Profile
My laboratory has developed expertise in genome-scale analysis of cancer and healthy population datasets. Our research in cancer is centered around detailed characterization of all genomic, epigenomic events that impacts on transcriptional landscape of the tumor and normal tissue samples of an individual patient. We aim to identify molecular alterations in genes and pathways that are associated with various clinical phenotypes of the cancer. Currently our studies are focused : [1] to understand multi-omics landscape of Oral Cancer and other Oral Precancers progression, recurrence and metastasis [2] understanding baseline DNA variation in contemporary normal human populations, and [3] development of flexible data-analytics pipelines for rapid processing of genomics bigdata.
Selected publication:
Das S, Biswas NK*, Basu A*. Mapinsights: deep exploration of quality issues and error profiles in high-throughput sequence data. Nucleic Acids Research. 2023 Jun 28:gkad539. doi: 10.1093/nar/gkad539.
Ghosh A, Das C, Ghose S, Maitra A, Roy B, Majumder PP, Biswas NK*. Integrative analysis of genomic and transcriptomic data of normal, tumour and co-occurring leukoplakia tissue triads drawn from patients with gingivobuccal oral cancer identifies signatures of tumour initiation and progression. Journal of Pathology. 2022 Mar 31. doi: 10.1002/path.5900.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature. (2020) ;578(7793):82-93. doi: 10.1038/s41586-020-1969-6. * Biswas NK is a member of PCWAG consortium.
GenomeAsia100K Consortium. The GenomeAsia 100K Project enables genetic discoveries across Asia. Nature. (2019) ;576(7785):106-111. doi:10.1038/s41586-019-1793-z. * Biswas NK is a member of analysis working group of GenomeAsia consortium.
Biswas NK*, Das C, Das S, Maitra A, Nair S, Gupta T, D'Cruz AK, Sarin R, Majumder PP. Lymph node metastasis in oral cancer is strongly associated with chromosomal instability and DNA repair defects. International Journal of Cancer. (2019) 145(9):2568-2579. doi: 10.1002/ijc.32305.
Biswas NK*, Das S, Maitra A, Sarin R, Majumder PP. Somatic mutations in arachidonic acid metabolism pathway genes enhance oral cancer post-treatment disease-free survival. Nature Communications. (2014) 17;5:5835. doi: 10.1038/ncomms6835.
India Project Team of the International Cancer Genome Consortium ( Maitra A, Biswas NK. et al) Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrently-mutated genes and molecular subgroups. Nature Communications. (2013) 4:2873. doi: 10.1038/ncomms3873.
# Corresponding author underlined.
Research
With the huge advances in DNA sequencing technology and computational algorithms, it is now possible to identify genomic alterations of a cancer genome in an unprecedented way. Now-a-days, massively parallel DNA sequencers can generate several terabytes of sequence data within a short span of time. We generate multi-omics datasets and apply stringent computational pipelines to analyze these large multi-omics datasets to answer important scientific questions in cancer and population genomics. In particular, our current research in cancer is to understand and study - (i) molecular signatures that captures progression states of oral pre-cancers and frank oral cancers, (ii) specific tumour features that are associated with local lymph-node metastasis and tumor recurrence and (iii) nature of immune contexture in various stages of oral cancer.
Our team provides major analysis support to the bioinformatics and statistical wing of the International Cancer Genome Consortium (ICGC) – India project on oral cancer, SyMeC project on oral cancer and cervical cancer and NIBMG-Flagship project on Cervical cancer. In these projects, we are identifying the nature and extent of genomic alterations in Indian oral cancer and cervical cancer patients. We are generating and analyzing data on whole-exome, whole-genome DNA sequencing, genome-wide CNV array, epigenomic array and RNA-sequencing from multiple gingivo-buccal oral and cervical cancer patients to discover the complete repertoire of genomic alteration of the patients and possible therapeutic options.
In past, I have worked extensively in human evolutionary genetics with special reference to natural selection. I have continued interest in human evolution and human population genetics. Presently, I am working with my colleague Dr Analabha Basu, to understand baseline genome variation in healthy individuals from whole genome sequencing data from multiple Indian ethnic population samples.
