* co-first authors, + co-corresponding authors

  • D. de Rie, I. Abugessaisa, …, A. Mathelier, …, M.J.L. de Hoon (~70 authors from the FANTOM5 Consortium). An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature Biotechnology, 2017. doi:10.1038/nbt.3947
  • A. Khan and A. Mathelier. Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. BMC Bioinformatics, 2017. doi:10.1186/s12859-017-1708-7
  • C.-Y. Chen, W. Shi, B.P. Balaton, A.M. Matthews, Y. Li, D.J. Arenillas, A. Mathelier, M. Itoh, H. Kawaji, T. Lassmann, Y. Hayashizaki, P. Carninci, A.R.R. Forrest, C.J. Brown, and W.W. Wasserman. YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses. Scientific Reports, 2016. doi:10.1038/srep37324
  • M. Lizio, J. Harshbarger, I. Abugessaisa, S. Noguchi, A. Kondo, J. Severin, C. Mungall, D. Arenillas, A. Mathelier, Y.A. Medvedeva, A. Lennartsson, F. Drabløs, J.A. Ramilowski, O. Rackham, J. Gough, R. Andersson, A. Sandelin, H. Ienasescu, H. Ono, H. Bono, Y. Hayashizaki, P. Carninci, A.R.R. Forrest, T. Kasukawa* and H. Kawaji*. Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Nucleic Acids Research, 2016. doi: 10.1093/nar/gkw995
  • A. Mathelier, B. Xin, T.-P. Chiu, L. Yang, R. Rohs, and W.W. Wasserman. DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo. Cell Systems, 2016. doi:10.1016/j.cels.2016.07.001
  • J.W. Hickmott, C.-Y. Chen, D.J. Arenillas, A.J. Korecki, S.L. Lam, L.L. Molday, R.J. Bonaguro, M. Zhou, A.Y. Chou, A. Mathelier, S.L. Boye, W.W. Hauswirth, R.S. Molday, W.W. Wasserman, and E.M. Simpson. PAX6 MiniPromoters drive restricted expression from rAAV in the adult mouse retina. Molecular therapy — Methods & Clinical Development, 2016. doi:10.1038/mtm.2016.51
  • W. Shi, O. Fornes, A. Mathelier, and W.W. Wasserman. Evaluating the impact of single nucleotide variants on transcription factor binding. Nucleic Acids Research, 2016. doi: 10.1093/nar/gkw691
  • D.J. Arenillas, A. Forrest, H. Kawaji, T. Lassman, the FANTOM consortium, W.W. Wasserman+, and A. Mathelier+. CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. Bioinformatics, 2016. doi: 10.1093/bioinformatics/btw337
  • S. Klein*, L.C. Dieterich*, A. Mathelier, C. Chong, A. Sliwa-Primorac, Y.-K. Hong, J.W. Shin, M. Lizio, M. Itoh, H. KawajiT. Lassmann, C.O. Daub, E. Arner, the FANTOM consortium, P. CarninciY. Hayashizaki, A.R.R. Forrest, W.W. Wasserman, and M. Detmar. DeepCAGE transcriptomics identify HOXD10 as transcription factor regulating lymphatic endothelial responses to VEGF-C. Journal of Cell Science, 2016. doi:10.1242/jcs.186767
  • R.A.G. De Souza, S.A. Islam, L.M. McEwen, A. Mathelier, A. Hill, S.M. Mah, W.W. Wasserman, M.S. Kobor, and B.R. Leavitt. DNA methylation profiling in human Huntington’s disease brain. Human Molecular Genetics, 2016. doi:10.1093/hmg/ddw076
  • A. Mathelier, O. Fornes, D.J. Arenillas, C.-Y. Chen, G. Denay, J. Lee, W. Shi, C. Shyr, G. Tan, R. Worsley-Hunt, A.W. Zhang, F. Parcy, B. Lenhard, A. Sandelin, and W.W. Wasserman. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. Nucleic Acids Research, database issue, 2016. doi:10.1093/nar/gkv1176
