Faculty Members

Research

The primary area of research in our group is Statistical Genomics with applications to genomics of complex diseases such as type-2 diabetes, cardiovascular disease, neuro-psychiatric diseases and autoimmune disorders. We use GWAS data and other high-throughput omics data available in the public domain to enhance our understanding of complex disease and at the same time we develop tools and techniques that enable other investigators to analysis and integration of their own datasets more efficiently. We also collaborate with scientists and clinicians who collect patient samples to generate their own genomics datasets to answer important scientific questions about complex diseases.

We have ongoing projects in the following areas:

Current Projects

• Prioritization of GWAS based on biological knowledge such as variant positional and functional annotations and gene-level knowledge from pathways and ontologies.
• Integrative Genomics: Utilizing transcriptomic studies, eQTL studies and epigenomic data to integrate with GWAS data for discovering additional genomic variants and to identify genes mediating the action of these variants.
• In-Silico Fine-Mapping and Functional Annotation: Guiding functional validation studies using statistical procedures to identify potential causal variants and regulatory variants with potential mechanisms of regulation.
• Gene-Gene and Gene-Environment Interactions: Understanding Interactions among genetic variants and between genes and environmental/lifestyle factors in the pathogenesis of complex diseases, that has a direct bearing on personalized risk assessment, therapy and/or management.
• Statistical Issues in High-throughput Genomics: We have been working towards addressing several statistical issues arising in analysis of genomics data such as
  • Large-scale Multiple Testing with locally correlated genomic tests.
  • Methods for large-scale genetic pleiotropy analysis.
  • Variable-selection in high-dimensional settings with sparsity restrictions
  • Statistical modelling of interactions between variants, genes, pathways and environmental factors.
• Computational Issues in High-Throughput Genomics: We create various software tools for methods that we develop and disseminate them freely for the genomics community. We are currently creating a user-friendly web-portal for remotely accessing, analyzing, integrating, and visualizing public domain genomic data.

Research Grant(s) as PI

Statistical Methods to Enhance the Power of Discovering Associations from Genome-wide Data. DBT/Wellcome Trust India Alliance Intermediate Fellowship Grant (Dec 2014-2019, Extended till: April 2021)

CV

• Education

Professional Appointments

October 2011 - June 2019 : Assistant Professor at National Institute of Biomedical Genomics, Kalyani, India

Sep 2008 - August 2011 : Research Fellow at the Biostatistics Branch of the Division of Cancer Epidemiology and Genetics, National Cancer Institute (NIH).

Professional Memberships

American Society of Human Genetics (2005 to 2008), American Statistical Association (2007-2011), ENAR-International Biometric Society (2008-2011), Indian Society of Human Genetics (since 2012), Calcutta Consortium of Human Genetics (since 2012), National Network for Mathematical and Computational Biology (since 2015)

Awards/Honors

Year Award

2010 Statistics in Epidemiology Young Investigator Award (Joint Statistical Meetings, 2010)

2011 Outstanding Research Paper by a Fellow (Division of Cancer Epidemiology and Genetics, 2010-11)

2014 Wellcome Trust/DBT India-Alliance Intermediate Fellowship (May, 2014)

Invited/Special lectures

Invited/Special lectures

Year Institute/meeting, Title of the talk

Past Major Projects

Pathway-driven Prioritization of GWAS (2014-2019)

Genetic Association for Heterogeneous traits and subtypes (2010-2014)

Gene-Gene Interactions in Presence of Population Stratification. (2008-2010)

Score Tests for QTL (Quantitative Trait Locus) Linkage Analysis. (2006-2008)

Publications

Research Articles

• Qi G, Chhetri SB, Ray D, Dutta D, Battle A, Bhattacharjee S*, Chatterjee N* (2024) Genome-wide large-scale multi-trait analysis characterizes global patterns of pleiotropy and unique trait-specific variants. Nat Commun 15, 6985 (2024). https://doi.org/10.1038/s41467-024-51075-5 [IF=14.7]

