Shreyas Joshi

  • PhD Candidate
  • Teaching Assistant
334 T H Morgan Building
Other Affiliations:
  • Society for Neuroscience
  • Bluegrass Society for Neuroscience
  • Complex Trait Community
  • International Society for Computational Biology
Research Interests:
Education

M.Sc. Bioinformatics, Nottingham Trent University
B.Sc. Microbiology, Barkatullah University

 

Graduate Training

University of Kentucky Ph.D. Biology (2011-Present)


 

Research

Identification of Novel Sleep Related Candidate Genes

Open access to mouse genomic and phenotypic data present an opportunity to perform meta-analyses and collectively study these data and identify novel sleep related genes using bioinformatics and statistical approaches. The NCBI GEO database is a repository of high throughput genomic data. Using this database, I have thus far analyzed several microarray datasets from sleep deprivation studies in mice. 

The knockout mouse project (KOMP) is a worldwide collaborative effort to produce embryonic stem (ES) cell lines each of which has one of mouse’s 21,000 protein coding genes knocked out. The objective of the next generation of this project (KOMP2) is to generate and phenotype mice for more than 5000 of these knockout ES lines from KOMP. The Jackson Laboratory (JAX) is  the primary center conducting phenotyping of these mice in the USA.  Currently, I am comparing control and KO mice using multivariate statistical approaches to identify genes that exhibit significant effects on sleep variables from Piezo data.  We have also suggested some of our best candidate genes for sleep for future knockout studies, which are now being generated. 

The data we collect from genomic datasets and phenotypic approaches are both dynamic in nature i.e. they gather observations and new information at multiple time-points. Our goal is to exploit this dynamicity of data to develop gene signaling networks using correlation statistics and computational machine learning techniques. Through experimental studies, our objective is to validate novel sleep related genes identified from bioinformatics and KOMP2 data analysis. 

Effect of meditation on performance

In a previous study conducted by our group to study the effects of meditation on performance, a significant short term performance boost was seen following meditation in both novice and experienced meditators. In the next step of this study, we want to study its effect on performance through the day and determine if experience improves longer term performance measures. Another aim is to study the effect on performance in novice meditators. I have been able to acquire a portable Electroencephalograph (EEG) system through a successful competitive internal grant. The IRB proposal has been approved and the study is currently underway.  


 

Selected Publications: 

Sethi M, Joshi SS, Webb RL, Beckett TL, Donohue KD, Murphy MP, O'Hara BF, Duncan MJ. Increased fragmentation of sleep wake cycles in the 5XFAD mouse model of Alzheimer's disease. Neuroscience. 2015 Apr 2;290:80-9.doi: 10.1016/j.neuroscience.2015.01.035. Epub 2015 Jan 28. PubMed PMID: 25637807.

Joshi S, O’Hara B. Identifying candidate genes for variation in sleep-related quantitative traits. BMC Bioinformatics. 2014;15(Suppl 10):P13. doi:10.1186/1471-2105-15-S10-P13. (Poster Abstract)

Sawant S1, Gokulan R, Dongre H, Vaidya M, Chaukar D, Prabhash K, Ingle A, Joshi S, Dange P, Joshi S, Singh AK, Makani V, Sharma S, Jeyaram A, Kane S, D'Cruz A. Prognostic role of Oct4, CD44 and c-Myc in radio-chemo-resistant oral cancer patients and their tumourigenic potential in immunodeficient mice. Clin Oral Investig. 2015 Apr 28.

Sawant SS, Chaukar DA, Joshi SS, Dange PP, Kannan S, Kane S, D'Cruz AK, Vaidya MM. Prognostic value of tissue polypeptide antigen in oral squamous cell carcinoma. Oral Oncol. 2011 Feb;47(2):114-20. doi: 10.1016/j.oraloncology.2010.11.005. Epub 2010 Dec 3. PubMed PMID: 21130025.

Mansi Sethi, Shreyas S Joshi, Martin Striz, Neil Cole, Jennifer Ryan, Michael E Lhamon, Anuj Agarwal, Stacey J Sukoff Rizzo, James M Denegre, Robert E Braun,David W Fardo, Kevin D Donohue, Elissa J Chesler, Karen L Svenson and Bruce F O'Hara. Analysis of sleep traits in knockout mice from the large-scale KOMP2 population using a non-invasive, high-throughput piezoelectric system. BMC Bioinformatics. 2015;16(Suppl 15):P15. doi: 10.1186/1471-2105-16-S15-P15. (Poster Abstract)

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