CURRENT ACADEMIC ROLE & RESPONSIBILITIES
- Engages undergraduate and postgraduate students for theory classes and practical sessions.
- Guides undergraduate and postgraduate students for research projects.
- Course administration and curriculum building.
- Conducting workshops and seminars.
- Core focus on genome and transcriptome bioinformatics.
- Bioinformatics analysis of high throughput data obtained from next generation sequencer (NGS).
- Development and automation of pipleline for DNA-Seq and RNA-Seq analysis.
- Big data handling and visualization.
P Sandeep Mallya is Lecturer in the Department of Bioinformatics at School of Life Sciences.
Academic
ACADEMIC QUALIFICATIONS
| Degree | Specialisation | Institute | Year of passing |
|---|---|---|---|
| MSc | Bioinformatics | School of Life Sciences, Manipal University | 2011 |
Experience
| Institution / Organisation | Designation | Role | Tenure |
|---|---|---|---|
| School of Life Sciences | Lecturer | Teaching and Research | July 2013 to present |
| School of Life Sciences | Junior Research Fellow | Nov 2011 - July 2013 |
MANIPAL: Mutation Detection and Annotation in Nucleotide Sequences with an Integrated Pipeline for Automation in Laboratories
Oral Presentation at 41st Indian Society of Human Genetics Annual Meeting and International Conference, Chennai, India, March 2016.
Scavenging small RNA-Seq data to predict mitochondrial encoded miRNA
Oral presentation at International Conference on Computational Methods in Engineering and Health, Manipal University, Manipal. Dec 2014 .
Meta-analysis of small RNA-Seq data to predict mitochondrial encoded miRNA and their targets
Poster presented at Indo-US Bilateral Workshops and Conferences on "Big Data Analysis and Translation in Disease Biology", Jawaharlal Nehru University, New Delhi. Jan 2015 .
BS-Seq Analysis Pipeline for Targeted Next Generation Sequencing Data
Poster presentated at 1st UAEU symposium on biological sciences - “Genomics and Bioinformatics", Al Ain, UAE, Dec 2016.
Identification and Annotation of Clinically Relevant Mutations from Sanger Sequencing Data
Poster presented at International conference on “Advances in Cellular, Genomic and Epigenomic Insights on Environmental Mutagenesis and Health”, Manipal, Jan 2017.
AREAS OF INTEREST, EXPERTISE AND RESEARCH
Area of Interest
Genome bioinformatics, Computational biology, Transcriptomics, High-throughput sequence data analysis.
Area of Expertise
Bioinformatics
DNA methylation analysis of phenotype specific stratified Indian population
2015-01-05 Harish Sandeep Mallya Shama Prasada Kabekkodu Sanjiban Chakrabarty Sameer Bhale Ramachandra Bharadwaj Balakrishna K. Bhat Kumarasamy Thangaraj Marthanda Varma Sankaran Valiathan Kapaettu Satyamoorthy
Click here
Abstract
Background: DNA methylation and its perturbations are an established attribute to a wide spectrum of phenotypic variations and disease conditions. Indian traditional system practices personalized medicine through indigenous concept of distinctly descriptive physiological, psychological and anatomical features known as prakriti. Here we attempted to establish DNA methylation differences in these three prakriti phenotypes.
Methods: Following structured and objective measurement of 3416 subjects, whole blood DNA of 147 healthy male individuals belonging to defined prakriti (Vata, Pitta and Kapha) between the age group of 20-30years were subjected to methylated DNA immunoprecipitation (MeDIP) and microarray analysis. After data analysis, prakriti specific signatures were validated through bisulfite DNA sequencing.
