Manu Shivakumara

Experience

• 

  Institute of Bioinformatics and Applied Biotechnology (IBAB)

  Jul 2017 - Dec 2017

  Phi-Psi Young Research Fellow - Bioinformatics

  Initiated and led a research project investigating human meiotic recombination hotspots using the 1000 Genomes Project data. Key accomplishments:✦ Developed efficient algorithms to identify recombination hotspots in human populations, leading to the discovery of thousands of new genomic regions with higher recombination.✦ Developed Python scripts to analyze, compare, and visualize recombination rates across 20 human populations, identifying thousands of unique recombination hotspots in each population with potential implications to genetic diversity and disease susceptibilities.✦ Published a preprint and presented the findings at the 2017 Indo-French international conference, receiving valuable feedback for the future directions of the project. Show less

• 

  Centre for Cellular and Molecular Biology

  Jan 2018 - now

  Spearheaded multiple genomics projects on diverse organisms ranging from microbes to mammals.Key accomplishments:✦ Sequenced and analyzed hundreds of whole genomes of primates, which contributed to identification of benign and pathogenic mutations, and evolutionarily constrained non-coding regulatory elements in the human genome using comparative genomics.✦ Developed efficient analysis workflows to assemble over 10 billion environmental DNA reads, enabling the discovery of thousands of novel genomes and functions of Viruses, Archaea, Bacteria, and Eukaryotes.✦ Assembled high-quality reference genomes of several Vertebrates and Invertebrates using Nanopore long reads and Illumina short reads, which helped in identifying the genomic basis of their unique physiology, adaptations, and genetic health.✦ Built amplicon sequencing analysis pipelines to study the microbiome structure, function, and its drivers in diverse ecosystems.✦ Presented the research findings at two international conferences and published over 15 peer-reviewed papers in international journals, including Nature and Science. Show less Initiated and led a research study to explore and assess biodiversity using environmental DNA.Key accomplishments:✦ Standardized and optimized a novel extraction protocol, enabling enrichment and library preparation of extracellular environmental DNA from water samples.✦ Developed complex analysis workflows using Snakemake and Python, which could sensitively classify environmental DNA reads to taxonomically identify any species.✦ Carried out a spatiotemporal study in a large lagoon, validating the entire workflow in a real-world ecosystem.✦ Performed statistical analyses and data visualization in R, inferring the diversity metrics and its ecological drivers. Show less

  • Senior Research Fellow - Bioinformatics

    Jan 2020 - now

  • Junior Research Fellow - Bioinformatics

    Jan 2018 - Dec 2019