Publications

• Predicting seizure episodes and high-risk events in autism through adverse behavioral patterns.
  Physiol Meas Volume: 46
  04/28/2025 Authors: Kiarashi Y; Lantz J; Reyna MA; Anderson C; Rad AB; Foster J; Villavicencio T; Hamlin T; Clifford GD
• Predicting Seizures Episodes and High-Risk Events in Autism Through Adverse Behavioral Patterns.
  medRxiv
  01/13/2025 Authors: Kiarashi Y; Lantz J; Reyna MA; Anderson C; Rad AB; Foster J; Villavicencio T; Hamlin T; Clifford GD
• Two-Layer Retrieval-Augmented Generation Framework for Low-Resource Medical Question Answering Using Reddit Data: Proof-of-Concept Study.
  J Med Internet Res Volume: 27 Page(s): e66220
  01/06/2025 Authors: Das S; Ge Y; Guo Y; Rajwal S; Hairston J; Powell J; Walker D; Peddireddy S; Lakamana S; Bozkurt S
• Off-Body Sleep Analysis for Predicting Adverse Behavior in Individuals With Autism Spectrum Disorder.
  IEEE J Biomed Health Inform Volume: 28 Page(s): 6886 - 6896
  11/01/2024 Authors: Kiarashi Y; B PS; Rad A; Reyna M; Anderson C; Foster J; Lantz J; Villavicencio T; Hamlin T; Clifford G
• 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
  09/25/2024 Authors: Reyna MA; Deepanshi; Weigle J; Koscova Z; Campbell K; Shivashankara KK; Saghafi S; Nikookar S; Motie-Shirazi M; Kiarashi Y
• ECG-Image-Database: A Dataset of ECG Images with Real-World Imaging and Scanning Artifacts; A Foundation for Computerized ECG Image Digitization and Analysis
  
  09/25/2024 Authors: Reyna MA; Deepanshi; Weigle J; Koscova Z; Campbell K; Shivashankara KK; Saghafi S; Nikookar S; Motie-Shirazi M; Kiarashi Y
• Off-body Sleep Analysis for Predicting Adverse Behavior in Individuals with Autism Spectrum Disorder.
  medRxiv
  06/11/2024 Authors: Kiarashi Y; Suresha PB; Rad AB; Reyna MA; Anderson C; Foster J; Lantz J; Villavicencio T; Hamlin T; Clifford GD
• From Sleep Patterns to Heart Rhythms: Predicting Atrial Fibrillation from Overnight Polysomnograms.
  medRxiv
  06/04/2024 Authors: Koscova Z; Rad AB; Nasiri S; Reyna MA; Sameni R; Trotti LM; Sun H; Turley N; Stone KL; Thomas RJ
• ECG-Image-Kit: a synthetic image generation toolbox to facilitate deep learning-based electrocardiogram digitization.
  Physiol Meas Volume: 45
  05/28/2024 Authors: Shivashankara KK; Deepanshi; Mehri Shervedani A; Clifford GD; Reyna MA; Sameni R
• A missense SNP in the tumor suppressor SETD2 reduces H3K36me3 and mitotic spindle integrity in Drosophila.
  Genetics Volume: 226
  04/03/2024 Authors: Brockett JS; Manalo T; Zein-Sabatto H; Lee J; Fang J; Chu P; Feng H; Patil D; Davidson P; Ogan K
• A Survey on Blood Pressure Measurement Technologies: Addressing Potential Sources of Bias.
  Sensors (Basel) Volume: 24
  03/07/2024 Authors: Mousavi SS; Reyna MA; Clifford GD; Sameni R
• From sleep patterns to heart rhythm: Predicting atrial fibrillation from overnight polysomnograms.
  J Electrocardiol Volume: 86 Page(s): 153759
  01/01/2024 Authors: Koscova Z; Rad AB; Nasiri S; Reyna MA; Sameni R; Trotti LM; Sun H; Turley N; Stone KL; Thomas RJ
• The International Cardiac Arrest Research Consortium Electroencephalography Database.
  Crit Care Med Volume: 51 Page(s): 1802 - 1811
  12/01/2023 Authors: Amorim E; Zheng W-L; Ghassemi MM; Aghaeeaval M; Kandhare P; Karukonda V; Lee JW; Herman ST; Sivaraju A; Gaspard N
• Heart murmur detection from phonocardiogram recordings: The George B. Moody PhysioNet Challenge 2022.
  PLOS Digit Health Volume: 2 Page(s): e0000324
  09/01/2023 Authors: Reyna MA; Kiarashi Y; Elola A; Oliveira J; Renna F; Gu A; Perez Alday EA; Sadr N; Sharma A; Kpodonu J
• The International Cardiac Arrest Research (I-CARE) Consortium Electroencephalography Database.
  medRxiv
  08/28/2023 Authors: Amorim E; Zheng W-L; Ghassemi MM; Aghaeeaval M; Kandhare P; Karukonda V; Lee JW; Herman ST; Sivaraju A; Gaspard N
• Beyond Heart Murmur Detection: Automatic Murmur Grading From Phonocardiogram.
  IEEE J Biomed Health Inform Volume: 27 Page(s): 3856 - 3866
  08/01/2023 Authors: Elola A; Aramendi E; Oliveira J; Renna F; Coimbra MT; Reyna MA; Sameni R; Clifford GD; Rad AB
• Combining crowd-sourcing, census data, and public review forums for real-time, high-resolution food desert estimation.
  Biomed Eng Online Volume: 22 Page(s): 69
  07/10/2023 Authors: Salari M; Kramer MR; Reyna MA; Taylor HA; Clifford GD
• ECG-Image-Kit: A Synthetic Image Generation Toolbox to Facilitate Deep Learning-Based Electrocardiogram Digitization
  
