Postdoctoral Researcher Computational Scientist
Resume:
CURRICULUM VITAE
Abhishek Choudhary
* ********** **, ******, ** 03060
****.**********@*****.*** • www.linkedin.com/in/abhiachoudhary EDUCATION
Rensselaer Polytechnic Institute (RPI), Troy, New York Doctor of Philosophy in Mathematics, July 2019
Indian Institute of Technology (IIT) Delhi, New Delhi, India Integrated M. Tech. in Mathematics & Computing, July 2013 RESEARCH EXPERIENCE
Medical & Population Genetics, Broad Institute of MIT and Harvard, Massachusetts Computational Scientist, December, 2022 – January, 2025
- Led statistical and computational analyses for an ambitious Developmental Genotype-Tissue Expression (dGTEx) project. Focus of the work was to map and study gene expression and regulation across multiple cells and tissues during the pediatric period towards understanding normal development and develop insights into disease processes that have origins in childhood development.
- Implemented a new STAR (Spliced Transcripts Alignment to a Reference) aligner for Bulk RNA- seq data that allows mapping reads to a diploid genome. Thoroughly established both the correctness and the benefits of the new aligner by benchmarking the new expression counts against their original values, and by validating the new and improved alignment of reads across novel splice junctions, that had created artifacts in the old haploid alignment due to the existence of rare personal splice site variants.
Division of Statistics, Amgen pharmaceuticals (deCODE Genetics), Iceland Postdoctoral researcher, October, 2020 – November, 2022
- Statistically analyzed the proteomics data at multiple timepoints in the global clinical trial of a lipid-lowering drug to demonstrate its efficacy and safety. Constructed the genetic framework using sequence variants and their effects on plasma protein levels to substantiate PCSK9- inhibitory action of the drug in patients with elevated cardiovascular risk.
- Built deep learning models for phenotypes predictions using DXA imaging data from UK biobank study. Conceived, implemented, and diagnosed in TensorFlow neural network architectures to predict binary as well as continuous phenotypes, and successfully applied to predict grip strengths using whole body scans and hip events using femur scans of patients. Department of Global and Community Health, HSDM, Harvard University, Massachusetts Postdoctoral Researcher, August, 2019 – August, 2020
- Analyzed the effect of healthcare interventions towards preventing HPV associated cancers in specific subpopulations.
- Using Markov cohort models and Monte Carlo simulations calculated the cost-effectiveness of an expanded vaccination program.
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- Designed the study and performed statistical analyses on electronic health records of patients to identify the relationship between periodontal disease and common birth related complications. Department of Mathematical Sciences, Rensselaer Polytechnic Institute, New York PhD Candidate, August, 2014 – July, 2019
Thesis: Stochastic Modeling of Intracellular Transport
- Developed the mathematical framework of transport processes inside living cells using stochastic differential equations for molecular motor and cargo.
- Analytically obtained effective transport properties on a specified microtubule structure, namely ordered and disordered polarized networks commonly found in biological systems. Epic Systems, Wisconsin
Software Developer, October, 2013 – May, 2014
- Develop a novel and highly customizable report printing interface with additional features for physicians to use in Epic’s web-based hyperspace framework. Using web technology and C#, .NET framework, created the new design of printing interface for use towards various tasks in inpatient treatment of patient
- Classified report groups based on specialization and made it convenient for the user to select the appropriate options and make changes to prescriptions. Department of Mathematics, Indian Institute of Technology, India Master’s Candidate, August, 2012 – July 2013
Thesis: The MacWilliams Identity and Cluster-Correcting Codes
- Studied different weight enumerators and respective MacWilliams identities for linear and non- linear codes. Analyzed and implemented construction models for two-dimensional codes, which could correct straight clusters of any given length and rectangular clusters containing up to 3 erroneous elements.
