Juan Felipe Ortiz
Singapore, Singapore ·
juanfortizq@gmail.com
10 years experience designing HPC and cloud-native scalable solutions to run NGS and comparative genomics analyses, from standardized to complex, in production environments.
Awards
Social Media Presence
Publications
This has been an arduous path, but it is satisfying to see the products of my work, big and small.
Oral presentation - A Novel Homology-Based Algorithm for Identifying Closely Spaced Clusters of Tandemly Duplicated Genes. Quest for Orthologs 5. Los Angeles, USA.
Closely spaced clusters of tandemly duplicated genes (CTDGs) contribute to the diversity of many phenotypes, including chemosensation, snake venom, and animal body plans. CTDGs have traditionally been identified subjectively as genomic neighborhoods containing several gene duplicates in close proximity; however, CTDGs are often highly variable with respect to gene number, intergenic distance, and synteny. This lack of formal definition hampers the study of CTDG evolutionary dynamics and the discovery of novel CTDGs in the exponentially growing body of genomic data. To address this gap, we developed a novel homology-based algorithm, CTDGFinder, which formalizes and automates the identification of CTDGs by examining the physical distribution of individual members of families of duplicated genes across chromosomes.
July 2018
Poster - Where did chromosome 19 got its gene clusters?. SMBE Conference. Yokohama, Japan
Clusters of duplicated genes (CTDGs) are great contributors to the diversity exhibited by many phenotypes, like snake venom, animal body plans, and olfaction. To systematically study CTDGs, we developed CTDGFinder, a homology-based algorithm that statistically takes into account the size and spacing of duplicate gene locations in a genome, and has been shown to identify several well-known mammalian CTDGs (e.g., the Hox, globin, and protocadherin CTDGs). We found that more than 20% of human genes belong to CTDGs and that CTDGs span 7% of the total length of the human genome.
July 2018
Oral presentation - Quests and adventures in Genomic Geography. Three Minutes Thesis Competition. Winner. Vanderbilt University. Department of Biological Sciences
The genome, that wonderful land. We, humble explorers, have cataloged many genes, many hills. Even more, as we mapped genes in different genomes, we discovered that many genes come in clusters of duplicated genes! Those mountain ranges, spanning large sections of our genomes, provide a lush environment for diverse phenotypes: olfaction, immunity, and body plan architecture are just some examples.
May 2017
Article - CTDGFinder: A Novel Homology-Based Algorithm for Identifying Closely Spaced Clusters of Tandemly Duplicated Genes
Juan Felipe Ortiz, Antonis Rokas
October 2016
![]()
Article - A genetic map of cassava ( Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes
Johana Carolina Soto, Juan Felipe Ortiz, Laura Perlaza-Jiménez, Andrea Ximena Vásquez, Luis Augusto Becerra Lopez-Lavalle, Boby Mathew, Jens Léon, Adriana Jimena Bernal, Agim Ballvora & Camilo Ernesto López
March 2015
![]()
Article - Identification of Immunity-related Genes in Arabidopsis and Cassava Using Genomic Data
Luis Guillermo Leal, Alvaro Perez, Andres Quintero, Angela Bayona, Juan Felipe Ortiz, Anju Gangadharan, David MacKey, Camilo Lopez, Liliana Lopez-Kleine
December 2013
![]()
Article - Genomic Survey of Pathogenicity Determinants and VNTR Markers in the Cassava Bacterial Pathogen Xanthomonas axonopodis pv. Manihotis Strain CIO151
Mario Arrieta-Ortiz [42 more including Ortiz, J. F.] Adriana Bernal
November 2013
![]()
Article - Did the prion protein become vulnerable to misfolding after an evolutionary divide and conquer event?
Kacy Richmond, Patrick Masterson, Juan Felipe Ortiz, Jessica Siltberg-Liberles
July 2013
![]()
Article - Rapid Evolutionary Dynamics of Structural Disorder as a Potential Driving Force for Biological Divergence in Flaviviruses
Juan Felipe Ortiz, Madolyn L. MacDonald, Patrick Masterson, Vladimir N. Uversky, Jessica Siltberg-Liberles
February 2013
![]()
Article - Notes on the marine algae of the International Biosphere Reserve Seaflower, Caribbean Colombia II: diversity of drift algae in San Andres island, Caribbean Colombia.
Juan Felipe Ortiz, Brigitte Gavio
January 2010
![]()
Experience
Lead Bioinformatics Engineer
Cancer Sciences Institute. National University of Singapore
- Design cloud-based (AWS) architecture for deploying and running scalable NGS workflows.
- Encode scalable and optimized NGS workflows using the WDL and Nextflow languages.
- Design full-stack web application for submitting and tracking NGS workflows.
- Design and execute research projects and collaborative initiatives in NGS science.
March 2022 - Present
Special postoctoral fellow
RIKEN Center for Integratice Medical Sciences
- Develop algorithms for the assessment of novel chromatin conformation capture experiments.
- Design and execute research projects on comparative chromatin dynamics and their association with ageing.
April 2020 - February 2022
Postdoctoral fellow
RIKEN Biosystems Dynamics Research
- Develop data analysis pipelines and downstream analysis for RNA-seq experiments.
- Design and execute research programs combining structural genomics and evolutionary biology methods.
- Deploy a genome browser integrating multi-omics data for the brownbanded bamboo shark genome.
April 2019 - April 2020
Education
Vanderbilt University
Doctor of Philosophy
Biological Sciences
Publication: Ortiz, J F Rokas, A . (2016). CTDGFinder: A Novel Homology-Based Algorithm for Identifying Closely Spaced Clusters of Tandemly Duplicated Genes. Molecular Biology and Evolution 34 (1) : 215-229.
2014 - 2019
University of Wyoming
Master of Science
Molecular Biology
MacDonald, M L Masterson, P Uversky, V N Siltberg-Liberles, J . (2013). Rapid Evolutionary Dynamics of Structural Disorder as a Potential Driving Force for Biological Divergence in Flaviviruses. Genome Biology and Evolution 5 (3) : 504-513.
2011 - 2012
National University of Colombia
Bachelor of Science
Biology
Publication: Ortiz, J F Gavio, B . (2010). Notes on the marine algae of the International Biosphere Reserve Seaflower, Caribbean Colombia II: diversity of drift algae in San Andres island, Caribbean Colombia. Caribbean Journal of Science 46 (2-3) : 313-321.
2006 - 2011