Research Publications

Research

Currently, I am working on leveraging large language models for phenotyping of rare disease patients.

During my PhD, I tackled a variety of phenomic and genomic problems. On the genomics side, I worked on:

Identifying epistatic mechanisms driving complex diseases
Multiomic data integration to study Alzheimer's disease using gene and pathway burden scores
Genome-wide association study and polygenic risk score development of neuroimaging phenotypes to identify genetic predictors of schizophrenia, autism, and major depressive disorder

On the phenomic and ML side, I worked on:

Implementing unsupervised clustering to subphenotype heart failure patient population using EHR and cardiac echo data
Elucidating comorbidity architecture of complex diseases using network medicine
Developing method DETECT to identify probabilistic disease trajectories and early indicators of severe cardiac clinical events

During my bachelors at Northeastern University, I researched the genetic mechanisms underlying limb regeneration in the axolotl model. Additionally, I did 2 co-op stints (2015, 2016) at Editas Medicine developing CRISPR based therapeutics for HSV1.

Research interest keywords: precision medicine, prognostics, EHR statistical genetics, machine learning, network science, time series, predictive modeling, patient-facing tool development

Publications

[17] Singhal P, Li Z, Yang Z, Nandi T, Morse C, Rodriguez Z, Pyeritz R, Sirugo G, Rodriguez A, Drivas T, Madduri R, Verma A. Leveraging Open-Source Large-Language Model-Enabled Identification of Undiagnosed Patients with Rare Genetic Aortopathies. {2025}. Manuscript under review at NPJ Digital Medicine.

[16] Rachit Kumar, Pankhuri Singhal, Chris Carson, Mitchell Conery, Alex Rodriguez, Tarak Nath Nandi, Marylyn D Ritchie, Mathialakan Thavappiragasm, Ravi K Madduri, Benjamin F Voight, Anurag Verma. Rapid Long-Range Linkage Disequilibrium Calculations at Biobank Scale using GPU Acceleration. {2025}. Manuscript under review.

[15] David S M Lee, Kathleen M Cardone, David Y Zhang, Noah L Tsao, Sarah Abramowitz, Pranav Sharma, John S DePaolo, Mitchell Conery, Krishna G Aragam, Kiran Biddinger, Ozan Dilitikas, Lily Hoffman-Andrews, Renae L Judy, Atlas Khan, Iftikhar Kulo, Megan J Puckelwartz, Nosheen Reza, Benjamin A Satterfield, Pankhuri Singhal; et al (2025). Common-variant and rare-variant genetic architecture of heart failure across the allele frequency spectrum. Nature Genetics. 10.1038/s41588-025-02140-2

[14] Tom Pollard, Edward Choi, Pankhuri Singhal, Michael Hughes, Elena Sizikova, Bobak Mortazavi, Irene Chen, Fei Wang, Tasmie Sarker, Matthew McDermott, Marzyeh Ghassemi. Proceedings of the fifth Conference on Health, Inference, and Learning, PMLR 248:1-6, (2024).

[13] Singhal P, Kumar R, Kumar N, Becker M, Hanish A, Xapakhdy K, Verma A. Leveraging GPT models to intuitively structure free-text clinical notes. (2024). Proceedings of American Medical Informatics Summit.

[12] Singhal P, Tan A, Drivas T, Ritchie MD, Beaulieu-Jones B. Opportunities and Challenges for Biomarker Discovery Using Electronic Health Record Data. (2023) 18 July 2023. Trends in Molecular Medicine. https://doi.org/10.1016/j.molmed.2023.06.006

[11] Singhal P, Verma SS, Ritchie MD. (2023) Gene Interactions in Human Disease Studies – Evidence is Mounting. 17 May 2023. Annual Review of Biomedical Data Science. https://www.annualreviews.org/doi/10.1146/annurev-biodatasci-102022-120818

[10] Pankhuri Singhal, Lindsay Guare, Colleen Morse, Anastasia Lucas, Marta Byrska-Bishop, Marie A Guerraty, Dokyoon Kim, Marylyn D Ritchie, Anurag Verma (2023) DETECT: Feature extraction method for disease trajectory modeling. 16 June 2023. Proceedings of American Medical Informatics Association Informatics Summit. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10283148/

[9] Pankhuri Singhal, Yogasudha Veturi, Scott M Dudek, … Marylyn D Ritchie, Shefali S Verma (2023) Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets. 6 Apr 2023. American Journal for Human Genetics. https://doi.org/10.1016/j.ajhg.2023.03.007

[8] Singhal P, Veturi Y, Judy R, Park Y, Vujkovic M, Veatch O, Kember R, Verma SS. (2023) Session Introduction: SALUD: Scalable Applications of cLinical risk Utility and preDiction. Pacific Sym on Biocomputing. https://doi.org/10.1142/9789811270611_0037

[7] Yonghyun Nam, Sang-Hyuk Jung, Jae-Seung Yun, Vivek Sriram, Pankhuri Singhal, Marta Byrska-Bishop, Anurag Verma, Hyunjung Shin, Woong-Yang Park, Hong-Hee Won, Dokyoon Kim (2023) Discovering comorbid diseases using an inter-disease interactivity network based on biobank-scale PheWAS data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac822

[6] Gyujoon Hwang, Junhao Wen, Susan Sotardi, Edward S Brodkin, Ganesh B Chand, Dominic B Dwyer, Guray Erus, Jimit Doshi, Pankhuri Singhal, et al (2023) Assessment of Neuroanatomical Endophenotypes of Autism Spectrum Disorder and Association With Characteristics of Individuals With Schizophrenia and the General Population. JAMA Psychiatry. doi:10.1001/jamapsychiatry.2023.0409

[5] Michael G. Levin, Noah L. Tsao, Pankhuri Singhal, … Benjamin F. Voight & Scott M. Damrauer (2022) Genome-wide association and multi-train analyses characterize the common genetic architecture of heart failure. Nature Communications. https://doi.org/10.1038/s41467-022-34216-6

[4] Ganesh B Chand, Pankhuri Singhal, Dominic B Dwyer, Junhao Wen, … Christos Davatzikos (2022) Schizophrenia imaging signatures and their associations with cognition, psychopathology, and genetics in the general population. American Journal of Psychiatry. https://doi.org/10.1176/appi.ajp.21070686

[3]NNosheen Reza, Yifan Yang, William Bone, Pankhuri Singhal, Anurag Verma, Srinivas Denduluri, Srinath Adusumali, Marylyn D. Ritchie, Thomas P. Cappola (2022) A supervised learning method for classification of electronic health-record based phenotypes. Preprint. https://doi.org/10.1101/2022.10.31.22281772

[2] Matthew Nguyen, Pankhuri Singhal, Judith W Piet, Sandra J Shefelbine, Malcolm Maden, S Randal Voss, James R Monaghan (2017) Retinoic acid receptor regulation of epimorphic and homeostatic regeneration in the axolotl. Development. 144: 601-611. https://doi.org/10.1242/dev.139873

[1] Ari E. Friedland, Reshica Baral, Pankhuri Singhal, Katherine Loveluck, Shen Shen, Minerva Sanchez, Eugenio Marco, Gregory M. Gotta, Morgan L. Maeder, Edward M. Kennedy, Anand V.R. Kornepati, Alexander Sousa, McKensie A. Collins, Hari Jayaram, Bryan R. Cullen & David Bumcrot (2015) Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications. Genome Biology 16: 257. https://doi.org/10.1186/s13059-015-0817-8

Pankhuri Singhal

Postdoctoral Fellow University of Pennsylvania Dept of Medicine

Research

Publications

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