Aritra Bose
I am a Research Staff Member in the Computational Genomics group at IBM T.J. Watson Research Center, Yorktown Heights, NY. I am also a visiting scientist at the Broad Institute of MIT and Harvard. I completed my PhD in Computer Science from Purdue University, West Lafayette, IN under the guidance of Petros Drineas.
I work in the intersection of Genomics, Machine Learning and Algorithms. I'm broadly interested in both the theoretical and practical aspects of population genetics in light of mathematical and statistical foundations.
Prior to this, I completed MS in Computer Science from Rensselaer Polytechnic Institute in Troy, NY. I grew up in Kolkata, the "City of joy" in India. I earned a BTech degree from the Department of Computer Science and Information Technology, West Bengal University of Technology, Kolkata. Apart from this, I am an avid traveler and photographer. When I am not working, you will find me doing one of these things: planning trips, reading books, watching soccer or playing racquet sports.
Research Statement
My research revolves around making sense of complex, high dimensional population genetic datasets with respect to the following directions:
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Inferring population sub-structure and detecting ancient archaic admixture among populations across the world. We have developed novel computational framework to find out how demographic factors influence gene flow within a population. Along with this, I am also interested in anthropological implications of population genetics, testing historical hypotheses in the light of genomics.
Developing scalable computational and statistical tools to tackle the ever-growing size of datasets being generated in the field of genomics and medicine.
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Develop Machine learning methods for neuropsychiatric disorder trait prediction as well as finding the biological underpinnings of psychiatric diseases.
Apart from this, I am also interested in developing mathematical models for understanding the complex evolutionary scenarios such as natural selection, epistatic interactions, demographic factors which govern genetic variation resulting in differences between and within species.
Recent Publications
2022
Agniva Chowdhury, Aritra Bose, Samson Zhou, David Woodruff, Petros Drineas A Fast, Provably Accurate Approximation Algorithm for Sparse Principal Component Analysis Reveals Human Genetic Variation Across the World, RECOMB (2021). (Equal Contribution)
2021
Sanjoy Dey, Aritra Bose, Subrata Saha, Prithwish Chakraborty, Mohamed Ghalwash, Aldo Guzman Saenz, Filipp Ultro, NG Kenney, Jianying Hu, Laxmi Parida, Daby Sow, Filippo Utro, Daniel E. Platt, Laxmi Parida, Impact of Clinical and Genomic Factors on COVID-19 Disease Severity, AMIA (2021). (Equal Contribution)
Aritra Bose, Filippo Utro, Daniel E. Platt, Laxmi Parida, Multiple Loci Selection with Multi-way Epistasis in Coalescence with Recombinations, Algorithms (2021)
Aritra Bose, Daniel E. Platt, Laxmi Parida, Peristera Paschou, Petros Drineas, Integrating linguistics, social structure and geography to model gene flow in India, Molecular Biology and Evolution (2021)
Aritra Bose, Daniel E. Platt, Niina Haiminen, Laxmi Parida, Cumulant-based genotype-phenotype interaction networks in Parkinson's Disease , under review (2021)
2020
Aritra Bose, Myson Burch, Agniva Chowdhury, Peristera Paschou, Petros Drineas CluStrat: a structure informed clustering strategy for population stratification , accepted in RECOMB (2020)
2019
Aritra Bose, Vassilis Kalantzis, Eugenia Kontopoulou, Mai Elkady, Peristera Paschou, Petros Drineas, TeraPCA: a fast and scalable software package to study genetic variation in tera-scale genotypes, Bioinformatics (2019)
2017
Aritra Bose, Daniel E. Platt, Laxmi Parida, Peristera Paschou, Petros Drineas, Dissecting Population Substructure in India via Correlation Optimization of Genetics and Geodemographics, bioRxiv (2017)
George Stamatoyannopoulos, Aritra Bose, Athanassios Teodasiadis, Fotis Tsetsos, Anna Plantiga, Nikoletta Psatha, Nikos Zogas, Evangelia Yannaki, Pierre Zalloua, Kenneth K Kidd, Brian L Browning, John Stamatoyannopoulos, Peristera Paschou, Petros Drineas, Genetics of the Peloponnesean populations and the theory of the extinction of the medieval Peloponnesean Greeks , European Journal of Human Genetics (2017).
Full list of publications on Google Scholar
Research profile on ResearchGate
News
- Our work on "Integrating linguistics, social structure and geography to model gene flow in India " has appeared in Molecular Biology and Evolution . Here is the paper and the code. Check out Purdue news release here and other articles here .
- Received a travel fellowship for RECOMB 2020 (held in Padova, Italy) from International Society for Computational Biology (ISCB).
