Amit Sinha

Amit Sinha


Summary

Post-doctoral researcher with interest in nematodes, genomics, genetics, evolution, evo-devo, aging and innate immunity. Currently working on comparative and functional genomics of new nematode models, using NGS, Illumina, PacBio, RNA-Seq, Whole-genome shotgun assembly.

Bioinformatics Computational Biology Developmental Biology Evolutionary Studies Genetics Genomics Molecular Biology

Work details

Post Doctoral Researcher

New England Biolabs, USA
April 2017
Genome Biology
Genome sequencing, assembly and annotation of parasitic filarial nematodes, Comparative genomics, Population genetics, Evolutionary Biology. RNA-Seq, Metagenomics, Symbiosis.

PhD student

Eberhard-Karls-Universität Tübingen
July 2008 - December 2012
Evolutionary Biology
Gene expression studies of evolution of development and innate immunity in the nematode Pristionchus pacificus * Developed the first ever microarray based gene expression platform for the nematode Pristionchus pacificus, and used it to study various biological processes including dauer formation, innate immunity, and the effect of germline on longevity and pathogen resistance. * Established the experimental protocols as well as data analysis methods. * Also conducted similar experiments in C. elegans and compared the results with P. pacificus to infer evolutionary trends.

Post-Doc

Max Planck Institute for Developmental Biology, Tübingen, Germany
January 2013 - September 2013
Evolutionary Biology
Discovering the micro-RNAs and other small non-coding RNAs in Pristionchus pacificus, a newly developed nematode model. * Established the protocols for RNA-Seq experiments to characterize small RNA populations * Performed RNA-Seq library preparation, sequencing and computational analysis to characterize small- RNAs in Pristionchus pacificus and its sister species Pristionchus expecstatus. * Conducted population genetics and evolutionary analysis on newly discovered miRNA genes in these two species. * Identified micro- and macro-evolutionary patterns in miRNA gene sequences.

Post-Doc

University of Massachusetts Medical School
November 2013 - November 2014
Neurobiology
Genetic basis of monarch butterfly migration

Post-Doc

University of Massachusetts Medical School
November 2014 - April 2017
Neurobiology
Investigating the genetic and genomic basis of extreme acid tolerance of the extremophilic nematode Turbatrix aceti. * Carried out whole genome sequencing and assembly of T. aceti genome using Illumina and Pacific Biosciences technologies, and the corresponding computational analysis. * Planned and carried out RNA-Seq experiments and computational analysis to identify candidate genes conferring acid resistance to T. aceti. * Established functional and pharmacological assays to monitor growth and survival of T. aceti under various physiological and genetic manipulations. * Explored methods to develop tools and methods for RNAi, transgenesis and CRISPR/Cas9 based genome-editing in T. aceti.

Websites

PeerJ Contributions