SysGenLab

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

Linkedin: https://in.linkedin.com/in/prashbio

Git: https://github.com/prashbio
ORCID: https://orcid.org/0000-0002-8535-278X
Twitter: https://twitter.com/prashbio

=====Systems Genomics Lab=====
A PhD in Systems Biology from Aalborg University, Denmark., Prashanth N Suravajhala (Prash) is known for his work in genomics, computational biology, and systems biology with a research primarily focusing on understanding complex biological systems, including the study of various biological networks, protein function prediction, and the development of computational tools for studying molecular biology. A Professor at Systems Genomics Laboratory at Manipal University Jaipur India, his 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.

He has interests exploring the known unknown regions in the human genomes, primarily working on the top-down systems biology approaches of hypothetical proteins besides long noncoding RNAs in humans, elucidating the mechanisms underpinning small molecular interactions through clinical exomes. His group’s focus in the areas of rare diseases primary Anorectal Malformation and CA Prostate consortium of India (CAPCI) where he leads the consortium efforts in ascertaining the genetic landscape of CA Prostate in India. He has benchmarked pipelines and developed methods for systems genomic integration. He has over 135+ publications in peer-reviewed journals and edited 4 books. Traveled over 90+ countries, he loves mentoring students and founded Bioclues.org in 2005,

=====Keywords=====
#KnownUnknowns #HypotheticalProteins #LncRNAs #RareDiseases #ProstateCancer #SystemsGenomics

=====Current PhD fellows=====

  • Soham Biswas, working on “Somatic Genetic Landscape of CA Prostate in Indian Sub-Populations”
  • Vandana, working on “Systems Genomics of Rare Annorectal Malformations: A cross-sectional study”
  • Gautham Manoj, working on “A Disease Model for Inferring Variants of Uncertain Significance”
  • Akshay Zawar, working on “Machine Learning Heuristics for Variants of Unknown Significance”
  • Poonam Sen, working on “Missing Link Between CA Prostate and Diabetes”
  • Sai Teja, working on “Systems Genomics of New-Born Screening and Blood-Related Disorders”
  • Nayeem N, working on “Machine Learning Approaches to Identify Key Genes in CA Prostate”
  • Ajay Joshi, working on ” Integration of Next-Generation Sequencing Pipelines Employing Systems Genomics  Approaches”

======Past PhD/Postdoc fellows======

  • Anchita Prasad, worked on “The known unknown regions in bacteria.” Defended her thesis in April 2026
  • Muskan Syed, worked on “Genome scale models in Mucorales”
  • Shalini Rajagopal worked on “Dissecting Vitamin K Pathways using Systems Genomics.” ”Postdoc in NIVEDI, Bangalore.”
  • Nidhi Shukla, worked on “Long non-coding RNAs in CA prostate.” ”Now Assistant Professor in CURAJ, Kishnagarh”
  • Harshita Bhargava, worked on “Recommender systems for a thorough health database integration.” ”Now Assistant Professor in IIS University, Jaipur”
  • Bhumandeep Kour worked on “Systems genomic approaches in understanding the role of diabetics in CA prostate.” ”Now a Postdoc”
  • Ashkan Dashtban, currently based in UK, worked on “Robust BAT algorithms for gene selection.” Now a Postdoc at 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 SMSHC, Jaipur.
  • Johny Ijaq, Worked on ” A nine point classification scoring scheme for deciphering function of hypothetical proteins.” Currently a Scientist in Elucidata
  • 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 Visiting Research Fellows=====

  • Bharat
  • Hunarpreet Kaur

=====Vacancies=====
The Systems Genomics Lab recently announced openings for a Postdoc and a couple of PhD fellows. The deadline is now closed:

=====Publication Highlights=====

All peer-reviewed PubMed publications are available here

  • Research: Suseelan V, Krishna A A, Zawar A, Prabhu PS, Bhatta P, Paliwal A, Mathur P, Medicherla KM, Polipalli SK, Suravajhala P. Distinct genetic variants from the whole-exome sequencing of syndromic anorectal malformations: A cross-sectional study. iScience. 2026 Apr 1;29(5):115576. doi: 10.1016/j.isci.2026.115576. PMID: 42058895; PMCID: PMC13123494.
  • ‘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
  • Perspective: 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=====

  • 2025: Next-Generation Sequencing Standard Operating Procedures and Applications. Edited By Prashanth N Suravajhala, Jeffrey W Bizzaro. Link
  • 2011: Your passport to a Career in Bioinformatics. Prashanth N Suravajhala. Link
  • 2006: Biotoons. Prashanth N Suravajhala. Link

=====Select Assignments=====

======Upcoming/Recently concluded======
** #ISMB2026 COSI Keynote speaker in Washington DC, USA during July 2026.
** India chair, #APJBC2026 in Singapore

======Recent Past======
** #GBES2026 and INBIX2026 in Ahmedabad during September 29-October 1, 2026.

** Invited talk at ISHG2026, PGIMER, Chandigarh during January 2026
** Invited talk at MAHE, Manipal during December 2025
** Invited talk at ICMR, Delhi during April 2025
** Program chair of InbixADNAT24 : inbix.bioclues.org
** Session organizer on Biological networks for non-coding RNA: Insights into interactions at IWBBIO, Granada, Spain during 2015- ’25
** Invited talk in Mangalore University on January 17, 2024.
** 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 [https://app.hopin.com/events/mitochondria-targeted-drug-development/reception Link] April 27-29, 2021
** Keynote at [https://bcc2020.github.io/schedule/ BCC2020]
** Conference co-chair for [https://incob.apbionet.org/incob20/ InCoB’20]
** Program chair for [http://www.inbix.bioclues.org 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 [https://bioinfo.bisr.res.in/workshop/2018-19/workshop_mar2019.php 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
** Frontiers in Systems Biology
** Gigabyte
** BMC Medical Genomics
** BMC Medical Supplements
** BMC Methods
** Bio-Protocol
** Biomolecules
** Frontiers in Genetics/Genomic Assay Technologies

*Review Editor for
** PeerJ
** Elsevier Software
** Plos ONE
** Frontiers in Oncology
** BMC Bioinformatics
** Current Science