Faculty Members

Research

Research Interests Population Genetics, Genetic Epidemiology, Statistical Genetics

My research interest is nested. There are two major components; one is to understand human genome diversity and evolution with special reference to India. This endeavor of understanding human genetic diversity and structure, not only provides us a window into human pre-history or understanding socio-cultural norms in historic times influencing social behavior; it also provides the framework to look at the multifactorial nature of disease causation considering host and exposure factors together. This automatically introduces the second component of my research, which is aimed at identification of genomic regions responsible for differential expression of heritable traits, i.e. connecting genotype with the phenotype. However, it is nested because I often work on problems where there are no off-the-shelf statistical methods. Thus, an important part of my work is in developing appropriate statistical and computational approaches that can yield new insights into biological data.

CV

Education

PhD in Statistics, Indian Statistical Institute, 2003
Thesis Title: Some statistical contributions to the analysis of human genome diversity and evolution

Master of Statistics (Applied Statistics and Data Analysis), Indian Statistical Institute, 1998

Past Appointments

Associate Professor, April 2016 to August 2023, National Institute of BioMedical Genomics, India

Assistant Professor, November 2012 to April 2016, National Institute of BioMedical Genomics, India

DBT-NIBMG Fellow, September 2009 to November 2012, National Institute of BioMedical Genomics, India

Post Doctoral Employee, January 2005 to July 2009, University of California San Francisco, California, USA

Post Doctoral Scholar, July 2004 to December 2004, Stanford University, California, USA

Awards & Honours

Fellow of the Indian Academy of Sciences, January 2023

Fellow of the West Bengal Association of Science and Technology, December 2016

Young Investigator Award at the 12th International Congress of Human Genetics/ 61st American Society of Human Genetics Meeting, Montreal 2011

Honorable Mention in USPROC 2011 Competition (Project with Sayar Karmakar and Dr Anil K Ghosh)

Orations & Special Lectures.

EMBL Symposium: Reconstructing the Human Past - Using Ancient and Modern Genomics at EMBL Heidelberg, Germany

Current Projects

GenomeIndia: Cataloguing the genetic Variation in Indians (Department of BioTechnology, Government of India) 

Integrating Multi-Omics Data Using Big Data Analytics to Infer Optimal Wellness Trajectories for Management of Non-communicable diseases (NCDs): Cervical Cancer as an Exemplar
(Department of BioTechnology, Government of India) 

Development of a fast, flexible, high performance computing framework to accelerate NGS omics-data analysis (National Supercomputing Mission (NSM) Platform for Genomics and Drug Discovery, Government of India)

Unbiased Profiling of Loci Relevant for Pharmacogenomics, Pharmacovigilance and Predisposition to Some Common Disorders in a Peri-Urban Population of West Bengal
(Department of BioTechnology, Government of West Bengal) 

A Unified Web-portal for Analysis, Integration and Visualization of Multi-omics Data
(Department of BioTechnology, Government of India) 

Past Major Projects 

ADVANCE (Atherosclerotic Disease, VAscular functioN, and genetiC Epidemiology) is a multicenter (Stanford University, Kaiser Permanente, UCSF) Study aimed at providing better care for patients with atherosclerotic coronary heart disease through the application of modern genetic approaches. (http://med.stanford.edu/advance/)

Family Blood Pressure Program (FBPP) is a large multi-center genetic study of high blood pressure and related conditions in multiple ethnic groups. The program in turn consists of four multi-center Networks: GenNet, GENOA, HyperGEN and SAPPHIRe.  (http://www.biostat.wustl.edu/fbpp/FBPP.shtml)

Publications

• Das S, Biswas N, BASU A* (2023) Mapinsights: deep exploration of quality issues and error profiles in high-throughput sequence data. Nucleic Acid Research 51:14 e75 
  
  
• Bhattacharyya C, Barman D, Tripathi D, Dutta S, Bhattacharya C, Alam M, Choudhury P, Devi U, Mahanta J, Rasaily R, BASU A*, Paine SK (2023) The influence of maternal Breast milk and Vaginal microbiome on Neonatal gut microbiome: A longitudinal study over the first year of birth. Microbiology Spectrum 11(3): e0496722
  