COVID-19 has impacted our research and daily life heavily in last two year. My team also contributed to the understanding of the ongoing viral evolution of SARS-CoV-2 lineages. We were trying to understand the host genomic factors that modulates the infection rate and disease severity in affected individuals.
My laboratory members are engaged in the following projects:
1. International Cancer Genome Consortium - India project on Oral Cancer. [Funded by Department of Biotechnology, India] Role: Co-Investigator Goal: Understanding molecular alteration landscape of oral cancer. [Completed]
2. Big Data in Biology project grant to develop web servers for analysis of large scale genomic datasets [Funded by Department of Biotechnology, India] Role: PI Goal: To create a large-scale database of germline and somatic mutations identified from Indian and world-wide studies. [Completed]
3. Systems Medicine Cluster project on Oral and Cervical Cancer. [Funded by Department of Biotechnology, India] Role: Co-PI Goal: Understanding genomic, epigenomic, transcriptomics, metabolomic landscape of oral tumours from a system point of view. [Completed]
4. Virtual National Oral Cancer Institute Grant. [Funded by Department of Biotechnology, India] Role: Co-PI [Completed]
5. National Supercomputing Mission Project Grant to develop fast and flexible NGS data analysis pipelines. [Ministry of Information Technology, India], Role: Co-PI Goal: To create an analysis framework to do rapid analysis of high-throughput OMIC datasets. [Ongoing]
6. National Genomics Core. [Funded by Department of Biotechnology, India] Role: Co-I Goal: To provide data generation and data analytics services for genomics research community. [Completed]
7. NIBMG Flagship Project on Cervical Cancer. [Funded by Department of Biotechnology, India] Role: Co-PI Goal: Understanding genomic, epigenomic, transcriptomics landscape of cervical cancers on a longitudinal framework. [Completed]
8. GenomeIndia Project : Cataloguing genome-scale variants for 20000 healthy Indian ethnic individuals. [Funded by Department of Biotechnology, India] Role: Co-PI Goal: To understand the baseline sequence variations that exists in normal individuals of India. [Ongoing]
9. INSACOG Project: Phase I - Role: Co-PI Goal: Genomic surveillance of SARS-CoV-2 lineages in India during COVID-19 pandemic. [Completed]
10. BRICS project: Role: Co-PI Goal: Genomic surveillance network for lineage tracing of SARS-CoV-2 infection in India, Brazil, Russia, China and South-Africa. [Ongoing]
CV
Education
|
Year |
Degree |
University |
|
2011 |
Ph.D |
Calcutta University (Research done at Indian Statistical Institute) |
|
2003 |
M.Sc |
Calcutta University ( Ballygaunge Science college) |
|
2001 |
B.Sc |
Calcutta University (Scottish Church College) |
Professional Appointments
- Assistant Professor, 2016-2021, NIBMG
- Young Biotechnologist Fellow, 2013 – 2016, NIBMG
-
Senior data analyst, 2011 - 2013, International Cancer Genome Consortium - India Project, NIBMG.
Professional Memberships
Member of Calcutta Consortium on Human Genetics, India.
Member, Society of Biological Chemists
Awards/Honors
|
Year |
Award |
|
2004 |
CSIR-JRF. |
|
2005 |
Best poster award – NCBS, India. |
|
2006 |
Best poster award – ISHG Meeting, Delhi. |
|
2006 |
International travel award – HUGO-AP meeting, Taipei, Taiwan. |
|
2008 |
International travel award – HUGO-AP meeting, Philippines. |
|
2008 |
CCTDS Travel Fellowship. |
|
2011 |
International travel award – HGM-2011, Dubai. |
|
2012 |
International travel award – NCKU, Tainan City,Taiwan. |
|
2012 |
Won data analysis competition – NCKU, Tainan city, Taiwan. |
|
2013 |
Wellcome trust meeting bursaries award – Genomics of complex disease Meeting, Oxford, UK. |
|
2013 |
Young Biotechnologist Fellowship Award |
|
2016 |
International Travel Award - 13th International Congress of Human Genetics, Tokyo. |
Selected Invited/Special lectures
|
Year |
Institute/meeting, Title of the talk |
|
2006 |
Workshop on Statistical Methods in the Analysis of SNP Marker Data - Indian Statistical Institute, Kolkata. |
|
2007 |
Indian Society of Human Genetics meeting, Kolkata. |
|
2008 |
Indian Society of Human Genetics meeting, Vizag. |
|
2008 |
Illumina User group meeting, HUGO-AP, Philippines. |
|
2010 |
Workshop on Human Genetics and Genomics - An Introduction, NIBMG. |
|
2012 |
Introduction to next generation sequencing: Learning the platforms and basics of data analysis – One day workshop for CU students, NIBMG.
