Developed bioinformatics platforms for engineered fungal strains, to identify human drug targets in biosynthetic gene clusters.• Identified representative transcriptomic features to assess fungal cluster activity, systematic coregulation, and core synthase correlation.• Established cross-functional data management strategies with bench collaborators, LIMS managers, and data scientists to facilitate reporting.• Conducted troubleshooting and quality control of sequence data… Show more Developed bioinformatics platforms for engineered fungal strains, to identify human drug targets in biosynthetic gene clusters.• Identified representative transcriptomic features to assess fungal cluster activity, systematic coregulation, and core synthase correlation.• Established cross-functional data management strategies with bench collaborators, LIMS managers, and data scientists to facilitate reporting.• Conducted troubleshooting and quality control of sequence data, collaborating closely with computational and experimental scientists to design experiments.• Led pipeline engineering and infrastructure development initiatives; planned, scheduled, and executed at all stages of implementation. Show less

Modeled heterogeneity of gene expression in single-cell data.• Processed and analyzed scRNA-seq data using both the 10X Genomics Chromium technology and the SMART-Seq protocol on Illumina MiSeq, HiSeq, and NovaSeq platforms.• Assessed intratumor heterogeneity by inferring the true distribution of counts from observed data. Applied statistical distributions to deconvolute scRNA-seq expression from sampling variability and technical/biological noise.• Developed, tested, and… Show more Modeled heterogeneity of gene expression in single-cell data.• Processed and analyzed scRNA-seq data using both the 10X Genomics Chromium technology and the SMART-Seq protocol on Illumina MiSeq, HiSeq, and NovaSeq platforms.• Assessed intratumor heterogeneity by inferring the true distribution of counts from observed data. Applied statistical distributions to deconvolute scRNA-seq expression from sampling variability and technical/biological noise.• Developed, tested, and documented single-cell sequencing pipelines to investigate tumor heterogeneity. Integrated multi-modal data to generate confident single-cell population profiles.• Supported assay development in targeted single-cell sequencing, collaborating and effectively communicating with interdisciplinary teams.• Supervised a six-month co-op student in data analysis, bioinformatics software development, project management, and professional communication. Show less

Conducted bioinformatics analysis in neoantigen discovery using genomic and transcriptomic datasets.• Integrated scientific literature and in-house tumor samples to discover new immunotherapy targets, using the company’s proprietary machine learning model.• Conducted troubleshooting and quality control of sequence data, collaborating closely with computational and experimental scientists to design experiments.• Incorporated model updates in established prediction pipelines to… Show more Conducted bioinformatics analysis in neoantigen discovery using genomic and transcriptomic datasets.• Integrated scientific literature and in-house tumor samples to discover new immunotherapy targets, using the company’s proprietary machine learning model.• Conducted troubleshooting and quality control of sequence data, collaborating closely with computational and experimental scientists to design experiments.• Incorporated model updates in established prediction pipelines to identify novel tumor-specific targets for immunotherapy.• Applied and resolved biological inaccuracies in open-source code for HLA type calling.• Established Kanban- and Wiki-based workflows for successful project management across and within departments. Show less

Developed tools to conduct bioinformatics analysis with Next Generation Sequencing.• Built and maintained pipelines for sequencing analysis, generating workflows to automate bioinformatics processes including quality control, read normalization, alignment, filtering, and variant calling.• Established significance of experimental results, developing probabilistic models to calculate statistical power.• Collaborated with interdisciplinary teams to design biological… Show more Developed tools to conduct bioinformatics analysis with Next Generation Sequencing.• Built and maintained pipelines for sequencing analysis, generating workflows to automate bioinformatics processes including quality control, read normalization, alignment, filtering, and variant calling.• Established significance of experimental results, developing probabilistic models to calculate statistical power.• Collaborated with interdisciplinary teams to design biological experiments.• Communicated computational biology principles to collaborators and funding agencies; wrote statistical sections of grant applications and scientific manuscripts.• Visualized analyses of large datasets, constructing cogent narratives from 500+ million read sequencing runs.• Trained lab members to use bioinformatics tools and perform exploratory data analysis; mentored undergraduate students by designing introductory bioinformatics projects. Show less

Trained and developed students into leaders of global impact.• Designed and led workshops on public speaking, cross-cultural communication, and event planning.• Fundraised $50,000+ yearly budget through alumni networks. • Led 80+ person service projects to New Orleans, rebuilding homes in the wake of Hurricane Katrina. Guided dialogue with local residents, as well as programmed discussions on economic injustice and racial reconciliation.