  • L.C. Dietriech*, S. Klein*, A. Mathelier, A. Primorac, Q. Ma, Y-K. Hong, J.W. Shin, M. Hamada, M. Lizio, M. Itoh, H. Kawaji, T. Lassman, C.O. Daub, E. Arner, P. Carninci, Y. Hayashizaki, the FANTOM5 consortium, A.R.R. Forrest, W.W. Wasserman, and M. Detmar. The transcription factor MAFB links VEGFR-3 signaling with PROX1 expression in lymphatic endothelial cells. Cell Reports, 2015. doi:10.1016/j.celrep.2015.10.002
  • A. Mathelier, C. Lefebvre, A.W. Zhang, D.J. Arenillas, J. Ding, W.W. Wasserman, and S.P. Shah. Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas. Genome Biology, 2015. doi:10.1186/s13059-015-0648-7
  • A. Mathelier, W. Shi, and W.W. Wasserman. Identification of altered cis-regulatory elements in human diseases. Trends in Genetics, 2015. doi:10.1016/j.tig.2014.12.003
  • A. Saumet, A. Mathelier, and C.H. Lecellier. The potential of miRNAs in personalized medicine against cancers. BioMed Research International, 2014. doi:10.1155/2014/642916
  • A. Mathelier and A. Carbone. Predicted human structural clusters of miRNAs target cancer genes. Atlas Genet. Cytogenet. Oncol. Haematol., 2014. doi:10.4267/2042/54379
  • R. Worsley-Hunt, A. Mathelier, L. Del Peso, and W.W. Wasserman. Improving detection and analysis of transcription factor binding sites within ChIP-seq data based on topological motif enrichment. BMC Genomics, 2014. doi:10.1186/1471-2164-15-472
  • A.R. Forrest, …, A. Mathelier, …, Y. Hayashizaki (~250 authors from the FANTOM5 consortium). A promoter-level mammalian expression atlas. Nature, 2014. doi:10.1038/nature13182
  • L. Yang, T. Zhou, I. Dror, A. Mathelier, W.W. Wasserman, R. Gordân, and R. Rohs. TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Research, database issue, 2014. doi:10.1093/nar/gkt1087
  • A. Mathelier*, X. Zhao*, A.W. Zhang, F. Parcy, R. Worsley-Hunt, D.J. Arenillas, S. Buchman, C-Y. Chen, A. Chou, H. Ienasescu, J. Lim, C. Shyr, G. Tan, M. Zhou, B. Lenhardt, A. Sandelin, and W.W. Wasserman. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Research, database issue, 2014. doi:10.1093/nar/gkt997
  • A. Mathelier and W.W. Wasserman. The next generation of transcription factor binding site prediction. PLOS Computational Biology, 2013. doi:10.1371/journal.pcbi.1003214
  • A. Mathelier and A. Carbone. Large scale chromosomal mapping of human microRNA structural clusters. Nucleic Acids Research, 2013. doi: 10.1093/nar/gkt112
  • J.-F. Schmouth, K.G. Banks, A. Mathelier, C.Y. Gregory-Evans, M. Castellarin, R. Holt, K. Gregory-Evans, W.W. Wasserman and E.M. Simpson. Retina restored and brain abnormalities ameliorated by single-copy knock-in of Human NR2E1 in null mice. Molecular and Cellular Biology, 2012. doi:10.1128/MCB.06016-11
  • A. Mathelier and A. Carbone. Chromosomal periodicity and positional networks of genes in Escherichia coli. Molecular Systems Biology, 2010. doi:10.1038/msb.2010.21
  • A. Mathelier and A. Carbone. MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. Bioinformatics, 2010. doi:10.1093/bioinformatics/btq329


  • A. Carbone and A. Mathelier, “Environmental and physiological insights from microbial genome sequences”. Elements of Computational Systems Biology, Huma Lodhi and Stephen Muggleton (eds.), Wiley Book Series in Bioinformatics, 2010. Pages 325-339