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NIIT UNIVERSITY
Utkarsh Raj

Dr Utkarsh Raj

  • Assistant Professor
  • Biotechnology & Bioinformatics
Utkarsh Raj

Dr Utkarsh Raj has earned his PhD from the Department of Bioinformatics & Applied Sciences at the Indian Institute of Information Technology-Allahabad, recognized as an Institute of National Importance by the Government of India. His research, encapsulated in his thesis, focuses on the nuanced exploration of targeting epigenetic regulators for cancer therapy. His methodologies involve a judicious blend of NGS data analysis, systems biology, and structural bioinformatics approaches.

Dr Raj has previously held significant roles at various institutions of repute across the country. In these capacities, he has consistently demonstrated a steadfast commitment to academic and research excellence. Notably, his contributions extend beyond the confines of the classroom, as reflected in his substantial body of research work. With over 50 publications in Scopus /Web of Science/ Peer-reviewed journals and conferences, Dr Raj’s research impact is underscored by a Google Scholar h-index of 16 and 1000+ citations to date. He has actively participated as a reviewer for esteemed peer-reviewed journals of Nature Publications, Taylor & Francis, IEEE, ACM, Springer, and Elsevier, thus significantly contributing to the advancement of scientific knowledge. Dr Raj’s research journey traverses diverse realms, encompassing protein motif discovery, gene expression meta-analysis, network biology, AI-driven drug discovery, and high-throughput sequencing data analysis. His proficiency in NGS data analysis, structural bioinformatics, computer-aided drug discovery, and database/tool development is accentuated by certifications from IBM and the Google Digital Academy.

In addition to his academic accomplishments, Dr Utkarsh Raj was honored with the designation of a Life Member of the National Academy of Sciences, India (NASI) in 2021, a testament to his acknowledged standing in the scientific community. His multifaceted expertise and contributions reflect a comprehensive and impactful approach to bioinformatics, making significant strides in the realms of healthcare and drug discovery.

Qualifications

  • PhD (Bioinformatics)
  • MTech (Bioinformatics)
  • BTech (Biotechnology)

Experience

  • 5+ years Post-PhD

Courses taught

  • Computational Biology
  • Genomics and Proteomics
  • Molecular Modeling & Drug Design
  • Biostatistics
  • Thermodynamics

Research Area(s)

  • Bioinformatics
  • Computational Biology

Consulting Area

  • NGS data analysis
  • Systems Biology
  • Computer Aided Drug Design
  • Structural Bioinformatics
  • Immunoinformatics
  • Microarray data analysis
  • Biostatistics
  • Cancer Epigenetics