- Our recent work on "CluStrat: a structure informed clustering strategy for population stratification" , got accepted in
RECOMB 2020 to be held in Padova, Italy in May, 2020.
2019
- Our recent work on "Structure informed clustering for population stratification and genetic risk prediction" , got accepted as a Poster in the American Society of Human Genetics 2019 meeting in Houston, TX.
- Our work on "TeraPCA: A fast and scalable method to study genetic variation in tera-scale genotypes" has appeared in Bionformatics. Here is the paper and the code. Check out this for the press release.
- The work that I've been doing at IBM for the past two summers, "Algorithms to modulate ARG by Selection", has been accepted as a platform presentation in RECOMB-Genetics, 2018. To be presented by Dr. Laxmi Parida at Paris in April, 2018.
- Our abstract on "TeraPCA: A fast and scalable method to study genetic variation in tera-scale genotypes", got accepted as a Poster in the American Society of Human Genetics 2017 > meeting in Orlando, FL.
- Our abstract on "COGG (Correlation Optimization of Genetics and Geodemographics) reveals sociolinguistic stratification in Indian subcontinent", got accepted for a poster in Biology of Genomes 2017, held at Cold Spring Harbor Laboratory, NY.
- Our paper on "Genetics of the Peloponnesean populations and the theory of the extinction of the medieval Peloponnesean Greeks" , got accepted for publication in European Journal of Human Genetics.
- Here [pdf] are the slides that I presented in ASHG 2016, platform presentation in Vancouver, BC, Canada on Oct 20, 2016.
- Our work on COGG(Correlation Optimization of Genetics and Geodemographics), a novel optimization method to model genetic relationships with social factors such as castes, languages, occupation, etc. and maximize their correlation with geography, was selected as a platform presentation (top 8% of all submitted abstracts) at the 2016 Annual Meeting of the American Society of Human Genetics.
2021
2020
2018
2017
2016
Talks and Posters
Dec '20
- Title: Computational Methods in Population Genetics
- Occasion: Invited
- Venue: Regeneron Genetics Center, Tarrytown, NY
Nov '20
- Title: Computational Methods in Population Genetics
- Occasion: Invited
- Venue: Allen Institute of Brain Science, Seattle, WA
Nov '20
- Title: Computational Methods in Population Genetics
- Occasion: Invited
- Venue: Inari Agriculture, Cambridge, MA
Jun '20
- Title: CluStrat: a structure informed clustering strategy for population stratification
- Occasion: 24th International Conference on REsearch in COMputational Molecular Biology (RECOMB)
- Venue: Virtual
Oct '19
- Title: Structure informed clustering for population stratification and genetic risk prediction
- Occasion: American Society of Human Genetics 2019 Meeting
- Venue: Houston, TX, USA
Aug '19
- Title: Computational methods in Population Genetics
- Occasion: Dissertation Defense
- Venue: Purdue University, West Lafayette, IN, USA
Feb '19
- Title: A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots
- Occasion: RandNLA Group Meet
- Venue: Purdue University, West Lafayette, IN, USA
Nov '18
- Title: Computational methods in Population Genetics
- Occasion: Preliminary Exam
- Venue: Purdue University, West Lafayette, IN, USA
Aug '18
- Title: Integrating linguistics, social structure and geography to model gene flow in India
- Occasion: Invited talk
- Venue: Bose Institute, Kolkata, India
Apr '18
- Title: TeraPCA: A fast and scalable method to study genetic variation in tera-scale genotypes
- Occasion: PUNLAG Meeting
- Venue: Purdue University, West Lafayette, IN, USA
Oct '17
- Title: TeraPCA: A fast and scalable method to study genetic variation in tera-scale genotypes
- Occasion: American Society of Human Genetics 2017 Meeting
- Venue: Orlando, FL, USA
Jul '17
- Title: Dissecting Population Substructure in India via Correlation Optimization of Genetics and Geodemographics
- Occasion: IBM Research Intern showcase
- Venue: Yorktown Heights, NY, USA
Jun '17
- Title: Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation
- Occasion: Computational Biology Center Group Meeting, IBM Research
- Venue: Yorktown Heights, NY, USA
May '17
- Title: Integrating linguistics, social structure and geography to model gene flow in India
- Occasion: Biology of Genomes 2017 Meeting
- Venue: Cold Spring Harbor Laboratory, NY, USA
Oct '16
- Title: Dissecting Population Substructure in India via Correlation Optimization of Genetics and Geodemographics
- Occasion: American Society of Human Genetics 2016 Meeting
- Venue: Vancouver, BC, Canada
May '16
- Title: Dissecting Population Substructure in India via Correlation Optimization of Genetics and Geodemographics
- Occasion: Biology of Genomes 2016 Meeting
- Venue: Cold Spring Harbor Laboratory, NY, USA