Publications

Preprints

  1. A.V. Pladsen, G. Nilsen, O.M. Rueda, M.R. Aure, Ø. Borgan, K. Liestøl, V. Vitelli, A. Frigessi, A. Langerød, OSBREAC, A. Mathelier, O. Engebråten, D.C. Wedge, P. Van Loo, C. Caldas, A.-L. Børresen-Dale, H.G. Russnes, O.C. Lingjærde. Copy number motifs expose genome instability type and predict driver events and disease outcome in breast cancer. bioRxiv, 2019. doi:10.1101/769356

Peer-reviewed manuscripts

* co-first authors, + co-senior authors, group members in bold

  1. O. Fornes*, J.A. Castro-Mondragon*, A. Khan*, R. van der Lee, X. Zhang, P.A. Richmond, B.P. Modi, S. Correard, M. Gheorghe, D. Baranašić, W. Santana-Garcia, G. Tan, J. Chèneby, B. Ballester, F. Parcy, A. Sandelin+, B. Lehnard+, W.W. Wasserman+, and A. Mathelier+. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Research, 2019. In press
  2. S. Salvatore, K.D. Rand, I. Grytten, E. Ferkingstad, D. Domanska, L. Holden, M. Gheorghe, A. Mathelier, I. Glad, G.K. Sandve. Beware the Jaccard: the choice of metric is important and non-trivial in genomic colocalisation analysis. Briefings in Bioinformatics, 2019. doi:10.1093/bib/bbz083
  3. B. Fromm, D. Domanska, E. Høye, V. Ovchinnikov, W. Kang, E. Aparicio-Puerta, M. Johansen, K. Flatmark, A. Mathelier, E. Hovig, M. Hackenberg, M.R. Friedländer, K.J. Peterson. MirGeneDB 2.0: The metazoan microRNA complement. Nucleic Acids Research, 2019. doi:10.1093/nar/gkz885
  4. T.J. Ha, P.G.Y. Zhang, R. Robert, J. Yeung, D.J. Swanson, A. Mathelier, W.W. Wasserman, S. Im, M. Itoh, H. Kawaji, T. Lassmann, C.O. Daub, E. Arner, The FANTOM Consortium, P. Carninci, Y. Hayashizaki, A.R.R. Forrest, and D. Goldowitz. Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis. BMC Genomics, 2019. doi:10.1186/s12864-019-6063-9
  5. H.M. Itkonen, A. Urbanucci, S.E.S. Martin, A. Khan, A. Mathelier, B. Thiede, S. Walker, I.G. Mills. High OGT activity is essential for MYC-driven proliferation of prostate cancer cells. Theranostics, 2019. doi:10.7150/thno.30834
  6. A.J. KoreckiJ.W. HickmottS.L. LamL. DreoliniA. MathelierO. BakerC. KuehneR.J. BonaguroJ. SmithC.-V. TanM. ZhouD. GoldowitzJ.M. DeussingA.F. StewartW.W. WassermanR.A. Holt, and E.M. Simpson. Twenty-Seven Tamoxifen-Inducible iCre-Driver Mouse Strains for Eye and Brain; Including Seventeen Carrying a New Inducible-First Constitutive-Ready Allele. Genetics, 2019. doi:10.1534/genetics.119.301984
  7. M. Gheorghe, G.K. Sandve, A. Khan, J. Chèneby, B. Ballester, and A. Mathelier. A map of direct TF-DNA interactions in the human genome. Nucleic Acids Research, 2018. doi:10.1093/nar/gky1210
  8. A. KhanA. Mathelier, and X. Zhang. Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers. Epigenetics, 2018. doi:10.1080/15592294.2018.1514231
  9. E. Simpson, A.J. Korecki, O. Fornes, T.J. McGill, J.L. Cueva-Vargas, J. Agostinone, R.A. Farkas, J.W. Hickmott, S.L. Lam, A. Mathelier, L.M. Renner, J. Stoddard, M.  Zhou, A. Di Polo, M. Neuringer, and W.W. Wasserman. New MiniPromoter Ple345 (NEFL) Drives Strong and Specific Expression in Retinal Ganglion Cells of Mouse and Primate Retina. Human Gene Therapy, 2018. doi:10.1089/hum.2018.118
  10. R.A.G. De Souza*, N. Kosior*, S.B. Thomson, A. Mathelier, A.W. Zhang, K. Becanovic, W.W. Wasserman, and B.R. Leavitt. Computational Analysis of Transcriptional Regulation Sites at the HTT Gene Locus. Journal of Huntington’s Disease, 2018. doi:10.3233/JHD-170272
  11. O. Fornes*, M. Gheorghe*, P. A. Richmond, D.J. Arenillas, W.W. Wasserman+, and A. Mathelier+. MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations. Scientific Data, 2018. doi:10.1038/sdata.2018.141
  12. C.-H. Lecellier+, W.W. Wasserman, and A. Mathelier+. Human enhancers harboring specific sequence composition, activity, and genome organization are linked to the immune response. Genetics, 2018. doi:10.1534/genetics.118.301116
  13. A. Khan, A. Montenegro-Montero, and A. Mathelier. Put science first and formatting later. EMBO Reports, 2018. doi:10.15252/embr.201845731
  14. D. Sugiaman-TrapmanM. VitezicE.-M. JouhilahtiA. MathelierG. LauterS. MisraC.O. DaubJ. Kere+, and P. Swoboda+. Characterization of the human RFX transcription factor family by regulatory and target gene analysis. BMC Genomics, 2018. doi:10.1186/s12864-018-4564-6
  15. A. Khan and A. Mathelier. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017. doi:10.1093/bioinformatics/btx804.
  16. A. Khan*, O. Fornes*, A. Stigliani*, M. GheorgheJ.A. Castro-Mondragòn, R. van der Lee, A. Bessy, J. Chèneby, S.R. Kulkarni, G. Tan, D. Baranasic, D.J. Arenillas, A. Sandelin+, K. Vandepoele, B. Lenhard+, B. Ballester, W.W. Wasserman+, F. Parcy, and A. Mathelier+. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Research, 2017. doi:10.1093/nar/gkx1126
  17. T. Fleischer*, X. Tekpli*, A. Mathelier, S. Wang, D. Nebdal, H.P. Dhakal, K. Kleivi Sahlberg, E. Schlichting, Oslo Breast Cancer Research Consortium (OSBREAC), A.-L. Børresen-Dale, E. Borgen, B. Naume, R. Eskeland, A. Frigessi, J. Tost, A. Hurtado, and V.N. Kristensen. DNA methylation at enhancers identifies distinct breast cancer lineages. Nature Communications, 2017. doi:10.1038/s41467-017-00510-x
  18. J. Chèneby, M. Gheorghe, M. Artufel, A. Mathelier, and B. Ballester. ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. Nucleic Acids Research, 2017. doi:10.1093/nar/gkx1092
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. A. Mathelier and A. Carbone. Large scale chromosomal mapping of human microRNA structural clusters. Nucleic Acids Research, 2013. doi: 10.1093/nar/gkt112
  41. 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
  42. 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
  43. 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

Collections

  • 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
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