Selected Publications

  • R. Semwal, I. Aier, U. Raj, and P. K. Varadwaj, “Pr[m]: An Algorithm for Protein Motif Discovery,” IEEE/ACM Trans. Comput. Biol. Bioinform., vol. 19, no. 1, pp. 585–592, Jan. 2022, doi: 10.1109/TCBB.2020.2999262.
  • M. Mondal*, R. Semwal*, U. Raj*, I. Aier*, and P. K. Varadwaj, “An entropy-based classification of breast cancerous genes using microarray data,” Neural Comput. Appl., vol. 32, no. 7, pp. 2397–2404, 2020, doi: 10.1007/s00521-018-3864-8. (*Authors having equal contribution)
  • U. Raj, I. Aier, R. Semwal, and P. K. Varadwaj, “Identification of novel dysregulated key genes in Breast cancer through high throughput ChIP-Seq data analysis,” Sci. Rep., vol. 7, no. 1, p. 3229, Jun. 2017, doi: 10.1038/s41598-017-03534-x.
  • I. Aier, P. K. Varadwaj, and U. Raj*, “Structural insights into conformational stability of both wild-type and mutant EZH2 receptor,” Sci. Rep., vol. 6, no. 1, pp. 1–10, 2016, doi: 10.1038/srep34984. (*Corresponding author)
  • U. Raj and P. K. Varadwaj, “Flavonoids as multi-target inhibitors for proteins associated with Ebola virus: in silico discovery using virtual screening and molecular docking studies,” Interdiscip. Sci. Comput. Life Sci., vol. 8, no. 2, pp. 132–141, 2016, doi: 10.1007/s12539-015-0109-8.
Research Papers/Articles
  • R. Semwal, I. Aier, U. Raj, and P. K. Varadwaj, “Pr[m]: An Algorithm for Protein Motif Discovery,” IEEE/ACM Trans. Comput. Biol. Bioinform., vol. 19, no. 1, pp. 585–592, 2022, doi: 10.1109/TCBB.2020.2999262.
  • U. Raj, S. Rai, S. K. Mathur, A. Saxena and A. C. Kaushik, “A comprehensive study on sars-cov-2 through gene expression meta-analysis and network biology approach,” J. Appl. Biotechnol. Rep., vol. 8, no. 3, pp. 242–253, 2021, doi: 10.30491/JABR.2021.275694.1360.
  • A. Saxena, N. Mathur, U. Chaudhary, U. Raj, S. Rai, and S. K. Mathur, “Meta-analysis of Type 2 diabetes and insulin resistance gene expression datasets to decipher their associated pathways,” Journal of Applied Biology and Biotechnology, vol. 11, no. 1, pp. 109–115, 2022, doi: 10.7324/JABB.2023.110116.
  • Aier, R. Semwal, U. Raj, and P. K. Varadwaj, “Comparative modeling and structure based drug repurposing of PAX2 transcription factor for targeting acquired chemoresistance in pancreatic ductal adenocarcinoma,” J. Biomol. Struct. Dyn., vol. 39, no. 6, pp. 2071–2078, 2021, doi: 10.1080/07391102.2020.1742793
  • G. Malik, T. Agarwal, U. Raj, V. S. Sundararajan, O. R. Bandapalli, and P. Suravajhala, “Hypothetical Proteins as Predecessors of Long Non-coding RNAs,” Curr. Genomics, vol. 21, no. 7, pp. 531–535, 2020, doi: 10.2174/1389202921999200611155418
  • A. C. Kaushik and U. Raj*, “Ai-driven drug discovery: A boon against covid-19?,” AI Open, vol. 1, pp. 1–4, 2020, doi: 10.1016/j.aiopen.2020.07.001. (*Corresponding author)
  • J. R. Kalli and U. Raj*, “Outbreak of COVID-19: An update on the status of the evolving mechanism with possible diagnostic, therapeutics, and future directions,” Int. J. Res. Pharm. Sci., pp. 763–773, 2020, doi: 10.26452/ijrps.v11iSPL1.3080. (*Corresponding author)
  • A. Saxena et al., “A lung transcriptomic analysis for exploring host response in COVID-19,” J Pure Appl Microbiol, vol. 14, no. suppl 1, pp. 1077–1081, 2020, doi: 10.22207/JPAM.14.SPL1.47. (*Corresponding author)
