard, Marius Gheorghe, Damir Baranasic, Walter Santana-Garcia, Ge Tan, Jeanne Chèneby, Benoît Ballester, François Parcy, Albin Sandelin, Boris Lenhard, Wyeth W. Wasserman, Anthony Mathelier
2020 J jnl
MirGeneDB 2.0: the metazoan microRNA complement.
Nucleic Acids Res.
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, Kevin J. Peterson
2018 J jnl
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.
Nucleic Acids Res.
Aziz Khan, 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, Albin Sandelin, Klaas Vandepoele, Boris Lenhard, Benoît Ballester, Wyeth W. Wasserman, François Parcy, Anthony Mathelier
2018 J jnl
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.
Nucleic Acids Res.
Aziz Khan, 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, Albin Sandelin, Klaas Vandepoele, Boris Lenhard, Benoît Ballester, Wyeth W. Wasserman, François Parcy, Anthony Mathelier
2018 J jnl
JASPAR RESTful API: accessing JASPAR data from any programming language.
Bioinform.
Aziz Khan, Anthony Mathelier
2018 J jnl
ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments.
Nucleic Acids Res.
Jeanne Chèneby, Marius Gheorghe, Marie Artufel, Anthony Mathelier, Benoît Ballester
2017 J jnl
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets.
BMC Bioinform.
Aziz Khan, Anthony Mathelier
2017 J jnl
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.
Nucleic Acids Res.
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, Jordan A. Ramilowski, Owen J. L. Rackham, Julian Gough, Robin Andersson, Albin Sandelin, Hans Ienasescu, Hiromasa Ono, Hidemasa Bono, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, Takeya Kasukawa, Hideya Kawaji
2016 J jnl
CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.
Bioinform.
David J. Arenillas, Alistair R. R. Forrest, Hideya Kawaji, Timo Lassmann, Wyeth W. Wasserman, Anthony Mathelier
2016 J jnl
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.
Nucleic Acids Res.
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, Boris Lenhard, Albin Sandelin, Wyeth W. Wasserman
2014 J jnl
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.
Nucleic Acids Res.
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, Ge Tan, Michelle Zhou, Boris Lenhard, Albin Sandelin, Wyeth W. Wasserman
2014 J jnl
NAR Breakthrough Article: TFBSshape: a motif database for DNA shape features of transcription factor binding sites.
Nucleic Acids Res.
Lin Yang, Tianyin Zhou, Iris Dror, Anthony Mathelier, Wyeth W. Wasserman, Raluca Gordân, Remo Rohs
2013 J jnl
The Next Generation of Transcription Factor Binding Site Prediction.
PLoS Comput. Biol.
Anthony Mathelier, Wyeth W. Wasserman
2010 J jnl
MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.
Bioinform.
Anthony Mathelier, Alessandra Carbone