Select Page

Genomicist

A molecular biologist, bioinformatician and genomics scientist with expertise in leading the development of assays, applications and products for next-generation sequencing, and microarray platforms.

  • Independently conceive, plan, conduct, and analyze experiments, along with coordinating with, managing, and technically guiding other scientists.
  • Lead application development and collaboration efforts with industry and academia. 
  • As a technical lead, perform feasibility/POC/development studies, design of experiments (DOEs), technical transfer, validation, and develop product specifications.
  • A team player in multidisciplinary product core and project teams to coordinate resolutions related to resource conflicts, quality, program costs, and budgeting.
  • 15 years of experience: Sequencing platform development microarray, 3D genomics, next-generation sequencing (NGS), Nanopore platform sequencing, human genetic disorders, Small RNA short-read sequencing (microRNAs & snoRNAs), microbiome, HIV and aging research.
  • Experience with human, vertebrate and invertebrate samples to describe the genetics of a wide variety of human diseases.
  • Bioinformatics: Genotyping and sequencing data analysis. I also developed an online directory for public repositories of genetic, genomic, and biological data. Proficient in bioinformatics tools and languages (HTML, dHTML, and CSS). 10+ years of experience in science communication and curation of biomedical resources.
  • Immigration Status: Permanent Resident (USA)

Scientific Citations

h-Index

i10-Index

Positions and Employment

  • Senior Scientist Applications and Collaborations, Dovetail Genomics (EdenRoc Sciences) (2020-Present)
  • Senior Scientist Product Development, Dovetail Genomics (EdenRoc Sciences) (2018-Present)
  • Scientist II Product Development, Centrilllion Technologies (2016-2018)
  • Post Doctoral Fellow, Buck Institute for Research on Aging, Novato, CA, USA (2011-2016)
  • Post Doctoral Fellow, Gheens Center on Aging University of Louisville, KY, USA (2010-2011)
  • Research Scholar, Unversity of Kentucky, Lexington, KY, USA (2006-2010)
  • Research fellow, Post-Graduate Institute of Medical Education and Research, Chandigarh India (2004-2006)

Research experience:

  • Product development for HTS and microarray technologies.
  •  Area of research: human genetic disorders, microbiome, HIV and aging research.
  • Strong background in cell and molecular biology, biochemical, and cell culture techniques.
  • Proficient in sample preparation and analysis of next generation sequencing (NGS) and microarray.
  • Experience with molecular biology platforms: Bioanalytical assays, Real Time-PCR, Fluorescent Imaging, Flow Cytometry and luminescent plate readers.
  • Experience with human samples to describe genetics of a wide variety of human diseases (AIDS and Prader-Willi syndrome).
  • Experience with generating stable recombinant cell lines for protein expression.
  • Experienced in using different in vivo vertebrate and invertebrate models.
  • Experienced in in situ hybridization, molecular cloning, and cDNA library generation.
  • Experienced with sample preparation and analysis of top-down/bottom-up protein mass spectrometry.
  • Developed a directory of resources for public repositories of genetic, genomic, and biological data.
  • 10+ years of experience in science communication and curation of biomedical resources.
  • Proficient in bioinformatics tools and languages (HTML, dHTML, and CSS).
  • Designed and webmaster of The Buck Institute for Research on Aging’s official Blog website. Link
  • Ph.D., Molecular and Cellular Biochemistry (2010)
    Friedrich-Alexander University/University of Kentucky
  • M.S., Human Genomics (2004)
    Panjab University, India
  • B.S., Biotechnology (2002)
    Panjab University, India

Cell Culture

  • Primary neuronal culture
  • Mammalian cell culture
  • Macrophage cell culture

Molecular Biology: RNA/DNA based techniques

  • Cloning of double-stranded RNAs (small and long RNAs)
  • RNase protection assay (RPA)
  • Next Generation Sequencing (NGS)
  • RNA Pull down assay
  • Northern Blotting
  • Southern Blotting
  • Colony Hybridization
  • Total RNA Isolation: Animal tissues and cells
  • Transient transfection.
  • PCR, Reverse Transcription PCR, and Real-Time PCR,
  • Minigene cloning
  • Restriction enzyme and bacteriophage lambda based cloning
  • Primer-Designing and Gene Arrays
  • Electrophoresis
  • In-situ hybridization and immunostaining
  • Primary Neuronal Culture

 Proteomics:

  • SDS-PAGE of Proteins,
  • Western Blot, Silver Staining of Proteins
  • Two-Dimensional Gel Electrophoresis

Cytogenetics:

  • Preparation and Staining of Metaphysics chromosomes & Barr Body.
  • Immunohistochemistry: Macrophage staining

Radiation Safety Certification from Radiation Safety University of Kentucky Animal Handling Mouse dissection: Mouse tissues and macrophage culture

Bioinformatics: BLAST Alignment of Pair sequences, Multiple Sequence Alignment, Prediction of RNA Secondary Structure Gene and SWISS-PROT, Database Search for Similar Sequences. 