Institut National de Recherche en Informatique et Automatique (INRIA), France Summer Visiting Researcher, June-August 2012
- Studied hybrid explanation algorithm Conseil for missing data as part of system Nautilus. Implemented the architecture for Data Flow in a general non-monotonous SQL Query and designed Data Provenance Model in Java along with creation of a dynamic user interface. Department of Mathematics, Indian Institute of Technology, India Research Assistant, January-June 2012
- Studied Decision theory in economic environment involving multiple criteria and stakeholders' choices. Implemented the outranking approaches ELECTRE III and PROMETHEE and built the platform for users to rank and analyze the alternatives with custom preferences. TEACHING EXPERIENCE
Department of Mathematical Sciences, Rensselaer Polytechnic Institute, New York Teaching Assistant
Weekly recitations, office hours, grading assignments and tests, proctoring exams
• Computational Optimization, January-May 2019
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• Ordinary Differential Equations and Dynamical Systems, August-December 2016
• Foundations of Applied Mathematics, August-December, 2016
• Numerical Computing, May-July 2016
• Introduction to Differential Equations, January-May 2016
• Probability Theory and Applications, August-December 2015
• Introduction to Differential Equations, May-July 2015
• Introduction to Differential Equations, January-May 2015
• Multivariable Calculus & Matrix Algebra, August-December 2014 Department of Mathematics, Indian Institute of Technology, India Teaching and Laboratory Assistant
Content organization, leading discussion sessions, grading assignments and quizzes, proctoring
• Scientific Software Laboratory (Masters’), January-May, 2013 SKILLS
Technical Skills
• Programming Languages: R, Python, MATLAB, Java, C++, C#, .NET, HTML, SQL, PHP, SAS, Latex, JavaScript, Stata
• Databases: MySQL, Microsoft SQL Server Management Studio, IBM DB2, Oracle
• Software Packages/OS: Windows, Unix/Linux, Mac OS, Microsoft office (Office, Excel, Access etc.), RStudio, Jupyter lab, Pycharm, Eclipse, Dreamweaver, Visual Studio, TreeAge
• Computational tools: numpy, scikit-learn, pandas, tensorflow, keras, matplotlib, seaborn, sklearn, opencv, tidyverse, dplyr, ggplot2, plotly, scanpy, anndata Data Science/Quantitative Skills
• Mathematics (general): Analytical research, Mathematical modeling, Probability, Stochastic processes, Numerical computation, Dynamical systems, Monte Carlo simulations
• Statistics: Data analysis, Diagnostic and predictive analysis, Association, Correlation metrics, Hypothesis Testing, Multivariate analysis, Principal Component Analysis (PCA), Generative models, Nonparametric tests, Bootstrap, Time Series (ARIMA) analysis, Bayesian statistics, Probabilistic graphical networks, Gaussian mixture models, MCMC
• Machine Learning: Supervised, Unsupervised learning, Linear Regression, Generalized Linear Model, Hierarchical Logistic Regression, Nonlinear models, Multi-class Classification, Clustering, Expectation-Minimization, Support Vector Machine, CART, Random Forest, Bagging and boosting, Elastic Net, Polynomial and radial basis function (RBF) kernel, Regularization, Cross validation, Hidden Markov models (HMM)
• Deep Learning: Feedforward neural networks, Convolutional neural networks (CNN), ResNet, Transfer learning, Data-centric approaches
• Biostatistics/bioinformatics: Healthcare data analytics, Cost effectiveness analysis, Disease modeling, Clinical trials design and assessment, Mendelian randomization, Statistical genetics, Genome wide association study (GWAS), Proteomics and multi-omics, Pharmacogenomics, Bulk- RNA-seq pipelines, Single cell and single nuclei analysis Page 4 of 5
HONORS AND AWARDS
• Bill and Nancy Siegmann Applied Mathematical Modeling Prize, Department of Mathematical Sciences, Rensselaer Polytechnic Institute
• SIAM Travel award for participation in International Congress on Industrial and Applied Mathematics, Conference on Life Sciences, and the Conference on Applications of Dynamical Systems, Society for Industrial and Applied Mathematics
• EGIDE Scholarship for pursuit of summer project in France, French Ministry of Foreign Affairs
• MHRD Scholarship for obtaining All India Rank 17 in GATE, Government of India
• CSIR Program on Youth for Leadership in Science, Central Electronics Engineering Research Institute (CEERI), Pilani, India
• Mamraj Agrawal National Award for academic excellence, Governor of State, Rajasthan, India PUBLICATIONS
1. The dGTEx Consortium (2025). The human and non-human primate developmental GTEx projects. Nature. 2025 Jan 16;637(8046):557-64.
2. Helgason, H., Eiriksdottir, T., Ulfarsson, M. O., Choudhary, A., Lund, S. H., Ivarsdottir, E. V., ... & Stefansson, K. (2023). Evaluation of large-scale proteomics for prediction of cardiovascular events. JAMA, 330(8), 725-735.
