Pallavi Singh, PhD
Cell and Molecular Biology
I am a Molecular Microbiologist, an avid traveler and a “veggie” foodie with severe case of sweet tooth! Born and raised in the beautiful country of India I moved to another awesome country, the US to pursue my doctoral degree in 2006. I have been here ever since, did quality science, made great friends, saw great lands and had amazing life experiences.
Currently I am a Senior Research Associate and Instructor. My research interests include microbial ecology, pathogenesis and genomics. Here is a peek into my scientific world and the professional experiences I have had. I intend to expand upon it as I progress in my journey!
Research Trainee 2004-2005
Department of Immunology
National Institute for Research in Tuberculosis
Chennai, TN, India.
Microbial ecology studies on intestinal microbial communities of patients with enteric infections, cattle that are reservoir for shiga-toxin producing E. coli (STEC) and chickens that were fed antibiotics based on 16S rRNA gene as well as whole genome shotgun sequencing. Read here for more information.
Bacterial genomics conducting whole genome assembly, genome mapping, comparative genomics for genome wide variation analysis in food-borne pathogens STEC, Salmonella, Campylobacter and invasive neonate pathogen Group B Streptococcus. Read here for more information.
Studies conducted to assess genetic diversity and characterization of bacterial pathogens, specifically by designing SNP panels based on Illumina platforms and novel molecular typing technique (MLST-seq). Read here for more information.
- Library preparations for Next generation sequencing for Roche and Illumina based paltforms for whole genome sequencing, 16S rRNA gene based microbial community analysis, metagenomics in bacterial and viral communities as well as RNA-sequencing.
- Bioinformatical analysis for studies related to microbial ecology, including diet and disease related effects on the community members based on tools such as QIIME, MOTHUR, MEGAN, MEGA, SeqMan Pro.
- Genome assembly and genome analysis including genetic characterization, SNP identification, inferring polygenetic relationship, linking epidemiological data.
- Analytical tools including both web-based and stand alone BLAST, Velvet, MUMmer, Mauve, BWA, Bowtie, GenomeStudio and BioNumerics to name a few.
- Familiarity in working on both windows as well as linux based open source tools.
- Microbial techniques including sample collection, enrichment, isolation techniques, biofilm assays.
- DNA and plasmid isolations, bacterial transformation and cloning.
- Hands on experience with gram positive and gram negative pathogens in BSL2 and BSL3 laboratories.
- Molecular techniques including PCR, Real-Time qPCR, SDS-PAGE gels, Western Blotting, Immuno-blotting.
- Quality control techniques inclusive of Bioanalyzer, Qubit, qPCR.
- Handling robots such as epMotion.