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Research Assistant Molecular Biology

Philadelphia, PA
April 17, 2024

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SHIKHA SINGH, 267-***-****


Tokyo Metropolitan University, Japan Oct 2018-March 2024

PhD, Evolutionary Genetics. D-5.

Banasthali Vidyapith University, India June 2010-May 2015

Master of Science, Bioinformatics.

Mahatma Jyotiba Phule Rohilkhand University June 2010- May 2013

Bachelor of Science, Biological Science.


Temple University (IGEM), PA-USA. July 2023-Present

Visiting faculty

Benchmarking methods on scRNA-seq, scATAC-seq, and single-cell omics sequencing.

University of Pennsylvania (Penn Vet), PA-USA. Dec 2022-July 2023

Visiting Research Scholar

Single cell transcription analysis.

Tokyo Metropolitan University, Japan. Oct 2018-Oct 2022

Research Assistant (Evolutionary Genetics laboratory)

Evolution of gene expression dynamics in response to cold in Drosophila albomicans.

Senior Teaching Assistance (Evolutionary Genetics laboratory)

Course: Next Generation Sequencing and Data Analysis.

Course: Perl programming and analyzing image data.

Teaching Assistants (Laboratory of Animal Ecology)

Course: PC maintenance and updating of software (R, ImageJ, etc.).

CSIR-NBRI (National Botanical Research Institute), India. Mar 2016-April 2018

Project Assistant level-2 (Computational Plant and Molecular Biology lab)

Handled and analyzed Next-Generation Sequencing data.


●Shikha Singh, Sakshi Srivastava, Divya Srivastava, and Meetali Sinha (2016) “Insilico identification of novel compound against Urinary Tract Infection” Int. Res. J. Biological Sci., 5(3), 51-55.

●Dhar, Yogeshwar V., Deepika Lakhwani, Ashutosh Pandey, Shikha Singh, Prabodh K. Trivedi, and Mehar H. Asif. "Genome-wide identification and interactome analysis of members of two-component system in Banana." BMC Genomics 20, no. 1 (2019): 1-15.

●Khare, Ria, Yogeshwar V. Dhar, Gurpreet Sandhu, Shikha Singh, Smita Kumar, Aruba Khan, Mehar Hasan Asif, and Prabodh Kumar Trivedi. "Genome-wide expression and variation in nucleotide sequences lead to differential response of Arabidopsis thaliana ecotypes towards arsenic stress under sulfur limiting condition." Environmental and Experimental Botany 195 (2022): 104764.

●Kumar, Vinod, Deepika Singh, Adity Majee, Shikha Singh, Mehar Hasan Asif, Aniruddha P. Sane, and Vidhu A. Sane. "Identification of tomato root growth regulatory genes and transcription factors through comparative transcriptomic profiling of different tissues." Physiology and Molecular Biology of Plants 27, no. 6 (2021): 1173-1189.

●In Lakhwani, Deepika, Yogeshwar Vikarm Dhar, Shikha Singh, Ashutosh Pandey, Prabodh Kumar Trivedi, and Mehar Hasan Asif. "Genome wide identification of MADS box gene family in Musa balbisiana and their divergence during evolution." Gene (2022): 146666.



Language: R, Basic PERL programming

Single cell RNA-Seq, scATAC-Seq, SNV calling in scRNA-Seq and bulk, Denovo genome and reference-based transcriptome assembly(Cufflinks, RSEM, Trinity), read mapping(STAR, Bowtie, TopHat), alignment(Clustal Omega, Clustalx, Tcoffee, BLAST), comparative genomics and transcriptomics, differential gene expression (EdgeR, Cuffdiff, NOIseq), functional annotation, data analyses and Clustering using R, MeV and various data visualization through R, network analyses using Cytoscape, quality trimming, tree topology comparison, Genome-wide identification of gene families, genome-wide SNP analyses, Pymol, Chimera, Autodock, Chemdraw, Sequence, and expression distance using megacc.

Technical (Wet Lab):

Hands-on expertise in basic molecular biology and Next generation sequencing practices like DNA/RNA extraction and quality analysis, PCR and Gel-electrophoresis, Library Preparation using –nanovue, PureLink mini kit, Bioanalyser-2100 Agilent RNA 6000, Bioanalyzer-2100 High Sensitivity DNA kit, and TapeStation-2200 High Sensitivity DNA Analysis, Qubit dsDNA High sensitivity, TruSeq Stranded mRNA Library Preparation. primer design, CRISPR/Cas9 design gene editing in mammalian cell culture.

PhD Project

Topic: “Evolution of gene expression dynamics in response to cold in Drosophila albomicans”.

Objective: Major objective of my current work is to find genes responsible for cold acclimation similar phenotypes and how species genetically modify for their adaptation to tropical to temperate regions within species.

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