Work experience

Bioinformatician (Scientist II)

2022 - Present• Oslo, Norway

Nykode Therapeutics AS, Oslo, Norway.

Design and analysis of RNA‑seq data. Establishment of bioinformatic workflows (prediction of MHC‑binding peptides, protease cleavage sites, RNA secondary structure). Train ML models to highlight protein features explaining experimental observations.

Post-doctoral researcher

2017 - 2022 • Oslo, Norway

Centre of Molecular Medicine Norway Oslo, Norway.
Supervisor: Anthony Mathelier.

Multi-omics integration by associating somatic mutations with changes in gene expression (RNA-seq, CNA, SNVs) in multiple cancer types. Also, I worked in the update of the JASPAR database as a curator and developer. I peer-reviewed publicationf for journals and trained students. As a side project, I continued working as part of the RSAT team by maintaining the tools I developed during my PhD and updating the motif databases.

Education

PhD in Bioinformatics

2014 - 2017• Marseille, France

Aix-Marseille Universite, France.
Supervisor: Jacques van Helden.
Goals:
(1) Development of a tool 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• Paris, 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• Cuernavaca, Mexico

I did a research internship 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 mainly focused on Bioinformatics of Transcriptional regulation (as user and developer), mainly in algorithms related to Transcription Factor (TF) Binding Motifs and prediction TF Binding Sites, although Ihave experience in RNA-seq, cancer genomics, miRNA biology, and protease cleavage prediction. I'm an active developer of RSAT which is a collection of tools to analize Cis-Regulatory sequences and I am also involved in the JASPAR database, as curator and processing data for the upcoming release.

Current Projects

I am part of the JASPAR consortium since 2017. With other colleagues, I lead the curation and development of JASPAR during 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.
I am an active developer of the Regulatory Sequences Analysis Tools RSAT since 2013. RSAT 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 Factor Binding Motifs.

Example here.

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 or open an issue 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

Peer-reviewed publications:

23.	RhizoBindingSites v2.0 Is a Bioinformatic Database of DNA Motifs Potentially Involved in Transcriptional Regulation Deduced From Their Genomic Sites Taboada-Castro H, AJ Hernández-Álvarez, Castro-Mondragon JA, and Encarnación-Guevara S (2024) Bioinformatics and Biology Insights.
22.	Identification of transcription factor co-binding patterns with non-negative matrix factorization. Rauluseviciute I, Launay T, Barzaghi G, Nikumbh S, Lenhard B, Krebs AR, Castro-Mondragon JA, and Mathelier A (2024) Nucleic Acids Research.
21.	JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles. Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R^, Castro-Mondragon JA^, Ferenc K^, Kumar V^, Berhanu Lemma R^, Lucas J^, Cheneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B#, Sandelin A#, Wasserman WW#, Parcy F#, and Mathelier A#. (2024) Nucleic Acids Research.
20.	Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of gene regulatory programs in cancers Castro-Mondragon JA, Ragle Aure M, Lingjærde OC, Langerød A, Martens JWM, Børresen-Dale AL, Kristensen VN, and Mathelier A (2022) Nucleic Acids Research.
19.	Genetic architecture of natural variations of cardiac performance in flies Saha S, Spinelli L, Castro-Mondragon JA, Kervadec A, Lynott M, Kremmer L, Roder L, Sallouha J, Torres M, Brun C, Vogler G, Bodmer R, Colas AR#, Ocorr K#, and Perrin L# (2021) eLife.
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]

Jaime A Castro-Mondragón's webiste

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