  • M. Mondal*, R. Semwal*, U. Raj*, I. Aier*, and P. K. Varadwaj, “An entropy-based classification of breast cancerous genes using microarray data,” Neural Comput. Appl., vol. 32, no. 7, pp. 2397–2404, 2020, doi: 10.1007/s00521-018-3864-8. (*Authors having equal contribution)
  • T. C. Yadav et al., “Exploration of interaction mechanism of tyrosol as a potent anti-inflammatory agent,” J. Biomol. Struct. Dyn., vol. 38, no. 2, pp. 382–397, 2020, doi: 10.1080/07391102.2019.1575283
  • N. Roy, U. Raj, S. Rai, and P. K. Varadwaj, “Deciphering the Novel Target Genes Involved in the Epigenetics of Hepatocellular Carcinoma Using Graph Theory Approach,” Curr. Genomics, vol. 20, no. 8, pp. 545–555, 2019, doi: 10.2174/1389202921666191227100441
  • A. Kumar et al., “Computational and in-vitro validation of natural molecules as potential acetylcholinesterase inhibitors and neuroprotective agents,” Curr. Alzheimer Res., vol. 16, no. 2, pp. 116–127, 2019, doi: 10.2174/1567205016666181212155147
  • N. Raghuwanshi, T. C. Yadav, A. K. Srivastava, U. Raj, P. Varadwaj, and V. Pruthi, “Structure-based drug designing and identification of Woodfordia fruticosa inhibitors targeted against heat shock protein (HSP70-1) as suppressor for Imiquimod-induced psoriasis like skin inflammation in mice model,” Mater. Sci. Eng. C, vol. 95, pp. 57–71, 2019, doi: 10.1016/j.msec.2018.10.061.
  • P. Kumar*, U. Raj*, I. Aier*, and P. K. Varadwaj, “Decoding methylation patterns in ovarian cancer using publicly available Next-Gen sequencing data,” Netw. Model. Anal. Health Inform. Bioinforma., vol. 7, no. 1, pp. 1–12, 2018, doi: 10.1007/s13721-018-0173-1. (*Authors having equal contribution)
  • S. Rai, U. Raj, and P. K. Varadwaj, “Systems biology: A powerful tool for drug development,” Curr. Top. Med. Chem., vol. 18, no. 20, pp. 1745–1754, 2018, doi: 10.2174/1568026618666181025113226.
  • B. Jain, U. Raj, and P. K. Varadwaj, “Drug target interplay: a network-based analysis of human diseases and the drug targets,” Curr. Top. Med. Chem., vol. 18, no. 13, pp. 1053–1061, 2018, doi: 10.2174/1568026618666180719160922.
  • S. Gupta, Y. Singh, H. Kumar, U. Raj, A. R. Rao, and P. K. Varadwaj, “Identification of novel abiotic stress proteins in Triticum aestivum through functional annotation of hypothetical proteins,” Interdiscip. Sci. Comput. Life Sci., vol. 10, no. 1, pp. 205–220, 2018, doi: 10.1007/s12539-016-0178-3
  • R. Semwal, I. Aier, U. Raj, and P. K. Varadwaj, “Pharmadoop: a tool for pharmacophore searching using Hadoop framework,” Netw. Model. Anal. Health Inform. Bioinforma., vol. 6, no. 1, pp. 1–9, 2017, doi: 10.1007/s13721-017-0161-x.
  • U. Raj, A. K. Sharma, I. Aier, and P. K. Varadwaj, “In silico characterization of hypothetical proteins obtained from Mycobacterium tuberculosis H37Rv,” Netw. Model. Anal. Health Inform. Bioinforma., vol. 6, no. 1, pp. 1–9, 2017, doi: 10.1007/s13721-017-0147-8.
  • G. Yadav*, R. Rao*, U. Raj*, and P. K. Varadwaj, “Computational modeling and analysis of prominent T-cell epitopes for assisting in designing vaccine of ZIKA virus,” J Appl Pharm Sci, vol. 7, no. 08 pp. 116–122, 2017, doi: 10.7324/JAPS.2017.70816. (*Authors having equal contribution)
  • U. Raj, I. Aier, R. Semwal, and P. K. Varadwaj, “Identification of novel dysregulated key genes in Breast cancer through high throughput ChIP-Seq data analysis,” Sci. Rep., vol. 7, no. 1, p. 3229, 2017, doi: 10.1038/s41598-017-03534-x.
