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Dr. Prashanth N. Suravajhala

Associate Professor, School of Biotechnology, Amritapuri

Qualification: BSc, MSc, Ph.D
prash@am.amrita.edu
Curriculum Vitae
ResearchGate Profile
Research Interest: Bioinformatics, Cancer Biology, lncRNA Biology, Systems Genomics

Bio Publications Professional Appointments Fellowships & Grants Skills & Activities Conference Talks/Organization Peer-review & Publication Records
Bio

A Ph.D. in Systems Biology from Aalborg University, Denmark., Prashanth N Suravajhala went on to gain more than 7 years of postdoctoral experience across four different laboratories. Prash worked for the 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 an interest in exploring the known unknown regions in the human genome, 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 is an Associate Editor of  Frontiers in Genetics/Systems Biology, Bio-Protocol, Biomolecules, and BMC Medical Genomics.  He strongly advocates open access and open science.

Education

  • 2000 – 2002: M.Sc in Biotechnology GG Central University, Bilaspur, India
  • 1997- 2000: B.Sc. in Microbiology (with Botany and Chemistry as auxiliary subjects),
    Kakatiya University, India
  • 1994 – 1996: Intermediate (Botany, Zoology, Physics and Chemistry)
    Board of Intermediate Education, Hyderabad
  • 1994: Class X.
    Board of Secondary education, Hyderabad, India.
Publications

Journal Article

Year : 2022

Systematic Understanding of Anti-tumor Mechanisms of Tamarixetin through network and Experimental Analyses

Cite this Research Publication : Sanu K. Shaji, Damu Sunilkumar, Dr. Geetha Kumar, and Dr. Bipin G. Nair, “Systematic understanding of anti-tumor mechanisms of tamarixetin through network and experimental analyses”, 39th Annual Conference of Indian Association for Cancer Research (IACR-2020): “Leading the Fight against Cancer”, Rajiv Gandhi Centre for Biotechnology (RGCB), Trivandrum, Kerala, India, February 5-7. 2020.

Publisher : Scientific reports

Year : 2021

The Omic Insights on Unfolding Saga of COVID-19

Cite this Research Publication : Kaur A, Chopra M, Bhushan M, Gupta S, Kumari P H, Sivagurunathan N, Shukla N, Rajagopal S, Bhalothia P, Sharma P, Naravula J, Suravajhala R, Gupta A, Abbasi BA, Goswami P, Singh H,
Narang R, Polavarapu R, Medicherla KM, Valadi J, Kumar S A, Chaubey G, Singh KK, Bandapalli OR, Kavi Kishor PB, Suravajhala P. The Omic Insights on Unfolding Saga of COVID-19. Front Immunol. 2021 Oct 20;12:724914. doi: 10.3389/fimmu.2021.724914. PMID: 34745097; PMCID: PMC8564481

Publisher : Front Immunol

Year : 2020

Decoding SARS-CoV-2 hijacking of host mitochondria in COVID-19 pathogenesis

Cite this Research Publication : Singh KK, Chaubey G, Chen JY, Suravajhala P. Decoding SARS-CoV-2 hijacking of host mitochondria in COVID-19 pathogenesis. Am J Physiol Cell Physiol. 2020 Aug 1;319(2):C258- C267. doi: 10.1152/ajpcell.00224.2020. Epub 2020 Jun 8. PMID: 32510973; PMCID: PMC7381712.

Publisher : Am J Physiol Cell Physiol.

Year : 2020

Deciphering LncRNA-protein interactions using docking complexes

Cite this Research Publication : Suravajhala R, Gupta S, Kumar N, Suravajhala P. Deciphering LncRNA-protein interactions
using docking complexes. J Biomol Struct Dyn. 2020 Dec 7:1-8. doi: 10.1080/07391102.2020.1850354. Epub ahead of print. PMID: 33280525

Publisher : J Biomol Struct Dyn.

Year : 2019

Systems Genomics of Thigh Adipose Tissue From Asian Indian Type-2 Diabetics Revealed Distinct Protein Interaction Hubs

Cite this Research Publication : Tiwari P, Saxena A, Gupta N, Medicherla KM, Suravajhala P, Mathur SK. Systems Genomics of Thigh Adipose Tissue From Asian Indian Type-2 Diabetics Revealed Distinct Protein Interaction Hubs. Front Genet. 2019 Jan 8;9:679. doi: 10.3389/fgene.2018.00679. PMID: 30671081; PMCID: PMC6331691.

