I obtained a bachelor degree in Genomic Sciences from UNAM (Universidad Nacional Autonoma de Mexico) in Cuernavaca, Mexico. After that I moved to France where I obtained a master degree in Systems Biology from the IMaLiS program at the ENS (Ecole normale Superieure) in Paris, France. Also in France I obtained a PhD degree from the Aix-Marseille Universite in Marseille in 2017. From 2017 to 2022 I worked as a post-doctoral researcher at Anthony Mathelier's lab in Oslo, Norway. Now I contiue working as researcher, but working mainly with protein sequences at Nykode Therapeutics AS in Oslo.
Jaime A Castro-Mondragon
Department of Bioinformatics at Nykode Therapeutics
Oslo Science Park
Gaustadalleen 21 0349 Oslo, Norway
E-mail: j.a.castro.mondragon@gmail.com
E-mail: jacmondragon@nykode.com
Twitter/X: @jaimicore
Mastodon : @jaimicore
Web of science (prev. Publons): P-6297-2019
ORCID: 0000-0003-4069-357X
Github: jaimicore
Bitbucket: jaimicore
Google scholar: pcevKk0AAAAJ
2017 - 2022 • Oslo, Norway
Centre of Molecular Medicine Norway Oslo, Norway.
Supervisor: Anthony Mathelier.
During this time I worked mainly in a project to associate somatic mutations with changes in gene expression across gene networks in multiple cancer types. Also, I worked in the update of the JASPAR database as a curator and developer. As a side project, I continued working as part of the RSAT team by maintaining the tools I developed during my PhD and updating the motif databases.
2014 - 2017• France
Aix-Marseille Universite, France. Supervisor: Jacques van Helden. Goals:(1) Development of a tool 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.
22. | Identification of transcription factor co-binding patterns with non-negative matrix factorization. Rauluseviciute I, Launay T, Barzaghi G, Nikumbh S, Lenhard B, Krebs AR, Castro-Mondragon JA, and Mathelier A (2024) Nucleic Acids Research. |
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21. | JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles. Rauluseviciute I*, Riudavets-Puig R*, Blanc-Mathieu R^, Castro-Mondragon JA^, Ferenc K^, Kumar V^, Berhanu Lemma R^, Lucas J^, Cheneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B#, Sandelin A#, Wasserman WW#, Parcy F#, and Mathelier A#. (2024) Nucleic Acids Research. |
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20. | Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of gene regulatory programs in cancers Castro-Mondragon JA, Ragle Aure M, Lingjærde OC, Langerød A, Martens JWM, Børresen-Dale AL, Kristensen VN, and Mathelier A (2022) Nucleic Acids Research. |
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19. | Genetic architecture of natural variations of cardiac performance in flies Saha S*, Spinelli L*, Castro-Mondragon JA, Kervadec A, Lynott M, Kremmer L, Roder L, Sallouha J, Torres M, Brun C, Vogler G, Bodmer R, Colas AR#, Ocorr K#, and Perrin L# (2021) eLife. |
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18. | RSAT 2022: regulatory sequence analysis tools Santana-Garcia W*, Castro-Mondragon JA*, Padilla-Galvez M, Nguyen NTT, Elizondo-Salas A, Ksouri N, Gerbes F, Thieffry D, Vincens P, Contreras-Moreira B#, van Helden J#, Thomas-Chollier M#, Medina-Rivera A#. (2022) Nucleic Acids Research |
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17. | JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles Castro-Mondragon JA*, Riudavets-Puig R*, Rauluseviciute I*, Berhanu Lemma R, Turchi L, Blanc-Mathieu R, Lucas J, Boddie P, Khan A, Manosalva Perez N, Fornes O, Leung TY, Aguirre A, Hammal F, Schmelter D, Baranasic D, Ballester B, Sandelin A#, Lenhard B#, Vandepoele K, Wasserman WW#, Parcy F#, and Mathelier A#. (2021) Nucleic Acids Research |
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16. | Epromoters function as a hub to recruit key transcription factors required for the inflammatory response Santiago-Algarra D, Souaid C, Singh H, Dao TML, Hussain S, Medina-Rivera A, Ramirez-Navarro L, Castro-Mondragon JA, Sadouni N, Charbonnier G, Spicuglia S. (2021) Nature Communications |
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15. | 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 (2021) BMC Genomics. |
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14. | Crosstalk between microRNA expression and DNA methylation drives 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, Tost J, Sahlberg KK, Mathelier A, Tekpli X#, Kristensen VN# (2021) Genome Medicine. |
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13. | 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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12. | 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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11. | 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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10. | 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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9. | 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) Microbiology. |
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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 |