CV
Current Role
Staff Scientist, Warren Lab, Clinical Research Division, Fred Hutchinson Cancer Center (April 2022 - Current)
- Investigating the role of T-cells within the tumor micro-environment of individuals with epidemic and endemic KS from sub-Saharan Africa. (Manuscript in preparation)
- Identifying the global diversity of Epstein Barr Virus (EBV) and understanding its impact on the immune response towards EBV and EBV-associated malignancies. (Manuscript submitted)
- Explored the impact of HLA Class II genotype on metastatic non-small cell lung cancer (mNSCLC) patients undergoing immune checkpoint inhibitor (ICI) therapy. (Nature Scientific Reports)
Research Interests
- T-Cell Specificity Prediction using Large Language Models
- 3D Structure Prediction of T-Cell Receptor-pMHC Complexes
- Multi-Instance Learning for T-Cell Repertoire Level Characteristic Identification
- Epitope Hotspot Identification in Kaposi Sarcoma Herpesvirus (KSHV)
Work experience
Bioinformatics Analyst, Warren Lab, Clinical Research Division, Fred Hutchinson Cancer Center. (October 2019 - April 2022)
- Investigating the impact of extended antiretroviral therapy (ART) on the T-cell receptor (\beta) -chain (TRB) repertoire in individuals living with HIV. (Frontiers in Immunology)
- Understanding the tumor micro-environment of Kaposi Sarcoma using single-cell RNA-Seq.
- Developing tools and pipelines for AIRR-Seq, scRNA-Seq analysis, and viral genome assembly.
SWEP Graduate Researcher, Malaria Branch, Centers for Disease Control and Prevention, Malaria Branch, Centers for Disease Control and Prevention. (January 2018 - August 2018)
- Developing a scalable NGS workflow for the identification of variations associated with drug resistance in \textit{Plasmodium falciparum}. (Antimicrobial agents and chemotherapy and bioRxiv)
- Constructed the first ever complete genome of the simian infecting malaria parasite \textit{Plasmodium brasilianum}. (Nature Scientific Reports)
Bioinformatics Intern, New York Genome Center. (June 2015 - August 2015)
- Developing a framework for Bisulfite-Seq analysis.
- Benchmarking tools for variant identification from Bisulfite-Seq data.
- Developing a tool for the detection of allele-specific methylation from Bisulfite-Seq data.
Junior Bioinformatics Analyst, Interpretomics India Pvt Ltd. (July 2013 - May 2014)
- Design and implementation of a Python based pipeline for Whole Genome/Exome Sequencing, RNA-Seq, ChIP-Seq, microRNA-Seq, and HLA-Typing for NGS-based cloud platform called iOMICS.
- Developing a tool for the detection of the complete spectrum of variations in WGS/WES data. (PLOS One)
Publications
First Full Draft Genome Sequence of Plasmodium brasilianum
Talundzic E, Ravishankar S, Nayak V, Patel DS, Olsen C, Sheth M, Batra D, Loparev V, Vannberg FO, Udhayakumar V, Barnwell JW. First full draft genome sequence of Plasmodium brasilianum. Genome Announcements. 2017 Feb 9;5(6):10-128.
TLR-exosomes exhibit distinct kinetics and effector function
Srinivasan, S., Su, M., Ravishankar, S. et al. TLR-exosomes exhibit distinct kinetics and effector function. Sci Rep 7, 41623 (2017). https://doi.org/10.1038/srep41623
Next-generation sequencing and bioinformatics protocol for malaria drug resistance marker surveillance
Talundzic E, Ravishankar S, Kelley J, Patel D, Plucinski M, Schmedes S, Ljolje D, Clemons B, Madison-Antenucci S, Arguin PM, Lucchi NW. Next-generation sequencing and bioinformatics protocol for malaria drug resistance marker surveillance. Antimicrobial Agents and Chemotherapy. 2018 Apr;62(4):10-128.
