Aditya Kumar Lankapalli
My research focuses on computational pathogen genomics with special interest in comparative genomics and methods development.
Main interests include:
- Screening for specific bacterial genomes from metagenomic data sequenced from bones/teeth isolated from archaeological remains from ancient time.
- Performing comparative analysis on the reconstructed ancient bacterial genomes to contemporary genomes.
- Phylogenetic Analyses
- Development of pipeline for detection of recombination patterns in bacterial genomes.
- Development of tools for bacterial genomic analyses.
Currently I am developing a pipeline for detection and characterisation of recombination patterns in bacterial genomes.We compare various tree models to a whole genome phylogeny and identify genomic regions with a contradicting tree model might be explained by recombination. By assessing genomic regions with respect to their phylogenetic signals possible recombinant regions across a bacterial genome of interest are identified.
Schuenemann VJ, Lankapalli A.K, Barquera R, Nelson EA, Iraíz Hernández D, et al.Historic Treponema pallidum genomes from Colonial Mexico retrieved from archaeological remains. PLOS Neglected Tropical Diseases 12(6):e0006447. https://doi.org/10.1371/journal.pntd.0006447 (2018)
Baddam, R., Kumar, N., Wieler, L.H., Lankapalli, A.K., Ahmed, N., Peacock, S.J., and Semmler, T. Analysis of mutations in pncA reveals non-overlapping patterns among various lineages of Mycobacterium tuberculosis. Sci Rep 8, 4628, doi:10.1038/s41598-018-22883-9 (2018).
Shaik, S., Kumar, N., Lankapalli, A.K., Tiwari, S.K., Baddam, R., and Ahmed, N. Contig-Layout-Authenticator (CLA): A Combinatorial Approach to Ordering and Scaffolding of Bacterial Contigs for Comparative Genomics and Molecular Epidemiology. PLoS One 11, e0155459, doi:10.1371/journal.pone.0155459 (2016).
Baddam, R., Kumar, N., Shaik, S., Lankapalli, A. K. & Ahmed, N. Genome dynamics and evolution of Salmonella Typhi strains from the typhoid-endemic zones. Sci Rep 4, 7457, doi:10.1038/srep07457 (2014).
Kumar, N., Mariappan, V., Baddam, R., Lankapalli, A.K., Shaik, S., Goh, K.L., Loke, M.F., Perkins, T., Benghezal, M., Hasnain, S.E., et al. Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution. Nucleic Acids Res 43, 324-335, doi:10.1093/nar/gku1271 (2015).
Conferences and Workshops
Aditya Kumar Lankapalli et al.,(2017) "An automated pipeline for identification of recombination in bacterial genomics" Poster presentation, 7th European Conference on Prokaryotic and Fungal Genomics (ProkaGENOMICS) , Göttingen , Germany.
Aditya Kumar Lankapalli et al.,(2017) "An automated pipeline for identification of recombination in bacterial genomics" Conference talk, Symposium on pathogen evolution, Kiel, Germany.
2015 - Current : PhD , Archaeogentics, Max Planck Institute for Science of Human History, Jena
Thesis (Provisional) : "Computational tools for detection of recombination patterns in ancient bacterial genomes".
2008 - 2013 : Masters in Systems Biology, University of Hyderabad, India
Thesis: "2Dimensional visualisation of chromosome architecture based on genome wide contact matrix".
2017 : "PhD Course in Analyses of Genotyping and Next-Generation Sequencing Data in Medical and Population Genetics" , Copenhagen, Denmark.
2013 - 2015 : Junior Research Fellow, University of Hyderabad, India
Topic : "Comparative genomic analysis of Helicobacter pylori strains".