• Dutta T, Sengupta S, Adhya S, Saha A, Sengupta D, Mondal R, Bhattacharjee S*, Sengupta M* (2024) Identification of TNF-α as major susceptible risk locus for vitiligo: A systematic review and meta-analysis study in Asian population. Dermatology.2024 Feb 20; https://doi.org/10.1159/000536480 [IF=3.4]

• Chakraborty S, Sharma A, Pal S, Sharma A, Sihota R, Bhattacharjee S, Acharya M* (2023) A quantitative trait GWAS on lens thickness identifies novel risk loci on PTPRM in the narrow angle individuals susceptible to PACG. Eur J Ophthalmol. 2023 Sep;33(5):1922-1930. doi: https://doi.org/10.1177/11206721231160988 [IF=1.7]

• Sengupta D, Mukhopadhyay P, Banerjee S, Ganguly K, Mascharak P, Mukherjee N, Mitra S, Bhattacharjee S, Mitra R, Sarkar A, Chaudhuri T, Bhattacharjee G, Nath S, Roychoudhury S, Sengupta M* (2023) Identifying polymorphic cis-regulatory variants as risk markers for lung carcinogenesis and chemotherapy responses in tobacco smokers from eastern India. Sci Rep. 2023 Mar 10;13(1):4019. https://doi.org/10.1038/s41598-023-30962-9  [IF=4.997]

• Ganesh S, Vemula A, Bhattacharjee S, Mathew K, Ithal D, Navin K, Nadella RK, Viswanath B, Sullivan PF, Jain S, Purushottam M* (2022) Whole exome sequencing in dense families suggests genetic pleiotropy amongst Mendelian and complex neuropsychiatric syndromes. Sci Rep. 2022 Dec 7;12(1):21128. https://doi.org/10.1038/s41598-022-25664-7 [IF=4.6]

• Sengupta D, Banerjee S, Mukhopadhyay P, Mitra R, Chaudhuri T, Sarkar A, Bhattacharjee G, Nath S, Roychoudhury S, Bhattacharjee S*, Sengupta M* (2021) A comprehensive meta-analysis and a case-control study give insights into genetic susceptibility of lung cancer and subgroups. Sci Rep. 2021 Jul 16;11(1):14572. https://doi.org/10.1038/s41598-021-92275-z [IF=4.996]

• Pandit B, Bhattacharjee S, Bhattacharjee B* (2021) Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. Infect Genet Evol. 2021 Jun;90:104734. https://doi.org/10.1016/j.meegid.2021.104734 [IF=4.393]

• Vipparthi K, Patel AK, Ghosh S, Das S, Das C, Das K, Sarkar A, Thatikonda V, Pal B, Remani ASKN, Arora N, Parihar M, Vijayakumar MV, Bhat MK, Boppana R, Bhattacharjee S, Biswas NK, Arun P, Sharan R, Singh S* (2021) Two novel cell culture models of buccal mucosal oral cancer from patients with no risk-habits of tobacco smoking or chewing. Oral Oncol. 2021 Feb;113:105131. https://doi.org/10.1016/j.oraloncology.2020.105131 [IF=5.972]

• Chakraborty S, Sharma A, Bagchi I, Pal S, Bhattacharyya C, Gupta V, Maitra A, Bhattacharjee S, Sharma A, Sihota R, Acharya M* (2021) A genomewide association study on individuals with occludable angles identifies potential risk loci for intraocular pressure. J Genet. 2021;100. https://pubmed.ncbi.nlm.nih.gov/34608871/  [IF=1.508]

• Chakraborty S, Sharma A, Sharma A, Sihota R, Bhattacharjee S, Acharya M* (2021) Haplotype-based genomic analysis reveals novel association of CNTNAP5 genic region with primary angle closure glaucoma. J Biosci. 2021;46. https://pubmed.ncbi.nlm.nih.gov/33737499/  [IF=2.795]

