Richa Rashmi

Bioinformatician and computational biologist with a PhD in Bioinformatics and 3+ years of postdoctoral research experience, complemented by a current industry role developing end-to-end NGS pipelines across 6 assay types. Expertise spans RNA-seq, ATAC-seq, scRNA-seq, spatial transcriptomics, CUT&RUN, and multi-omics data integration using R, Python, and HPC environments. First-author publications in peer-reviewed journals including Genome Research.

Experienced working across academic, clinical, and cross-functional research settings.

Bioinformatician II - Georgia Cancer Center

(2025-10)

• Designed and deployed end-to-end NGS analysis pipelines on HPC (SLURM) across 6 assay types and >100 samples: ddRAD-seq, ATAC-seq, scRNA-seq, spatial transcriptomics, BD Rhapsody WTA, and CUT&RUN
• Built a ddRAD-seq demultiplexing pipeline processing 58 samples across 2 sequencing lanes using combinatorial inline x i7 barcoding (BCL, FASTQ, Stacks)
• Developed an ATAC-seq differential accessibility pipeline for 22 samples: MACS2 peak calling, DiffBind/DESeq2 (11 donors, ~20 contrasts), HOMER motif enrichment, TOBIAS TF footprinting, and promoter accessibility scoring
• Implemented 10x Genomics scRNA-seq workflows integrating 4 samples via SCTransform + RPCA, identifying 31 cell clusters; performed per-subset DE analysis, pathway scoring (IFN-I, IL-6), and Loupe Browser export
• Processed Visium spatial transcriptomics data (4 sections, 2 CytAssist slides) using Space Ranger count/aggr with probe-based and poly-A library configurations
• Configured and executed a BD Rhapsody WTA + TCR CWL pipeline for whole-transcriptome single-cell analysis
• Built a modular CUT&RUN pipeline (FastQC, Trim Galore, Bowtie2, Picard dedup, MACS2, HOMER annotation) with non-specific binding QC using SKF1 KO controls

Postdoctoral Research Associate - Texas A&M Health Science Center

(2022-05 - 2025-09)

• Developed and implemented IPAseek, an R-based algorithm to detect intronic polyadenylation sites (IPA) from RNA-seq data, improving detection accuracy
• Performed DNA methylation analysis to study epigenetic biogenesis of IPA
• Analyzed large-scale multi-omics datasets (TCGA, GTEx, ENCODE) to identify novel regulatory elements involved in gene regulation
• Mentored >5 undergraduate and graduate students in bioinformatics data analysis and algorithm development, resulting in completion of theses and presentations at conferences
• Performed lab purchasing and financial management

Teaching Assistant, Bioinformatics & Computational Biology (BE691-III) - Indian Institute of Technology Gandhinagar

(2021-07 - 2021-12)

• Instructed a class of 20 undergraduate, master's, and PhD students in bioinformatics and computational biology
• Collaborated with faculty to design assessments aligned with course learning outcomes
• Held office hours and provided 1:1 student support as needed

Data Science Intern - Kvantum Inc.

(2017-09 - 2017-10)

• Analyzed marketing data using Python and Scikit-learn to identify key trends in customer behavior, leading to an increase in targeted marketing campaign effectiveness
• Developed data visualizations to communicate findings to stakeholders, improving data-driven decision-making

Research Intern - CSIR-Institute of Genomics & Integrative Biology

(2016-05 - 2017-05)

• Performed microarray data analysis using R and Bioconductor to identify differentially expressed genes in Type 2 Diabetes Mellitus, contributing to understanding of disease mechanisms

Doctor of Philosophy - Bioinformatics.

Dissertation: "Investigating conservation and disease association of THAP9 using sequence, structure, and expression data." Advisor: Dr. Sharmis - Indian Institute of Technology Gandhinagar (2022-10)

Master of Technology - Computational Biology.

Thesis: "An integrated gene expression analysis of normal healthy controls across all datasets available for genes implicated in Type 2 d - Indraprastha Institute of Information Technology Delhi (2017-08)

Bachelor of Technology - Electronics and Communication Engineering - Punjab Technical University (2014-07)