Dr. Piyush Agrawal

Introduction

Dr. Piyush Agrawal holds a Ph.D. in the field of Bioinformatics and Computational Biology from CSIR-IMTech, Chandigarh, India, supervised by Prof. G.P.S. Raghava. His doctoral research primarily delved into computer-aided drug design, with a focus on the computational aspects of protein-ligand interactions. In addition to substantial contributions to methodological advancements, Dr. Agrawal developed web-based resources and user-friendly machine learning tools for predicting therapeutic properties of ligands.

For his Postdoctoral Fellowship, Dr. Agrawal joined Dr. Hannenhalli’s lab at the National Cancer Institute, NIH, USA, where he extensively explored cancer genomics. His postdoctoral research was centered on unraveling tumor heterogeneity, deciphering molecular mechanisms underlying metastasis, and studying responses to drug treatments.

In April 2024, Dr. Agrawal assumed the role of Assistant Professor at the Faculty of Medical & Health Sciences, SRM Institute of Science & Technology, Chennai, India. His research group, the “Computational and System Biology” lab, is dedicated to leveraging AI/ML-based computational approaches to analyze multi-omics data, aiming to elucidate mechanisms associated with cancer metastasis, drug toxicity, and identification of potential biomarkers from various imaging modalities (such as H&E and IHC staining). Additionally, the lab investigates splicing events in host-microbe interactions.

Dr. Agrawal collaborates closely with researchers at both international and national levels. Notably, he collaborates with Dr. Hannenhalli at NCI, NIH, USA, focusing on various aspects of cancer genomics. Additionally, his collaboration with Dr. Patiyal and Dr. Mukherjee at NCI, NIH, USA focuses on investigating the mechanism of alternative splicing in cancer metastasis. Moreover, Dr. Agrawal collaborates with Dr. Sharma at IIT Hyderabad, concentrating on the development of AI/ML tools for exploring properties associated with peptides derived from microbes. Furthermore, he collaborates with Dr. Singh at the University of Delhi, with a broad focus on chemoinformatics.

A. Education

B. Publications

B1. Original Research Articles

• Piyush Agrawal*, Navami Jain, Vishaka Gopalan, Annan Timon, Arashdeep Singh, Padma S. Rajagopal, Sridhar Hannenhalli*. Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in Triple Negative Breast Cancer. Cell Press iScience, 2024. [IF: 6.0]
• Piyush Agrawal, Narmada Sambaturu, Gulden Olgun, Sridhar Hannenhalli*. A path-based analysis of infected cell line and COVID-19 patient transcriptome reveals novel potential targets and drugs against SARS-CoV-2. Frontiers in Immunology, 2022, 13:918817, [IF: 8.78]
• Arashdeep Singh, Arati Rajeevan, Vishaka Gopalan, Piyush Agrawal, Chi-Ping-Day, Sridhar Hannenhalli*. Broad misappropriation of developmental splicing profile by cancer in multiple organs. Nature Communication, 2022, 13:7664-7682, [IF: 16.6]
• Piyush Agrawal, Dhruv Bhagat, Manish Mahalwal, Neelam Sharma, Gajendra P.S. Raghava*. AntiCP 2.0: an updated model for predicting anticancer peptides. Oxford Briefings in Bioinformatics 2020, 22(3):bbaa153, [IF: 13.99].
• Piyush Agrawal, Sumit Kumar, Archana Singh, Gajendra P. S. Raghava*, Indrakant K Singh*. NeuroPIpred: a tool to predict, design, and scan insect neuropeptides. Nature Scientific Reports, 2019, 9:5129-40, [IF: 4.6]
• Piyush Agrawal#, Harinder Singh#, Hemant Kumar Srivastava, Sandeep Singh, Gaurav Kishore, Gajendra P.S. Raghava*. Benchmarking of different molecular docking methods for protein-peptide docking. BMC Bioinformatics, 2019, 19:105-124, [IF: 3.3]
• Piyush Agrawal, Sumeet Patiyal, Rajesh Kumar, Vinod Kumar, Harinder Singh, Pawan Kumar Raghav, Gajendra P.S. Raghava*. ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank. Oxford Database, 2019, 2019, bay142, [IF: 5.8].
• Piyush Agrawal and Gajendra P. S. Raghava*. Prediction of antimicrobial potential of a chemically modified peptide from its tertiary structure. Frontiers in Microbiology, 2018, 9:2551, [IF: 5.8]
• Piyush Agrawal#, Sherry Bhalla#, Kumardeep Chaudhary, Rajesh Kumar, Meenu Sharma, Gajendra P.S. Raghava*. In Silico Approach for Prediction of Antifungal Peptides. Frontiers in Microbiology 2018, 9:323 [IF: 5.2]
• Piyush Agrawal#, Sherry Bhalla#, Salman Sadullah Usmani#, Sandeep Singh, Kumardeep Chaudhary, Gajendra PS Raghava, Gajendra P.S. Raghava*, Ankur Gautam. CPPsite 2.0: a repository of experimentally validated cell-penetrating peptides. Nucleic Acids Research 2016, 44:D1098-D1103 [IF: 14.9].

