Aronow Lab

Publications

Pryhuber, GS; Nawijn, M; Alam, DA; Aronow, B; Banchero, M; Banovich, N; Barbry, P; Basil, M; Burns, K; Burgess, J; Walters, MS; Wikenheiser-Brokamp, KA; Xu, Y; Zaragosi, L-E. Consensus Lung Cell Reference: The Collaborative Cross-Consortium and Country Lung Cell Nomenclature Project (C3LCN). An Official American Thoracic Society Workshop Report. American Journal of Respiratory Cell and Molecular Biology. 2026.

Groenendijk, A; Aronow, BJ; Cost, N; Cajaiba, M; Renfro, LA; Perlman, EJ; Dyer, L; Smolarek, TA; Mullen, EA; Pervaiz, S; Ehrlich, PF; Van Den Heuvel-Eibrink, MM; Dome, JS; Geller, JI. Integrated Molecular, Genomic, and Clinical Characterization of Pediatric and Adolescent Translocation Renal Cell Carcinoma: A Report from the Children's Oncology Group. Biomedicines. 2026; 14(5).

Shirae, S; Debsarkar, SS; Kawanaka, H; Aronow, BJ; Prasath, VBS. End-to-End Multimodal Multiple Instance Learning for Cancer Histopathology Classification with Dual-Attention Fusion. Journal of Medical Systems. 2026; 50(1).

Fisher, EG; Glass, SE; Sievers, CK; Cao, Z; Bechard, ME; Ellis, ST; Aramnadla, R; Zhao, P; Smith, RT; Wang, Y; Liu, Q; Lau, KS; Aronow, B; Coffey, RJ. Abstract 4760: Uncovering a highly transforming, Myc-stabilizing isoform of dipeptidase-1 in colorectal cancer. Cancer Research. 2026; 86(7_Supplement):4760-4760.

Debsarkar, SS; Aronow, B; Prasath, VBS. Unsupervised biomarker discovery leveraging foundation models: a multimodal approach to clinical data integration. Neural Computing and Applications. 2026; 38(5):93.

Glaser, K; Depasquale, EAK; Berklite, L; Hickner, BT; Rao, P; Patel, RH; Badachhape, AA; Roy, S; Schepers, E; Timchenko, NA; Takebe, T; Woodfield, SE; Vasudevan, SA; Bondoc, AJ. Investigating the oncogenic role of aberrant EZH2 in hepatoblastoma. Scientific Reports. 2026; 16(1).

Kamsheh, AM; Ware, SM; Bhatnagar, S; Martin, LJ; Lee, TM; Towbin, JA; Kantor, PF; Lal, AK; Bansal, N; Ballweg, JA; Colan, SD; Aronow, BJ; Canter, CE; Lipshultz, SE. Cardiomyopathy-Associated Pathogenic Variants in Pediatric Myocarditis: A Study From the Pediatric Cardiomyopathy Registry. Circulation: Heart Failure. 2026; 19(1):e013104.

Boudissa, S; Kawanaka, H; Aronow, B; Prasath, VBS. Cross-Architecture Knowledge Distillation for Histopathological Image Analysis. IEEE Access. 2026; 14:58187-58209.

Jin, K; Zhang, Z; Zhang, K; Viggiani, F; Callahan, C; Tang, J; Aronow, BJ; Shu, J. Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings. Nature Communications. 2025; 16(1):6618.

Iyer, B; Deoghare, S; Ranjan, K; Aronow, BJ; Prasath, VBS. Benchmarking HEp-2 cell segmentation methods in indirect immunofluorescence images - standard models to deep learning. Computers in Biology and Medicine. 2025; 192(Pt A):110150.

Mihalas, AB; Arora, S; O'connor, SA; Feldman, HM; Cucinotta, CE; Mitchell, K; Bassett, J; Kim, D; Jin, K; Hoellerbauer, P; Aronow, B; Plaisier, CL; Patel, AP; Paddison, PJ. KAT5 regulates neurodevelopmental states associated with G0-like populations in glioblastoma. Nature Communications. 2025; 16(1):4327.