|
|
2013 |
NIBMG-EBI winter school on “Analysis of Massively-Parallel Sequencing Data”, NIBMG |
|
2013 |
Applications of Bioinformatics in Modern Molecular Biology, ICGEB. |
|
2014 |
CC-HUGE Meeting. IPGMER. |
|
2014 |
NIBMG winter school on "From GWAS hits to targeted resequencing" |
|
2015 |
NIBMG winter school on "Analysis of Massively-Parallel Sequencing Data" |
|
2015 |
First advanced training workshop on "Understanding human disease and improving human health using genomic-driven approaches", NIBMG.
|
|
2016 |
NIBMG-UChichago Workshop on " Big data analysis in Biomedical Genomics" |
|
2016 |
13th International Congress of Human Genetics, Kyoto - Japan. |
|
2018 |
Annual meeting of Indian association of cancer research, Bose Institute. |
|
2019 |
Presidency University, “Crafting your career”. |
|
2020 |
BITS-Mesra, Webinar format - “Temporal and Geographical Spread Of Subtypes Of SARS-CoV-2: New Insights From Host Genetics”
|
Past Major Projects
Big Data in Biology project grant to develop web servers for analysis of large scale genomic datasets [Funded by Department of Biotechnology, India] Role: PI Goal: To create a large-scale database of germline and somatic mutations identified from Indian and world-wide cancer studies.
Publications
*Corresponding author publications are marked with a star (*).
- Kurkalang S, Roy S, Acharya A, Mazumder P, Mazumder S, Patra S, Ghosh S, Sarkar S, Kundu S, Biswas NK, Ghose S, Majumder PP, Maitra A. Single-cell transcriptomic analysis of gingivo-buccal oral cancer reveals two dominant cellular programs. Cancer Sci. 2023 Oct 4. doi: 10.1111/cas.15979.
- Chatterjee, A, Chaudhary, A, Ghosh, A, .., Biswas NK, Majumder PP. Overexpression of CD73 is associated with recurrence and poor prognosis of gingivobuccal oral cancer as revealed by transcriptome and deep immune profiling of paired tumor and margin tissues. Cancer Med. 2023; 00: 1- 14. doi:10.1002/cam4.6299
- Das S, Biswas NK*, Basu A*. Mapinsights: deep exploration of quality issues and error profiles in high-throughput sequence data. Nucleic Acids Research. 2023 Jun 28:gkad539. doi: 10.1093/nar/gkad539.
- Ghosh S, Mitra P, Saha U, Nandi R, Jena S, Ghosh A, Roy SS, Acharya M, Biswas NK, Singh S. NOTCH pathway inactivation reprograms stem-like oral cancer cells to JAK-STAT dependent state and provides the opportunity of synthetic lethality. Transl Oncol. 2023 Jun;32:101669. doi: 10.1016/j.tranon.2023.101669. Epub 2023 Apr 11. PMID: 37054548.
- Paine SK, Das S, Bhattacharyya C, Biswas NK, Rao R, De A, Basu A. Autosomal recessive inheritance of a novel missense mutation of ITGB4 for Epidermolysis-Bullosa pyloric-atresia: a case report. Mol Genet Genomics. 2022 Nov;297(6):1581-1586. doi: 10.1007/s00438-022-01941-y. Epub 2022 Aug 23. PMID: 35997841.
- Banerjee A, Mazumder A, Roy J, Das J, Majumdar A, Chatterjee A, Biswas NK, Sarkar MC, Das S, Dutta S, Maitra A. Emergence of a unique SARS-CoV-2 Delta sub-cluster harboring a constellation of co-appearing non-Spike mutations. J Med Virol. 2022. doi: 10.1002/jmv.28413. PMID: 36541745.
- Singh AK, Laskar R, Banerjee A, Mondal RK, Gupta B, Deb S, Dutta S, Patra S, .., Das S, Maitra A, Biswas NK*. Contrasting Distribution of SARS-CoV-2 Lineages across Multiple Rounds of Pandemic Waves in West Bengal, the Gateway of East and North-East States of India. Microbiology Spectrum. 2022 :e0091422. doi:10.1128/spectrum.00914-22.
- Vipparthi K., Hari K., Chakraborty P., Ghosh S., Patel AK., Ghosh A., Biswas NK., Sharan R., Arun P., Jolly MK., Singh S., Emergence of hybrid states of stemlike cancer cells correlates with poor prognosis in oral cancer, iScience (2022), doi.org/10.1016/j.isci.2022.104317.
- Ghosh D, Ghosh Dastidar D, Roy K, Ghosh A, Mukhopadhyay D, Sikdar N, Biswas NK, Chakrabarti G, Das A. Computational prediction of the molecular mechanism of statin group of drugs against SARS-CoV-2 pathogenesis. Sci Rep. 2022 Apr 14;12(1):6241
- Ghosh A, Das C, Ghose S, Maitra A, Roy B, Majumder PP, Biswas NK*. Integrative analysis of genomic and transcriptomic data of normal, tumour and co-occurring leukoplakia tissue triads drawn from patients with gingivobuccal oral cancer identifies signatures of tumour initiation and progression. Journal of Pathology. 2022 Mar 31. doi: 10.1002/path.5900.
- Reciprocal interplay between asporin and decorin: Implications in gastric cancer prognosis. Basak D, Jamal Z, Ghosh A, Mondal PK, Dey Talukdar P, Ghosh S, Ghosh Roy B, Ghosh R, Halder A, Chowdhury A, Dhali GK, Chattopadhyay BK, Saha ML, Basu A, Roy S, Mukherjee C, Biswas NK, Chatterji U, Datta S. PLoS One. 2021 Aug 11;16(8):e0255915.
- Pradhan, S., Das, S., Singh, A.K, Das C, Basu A, Majumder PP, Biswas NK*. dbGENVOC: database of GENomic Variants of Oral Cancer, with special reference to India. Database (2021) Vol. 2021: article ID baab034.
- Bhattacharyya C, Das C, Ghosh A, Singh AK, Mukherjee S, Majumder PP, Basu A, Biswas NK*. SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. Infect Genet Evol. (2021) ;90:104760. doi: 10.1016/j.meegid.2021.104760.
- Vipparthi K, Patel AK, Ghosh S, Das S, Das C, Das K, Sarkar A, Thatikonda V, Pal B, Remani AS, Arora N, Parihar M, Vijayakumar MV, Bhat MK, Boppana R, Bhattacharjee S, Biswas NK, Arun P, Sharan R, Singh S. Two novel cell culture models of buccal mucosal oral cancer from patients with no risk-habits of tobacco smoking or chewing. Oral Oncology, Feb;113:105131 (2021).
- Mukhopadhyay S, Ghosh S, Das D, Arun P, Roy B, Biswas NK, Maitra A, Partha Majumder. Analysis Using Random Forest and Data Integration Methods of Non-promoter Methylation and Expression Data Identifies Dysregulated Genes in Central Carbon Metabolism Pathway in Oral Cancer. BMC Cancer 20, 1219 (2020).
- Sanga S, Ghosh A, Kumar K, Polavarapu K, Preethish-Kumar V, Vengalil S, Nashi S, Bardhan M, Arunachal G, Raju S, Gayathri N, Biswas NK, Chakrabarti S, Nalini A, Roy S, Acharya M. Whole-exome analyses of congenital muscular dystrophy and congenital myopathy patients from India reveal a wide spectrum of known and novel mutations. Eur J Neurol. 2020 Oct 30. doi: 10.1111/ene.14616.
- Saha G, Singh R, Mandal A, Das S, Chattopadhyay E, Panja P, Roy P, DeSarkar, N, Gulati S, Ghatak S, Ghosh S, Banerjee S, Roy B, Ghosh S, Chaudhuri D, Arora N, Biswas NK, Sikdar N. A novel hotspot and rare somatic mutation p.A138V, at TP53 is associated with poor survival of pancreatic ductal and periampullar adenocarcinoma patients. Mol Med. 2020 Jun 17,26(1):59. doi:10.1186/s10020-020-00183-1.
- Maitra A, Sarkar MC, Raheja H, Biswas NK, Chakraborti S, Singh AK, Ghosh S, Sarkar S, Patra S, Mondal RK, Ghosh T, Chatterjee A, Banu H, Majumdar A, Chinnaswamy S, Srinivasan N, Dutta S, DAS S. Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. J Biosci. 2020,45(1):76. doi: 10.1007/s12038-020-00046-1.
- Singh R, Das S, Datta S, Mazumdar A, Biswas NK, Maitra A, Majumder PP, Ghose S, Roy B. Study of Caspase 8 mutation in oral cancer and adjacent precancer tissues and implication in progression. PLoS One. 2020 Jun 3,15(6):e0233058. doi: 10.1371/journal.pone.0233058.
- Biswas NK, Majumder PP. Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. Indian J Med Res. 2020 May,151(5):450-458. doi: 10.4103/ijmr.IJMR_1125_20.
- ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature. 2020 Feb;578(7793):82-93. doi:10.1038/s41586-020-1969-6. 2020 Feb 5. #Biswas NK is a member of the PCWAG consortium.
- GenomeAsia100K Consortium. The GenomeAsia 100K Project enables genetic discoveries across Asia. Nature. 2019 Dec;576(7785):106-111. doi:10.1038/s41586-019-1793-z. 2019 Dec 4. #Biswas NK is a member of analysis working group of GenomeAsia consortium.
- Das D, Ghosh S, Maitra A, Biswas NK, Panda CK, Roy B, Sarin R, Majumder PP. Epigenomic dysregulation-mediated alterations of key biological pathways and tumor immune evasion are hallmarks of gingivo-buccal oral cancer. Clin Epigenetics. 2019 Dec 3;11(1):178. doi: 10.1186/s13148-019-0782-2. PMID: 31796082; PMCID: PMC6889354.
- Biswas NK*, Das C, Das S, Maitra A, Nair S, Gupta T, D'Cruz AK, Sarin R, Majumder PP. Lymph node metastasis in oral cancer is strongly associated with chromosomal instability and DNA repair defects. Int J Cancer. 2019 Nov 1;145(9):2568-2579. doi: 10.1002/ijc.32305. Epub 2019 Apr 16.
- Palodhi A, Ghosh S, Biswas NK, Basu A, Majumder PP, Maitra A. Profiling of genomic alterations of mitochondrial DNA in gingivobuccal oral squamous cell carcinoma: Implications for disease progress. Mitochondrion. 2019 May;46:361-369. doi: 10.1016/j.mito.2018.09.006. Epub 2018 Sep 24.
- Singh R, De Sarkar N, Sarkar S, Roy R, Chattopadhyay E, Ray A, Biswas NK, Maitra A, Roy B. Analysis of the whole transcriptome from gingivo-buccal squamous cell carcinoma reveals deregulated immune landscape and suggests targets for immunotherapy. PLoS One. 2017 Sep 8;12(9):e0183606. doi:10.1371/journal.pone.0183606.
- Chandra V, Das T, Gulati P, Biswas NK, Rote S, Chatterjee U, Ghosh SN, Deb S, Saha SK, Chowdhury AK, Ghosh S, Rudin CM, Mukherjee A, Basu A, Dhara S. Hedgehog signaling pathway is active in GBM with GLI1 mRNA expression showing a single continuous distribution rather than discrete high/low clusters. PLoS One. 2015 Mar 16;10(3):e0116390. doi: 10.1371/journal.pone.0116390.
