Prash
From Bioinformatics.Org Wiki
”The only thing that interferes with my learning is my education” ~ Albert Einstein
Contents |
About me
Namasté! I am a Principal Scientist in Systems Biology at Amrita School of Biotechnology, India. I obtained my PhD from Aalborg University, Denmark after having worked in [http://icmm.ku.dk/english/research-groups/juel-rasmussen-group/ Lene Juel Rasmussen's lab. I went on to gain seven years of post-doctoral experience and sabbatical visits in various laboratories before taking up independent investigatorial position in 2016 whence my return to India. I love traveling and had been to over 70+ countries.
Keywords
- KnownUnknowns
- HypotheticalProteins
- VitaminGenomics
- LncRNAs
- ProstateCancer
- SystemsGenomics
Interests
I'm a dry biologist curious to know how of a biology of a system. My interests are to study protein-protein interactions and top-down systems biology of hypothetical proteins, long noncoding RNAs in human, focusing on next generation sequencing sequencing approaches to identify regulatory aspects of the genome. My recent interests have been into elucidating the known unknown mechanisms underpinning small molecular interactions through clinical exomes. Apart from this, I have had intermittently worked on identifying the candidate genes involved in synthetic framework in bacteria. Besides this, I am an opportunist helper in providing bioinformatics/systems solutions to scientists in other allied fields.
Mentoring
I mentor students online through Bioclues. You may find my favorite articles that I compile through Citeulike from time to time.
PhD fellows
- Nidhi Shukla, working on "Long non-coding RNAs in cancer prostate."
- Harshita Bhargava, working on "Recommender systems for a thorough health database integration"
- Ayam Gupta working on "Regulating vitamin K and cancer Prostate transcriptomes in humans"
- Shalini Rajgopal working on "Dissecting Vitamin K Pathways using Systems Genomics"
- Bhumandeep Kour working on "Systems genomic approaches in understanding the role of diabetics in cancer prostate"
- Anchita Prasad, working on "The known unknown regions in bacteria"
- Shazia Naqshbandi: working on "The annotation and machine learning approaches for classifying hypothetical proteins in fungi"
Visiting/Graduate fellows
- Saloni Someshwar: Working on "Systems genomics of dental cancers"
- Tanvi Balyan: Working on "Machine Learning heuristics of cancers"
Past PhD/Postdoc fellows
- Ashkan Dashtban, currently based in UK, worked on "Robust BAT algorithms for gene selection." Awarded and currently at University of UCL, London.
- Purva Bhalothia, Postdoc. Worked on "Identifying Regulatory Elements in Diabetic Nephropathies"
- Johny Ijaq, Osmania University, Hyderabad.Worked on " A nine point classifications coring scheme for deciphering function of hypothetical proteins."
- Sonal Gupta, Birla Institute of Scientific Research, Jaipur working on "Identifying lncRNA-protein interactions in Congenital Pouch Colon"
Vacancies
The group has recently advertised for three positions. If you are a CSIR JRF/GATE fellow, you are always welcome to contact me. Grad project fellows can contact me throughout the year. Applications considered on a rolling basis.
Publication Highlights
All peer-reviewed PubMed publications are available here
- Editorial perspective: Shukla N, Prasad A, Kanga U, Suravajhala R, Nigam VK, Kishor PK, Polavarapu R, Chaubey G, Singh KK, Suravajhala P. SARS-CoV-2 Transgressing LncRNAs Uncovers the Known Unknowns. Physiol Genomics. 2021 Sep 7. doi: 10.1152/physiolgenomics.00075.2021. Epub ahead of print. PMID: 34492207.
- Research: Gupta A, Shukla N, Nehra M, Gupta S, Malik B, Mishra AK, Vijay M, Batra J, Lohiya NK, Sharma D and Suravajhala P (2020) A Pilot Study on the Whole Exome Sequencing of Prostate Cancer in the Indian Phenotype Reveals Distinct Polymorphisms. Front. Genet. 11:874. doi: 10.3389/fgene.2020.00874
- Perspectives: Singh KK, Chaubey G, Chen JY, Suravajhala P. Decoding SARS-CoV-2 Hijacking of Host Mitochondria in Pathogenesis of COVID-19 [published online ahead of print, 2020 Jun 8]. Am J Physiol Cell Physiol. 2020;10.1152/ajpcell.00224.2020. Link
- Research: Mathur P, Medicherla KM, Chaudhary S, Patel M, Bagali S and Suravajhala P. Whole Exome Sequencing reveals rare variants linked to Congenital Pouch Colon. Scientific Reports. 2018; 8:6646. Link
- Research: Suravajhala P, Benso A. Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis. Adv Appl Bioinform Chem. 2017 Jun 12;10:57-64. Link
- Research: Dashtban M, Balafar M, Suravajhala P.Gene selection for tumor classification using a novel bio-inspired multi-objective approach. Genomics. 2017 Aug 3. pii: S0888-7543(17)30067-8. Link
- Review: Suravajhala P, Kogelman LJ, Kadarmideen HN. Multi-omic data integration and analysis using systems genomics approaches: Methods and application in animal production, and health and welfare. Genetics, Selection and Evolution. 2016: 48:38. Link
- Research: Suravajhala P, Kogelman LJ, Mazzoni G, Kadarmideen HN. Potential role of lncRNA cyp2c91-protein interactions on diseases of the immune system. Front Genet. 2015 Jul 28;6:255. Link
- Protocol: Suravajhala P and Bizzaro JW: A Conceptual Outline for ‘Omics Experiments Using Bioinformatics Analogies. Bioprotocol. 01/2015; Link
Books
Select Assignments
Upcoming/Recently concluded
- Workshop on Systems Genomics in the Age of Next Generation Sequencing: October-December 2021. Please stay tuned!
Recent Past
- Workshop co-organizer on the known unknowns of SARS-CoV-2 infection and role of Mitochondria Link April 27-29, 2021
- Keynote at BCC2020
- Conference co-chair for InCoB'20
- Program chair for Inbix'20
- Plenary talk for Indonesia Medical Association (IMERI) conference, November 9, 2020.
- Workshop on 'Bioinformatics to Systems Genomics' during September 22-30, 2020.
- Systems genomic approaches of COVID at various schools
- Workshop on Systems Biology in 2020.
- Workshop on Prioritizing variants from NGS data in PAG Asia in Seoul during May 30-June 1, 2018.
- Workshop on Systems genomics in University of Jayawardenapura, Colombo during June 2-4, 2018.
Reviewing Assignments
- Associate Editor for
- BMC Medical Genomics
- Frontiers in Genetics/Genomic Assay Technologies
- Bio-Protocol
- Biomolecules
- Recently reviewed for
- PeerJ
- Elsevier Software
- Plos ONE
- Frontiers in Oncology
- MDPI journals
- BMC Bioinformatics
- Current Science