Debsarkar, SS; Aronow, B; Prasath, VBS. Advancements in automated nuclei segmentation for histopathology using you only look once-driven approaches: A systematic review. Computers in Biology and Medicine. 2025; 190:110072.

Börner, K; Blood, PD; Silverstein, JC; Ruffalo, M; Satija, R; Teichmann, SA; Pryhuber, GJ; Misra, RS; Purkerson, JM; Fan, J; Qaurooni, D; Kong, Y; Bueckle, A; Herr, BW. Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage. Nature Methods. 2025; 22(4):845-860.

Greve, K; Bailes, AF; Zhang, N; Long, J; Aronow, B; Mitelpunkt, A. Physical Therapy Dose After Orthopedic Multilevel Surgery Varies by Ambulatory Status in Children With Cerebral Palsy: A Pilot Study. Pediatric Physical Therapy. 2025; 37(1):37-44.

Shirae, S; Debsarkar, SS; Kawanaka, H; Aronow, B; Prasath, VBS. Multimodal Ensemble Fusion Deep Learning Using Histopathological Images and Clinical Data for Glioma Subtype Classification. IEEE Access. 2025; 13:57780-57797.

Boudissa, S; Debsarkar, SS; Kawanaka, H; Aronow, B; Prasath, VBS. Vision Transformers for Histopathological Image Classification with Efficient Head Pruning. Procedia Computer Science. 2025; 270:2274-2283.

Shirae, S; Debsarkar, SS; Kawanaka, H; Aronow, B; Prasath, VBS. Multiple Instance Learning Using Reduced Deep Learning Model For Glioma Subtype Classification. Procedia Computer Science. 2025; 270:2434-2442.

Zachariasse, JM; Gutiérrez-Sacristán, A; Makwana, S; Li, X; Bhatnagar, S; Hanauer, DA; Kainth, MK; Morris, M; Rubio-Mayo, P; Sáez, C; Visweswaran, S; Xia, Z; Bourgeois, FT; Avillach, P. Impact of COVID-19 non-pharmaceutical interventions on bacterial infections in children: an international electronic health record-based study. BMJ Public Health. 2025; 3(2):e002671.

Boudissa, S; Debsarkar, SS; Kawanaka, H; Aronow, B; Prasath, VBS. Vision Transformers and CNN-Based Knowledge-Distillation for Histopathological Image Classification. In: Fuzzy Systems and Data Mining X. IOS Press; 2024.

Lee, Y; Kim, KH; Park, J; Kang, HM; Kim, S-H; Jeong, H; Lee, B; Lee, N; Cho, Y; Kim, GD; Aronow, BJ; Lim, K-M; Coffey, RJ; Nam, KT. Regenerative Role of Lrig1+ Cells in Kidney Repair. Journal of the American Society of Nephrology. 2024; 35(12):1702-1714.

Lee, TM; Miller, E; Sridhar, A; Fan, X; Dexheimer, PJ; Bansal, N; Godown, J; Hsu, DT; Kantor, P; Kirmani, S; Ware, SM; Chung, WK; Wilkinson, JD; Lipshultz, SE. Pediatric cardiomyopathy illustrates the importance of reinterpreting the significance of genetic variants. Progress in Pediatric Cardiology. 2024; 74:101732.

Nakagaki, R; Debsarkar, SS; Kawanaka, H; Aronow, BJ; Prasath, VBS. Deep learning-based IDH1 gene mutation prediction using histopathological imaging and clinical data. Computers in Biology and Medicine. 2024; 179:108902.

Yuan, W; Stevenson, CB; Moretti, P; Mangano, FT; Pavanello, M; Cama, A; Tortora, D; Tacchino, C; Bailes, AF; Greve, KR; Harpster, K; Kurowski, BG; Mitelpunkt, A; Aronow, B. White matter characteristics in children with cerebral palsy prior to selective dorsal rhizotomy: a multicenter diffusion tensor imaging study. Journal of Neurosurgery: Pediatrics. 2024; 34(3):268-277.