• Chhatriya B, Mukherjee M, Ray S, Saha B, Lahiri S, Halder S, Ghosh I, Khamrui S, Das K, Bhattacharjee S, Mohapatra SK, Goswami S* (2020) Transcriptome analysis identifies putative multi-gene signature distinguishing benign and malignant pancreatic head mass. J Transl Med. 2020 Nov 7;18(1):420. https://doi.org/10.1186/s12967-020-02597-1  [IF=5.531]

• Biswas S, Pal S, Majumder PP, Bhattacharjee S* (2020) A framework for pathway knowledge driven prioritization in genome-wide association studies. Genet Epidemiol. 2020 Nov;44(8):841-853. https://doi.org/10.1002/gepi.22345 [IF=2.135]

• Sengupta D, Banerjee S, Mukhopadhyay P, Guha U, Ganguly K, Bhattacharjee S, Sengupta M* (2020) A meta-analysis and in silico analysis of polymorphic variants conferring breast cancer risk in the Indian subcontinent. Future Oncol. 2020 Sep;16(27):2121-2142. https://doi.org/10.2217/fon-2020-0333 [IF=3.404]

• Patel AK, Vipparthi K, Thatikonda V, Arun I, Bhattacharjee S, Sharan R, Arun P, Singh S* (2018) A subtype of cancer-associated fibroblasts with lower expression of alpha-smooth muscle actin suppresses stemness through BMP4 in oral carcinoma. Oncogenesis. 2018 Oct 5;7(10):78. https://doi.org/10.1038/s41389-018-0087-x [IF=6.634]

• Sengupta D, Guha U, Mitra S, Ghosh S, Bhattacharjee S*, Sengupta M* (2018) Meta-Analysis of Polymorphic Variants Conferring Genetic Risk to Cervical Cancer in Indian Women Supports CYP1A1 as an Important Associated Locus. Asian Pac J Cancer Prev. 2018 Aug 24;19(8):2071-2081. https://doi.org/10.22034/APJCP.2018.19.8.2071  [IF=1.307]

• Sengupta D, Guha U, Bhattacharjee S*, Sengupta M* (2017) Association of 12 polymorphic variants conferring genetic risk to lung cancer in Indian population: An extensive meta-analysis. Environ Mol Mutagen. 2017 Dec;58(9):688-700. https://doi.org/10.1002/em.22149 [IF=3.254]

• Bhushan A, Ghosh S, Bhattacharjee S, Chinnaswamy S* (2017) Confounding by Single Nucleotide Polymorphism rs117648444 (P70S) Affects the Association of Interferon Lambda Locus Variants with Response to Interferon-α-Ribavirin Therapy in Patients with Chronic Genotype 3 Hepatitis C Virus Infection. J Interferon Cytokine Res. 2017 Aug;37(8):369-382. https://doi.org/10.1089/jir.2017.0002 [IF=2.446]

• Mukhopadhyay S, Thatoi PK, Pandey AD, Das BK, Ravindran B, Bhattacharjee S, Mohapatra SK* (2017) Transcriptomic meta-analysis reveals up-regulation of gene expression functional in osteoclast differentiation in human septic shock. PLoS One. 2017;12(2):e0171689. https://doi.org/10.1371/journal.pone.0171689 [IF=2.992]

• Li WQ, Pfeiffer RM, Hyland PL, Shi J, Gu F, Wang Z, Bhattacharjee S, Luo J, Xiong X, Yeager M, Deng X, Hu N, Taylor PR, Albanes D, Caporaso NE, Gapstur SM, Amundadottir L, Chanock SJ, Chatterjee N, Landi MT, Tucker MA, Goldstein AM, Yang XR* (2014) Genetic polymorphisms in the 9p21 region associated with risk of multiple cancers. Carcinogenesis. 2014 Dec;35(12):2698-705. https://doi.org/10.1093/carcin/bgu203 [IF=5.89]

