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 - 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 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.

Current Projects

My main project for the moment is the study of mutations in TFBSs associated with trans-effect on gene expression. We associated TFBSs with protein-coding and miRNA genes and the assesed the likely association of observing TFBS mutations with changes in expression in the networks of the protein-coding and miRNAs. The methodlogy is based on a bayesian network and we applied it to 7 different cancer types from TCGA. Check out the preprint of this project.
I am part of the JASPAR consortium. My job contribution was 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 processes for the upcoming 2022 release.
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.
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 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.

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Research articles and book chapters

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

Preprints:

2.	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# (2020) 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:

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]

Jaime A Castro-Mondragón's webiste

In brief

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