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. Recently I obtained a PhD degree at the Aix-Marseille Universite in Marseille, France. Currenly I am working as a post-doctoral researcher at Anthony Mathelier's lab.
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. Currently I'm an active developer of RSAT which is a collections of tools to analize Cis-Regulatory sequences.
We are working in a new release of RSAT with new programs.
This tool can merge different files containing (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 JASPAR website.
The matrix-clustering paper can be found on this link.
This tool separates the type of positional profiles which allows to identify enrichment or depletion of TF binding sites at certain positions of a set of sequences with the same length.
The TF enrichment can be measured simultaneously in several set of sequences.
This databases and other examples ara available in this link. In the future I will include the databases for worms, fungi and bacteria.
|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#, Lenhard Thomas-Chollier M#. (2018) Nucleic Acids Research
|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