Dr. Arnab Nayek

Dr. Arnab Nayek completed his M.Tech degree in Bioinformatics from West Bengal University of Technology (WBUT), Kolkata, West Bengal in 2010 and received a PhD in Bioinformatics in 2018 from The University of Burdwan, Burdwan, West Bengal. The title of his PhD thesis was “Bioinformatic analysis of sequence and structure of halophilic protein in comparison with mesophilic ones”. In his tenure of PhD, he got opportunity to present his thesis work in “The 29th Annual Symposium of the Protein Society”, Barcelona, Spain, organised by The protein Society and also received the Travel Award in graduate category.

As a professional carrear Dr. Arnab started his journey as a Research Assistant at Biomedical Informatics Center, ICMR – National Institute of Pathology, New Delhi from December, 2013 and later worked as a Scientist- I (Non-Medical) in the same center till March, 2019. He also worked as a Consultatnt (Data management) in the project “India TB research consortium” for a short period of time at Indian Council of Medical Research, New Delhi. He also worked as a Research Associate -III in DRDO funded project entitled “Exome sequencing based detection of novel and causal mutations associated with juvenile onset open angle glaucoma (JOAG)”, in the Department of Ophthalmology, Dr. R. P Center for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi from September, 2019 to August, 2020.

Currently, Dr. Arnab is working as a Research Associate (Bioinformatician), in the department of Biochemistry, All India Institute of Medical Sciences, New Delhi, under the guidance of Dr. Subhradip Karmakar, Additional Professor, Department of Biochemistry. He is associated with the transcriptomics (RNA-seq) data analysis from RNA sequencing data generated from the lab as well as publicly available data from the The Cancer Genome Atlas (TCGA) database, development of integrated pipelines for NGS data analysis etc.

His research credentials supported with 13 publications in referred journals and his research interest includes Next generation sequencing (NGS) data analysis from human samples to improve the disease diagnosis for clinicians, development of integrated pipelines for NGS data analysis, protein structure modelling, protein engineering, Molecular dynamics simulations.

Research Publications:

  1. Rajesh Kumar Meher, Pratyush Pragyandipta, Ravi K Pedapati, Praveen K R Nagireddy, Srinivas Kantevari, Arnab Nayek and Pradeep K. Naik (2021). Rational design of novel N-alkyl amine analogues of noscapine, their chemical synthesis and cellular activity as potent anticancer agents. Chemical Biology & Drug Design. 00, 1-21.
  1. Parth Sarthi Sen Gupta, Rifat Nawaz UI Islam, Sahini Banerjee, Arnab Nayek, Malay Kumar Rana & Amal Kumar Bandyopadhyay (2020). Screening and molecular characterization of lethal mutations of human homogentisate 1, 2 dioxigenase. Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2020.1736158.
  1. Aditya Verma, Arnab Nayek, Amit Kumar, Ruchi Singh & Poonam Salotra (2019). Elucidation of role of an acetyltransferase like protein in paromomycin resistance in Leishmania donovani using in silico and in vitro approaches. Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2019.1682674.
  1. S Singh, D Pradhan, P Puri, V Ramesh, S Aggarwal, A Nayek and A K Jain (2019). Genomic alterations driving psoriasis pathogenesis. Gene. 683 (2019) 61-71.
  1. Noor Saba Khan, Rashi Verma, Dibyabhaba Pradhan, Arnab Nayek, Rajabrata Bhuyan, Tanmaya Kumar Sahu & Arun Kumar Jain (2018). Analysis of interleukin23 and 7G10 interactions for computational design of lead antibodies against immune-mediated inflammatory diseases. Journal of Receptors and Signal Transduction. 38:4, 327 – 334.
  1. Shweta Aggarwal & Arnab Nayek, Rashi Verma, Monika Yadav, Dibyabhaba Pradhan, Ponnusamy Kalaiarasan, & Arun Kumar Jain (2017). dbGAPs: a comprehensive database of genes and genetic markers associated with psoriasis. Genomics. S0888-7543(17)30115-5.
  1. Rashi Verma, Monika Yadav, Dibyabhaba Pradhan, Rajabrata Bhuyan, Shweta Aggarwal, Arnab Nayek & Arun Kumar Jain (2016). Probing binding mechanism of interleukin- 6 andolokizumab: in silico design of potential lead antibodies for autoimmune and inflammatory diseases. Journal of Receptors and Signal Transduction. DOI: 10.3109/10799893.2016.1147584.
  1. Arnab Nayek, Parth Sarthi Sen Gupta, Shyamashree Banerjee, Vishma Pratap Sur, Pratyay Seth, Sunit Das, Rifat Nawaz Ul Islam, Amal Kumar Bandyopadhyay (2015). ADSBET2: Automated Determination of Salt-Bridge Energy-Terms version 2. Bioinformation 8(11): 413-415.
  1. Arnab Nayek, Parth Sarthi Sen Gupta, Shyamashree Banerjee, Sunit Das, Vishma Pratap Sur, Pratyay Seth, Rifat Nawaz Ul Islam, Amal K Bandyopadhyay (2015). ADSBET: AUTOMATED DETERMINATION OF SALT-BRIDGE ENERGY TERMS. International Journal Of Institutional Pharmacy And Life Sciences 3(5): 28-36.
  1. Parth Sarthi Sen Gupta, Arnab Nayek, Shyamashree Banerjee, Pratyay Seth, Sunit Das, Vishma Pratap Sur, Chittran Roy & Amal Kumar Bandyopadhyay (2015). SBION2: Analysis of Salt Bridges from Multiple Structure Files, Version 2. Bioinformation. 11(1): 039-042.
  1. Shyamashree Banerjee, Parth Sarthi Sen Gupta, Arnab Nayek, Sunit Das, Vishma Pratap Sur, Pratyay Seth, Rifat Nawaz Ul Islam, Amal K Bandyopadhyay (2015). PHYSICO2: An UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2. Bioinformation 7(11): 366
  1. Dibyabhaba Pradhan, Vani Priyadarshini, Shweta Aggarwal, Nataranjan Pradeep, Arnab Nayek, Arun Kumar Jain, Amineni Umamaheswari (2015). Discovery of potential inhibitors of BMX non-receptor tyrosine kinase through e-pharmacophore based virtual screening. Journal of Biomolecular Structure and Dynamics, 33: sup1, 118-120.
  1. Arnab Nayek, Parth Sarthi Sen Gupta, Shyamashree Banerjee, Buddhadev Mondal and Amal K. Bandyopadhyay (2014). Salt-Bridge Energetics in Halophilic Proteins. PLOS ONE 9(4): e93862.

Abstracts Published in Conferences/workshops:

  1. Arnab Nayek, Monica Saxena, and Amal K. Bandyopadhyay (2012). Differential Salt-Bridge Stabilization in Halophilic Ferredoxin: In Silico Studies. Frontiers in Modern Biology (FIMB)”, Indian Institute of Science Education and Research (IISER), Kolkata.
  1. Arnab Nayek, Shyamashree Banerjee, Parth Sarthi Sen Gupta, Biswa pratap Sur, Pratay Seth, Sunit Das, Nathan A Baker and Amal K Bandyopadhyay (2015). ADSETMEAS: Automated Determination of Salt-bridge Energy Terms and Micro Environment from Atomic Structures using APBS method, version 1.0. The 29th Annual Symposium of The Protein Society, Barcelona, Spain.
  1. Dibyabhaba Pradhan, Vani Priyadarshini, Shweta Aggarwal, Nataranjan Pradeep, Arnab Nayek, Arun Kumar Jain, Amineni Umamaheswari (2015). Discovery of potential inhibitors of BMX non-receptor tyrosine kinase through e-pharmacophore based virtual screening. Albany, 2015.

Award/Scholarship:

  1. Travel Award winner of “The 29th Annual Symposium of the Protein Society”, Barcelona, Spain for poster presentation, 2015 in Graduate category.
  1. Awarded scholarship from DBT, Govt. of India, under Biotechnology Finishing School (BTFS) program, KBITS, Govt. of Karnataka (2013).