I am interested in the study of early development gene regulatory networks and their role in animal form and function using a marine worm model system, the annelid Platynereis dumerilii. My research includes the design of computational tools for the analysis, and visualiztion of NGS data in order to assess patterns in gene expression, and in the transcriptional regulatory mechanisms during early asymmetric cell divisions.
PAST RESEARCH EXPERIENCE:
National Institutes of Health, National Center for Biotechnology Information, NCBI. Computational Biology Branch. April 2011 to 2014.
- My research project at NCBI aimed to identify the relationship between the binding site positions of transcription factors within a regulatory module and their function. Our approach involved intensive computations as we developed a computer program to categorize Transcription Factor Binding Sites (TFBS) motifs according to positional preference, and possibly to use positional preference to discover combinations of TFBS in cis-regulatory modules in the human genome.
Pontificia Universidad Javeriana, GeBiX: Colombian Center for Genomics and Bioinformatics of Extreme Environments, Research assistant with Jose Salvador Montana, February 2010 to March 2011.
- Project: “Molecular characterization of Sclerotium cepivorum strains associated with garlic crops in three of the major production zones in Colombia”. Sponsored by the Colombian Government through a grant from the Ministry of Agricultural and rural development under the project: “Technology innovation to improve garlic competitiveness in the national market”. Aimed to assess the genetic diversity of different strains of the phytopathogen fungi Sclerotium cepivorum in order to design better strategies to control the fungi pest in garlic crops. My participation in the project involved bench laboratory work as well as computational approaches.
National Institutes of Health, National Center for Biotechnology Information, Computational Biology Branch, Undergraduate Internship with Dr. David Lansman and Dr. Leonardo Marino, Fall 2006.
- Project: "Identification and localization of beta-Globin cluster regulatory sequences in different species". I developed novel computational approaches to identify regulatory elements of the Beta globin genes in different species. The project involved handling of databases and phylogenetic analysis. Our findings generated interesting conclusions about the evolutionary pattern of the regulatory mechanisms in the Beta globin cluster.
Pontificia Universidad Javeriana, Bogota, Colombia, Human Genome Institute, Undergraduate internship with Dr. Jaime Bernal, January 2005 to August 2006.
- Project: "Molecular Characterization of Carollia Bats Populations across an altitudinal gradiant". Evaluated the gene flow between isolated populations of Carollia perspicillata and Carollia castanea bats along a braod range of altitudinal distriution using microsatellite markers. The project involved taxonomic identification of Carollia bats, siolation of DNA from different tissues, amplification of heterologous VNTR DNA regions, Agarose and Acrylamide Electrophoresis, Population Genetics and Phylogenetic analysis using Arlequin software. The results were published and shared in the intramural research meeting at the Institute.
Fall 2015 to Fall 2018: Bio211L Teacher Assistant at Iowa State University, Genetics, Development and Cell Biology Department (GDCB)
Introduction to Biological Diversity (Bio211L). This introductory laboratory course in biology is intended for major and non-major freshman students.
Summer 2018: Elementary Spanish 101 - Online Session - Instructor at Iowa State University Department of World Languages and Cultures.
This Spanish class is a communicative approach to grammar and vocabulary within the context of Hispanic culture. For students whose native language is not Spanish.
- PdumBase: a transcriptome database and research tool for Platynereis dumerilii and early development of other metazoans.
Aug 16, 2018 BMC Genomics. See Publication
Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules.
Nov 21, 2016 BMC Bioinformatics. See Publication
- Identificacion y Localizacion de Secuencias de Regulacion de la Familia de Genes de Beta-Globina en Diferentes Especies - Abstract. In [X Congreso La Investigacion en la Pontificia Universidad Javeriana: Resumentes. Compiladora Doris Morales Alarcon. - 1ra Ed. Bogota: Editorial Pontificia Universidad Javeriana, 2009] (In Spanish)
Interests: I like hiking and biking. I also enjoy photography.