  
• Tagore D, Majumder PP, Chatterjee A, BASU A* (2022) Multiple migrations from East Asia led to linguistic transformation in Northeast India and mainland Southeast Asia. Frontiers in genetics (https://doi.org/10.3389/fgene.2022.1023870)
  
  
• Paine SK, Das S, Bhattacharyya C, Biswas NK, Rao R, De A, BASU A* (2022) Autosomal recessive inheritance of a Novel missense mutation of ITGB4 for Epidermolysis-Bullosa Pyloric-Atresia: A Case report. Molecular Genetics and Genomics 297(6):1581-1586.
  
  
• Paine SK, Rout U, Bhattacharyya C, Parai D, Alam M, Nanda R, Tripathi D, Choudhury P, Kundu C, Pati S, Bhattacharya D, BASU A* (2022) Temporal Dynamics of Oropharyngeal Microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance. NPJ Biofilms and Microbiomes 67 (8) 
  
  
• Pal Bhowmick I, Pandey A, Subbarao SK, Pebam R, Majumder T, Nath A, Nandi D, BASU A, Sarkar A, Majumder S, Debbarma J, Dasgupta D, Borgohain A, Chanda R, Das M, Gogoi K, Gogoi K, Joshi PL, Kaur H, Borkakoty BJ, Bhattacharya DR, Khan AM, Sen S, Narain K (2022) Diagnosis of indigenous non-malarial vector-borne infections from malaria negative samples from community and rural hospital surveillance in a high malaria-endemic forested region of Dhalai District, Tripura, North-East India. Diagnostics 12:2 
  
  
• Kakati P, Paine SK, Bhattacharjee CK, Bhattacharyya C, Sharma A, Phukan D, Barman NN, BASU A* (2021) Gut microbiome architecture of wild Greater One Horned (GoH) Rhinoceros, a vulnerable species from Kaziranga National Park, India. Journal of Genetics 100:84 
  
  
• Pradhan S, Das S, Singh AK, Das C, BASU A, Majumder PP, Biswas NK (2021) dbGENVOC: database of GENomic Variants of Oral Cancer, with special reference to India. Database 2021 baab034 
  
  
• Tagore D, Aghakhanian F, Naidu R, Phipps ME, BASU A* (2021) Insights into the demographic history of Asia from common ancestry and admixture in the genomic landscape of present-day Austroasiatic speakers. BMC Biology 19(1):61 
  
  
• Bhattacharyya C, Das C, Ghosh A, Singh AK, Mukherjee S, Majumder PP, BASU A, Biswas NK (2021) SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. Infection, Genetics and Evolution 90, 104760 
  
  
• Chatterjee A, BASU A, Das K, Chowdhury A, Basu P (2021) Exome-wide scan identifies significant association of rs4788084 in IL27 promoter with increase in hepatic fat content among Indians. Gene 775, 14543 
  
  
• Paine SK, Bhattacharjee CK, Bhaduri G, Pramanik S, Borah PK, Mahanta J, BASU A, Mondal LK (2021) Pre-therapeutic Biomarkers for Ranibizumab Therapy among Type 2 Diabetic Patients with Diabetic Macular Edema. Optometry and Vision Science 98 (1), 81-87 
  
  
• Chakraborty S, BASU A*, GenomeAsia 100K Consortium (2020) Whole genomes reveal severe bottleneck among Asian hunter-gatherers following the invention of agriculture. bioRxiv

• Bhattacharyya C, Das C, Ghosh A, Singh AK, Mukherjee S, Majumder PP, BASU A, Biswas NK (2020) 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

• Chatterjee A, BASU A, Das K, Singh P, Mondal D, Bhattacharyya B, Roychoudhury S, Majumder PP, Chowdhury A, Basu P (2020) Hepatic transcriptome signature correlated with HOMA-IR explains early Nonalcoholic Fatty Liver Disease pathogenesis. Annals of Hepatology 19 (5), 472-481

