Platform Coordination & Strategic Leadership: Orchestrating medical and genomic data ecosystems through partnerships with industry and academic institutions, while supervising deployment of cancer research analytics frameworks and driving research collaboration initiatives
Technical Innovation & Research Advancement: Guiding implementation of breast cancer investigation toolsets and computational resources, overseeing patient data processing systems, and pioneering solutions that enhance research outcomes across partner networks
Program Management & Stakeholder Engagement: Leading multi-disciplinary teams in research initiatives, establishing operational protocols between external collaborators, and cultivating strategic relationships with academic and industry partners to accelerate scientific discovery

Integration of Genomic Tools: Lead development (containerization, python API layers, user interface) of 60+ analytics modules and 90 pipelines
‍Research Analysis and Insights: Analyzed molecular datasets for customers and team research needs using bioinformatics tools in diverse areas
‍Documentation and QA Standards: Created 50+ QA test datasets and internal documentation, increasing code maintainability and testing efficiency
‍Pipeline Development and Innovation: Designed and implemented custom pipelines, executing a vigorous infrastructure for fault-tolerant multi-omics analytics filling critical analysis gaps to improve service offerings by 30%
Leadership and Project Management: Presented and strategized novel processes aimed at enhancing operational efficiency to executive leadership while mentoring team members in codebase best practices, expediting high-quality analytics and pipeline delivery

TRANSCRIPTOMICS
RNA-Seq: Analyzing RNA-Seq data to quantify gene expression levels across different conditions or cell types, with expertise in alignment, normalization, and differential expression analysis
‍scRNA-Seq (Single-Cell): Processing and analyzing single-cell RNA-Seq data to understand cellular heterogeneity, including cell clustering, trajectory inference, and differential expression across cell types
Differential Isoforms: Skilled in identifying and quantifying alternative splicing events and isoforms using RNA-Seq data, contributing to the understanding of gene regulation and functional diversity
‍Cell Deconvolution: Proficient in computational techniques to deconvolute bulk RNA-Seq data into its constituent cell types, enabling the estimation of cell type proportions in heterogeneous tissue samples
Gene Fusions: Expertise in detecting and characterizing gene fusion events from RNA-Seq data, which are critical in cancer genomics and other disease contexts
GENOMICS
WGS (Whole Genome Sequencing): Experienced in the analysis of whole genome sequencing data, including alignment to reference genomes, variant calling, and annotation of genomic variants
Variant Detection: Skilled in identifying single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variants from genomic data, with an emphasis on filtering, prioritization, and clinical interpretation
Genome Assembly: Proficient in assembling genomes from short-read or long-read sequencing data, using de novo or reference-guided methods, to reconstruct the complete genome of an organism
GENE-EDITING
Off-Target Prediction: Predict potential off-target effects of CRISPR/Cas9 gene-editing, ensuring specificity and minimizing unintended genomic alterations
Viral Integration: Detecting viral integration sites in host genomes, particularly in the context of gene therapy, to assess the safety and efficacy of viral vectors
Metagenomics: Study the composition, function, and diversity of microbial communities, including taxonomic profiling, functional annotation, and comparative analysis across environments or conditions
QUALITY CONTROL
Read Filtering and Trimming: Applying quality control measures to NGS data, including the removal of low-quality reads and adapter sequences, ensuring high-quality downstream analysis
‍File Conversion: Various NGS data formats (e.g., FASTQ, BAM, VCF) and converting between them as necessary for different analysis pipelines
EPIGENOMICS
ChIP-Seq (Chromatin Immunoprecipitation Sequencing): Map protein-DNA interactions, including peak calling, motif analysis, and integration with gene expression data
ATAC-Seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing): Assess chromatin accessibility and identify regulatory elements across the genome
PROTEOMICS
Mass-Spectrometry: Identify and quantify proteins, post-translational modifications, and protein complexes in biological samples
Flow Cytometry: Characterize cell populations, surface markers, and intracellular signaling pathways
Gene Ontology and Annotation: Providing insights into the biological processes, molecular functions, and cellular components associated with gene sets

Bioinformatics Implementation: Initiated and implemented bioinformatic processes in research labs where previous work was outsourced to external vendors saving significant grant funding
High-Throughput Approaches: Utilized high-throughput, unbiased sequencing approaches to identify alternatively spliced genes during S. Typhimurium and M. tuberculosis infection to determine host factors required for controlling and/or establishing infection

Function and Regulation of Phosphorylation: Defined the function and regulation of phosphorylation of splicing factors and its impact on host outcomes during Salmonella Typhimurium and Mycobacterium tuberculosis infection
RNA-Binding Proteins and Immune Processes: Investigated how innate immune signaling affects RNA processing, highlighting the roles of RNA-binding proteins in viral and bacterial infections
Post-Transcriptional Gene Regulation: Elucidated post-transcriptional gene regulation during innate immune signaling, specifically pre-mRNA splicing, in modulating host responses to bacterial infection using bioinformatics and molecular techniques

NSAIDs Side Effects Characterization: Analyzed gastrointestinal, urinary, and pharmacokinetic parameters using statistical programs such as SAS, SPSS, and R to evaluate side effects of nanoparticle drug formulations in commonly used nonsteroidal anti-inflammatory drugs (NSAIDs), Diclofenac and Celecoxib
Data Collection and Analysis: Collected epidemiological data through community surveys and interviews in Nueva Vida, Nicaragua to study risk factors associated with global public health priorities, including type II diabetes, biosand water filters, HIV/AIDS, and pap smear utilization
Community Engagement: Facilitated focus groups and a Community Health Status Assessment (CHSA) across a 29-county region to identify major healthcare needs
Evidence-based Methods and Reporting: Conducted qualitative data analysis to produce an inclusive report with evidence-based intervention recommendations for identified health priorities, shared with the community and healthcare professionals

Infection Models: Setting up and maintaining infection models in cell culture systems, handling a variety of pathogens under controlled conditions
BSL3 and BSL2 Training: Trained and certified to work in Biosafety Level 2 and 3 laboratories, adhering to rigorous safety protocols while conducting high-risk pathogen research
Lentiviral Production: Proficient in the generation and titration of lentiviral vectors for stable gene expression, knockdown, or overexpression studies in mammalian cells
Site-Directed Mutagenesis: Introducing specific nucleotide changes into the DNA sequence to study gene function or protein activity
shRNA Knockdown: Designing and applying shRNA constructs to silence gene expression, optimizing conditions for effective knockdown and minimal off-target effects
CRISPR/Cas9 and gRNA Design: Design and application of CRISPR/Cas9 gene-editing technology, including guide RNA (gRNA) design, to create targeted gene knockouts or modifications
Molecular Assays: RT-qPCR, ChIP (Chromatin Immunoprecipitation)
Immunofluorescence: Confocal microscopy for high-resolution imaging of cells and tissues, with experience in multi-color staining, image analysis, and 3D reconstruction to study cellular structures and protein localization
Protein Detection: Protein extraction, SDS-PAGE, and immunoblotting techniques to detect and quantify specific proteins, including optimization of antibody conditions and detection methods
Immunoprecipitation: Isolating specific proteins from complex mixtures using antibodies, followed by analysis through Western blotting or mass spectrometry
ELISA (Enzyme-Linked Immunosorbent Assay): Performing ELISAs for the quantification of proteins, cytokines, or other biomolecules in various sample types
Cellular Fractionation: Subcellular fractionation techniques to separate cellular components, enabling the study of specific organelles or protein complexes.
BioID (Proximity-Dependent Biotin Identification): BioID technology for mapping protein-protein interactions and identifying potential interacting partners within the cellular context