Amal Thomas Email & Phone Number

Foster City, California, United States

- Design, development, and implementation of Bioinformatics and Machine Learning methods to integrate multi-modal genomics datasets to support clinical development- Developed and implemented bioinformatics pipelines, including gene-expression quantification (RNA-Seq), mutation calls (WES/WGS), detecting fusion transcripts, and ctDNA annotation for Omics.

South San Francisco, California, United States

• Contributed to algorithms and eQTL detection pipelines to enable functional annotation of genetic associations to identify genetically-informed drug targets
• Improved existing RNA-Seq analysis pipeline to quantify overlapping genes accurately and streamlined the workflow to reduce computational expenses
• Worked on assessing lncRNAs as explanations of association signals and as potential drug targets
• Worked on evaluating scRNA-seq eQTLs as a gene mapping source
• Received 23andMe Therapeutics recognition award for reducing computational cost (> $40K) associated with reprocessing gene-expression datasets
• Honored with two 23andMe Therapeutics Phenomenal Thanks awards for exceptional contributions in assisting colleagues

Los Angeles Metropolitan Area

Los Angeles

• Developed a homology-independent algorithm to analyze and query gene expression data across species. Characterized functionally important genes from cross-species gene expression datasets.
• Developed bioinformatics pipelines to analyze RNA-Seq, ATAC-Seq, ChIP-Seq, WES, single-cell omics data, and other epigenetic next-generation sequencing data
• Collaborated on projects studying the metastasis mechanisms of circulating tumor cells (CTCs)
• Proficient in using bioinformatics tools for analyzing genomics datasets, including Bioconductor packages, GATK, BWA, STAR, Salmon, VEP, etc.
• Extensive experience with biological databases: NCBI, Ensembl, GEO/ArrayExpress, SRA, GTEx, ENCODE, GDC, and TCGA

Los Angeles Metropolitan Area

United States

• Mentor, gtfBase project, Open Bioinformatics Foundation
• Help and evaluate GSoC contributor participation
• Development of curated resource of multispecies genomic regions

United States

• Mentor, pysradb project, Open Bioinformatics Foundation
• Development of a method to retrieve information from NCBI’s SRA database
• Help and evaluate GSoC contributor participation

Kharagpur Area, India

• Undergraduate Research Assistant at Computational Structural Biology Group, IIT Kharagpur
• Computational prediction of microRNAs & Structural analysis of ribosomal complexes

Pune, Maharashtra, India

Development of alignment-based filters for efficient classification of 16S rDNA sequences

Singapore

Identifying the regulation of microRNA 5′ selection in fruit flies by analyzing small RNA sequencing data

Doctor Of Philosophy (Ph.D.), Computational Biology And Bioinformatics

Bachelor And Master Of Technology (B.Tech + M.Tech), Biotechnology And Biochemical Engineering

Education record