• Chhatriya B, Paine SK, Das S, Chatterjee A, Nath D, Mukherjee A, BASU A, Goswami S (2020) Single nucleotide polymorphisms in PRSS1 and CASR genes are associated with chronic pancreatitis in North-Eastern region of India. Journal of Gastrointestinal and Liver Diseases 29 (2), 267-268

• Giri AK, Prasad G, Bandesh K, Parekatt V, Mahajan A, Banerjee P, Kauser Y, Chakraborty S, Rajashekar D, INDICO, Sharma A, Mathur SK, BASU A, McCarthy MI, Tandon N, Bharadwaj D (2020) Multifaceted genome-wide study identifies novel regulatory loci for body mass index in Indians. Molecular Genetics and Genomics 295(4), 1013-26

• Wall JD, Ratan A, Stawiski E, Kim HL, Kim C, Gupta R, Suryamohan K, GenomeAsia 100K Consortium (2020) Identification of African-Specific Admixture between Modern and Archaic Humans. The American Journal of Human Genetics 105 (6), 1254-1261

• GenomeAsia 100K Consortium (2020) The GenomeAsia 100K Project enables genetic discoveries across Asia. Nature 576, 106–111

• Chakraborty S, Prasad G, Marwaha RK, BASU A, Tandon N, Bharadwaj D (2020) An Assessment of plasma adipocytokines and C-reactive protein levels in healthy school-going adolescents from private and government-funded schools of Delhi, India. Indian Journal of Medical Research 151 (1), 47-58

• Prasad G, Bandesh K, Giri AK, Kauser Y, Chanda P, Parekatt V, Mathur S, Madhu SV, Venkatesh P, Bhansali A, Marwaha RK, BASU A, Tandon N, Bharadwaj D and INDICO (2019) Genome-Wide Association Study of Metabolic Syndrome Reveals Primary Genetic Variants at CETP Locus in Indians. Biomolecules, 9(8), 321; (This article belongs to the Special Issue: Atherosclerosis and Related Diseases: Particular Focus on Molecular Biology)

• Chakraborty S*, BASU A* (2019) Reconstruction of ancestral footfalls in South Asia using genomic data. Journal of Biosciences 44: 74. https://doi.org/10.1007/s12038-019-9875-5
  
  
• Bandesh K, Prasad G, Giri AK, Kauser Y, Upadhyay M, INDICO, BASU A, Tandon N, Bharadwaj D (2019) GWAS of Total Cholesterol, LDL, HDL and Triglycerides in Indians confirms universality of established variants. Journal of Human Genetics 64(6), 573
  
  
• Prasad G, Giri AK , INDICO, BASU A, Tandon N, Bharadwaj D (2019) Genome-wide association study for C-reactive protein in Indians replicates known associations of common variants. Journal of Genetics 98(1), 20
  
  
• Palodhi A, Ghosh S, Biswas NK, BASU A, Majumder PP, Maitra A (2019) Profiling of genomic alterations of mitochondrial DNA in gingivobuccal oral squamous cell carcinoma: Implications for disease progress. Mitochondrion (46), 361-369
  
  
• Paine SK, BASU A, Gon Choudhury R, Bhattacharya B, Chatterjee S, Bhattacharya C (2018) Multiplex PCR from Menstrual Blood: A Non-Invasive Cost Effective Approach to Reduce Diagnostic Dilemma for Genital Tuberculosis. Molecular Diagnosis and Therapy 22 (3), 391-396
  
  
• Giri AK, Bhardwaj S, Banerjee P, Chakraborty S, Parekatt V, Rajashekar D, Tomar A, Ravindran A, BASU A, Tandon N, Bharadwaj D (2017) DNA methylation profiling reveals the presence of population-specific signatures correlating with phenotypic characteristics. Molecular Genetics and Genomics. 292(3):655-662.
  
  
• Sengupta D, Choudhury A, BASU A*, Ramsay M (2016) Population stratification and underrepresentation of Indian subcontinent genetic diversity in the 1000 Genomes Project dataset. Genome Biol Evol. 8 (11): 3460-3470.
  
