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.
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.
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.
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.
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.
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. [Ongoing]
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. [Ongoing]
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]
| 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
Member of Calcutta Consortium on Human Genetics, India.
Member, Society of Biological Chemists
| 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”
|
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.
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.
PhD
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