Publications

Please see my Google Scholar, PubMed, and ORCID pages for more publications, including my most recent work.

Highlighted Publications

2026

Tripathi A, Gupta A, Ganglberger W, Waters S, Sun H, Nasiri S, Mitra A, Stone KL, Mignot E, Hwang D, Reyna MA, Trotti LM, Clifford GD, Maski K, Katwa U, Thomas RJ, Westover MB.Pediatric SleepNet: a deep learning network for reliable pediatric sleep staging across developmental stages. Sleep. 2026 Mar 10: zsag064. PMID: 41804802

Koscova Z, Li Q, Robichaux C, Moura Junior V, Ghanta M, Gupta A, Rosand J, Aguirre AD, Reinertsen E, Song S, Hong S, Albert DE, Xue J, Parekh A, Sameni R, Reyna MA, Westover MB, Clifford GD. The Harvard-Emory ECG database. Sci Data. 2026 Feb 25;13:516. PMID: 41741499

2025

Tripathi A, Nasiri S, Ganglberger W, Nassi T, Meulenbrugge EJ, Sun H, Stone KL, Mignot E, Hwang D, Trotti LM, Reyna MA, Clifford GD, Katwa U, Thomas RJ, Westover MB. Automated analysis of the American Academy of Sleep Medicine inter-scorer reliability gold-standard polysomnogram dataset. J Clin Sleep Med. 2025 Nov 1;21(11):1821-1829.
Reyna MA, Koscova Z, Pavlus J, Saghafi S, Weigle J, Elola A, Seyedi S, Campbell K, Li Q, Bahrami Rad A, Ribeiro AH, Ribeiro ALA, Sameni R, Clifford GD. Detection of Chagas disease from the ECG: the George B. Moody PhysioNet Challenge 2025. 2025 Computing in Cardiology (CinC), vol. 52, pp. 1-4. 2024.
Tripathi A, Ganglberger W, Sun H, Alcott C, Turley N, Fitzgerald R, Mitra A, Waters S, Gupta A, Gupta A, Ghanta M, Moura Junior V, Nasiri S, Nearing B, Stone KL, Mignot E, Hwang D, Reyna MA, Koscova Z, Robichaux C, Zhang Z, Li Q, Ganjoo G, Trotti LM, Clifford GD, Silvers CT, Gunapati B, Thomas RJ, Westover MB, Maski K, Katwa U. The Boston Children’s Hospital sleep corpus: a collection of 15,695 annotated pediatric polysomnograms. Sleep. 2025 Sep 16: zsaf273. PMID: 40971987
Ardeshir Larijani F, Bozkurt S, Barnett R, Ali A, Bou Zerdan M, Campbell K, Canaslan K, Reyna MA. Genomic and circulating tumor DNA landscape in young-onset non-small cell lung cancer. J Clin Oncol. 2025 Jun 1;43(16_suppl):8528.
Das S, Ge Y, Guo Y, Rajwal S, Hairston J, Powell J, Walker D, Peddireddy S, Lakamana S, Bozkurt S, Reyna MA, Sameni R, Xiao Y, Kim S, Chandler R, Hernandez N, Mowery D, Wightman R, Love J, Spadaro A, Perrone J, Sarker A. Two-layer retrieval-augmented generation framework for low-resource medical question answering using Reddit data: proof-of-concept study. J Med Internet Res. 2025 Jan 6;27:e66220. doi: 10.2196/66220. PMID: 39761554.
Koscova Z, Li Q, Robichaux C, Moura Junior V, Ghanta M, Gupta A, Rosand J, Aguirre A, Hong S, Albert DE, Xue J, Parekh A, Sameni R, Reyna MA, Westover MB, Clifford GD. The Harvard-Emory ECG Database. medRxiv. 2024 Oct 1:2024.09.27.24314503.

