Publications

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

2023

  1. I. Rauluseviciute, T. Launay, G. Barzaghi, S. Nikumbh, B. Lenhard, A.R. Krebs, J.A. Castro-Mondragon, A. Mathelier. Identification of transcription factor co-binding patterns with non-negative matrix factorization. biorXiv, 2023. doi:10.1101/2023.04.28.538684
  2. O. Fornes, T.V. Av-Shalom, A.J. Korecki, R.A. Farkas, D.J. Arenillas, A. Mathelier, E.M. Simpson, W.W. Wasserman.  OnTarget: in silico design of MiniPromoters for targeted delivery of expression. Nucleic Acids Research, 2023. doi:10.1093/nar/gkad375

2022

  1. J.A. Castro-Mondragon, M. Ragle Aure, O.C. Lingjærde, A. Langerød, J.W.M. Martens, A.-L. Børresen-Dale, V. Kristensen, and A. Mathelier. Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of gene regulatory programs in cancers. Nucleic Acids Research, 2022. doi:10.1093/nar/gkac1143
  2. R. Rossini, V. Kumar, A. Mathelier, T. Rognes, J. Paulsen. MoDLE: High-performance stochastic modeling of DNA loop extrusion interactions. Genome Biology, 2022. doi:10.1186/s13059-022-02815-7
  3. S. Bjørklund, M. Ragle Aure, J. Häkkinen, J. Vallon-Christersson, S. Kumar, K. Bull Evensen, T. Fleischer, J. Tost, A. Mathelier, G. Bhanot, S. Ganesan, X. Tekpli, V.N. Kristensen. Subtype and cell type specific expression of lncRNAs provide insight into breast cancer. Communications Biology, 2022. doi:10.1038/s42003-022-03559-7
  4. R.B. Lemma, T. Fleischer, E. Martinsen, M. Ledsaak, V. Kristensen, R. Eskeland, O.S. Gabrielsen, and A. Mathelier. Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers. Epigenetics and Chromatin, 2022. doi:10.1186/s13072-022-00444-9
  5. J.M. Strømme, B. Johannessen, S.G. Kidd, M. Bogaard, K.T. Carm, X. Zhang, A. Sveen, A. Mathelier, R.A. Lothe, U. Axcrona, K. Axcrona, and R.I. Skotheim. Expressed prognostic biomarkers for primary prostate cancer independent of multifocality and transcriptome heterogeneity. Cancer Gene Therapy, 2022. doi:10.1038/s41417-022-00444-7
  6. J.A. Castro-Mondragon*, R. Riudavets-Puig*, I. Rauluseviciute*, R.B. Lemma, L. Turchi, R. Blanc-Mathieu, J. Lucas, P. Boddie, A. Khan, N. Manosalva Pérez, O. Fornes, T.Y. Leung, A. Aguirre, F. Hammal, D. Schmelter, D. Baranasic, B. Ballester, A. Sandelin+, B. Lenhard+, K. Vandepoele, W.W. Wasserman+, F. Parcy+, and A. Mathelier+. JASPAR 2022: the 9th release of the open-acess database of transcription factor binding profiles. Nucleic Acids Research, 2022. doi:10.1093/nar/gkab1113

2021

  1. R. Riudavets Puig, P. Boddie, A. Khan, J.A. Castro Mondragon, and A. Mathelier. UniBind: maps of high-confidence direct TF-DNA interactions across nine species. BMC Genomics, 2021. doi:10.1186/s12864-021-07760-6
  2. M. Ragle Aure, T. Fleischer, S. Bjørklund, J. Ankill, J.A. Castro-Mondragon, OSBREAC, A.-L. Børresen-Dale, K.K. Sahlberg, A. Mathelier, X. Tekpli, and V.N. Kristensen. Crosstalk between microRNA expression and DNA methylation drive the hormone-dependent phenotype of breast cancer. Genome Medicine, 2021. doi:10.1186/s13073-021-00880-4
  3. E. Mileti, K.H.M. Kwok, D.P. Andersson, A. Mathelier, A. Raman, J. Bäckdahl, J. Jalkanen, L. Massier, A. Thorell, H. Gao, P. Arner, N. Mejhert, C.O. Daub, M. Rydén. Human white adipose tissue displays selective insulin resistance in the obese state. Diabetes, 2021. doi:10.2337/db21-0001
  4. A.J. Korecki, J.L. Cueva-Vargas, O. Fornes, J. Agostinone, R.A. Farkas, J.W. Hickmott, S.L. Lam, A. Mathelier, M. Zhou, W.W. Wasserman, A. Di Polo, E.M. Simpson. Human MiniPromoters for ocular-rAAV expression in ON bipolar, cone, corneal, endothelial, Müller glial, and PAX6 cells. Gene Therapy, 2021. doi:10.1038/s41434-021-00227-z

2020

  1. A. Khan, R. Riudavets Puig, P. Boddie, and A. Mathelier. BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences. Bioinformatics, 2020. doi:10.1093/bioinformatics/btaa928
  2. 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, and O.C. Lingjærde. DNA copy number motifs are strong and independent predictors of survival in breast cancer. Communications Biology, 2020. doi:10.1038/s42003-020-0884-6
  3. 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, 2020. doi:10.1093/nar/gkz1001

2019

  1. 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
  2. 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
  3. 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
  4. 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
  5. A.J. Korecki, J.W. Hickmott, S.L. Lam, L. Dreolini, A. Mathelier, O. Baker, C. Kuehne, R.J. Bonaguro, J. Smith, C.-V. Tan, M. Zhou, D. Goldowitz, J.M. Deussing, A.F. Stewart, W.W. Wasserman, R.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

2018

  1. 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
  2. A. Khan, A. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. A. Khan, A. Montenegro-Montero, and A. Mathelier. Put science first and formatting later. EMBO Reports, 2018. doi:10.15252/embr.201845731
  8. D. Sugiaman-Trapman, M. Vitezic, E.-M. Jouhilahti, A. Mathelier, G. Lauter, S. Misra, C.O. Daub, J. 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

2017

  1. A. Khan and A. Mathelier. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017. doi:10.1093/bioinformatics/btx804.
  2. A. Khan*, O. Fornes*, A. Stigliani*, M. Gheorghe, J.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
  3. 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
  4. 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
  5. 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
  6. 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

2016

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. S. Klein*, L.C. Dieterich*, A. Mathelier, C. Chong, A. Sliwa-Primorac, Y.-K. Hong, J.W. Shin, M. Lizio, M. Itoh, H. Kawaji, T. Lassmann, C.O. Daub, E. Arner, the FANTOM consortium, P. Carninci, Y. 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
  8. 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
  9. 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

2015

  1. 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. DeepCAGE transcriptomics reveals an important role of the transcription factor MAFB in the lymphatic endothelium. Cell Reports, 2015. doi:10.1016/j.celrep.2015.10.002
  2. 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
  3. 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

2014

  1. 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
  2. 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
  3. 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
  4. 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, 2014. doi:10.1093/nar/gkt1087
  5. 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, 2014. doi:10.1093/nar/gkt997

2013

  1. 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
  2. A. Mathelier and A. Carbone. Large scale chromosomal mapping of human microRNA structural clusters. Nucleic Acids Research, 2013. doi: 10.1093/nar/gkt112

2012

  1. 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

2010

  1. 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
  2. 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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