  
• BASU A* (2016) The Dazzling Diversity and the Fundamental Unity: Peopling and the Genomic Structure of Ethnic India. Indian Journal of History of Science 51.2.2  406-416
  
  
• Vishal M, Sharma A, Kaurani L, Alfano G, Mookherjee S, Narta K, Agrawal J, Bhattacharya I, Roychoudhury S, Ray J, Waseem N, Bhattacharya S, BASU A, Sen A, Ray K, Mukhopadhyay A (2016) Genetic association and stress mediated down regulation in trabecular meshwork implicates MPP7 as a novel candidate gene in primary open angle glaucoma. BMC Medical Genomics 9: 15
  
  
• BASU A*, Sarkar-Roy N, Majumder PP (2016) Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure. Proc Natl Acad Sci U S A. Feb 9;113(6):1594-9.
  
  
• Datta S, Ray A, Singh R, Mondal P, BASU A, De Sarkar N, Majumder M, Maiti G, Baral A, Jha GN, Mukhopadhyay I, Panda C, Chowdhury S, Ghosh S, Roychoudhury S, Roy B (2015) Sequence and expression variations in 23 genes involved in mitochondrial and non-mitochondrial apoptotic pathways and risk of oral leukoplakia and cancer. Mitochondrion. 25: 28-33
  
  
• Esteban ME, BASU A, Calo CM, Moral P (2015) Biomedical Insights of Human Genetic Diversity in Complex Diseases. BioMed Research International Volume 2015 (2015) http://dx.doi.org/10.1155/2015/974809,  Editorial
  
  
• 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 and Dhara S (2015) DNA repair, amino acid degradation and sonic hedgehog signaling pathways are associated with cellular senescence versus quiescence in GBM neoplastic cells in response to TMZ . Scientific Reports 5
  
  
• 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 and Dhara S (2015) An objective clustering of GBM patients to identify clinically relevant subgroups with hedgehog pathway activity. PLoS One 10(3)
  
  
• Chatterjee A, BASU A,Chowdhury A, Das K, Sarkar-Roy N, Majumder PP and Basu P (2015) Comparative analyses of genetic risk prediction methods reveal extreme diversity of genetic predisposition to nonalcoholic fatty liver disease (NAFLD) among ethnic populations of India. Journal of Genetics 94(1):105-113
  
  
• Karmakar B, Dhara K, Dey KK, BASU A, Ghosh AK (2015) Tests for Statistical Significance of a Treatment Effect in the Presence of Hidden Sub-populations. Statistical Methods and Applications 24(1), 97-119
  
  
• Datta S, Ghosh A, Dasgupta D, Ghosh A, Roychoudhury S, Roy G, Das S, Das K, Gupta S, Basu K, BASU A, Datta S, Chowdhury A, Banerjee S (2014) Novel Point and Combo-Mutations in the Genome of Hepatitis B Virus-Genotype D: Characterization and Impact on Liver Disease Progression to Hepatocellular Carcinoma. PLoS One 9(10): e110012.
  
  
• Majumder PP, BASU A (2014) A Genomic view of peopling and population structure of India Cold Spring Harb Perspect Biol. pii: a008540.
  
  
• Giri AK, Khan NM, Grover S, Kaur I, BASU A, Tandon N, Scaria V, IGV Consortium, INDICO, Kukreti R, Brahmachari SK, Bharadwaj D (2014) Genetic epidemiology of pharmacogenetic variations in CYP2C9, CYP4F2 and VKORC1 genes associated with warfarin dosage in the Indian population. Pharmacogenomics 15(10), 1337–1354
  
  
• Giri AK, Khan NM, BASU A, Tandon N, Scaria V, Bharadwaj D.(2014) Pharmacogenetic landscape of clopidogrel in north Indians suggest distinct interpopulation differences in allele frequencies. Pharmacogenomics 15(5):643-53
  
  
• 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.
  
