In brief

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.

Contact Details

Jaime Castro-Mondragon
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


PhD in Bioinformatics

2014 - 2017 France

Aix-Marseille Universite, France.
Supervisor: Jacques van Helden.
(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.

Master degree 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 - 2013Mexico

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.

Current Projects

  1. I am an active developer of the Regulatory Sequences Analysis Tools RSAT that is a modular software suite for the analysis of cis-regulatory elements in genome sequences (ChIP-seq, ATAC-seq).


    We are working in a new release of RSAT with new programs.

  2. I contributed to the JASPAR 2018 release. My contribution was to develop a motif browser for all the TF binding motifs in several taxa.


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


    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.

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


    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.

    We used this software to detect TF binding motif enriched at human promoters acting as enhancer (Epromoters) on two cell lines, see supp figures.
  5. RSAT matrix-enrichment: a tool to detect gloablly enriched or depleted Transcription Factors in a set of sequences.


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

  6. Using the tool RSAT matrix-clustering 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.


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


Research articles and book chapters

* = equal contributions (first-author)
^ = equal contributions (second-author)
# = co-corresponding authors
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


  • 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]


Parallel dimensions: random stuff and examples

    I will start a blog as soon as I have time to write ...