• Datta S*, Xia XQ, Bhattacharjee S, Jia Z (2014) Advances in statistical medicine. Comput Math Methods Med. 2014;2014:316153. https://doi.org/10.1155/2014/316153 [IF=1.354]

• Carty CL, Bhattacharjee S, Haessler J, Cheng I, Hindorff LA, Aroda V, Carlson CS, Hsu CN, Wilkens L, Liu S, Selvin E, Jackson R, North KE, Peters U, Pankow JS, Chatterjee N, Kooperberg C* (2014) Analysis of metabolic syndrome components in >15 000 african americans identifies pleiotropic variants: results from the population architecture using genomics and epidemiology study. Circ Cardiovasc Genet. 2014 Aug;7(4):505-13. https://doi.org/10.1161/CIRCGENETICS.113.000386 [IF=5.337]

• Chinnaswamy S*, Chatterjee S, Boopathi R, Mukherjee S, Bhattacharjee S, Kundu TK (2013) A single nucleotide polymorphism associated with hepatitis C virus infections located in the distal region of the IL28B promoter influences NF-κB-mediated gene transcription. PLoS One. 2013;8(10):e75495. https://doi.org/10.1371/journal.pone.0075495 [IF=4.034]

• Gu F, Pfeiffer RM, Bhattacharjee S, Han SS, Taylor PR, Berndt S, Yang H, Sigurdson AJ, Toro J, Mirabello L, Greene MH, Freedman ND, Abnet CC, Dawsey SM, Hu N, Qiao YL, Ding T, Brenner AV, Garcia-Closas M, Hayes R, Brinton LA, Lissowska J, Wentzensen N, Kratz C, Moore LE, Ziegler RG, Chow WH, Savage SA, Burdette L, Yeager M, Chanock SJ, Chatterjee N, Tucker MA, Goldstein AM, Yang XR* (2013) Common genetic variants in the 9p21 region and their associations with multiple tumours. Br J Cancer. 2013 Apr 2;108(6):1378-86. https://doi.org/10.1038/bjc.2013.7  [IF=5.238]

• Leenders M, Bhattacharjee S, Vineis P, Stevens V, Bueno-de-Mesquita HB, Shu XO, Amundadottir L, Gross M, Tobias GS, Wactawski-Wende J, Arslan AA, Duell EJ, Fuchs CS, Gallinger S, Hartge P, Hoover RN, Holly EA, Jacobs EJ, Klein AP, Kooperberg C, LaCroix A, Li D, Mandelson MT, Olson SH, Petersen G, Risch HA, Yu K, Wolpin BM, Zheng W, Agalliu I, Albanes D, Boutron-Ruault MC, Bracci PM, Buring JE, Canzian F, Chang K, Chanock SJ, Cotterchio M, Gaziano JM, Giovanucci EL, Goggins M, Hallmans G, Hankinson SE, Hoffman-Bolton JA, Hunter DJ, Hutchinson A, Jacobs KB, Jenab M, Khaw KT, Kraft P, Krogh V, Kurtz RC, McWilliams RR, Mendelsohn JB, Patel AV, Rabe KG, Riboli E, Tjønneland A, Trichopoulos D, Virtamo J, Visvanathan K, Elena JW, Yu H, Zeleniuch-Jacquotte A, Stolzenberg-Solomon RZ* (2013) Polymorphisms in genes related to one-carbon metabolism are not related to pancreatic cancer in PanScan and PanC4. Cancer Causes Control. 2013 Mar;24(3):595-602. https://doi.org/10.1007/s10552-012-0138-0 [IF=3.428]

• Bhattacharjee S, Rajaraman P, Jacobs KB, Wheeler WA, Melin BS, Hartge P, Yeager M, Chung CC, Chanock SJ, Chatterjee N* (2012) A subset-based approach improves power and interpretation for the combined analysis of genetic association studies of heterogeneous traits. Am J Hum Genet. 2012 May 4;90(5):821-35.  https://doi.org/10.1016/j.ajhg.2012.03.015 [IF=11.11]

