Utrecht Center for Quantitative Immunology
Theoretical Biology and Bioinformatics
Faculty of Sciences
Host-pathogen interactions can be classified as an "arms race", where pathogens replicate using host's molecular resources, while hosts try to eliminate the pathogen. Human hosts are equipped with diverse multi-layered immune system, which is capable of eliminating most pathogens. Pathogens like HIV, however, can mutate rapidly to escape host's immune response.
Using bioinformatic and mathematical models, I study the diversity and complexity of the human immune system and the mechanisms by which the pathogens escape the human immune system. Specifically, I am involved in the following projects:
- development of bioinformatics pipelines to study the within-host viral evolution using deep sequencing data sets.
- development of agent-based model to study the evolution of diversity in antigen presentation pathways.
- development of stochastic mathematical models to study the commitment of T cells to different lineages for immediate and long-term immune response.
Pandit A, de Boer RJ (2013) Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants. arXiv:1309.6939.
Pandit A, Dasanna AK, Sinha S (2012) Multifractal analysis of HIV-1 genomes. Mol Phylo Evol 62(2): 756.
Pandit A, Sinha S (2011) Differential Trends in the Codon Usage Patterns in HIV-1 Genes. PLoS ONE 6(12): e28889.
Pandit A, Sinha S (2010) Using genomic signatures for HIV-1 sub-typing. BMC Bioinformatics 11(S1): S26.
For contact information see my home page
at Utrecht University.