Hey, I'm Datta (Sai Rama Sridatta Prakki)!
Doctoral Candidate @ Helmholtz Center Munich
Diving deep into the fascinating world of lung single-cell genomics. With 15+ years of bioinformatics experience spanning genomics, infectious diseases, and now single cell genomics, I decode what our cells are whispering to us using Python, R, and AI tools.
Download CVResearch
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.
- sc/snRNA-seq analysis — Processing and analyzing single-cell/nucleus RNA-seq data from lung tissues (human/mouse)
- Spatial transcriptomics — Integrating spatial context with gene expression
- Interactive 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
- Bleomycin Aging App — Interactive R Shiny application for exploring lung aging data
Supervisors
- Prof. Dr. Herbert Schiller
Director, Research Unit for Precision Regenerative Medicine - Prof. Dr. Fabian Theis
Director, Institute of Computational Biology
Experience
Doctoral Candidate
Helmholtz Center Munich
- sc/snRNA-seq data analysis from lung tissues (human/mouse)
- Developing applications for the lung research community
- Training colleagues on bioinformatics skills
Senior Bioinformatician
National Centre for Infectious Diseases (NCID)
- Bacterial genome sequence analysis and reporting for infection control
- Developed and published R package CPgeneProfiler
- Automated clinical bioinformatics using workflow management systems
- HPC data management and analysis pipeline development
Research Associate
Saw Swee Hock School of Public Health, NUS (External Staff at NCID)
- Developed SOPs for bioinformatics data analysis
- Bacterial genome data and metadata management
- HPC performance analysis and optimization
Bioinformatics Engineer
Temasek Life Sciences Laboratory, NUS
- Participated in the Asian Seabass Genome Project with the South African National Bioinformatics Institute (SANBI), focusing on bioinformatics analysis
- Involved in transcriptome analysis and genome assembly of Asian Seabass
- Applied comparative genomics methods to Tilapia and Arowana datasets
Research Intern
Genome Institute of Singapore, A*STAR
- Computational analysis of algal organism Botryococcus genomes and transcriptomes
Education
Doctoral Candidate in Bioinformatics
Helmholtz Center Munich, Germany
Master of Science in Bioinformatics
Nanyang Technological University (NTU), Singapore
Bachelor of Technology in Bioinformatics
Bharath University, Chennai, India
Publications
15+ peer-reviewed publications in genomics, infectious diseases, and single-cell biology.
Selected Publications
Single cell decomposition of multicellular aging programs associated with impaired lung regeneration.
Gote-Schniering J, Melo-Narváez MC, Boosarpu G, Lauer D, Prakki SRS, et al.
bioRxiv | DOI
Plasmid dynamics driving carbapenemase gene dissemination in healthcare environments.
Koh V, Cabrera R, Prakki SRS, et al.
Nature Communications 16:9522 | DOI
Dissemination of Pseudomonas aeruginosa blaNDM-1 positive ST308 clone in Singapore.
Prakki SRS, Ng OT, et al.
Microbiology Spectrum | DOI
Whole Genome Sequencing Reveals Hidden Transmission of Carbapenemase-producing Enterobacterales.
Marimuthu K, Venkatachalam I, Prakki SRS, Ng OT, et al.
Nature Communications | DOI
CPgeneProfiler: A lightweight R package to profile the Carbapenamase genes from genome assemblies.
Prakki SRS, et al.
Journal of Open Source Software 5(54):2473 | DOI
Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding.
Vij S, Kuhl H, ..., Prakki SRS, et al.
PLoS Genetics 12(4):e1005954 | DOI
Presentations
Conference Presentations
-
Single Cell Genomics (SCG) — Stockholm, Sweden, 2025
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, 2024
Poster: Towards perturbation analysis of cell lineage specific transcriptional regulons in pulmonary fibrosis -
Singapore Health and Biomedical Conference (SHBC) — Singapore, 2022
Poster: Dissemination of Pseudomonas aeruginosa blaNDM-1 positive ST308 clone in Singapore -
European Society of Clinical Microbiology and Infectious Diseases (ECCMID) — Amsterdam, Netherlands, 2019
Poster: Tracking plasmid-mediated horizontal gene transmission of blaNDM across Enterobacteriaceae -
European Society of Clinical Microbiology and Infectious Diseases (ECCMID) — Madrid, Spain, 2018
Poster: Population whole-genome sequencing uncovers plasmid-mediated NDM persistence -
Plant and Animal Genome (PAG) Asia — Singapore, 2014
Poster: Improved Assembly of the Asian Seabass Transcriptome -
Plant and Animal Genome (PAG) — San Diego, California, 2013
Poster: Sequencing and Assembly of the Asian seabass Transcriptome
Technical Skills
Programming
Generative AI
Domains with Bioinformatics experience
WebApp development
Infrastructure
Contributions
Open Source
-
CPgeneProfiler — R package for profiling Carbapenamase genes
GitHub | JOSS Publication -
Bleomycin Aging App — Interactive R Shiny application
Live App -
GitHub Profile — Various bioinformatics tools and analyses
github.com/ramadatta
Community
-
Biostar — Active community member
Profile: Prakki Rama -
Tutorial Videos — Bioinformatics related content
A Search For Solutions -
Blog — Fixes in software/bugs/myrants in the past years
asearchforsolutions.blogspot.com
Certifications
Grants & Awards
-
Environmental Health and Lung Research School (EHLRS) Grant Award (2,000 EUR) — 2025
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 -
Best Performer Award — 2009
Poster presentation at National Symposium on "Insilico Drug Design against Leishmaniasis"
SRM University, Chennai, India
Contact
I'd be happy to connect! Feel free to reach out: