Dr. Soumyadeep Nandi

My research is aimed to study the correlation of different determinants of gene regulation. Cells in the multicellular organisms develop to a distinct cellular lineage, albeit they all carry an identical genome. This differentiation is primarily done by controlled gene expression at different stages of development. This complex program of gene expression is regulated by transcription factors and epigenetic factors like, non-coding RNA, polycomb group proteins and DNA methylation. The focus of my study is to characterize the interplay among these regulators by exploiting massive amounts of experimental data and using different computational methods


  • PhD: Data analysis pipelines in computational biology using a three tier architecture. School of Computational and Integrative Sciences (SC&IS), Jawaharlal Nehru University, New Delhi, India.
  • Masters of Science in Zoology, Specialized in Cell Biology, Department of Zoology, Gauhati University, Assam, India
  • Bachelor of Science in Zoology, Specialized in Zoology, Arya Vidyapeeth College, Gauhati University, Assam, India


  • 2015-till date
    Ramalingaswami Fellow at Institute of Advanced Study in Science and Technology, Guwahati- 781035, Assam, India.
  • 2012-2015

    Postdoctoral Fellow
    Research: Study the recruitment of epigenetic factor, Polycomb group proteins to their site of activity.
    Molecular Biology Department and Computational Life Science Cluster (CLiC) Umea University, SE-901 87 Umea, Sweden

  • 2009-2012
    Postdoctoral Fellow
    Research: Study the optimization of Position Weight Matrics for transcription factors and identify cis-regulatory modules of transcription factors.
    Ottawa Institute of Systems Biology (OISB), Department of Biochemistry, Microbiology and Immunology (BMI), Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.

  • Alignment-free method for DNA sequence clustering using Fuzzy integral similarity. Ajay Kumar Saw, Garima Raj, Manashi Das, Narayan C. Talukdar, Binod Chandra Tripathy, Soumyadeep Nandi. Scientific Reports (In press) 2019.

  • Alignment-free similarity analysis for protein sequences based on fuzzy integral. Ajay Kumar Saw, Binod Chandra Tripathy, Soumyadeep Nandi. Scientific Reports (In press) 2019.

  • PTE, a novel module to target Polycomb Repressive Complex 1 to the human Cyclin D2 oncogene. Sarina Cameron, Soumyadeep Nandi, Tatyana G. Kahn, Juan I. Barrasa, Per Stenberg, Yuri B. Schwartz. Journal of Biological Chemistry 2018, 293(37):14342-14358 doi: 10.1074/jbc.RA118.005010.
  • Fuzzy code on RNA secondary structure. Ajay Saw, Soumyadeep Nandi, Binod Chandra Tripathy. International Journal of Pure and Applied Mathematics 2017, 114(3):483-501 doi: 10.12732/ijpam.v114i3.6.
  • Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors. Soumyadeep Nandi , Alexandre Blais and Ilya Ioshikhes. Nucleic Acids Research 2013, first published online August 2, 2013 doi: 10.1093/nar/gkt578.
  • Optimizing the GATA-3 Position Weight Matrix to improve the identification of novel binding sites. Soumyadeep Nandi and Ilya Ioshikhes. BMC Genomics 2012, 13:416.
  • Discovery, optimization and validation of an optimal DNA-binding sequence for the Six1 homeodomain transcription factor. Yubing Liu, Soumyadeep Nandi, Andr Martel, Alen Antoun, Ilya Ioschikhes, Alexandre Blais. Nucleic Acids Res 2012, 1;40(17):8227-39. Epub 2012 Jun 22.
  • ModEnzA – accurate identification of metabolic enzymes using function specific profile HMMs with optimised discrimination threshold and modified emission probabilities. Dhwani K. Desai, Soumyadeep Nandi, Prashant Kr Srivastava, and Andrew M. Lynn. Advances in Bioinformatics 2011, 2011:743782.
  • Serological microarray for a paradoxical diagnostic of Whipple’s disease. C Bonhomme, P Renesto, S Nandi, A Lynn, D Raoult. Eur J Clin Microbiol Infect Dis 2008, 27(10):959-68. Epub 2008 Jul 2.
  • HMM-ModE – Improved classification using profile hidden Markov models by optimizing the discrimination threshold and modifying emission probabilities with negative training sequences. Prashant K Srivastava, Dhwani K Desai, Soumyadeep Nandi and Andrew M Lynn. BMC Bioinformatics 2007, 8:104.
  • A genomewide steroid response study of major human fungal pathogen Candida albicans. D. Banerjee, N Martin, S Nandi, S Shukla, A Dominguez, G Mukhopadhyay, R Prasad. Mycopathologia 2007, 164(1):117. Epub 2007 Jun 16.
  • Improved Classification using HMM by Removal of Nondiscriminating Signals. Prashant Srivastava, Dhwani K Desai, Soumyadeep Nandi and Andrew M Lynn. Proceedings of National Seminar and Workshop on Bioinformatics and Computational Biology, 2006, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi, India
  • Comparison of theoretical proteomes: Identification of COGs with conserved and variable pI within the multimodal pI distribution. Soumyadeep Nandi, Nipun Mehra, Andrew M Lynn and Alok Bhattacharya. BMC Genomics 2005, 6:116.
  1.  Ramalingaswami Fellowship project. Correlation study of the determinant of gene regulators Period: February 18, 2015-February 17, 2020. Ongoing)
  2. DBTs Twinning Program for NER. Development of an integrated multi-omics analysis platform, and its application to elucidate the differential process of silk colouration in the Muga silkworm Antheria assamensis Helfer Period: September 4, 2018-September 3, 2021. (Ongoing)