  07/04/2023 Authors: Shivashankara KK; Deepanshi; Shervedani AM; Clifford GD; Reyna MA; Sameni R
• A Survey on Blood Pressure Measurement Technologies: Addressing Potential Sources of Bias
  
  06/14/2023 Authors: Mousavi SS; Reyna MA; Clifford GD; Sameni R
• Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers.
  Nat Genet Volume: 55 Page(s): 892
  05/01/2023 Authors: Yuan Y; Ju YS; Kim Y; Li J; Wang Y; Yoon CJ; Yang Y; Martincorena I; Creighton CJ; Weinstein JN
• Author Correction: Butler enables rapid cloud-based analysis of thousands of human genomes.
  Nat Biotechnol Volume: 41 Page(s): 577
  04/01/2023 Authors: Yakneen S; Waszak SM; PCAWG Technical Working Group; Gertz M; Korbel JO; PCAWG Consortium
• Author Correction: Pan-cancer analysis of whole genomes.
  Nature Volume: 614 Page(s): E39
  02/01/2023 Authors: ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium
• Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes.
  Nat Commun Volume: 13 Page(s): 7566
  12/08/2022 Authors: Reyna MA; Haan D; Paczkowska M; Verbeke LPC; Vazquez M; Kahraman A; Pulido-Tamayo S; Barenboim J; Wadi L; Dhingra P
• Author Correction: Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig.
  Nat Commun Volume: 13 Page(s): 7567
  12/08/2022 Authors: Rubanova Y; Shi R; Harrigan CF; Li R; Wintersinger J; Sahin N; Deshwar AG; PCAWG Evolution and Heterogeneity Working Group; Morris QD; PCAWG Consortium
• Issues in the automated classification of multilead ecgs using heterogeneous labels and populations.
  Physiol Meas Volume: 43
  08/26/2022 Authors: Reyna MA; Sadr N; Perez Alday EA; Gu A; Shah AJ; Robichaux C; Bahrami Rad A; Elola A; Seyedi S; Ansari S
• Rethinking Algorithm Performance Metrics for Artificial Intelligence in Diagnostic Medicine.
  JAMA Volume: 328 Page(s): 329 - 330
  07/26/2022 Authors: Reyna MA; Nsoesie EO; Clifford GD
• Exploring novel algorithms for atrial fibrillation detection by driving graduate level education in medical machine learning.
  Physiol Meas Volume: 43
  07/07/2022 Authors: Rohr M; Reich C; Hhl A; Lilienthal T; Dege T; Plesinger F; Bulkova V; Clifford G; Reyna M; Hoog Antink C
• Systematic discovery of mutation-directed neo-protein-protein interactions in cancer.
  Cell Volume: 185 Page(s): 1974 - 1985.e12
  05/26/2022 Authors: Mo X; Niu Q; Ivanov AA; Tsang YH; Tang C; Shu C; Li Q; Qian K; Wahafu A; Doyle SP
• Age, sex and race bias in automated arrhythmia detectors.
  J Electrocardiol Volume: 74 Page(s): 5 - 9
  01/01/2022 Authors: Perez Alday EA; Rad AB; Reyna MA; Sadr N; Gu A; Li Q; Dumitru M; Xue J; Albert D; Sameni R
• NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks.
  J Comput Biol Volume: 28 Page(s): 469 - 484
  05/01/2021 Authors: Reyna MA; Chitra U; Elyanow R; Raphael BJ
• Prediction of Acute Respiratory Failure Requiring Advanced Respiratory Support in Advance of Interventions and Treatment: A Multivariable Prediction Model From Electronic Medical Record Data.
  Crit Care Explor Volume: 3 Page(s): e0402
  05/01/2021 Authors: Wong A-KI; Kamaleswaran R; Tabaie A; Reyna MA; Josef C; Robichaux C; de Hond AAH; Steyerberg EW; Holder AL; Nemati S
• An expanded universe of cancer targets.
  Cell Volume: 184 Page(s): 1142 - 1155
  03/04/2021 Authors: Hahn WC; Bader JS; Braun TP; Califano A; Clemons PA; Druker BJ; Ewald AJ; Fu H; Jagu S; Kemp CJ
• Classification of 12-lead ECGs: the PhysioNet/Computing in Cardiology Challenge 2020.
  Physiol Meas Volume: 41 Page(s): 124003
  01/01/2021 Authors: Perez Alday EA; Gu A; J Shah A; Robichaux C; Ian Wong A-K; Liu C; Liu F; Bahrami Rad A; Elola A; Seyedi S
• 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
  
