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. At the moment we are collaborating with researchers in Corpoica, Colombia to continue the characterization of the Cape gooseberry transcriptome with additional data generated by next-generation sequencing technologies and have finalized the construction of a database using NCBI tools to display the newly assembled Cape gooseberry transcriptome. Additionally, we are in the process of analyzing interactions between plant growth promoting bacteria and banana plants. This is done in collaboration with Richa Agarwala and Roberto Vera Alvarez. In collaboration with John Spouge, we have studied the co-localization of transcription factor binding sites (TFBSs) within regulatory modules (RMs) and found that their tight positional conservation explains much of the TFBS positional preferences near the transcription start site (TSS). In another study related to the investigation of repeated sequences in genomes in collaboration with I. King Jordan we studied the human population-specific gene expression and transcriptional network modification with polymorphic transposable elements. We presented a systematic analysis of the regulatory contributions of polyTE loci that were generated by recent transpositional activity and thereby differ between individuals. We found that the phenotypic impact of human TE activity is not limited to deleterious effects; it also includes the generation of regulatory differences that fall within the scope of naturally occurring human variation and are involved in population-specific gene regulation as well as transcriptional network modification. We contributed to the genome assembly and annotation of 26 genome sequences of Vibrio cholerae strains obtained from clinical and environmental sources. Assemblies were constructed using Illumina and the genomes were annotated with the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP). This research was done in collaboration with I. King Jordan and Brian K. Hammer (Georgia Tech).
| 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 |
| Duplat-Bermúdez, L; Ruiz-Medrano, R; Landsman, D et al. (2016) Dataset of Arabidopsis plants that overexpress FT driven by a meristem-specific KNAT1 promoter. Data Brief 8:520-8 |
| Medina-Rivas, Miguel A; Norris, Emily T; Rishishwar, Lavanya et al. (2016) Chocó, Colombia: a hotspot of human biodiversity. Rev Biodivers Neotrop 6:45-54 |
| Bernal, Johan F; Donado-Godoy, Pilar; Arévalo, Alejandra et al. (2016) Whole-Genome Sequence of Multidrug-Resistant Campylobacter coli Strain COL B1-266, Isolated from the Colombian Poultry Chain. Genome Announc 4: |
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