2024

Kiarashi Y, B PS, Rad A, Reyna MA, Anderson C, Foster J, Lantz J, Villavicencio T, Hamlin T, Clifford GD. Off-Body Sleep Analysis for Predicting Adverse Behavior in Individuals With Autism Spectrum Disorder. IEEE J Biomed Health Inform. 2024 Nov;28(11):6886-6896. Epub 2024 Nov 6. doi: 10.1109/JBHI.2024.3455942. PMID: 39240748.
Reyna MA, Deepanshi, Weigle J, Koscova Z, Campbell K, Seyedi S, Elola A, Bahrami Rad A, Shah AJ, Bhatia NK, Clifford GD, Sameni R. Digitization and classification of ECG images: The George B. Moody PhysioNet Challenge 2024. 2024 Computing in Cardiology (CinC), vol. 51, pp. 1-4. 2024.
Reyna MA, Deepanshi, Weigle J, Koscova Z, Campbell K, Shivashankara KK, Saghafi S, Nikookar S, Motie-Shirazi M, Kiarashi Y, Seyedi S, Clifford GD, Sameni R. ECG-Image-Database: A Dataset of ECG Images with Real-World Imaging and Scanning Artifacts; A Foundation for Computerized ECG Image Digitization and Analysis. ArXiv. 2024 Sep 25; PMID: 39398215.
Koscova Z, Rad AB, Nasiri S, Reyna MA, Sameni R, Trotti LM, Sun H, Turley N, Stone KL, Thomas RJ, Mignot E, Westover B, Clifford GD. From sleep patterns to heart rhythm: Predicting atrial fibrillation from overnight polysomnograms. J Electrocardiol. 2024 Sep-Oct;86:153759. doi: 10.1016/j.jelectrocard.2024.153759. PMID: 39067281.
Shivashankara KK, Deepanshi, Mehri Shervedani A, Clifford GD, Reyna MA, Sameni R. ECG-Image-Kit: a synthetic image generation toolbox to facilitate deep learning-based electrocardiogram digitization. Physiol Meas. 2024 May 28;45(5). doi: 10.1088/1361-6579/ad4954. PMID: 38290049.
Brockett JS, Manalo T, Zein-Sabatto H, Lee J, Fang J, Chu P, Feng H, Patil D, Davidson P, Ogan K, Master VA, Pattaras JG, Roberts DL, Bergquist SH, Reyna MA, Petros JA, Lerit DA, Arnold RS. A missense SNP in the tumor suppressor SETD2 reduces H3K36me3 and mitotic spindle integrity in Drosophila. Genetics. 2024 Apr 3;226(4): iyae015. doi: 10.1093/genetics/iyae015. PMID: 38290049.
Mousavi SS, Reyna MA, Clifford GD, Sameni R. A Survey on Blood Pressure Measurement Technologies: Addressing Potential Sources of Bias. Sensors (Basel). 2024 Mar 7;24(6):1730. doi: 10.3390/s24061730. PMID: 38543993.

2023

Amorim E, Zheng WL, Ghassemi MM, Aghaeeaval M, Kandhare P, Karukonda V, Lee JW, Herman ST, Sivaraju A, Gaspard N, Hofmeijer J, van Putten MJAM, Sameni R, Reyna MA, Clifford GD, Westover MB. The International Cardiac Arrest Research Consortium Electroencephalography Database. Critical Care Medicine. 2023 Dec 1;51(12):1802-1811. doi: 10.1097/CCM.0000000000006074. PMID: 37855659.
Reyna MA, Amorim E, Sameni R, Weigle J, Elola A, Rad AB, Seyedi S, Kwon H, Zheng WL, Ghassemi MM, van Putten MJAM, Hofmeijer J, Gaspard N, Sivaraju A, Herman ST, Lee JW, Westover MB, Clifford GD. Predicting Neurological Recovery from Coma After Cardiac Arrest: The George B. Moody PhysioNet Challenge 2023. 2023 Computing in Cardiology (CinC), vol. 50, pp. 1-4. IEEE, 2023.
Reyna MA, Kiarashi Y, Elola A, Oliveira J, Renna F, Gu A, Perez Alday EA, Sadr N, Sharma A, Kpodonu J, Mattos S, Coimbra MT, Sameni R, Rad AB, Clifford GD. Heart murmur detection from phonocardiogram recordings: The George B. Moody PhysioNet Challenge 2022. PLOS Digital Health. 2023 Sep 11;2(9): e0000324. doi: 10.1371/journal.pdig.0000324. PMID: 37695769.
Elola A, Aramendi E, Oliveira J, Renna F, Coimbra MT, Reyna MA, Sameni R, Clifford GD, Rad AB. Beyond Heart Murmur Detection: Automatic Murmur Grading from Phonocardiogram. IEEE Journal of Biomedical Health Informatics. 2023 Aug;27(8):3856-3866. doi: 10.1109/JBHI.2023.3275039. PMID: 37163396.
Salari M, Kramer MR, Reyna MA, Taylor HA, Clifford GD. Combining crowd-sourcing, census data, and public review forums for real-time, high-resolution food desert estimation. BioMedical Engineering OnLine. 2023 Jul 10;22(1):69. doi: 10.1186/s12938-023-01108-9. PMID: 37430279.

