A computationally aided strategy to recover gene activity profiles from post-mortem HIV+ brains

This video is a record of geneXplain's webseminar "A computationally aided strategy to recover gene activity profiles from post-mortem HIV+ brain specimens" that was given on 19th of May 2021 by geneXplain's invited speaker Dr. Cecilia Marcondes, Associate Professor at San Diego Biomedical Research Institute.

Dr. Marcondes talked about her group’s attempt to overcome a challenge in the research of human tissues, where post-mortem intervals may impair the retrieval of quality information from the transcriptome.

Using epigenetic marks and computational analytical strategies, her group has successfully identified gene networks associated with critical biological processes in post-mortem brains from HIV+ cases, using resources from the National NeuroAIDS Tissue Consortium (NNTC). The combination of systems biology and visualization tools, including IPA, DAVID Bioinformatics Resources, Cytoscape, GeneMania, TRANSFAC FMatch, and iRegulon, led to the identification of genomic regions functionally annotated to inflammation, anti-viral response, and to synaptic pathways with the ability to distinguish individuals with history of substance use disorder in the context of HIV infection. This work demonstrates how creative strategies and computer aided analysis can help increase the power of association studies using valuable post-mortem human tissue.