San Diego, California, United States
Computational biology leader with 9 years of industry experience supporting drug discovery and therapeutic development. I currently lead an analyst team, in direct contact with clients, managing cross-functional parties to deliver data-driven insights from complex genomic and transcriptomic datasets. I have worked with 35+ companies across the biopharma industry, with expertise in next-generation sequencing, single-cell gene expression, RNA-seq, genomics, epigenetics, and oligonucleotide therapeutics. Known for clear communication, scientific rigor, and collaborative leadership across computational, experimental, and therapeutic teams. Core expertise: Bioinformatics, NGS data analysis, RNA-seq, single-cell RNA-seq, genomics, ChIP-seq, RIP-seq, oligonucleotide therapeutics, epigenetics, molecular biology.
- Led and performed the NGS analysis pipeline development - Integrated automated NGS pipeline with our LIMS (Laboratory information management system) - Supported three project teams to accomplish their research goals with data analysis and interpretation for PD signature development, gene and microRNA expression characterization of organ cell types and cell lines, and for efficacy studies in mice and humans - Developed four web applications (in Shiny) for screening data analysis automation and for data visualization and interpretation - Reorganized Linux bioinformatics infrastructure while supervising a system administrator to facilitate cross-server analyses and parallel processing
- Identified and isolated four subpopulations of fibroadipogenic population of mesenchymal cells in skeletal muscles by single cell gene expression quantification in the context of either acute or chronic injury. Phenotypically and transcriptionally characterized those FAPs subpopulations - Uncovered the role of a SWI-SNF protein, Baf60c, in directing the binding of a master transcription factor, MyoD, on specific E-boxes motifs and in restricting the transcriptional activity of alternative lineages in MyoD-expressing hESC (human Embryonic Stem Cells) - Contributed to several publications with NGS data analysis and interpretation - Designed and developed an internal NGS database.
Teaching Assistant at the CURE Summer Science Enrichment Program for high school students.
- Uncovered novel indirect mechanisms of epigenetic regulation of gene expression in Immunodeficiency, Centromere instability and Facial anomalies syndrome (ICF), where mutations in DNA methyltransferase 3B (DNMT3B) protein cause DNA hypomethylation. Integration of data from ChIP-seq, RNA-seq, RIP-seq and Bisulfite-seq - Studied microRNA roles in the pathogenesis of ICF syndrome. Found that altered miRNAs have altered histone modifications more than altered DNA methylation in this context - Studied the epigenetic pathogenesis of an unbalanced X;2 translocation in a patient with Incontinentia Pigmenti, providing new insights into long-range gene silencing and their impact on human diseases
- Mastered ChIP-seq techniques by performing every step with experts in the lab - Worked closely with the bioinformatics core to improve my analysis pipeline and extend it to identify histone modifications enrichment within repeated sequences in the genome