  • S. Gupta, B. S. Yadav, U. Raj, S. Freilich, and P. K. Varadwaj, “Transcriptomic analysis of soil grown T. aestivum cv. root to reveal the changes in expression of genes in response to multiple nutrients deficiency,” Front. Plant Sci., vol. 8, article no. 1025, pp. 1-19 2017, doi: 10.3389/fpls.2017.01025.
  • U. Raj, H. Kumar, and P. K. Varadwaj, “Molecular docking and dynamics simulation study of flavonoids as BET bromodomain inhibitors,” J. Biomol. Struct. Dyn., vol. 35, no. 11, pp. 2351–2362, 2017, doi: 10.1080/07391102.2016.1217276
  • P. Varadwaj, U. Raj, S. Pathak, I. Aier, and S. Gupta, “In Silico Finding of the Putative Drug Targets from Hypothetical Set of Proteins for Mycobacterium Leprae ln,” Int. J. Pharm. Sci. Res., vol. 8, no. 5, pp. 2100-2121, 2017, doi: 10.13040/IJPSR.0975-8232.8(5).2100-21.
  • S. Kumar Gupta, K. Kumar Chaudhary, U. Raj, and N. Mishra, “Computational Identification of Inhibitors Against DPP-IV for Checking Type-2 Diabetes,” Lett. Drug Des. Discov., vol. 14, no. 1, pp. 66–73, 2017, doi: 10.2174/1570180813666160720121718.
  • V. Kumari, R. Tripathi, S. Patel, U. Raj, and P. K. Varadwaj, “DUSR (Distributed Ultrafast Shape Recognition): a Hadoop Based Tool to Identify Similar Shaped Ligand Molecules,” Indian J. Pharm. Educ. Res., vol. 51, no. 1, pp. 34–42, 2017, doi: 10.5530/ijper.51.1.6.
  • U. Raj, H. Kumar, S. Gupta, and P. Kumar Varadwaj, “Identification of Novel Inhibitors for Disrupting EZH2-EED Interactions Involved in Cancer Epigenetics: An In-Silico Approach,” Curr. Proteomics, vol. 13, no. 4, pp. 313–321, 2016, doi: 10.2174/1570164613666161124095758.
  • I. Aier, P. K. Varadwaj, and U. Raj*, “Structural insights into conformational stability of both wild-type and mutant EZH2 receptor,” Sci. Rep., vol. 6, no. 1, pp. 1–10, 2016, doi: 10.1038/srep34984. (*Corresponding author)
  • H. Kumar, U. Raj, S. Gupta, and P. K. Varadwaj, “In-silico identification of inhibitors against mutated BCR-ABL protein of chronic myeloid leukemia: a virtual screening and molecular dynamics simulation study,” J. Biomol. Struct. Dyn., vol. 34, no. 10, pp. 2171–2183, 2016, doi: 10.1080/07391102.2015.1110046.
  • U. Raj, H. Kumar, S. Gupta, and P. K. Varadwaj, “Exploring dual inhibitors for STAT1 and STAT5 receptors utilizing virtual screening and dynamics simulation validation,” J. Biomol. Struct. Dyn., vol. 34, no. 10, pp. 2115–2129, 2016, doi: 10.1080/07391102.2015.1108870.
  • K. Kumar Chaudhary, U. Raj, P. K. Varadwaj, and N. Mishra, “Novel Potent Plasmepsin-I (PMI) Inhibitors: An In-Silico Approach,” Curr. Proteomics, vol. 13, no. 3, pp. 196–205, 2016.
  • H. Kumar, U. Raj, S. Srivastava, S. Gupta, and P. K. Varadwaj, “Identification of dual natural inhibitors for chronic myeloid leukemia by virtual screening, molecular dynamics simulation and ADMET analysis,” Interdiscip. Sci. Comput. Life Sci., vol. 8, no. 3, pp. 241–252, 2016.
  • U. Raj and P. K. Varadwaj, “Flavonoids as multi-target inhibitors for proteins associated with Ebola virus: in silico discovery using virtual screening and molecular docking studies,” Interdiscip. Sci. Comput. Life Sci., vol. 8, no. 2, pp. 132–141, 2016, doi: 10.1007/s12539-015-0109-8.