Publisher : Front Genet.

Year : 2019

A model to predict the function of hypothetical proteins through a nine-point classification scoring schema

Cite this Research Publication : Ijaq J, Malik G, Kumar A, Das PS, Meena N, Bethi N, Sundararajan VS, Suravajhala P. A model to predict the function of hypothetical proteins through a nine-point classification scoring schema. BMC Bioinformatics. 2019 Jan 8;20(1):14. doi: 10.1186/s12859-018-2554-y. PMID: 30621574; PMCID: PMC6325861.

Publisher : BMC Bioinformatics

Year : 2018

Whole Exome Sequencing reveals rare variants linked to Congenital Pouch Colon.

Cite this Research Publication : Mathur, P., Medicherla, K.M., Chaudhary, S. et al. Whole exome sequencing reveals rare variants linked to congenital pouch colon. Sci Rep 8, 6646 (2018). https://doi.org/10.1038/s41598-018-24967-y

Publisher : Scientific Reports. 2018: 8:6646.

Year : 2018

Genetics of Lipodystrophy: Can It Help in Understanding the Pathophysiology of Metabolic Syndrome?

Cite this Research Publication : Mathur SK, Tiwari P, Gupta S, Gupta N, Nimesh S, Medicherla KM, Suravajhala P. Genetics of Lipodystrophy: Can It Help in Understanding the Pathophysiology of Metabolic Syndrome? Biomolecules. 2018 Jul 6;8(3).

Publisher : Biomolecules. 2018 Jul 6;8(3).

Year : 2018

HYPO: A database of hypothetical human proteins

Cite this Research Publication : Sundararajan VS, Malik G, Ijaq J, Kumar A, Das PS, P R S, Nair AS, Dhar PK, Suravajhala P. HYPO: A Database of Human Hypothetical Proteins. Protein Pept Lett. 2018;25(8):799-803. doi: 10.2174/0929866525666180828110444. PMID: 30152276.

Publisher : Protein Pept Lett. 2018 Aug 27.

Year : 2018

Lnc-EPB41-Protein Interactions Associated with Congenital Pouch Colon

Cite this Research Publication : Gupta S, Gupta N, Tiwari P, Menon S, Mathur P, Kothari SL, Nallapeta S, Medicherla KM, Suravajhala P. Lnc-EPB41-Protein Interactions Associated with Congenital Pouch Colon. Biomolecules. 2018 Sep 17;8(3).

Publisher : Biomolecules. 2018 Sep 17;8(3)

Year : 2017

Gene selection for tumor classification using a novel bio-inspired multi -objective approach

Cite this Research Publication : 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

Publisher : Genomics. 2017 Aug 3. pii: S0888-7543(17)30067 -8.

Year : 2017

Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis.

Cite this Research Publication : Suravajhala P, Benso A. Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis. Adv Appl Bioinform Chem. 2017 Jun 12;10:57-64

Publisher : Adv Appl Bioinform Chem. 2017 Jun 12;10:57-64.

Year : 2016

Multi-omic data integration and analysis using systems genomics approaches: Methods and application in animal production, and health and welfare.

Cite this Research Publication : 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. Highly accessed and featured review

Publisher : Genetics, Selection and Evolution. 2016: 48:38.

Year : 2015

Is HNF4A a candidate to study zinc finger protein slug?

Cite this Research Publication : Suravajhala P, Singh TR. Is HNF4A a candidate to study zinc finger protein slug? Int J Bioinform Res Appl. 2015;11(4):366-73. PubMed PMID: 26561320

Publisher : Int J Bioinform Res Appl. 2015;11(4):366-73. PubMed PMID: 26561320

Year : 2015

A Conceptual Outline for ‘Omics Experiments Using Bioinformatics Analogies

Cite this Research Publication : Prashanth Suravajhala, Jeffrey W Bizzaro: A Conceptual Outline for ‘Omics Experiments Using Bioinformatics Analogies. Bioprotocol. 01/2015

Publisher : Bioprotocol. 01/2015

Year : 2015

Potential role of lncRNA cyp2c91-protein interactions on diseases of the immune system

Cite this Research Publication : 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. doi: 10.3389/fgene.2015.00255. eCollection 2015. PubMed PMID: 26284111

Publisher : Front Genet. 2015 Jul 28;6:255.

