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Aridaman Pandit

Dr. Aridaman Pandit

Experienced Researcher / Post-doc

Theoretical Biology & Bioinformatics
University of Utrecht

August 2013 - July 2015

Biography

Aridaman did his PhD on "Theoretical Analysis of Host-Pathogen Interactions" (2007-2012) under the guidance of Dr. Somdatta Sinha, Centre for Cellular & Molecular Biology, Hyderabad, India. Major results from the thesis are:
a) HIV-1 subtypes can be differentiated on the basis of subtle yet important variations in genome signatures (DNA words).
b) Genome signatures in RNA viruses from multiple families are modulated by host-pathogen interactions.
c) HIV-1 mimicks host's codon usage pattern for its genes to efficiently translate in human cells. However, the trend towards human codon bias is more in functionally important genes.

He achieved his Bachelor of Technology in Bioinformatics (2003-2007) from Vellore Institute of Technology University, Vellore, India.

He was awarded Young Scientist Award 2011-2012 by Dr. KV Rao Scientific Society in the field of Biological Sciences.

Areas of Interest:
Computational Immunology; Comparative Genomics; Evolution of variation in host-pathogen systems

Aridaman started his ER (Post-doctoral) research at Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands in August 2013 and he is working on:
a) Reconstruction of HIV-1 whole genome haplotypes from next generation sequencing datasets to study within-host epitope escape dynamics.
b) Analysis and development of novel approaches (both computational and experimental) for T-cell receptor deep sequencing to study TCR diversity in humans.
c) A host-pathogen agent based model to study the mechanisms underlying antigen presentation pathway polymorphism.

QuanTI Research project

Quantification of T lymphocyte dynamics by in vivo labelling (Theoretical Study)

T cells are an important component of adaptive immune response in humans. T cell populations consist of billions of clones which can recognize pathogen-specific peptides. A T cell clones can be characterized into different classes, namely, naive, activated, effector, effector memory and central memory. Naive T cells are generated in the thymus and circulate in the blood. Naive T cells have a small chance to get activated if they recognize a foreign pathogen-specific peptide. These activated T cells then expand rapidly to form effector short lived effector cells and long-lived memory cells. The exact processes underlying the differentiation of naive cells into short-lived effector cells, and long-lived memory cells is not yet clear.
In this project, we will be studying at what point during T cell responses, T cells commit to either short-lived effector or long-lived memory cell fate. We will also study how the time of commitment is influenced by infection conditions. We will develop deterministic and stochastic mathematical models to study CFSE labelling and deep-sequencing barcoded data to trace individual cell fates over time.

Supervisors

Prof. Rob J de Boer, Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands.

Co-supervisors:
Prof. Ton Schumacher, Division of Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands.
Dr. Thomas Eißing, Computational Systems Biology, Bayer Technology Services GmbH, Leverkusen, Germany

Publications

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 preprint 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

 




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Funded by the EU
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Associated partners
Universidade de Vigo

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Last update: 11 June 2017