  • H. Kumar, S. Tichkule, U. Raj, S. Gupta, S. Srivastava, and P. K. Varadwaj, “Effect of STAT3 inhibitor in chronic myeloid leukemia associated signaling pathway: a mathematical modeling, simulation and systems biology study,” 3 Biotech, vol. 6, no. 1, pp. 1–12, 2016, doi: 10.1007/s13205-015-0357-7.
  • R. H. Bedre, U. Raj, S. P. Misra, and P. K. Varadwaj, “Antiviral therapy with nucleotide/nucleoside analogues in chronic hepatitis B: A meta-analysis of prospective randomized trials,” Indian J. Gastroenterol., vol. 35, no. 2, pp. 75–82, 2016, doi: 10.1007/s12664-016-0632-5.
  • U. Raj, H. Kumar, and P. K. Varadwaj, “3D structure generation, molecular dynamics and docking studies of IRHOM2 protein involved in cancer & rheumatoid arthritis,” Curr. Comput. Aided Drug Des., vol. 11, no. 4, pp. 325–335, 2015, doi: 10.2174/1573409912666151124234008.
  • H. Kumar, S. Tichkule, U. Raj, S. Gupta, S. Srivastava, and P. K. Varadwaj, “Parameters Involved in Autophosphorylation in Chronic Myeloid Leukemia: a Systems Biology Approach,” Asian Pac. J. Cancer Prev., vol. 16, no. 13, pp. 5273–5278, 2015, doi: 10.7314/apjcp.2015.16.13.5273
  • S. Gupta, A. Jadaun, H. Kumar, U. Raj, P. K. Varadwaj, and A. R. Rao, “Exploration of new drug-like inhibitors for serine/threonine protein phosphatase 5 of Plasmodium falciparum: a docking and simulation study,” J. Biomol. Struct. Dyn., vol. 33, no. 11, pp. 2421–2441, 2015, doi: 10.1080/07391102.2015.1051114.
  • U. Raj, H. Kumar, S. Gupta, and P. K. Varadwaj, “Novel DOT1L receptor natural inhibitors involved in mixed lineage leukemia: a virtual screening, molecular docking and dynamics simulation study,” Asian Pac. J. Cancer Prev., vol. 16, no. 9, pp. 3817–3825, 2015, 10.7314/apjcp.2015.16.9.3817.
  • S. Sahi, U. Raj, M. Chaudhary, and V. Nain, “Modelling of human leucyl aminopeptidases for in silico off target binding analysis of potential Plasmodium falciparum leucine aminopeptidase (PfA-M17) specific inhibitors,” Recent Pat. Endocr. Metab. Immune Drug Discov., vol. 8, no. 3, pp. 191–201, 2014, doi: 10.2174/1872214808666141001125057.
Conference Papers
  • R. Semwal, I. Aier, P. Tyagi, U. Raj and P. K. Varadwaj, "DeepLBS: A deep Convolutional Neural Network-Based Ligand-Binding Site Prediction Tool," 2023 6th International Conference on Information Systems and Computer Networks (ISCON), Mathura, India, 2023, pp. 1-4, doi: 10.1109/ISCON57294.2023.10112034.
  • U. Raj, S. K. Mishra, C. Bhatia, P. K. Varadwaj, and G. Harit, “A Comprehensive Knowledgebase on Cancer Epigenetics,” in 2018 International Conference on Bioinformatics and Systems Biology (BSB), 2018, pp. 198–202, doi: 10.1109/BSB.2018.8770626.
  • I. Aier and U. Raj, “Exploring the role of EZH2 (PRC2) as epigenetic target,” in 2016 International Conference on Bioinformatics and Systems Biology (BSB), 2016, pp. 1–4, doi: 10.1109/BSB.2016.7552131.
  • S. Gupta, U. Raj, H. Kumar, P. K. Varadwaj, and A. Gupta, “Embryo and endosperm specific comparative transcriptome analysis of triticum aestivum in response to ABA and H2O2 stress,” in 2016 International Conference on Bioinformatics and Systems Biology (BSB), 2016, pp. 1–4, doi: 10.1109/BSB.2016.7552157.
  • S. Srivastava, H. Kumar, S. Tandon, U. Raj, C. Prasad, and P. Varadwaj, “Classification of the Genes Responsible for Stem Cells Differentiation and Regeneration by Rotation Forest: An Ensemble Method,” in Exploring Basic and Applied Sciences for Next Generation Frontiers (EBAS-LPU), 2014, pp.133-137.

