I obtained a bachelor degree in Genomic Sciences from the UNAM (Universidad Nacional autonoma de Mexico) in Cuernavaca, Mexico. I have a master degree in Systems Biology from the IMaLiS program at the ENS (Ecole normale Superieure) in Paris, France. I obtained a PhD degree at the Aix-Marseille Universite in Marseille, France in 2017. Currenly I am working as a post-doctoral researcher at Anthony Mathelier's lab. My research projects is focused on the characterization of mutations dysregulating miRNA networks and I am also contributing to the next JASPAR motif database release.
Jaime A Castro-Mondragon
E-mail:
j.a.c.mondragon@ncmm.uio.no
Computational biology & Gene Regulation group
Centre for Molecular Medicine Norway (NCMM)
NCMM, P.O. Box 1137 Blindern, 0318
Oslo, Norway
Twitter: @jaimicore
Publons: 1499198
ORCID: 0000-0003-4069-357X
Github: jaimicore
Bitbucket: jaimicore
2014 - 2017• France
Aix-Marseille Universite, France. Supervisor: Jacques van Helden. Goals:(1) Development tools to cluster, align and reduce redundance of Transcription Factors Binding Motifs.(2) Development of a tool to detect positionally enriched/depleted motifs. Title: Development of bioinformatics methods for the analysis of large collections of transcription factor binding motifs: positional motif enrichment and motif clustering.
2014• France
École Normale Supérieure Paris, France. Courses taken included: Bioinformatics, Genomics, Logical Modelling, Microscopy, Evolution, Molecular Biology. Master thesis at Aix-Marseille Université TAGC in the TAGC Laboratory in Marseille, France. Supervisor: Jacques van Helden. Title: matrix-clustering: a novel tool to cluster and align Transcription Factor binding motifs.
2009 - 2013•Mexico
I did a research project at the Computational Genomics Lab, Centro de Ciencias Genómicas, UNAM, Cuernavaca, Mexico.
Supervisors : Julio Collado-Vides & Alejandra Medina-Rivera.
"Prediction of novel regulons based on several properties of the regulatory network." Based in that most knowns TFs in E. coli K12 are autorregulated, we searched the motifs for the unknown TFs. (Ongoing project).
4. | UniBind: maps of high-confidence direct TF-DNA interactions across nine species Riudavets Puig R, Boddie P, Khan A, Castro-Mondragon JA, and Mathelier A# (2020) bioRxiv. |
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3. | Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of the gene regulatory program in cancers Castro-Mondragon JA, Ragle Aure M, Lingjærde OC, Langerød A, Martens JWM, Børresen-Dale AL, Kristensen VN, and Mathelier A# (2020) bioRxiv. |
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2. | Crosstalk between microRNA expression and DNA methylation drive the hormone-dependent phenotype of breast cancer Ragle Aure M, Fleischer T, Bjørklund S, Ankill J, Castro-Mondragon JA, OSBREAC (Oslo Breast Cancer Research Consortium), Børresen-Dale AL, Sahlberg KK, Mathelier A, Tekpli X#, Kristensen VN# (2020) bioRxiv. |
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1. | Proteins in the periplasmic space and outer membrane vesicles of Rhizobium etli CE3 grown in minimal medium are largely distinct and change with growth phase Taboada H*, Meneses N*, Dunn MF*, Vargas-Lagunas C, Buchs N, Castro-Mondragon JA, Heller M, and Encarnacion S# (2018) bioRxiv. |
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12. | Tuning promoter boundaries improves regulatory motif discovery in non-model plants: the peach example Ksouri N, Castro-Mondragon JA, Montardit-Tarda F, van Helden J, Contreras-Moreira B#, and Gogorcena Y# (2021) Plant Physiology. |
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11. | RhizoBindingSites, a Database of DNA-Binding Motifs in Nitrogen-Fixing Bacteria Inferred Using a Footprint Discovery Approach Taboada-Castro H, Castro-Mondragon JA, Aguilar-Vera A, Hernandez-Alvarez AJ, van Helden J, and Encarnacion-Guervara S#. (2020) Frontiers in Microbiology |
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10. | JASPAR 2020: update of the open-access database of transcription factor binding profiles Fornes O*, Castro-Mondragon JA*, Khan A*, van der Lee Robin, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Baranasic D, Santana-Garcia Walter, Tan G, Cheneby J, Ballester B, Parcy F, Sandelin A#, Lenhard B#, Wasserman WW#, and Mathelier A#. (2019) Nucleic Acids Research |
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9. | RSAT 2018: regulatory sequence analysis tools 20th anniversary Nguyen NTT*, Contreras-Moreira B*, Castro-Mondragon JA, Santana-Garcia W, Ossio R, Robles-Espinoza CD, Bahin M, Collombet S, Vincens P, Thieffry D, van Helden J#, Medina-Rivera A#, Thomas-Chollier M#. (2018) Nucleic Acids Research |
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8. | JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework Khan A*, Fornes O*, Stigliani A*, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni S, Tan G, Baranasic D, Arenillas D, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman W, Parcy F, Mathelier A. (2017) Nucleic Acids Research |
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7. | Genome-wide characterization of mammalian promoters with distal enhancer functions Dao LM*, Galindo-Albarran AO*, Castro-Mondragon JA^, Andireu-Soler C^, Medina-Rivera A^, Souadi C, Charbonnier G, Griffon A, Vanhille L, Stephen S, Alomairi J, Soler C, Stephen T, Martin D, Torres M, Fernandez N, Soler E, van Helden J, Puthier D, Spicuglia S (2017) Nature Genetics |
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6. | RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections Castro-Mondragon JA, Jaeger S, Thieffry D, Thomas-Chollier M#, and van Helden J# (2017) Nucleic Acids Research |
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5. | RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes Castro-Mondragon JA, Rioualen C, Contreras-Moreira B, van Helden J (2016) Plant Synthetic Promoters - Springer Protocol |
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4. | RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes Contreras-Moreira B#, Castro-Mondragon JA, Rioualen C, Cantalapiedra CP, van Helden J (2016) Plant Synthetic Promoters - Springer Protocol |
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3. | RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond Gama-Castro S*, Salgado H*, Santos-Zavaleta A, Ledezma-Tejeida D, Muñiz-Rascado L, García-Sotelo JS, Alquicira-Hernández K, Martínez-Flores I, Pannier L, Castro-Mondragón JA, Medina-Rivera A, Solano-Lira H, Bonavides-Martínez C, Pérez-Rueda E, Alquicira-Hernández S, Porrón-Sotelo L, López-Fuentes A, Hernández-Koutoucheva A, Del Moral-Chávez V, Rinaldi F, Collado-Vides J (2015) Nucleic Acids Research |
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2. | RSAT 2015 : Regulatory Sequence Analysis Tools Medina-Rivera A*, Defrance M*, Sand O*, Herrmann C, Castro-Mondragon JA, Delerce J, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier–Khamvongsa L, Hernandez C, Thieffry D, Thomas-Chollier M#, van Helden J# (2015) Nucleic Acids Research |
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1. | Genomic basis of symbiovar mimosae in Rhizobium etli Rogel MA, Bustos P, Santamaría RI, González V, Romero D, Miguel AC, Lozano L, Castro-Mondragon JA, Martínez-Romero J, Ormeño-Orrillo E, Martínez-Romero E# (2014) BMC Genomics |
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