2022

Perez Alday EA, Rad AB, Reyna MA, Sadr N, Gu A, Li Q, Dumitru M, Xue J, Albert D, Sameni R, Clifford GD. Age, sex and race bias in automated arrhythmia detectors. Journal of Electrocardiology. 2022 Sep-Oct;74:5-9. doi: 10.1016/j.jelectrocard.2022.07.007. PMID: 35878534.
Reyna MA, Sadr N, Perez Alday EA, Gu A, Shah AJ, Robichaux C, Bahrami Rad A, Elola A, Seyedi S, Ansari S, Ghanbari H, Li Q, Sharma A, Clifford GD. Issues in the automated classification of multilead ECGs using heterogeneous labels and populations. Physiological Measurement. 2022 Aug 26;43(8):10.1088/1361-6579/ac79fd. doi: 10.1088/1361-6579/ac79fd. PMID: 35815673.
Reyna MA, Nsoesie EO, Clifford GD. Rethinking Algorithm Performance Metrics for Artificial Intelligence in Diagnostic Medicine. JAMA. 2022 Jul 26;328(4):329-330. doi: 10.1001/jama.2022.10561. PMID: 35802382.
Rohr M, Reich C, Höhl A, Lilienthal T, Dege T, Plesinger F, Bulkova V, Clifford G, Reyna M, Hoog Antink C. Exploring novel algorithms for atrial fibrillation detection by driving graduate level education in medical machine learning. PhysiolOgical Measurement. 2022 Jul 7;43(7). doi: 10.1088/1361-6579/ac7840. PMID: 35697013.
Mo X, Niu Q, Ivanov AA, Tsang YH, Tang C, Shu C, Li Q, Qian K, Wahafu A, Doyle SP, Cicka D, Yang X, Fan D, Reyna MA, Cooper LAD, Moreno CS, Zhou W, Owonikoko TK, Lonial S, Khuri FR, Du Y, Ramalingam SS, Mills GB, Fu H. Systematic discovery of mutation-directed neo-protein-protein interactions in cancer. Cell. 2022 May 26;185(11):1974-1985.e12. doi: 10.1016/j.cell.2022.04.014. PMID: 35512704.
Oliveira J, Renna F, Costa P, Nogueira M, Oliveira AC, Elola A, Ferreira C, Jorge A, Bahrami Rad A, Reyna M, Sameni R, Clifford G, Coimbra M. The CirCor DigiScope Phonocardiogram Dataset (version 1.0.3). PhysioNet (2022). doi: 10.13026/tshs-mw03.

2021

Reyna MA, Sadr N, Alday EAP, Gu A, Shah AJ, Robichaux C, Rad AB, et al. Will two do? Varying dimensions in electrocardiography: the PhysioNet/Computing in Cardiology Challenge 2021. In 2021 Computing in Cardiology (CinC), vol. 48, pp. 1-4. IEEE, 2021. doi: 10.23919/CinC53138.2021.9662687.
Wong AI, Kamaleswaran R, Tabaie A, Reyna MA, Josef C, Robichaux C, de Hond AAH, Steyerberg EW, Holder AL, Nemati S, Buchman TG, Blum JM. Prediction of Acute Respiratory Failure Requiring Advanced Respiratory Support in Advance of Interventions and Treatment: A Multivariable Prediction Model from Electronic Medical Record Data. Critical Care Exploration. 2021 May 12;3(5): e0402. doi: 10.1097/CCE.0000000000000402. PMID: 34079945.
Hahn WC, Bader JS, Braun TP, Califano A, Clemons PA, Druker BJ, Ewald AJ, Fu H, Jagu S, Kemp CJ, Kim W, Kuo CJ, McManus M, Mills GB, Mo X, Sahni N, Schreiber SL, Talamas JA, Tamayo P, Tyner JW, Wagner BK, Weiss WA, Gerhard DS; Cancer Target Discovery and Development Network. (2021). An expanded universe of cancer targets. Cell, 184(5), 1142-1155. doi: 10.1016/j.cell.2021.02.020. PMID: 33667368.
Reyna MA, Chitra U, Elyanow R, Raphael BJ. NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks. Journal of Computational Biology. 2021 May;28(5):469-484. doi: 10.1089/cmb.2020.0435. PMID: 33400606.
Salari M, Reyna M, Kramer MD, Taylor HA, Clifford GD. Food Desert Assessment: An Analytical Framework for Comparing Utility of Metrics and Indices; Case Study of Key Factors, Concurrences, and Divergences. SSRN. 2021 April 10. doi: 10.2139/ssrn.3823677