B2. Book Chapter

• Animesh Awasthi, Gaurav Sharma*, Piyush Agrawal*. Book Chapter 20: Computational approaches for vaccine designing. Book Name "Bioinformatics: Methods and Applications" by Elsevier Publications. 2021

B3. Conference Abstracts

• Piyush Agrawal*, Gulden Olgun, Arashdeep Singh, Vishaka Gopalan, Sridhar Hannenhalli*. Characterizing the role of exosomal miRNAs in metastasis. Cancer Research. 2024.
• Piyush Agrawal*, Navami Jain, Vishaka Gopalan, Sridhar Hannenhalli*. Network-based approach elucidates critical genes in BRCA subtypes. Cancer Immunology Research. 2022.

C. Awards & Achievements

• The Fellows Award for Research and Excellence (FARE) for outstanding research work entitled “Netwrok based approach elucidates critical genes in BRCA subtypes and chemotherapy response in Triple Negative Breast Cancer” by National Institutes of Health (NIH), Bethesda, USA. 2023
• Intramural Research Training Award (IRTA) for doing Postdoctoral Research at Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, USA as Visiting Postdoctoral Fellow. 2020
• DST SERB Travel Fellowship to attend 12th International Biocuration Conference 2019, Cambridge, UK. 2019
• 2nd prize in Oral Paper Presentation for the work entitled “Benchmarking of different molecular docking methods for protein-peptide docking” during 17th International Conference on Bioinformatics 2018 (Incob2018), JNU, New Delhi. 2018
• Recognized as “B4 Fellow” for being selected among Top 25 Candidates for “Genomics in Healthcare and Translational Research”, 14 days hands on workshop organized by joint association of Lakshmi Mittal South Asia Institute, Harvard University and Department of Biotechnology (DBT), Govt. of India at IBAB, Bangalore, India. 2017
• 2nd prize in Scientific Paper Presentation in Hindi, CSIR-Institute of Microbial Technology, Chandigarh, India. 2016
• Senior Research Fellowship from Department of Science and Technology -INSPIRE, Govt. of India. 2016
• Junior Research Fellowship from Department of Science and Technology -INSPIRE, Govt. of India. 2015
• AIR-1035, GATE 2014 (Biotechnology), NCB-GATE, Ministry of Human Resource Development (MHRD), Govt. of India. 2014
• Gold Medalist for being university topper and securing 1st rank in M.Sc. Bioinformatics course, awarded by Maharishi Dayanand University, Rohtak, India. 2013
• Department of Biotechnology (DBT) Scholarship during master’s, awarded by Maharishi Dayanand University, Rohtak, India and Department of Biotechnology (DBT), Govt. of India. 2011

D. Workshops/Conferences/Seminars

D1. Conferences/Symposium/Workshops

• AACR Annual Meeting 2024, (April 5-10, 2024) organized by American Association for Cancer Research, San Diego Convention Center, San Diego, California.
• 40th Anniversary of Cancer Epigenetics Symposium, (October 20, 2023), organized by National Institutes of Health, The Ruth Kirschstein Auditorium, Natcher Conference Center (Building 45), NIH Main Campus, Bethesda, USA.
• AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics, (October 11- 15, 2023), organized by American Association for Cancer Research, Hynes Convention Center, Boston, Massachusetts.
• AACR Special Conference: Tumor Immunology and Immunotherapy, (October 21-24, 2022), organized by American Association for Cancer Research, Shearton Boston Hotel, Boston, Massachusetts.
• Multidisciplinary Approaches to Understand Cancer Treatment Resistance (November 2020-December 2020) organized by National Cancer Institute Cancer Target Discovery and Development and Network and Cancer Systems Biology Consortium. Virtual Symposium.
• 12th Biocuartion Conference, (April 7-10, 2019), organized by International Society for Biocuration, West Road Concert Hall, Cambridge, UK.
• National Workshop on Computation for Biomedicine and Healthcare, (December 10-14, 2018), organized by Centre for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
• Symposium on Computational gastronomy, (December 8, 2018), organized by Centre for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.
• 17th International Conference on Bioinformatics 2018 (Incob2018), (September 26-28, 2018), Jawaharlal Nehru University, New Delhi, India.
• Genomics in Healthcare and Translational Research, (December 10-23, 2017), 14 days hands on workshop organized by joint association of Lakshmi Mittal South Asia Institute, Harvard University and Department of Biotechnology (DBT), Govt. of India at IBAB, Bangalore, India.
• Symposium On Functional Genomics, (December 2, 2017), organized by Centre for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.
• Symposium On Network Biology, (October 28, 2017), organized by Centre for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.
• Breaking Barriers through Bioinformatics and Computational Biology, (July 31-August 1, 2017), organized by Centre for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.
• National Workshop on Bioinformatics Approaches on Genome Resources, Assembly and Annotation, (February 9-12, 2016), organized by Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India

