Suhas Srinivasan

Methods & Tools

Tools released with published research, contributions to open-source computational biology tools and utilities for high-performance computing.

Methods & Tools

  • PLI Analyzer (PLIA)

    Extracts the interaction interfaces of protein, RNA and DNA complexes and compares them with known binding motifs and interaction domains, to validate AI-generated biomolecular complex structures.

  • DUSC: Deep Unsupervised Single-cell Clustering

    Hybrid method that couples deep-learning feature generation with model-based clustering for cell-type discovery in single-cell RNA-seq data.

  • Infection Dynamics (AGID model)

    Agent-based host–pathogen simulation that integrates a 3D GIS model of a confined environment, host behaviour and pathogen-specific parameters to track outbreaks and test containment protocols.

  • Dissociative disorder psychometrics analysis

    Data augmentation and supervised learning methods for psychometric data in trauma-related dissociation.

Open-source Contribution

  • RoseTTAFold2NA

    Extends the RoseTTAFold structure-prediction network to model protein–DNA and protein–RNA complexes, producing three-dimensional models with confidence estimates.

  • AlphaFold 3

    Inference pipeline for AlphaFold 3, a diffusion-based model that predicts the joint structure of complexes of proteins, nucleic acids, small molecules, ions and modified residues.

  • ORFik

    R/Bioconductor toolkit for processing, analysing and visualising translation data, including Ribo-seq, RNA-seq, CAGE and TCP-seq.

High Performance Computing

  • space-jam

    Parallel (pigz) compression and decompression scripts that reduce storage of text-based omics files, runnable as Slurm jobs.

  • elm-utils

    Slurm and shell utilities for preparing data for Stanford Research Computing's Elm archival storage and extracting data retrieved from it.

  • centos-rjags

    Installation steps for JAGS and rjags on CentOS.

Miscellaneous

  • multiplexed-scrna

    Analysis of multiplexed droplet single-cell RNA-seq data from Kang et al. (Nature Biotechnology, 2018) on cell-type-specific responses to IFN-β in lupus patients.

  • delivery-time

    Predictive analytics of delivery patterns and the time to fulfil a delivery, in an R notebook.

  • ad-campaign

    Time-series analysis of online advertisements, in an R notebook.