2020

Perez Alday EA, Gu A, Shah A J, Robichaux C, Wong AKI, Liu C, Liu F, Bahrami Rad A, Elola A, Seyedi S, Li Q, Sharma A, Clifford GD, Reyna MA. Classification of 12-lead ECGs: the PhysioNet/Computing in Cardiology Challenge 2020. Physiological Measurement. 2020 Dec;41(12):124003. doi: 10.1088/1361-6579/abc960. PMID: 33176294.
Reyna MA, Alday EAP, Gu A, Liu C, Seyedi S, Rad AB, Elola A, Li Q, Sharma A, Clifford GD. Classification of 12-lead ECGs: the PhysioNet/Computing in Cardiology Challenge 2020. In 2020 Computing in Cardiology, pp. 1-4.IEEE. doi: 10.22489/CinC.2020.236.
Reyna MA, Clifford GD. Voting of predictive models for clinical outcomes: consensus of algorithms for the early prediction of sepsis from clinical data and an analysis of the PhysioNet/Computing in Cardiology Challenge 2019. Preprint arXiv:2012.11013 (2020). doi: 10.48550/arXiv.2012.11013.
Hegde C, Jiang Z, Suresha PB, Zelko J, Seyedi S, Smith M, Wright D, Kamaleswaran R, Reyna M, Clifford G. AutoTriage - An Open Source Edge Computing Raspberry Pi-based Clinical Screening System. Preprint. 2020. doi: 10.1101/2020.04.09.2005984.
Shahamatdar S, He MX, Reyna MA, Gusev A, AlDubayan SH, Van Allen EM, Ramachandran S. Germline Features Associated with Immune Infiltration in Solid Tumors. Cell Reports. 2020 Mar 3;30(9):2900-2908.e4. doi: 10.1016/j.celrep.2020.02.039. PMID: 32130895.
Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A; PCAWG Drivers and Functional Interpretation Working Group; Reimand J, Stuart JM, Raphael BJ; PCAWG Consortium. Pathway and network analysis of more than 2500 whole cancer genomes. Nature Communications. 2020 Feb 5;11(1):729. doi: 10.1038/s41467-020-14367-0. Erratum in: Nat Commun. 2022 Dec 8;13(1):7566. PMID: 32024854.
Reyna MA, Josef CS, Jeter R, Shashikumar SP, Westover MB, Nemati S, Clifford GD, Sharma A. Early Prediction of Sepsis from Clinical Data: The PhysioNet/Computing in Cardiology Challenge 2019. Critical Care Medicine. 2020 Feb;48(2):210-217. doi: 10.1097/CCM.0000000000004145. PMID: 31939789.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature. 2020 Feb;578(7793), 82-93. doi: 10.1038/s41586-020-1969-6. Epub 2020 Feb 5. PMID: 32025007.

2019

Reyna MA, Josef CS, Jeter R, Shashikumar SP, Westover MB, Nemati S, Clifford GD, Sharma A. Early Prediction of Sepsis From Clinical Data: The PhysioNet/Computing in Cardiology Challenge 2019. In 2019 Computing in Cardiology (CinC), pp. 1-4. IEEE. doi: 10.22489/CinC.2019.412.

2018

Reyna MA, Leiserson MDM, Raphael BJ. Hierarchical HotNet: identifying hierarchies of altered subnetworks. Bioinformatics. 2018 Sep 1;34(17): i972-i980. doi: 10.1093/bioinformatics/bty613. PMID: 30423088.

2016

Leiserson MD, Reyna MA, Raphael BJ. A weighted exact test for mutually exclusive mutations in cancer. Bioinformatics. 2016 Sep 1;32(17): i736-i745. doi: 10.1093/bioinformatics/btw462. PMID: 27587696.

2015

Rieder LE, Savva YA, Reyna MA, Chang YJ, Dorsky JS, Rezaei A, Reenan RA. Dynamic response of RNA editing to temperature in Drosophila. BMC Biology. 2015 Jan 3; 13:1. doi: 10.1186/s12915-014-0111-3. PMID: 25555396.
Reyna MA, Li F. Operator Bounds and Time Step Conditions for the DG and Central DG Methods. Journal of Scientific Computing. 2015; 62:532-554. doi:10.1007/s10915-014-9866-5.

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