D2. Oral Presentations

• Piyush Agrawal# et.al. ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank. 12th International Biocuration Conference 2019, April 7-10, 2019, West Road Concert Hall, Cambridge, UK
• Piyush Agrawal#, Singh H#, Srivastava HK, Singh S, Kishore G and Raghava GPS. Benchmarking of different molecular docking methods for protein-peptide docking. 17th International Conference on Bioinformatics 2018 (Incob2018), Jawaharlal Nehru University, New Delhi, SFIB-4, Page No.54, 2018.

D3. Poster Presentations

• Piyush Agrawal*, Gulden Olgun, Arashdeep Singh, Vishaka Gopalan, Sridhar Hannenhalli*. Characterizing the role of exosomal miRNAs in metastasis. Cancer Research. 2024.
• Piyush Agrawal#, Navami Jain#, Vishaka Gopalan, Annan Timon, Arashdeep Singh, Padma S. Rajagopal, Sridhar Hannenhalli. Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in Triple Negative Breast Cancer. 23rd Annual CCR Fellows and Young Investigators Colloquium, “Drugging the undruggable, novel targets and targeted therapeutic strategies”. May 4-5, 2023. NCI Shady Grove Campus in Rockville, MD.
• Piyush Agrawal#, et.al. ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank. 12th International Biocuration Conference 2019, April 7-10, 2019, West Road Concert Hall, Cambridge, UK.
• Piyush Agrawal, Singh S, Nagpal G, Sethi D and Raghava GPS. Prediction of residue-residue contacts in CASP12 target. 17th International Conference on Bioinformatics 2018 (Incob2018), Jawaharlal Nehru University, New Delhi, Page No.74, 2018

D4. Invited Lectures

• Bioinformatics for Vaccine Design, Dollar Education, 2022.
• Application of Bioinformatics in Life Sciences, Ram Lal Anand College, University of Delhi, 2019. Event: Alumni Lecture Series.
• Machine Learning Application in Bioinformatics, Maharshi Dayanand University, Rohtak, 2019. Event: Alumni Lecture Series,
• Role of Bioinformatics in Healthcare, Multanimal Modi College, Modinagar, Uttar Pradesh, 2020.
• Advancements in the biological databases and prediction algorithm and their potential application in Healthcare, GGDSD College, Chandigarh, 2020. Event: Faculty cum Student Skill Development programme “Biological Data analysis & Data Science”.

E. Work Experience

E1. Academic Experience

• Assistant Professor, Faculty of Medical & Health Sciences, SRM Institute of Sciences & Technology, Kattankulathur – 603202, Tamil Nādu, India. (April 2024- Ongoing)
• Visiting Postdoctoral Fellow at National Cancer Institute, NIH, USA from Aug 2020-April 2024.
• Research Associate-I at Indraprastha Institute of Information Technology Delhi (IIITD), Okhla Phase-III, New Delhi. Jan 2020-March 2020.

F. Membership

• Associate Member of ‘American Association for Cancer Research (AACR)’
• Life Member of ‘BIOinformatics CLUB for Experimenting Scientists (BIOCLUES)

G. Responsibilities Held

G1. Mentoring Experience

• Co-Supervised Navami Jain, Summer Intern at National Cancer Institute, NIH, USA on the Project “Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in Triple Negative Breast Cancer”.
• Co-Supervised Ilana Borison, Summer Intern at National Cancer Institute, NIH, USA on the Project “Application of PathExt to identify cell state markers in single cell transcriptome data”.

G2. Editor and Reviewer’s Role

• Frontiers Review Editor for Frontiers in Genetics [Section: Computational Genomics] and Frontiers in Public Health [Section: Digital Public Health]
• Oxford Review Editor for Briefings in Bioinformatics,
• Peer Reviewer: STAR Protocols, Oxford Briefings in Bioinformatics, Oxford Integrative Biology, Nature Scientific Reports, ACS Pharmacology & Translational Medicine, Frontiers in Genetics, Frontiers in Bioinformatics, Frontiers in Bioengineering and Biotechnology, Medical Oncology, Journal of Biomolecular Structure and Dynamics, Aging Medicne, Clinical and Translational Medicine (Wiley Online Library)