Seeking Senior Scientist roles in therapeutics companies: Translational Multi-omics, Target Discovery & Biomarkers, with a focus on single-cell and spatial biology.
Presented a poster at the Lung Science Conference (2026), Estoril, Portugal · Awarded the EHLRS Grant (2025) for PULP-in-PEAR.
About Me
I am a computational biologist and final-year PhD candidate with 15+ years of experience spanning clinical genomics, NGS workflows, scientific computing, and single-cell disease biology.
My doctoral research applies human and mouse lung multi-omics to study fibrotic disease states, gene regulatory programs, and perturbation responses with relevance to translational research. As I move toward the final stage of my PhD, I am preparing to transition into industry R&D, where I hope to contribute to computational biology strategies in target discovery, biomarker development, translational medicine, and precision medicine.
Technically, I work day-to-day in Python and R for single-cell and multi-omics analysis, including Scanpy, Seurat, and Bioconductor. I also bring a strong foundation in UNIX/Linux, shell scripting, AWK/SED, HPC environments, AWS, GitHub-based version control, and reproducible workflow development. Earlier in my career, Perl was a major part of my bioinformatics toolkit, and that background still shapes how I think about robust, practical data handling.
I care deeply about making analyses reproducible, well-documented, and easy for others to understand, reuse, and build upon. My code and selected projects are available on GitHub.
Beyond my research, I enjoy practical scientific community-building. I have spent 14+ years learning from and contributing to BioStars, long before LLM-based tools became part of everyday bioinformatics workflows.
I also maintain a blog where I document discoveries, mistakes, and learning moments from my PhD journey, and I run a small YouTube channel with tutorials and walkthroughs for researchers working through similar problems.
Sharing what I learn has become one of the most rewarding parts of my work. If something I wrote, answered, or explained ever saved your time without me knowing, let me know! :)
I value conversations that move naturally between science, technology, ideas, and everyday life. If my work or outlook resonates with you, I would be happy to connect here.
“To ensure that the community can explore and build upon our results without specialized bioinformatics expertise, we have developed an interactive browser-based webtool… Really nice work by the talented Sai Rama Sridatta Prakki.”
Research
My current research focuses on understanding lung biology at single-cell resolution at the Research Unit for Precision Regenerative Medicine and Institute of Computational Biology, Helmholtz Munich, as a doctoral candidate affiliated with the Technical University of Munich (TUM).
Focus areas
sc/snRNA-seq analysis
Processing and analyzing single-cell/nucleus RNA-seq data from lung tissues (human/mouse)
Interactive web applications
Building tools for the lung research community
Training & mentorship
Helping colleagues improve their bioinformatics skills
Current projects
Profiling of in vivo IPF Lung Tissues
Characterizing Early Disease Cell States in Idiopathic Pulmonary Fibrosis (IPF) Using MicroCT Staging and Single-Nucleus Transcriptomics
Exploring of fibrosis induced ex vivo Lung Tissues
Time-Resolved Single-Nuclei RNA-Seq in Fibrotic Human Precision-Cut Lung Slices coupled to perturbations
Web apps
Bleomycin Aging App
Interactive R Shiny application for exploring lung aging data
Open the app ↗Galapagos Dataset Explorer
Interactive explorer for the Galapagos lung dataset
Public release upcomingEx Vivo Time-Course Explorer
Explore time-resolved single-nuclei RNA-seq of fibrotic human precision-cut lung slices
Public release upcomingIn Vivo Lung Cell Atlas
Explore single-nuclei RNA-seq of fibrotic human lung tissue across epithelial, endothelial, mesenchymal and immune compartments
Public release upcomingTools I've built
MAPLE
Turns marker genes into literature-backed cell type labels, with every call traced to a supporting sentence and PMID.
Try it on Hugging Face ↗MarkerMind
AI-powered literature mining: extracts cell types, their marker genes, the methods used to identify them, and the biological context from pasted text or uploaded PDFs.
RUMAPS
A Python package for refined UMAP visualizations with clean labeling and interactive exploration, built to fit into single-cell workflows with scanpy and anndata.
View on GitHub ↗CPgeneProfiler
A lightweight R package to profile the Carbapenamase genes from genome assemblies.
View on GitHub ↗Supervisors
Prof. Dr. Herbert Schiller
Director, Research Unit for Precision Regenerative Medicine
Prof. Dr. Fabian Theis
Director, Institute of Computational Biology
Experience
Doctoral Candidate — Computational Biology
Helmholtz Center Munich · Technical University of Munich (TUM) · Germany
- Co-lead and drive single-nucleus analysis of microCT-staged human IPF lung tissue to identify early-disease cell states as candidate targets and biomarkers.
- Profile time-resolved, perturbed human precision-cut lung slices, using ex vivo models to test cellular responses to fibrosis-relevant interventions.
- Built and deployed interactive single-cell atlases (~605k cells), including a 12.5× storage reduction that made a 20 GB atlas deployable; the Bleomycin Aging app is openly accessible with no sign-in required.
- Built MAPLE, an LLM-based tool that annotates cell types from the literature and traces every label to a supporting citation.
- Partner with wet-lab scientists on experimental design and interpretation, and train colleagues in single-cell and reproducible analysis workflows.
Senior Bioinformatician
National Centre for Infectious Diseases · Singapore
- Delivered bacterial whole-genome sequencing analysis in a clinical production setting, with results informing infection-control and outbreak investigations; single projects spanned 1,000–1,500 bacterial genomes.