Year : 2014

Introducing the hypothome. A way to integrate predicted proteins in interactomes.

Cite this Research Publication : Claus Desler, Prashanth Suravajhala, Sine Zambach and Lene Juel Rasmussen: Introducing the hypothome. A way to integrate predicted proteins in interactomes. International Journal of Bioinformatics Research and Applications 01/2014

Publisher : International Journal of Bioinformatics Research and Applications 01/2014

Year : 2014

Making novel proteins from pseudogenes

Cite this Research Publication : P. R. Shidhi, Prashanth Suravajhala, Aysha Nayeema, Achuthsankar S. Nair, Shailja Singh, Pawan K. Dhar: Making novel proteins from pseudogenes. Bioinformatics 09/2014

Publisher : Bioinformatics 09/2014;

Year : 2013

A combined approach for genome wide protein function annotation/prediction

Cite this Research Publication : Alfredo Benso, Stefano Di Carlo, Hafeez Ur Rehman, Gianfranco Politano, Alessandro Savino, Prashanth Suravajhala: A combined approach for genome wide protein function annotation/prediction. Proteome Science 11/2013; 11(Suppl 1):S1

Publisher : Proteome Science 11/2013; 11(Suppl 1):S1

Professional Appointments

Work Experience

Year Affiliation
September 2021 Principal Scientist, Amrita school of Biotechnology, Amrita University, Kerala, India
Achievements

  • Principal Investigator and Leader of two projects on analyzing the next generation sequencing of Prostate cancer/clinical exomes/rare diseases and Vitamin K Genetics
August 2016 – August 2021 Senior Scientist, Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India.
Achievements

  • Principal Investigator and successfully lead three projects in rare diseases, viz. Congenital Pouch Colon (CPC), aplastic Anemia, cancer phenotypes and Diabetes genomics.
  • Benchmarked Whole Exome/Transcriptome Sequencing pipelines for research community
  • Characterized a couple of lncRNAs and assessed their interactions with proteins for a phenotype of our interest.
September 2014 – August 2015 Postdoc/Bioinformatics Manager at Faculty of Health and Medicine, University of Copenhagen, Denmark Project: EU-FP7 Marie Curie Actions Grant (CIG-293511)
Achievements

  • Identified variant and regulatory regions in animal genomes.
  • Analyzed next generation sequencing (NGS) datasets of Clinical samples, RNA-Seq
  • Analyzed metabolic and immunomodulary pathway specific genes
June 2008 – August 2014 Visiting Postdoc/collaborative scientist at

  • Bioinformatic.Org, USA
  • Jaak Vilo’s lab, University of Tartu, Estonia
  • Institute for Protein Research (IPR) at Osaka University, Japan
  • South African National Bioinformatics Institute, Cape Town
  • Bioinformatics Division, CDAC, Pune, India.

Achievements

  • Compared and analyzed wide variety of sequencing and biochemical data.
  • Raised successful collaborations in delivering impactful systems genomics approaches
  • Proactively engaged in knowledge sharing thereby building expertise in the niche area of Bioinformatics critical to Systems and Synthetic Biology.
  • Worked with network of peers to understand and agree project priorities in lessening the scale of experimentation
  • Discussed and peer-reviewed the works submitted by the researchers: partly involved in regulatory affairs of the organization
2004 – 2008 PhD fellow at Department of Nature, Systems and Models, Roskilde University, Denmark Awarded PhD in soft and biological matter, Faculty of Science and Technology , Aalborg University, Denmark. Convocation/Award: 2012

Title of the thesis: Hypothetical proteins in Human: An emphasis of proteins targeted to mitochondria

Summary: We presented an in silico selection strategy where eukaryotic hypothetical proteins are sorted according to two criteria that can be reliably identified in silico: the presence of subcellular targeting signals and presence of characterized protein domains. The PhD work was aimed at providing a way to characterize the hypothetical proteins through the validation of selection strategies. For the comparison we focused on mitochondrial proteins to find any leads specific to DNA mismatch repair and in this process, many proteins, defined as hypothetical in 2006, have later been characterized as mitochondrial.

