Computational biologist working at the intersection of genomics, statistics and software. My PhD (Washington University in St. Louis, 2023) used single-cell sequencing and statistical modeling to study why genetically identical cells express genes differently. I have also built tools for calling mutations and checking sample identity in large sequencing studies.
Languages: Python, R, C/C++
Methods: single-cell RNA-seq analysis, variant calling, statistical
modeling, supervised cell-state classification, massively parallel reporter
assays
Tools: Seurat, Monocle 3, Garnett, Bioconductor, samtools/htslib, CMake
- hedgehog-variability: single-cell RNA-seq analysis showing that transcription factor fluctuations drive variable Hedgehog signaling responses, including a trained cell-state classifier
- arnav: mutation calling from RNA-seq using site-specific binomial error models (C++), used on GTEx data
- maury: R package to detect sample swaps and relatedness in NGS data
- castools: processing and analysis code for SARGENT, single-cell measurement of reporter-gene noise across the genome (Genome Biology 2024)
- regtools: integrates tumor DNA-seq and RNA-seq to find splice-altering variants in cancer; I was a lead developer (Nature Communications 2023)
- mpileup2readcounts: per-nucleotide read counts from samtools mpileup
- bam-parser-tutorial: getting started with parsing BAM and VCF files using htslib
- Ramu A, Cohen BA. Transcription factor fluctuations underlie cell-to-cell variability in a signaling pathway response. GENETICS (2023). bioRxiv
- Hong CKY, Ramu A, Zhao S, Cohen BA. Effect of genomic and cellular environments on gene expression noise. Genome Biology (2024). link
- Cotto KC, Feng YY, Ramu A, et al. Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer. Nature Communications (2023). link
- Rockweiler NB, Ramu A, et al. The origins and functional effects of postzygotic mutations throughout the human life span. Science (2023). link
- Ramu A. Arnav: Site specific error models to identify variants in RNA. bioRxiv (2018). link
- Full list on Google Scholar