  12/20/2020 Authors: Reyna MA; Clifford GD
• Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
  Nat Commun Volume: 11 Page(s): 4748
  09/21/2020 Authors: Bailey MH; Meyerson WU; Dursi LJ; Wang L-B; Dong G; Liang W-W; Weerasinghe A; Li S; Li Y; Kelso S
• Sex differences in oncogenic mutational processes.
  Nat Commun Volume: 11 Page(s): 4330
  08/28/2020 Authors: Li CH; Prokopec SD; Sun RX; Yousif F; Schmitz N; PCAWG Tumour Subtypes and Clinical Translation; Boutros PC; PCAWG Consortium
• Germline Features Associated with Immune Infiltration in Solid Tumors.
  Cell Rep Volume: 30 Page(s): 2900 - 2908.e4
  03/03/2020 Authors: Shahamatdar S; He MX; Reyna MA; Gusev A; AlDubayan SH; Van Allen EM; Ramachandran S
• Combined burden and functional impact tests for cancer driver discovery using DriverPower.
  Nat Commun Volume: 11 Page(s): 734
  02/05/2020 Authors: Shuai S; PCAWG Drivers and Functional Interpretation Working Group; Gallinger S; Stein LD; PCAWG Consortium
• Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.
  Commun Biol Volume: 3 Page(s): 56
  02/05/2020 Authors: Carlevaro-Fita J; Lanzs A; Feuerbach L; Hong C; Mas-Ponte D; Pedersen JS; PCAWG Drivers and Functional Interpretation Group; Johnson R; PCAWG Consortium
• Integrative pathway enrichment analysis of multivariate omics data.
  Nat Commun Volume: 11 Page(s): 735
  02/05/2020 Authors: Paczkowska M; Barenboim J; Sintupisut N; Fox NS; Zhu H; Abd-Rabbo D; Mee MW; Boutros PC; PCAWG Drivers and Functional Interpretation Working Group; Reimand J
• Pathway and network analysis of more than 2500 whole cancer genomes.
  Nat Commun Volume: 11 Page(s): 729
  02/05/2020 Authors: Reyna MA; Haan D; Paczkowska M; Verbeke LPC; Vazquez M; Kahraman A; Pulido-Tamayo S; Barenboim J; Wadi L; Dhingra P
• Analyses of non-coding somatic drivers in 2,658cancer whole genomes.
  Nature Volume: 578 Page(s): 102 - 111
  02/01/2020 Authors: Rheinbay E; Nielsen MM; Abascal F; Wala JA; Shapira O; Tiao G; Hornshj H; Hess JM; Juul RI; Lin Z
• Pan-cancer analysis of whole genomes.
  Nature Volume: 578 Page(s): 82 - 93
  02/01/2020 Authors: ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium
• Early Prediction of Sepsis From Clinical Data: The PhysioNet/Computing in Cardiology Challenge 2019.
  Crit Care Med Volume: 48 Page(s): 210 - 217
  02/01/2020 Authors: Reyna MA; Josef CS; Jeter R; Shashikumar SP; Westover MB; Nemati S; Clifford GD; Sharma A
• Classification of Subsequent Acute Respiratory Failure (ARF) Requiring Prolonged Mechanical Ventilation by Basic Machine Learning Algorithms
  Volume: 201
  01/01/2020 Authors: Wong AI; Tabaie A; Holder AL; Reyna MA; Josef C; Robichaux C; Nemati S; Buchman T; Blum JM
• Assessment of EMR Data Availability Within the First 12 Hours of Admission for Prediction by Machine Learning Methods
  Volume: 201
  01/01/2020 Authors: Wong AI; Tabaie A; Holder AL; Reyna M; Nemati S; Josef C; Robichaux C; Blum JM
• Early Prediction of Sepsis From Clinical Data: The PhysioNet/Computing in Cardiology Challenge 2019.
  Crit Care Med
  12/17/2019 Authors: Reyna MA; Josef CS; Jeter R; Shashikumar SP; Westover MB; Nemati S; Clifford GD; Sharma A
• Hierarchical HotNet: identifying hierarchies of altered subnetworks.
  Bioinformatics Volume: 34 Page(s): i972 - i980
  09/01/2018 Authors: Reyna MA; Leiserson MDM; Raphael BJ
• A weighted exact test for mutually exclusive mutations in cancer.
  Bioinformatics Volume: 32 Page(s): i736 - i745
  09/01/2016 Authors: Leiserson MDM; Reyna MA; Raphael BJ
• Dynamic response of RNA editing to temperature in Drosophila.
  BMC Biol Volume: 13 Page(s): 1
  01/03/2015 Authors: Rieder LE; Savva YA; Reyna MA; Chang Y-J; Dorsky JS; Rezaei A; Reenan RA