Mapping-free variant calling using haplotype reconstruction from k-mer frequencies
Peter A Audano, Shashidhar Ravishankar, Fredrik O Vannberg, Mapping-free variant calling using haplotype reconstruction from k-mer frequencies, Bioinformatics, Volume 34, Issue 10, May 2018, Pages 1659–1665, https://doi.org/10.1093/bioinformatics/btx753
Next-generation Sequence-analysis Toolkit (NeST): A standardized bioinformatics framework for analyzing Single Nucleotide Polymorphisms in next-generation sequencing data
Ravishankar S, Schmedes SE, Patel DS, Plucinski M, Udhayakumar V, Talundzic E, Vannberg F. Next-generation Sequence-analysis Toolkit (NeST): A standardized bioinformatics framework for analyzing Single Nucleotide Polymorphisms in next-generation sequencing data. bioRxiv. 2018 May 16:323535.
Evolution and Genetic Diversity of the k13 Gene Associated with Artemisinin Delayed Parasite Clearance in Plasmodium falciparum
Pacheco MA, Kadakia ER, Chaudhary Z, Perkins DJ, Kelley J, Ravishankar S, Cranfield M, Talundzic E, Udhayakumar V, Escalante AA. Evolution and genetic diversity of the k13 gene associated with artemisinin delayed parasite clearance in Plasmodium falciparum. Antimicrobial Agents and Chemotherapy. 2019 Aug;63(8):10-128.
Targeted deep amplicon sequencing of antimalarial resistance markers in Plasmodium falciparum isolates from Cameroon
L’Episcopia M, Kelley J, Dongho BG, Patel D, Schmedes S, Ravishankar S, Perrotti E, Modiano D, Lucchi NW, Russo G, Talundzic E. Targeted deep amplicon sequencing of antimalarial resistance markers in Plasmodium falciparum isolates from Cameroon. International Journal of Infectious Diseases. 2021 Jun 1;107:234-41.
RNA helicase, DDX3X, is actively recruited to sites of DNA damage in live cells
Cargill MJ, Morales A, Ravishankar S, Warren EH. RNA helicase, DDX3X, is actively recruited to sites of DNA damage in live cells. DNA repair. 2021 Jul 1;103:103137.
Serial Analysis of the T-Cell Receptor β-Chain Repertoire in People Living With HIV Reveals Incomplete Recovery After Long-Term Antiretroviral Therapy
Towlerton AMH, Ravishankar S, Coffey DG, Puronen CE and Warren EH (2022) Serial Analysis of the T-Cell Receptor β-Chain Repertoire in People Living With HIV Reveals Incomplete Recovery After Long-Term Antiretroviral Therapy. Front. Immunol. 13:879190. doi: 10.3389/fimmu.2022.879190
The first complete genome of the simian malaria parasite Plasmodium brasilianum
Bajic, M., Ravishankar, S., Sheth, M. et al. The first complete genome of the simian malaria parasite Plasmodium brasilianum. Sci Rep 12, 19802 (2022). https://doi.org/10.1038/s41598-022-20706-6
Class II HLA-DRB4 is a predictive biomarker for survival following immunotherapy in metastatic non-small cell lung cancer
Jiang, C.Y., Zhao, L., Green, M.D. et al. Class II HLA-DRB4 is a predictive biomarker for survival following immunotherapy in metastatic non-small cell lung cancer. Sci Rep 14, 345 (2024). https://doi.org/10.1038/s41598-023-48546-y
Talks
Talk 1 on Relevant Topic in Your Field
Talk at UC San Francisco, Department of Testing, San Francisco, California
Tutorial 1 on Relevant Topic in Your Field
Tutorial at UC-Berkeley Institute for Testing Science, Berkeley CA, USA
Talk 2 on Relevant Topic in Your Field
Talk at London School of Testing, London, UK
Conference Proceeding talk 3 on Relevant Topic in Your Field
Conference proceedings talk at Testing Institute of America 2014 Annual Conference, Los Angeles, CA
Teaching
Service and leadership
- Currently signed in to 43 different slack teams