- Biswas NK, Chandra V, Sarkar-Roy N, Das T, Bhattacharya RN, Tripathy LN,Basu SK, Kumar S, Das S, Chatterjee A, Mukherjee A, Basu P, Maitra A, Chattopadhyay A, Basu A, Dhara S. Variant allele frequency enrichment analysis in vitro reveals sonic hedgehog pathway to impede sustained temozolomide response in GBM. Sci Rep. 2015 Jan 21;5:7915. doi: 10.1038/srep07915.
- Biswas NK*, Das S, Maitra A, Sarin R, Majumder PP. Somatic mutations in arachidonic acid metabolism pathway genes enhance oral cancer post-treatment disease-free survival. Nature Communications. 2014 Dec 17;5:5835. doi: 10.1038/ncomms6835.
- Das D, Kaur I, Ali MJ, Biswas NK, Das S, Kumar S, Honavar SG, Maitra A, Chakrabarti S, Majumder PP. Exome sequencing reveals the likely involvement of SOX10 in uveal melanoma. Optom Vis Sci. 2014 Jul;91(7):e185-92. doi: 10.1097/OPX.0000000000000309.
- India Project Team of the International Cancer Genome Consortium. (2013) Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrently-mutated genes and molecular subgroups. Nature Communications. 4:2873. doi: 10.1038/ncomms3873. ( ICGC-India Project Team: Maitra A, Biswas NK, Amin K, Kowtal P, Kumar S, Das S, Sarin R, Majumder PP, Bagchi I, Bairagya BB, Basu A, Bhan MK, Chaturvedi P, Das D, D'Cruz A, Dhar R, Dutta D, Ganguli D, Gera P, Gupta T, Mahapatra S, Mujawar MH, Mukherjee S, Nair S, Nikam S, Nobre M, Patil A, Patra S, Rama-Gowtham M, Rao TS, Roy B, Roychowdhury B, Sarkar D, Sarkar S, Sarkar-Roy N, Sutradhar D. )
- Sarkar S, Biswas NK, Dey B, Mukhopadhyay D, Majumder PP. A large, systematic molecular-genetic study of G6PD in Indian populations identifies a new non- synonymous variant and supports recent positive selection. Infect Genet Evol. 2010 Dec;10(8):1228-36. doi: 10.1016/j.meegid.2010.08.003. Epub 2010 Aug 14. PMID: 20713184.
- Datta S, Majumder M, Biswas NK, Sikdar N, Roy B. Increased risk of oral cancer in relation to common Indian mitochondrial polymorphisms and Autosomal GSTP1 locus. Cancer. 2007 Nov 1;110(9):1991-9. doi: 10.1002/cncr.23016. PMID: 17886251
- Biswas NK, Dey B, Majumder PP. Using HapMap data: a cautionary note. Eur J Hum Genet. 2007 Feb;15(2):246-9. doi: 10.1038/sj.ejhg.5201743. Epub 2006 Nov 29. PMID: 17133257.
Preprint:
- Maitra A, Raghav S, .., Biswas NK,…, The PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Consortium, Saumitra Das. PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Reveals Important Insights into the Outbreak. bioRxiv 2020.08.03.233718; doi: https://doi.org/10.1101/2020.08.03.233718.
- Bhattacharyya C, Das C, Ghosh A, Singh AK, Mukherjee S, Majumder PP, Basu A, Biswas NK*. Global Spread of SARS-CoV-2 Subtype with Spike Protein Mutation D614G is Shaped by Human Genomic Variations that Regulate Expression of TMPRSS2 and MX1 Genes. bioRxiv 2020.05.04.075911; doi: https://doi.org/10.1101/2020.05.04.075911. (50+ Citation)
- · *Corresponding author.
Lab members
PhD
Shouvik Chakravarty
Arnab Ghosh
Pratyusha Chikkala
Tuneer Ranjan Mallick
iPhD
Sneha Saha
Project
Subrata Das
Animesh K Singh
Vatsal Patel
Rezwanuzzaman Laskar
Kuntal K Dey
Hriday Home Chowdhury
Lab Picture