Animal Handling Mouse dissection: Mouse tissues extraction, primary neuronal and macrophage culture

Softwares

  • Multifactor Dimensionality Reduction (MDR) software for Gene-Gene and Gene-Environment interactions.
  • MASCOT software for analyzing the MALDI-TOF results
  • PD quest for analyzing the 2D dimensional results
  • ImageJ and Quantity One 3.1 software for studying the DNA/PCR results.
  • Haploview version 3.2 for studying the Linkage disequilibrium for the association between SNPs.
  • PHASE version 2.1 for generating Haplotypes of genes
  • Primer 3 software for designing the primers/oligos.
  • End Note 9 software
  • Khanna A, Kumar J, Misha VA, et al. (2020). Trimethylamine, a human gut flora metabolite, modulates nutrient sensing and lifespan in C. elegans Cell Reports (Under Submission).
  • Khanna A*, Kumar J*, Misha VA*, et al (2016). The influence of dietary bacteria genotypes on dauer formation in C. elegans Scientific Reports (*Equal Contributions) PMID:27958277
  • Katewa SD, Khanna A, Kapahi P (2014) Mitobolites: the elixir of life. (Cell Metab.) PMC4103626
  • Khanna A, Muthusamy S, Liang R, et al. (2011) Gain of survival signaling by down-regulation of three key miRNAs in brain of calorie-restricted mice. Aging (Albany NY) PMC3091518
  • Liang R*, Khanna A*, Muthusamy S, Li N, Sarojini H, Kopchick JJ, Masternak MM, Bartke A and Wang E. (2011)Post­transcriptional regulation of IGF1Rby key microRNAs inlong­livedmutant mice. (Aging Cell) (*Equal Contributions)
  • Khanna A and Kapahi P. (2011) Rapamycin: Killing two birds with one stone. Aging (Albany NY)
  • Li X, Khanna A, Li N, Wang E. (2011) Circulatory miR34a as an RNA based, noninvasive biomarker for brain aging. (Aging (Albany NY))
  • Shen M, Eyras E, Wu J, Khanna A, Josiah S, Rederstorff M, Zhang MQ, Stamm S. (2011) Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression. (Nucleic Acids Res.)
  • Khanna A and Stamm (2010) S Regulation of alternative splicing by short non-coding nuclear RNAs. (RNA Biol.)
  • Kishore S*, Khanna A*, Zhang Z, Hui J, Balwierz PJ, Stefan M, Beach C, Nicholls RD, Zavolan M, Stamm S. (2010) The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. (Hum Mol Genet.)  *Co-first authors
  • Kishore S, Khanna A, Stamm S. (2008) Rapid generation of splicing reporters with pSpliceExpress. (Gene)
  • Kaul D, Anand PK, Khanna A. (2006) Functional genomics of PPAR-gamma in human immunomodulatory cells. (Mol Cell Biochem.)
  • Kaul D, Khanna A, Suman (2006) Detection of novel miRNA in HIV-1 genome and its role in cd4T-cell deletion. (PINAS India)

Book Chapters

  • Hui J, Kishore S, Khanna A and Stamm S. (2009) Analysis of Alternative splicing with Microarrays. Bioinformatics for Systems Biology, Part III, 267-279, DOI: 10.1007/978-1-59745-440-7_14
  • Zhang Z, Khanna A and Stamm S. (2011) Fast cloning of splicing reporter minigenes. Alternative Pre-mRNA Splicing: Theory and Protocols.

Awards

  • Selected chair to organize Gordon Research seminar on aging and metabolism held in Italy, (2013)
  • Invited as an instructor for the workshop on “Alternative Splicing and Disease” organized by European Alternative Splicing Network (EURASNET) (2009)
  • Thomas C. Vanaman Graduate student best talk award at Spring research conference University of Kentucky (2009)
  • Research assistant fellowship in DBT funded project (2006)

Memberships

  • Webmaster/Member of European Alternative Splicing Network (EURASNET) (2007-2010)
  • Student Member of Indian Science Congress (2004-2006)

Email: AKhannaPhD@gmail.com
Ph: +1 859-608-6028

I believe in passion and intensity; there is training for everything else.

Mystic Aura

Poems

 Life is mystic and everything associated with it has an aura. I wish to share a few poems celebrating that aura.

Message me!

8 + 4 =

+1 859 608 6028

AKhannaPhD@gmail.com