- Built automated, reproducible pipelines for clinical genomics and moved them into routine use; contributed to Nextflow-based processing of SARS-CoV-2 nanopore data.
- Developed and published the R package CPgeneProfiler for bacterial genomic feature profiling.
- Managed sequencing data, HPC pipelines and computational infrastructure for national clinical and public health genomics projects.
Research Associate
Saw Swee Hock School of Public Health, NUS / NCID · Singapore
- Established standard operating procedures for bacterial genome analysis and optimized HPC workflows for large-scale sequencing studies.
Bioinformatics Engineer
Temasek Life Sciences Laboratory, NUS · Singapore
- Contributed to the Asian Seabass Genome Project (with the South African National Bioinformatics Institute), performing genome assembly, transcriptomics and comparative genomics.
- Applied these methods across Asian seabass, tilapia and arowana genomes.
Research Intern
Genome Institute of Singapore, A*STAR · Singapore
- Conducted computational analysis of algal genome and transcriptome datasets, including Botryococcus species.
Education
Doctoral Candidate in Bioinformatics
Technical University of Munich (TUM) · Helmholtz Center Munich, Germany
Master of Science in Bioinformatics
Nanyang Technological University (NTU), Singapore
Bachelor of Technology in Bioinformatics
Bharath University, Chennai, India
Selected publications All on Google Scholar →
15+ peer-reviewed publications in genomics, infectious diseases, and single-cell biology.
Single cell decomposition of multicellular aging programs associated with impaired lung regeneration.preprint
bioRxiv · DOI
Plasmid dynamics driving carbapenemase gene dissemination in healthcare environments.
Nature Communications 16:9522 · DOI
Dissemination of Pseudomonas aeruginosa blaNDM-1 positive ST308 clone in Singapore.
Microbiology Spectrum · DOI
Whole Genome Sequencing Reveals Hidden Transmission of Carbapenemase-producing Enterobacterales.
Nature Communications · DOI
Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding.
PLoS Genetics 12(4):e1005954 · DOI
Poster presentations
ERS Lung Science Conference (LSC) — Estoril, Portugal
Poster: Time-Resolved Single-Nuclei RNA-Seq in Fibrotic Human Precision-Cut Lung Slices coupled to Perturbations · ERJ Open Research 12(suppl 18):PS336 · DOI
Single Cell Genomics (SCG) — Stockholm, Sweden
Poster: Dissecting Early Disease Cell States in Idiopathic Pulmonary Fibrosis (IPF) Using MicroCT Staging and Single-Nucleus Transcriptomics
Deutsches Zentrum für Lungenforschung (DZL) — Bad Nauheim, Germany
Poster: Towards perturbation analysis of cell lineage specific transcriptional regulons in pulmonary fibrosis
Singapore Health and Biomedical Conference (SHBC) — Singapore
Poster: Dissemination of Pseudomonas aeruginosa blaNDM-1 positive ST308 clone in Singapore
European Society of Clinical Microbiology and Infectious Diseases (ECCMID) — Amsterdam, Netherlands
Poster: Tracking plasmid-mediated horizontal gene transmission of blaNDM across Enterobacteriaceae
European Society of Clinical Microbiology and Infectious Diseases (ECCMID) — Madrid, Spain
Poster: Population whole-genome sequencing uncovers plasmid-mediated NDM persistence
Plant and Animal Genome (PAG) Asia — Singapore
Poster: Improved Assembly of the Asian Seabass Transcriptome
Plant and Animal Genome (PAG) — San Diego, California
Poster: Sequencing and Assembly of the Asian seabass Transcriptome
Technical skills
Programming
AI app development
AI-assisted coding
AI for research
Domains with Bioinformatics experience
WebApp development
Infrastructure
Languages
Community
Journal reviewer
- Journal of Open Source Software: PPanGGOLiN v2, a prokaryotic pangenome analysis tool (software, documentation and paper), 2026 · Review thread ↗
- BMC Infectious Diseases (Springer Nature), 2023
Tutorial Videos
Tutorials and walkthroughs for researchers working through bioinformatics problems
A Search For Solutions ↗Blog
Fixes in software/bugs/myrants in the past years
asearchforsolutions.blogspot.com ↗Certifications
- IdeaLab, two-day start-up workshop, UnternehmerTUM & TUM Venture Labs Aug 2026
- Data Analysis and Statistical Inference Duke University
- The Data Scientist's Toolbox Johns Hopkins
- R Programming Johns Hopkins
- Bioinformatics: Life Sciences on Your Computer Johns Hopkins
- Data Wrangling in R LinkedIn Learning
- Data Visualization with ggplot2 LinkedIn Learning
- Tools for Data Science IBM
- Big Data Systems Management Temasek Polytechnic
Grants & awards
Environmental Health and Lung Research School (EHLRS) Grant Award (€2,000)
Project: "Plasticity Unforeseen: Loss of PTK7/SOX4 in human fibrotic lung slices drives Pulmonary Epithelial AT2 Reprogramming (PULP-in-PEAR)"
Helmholtz Munich, Comprehensive Pneumology Center
Winner, Theis Lab Christmas Competition: “Ugly Plot” Design
Custom ggplot recognized for “exceptional excellence in the field of ugly plot design”
Institute of Computational Biology, Helmholtz Munich · Post ↗
Best Performer Award
Poster presentation at National Symposium on "Insilico Drug Design against Leishmaniasis"
SRM University, Chennai, India
Recent writing The Lab Notebook →
Contact
I'd be happy to connect! Feel free to reach out: