Akshaya Annapragada

Research Description

My research interests include cancer genomics, public health modeling, and artificial intelligence approaches to precision medicine. I build machine learning models that mine clinical data – from whole genome data, to free text, to images – and achieve tasks such as the early detection of cancer, prediction of respiratory failure in COVID-19 patients, and identification of possible child abuse.

I am currently an MD/PhD student at Johns Hopkins. My research in the Biomedical Engineering PhD Program focuses on genomic approaches to early detection of cancer. As an undergraduate at Harvard, I was a research assistant at the School of Public Health and the School of Engineering and Applied Sciences.

Peer Reviewed Publications

*Indicates these authors contributed equally

J.E. Medina*, A.V. Annapragada*, P. Lof, S. Short, A. Bartolomucci, D. Mathios, S. Koul, N. Niknafs, M. Noë, Z. H. Foda, D. C. Bruhm, C. Hruban, N.A. Vulpescu, E. Jung, R. Dua, J. Canzoniero, S. Cristiano, V. Adleff, H. Symecko, D. van de Broek, L. Sokoll, S. B. Baylin, M. F. Press, D. Slamon, G. Konecny, C. Therkildsen, B. Carvalho, G.A. Meijer, C.L. Andersen, S. Domchek, R. Drapkin, R. B. Scharpf, J. Phallen, C. Lok, V. E. Velculescu. Early detection of ovarian cancer using cell-free DNA fragmentomes and protein biomarkers. Cancer Discovery, 15(1), 105–118 (2024). https://doi.org/10.1158/2159-8290.CD-24-0393 (*These authors contributed equally).
M. Noe, D. Mathios, A.V. Annapragada, S. Koul, Z.H. Foda, J.E. Medina, S. Cristiano, C. Cherry, D.C. Bruhm, N. Niknafs, V. Adleff, L. Ferreira, H. Easwaran, S. Baylin, J. Phallen, R.B. Scharpf, V.E. Velculescu. DNA methylation and gene expression as determinants of genome-wide cell-free DNA fragmentation. Nature Communications., 15, 6690 (2024). https://doi.org/10.1038/s41467-024-50850-8
A.V. Annapragada, N. Niknafs, J.R. White, D.C. Bruhm, C. Cherry, J.E. Medina, V. Adleff, C. Hruban, D. Mathios, Z.H. Foda, J. Phallen, R.B. Scharpf, V.E. Velculescu, Genome-wide repeat landscapes in cancer and cell-free DNA. Sci Transl Med., 16,eadj9283 (2024). DOI:10.1126/scitranslmed.adj9283
D. C. Bruhm, D. Mathios, Z. H. Foda, A. V. Annapragada, J. E. Medina, V. Adleff, E. J. Chiao, L. Ferreira, S. Cristiano, J. R. White, S. A. Mazzilli, E. Billatos, A. Spira, A. H. Zaidi, J. Mueller, A. K. Kim, V. Anagnostou, J. Phallen, R. B. Scharpf, V. E. Velculescu, Single-molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer. Nat. Genet., 1–10 (2023). https://doi.org/10.1038/s41588-023-01446-3
A. J. Ferrari, P. Rawat, H. S. Rendulich, A. V. Annapragada, Y. Kinose, X. Zhang, K. Devins, A. Budina, R. B. Scharpf, M. A. Mitchell, J. L. Tanyi, M. A. Morgan, L. E. Schwartz, T. R. Soong, V. E. Velculescu, R. Drapkin, H2Bub1 loss is an early contributor to clear cell ovarian cancer progression. JCI insight. 8, e164995 (2022). https://doi.org/10.1172/jci.insight.164995
Z. H. Foda*, A. V. Annapragada*, K. Boyapati, D. C. Bruhm, N. A. Vulpescu, J. E. Medina, D. Mathios, S. Cristiano, N. Niknafs, H. T. Luu, M. G. Goggins, R. A. Anders, J. Sun, S. H. Meta, D. L. Thomas, G. D. Kirk, V. Adleff, J. Phallen, R. B. Scharpf, A. K. Kim, V. E. Velculescu, Detecting Liver Cancer Using Cell-Free DNA Fragmentomes. Cancer Discov. 13, 616–631 (2022). https://doi.org/10.1158/2159-8290.cd-22-0659 (* these authors contributed equally)
A. V. Annapragada, P. Meshram, S. G. Jenkins, A. Jain, K. K. Middleton, S. C. Thakkar, A. S. Levin, U. Srikumaran, Age and Racial Disparities in Telemedicine Utilization in an Academic Orthopedic Surgery Department. Telemed. e-Heal. 28, 970–975 (2022). https://doi.org/10.1089/tmj.2021.0330
A. V. Annapragada, J. L. Greenstein, S. N. Bose, B. D. Winters, S. V. Sarma, R. L. Winslow, SWIFT: A deep learning approach to prediction of hypoxemic events in critically-Ill patients using SpO2 waveform prediction. Plos Comput Biol. 17, e1009712 (2021). https://doi.org/10.1371/journal.pcbi.1009712
D. Mathios, J. S. Johansen, S. Cristiano, J. E. Medina, J. Phallen, K. R. Larsen, D. C. Bruhm, N. Niknafs, L. Ferreira, V. Adleff, J. Y. Chiao, A. Leal, M. Noe, J. R. White, A. S. Arun, C. Hruban, A. V. Annapragada, S. Ø. Jensen, M.-B. W. Ørntoft, A. H. Madsen, B. Carvalho, M. de Wit, J. Carey, N. C. Dracopoli, T. Maddala, K. C. Fang, A.-R. Hartman, P. M. Forde, V. Anagnostou, J. R. Brahmer, R. J. A. Fijneman, H. J. Nielsen, G. A. Meijer, C. L. Andersen, A. Mellemgaard, S. E. Bojesen, R. B. Scharpf, V. E. Velculescu, Detection and characterization of lung cancer using cell-free DNA fragmentomes. Nat. Commun. 12, 5060 (2021). https://doi.org/10.1038/s41467-021-24994-w
A. V. Annapragada, S. G. Jenkins, A. L. Chang, A. Jain, D. Srikumaran, U. Srikumaran, Factors Driving Rapid Adoption of Telemedicine in an Academic Orthopedic Surgery Department. Telemed. e-Heal. 28, 415–421 (2021). https://doi.org/10.1089/tmj.2020.0539
A. V. Annapragada, C. E. Brook, M. S. Luskin, R. P. Rahariniaina, M. Helin, O. Razafinarivo, R. A. Ralaiarison, H. J. Randriamady, L. E. Olson, S. M. Goodman, C. D. Golden, Evaluation of tenrec population viability and potential sustainable management under hunting pressure in northeastern Madagascar. Anim. Conserv. 24, 1059–1070 (2021). https://doi.org/10.1111/acv.12714
A. V. Annapragada, M. M. Donaruma-Kwoh, A. V. Annapragada, Z. A. Starosolski, A natural language processing and deep learning approach to identify child abuse from pediatric electronic medical records. Plos One. 16, e0247404 (2021). https://doi.org/10.1371/journal.pone.0247404
B. L. Rice, A. V. Annapragada, R. E. Baker, M. Bruijning, W. Dotse-Gborgbortsi, K. Mensah, I. F. Miller, N. V. Motaze, A. Raherinandrasana, M. Rajeev, J. Rakotonirina, T. Ramiadantsoa, F. Rasambainarivo, W. Yu, B. T. Grenfell, A. J. Tatem, C. J. E. Metcalf, Variation in SARS-CoV-2 outbreaks across sub-Saharan Africa. Nat. Med. 27, 447–453 (2021). https://doi.org/10.1038/s41591-021-01234-8
C. D. Golden, B. L. Rice, H. J. Randriamady, A. M. Vonona, J. F. Randrianasolo, A. N. Tafangy, M. Y. Andrianantenaina, N. J. Arisco, G. N. Emile, F. Lainandrasana, R. F. F. Mahonjolaza, H. P. Raelson, V. R. Rakotoarilalao, A. A. N. A. Rakotomalala, A. D. Rasamison, R. Mahery, M. L. Tantely, R. Girod, A. V. Annapragada, A. Wesolowski, A. Winter, D. L. Hartl, J. Hazen, C. J. E. Metcalf, Study Protocol: A Cross-Sectional Examination of Socio-Demographic and Ecological Determinants of Nutrition and Disease Across Madagascar. Front. Public Heal. 8, 500 (2020). https://doi.org/10.3389/fpubh.2020.00500
A. Sarode, A. V. Annapragada, J. Guo, S. Mitragotri, Layered self-assemblies for controlled drug delivery: A translational overview. Biomaterials. 242, 119929 (2020). https://doi.org/10.1016/j.biomaterials.2020.119929
A. V. Annapragada, C. Borgerson, S. Iams, M. A. Ravelomanantsoa, G. C. Crawford, M. Helin, E. J. G. Anjaranirina, H. J. Randriamady, C. D. Golden, Modeling the Impact of Newcastle Disease Virus Vaccinations on Chicken Production Systems in Northeastern Madagascar. Front. Vet. Sci. 6, 305 (2019). https://doi.org/10.3389/fvets.2019.00305
Q. Mu, A. V. Annapragada, M. Srivastava, X. Li, J. Wu, V. Thiviyanathan, H. Wang, A. Williams, D. Gorenstein, A. Annapragada, N. Vigneswaran, Conjugate-SELEX: A High-throughput Screening of Thioaptamer-liposomal Nanoparticle Conjugates for Targeted Intracellular Delivery of Anticancer Drugs. Mol. Ther. - Nucleic Acids. 5, e382 (2016). https://doi.org/10.1038/mtna.2016.81
R. Bhavane, C. Badea, K. B. Ghaghada, D. Clark, D. Vela, A. Moturu, A. V. Annapragada, G. A. Johnson, J. T. Willerson, A. Annapragada, Dual-Energy Computed Tomography Imaging of Atherosclerotic Plaques in a Mouse Model Using a Liposomal-Iodine Nanoparticle Contrast Agent. Circ.: Cardiovasc. Imaging. 6, 285–294 (2013). https://doi.org/10.1161/circimaging.112.000119

Abstracts

*Indicates these authors contributed equally

A.V. Annapragada, Z.H. Foda, N. Niknafs, S. Short, D. Mathios, S. Koul, K. Boyapati, A. Bartolomucci, J.E. Medina, N.A. Vulpescu, C. Cherry, D.C. Bruhm, V. Adleff, A. Kim, A. Sorop, R. Iacob, S. Iacob, L. Gheorghe, S. Dima, K.A. McGlynn, M. Ramirez-Zea, J. Groopman, J. Phallen, R.B. Scharpf, V.E. Velculescu. Cell-free DNA fragmentomes enable early identification of liver cirrhosis to facilitate cancer surveillance [Oral Presentation. AACR 2025. April 25-30. Chicago, IL].
S. Short, S. Koul, A.V. Annapragada, D. Mathios, J.E. Medina, Z.H. Foda, C. Hruban, J.Y. Chiao, V. Adleff, R.B. Scharpf, V.E. Velculescu, J. Phallen. Evaluation of mono- and di-nucleosomal cell-free DNA in fragmentome analyses. [Abstract. AACR 2025. April 25-30. Chicago, IL].
C. Hruban, D.C. Bruhm, I. Chen, S. Koul, A. V. Annapragada, N. Vulpescu, S. Short, S. Thiele, K. Boyapati, A. Leal, S. Cristiano, V. Adleff, J. Johansen, R.B. Scharpf, Z.H. Foda, J. Phallen, V.E. Velculescu. Genome-wide analyses of cell-free DNA for therapeutic monitoring of patients with pancreatic cancer. [Abstract. AACR Special Conference in Cancer Research: Liquid Biopsy. Nov 13-16, 2024. San Diego, CA].
Z. H. Foda, D.C. Bruhm, A.V. Annapragada, S. Koul, S. Short, K. Boyapati, A. Bartolomucci, V. Adleff, N. Vulpescu, H. Orjuela, A. Sorop, R. Iacob, S. Iacob, L. Gheorghe, S. Dima, K.A. McGlynn, M. Ramirez-Zea, J. Phallen, J. Groopman, R.B. Scharpf, V.E. Velculescu. Early detection of liver cancer from diverse populations using cfDNA fragmentome and protein biomarkers. [Abstract. AACR Special Conference in Cancer Research: Liquid Biopsy. Nov 13-16, 2024. San Diego, CA].
A.V. Annapragada, N. Niknafs, J.R. White, D.C. Bruhm, C. Cherry, J.E. Medina, V. Adleff, C. Hruban, D. Mathios, Z.H. Foda, J. Phallen, R.B. Scharpf, V.E. Velculescu. Genome-Wide Repeat Element Landscapes Enhance Non-Invasive Detection and Characterization of Cancer [Oral Presentation. BMES 2024. Oct 23-26 2024. Baltimore, MD].
A.V. Annapragada, J.E. Medina, P. Lof, S. Short, A. Bartolomucci, K. Boyapati, A. Li, N. Niknafs, D. Roche, S. Patterson, D. Kaplin, E. Jung, H. Symecko, V. Adleff, C. Jackson, J. Weingart, K. Redmond, S. Domchek, R. Drapkin, L. Kleingberg, C. Lok, J. Phallen, D. Mathios, R.B. Scharpf, V.E. Velculescu. Cell-free DNA Fragmentation as a Non-Invasive Biomarker Across Different Oncology Settings [Oral Presentation. BMES 2024. Oct 23-26 2024. Baltimore, MD].
A.V. Annapragada, S. Short, A. Bartolomucci, K. Boyapati, A. Li, D. Roche, S. Patterson, D.M. Bruno, D. Kaplin, C. Jackson, J. Weingart, K. Redmond, V.E. Velculescu, R.B. Scharpf, J. Phallen, D. Mathios, L. Kleinberg. Genome-wide Cell-free DNA Fragmentation Analyses for Early, Non-invasive Detection of Treatment Response to Standard of Care Adjuvant Radiation Treatment in High-grade Gliomas. [Abstract. ASTRO 2024. Sep 29 – Oct 2 2024. Washington DC].
A.V. Annapragada, N. Niknafs, J.R. White, D.C. Bruhm, C. Cherry, J.E. Medina, V. Adleff, C. Hruban, D. Mathios, Z.H. Foda, J. Phallen, R.B. Scharpf, V.E. Velculescu. Genome-wide repeat landscapes in cancer and cell-free DNA. [Abstract. AACR 2024. April 5-10 2024. San Diego, CA].
J.E. Medina*, A.V. Annapragada*, P. Lof, D. Mathios, Z. H. Foda, M. Noë, S. Short, A. Bartolomucci, D. C. Bruhm, E. Jung, J. Canzoniero, N. Niknafs, S. Cristiano, V. Adleff, H. Symecko, D. van de Broek, S. B. Baylin, M. F. Press, D. Slamon, G. Konecny, S. Domchek, R. Drapkin, J. Phallen, R. B. Scharpf, C. Lok, V. E. Velculescu. Early detection of ovarian cancer using cell-free DNA fragmentomes and protein biomarkers. [Abstract. AACR 2024. April 5-10 2024. San Diego, CA]. (*These authors contributed equally).
M. Noe, A.V. Annapragada, Z.H. Foda, J.E. Medina, D. M. Mathios, S. Cristiano, C. Cherry, D.C. Bruhm, N. Niknafs, V. Adleff, L. Ferreira, H. Easwaran, S. Baylin, J. Phallen, R.B. Scharpf, V.E. Velculescu. DNA methylation and gene expression as determinants of genome-wide cell-free DNA fragmentation. [Abstract. AACR 2024. April 5-10 2024. San Diego, CA].
S. Short, A.V. Annapragada, J.E. Medina, Z.H. Foda, D. Mathios, J.Y. Chiao, K. Boyapati, A. Bartolomucci, K. Boyapati, V. Adleff, R.B. Scharpf, V.E. Velculescu, J. Phallen. Variation of cfDNA concentrations in liquid biopsies. [Abstract. AACR 2024. April 5-10 2024. San Diego, CA].
B.V. Landon, K. Marrone, M.J. Topper, A.V. Annapragada, H. Tsai, A. Balan, N. Niknafs, C. Cherry, J.R. White, G. Pereira, V. Adleff, C. Hu, J. Riemer, M. Fitzpatrick, P. Forde, C. Hann, R. Kelly, D. Ettinger, B. Levy, J. Nieva, J. Herman, V.E. Velculescu, S. Baylin, J. Brahmer, V. Anagnostou. Comprehensive genomic and transcriptomic analyses capture the effects of epigenetic therapy priming on immune checkpoint blockade response in non-small cell lung cancer. [Abstract. AACR 2024. April 5-10 2024. San Diego, CA].
C. Hruban, I. Chen, D.C. Bruhm, S. Koul, J. Yao, K. Boyapati, N. Vulpescu, A.V. Annapragada, L. Ferreira, S. Cristiano, Z.H. Foda, V. Adleff, J. Johansen, J. Phallen, R.B. Scharpf, V.E. Velculescu. Liquid Biopsy Approaches for Monitoring Metastatic Pancreatic Cancer in Immunotherapy Treated Patients. [Abstract. AACR 2024. April 5-10 2024. San Diego, CA].
A. V. Annapragada, J. E. Medina, Z. H. Foda, P. Lof, D. Mathios, S. Short, A. Bartolomucci, D. C. Bruhm, N. A. Vulpescu, E. Jung, V. Adleff, H. Symecko, H.T. Luu, D. van de Broek, S. B. Baylin, M. F. Press, D. Slamon, G. Konecny, S. Domchek, R. Drapkin, A. K. Kim, J. Phallen, R. B. Scharpf, C. Lok, V. E. Velculescu, Early Detection of Human Cancers Using a Cost-Effective, Non-Invasive Assay of the cfDNA Fragmentome. [Oral Presentation. BMES 2023. October 11-15 2023. Seattle, WA.
A. V. Annapragada*, J. E. Medina*, P. Lof, D. Mathios, Z. H. Foda, M. Noë, S. Short, A. Bartolomucci, D. C. Bruhm, E. Jung, J. Canzoniero, N. Niknafs, S. Cristiano, V. Adleff, H. Symecko, D. van de Broek, S. B. Baylin, M. F. Press, D. Slamon, G. Konecny, S. Domchek, R. Drapkin, J. Phallen, R. B. Scharpf, C. Lok, V. E. Velculescu, Abstract 773: Early detection of ovarian cancer using cell-free DNA fragmentomes. Cancer Res. 83, 773–773 (2023). [Abstract. AACR 2023. April 14-19 2023. Orlando, FL.] (* these authors contributed equally)
Z. Foda*, A.V. Annapragada*, K. Boyapati, D.C. Bruhm, N.A. Vulpescu, J.E. Medina, D. Mathios, S. Cristiano, N. Niknafs, H. Luu, M.G. Goggins, R.A. Anders, R.B. Scharpf, V.E. Velculescu, A. Kim. Cell-free DNA Fragmentomes for Detection of Liver Cancer. [Abstract. AASLD 2022 Meeting. November 4-8 2022. Washington, D.C.] (* these authors contributed equally)
Z. Starosolski, A.V. Annapragada, M. Donaruma-Kwoh, A. Annapragada. Improved prediction of child abuse and neglect based on Electronic Health Records and dedicated pediatric word embeddings. [Abstract. 2022 Annual Meeting of the Society for Imaging Informatics in Medicine. June 9-11 2022.]
A. V. Annapragada, D. Mathios, S. Cristiano, J. E. Medina, V. Adleff, N. Niknafs, J. Carey, N. Dracopoli, P. Bach, J. Phallen, V. E. Velculescu, R. B. Scharpf, Abstract 5159: Towards population-scale screening of human cancer using genome-wide fragmentation profiles of cell-free DNA. Cancer Res. 82, 5159–5159 (2022). [Abstract. AACR Annual 2022. April 18-13, 2022. New Orleans, LA.]
A.V. Annapragada, M. Donaruma-Kwoh, Z. Starosolski, A. Annapragada. Identification of Child Abuse Cases based on Electronic Health Records Containing Radiology Reports Using Convolutional Neural Networks. [Abstract. Society of Pediatric Radiology 2020 Conference. May 9-15, 2020. Miami, FL.]
A.V. Annapragada, B.L. Rice, H.J. Randriamady, C.D. Golden. Machine Learning Approaches to Better Understanding Drivers of P. falciparum Malaria and Anemia Co-incidence in Southwestern Madagascar. [Abstract. ASTMH 68th Annual Meeting. November 20-24, 2019. National Harbor, MD.]
Q. Mu, A. V. Annapragada, M. Srivastava, V. Thiviyanathan, X. Li, D. Gorenstein, A. Annapragada, N. Vigneswaran, Abstract 3913: Conjugate-SELEX, a novel screening method, identifies aptamers that deliver payload to the cytosol of target cells. Cancer Res. 76, 3913–3913 (2016). [Abstract. AACR 2016. April 16 - 20, 2016. New Orleans, LA.]

Other Writing

You can find my writing in the Johns Hopkins Biomedical Odyssey Blog and the Harvard Political Review.

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