Supervisory and Teaching Experience

  • Supervised 4 PhD fellows, currently with 7 PhD fellows with one PhD student submitting
  • Mentored and supervised 5 Postdocs, several graduate students through org, India’s largest professional society that I founded in 2005.
  • Adviser to 5 companies based in USA and
  • Designed course-ware, Systems Biology and bioinformatics curriculum for well known universities such as Central University of Himachal Pradesh (CUHP) etc.
  • Board member/paper setter and examiner for universities,e.g. Rajasthan
  • Involved in teaching in the domains of systems biology, protein interactions and mitochondrial
  • The following are the two upcoming courses:
    • An annual online course on “Biochemical Interactions: Proteins to non-coding RNAs” Next course planned during December 2021
    • A course on ‘Mitochondriomics: Tools and Techniques’ which I have been teaching online since Next course planned in March 2022.
Fellowships & Grants
Year Fellowships and Grants
September 2018 Principal Investigator for “Dissecting Vitamin K Pathways in Human Subjects Using Next Generation Sequencing” Funded by SERB-DST-IRRD ( 88.45 lakhs/8.845 million INR): Ongoing.
June 2018 Principal Investigator for “Whole Exome Sequencing of Prostate Cancer Subjects Specific to India” (28 lakhs/2.8 million INR), funded by BrainPan.
January 2018 Grant Recipient as a co-investigator for project titled, “Validation of Gene sets identified from Transcriptomic data of Adipose tissue of Asian Indian T2DM patients” by Research Society for the Study of Diabetes in India (10.2 lakhs/1.02 million INR)
2016-2019 Sentinels of Science : Peer-Review Publons award (Top 1%) for consecutive years
January 2015 PloS. T shirt design winner
September 2014 Bayer Postdoc/visiting fellowship, Boston.
April 2013 Visiting Scientist, Jaak Vilo’s laboratory, University of Tartu, Estonia.
February 2012 Visiting Scientist, South African National Bioinformatics Institute, Cape Town.
June 2011 Scholarship: The Biobricks young investigator award- Stanford University: Presented work on Synthetic Proteins to Hypothetical Proteins: A case study on Domain of Unknown Function (DUF)
July 2010 Scholarship: The International Society for Computational Biology-NY Cornell Fellowship for Cornell University Computational Biology.
June 2008 Scholarship: Recomb fellowship, Singapore
March 2008 Scholarship: ISMB/ISCB Travel fellowship, Taipei, Taiwan
July 2007 Scholarship: BioComp 2007 Travel fellowship, United States
Skills & Activities
Technical Skills Functional Genomics, Systems Genetics, Gene Expression, Computational Genomics and Proteomics, Pull-down assays, Protein-Protein Interaction, NGS Data Analysis, Statistics and Linux programming, Genome Annotation
Languages (All good) English, Hindi, Danish, Italian, Sanskrit, Telugu
Scientific Memberships
  • American Association for the Advancement of Science
  • Asia Pacific Bioinformatics Network
  • International Society for Computational Biology
  • Danish Biochemical Society
  • The Science Advisory Board
  • European Federation of Biotechnology
  • Indian Society for Human Genetics
  • Rotary.Org International since 1998
  • Mitochondrial Research Society
Conference Talks/Organization
  • Keynote speaker at recently held BCC2020/Galaxy conference organised in
  • Program chair of Indian Conference on Bioinformatics 2020 (Inbix’20)
  • Session organizer on Biological networks for non-coding RNA: Insights into interactions at IWBBIO, Granada, Spain during 2015- ’20
  • Co-organized series of Bioinformatics and Systems Biology (BSB) and participated in several ISMB/Molecular Biology/ISCB affiliate conferences since
  • 45+ invited talks and several workshops organized
Peer-review & Publication Records
  • 80+ peer-reviewed publications with 6 manuscripts under review and 2 in press
  • Authored 3 books, two for One widely accessed book titled, “Your passport to a Career in Bioinformatics” Second edition of the latter released in March 2021
  • Associate Editor for
    • Frontiers in Genetics
    • BMC Medical Genomics
    • Bio-Protocol
    • Gigabyte
    • MDPI Biomolecules
  • Recently Reviewed for Stem Cell and Therapy, BMC Medical Genetics, IJMS, Molecules, BMC Bioinformatics, Plos one, Current Trends in Biotechnology and Pharmacy
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