About

I am currently a PhD student in the School of Computational Science and Engineering at Georgia Institute of Technology (CSE), home department: Bioinformatics, advised by Dr. Srinivas Aluru.

I specialize in designing and scaling computational algorithms to solve problems at the intersection of biology and high-performance computing. My work leverages parallel computing to analyze large-scale, complex, high-dimensional single cell genomics datasets. This includes developing novel methods for integrating diverse, multi-modal data types, such as gene expression and chromatin accessibility. By creating these scalable frameworks, my research aims to uncover complex cellular relationships and provide deeper insights into biological systems. A primary focus of this work is scSAGA, a single-cell sampled Gromov-Wasserstein alignment framework I developed for the scalable and memory-efficient integration of multi-modal data. By utilizing matrix-safe joint embeddings, scSAGA ensures numerical stability during optimal transport based large-scale single cell multimodal integration.Moving forward, I am exploring ways to parallelize Normalized Mutual Information (NMI) for single-cell multimodal integration and non-anchor based optimal transport methods for integration.

I also work on scalable tools for protein analysis, most notably CAHS (Context-Aware Homology Search). CAHS is a lightweight, knowledge-guided framework that augments trusted profile hidden Markov models (pHMMs), such as HMMER, with query-specific adaptation to local sequence contexts. By integrating protein language model embeddings and an intrinsic structural disorder prior, CAHS dynamically modulates gap-open and gap-extension probabilities for flexible regions while preserving strict statistical calibration and E-values. This context-aware approach expands the detection of remote homologs and accelerates end-to-end wall-clock runtimes on HPC clusters without inflating false positives.

Aside from my professional and academic interests, I love to pursue music as a hobby: I play the piano, cello, and pursue Indian classical singing! As a California-Bay Area native, I enjoy spending time outdoors and exploring the numerous hiking/running trails!

Reach me at sbhattaram6@gatech.edu.

Publications

CAHS: Context Aware Homology Search
S Bhattaram, D Bhowmik, R Kannan
ACM KDD 2026, AI for Sciences Track

scSAGA: Single-cell Sampled Gromov Wasserstein Alignment for Scalable and Memory-efficient Integration of Multi-modal Single Cell Data
S Bhattaram, S Chockalingam, M Aluru, S Aluru
Under Review