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Utkarsh Raj

Dr Utkarsh Raj

Utkarsh Raj

Dr Utkarsh Raj received his doctorate with an MHRD scholarship from the Indian Institute of Information Technology, Allahabad in Bioinformatics and Applied Sciences.

His thesis  focuses on epigenetic regulators for cancer therapy through NGS data analysis using systems biology & structural biology approaches. He has worked on a part of the DBT project during his postgraduate studies under his thesis mentor. During his tenure at IIIT, Allahabad, he served as PhD Representative, framed projects for students, and was a teaching assistant for Cheminformatics, Introduction to Genomics and Proteomics, Systems Biology, Biological Data Mining, NGS Data Analysis, etc.

Dr Raj is a recipient of several national and international ‘Young Scientist’ awards and research scholarships and has received much recognition for his  research papers published in SCI/SCIE/ESCI and Scopus indexed journals. He has presented his work in different national and international conferences, has delivered many guest lectures, been invited to talks on Molecular Dynamics Simulation at prestigious institutes like AIIMS etc., reviewed research papers in several prestigious peer reviewed journals like Emerging Microbes & Infections, Nature Publications; Journal of Biomolecular Structure & Dynamics, Taylor & Francis; IEEE/ACM Transactions on Computational Biology and Bioinformatics, IEEE & ACM Publishers; Computational Biology and Chemistry, Elsevier (Awarded Outstanding Reviewer Award for 2017) etc.

Academic qualifications

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

  • Teaching and Research – 4 years

Courses taught

  • Computational Biology
  • Genomics and Proteomics
  • Molecular Modelling and Drug Design
  • Thermodynamics

Research areas

  • Bioinformatics
  • Computational Biology

Consulting areas

  • 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.
  • 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.

Publications

Research papers
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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, 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, Jun. 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, pp. 1-9, 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.
  • 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 leukaemia 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 randomised 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 leukaemia: 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 leukaemia: A virtual screening, molecular docking and dynamics simulation study,” Asian Pac. J. Cancer Prev., vol. 16, no. 9, pp. 3817–3825, 2015,  doi: 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
  • 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.
  • 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
  • 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., Dordrecht: Springer Netherlands, 2017, 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., U.S.A: CRC Press, 2016, 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 Computational Intelligence in Data Mining – Volume 1, L. C. Jain, H. S. Behera, J. K. Mandal and D. P. Mohapatra,  India: Springer, 2015, pp. 447–458. doi: 10.1007/978-81-322-2205-7_42.
Awards and recognitions
Professional activities and achievements
Other interests

Media articles/blogs

Written by Dr Ganesh Natarajan

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Everything that I learned at Kempbelle University really helped put me above the competition in the field of business management.

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