Book Chapters

  • A. Kumar, N. K. Mishra, U. Raj, and T. R. Singh, “Sequence-Based Algorithms in Computational Biology,” in Bioinformatics and Computational Biology, Chapman and Hall/CRC, 2024, ch. 02, pp. 16–26, doi: 10.1201/9781003331247-3
  • N. K. Mishra, A. Kumar, U. Raj, and T. R. Singh, “Structure-Based Algorithms in Computational Biology,” in Bioinformatics and Computational Biology, Chapman and Hall/CRC, 2024, ch. 03, pp. 27–37, doi: 10.1201/9781003331247-4
  • U. Raj and P. K. Varadwaj, “Epigenetics and its role in human cancer,” in Translational Bioinformatics and Its Application, D.-Q. Wei, Y. Ma, W. C. S. Cho, Q. Xu, and F. Zhou, Eds. Netherlands : Springer, 2017, ch. 11, pp. 249–267, doi: 10.1007/978-94-024-1045-7_11.
  • S. Mishra, U. Raj, and P. K. Varadwaj, “Annotation of hypothetical proteins: a functional genomics approach,” in Comput. Biol. Bioinforma., K.-C. Wong, Ed. USA: CRC Press, 2016, ch. 6, pp. 135–158, doi: 10.1201/b20026.
  • P. Gupta, U. Raj, and P. K. Varadwaj, “Prediction of Blood Brain Barrier Permeability of Ligands Using Sequential Floating Forward Selection and Support Vector Machine,” in Jain L., Behera H., Mandal J., Mohapatra D. (eds) Computational Intelligence in Data Mining - Volume 1. Smart Innovation, Systems and Technologies vol 31. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2205-7_42.

Awards & Recognition

  • Young Achiever Award (ICMRP-2023) organized by Koshambi Foundation, India and Department of History and Culture, Dr. B. R. Ambedkar University, Agra, India.
  • Selected 'Life Member' - National Academy of Sciences, India (2021).
  • Best Paper Presentation Award at 25th International Conference on Researches in Science and Technology (ICRST), Kuala Lumpur, Malaysia (2017).
  • Selected for Young Research Scholarship for attending the 15th International Conference on Healthcare and Life-Science Research (ICHLSR), Kuala Lumpur, Malaysia (2017).
  • First award of 500 US dollars for being amongst the Authors of Excellent Papers in the journal of Interdisciplinary Sciences: Computational Life Sciences - Springer (2016).
  • BRICPL Young Scientist Award (ICET-2016) jointly organized by Biotechnology Society of Nepal and Biologix Research and Innovation Centre Private Limited, India (2016).
  • 1st Prize in Oral Presentation at National Conference on Bioinformatics Panorama in Agriculture and Health (NCBPAH) organized by Dept. of Computational Biology and Bioinformatics, SHUATS, Allahabad (2015).
  • 1st Prize in Poster Presentation at National Conference on Lead Development and Drug Designing: Emerging Opportunities, organized by UIP in association with Indian Science Congress Association, Allahabad (2014).
  • Received MHRD scholarship during Ph.D. at IIIT-Allahabad.
  • First Rank Holder in M. Tech (Specialization: Bioinformatics) at Gautam Buddha University (2011-2013).

Professional Activities and Achievements

  • Travel grant from IIIT-Allahabad to attend 25th International Conference on Researches in Science and Technology (ICRST), Kuala Lumpur, Malaysia (2017).

Other Interests

  • Cricket
  • Singing
  • Cooking

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