  
• Banerjee D, Banerjee A, Mookherjee S, Vishal M, Mukhopadhyay A, Sen A, BASU A*, Ray K (2013) Mitochondrial genome analysis of primary open angle glaucoma patients. PLoS One 5;8(8):e70760
  
  
• Tabassum R, Chauhan G, Dwivedi OP, Mahajan A, Jaiswal A, Kaur I, Bandesh K, Chidambaram M, Sharma A, Chavali S, Sengupta S, Ramakrishnan L,Venkatesh P, Aggarwal SK, Ghosh S, Prabhakaran D, Srinath RK Saxena M, Banerjee M, Mathur S, Bhansali A, Shah VN, Madhu SV, Marwaha RK, BASU A, Scaria V, McCarthy MI, DIAGRAM, INDICO, Venkatesan R, Mohan V, Tandon N, Bharadwaj D (2013) Genome wide association study for type 2 diabetes in Indians identifies a new susceptibility locus at 2q21. Diabetes 62(3):977-86

• Majumdar A, Bhattacharya S, BASU A, Ghosh S (2013) A novel Bayesian semi-parametric algorithm for inferring population structure and adjusting for case-control association tests. Biometrics 69(1):164-73.
  
  
• Paine SK, BASU A, Mondal LK, Sen A, Choudhuri S, Chowdhury IH, Saha A, Bhadhuri G, Mukherjee A, Bhattacharya B (2012) Association of  VEGF, TGFβ1 and IFN-γ gene polymorphism with proliferative diabetic retinopathy in type2 diabetic subjects. Molecular Vision 18:2749-57
  
  
• Narayanasamya K, Chery L, BASU A, Duraisingh MT, Escalante A, Fowble J, Guler JL, Herricks T, Kumar A, Majumder PP, Maki J, Mascarenhas A, Rodrigues J, Roy B, Sen S, Shastri J, Smith J, Valecha N, White J, Rathod PK (2012) Malaria Evolution in South Asia: Knowledge for Control and Elimination. Acta Tropica 121: 256-266
  
  
• Narang A, Jha P, Rawat V, Mukhopadhayay A, Dash D, BASU A*, Mukerji M (2011) Recent Admixture in an Indian Population of African Ancestry. American Journal of Human Genetics 89(1): 111 – 120. 
  
  
• Paine SK, Sen A, Choudhuri S, Mondal LK, Chowdhury IH, BASU A, Mukherjee A and Bhattacharya B (2011) Association of TNF-α, IL-6 and IL-10 promoter polymorphism with proliferative diabetic retinopathy in type2 diabetic subjects. Retina 32:1197-1203
  
  
• Jha P, Kanchan K, Qidwai T, Pati SS, Mohanty S, Mishra SK, Sharma SK, Awasthi S, Venkatesh V, Jain S, BASU A, Shuhua X, IGVC, Mukerji M, Habib S (2011) Deletion of the APOBEC3B gene strongly impacts susceptibility to falciparum malaria. Infection, Genetics and Evolution 12:142-148.
  
  
• Farheen S, BASU A, Majumder PP (2011) Haplotype variation in the ACE gene in global populations, with special reference to India, and an alternative model of evolution of haplotypes. The HUGO Journal  5:35-45
  
  
• Zakharia F, BASU A, Absher D, Assimes T, Fortmann S, Go A, Hlatky M, Iribarren C, Knowles J, Li J, Narasimhan B, Olshen R, Sidney S, Southwick A, Myers R, Quertermous T, Risch N, Tang H (2009) Characterizing the Admixed African Ancestry of African Americans. Genome Biology 10(12):R141. Epub 2009 Dec 22.
  
  
• Risch N, Choudhry S, Via M, BASU A, Sebro R, Eng C, Beckman K, Thyne S, Chapela R, Rodriguez-Santana JR, Rodriguez-Cintron W, Avila PC, Ziv E, Gonzalez Burchard E (2009) Ancestry-related assortative mating in Latino populations. Genome Biology 10(11): R132. Epub 2009 Nov 20.
  
