In brief

I obtained a bachelor degree in Genomic Sciences from the 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 at the Aix-Marseille Universite in Marseille in 2017. From 2017 to 2022 I worked as a post-doctoral researcher at Anthony Mathelier's lab.

Contact Details

Jaime A Castro-Mondragon
Department of Bioinformatics at Nykode Threapeutics
Oslo Science Park
Gaustadalleen 21 0349 Oslo, Norway

E-mail: j.a.castro.mondragon@gmail.com
E-mail: jacmondragon@nykode.com

Twitter: @jaimicore
Publons: 1499198
ORCID: 0000-0003-4069-357X
Github: jaimicore
Bitbucket: jaimicore
Google scholar: pcevKk0AAAAJ


Work experience

Bioinformatician

2022 - Present Norway

Nykopde Threapeutics AS, Oslo, Norway.

Post-doctoral researcher

2017 - 2017 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 and updating the motif databases.

Education

PhD in Bioinformatics

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.

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.

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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, 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 upcoming 2024 release.


Current Projects

    These are the projects I currently work in (whenever possible).

  1. I am part of the JASPAR consortium since 2017. With other colleagues, I lead the curation and development of JASPAR, for the 2020 and 2022 releases. My contributions were to develop a workflow (using Snakemake) to ease the motif curation. This workflow performs the motif discovery and the ChIP-seq centrality enrichment score calculation; I am also behind the motif curation, and the visualization of the TF motif clusters.

    sample-image



  2. 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).

    sample-image


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


  3. 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 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.

    sample-image



    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.



    In this repository you can find a faster and stand-alone version (functional but still under active development).


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Research articles and book chapters

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

You can see here my contribution on each of the following papers.

Citations

Profile as reviewer

Preprints:

2. Genetic architecture of natural variations of cardiac performance in flies
Saha S*, Spinelli L*, Castro-Mondragon JA, Kervadec A, Kremmer L, Roder L, Sallouha J, Torres M, Brun C, Vogler G, Bodmer R, Colas AR#, Ocorr K#, and Perrin L# (2021) bioRxiv.
1. Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of the gene regulatory program in cancers
Castro-Mondragon JA, Ragle Aure M, Lingjærde OC, Langerød A, Martens JWM, Børresen-Dale AL, Kristensen VN, and Mathelier A (2020) bioRxiv.

Peer-reviewed publications:

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
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
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
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.
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.
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.
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
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#, 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) Microbiology.
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

Posters presented in conferences
  • Castro-Mondragon JA, Ragle Aure M, Kristensen V, Mathelier A
    "Combining transcriptional and post-transcriptional regulation to predict mutations altering the gene regulatory program in cancer cells".
    Systems Biology; Global Regulation of Gene Expression, CSHL, USA. [Full text]
  • Castro-Mondragon JA, Ragle Aure M, Kristensen V, Mathelier A
    "Combining transcriptional and post-transcriptional regulation to predict mutations altering the gene regulatory program in cancer cells".
    ISMB/ECCB 2019, Basel, Switzerland. [Full text]
  • 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]

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Parallel dimensions

  • I tried to (randomly) generate the work of Antonieta Sosa entitled 'Ajedrez Visual (Visual Chess)' through this shiny app: Random Visual Chess.
  • I am a core member of the ISCB Regional Student Group (RSG) Norway, a non-profit organisation aimed at creating a platform that will have a crucial role in fostering interactions and networking among students, early-career researchers and professionals in computational biology and related fields.
  • Among my interest is understanding the Mayan arithmetic to measure time, for example the vigesimal system, how they measured time using different calendars, and how these calendars are synchronized.