3. Choi, S. E., Choudhary, A., Huang, J., Sonis, S., Giuliano, A. R., & Villa, A. Increasing HPV Vaccination Coverage on Preventing Oropharyngeal Cancer: A Cost-Effectiveness Analysis. Tumour Virus Research, 200234 (2022).
4. Simon, L., Choudhary, A., Ticku, S., Barrow, J., & Tobey, M. Dental care utilization in Massachusetts before and after initiation of medication for opioid use disorder: A cross sectional study of a state all payer claims database. Journal of Public Health Dentistry (2021). 5. Choi, S. E., Choudhary, A., Ahern, J. M., Palmer, N., & Barrow, J. R. Association between maternal periodontal disease and adverse pregnancy outcomes: an analysis of claims data. Family Practice, 38(6), 718-723 (2021).
6. Choi, S. E., Choudhary, A., Sonis, S., & Villa, A. Benefits of the Involvement of Dentists in Managing Oral Complications Among Patients With Oral Cavity and Oropharyngeal Cancer: An Analysis of Claims Data. JCO Oncology Practice, OP-20 (2021). 7. Dipple S., Choudhary A., Flamino J., Szymanski B.K., Korniss G. Using Correlated Stochastic Differential Equations to Forecast Social Media Activity and Cryptocurrency Exchange Rates. Applied Network Science 5, 17 (2020).
PRESENTATIONS
• Invited talk at The NIH Common Fund Data Ecosystem (CFDE) All-Hands Meeting, March 2024
• Poster presentation at Chan Zuckerberg Initiative (CZI) Single Cell Biology Annual Meeting, San Diego, California, November 2023
• Poster presentation at The NIH Common Fund Data Ecosystem (CFDE) All-Hands Meeting, April 2023
• Invited talk at Annual Meeting and Conference of the Society for Mathematical Biology (SMB), Montréal, Canada, July 2019
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• Contributed talk at 9th International Congress on Industrial and Applied Mathematics (ICIAM), Valencia, Spain, July 2019
• Talk at Biology and Medicine Through Mathematics Conference (BAMM), Richmond, Virginia, May 2019
• Poster presentation at Conference on Multiscale Modeling in Biology (MMB), Minneapolis, Minnesota, May 2019
• Speaker at Applied Math Days (AMD), Troy, New York, April 2019
• Student chapter presentation at SIAM Conference on Computational Science and Engineering
(CSE), Spokane, Washington, February 2019
• Invited talk at SIAM Conference on Life Sciences (LS), Minneapolis, Minnesota, August 2018
• Talk at Biology and Medicine Through Mathematics Conference (BAMM), Richmond, Virginia, May 2018
• Speaker at 3rd Graduate Research Symposium (GRS), Troy, New York, March 2018
• Seminar talk at RTG Dynamical Systems forum, Troy, New York, January 2018
• Poster presentation at Frontiers in Applied and Computational Mathematics (FACM), Newark, New Jersey, June 2017
• Poster presentation at SIAM Conference on Dynamical Systems (DS), Snowbird, Utah, May 2017 PROFESSIONAL ACTIVITIES
• Broad Institute of MIT and Harvard Retreat Organization Committee, poster subcommittee co- chair, 2024
• Mathematical Problems in Industry Workshop (MPI), Claremont Center for Mathematical Sciences, California, June, 2018
• Data Analytics Research Laboratory (DARL), Rensselaer Polytechnic Institute, August-December, 2017
• Graduate Student Mathematics Modeling Camp (GSMMC), Rensselaer Polytechnic Institute, June, 2017
• Joint NIMBioS-MBI-CAMBAM Summer Graduate Program Connecting Models with Biological Data, University of Tennessee, Knoxville, Tennessee, June, 2017
• Symposium on Probabilistic Modeling in Engineering and Science, Lehigh University, Bethlehem, Pennsylvania, October 2016
• SIAM Chapter Graduate Student Representative, Rensselaer Polytechnic Institute, 2014-2015 PROFESSIONAL ASSOCIATIONS
• American Mathematical Society (AMS)
• Biophysical Society (BPS)
• INFORMS
• Society for Industrial and Applied Mathematics (SIAM)
• Society for Mathematical Biology (SMB)
• Pharmacogenomics Global Research Network (PGRN)
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