Prash

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”The only thing that interferes with my learning is my education” ~ Albert Einstein

Contents 1 About 1.1 Keywords 1.2 Systems Genomics Lab 1.3 Mentoring 1.4 Current PhD fellows 1.4.1 Past PhD/Postdoc fellows 1.5 Current Graduate students 1.6 Vacancies 1.7 Publication Highlights 1.8 Books 1.9 Select Assignments 1.9.1 Upcoming/Recently concluded 1.9.2 Recent Past 1.9.3 Reviewing Assignments

About

A PhD in Systems Biology from Aalborg University, Denmark., Prashanth N Suravajhala went on to gain more than 8 years of postdoctoral experience across four different laboratories. Prash worked for Birla Institute of Scientific Research, Jaipur on his return to India where he successfully led three projects in the areas of systems genomics of rare diseases and next generation sequencing analysis of cancers and diabetes. He has interests exploring the known unknown regions in the animal/human genomes, primarily working on the top-down systems biology approaches of hypothetical proteins. Over the last eight years, he has developed an interest in long noncoding RNAs in humans, elucidating the mechanisms underpinning small molecular interactions through clinical exomes. His group has benchmarked pipelines and developed methods for systems genomic integration. He has over 90 publications in peer-reviewed journals and edited 3 books. He strongly advocates open access and open science.

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Keywords

1. KnownUnknowns
2. HypotheticalProteins
3. LncRNAs
4. RareDiseases
5. ProstateCancer
6. SystemsGenomics

Systems Genomics Lab

I am a group leader of Systems Genomics laboratory at Amrita School of Biotechnology, Amrita Vishwavidyapeetham, Kerala, India. Our group is curious to know how of a biology of a system with special interests 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. A larger interests have been into elucidating the known unknown mechanisms underpinning small molecular interactions through clinical exomes. Apart from this, we have had intermittently worked on identifying the candidate genes involved in synthetic framework in bacteria and viruses.

Mentoring

I mentor students online through Bioclues, India's largest bioinformatics society which I founded in 2005

Current PhD fellows

• Anjali Krishna, working on "Inferring Variants of Unknown Significance (VOUS) in Rare Disease Genetics: An India-centric Study​​"
• Bhargavi Rajarathinam, working on "Integrated Systems Genomics Approaches for Deciphering Candidate Genes Regulating the Prostate Cancer Phenotype in India" 
• Anchita Prasad, working on "The known unknown regions in bacteria."
• Anandhu Presannan, working on "Evaluating bona fide pathogenic SNPs using an integrated systems genomic and agnostic framework"
• Gautham Manoj, working on "Amrita Disease Measure for Inferring Risk Epidemiology."
• Muskan Syed, working on "Identification of fungal AMR using metagenomic approaches in animals"

Past PhD/Postdoc fellows

• Shalini Rajgopal worked on "Dissecting Vitamin K Pathways using Systems Genomics." Submitted her thesis in December 2023.
• Nidhi Shukla, worked on "Long non-coding RNAs in CA prostate." Submitted her thesis in August 2023.
• Harshita Bhargava, worked on "Recommender systems for a thorough health database integration." Submitted her thesis in January 2024.
• Bhumandeep Kour worked on "Systems genomic approaches in understanding the role of diabetics in CA prostate." Submitted her thesis in December 2023.
• 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." Currently a Postdoc in the UK.
• Pradeep Tiwari, Birla Institute of Scientific Research, Jaipur worked on " Systems Phenome Interatcome Networks in Asian Indian Type -2 Diabetes Mellitues (AIT2DM)." Currently a Postdoc in Johns Hokins.
• Johny Ijaq, Worked on " A nine point classifications coring scheme for deciphering function of hypothetical proteins." Currnetly a Postdoc in CCMB, Hyderabad.
• Sonal Gupta, Birla Institute of Scientific Research, Jaipur worked on "Identifying lncRNA-protein interactions in Congenital Pouch Colon." Currently a Postdoc in Delhi.
• Urvashi Vijay, Birla Institute of Scientific Research, Jaipur worked on " Rare disease genomics inferring assays to screens the mutations" Currently a Scientist at SMS Medical College, Jaipur.

Current Graduate students

• Anupama Anil
• Anupama Vijay

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

• Perspective: Işık EB, Brazas MD, Schwartz R, Gaeta B, Palagi PM, van Gelder CWG, Suravajhala P, Singh H, Morgan SL, Zahroh H, Ling M, Satagopam VP, McGrath A, Nakai K, Tan TW, Gao G, Mulder N, Schönbach C, Zheng Y, De Las Rivas J, Khan AM. Grand challenges in bioinformatics education and training. Nat Biotechnol. 2023 Aug;41(8):1171-1174. doi: 10.1038/s41587-023-01891-9. PMID: 37568018.

• 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

• Your passport to a Career in Bioinformatics
• Biotoons

Select Assignments

Upcoming/Recently concluded

Invited talk in Mangalore University on January 17, 2024.

Recent Past

• • Invited talk in GATC, InStem conference in Bangalore: April 7-9, 2023.
  • Invited talk in ISSRF conference in Cuttack: February 24-26, 2023.
  • Invited talk in #ADNAT2023: March 10-12, 2023.
  • Invited talk in International Genetics conference in Malaysia: March 7-9, 2023.
  • PhD course on Integrated Systems Genomics January-June 2023.
  • PhD course on Ethic/FAIR/PRISMA guidelines January-June 2023.
  • Meetings/Talks in Mumbai Haematology Group during January 2023.
  • 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

• Publons profile

• Associate Editor for
  • Gigabyte
  • BMC Medical Genomics
  • BMC Medical Supplements
  • BMC Methods
  • Bio-Protocol
  • Biomolecules
  • Frontiers in Genetics/Genomic Assay Technologies

• Review Editor for
  • MDPI journals
  • PeerJ
  • Elsevier Software
  • Plos ONE
  • Frontiers in Oncology
  • BMC Bioinformatics
  • Current Science