Abstract

Technological advances in DNA sequencing are enabling new areas of genomic research allowing fine connections between genomic variants and phenotype. We are studying transcriptomes and genomes from a variety of eukaryotic and prokaryotic non model organisms and have contributed to gain biological insights. We have used the generalized Ruzzo-Tompa algorithm to find repeats in genomic sequences and made an implementation of the algorithm called RepWords. In another study related to the investigation of repeated sequences in genomes we tested the possibility that mammalian-wide interspersed repeats (MIRs) contribute functional enhancers to the human genome. We found that MIRs are highly concentrated in enhancers of the K562 and HeLa human cell-types and MIR-derived enhancers were found to be a rich source of transcription factor binding sites. Therefore, MIRs can exercise a regulatory function in the human genome and this study contributes to explain why their role as the most ancient family of transposable elements.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Library of Medicine (NLM)
Type
Investigator-Initiated Intramural Research Projects (ZIA)
Project #
1ZIALM082713-02
Application #
8943234
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
2
Fiscal Year
2014
Total Cost
Indirect Cost

  Institution

Name
National Library of Medicine
Department
Type
DUNS #
City
State
Country
Zip Code

  Publications

Medina-Cordoba, Luz K; Chande, Aroon T; Rishishwar, Lavanya et al. (2018) Genome Sequences of 15 Klebsiella sp. Isolates from Sugarcane Fields in Colombia's Cauca Valley. Genome Announc 6:
Conley, Andrew B; Rishishwar, Lavanya; Norris, Emily T et al. (2017) A Comparative Analysis of Genetic Ancestry and Admixture in the Colombian Populations of Chocó and Medellín. G3 (Bethesda) 7:3435-3447
Rishishwar, Lavanya; Mariño-Ramírez, Leonardo; Jordan, I King (2017) Benchmarking computational tools for polymorphic transposable element detection. Brief Bioinform 18:908-918
Wang, Lu; Rishishwar, Lavanya; Mariño-Ramírez, Leonardo et al. (2017) Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements. Nucleic Acids Res 45:2318-2328
Vera Alvarez, Roberto; Medeiros Vidal, Newton; Garzón-Martínez, Gina A et al. (2017) Workflow and web application for annotating NCBI BioProject transcriptome data. Database (Oxford) 2017:
Hernández-Fernández, Javier; Pinzón, Andrés; Mariño-Ramírez, Leonardo (2017) De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean. Genom Data 13:18-20
Rishishwar, Lavanya; Wang, Lu; Clayton, Evan A et al. (2017) Population and clinical genetics of human transposable elements in the (post) genomic era. Mob Genet Elements 7:1-20
Acevedo-Luna, Natalia; Mariño-Ramírez, Leonardo; Halbert, Armand et al. (2016) Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules. BMC Bioinformatics 17:479
Bernal, Johan F; Donado-Godoy, Pilar; Valencia, María Fernanda et al. (2016) Whole-Genome Sequences of Two Campylobacter coli Isolates from the Antimicrobial Resistance Monitoring Program in Colombia. Genome Announc 4:
Watve, Samit S; Chande, Aroon T; Rishishwar, Lavanya et al. (2016) Whole-Genome Sequences of 26 Vibrio cholerae Isolates. Genome Announc 4:

Showing the most recent 10 out of 37 publications