• Menashe I, Maeder D, Garcia-Closas M, Figueroa JD, Bhattacharjee S, Rotunno M, Kraft P, Hunter DJ, Chanock SJ, Rosenberg PS, Chatterjee N* (2010) Pathway analysis of breast cancer genome-wide association study highlights three pathways and one canonical signaling cascade. Cancer Res. 2010 Jun 1;70(11):4453-9. https://doi.org/10.1158/0008-5472.CAN-09-4502 [IF=8.474]

• Bhattacharjee S, Wang Z, Ciampa J, Kraft P, Chanock S, Yu K, Chatterjee N* (2010) Using principal components of genetic variation for robust and powerful detection of gene-gene interactions in case-control and case-only studies. Am J Hum Genet. 2010 Mar 12;86(3):331-42. https://doi.org/10.1016/j.ajhg.2010.01.026 [IF=11.344]

• Henson BJ, Bhattacharjee S, O'Dee DM, Feingold E, Gollin SM* (2009) Decreased expression of miR-125b and miR-100 in oral cancer cells contributes to malignancy. Genes Chromosomes Cancer. 2009 Jul;48(7):569-82. https://doi.org/10.1002/gcc.20666 [IF=4.066]

• Bhattacharjee S, Kuo CL, Mukhopadhyay N, Brock GN, Weeks DE, Feingold E* (2008) Robust score statistics for QTL linkage analysis. Am J Hum Genet. 2008 Mar;82(3):567-82. https://doi.org/10.1016/j.ajhg.2007.11.012 [IF=9.565]

• Mukhopadhyay N, Halder I, Bhattacharjee S, Weeks DE* (2007) Two-dimensional linkage analyses of rheumatoid arthritis. BMC Proc. 2007;1 Suppl 1(Suppl 1):S68. https://doi.org/10.1186/1753-6561-1-s1-s68 [IF=1.16]

• Bartlett CW*, Vieland VJ, Bartlett J, Bell JT, Bhattacharjee S, Clerget-Darpoux F, Bush WS, Edwards TL, Gao G, Halder I, Huang Y, Kotti S, Larkin EK, Li H, Motsinger AA, Mukhopadhyay N, Namkung J, Park T, Ritchie MD, Stein CM, Zhou JY (2007) Discussing gene-gene interaction: warning--translating equations to English may result in jabberwocky. Genet Epidemiol. 2007;31 Suppl 1:S61-7. https://doi.org/10.1002/gepi.20281 [IF=3.507]

• Sengul H, Bhattacharjee S, Feingold E, Weeks DE* (2007) The elusive goal of pedigree weights. Genet Epidemiol. 2007 Jan;31(1):51-65. https://doi.org/10.1002/gepi.20188 [IF=3.507]

• Ghosh S, Bhattacharjee S, Basu G, Pal S, Majumder PP* (2005) Linkage mapping of a complex trait in the New York population of the GAW14 simulated dataset: a multivariate phenotype approach. BMC Genet. 2005 Dec 30;6 Suppl 1(Suppl 1):S19. https://doi.org/10.1186/1471-2156-6-S1-S19 [IF=1.847]

Software

• FAST-ASSET (http://www.bioconductor.org/packages/release/bioc/html/ASSET.html): Part of ASSET V2.13 and above.
• GKnowMTest (https://github.com/sbstatgen/GKnowMTest): R package for pathway knowledge-based prioritization of GWAS results.
• TMVNSIM (https://cran.r-project.org/web/packages/tmvnsim/index.html): R package for importance sampling from the truncated multivariate normal distribution (2015).
• ASSET (http://www.bioconductor.org/packages/release/bioc/html/ASSET.html): R package for combined analysis of heterogeneous traits and disease subtypes (2012).

Lab members

Ph.D. Students:

Prasun Panja

Kallol Datta

Gaurav R. Amale

Diptanil Biswas

Graduated:

Shrayashi Biswas