Research
Current and past research positions across multiple institutions.
Current Positions
Graduate Research Assistant (Dissertation)
Tulane University School of Medicine, New Orleans, LA
PI: Loren Gragert, PhD (Center for Biomedical Informatics & Genomics)
Developed and validated a probabilistic HLA Molecular Typing model to automate manual histocompatibility review in donor-recipient HLA matching. Built dual large-scale imputation models: HaploFreqImpute (high-resolution; EM over ~10M NMDP haplotype frequencies) and AlleleFreqImpute (single-locus baseline comparator), converting intermediate-resolution donor typing into calibrated allele-level posteriors. Engineered a four-step simulated allocation framework (SSO ambiguities via AlleleAmbiguityUtility v2.0; per-allele uncertainty estimation; UNet allocation simulation; benchmarking against ground-truth typing); calibrated on a multi-population OPTN cohort using Brier scores and the Paynter et al. open-source framework. Built the first U.S. individualized HLA matching-opportunity metric (HLA Matchability): a public Django web tool deployed on AWS EC2 (transplanttoolbox.org/matchability), validated against the national SRTR transplant-candidate cohort using a 2.17M-genotype NMDP nine-locus reference panel. Demonstrated that the longstanding matching-vs-equity tradeoff can be resolved in U.S. kidney allocation via the Personalized Immunologic Compatibility Likelihood (PICL) framework: a frequency-weighted HLA-match priority for candidates with NYU OASIM platform shows that allocation can be made more equitable across racial groups while preserving HLA matching gains. Race is not used as a scoring variable. Built HLA-RAG (~3,500 articles) and ILC3-RAG (~2,600 articles) retrieval systems via Model Context Protocol for citation-grounded LLM querying; modernized the Transplant Toolbox platform. Industry partnership with Werfen (Norcross, GA): contributed to AlleleAmbiguityUtility v2.0 updates. Two first-author manuscripts in advisor final review, targeted for the American Journal of Transplantation; co-author on companion NYU OASIM manuscript.
Research Collaborator
Harbor-UCLA Medical Center, Los Angeles, CA
Collaborator: Kristen Nordham, MD (Department of Surgery)
Performed post-review statistical revision for an EAST multicenter trauma trial (J Trauma Acute Care Surg 2025). Methods: generalized linear mixed models with center random intercept, DAG-based covariate selection, counterfactual causal mediation, IPTW, MICE, E-value sensitivity, and nine prespecified sensitivity analyses.
Research Collaborator
NYU Langone Health, New York, NY
Collaborating PI: Michal A. Mankowski, PhD (Department of Surgery, NYU Grossman School of Medicine)
Provided HLA Matchability metrics and the Monte Carlo policy-mechanism foundation for the PICL-based deceased-donor kidney allocation framework. Simulated via SRTR Organ Allocation Simulator (OASIM) using evolutionary graph algorithms; balances medical urgency and population-informed organ access without compromising HLA compatibility.
Research Collaborator
University of Pennsylvania, Philadelphia, PA
Collaborating PI: Professor Malek Kamoun, MD, PhD (Department of Pathology and Laboratory Medicine, Perelman School of Medicine)
Built three production-grade clinical HLA typing ingestion pipelines: a PDF-to-structured-data extractor; an RT-PCR SureTyper XML-to-GL-String parser; and a nine-locus LinkSeq XML-to-GL-String parser. Pipelines bridge simulated and real-world validation of the Probabilistic Offer Filter and are now in production use by the Kamoun group for multi-laboratory deceased-donor typing extraction.
Past Positions
Graduate Research Assistant
Tulane University School of Medicine, New Orleans, LA
PI: Professor Jay Kolls, MD (Center for Translational Research in Infection and Inflammation, CTRII)
Identified and validated LIF-Fc as a candidate host-directed therapeutic against multidrug-resistant Klebsiella pneumoniae ST258 pulmonary infection; computationally delineated the hepatocyte STAT3 / acute-phase response (Saa1/Saa2, complement C3) / pulmonary IL-22 & IL-17A signaling axis driving efficacy across Rag2⁻/⁻Il2rg⁻/⁻ and FK506-pretreated WT C57BL/6 models. Integrated and analyzed high-dimensional multi-omics data (bulk RNA-Seq, single-cell RNA-Seq, ATAC-Seq, and CITE-Seq); applied GSEA and pathway analysis for mechanistic target identification, with differential-expression and signature-based biomarker discovery; characterized T-cell and ILC3 transcriptional, metabolic, and phenotypic programs. Established the CCR7-Cre Icosl^fl/fl transgenic mouse line; characterized lung ILC3 populations via FACS-sorted scRNA-Seq, qPCR, lung histology, and bronchoalveolar lavage (BAL) analysis.
Graduate Rotations (Three Labs)
Tulane University School of Medicine, New Orleans, LA
PI: Hong-Wen Deng Lab; Yi-Ping Li Lab; Jay Kolls Lab
Three first-year graduate rotations across complementary computational and immunology labs: • Hong-Wen Deng Lab: machine learning for biomedical data. • Yi-Ping Li Lab: scRNA-Seq analysis with Seurat and VISION. • Jay Kolls Lab: T-cell metabolism via scRNA-Seq of immunized mice (the rotation that led to my dissertation work in the Kolls and Gragert labs).
Faculty (Lecturer → Senior Lecturer → Assistant Professor); concurrent research appointment
Department of Microbiology, Khwaja Yunus Ali University (KYAU); Khwaja Yunus Ali Medical College Hospital (KYAMCH), Bangladesh
Founding Chair, Department of Microbiology, KYAU (2013–2020). Clinical microbiology research program (2015–2020) — PI: Prof. Dr. Abdullah Akhtar Ahmed, Head of Microbiology, Khwaja Yunus Ali Medical College & Hospital (KYAMCH). Established and led a newly-founded Microbiology department at this private university across a 7.5-year appointment. Concurrent co-investigator on a clinical microbiology research program studying antimicrobial resistance (AMR) patterns and bacteremia surveillance in clinical isolates at KYAMCH. Contributed to data analysis, statistical interpretation, and manuscript preparation across four peer-reviewed publications: - First-author: Hossain MS, Khatun R, Solayman M, Aktar B, Ahmed AA. "Antibiotic Susceptibility Pattern of Clinical Isolates of Escherichia coli at a Tertiary Care Hospital." KYAMC Journal 7(1):681–686 (2017). - Co-author: Ahmed AA, Hossain MS, Aktar B, Juyee NA, Hasan SA. "Prevalence of Methicillin-Resistant Staphylococcus aureus in Khwaja Yunus Ali Medical College Hospital." KYAMC Journal 7(1):673–677 (2017). - Co-author: Ahmed AA, Salam MA, Hossain MS, Aktar MB, Juyee NA, Hasan SA. "Trends in Antibiotic Resistance Patterns of MRSA and MSSA in Khwaja Yunus Ali Medical College Hospital." KYAMC Journal 9(1):6–10 (2018). - Co-author: Abedin MZ, Ahmed AA, Hossain MS, Aktar MB. "Laboratory-Based Diagnosis of Bacteremia among Inpatients and Outpatients with Acute Febrile Illness at Khwaja Yunus Ali Medical College and Hospital in Bangladesh." European Journal of Medical and Health Sciences 2(3):46–51 (2020). Mentored undergraduate research projects; led departmental research direction. Full teaching responsibilities and course list: see Teaching tab.
Research Officer
icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh), Matlab Health Research Centre
PI: Dr. Md. Khalequzzaman (Emeritus Scientist, Enteric and Respiratory Infections, Infectious Diseases Division, icddr,b). Direct supervisor: Md. Mustafizur Rahman, PhD.
Coordinated GCP-regulated Rotarix (oral live human rotavirus) vaccine immunogenicity and effectiveness multicenter study at the Matlab Health Research Centre, part of icddr,b's Rotavirus Vaccine Program supported by Gavi, PATH, U.S. CDC, NIH, USAID, UNICEF, and GSK (the Rotarix manufacturer). Contributed to a parallel Japanese encephalitis vaccine immunogenicity study. Performed norovirus surveillance, virus isolation, immunogenicity data analysis, and clinical reporting. Co-authored a peer-reviewed publication in Journal of Medical Virology.
Graduate Research Student
Virology Laboratory, icddr,b, Bangladesh
Supervisor: Md. Mustafizur Rahman, PhD; Senior Director, Infectious Diseases, icddr,b. Characterized respiratory human adenovirus in Bangladeshi children through viral genome extraction, qPCR, and phylogenetic analysis; deposited 74 sequences in NCBI GenBank (Accession KP268083–KP268156). This work formed the basis of my M.Sc. thesis at the University of Dhaka.