About
A Bioinformatician Navigating the Frontiers of Genomics!
With over a decade of experience in genomics research, I specialize in applying computational methods to understand crop genomics. Currently pursuing my PhD in lettuce genomics, my work connects large-scale genomic data with biological insight. My interests lie in population genomics and pan-transcriptomics, where I explore the genetic diversity, allelic expression, and evolution that could shape plant breeding.
Interest: Bioinformatics, Computational Genomics, Pan-Transcriptomics
- Degree: MSc
- Email: c.s.sivasubramani@gmail.com
- ResearchGate: Click HERE
- ORCID: Click HERE
- GitHub: Click HERE
Resume
Here is a brief overview of my career to date.
Education
Doctor of Philosophy (PhD)
Feb 2022 - Till Date
Comparative Genomics in Lactuca, Wagenigen University and Research (WUR), The Netherlands
Work chapters:
- KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles (Bioinformatics tool)
- Introgression-aware comparative transcriptomics in Lactuca highlights non-host resistance to downy mildew
- Introgressions and gene flow in Lactuca sp.
- Meganome: Graph-based pan-transcriptome framework for cross-species transcriptomics (Bioinformatics tool)
- Allele-specific expression in Lactuca sp.
Supervisor: Prof. Dr. M Eric. Schranz
Co-supervisor: Dr. Sandra Smit
Master of Science (MSc - Distance) Bioinformatics
Aug 2018 - May 2021
Bharathiar Univeristy, Coimbatore, India
Bachelor of Technology (BTech) Biotechnology
Aug 2008 - May 2011
PSG College of Technology, Coimbatore, India
Professional Experience
Doctoral Researcher
Feb 2022 - Till Date
Comparative Genomics in Latuca, Wageningen Univeristy and Research (WUR), The Netherlands
- Performed a novel cross-species comparative transcriptomics study on L. sativa × L. saligna introgressions, exploring resistance against lettuce downy mildew
- Developed a novel k-mer based approach to screen the introgression signals from sequencing data
- Studying introgression and variable regions in domesticated lettuce to study the trait evolution
- Developing a graph based Pan-Transcriptome pipeline to study cross species allele specific expression in Lactuca
Senior Scientific Analyst
Oct 2016 - Jan 2022
International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Worked with diverse Genomics applications in the ICRISAT mandate crops (Sorghum, Pearl Millet, Chickpea, Groundnut, Pigeonpea, and Finger millet)
- Developed methods that involve handling seed purity and verifications in F1 generations
- Designed marker panels for various applications such as Genomic Selection and Trail specific applications
- Worked as one of the core java developer under the globally acclaimed crop genomics management system - Genomic Open-source Breeding Informatics Initiative (GOBii)
- Involved in the development of a GUI-based genomic selection tool for large-scale datasets ISMU v2.
Programmer
Nov 2013 - Oct 2016
International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Handled different genomics applications of the Sorghum crop
- Written pipeline used on skim sequencing (GBS) variant calling based on the open-source applications
- Supported the molecular breeding group with GWAS, and GS analysis
Scientific Analyst
March 2011 - Oct 2013
Genotypic Technology PVT. LTD., Bengaluru, India
- Have extensively worked on human diagnostic markers and ancestral studies
- Designing Agilent based microarray chips for a variety of applications like gene expression, CHiP-on-Chip, SNP Array
- Co-developer at SeqQC (a sequence QC and summary tool for NGS data)
- Developed a web-server (SeqANNOT) to handle contig annotations based on homology search (as part of internship)
Research Projects/applications
My research areas mainly focuses on the side of bioinformatics involved in developing genomic applications/tools and studying crop genomics
Bioinformatics, Comparative Genomics, Computational Genomics, Pan-Transcriptomics, Population Genomics
LettuceKnow: Collaborative research program that uses lettuce as model crop
Under supervison of Prof. Dr. M. Eric. Schranz (WUR | Biosystematics) and Dr. Sandra Smit (WUR | Bioinformatics)
comparative genomics
pan-transcriptomics
population gentics
RNAseq
Using the vast amount of genomics and transcriptomics data generated from the selected elite 500 lettuce accessions, we are trying to understand the gentic architecture and trait evolution to improve the lettuce breerding. In order to achive that we have developed novel methods and pipelines that could benifit other crops as well.
KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles
Under supervison of Prof. Dr. M. Eric. Schranz (WUR | Biosystematics) and Dr. Sandra Smit (WUR | Bioinformatics)
k-mer
GWAS
introgression
plant breeding
Developed kcftools, a Java-based toolkit for alignment-free genotype analysis using k-mer presence/absence in genomic windows. Designed to detect introgressed and structurally variable regions more efficiently than traditional SNP-based pipelines. Extended the toolkit to generate genotype matrices compatible with GWAS, enabling discovery of loci(regions) linked to phenotypic traits. Demonstrated its effectiveness for high-resolution, reference-agnostic population genetic analysis.
Genomic Open-source Breeding Informatics Initiative (GOBii)
Under the supervision of Dr. Abhishek Rathore (ICRISAT | SBDM), and collaborators from other CGIAR institutes and researchers from Cornel Univeristy
breeding informatics
GWAS
java
molecuar markers
SNP/InDel
As part of a large team of developers from different institutions, the goal is to build a open source system to host and serve molecular markers and breeding informatics solutions. I was working in the back end development (Java) to parse and host the VCF and HapMap formated variations and link them to the sequencing technoloies. Later this project had become one of the core applications behind Excellence in breeding (EiB) Initiative
lgctools: Command-line utility toolkit to analyze Intertek data
Under supervision of Dr. Abhishek Rathore(ICRISAT | SBDM)
forward breeding
F1 verification
Purity Check
Diversity panels
Developed a python-based command line utility tool to hadle the Intertek genotyping data. The application of this utility includes selecting markers to test the purity of the genotypes, F1/Hybrid verification, quality test on genotypes/accessions based on the genotyped data.
Publications
2025
KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles
Sivasubramani Selvanayagam, Jesus Quiroz-Chavez, Ricardo H. Ramirez-Gonzalez, Cristobal Uauy, Sandra Smit, M. Eric Schranz
Preprint
Original Research
2024
Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696)
Prasad Gandham, Nandini Vadla, ..., Sivasubramani Selvanayagam, Rachit K. Saxena, Abhishek Rathore, Subramaniam Gopalakrishnan & Vivek Thakur
Scientific Reports
Original Research
2023
Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources
Pradeep Ruperao, Prasad Gandham, ..., Sivasubramani Selvanayagam, Nepolean Thirunavukkarasu, ..., Abhishek Rathore
Frontiers in Plant Science
Original Research
Development of a new AgriSeq 4K mid-density SNP genotyping panel and its utility in pearl millet breeding
Janani Semalaiyappan, Sivasubramani Selvanayagam, Abhishek Rathore..., Nepolean Thirunavukkarasu
Frontiers in Plant Science
Original Research
2022
Genetic Dissection and Quantitative Trait Loci Mapping of Agronomic and Fodder Quality Traits in Sorghum Under Different Water Regimes
Vinutha K. Somegowda, Kodukula V. S. V. Prasad, ..., Sivasubramani Selvanayagam, Abhishek Rathore1, ..., Santosh P. Deshpande
Frontiers in Plant Science
Original Research
Understanding Heterosis, Genetic Effects, and Genome Wide Associations for Forage Quantity and Quality Traits in Multi-Cut Pearl Millet
Ponnaiah Govintharaj, Marappa Maheswaran, ..., Selvanayagam Sivasubramani, ..., Rajeev Kumar Varshney, Shashi Kumar Gupta2
Frontiers in Plan Science
Original Research
Genome-Wide Association Study for Major Biofuel Traits in Sorghum Using Minicore Collection
Laavanya Rayaprolu, Sivasubramani Selvanayagam, ..., Santosh P. Deshpande and Ashok Kumar Are
Protein and Peptide Letters
Original Research
Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain
Pradeep Ruperao, Nepolean Thirunavukkarasu,..., Sivasubramani Selvanayagam, Mahalingam Govindaraj, ..., AbhishekRathore
Frontiers in Plant Science
Original Research
2020
Development of genomic microsatellite markers in cluster bean using next-generation DNA sequencing and their utility in diversity analysis
Sushil Kumar, Adinath S Palve, ..., Sivasubramani Selvanayagam, Ramavtar Sharma, Abhishek Rathore
Current Plant Biology
Original Research
2020
Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed Senescence
K. N. S. Usha Kiranmayee, C. Tom Hash, S. Sivasubramani, P. Ramu..., Santosh P. Deshpande
MDPI Genes
Original Research
2015
Population Genetics and Structure of a Global Foxtail Millet Germplasm Collection
Hari D. Upadhyaya, Mani Vetriventhan, ..., Selvanayagam Sivasubramani, ..., Punna Ramu
The Plant Genome
Original Research