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.
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.
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).
My projects are focused on Bioinformatics of Transcriptional regulation (as user and developer), mainly in algorithms to discover Transcription Factor Binding Motifs and to predict Transcription Factor Binding Sites and in the miRNa transcriptional regulation. Currently I'm an active developer of RSAT which is a collections of tools to analize Cis-Regulatory sequences and I am also involved in the JASPAR database, as curator and processing data for the next release.
We are working in a new release of RSAT with new programs.
This tool can merge different files containing TF binding motifs (i.e. motifs dicovered with different tools) and manually or automatically reduce the redundancy.
I recently extended the algorithm to generate radial (circular) tress including link to databases, some examples can be found on the JASPAR website.
The matrix-clustering paper can be found on this link.
I am actively maintaining this tool, send me an email in case you want to report a problem.
|13.|| 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.
|12.|| Motif analysis in co-expression networks reveals regulatory elements in plants: The peach as a model
Ksouri N, Castro-Mondragon JA, Montardit-Tarda F, van Helden J, Contreras-Moreira B#, and Gogorcena Y# (2020) bioRxiv.
|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
|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#, Lenhard Thomas-Chollier M#. (2018) Nucleic Acids Research
|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) bioRxiv.
|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
|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
|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
|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
|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
|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
|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
|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