  
• Theusch E, BASU A, Gitschier J (2009) Genome-wide study of families with absolute pitch reveals linkage to 8q24.21 and locus heterogeneity. American Journal of Human Genetics 85(1):112-19.
  
  
• BASU A*, Tang H, Lewis CE, North K, Curb DJ,  Quertermous T, Mosley TH, Boerwinkle E, Zhu X, Risch N (2009) Admixture Mapping of Quantitative Trait Loci for Blood Lipids in African Americans. Human Molecular Genetics 18(11):2091-98. 
  
  
• BASU A, Tang H, Arnett D, Gu CC, Mosley TH, Kardia S, Luke A, Tayo B, Cooper R, Zhu X, Risch N (2009) Admixture Mapping of Quantitative Trait Loci for BMI in African Americans: Evidence for Loci on Chromosomes 3q, 5q and 15q. Obesity 17(6): 1226-31.
  
  
• BASU A*, Tang H, Zhu X, Gu CC, Hanis C, Boerwinkle E, Risch N (2008) Genome-wide distribution of ancestry in Mexican Americans. Human Genetics 124(3):207-214. 
  
  
• Assimes TL, Knowles JW, BASU A, Iribarren C, Southwick A, Tang H, Absher D, Li J, Fair JM, Rubin GD, Sidney S, Fortmann SP, Go AS, Hlatky MA, Myers RM, Risch N, Quertermous T (2008) Susceptibility locus for clinical and subclinical coronary artery disease at chromosome 9p21 in the multi-ethnic ADVANCE study. Human Molecular Genetics 17(15):2320-28.
  
  
• Assimes TL, Knowles JW, Priest JR, BASU A, Volcik KA, Southwick A, Tabor HK, Hartiala J, Allayee H, Grove ML, Tabibiazar R, Sidney S, Fortmann SP, Go A, Hlatky M, Iribarren C, Boerwinkle E, Myers R, Risch N, Quertermous T (2008) Common polymorphisms of ALOX5 and ALOX5AP and risk of coronary artery disease. Human Genetics 123(4):399-408.
  
  
• Assimes TL, Knowles JW, Priest JR, BASU A, Borchert A, Volcik KA, Grove ML, Tabor HK, Southwick A, Tabibiazar R, Sidney S, Boerwinkle E, Go AS, Iribarren C, Hlatky MA, Fortmann SP, Myers RM, Kuhn H, Risch N, Quertermous T (2008) A near null variant of 12/15-LOX encoded by a novel SNP in ALOX15 and the risk of coronary artery disease. Atherosclerosis 198(1):136-44.
  
  
• Chan TF, Poon A, BASU A, Addleman NR, Chen J, Phong A, Byers PH, Klein TE, Kwok PY (2008) Natural variation in four human collagen genes across an ethnically diverse population. Genomics 91(4):307-14.
  
  
• BASU A, Chaudhuri P, Majumder PP. (2005) Identification of polymorphic motifs using probabilistic search algorithms. Genome Research 15(1):67-77
  
  
• BASU A, Mukherjee N, Roy S, Sengupta S, Banerjee S, Chakraborty M, Dey B, Roy M, Roy B, Bhattacharyya NP, Roychoudhury S, Majumder PP (2003) Ethnic India: a genomic view, with special reference to peopling and structure. Genome Research 13(10):2277-90
  
  
• BASU A, Majumder PP. (2003) A comparison of two popular statistical methods for estimating the time to most recent common ancestor (TMRCA) from a sample of DNA sequences. Journal of Genetics 82(1-2):7-12
  
  
• Roychoudhury S, Roy S, BASU A, Banerjee R, Vishwanathan H, Usha Rani M, Sil SK, Mitra M and Majumder PP. (2001) Genomic structures and population histories of linguistically distinct tribal groups of India. Human Genetics 109(3): 339-50

Book Chapters

BASU A, Majumder PP (2021) Peopling and population structure of West and South Asia. Evolution of Human Genome II. Springer 978-84, (Chapter 7)
Editor: Naruya Saitou

Lab members

Analabha Basu