In brief

I studied a bachelor in Genomic Sciences at UNAM in Cuernavaca, Mexico. I got a master degree in Systems Biology with IMaLiS program at the ENS in Paris, France. Currently I do my 3rd PhD year at the TAGC laboratory in Marseille, France, under the supervision of the professor Jacques van Helden.

Contact Details

Jaime Castro-Mondragon
E-mail: jcastro@lcg.unam.mx
TAGC
Unité INSERM U1090
163, Avenue de Luminy, 13288
Marseille, France

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Education

PhD student in Bioinformatics

2014 - now• 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) Study the combinatorial and positioning of Transcription Factors regulating specific conditions using ChIP-seq data.

Master2 in Systems Biology

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.

Bachelor in Genomic Sciences

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).

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Research


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.

Current Projects

  1. RSAT matrix-clustering: a tool to cluster, align and create non-redundant collections of Transcription Facotr Binding Motifs.

    sample-image


    This tool can merge different files containing (i.e. motifs dicovered with different tools) and manually or automatically reduce the redundancy.

  2. RSAT position-scan: a tool to detect Transcription Factors positionally biased in sequences (e.g. centered around ChIP-seq peak summits, located near TSS).

    sample-image


    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.

  3. RSAT matrix-enrichment: a tool to detect gloablly enriched or depleted Transcription Factors in a set of sequences.

    sample-image


    The TF enrichment can be measured simultaneously in several set of sequences.

  4. Using the tool RSAT matrix-enrichment I have merged several complete databases with motifs from different taxa (vertebrates, plants and insects) in order to create automatically non-redundant taxon-wise motifs collection.

    sample-image


    This databases and other examples ara available in this link. In the future I will include the databases for worms, fungi and bacteria.

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Research articles and book chapters

* = equal contributions
# = co-corresponding authors
  1. Castro-Mondragon JA, Rioualen C, Contreras-Moreira B, van Helden J
    "RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes",
    Plant Synthetic Promoters - Springer Protocol (2016) [Full text]
  2. Contreras-Moreira B#, Castro-Mondragon JA, Rioualen C, Cantalapiedra CP, van Helden J
    "RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes",
    Plant Synthetic Promoters - Springer Protocol (2016) [Full text]
  3. 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
    "RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond",
    Nucleic Acids Research (2015) [Full text]

  4. 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#
    "RSAT 2015 : Regulatory Sequence Analysis Tools",
    Nucleic Acids Research (2015) [Full text]

  5. 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
    "Genomic basis of symbiovar mimosae in Rhizobium etli" ,
    BMC Genomics (2014) [Full text]

Posters

  • Castro-Mondragon JA, Thieffry D, Thomas-Chollier M, van Helden J
    "Clustering and redundancy reduction of transcription factor binding motifs".
    European Conference on Computational Biology (ECCB16), The Hague, Netherlands. [Full text]
  • Castro-Mondragon JA, Thomas-Chollier M, van Helden J
    "Comparing and clustering multiple collections of DNA motifs using RSAT".
    Basel Computational Biology Conference (BC2 2015), Basel, Switzerland. [Full text]
  • Castro-Mondragon JA, Thomas-Chollier M, Thieffry D, van Helden J
    "Comparing, clustering and aligning Transcription Factor Binding Motifs with RSAT".
    European Conference on Computational Biology (ECCB14), Strasbourg, France. [Full text]