Results: Differentially methylated regions in CpG islands and shores were significantly enriched in promoters/UTRs and gene body regions. Phenotypes characterized by higher metabolism (Pitta prakriti) in individuals showed distinct promoter (34) and gene body methylation (204), followed by Vata prakriti which correlates to motion showed DNA methylation in 52 promoters and 139 CpG islands and finally individuals with structural attributes (Kapha prakriti) with 23 and 19 promoters and CpG islands respectively. Bisulfite DNA sequencing of prakriti specific multiple CpG sites in promoters and 5′-UTR such as; LHX1 (Vata prakriti), SOX11 (Pitta prakriti) and CDH22 (Kapha prakriti) were validated. Kapha prakriti specific CDH22 5′-UTR CpG methylation was also found to be associated with higher body mass index (BMI).
Genome sequence of a Burkholderia pseudomallei clinical isolate from a patient with community-acquired pneumonia and septicemia
2015-01-08 Chiranjay Mukhopadhyay K. E. Vandana T. A. K. Chaitanya Tushar Shaw H. Vinod Bhat Sanjiban Chakrabarty Bobby Paul Sandeep Mallya T. S. Murali Kapaettu Satyamoorthy
http://genomea.asm.org/content/3/4/e00915-15.full
Mitochondrial DNA variation analysis in cervical cancer
2014-01-05 Shama Prasada Kabekkodu Samatha Bhat Roshan Mascarenhas Sandeep Mallya Manoj Bhat Deeksha Pandey Pralhad Kushtagi Kumarasamy Thangaraj P. M. Gopinath Kapaettu Satyamoorthy
http://www.sciencedirect.com/science/article/pii/S1567724913001001
Immunophenotyping of normal individuals classified on the basis of human dosha prakriti.
2014-14-01 Harish Rotti Kanive Parashiva Guruprasad Jayakrishna Nayak Shama Prasada Kabekkodu Harpreet Kukreja Sandeep Mallya Jyothi Nayak P. M. Gopinath Paturu Kondaiah Kapaettu Satyamoorthy
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012362/
DNA methylation detection at single base resolution using targeted next generation bisulfite sequencing and cross validation using capillary sequencing.
2016-01-09 Smitha Bhat Sandeep Mallya Vinay Koshy Varghese Pradyumna Jayaram Sanjiban Chakrabarty Kalpana S. Joshi Tanuja M. Nesari Kapaettu Satyamoorthy
http://www.sciencedirect.com/science/article/pii/S0378111916307351
Complete Genome Sequences of the Endophytic Streptomyces Strains EN16, EN23, and EN27, Isolated from Wheat Plants.
2016-01-12 Christopher MM Franco Ricardo Araujo Eric Adetutu Shanan S. Tobe Sandeep Mallya Bobby Paul Kapaettu Satyamoorthy
http://genomea.asm.org/content/4/6/e01342-16.full
A compilation of Web-based research tools for miRNA analysis.
2017-01-02 Vaibhav Shukla Vinay Koshy Varghese Shama Prasada Kabekkodu Sandeep Mallya Kapaettu Satyamoorthy
https://academic.oup.com/bfg/article-abstract/doi/10.1093/bfgp/elw042/3053315/A-compilation-of-Web-based-research-tools-for?redirectedFrom=fulltext
Aberrant gene-specific DNA methylation signature analysis in cervical cancer.
2017-01-03 Samatha Bhat Shama Prasada Kabekkodu Vinay Koshy Varghese Sanjiban Chakrabarty Sandeep P. Mallya Harish Rotti Deeksha Pandey Pralhad Kushtagi Kapaettu Satyamoorthy
http://journals.sagepub.com/doi/10.1177/1010428317694573
Complete Genome Sequences of the Endophytic Streptomyces sp. Strains LUP30 and LUP47B, Isolated from Lucerne Plants
2017-01-06 Christopher MM Franco Eric M. Adetutu Hoang X. Le Ross A. Ballard Ricardo Araujo Shanan S. Tobe Bobby Paul Sandeep Mallya Kapaetu Satyamoorthy
http://genomea.asm.org/content/5/24/e00556-17.full