Bhatnagar, S; Mitelpunkt, A; Rizzo, JJ; Zhang, N; Guzman, T; Schuetter, R; Vargus-Adams, J; Bailes, AF; Greve, K; Gerstle, M; Pedapati, E; Aronow, B; Kurowski, BG. Mental Health Diagnoses Risk Among Children and Young Adults With Cerebral Palsy, Chronic Conditions, or Typical Development. JAMA Network Open. 2024; 7(7):e2422202.

銀河, 鷲; 巧海, 北; 普晴, 川; Iyer, B; Prasath, VBS; Aronow, BJ. 教師なし深層学習モデルを用いた脳性麻痺患者のための歩行機能評価手法の提案と基礎的検討. Journal of Japan Society for Fuzzy Theory and Intelligent Informatics. 2024; 36(1):527-531.

Gaddis, N; Fortriede, J; Guo, M; Bardes, EE; Kouril, M; Tabar, S; Burns, K; Ardini-Poleske, ME; Loos, S; Schnell, D; Xu, Y; Tickle, T; Aronow, BJ; Salomonis, N. LungMAP Portal Ecosystem: Systems-level Exploration of the Lung. American Journal of Respiratory Cell and Molecular Biology. 2024; 70(2):129-139.

Mitelpunkt, A; Stodola, MA; Vargus-Adams, J; Kurowski, BG; Greve, K; Bhatnagar, S; Aronow, B; Zahner, J; Bailes, AF. A big data approach to evaluate receipt of optimal care in childhood cerebral palsy. Disability and Rehabilitation. 2024; 46(4):723-730.

Rajdeo, P; Aronow, B; Surya Prasath, VB. Deep learning-based multimodal spatial transcriptomics analysis for cancer. 2024:1-38.

Dagliati, A; Strasser, ZH; Hossein Abad, ZS; Klann, JG; Wagholikar, KB; Mesa, R; Visweswaran, S; Morris, M; Luo, Y; Henderson, DW; Bellazzi, R; Murphy, SN; Holmes, JH; Estiri, H. Characterization of long COVID temporal sub-phenotypes by distributed representation learning from electronic health record data: a cohort study. EClinicalMedicine. 2023; 64:102210.

Sperotto, F; Gutiérrez-Sacristán, A; Makwana, S; Li, X; Rofeberg, VN; Cai, T; Bourgeois, FT; Omenn, GS; Hanauer, DA; Sáez, C; Xia, Z; Zachariasse, JM; Newburger, JW; Avillach, P. Clinical phenotypes and outcomes in children with multisystem inflammatory syndrome across SARS-CoV-2 variant eras: a multinational study from the 4CE consortium. EClinicalMedicine. 2023; 64:102212.

Guo, M; Morley, MP; Jiang, C; Wu, Y; Li, G; Du, Y; Zhao, S; Wagner, A; Cakar, AC; Kouril, M; Sun, X; Morrisey, EE; Whitsett, JA; Xu, Y. Guided construction of single cell reference for human and mouse lung. Nature Communications. 2023; 14(1):4566.

Sebastian, R; Jin, K; Pavon, N; Bansal, R; Potter, A; Song, Y; Babu, J; Gabriel, R; Sun, Y; Aronow, B; Pak, C. Schizophrenia-associated NRXN1 deletions induce developmental-timing- and cell-type-specific vulnerabilities in human brain organoids. Nature Communications. 2023; 14(1):3770.

Zhang, HG; Honerlaw, JP; Maripuri, M; Samayamuthu, MJ; Beaulieu-Jones, BR; Baig, HS; L'yi, S; Ho, Y-L; Morris, M; Panickan, VA; Xia, Z; Cho, K; Cai, T; Brat, GA. Potential pitfalls in the use of real-world data for studying long COVID. Nature Medicine. 2023; 29(5):1040-1043.

Bedard, MC; Chihanga, T; Carlile, A; Jackson, R; Brusadelli, MG; Lee, D; Vonhandorf, A; Rochman, M; Dexheimer, PJ; Chalmers, J; Lambert, PF; Adam, M; Steven Potter, S; Wells, SI. Single cell transcriptomic analysis of HPV16-infected epithelium identifies a keratinocyte subpopulation implicated in cancer. Nature Communications. 2023; 14(1):1975.

Tan, ALM; Getzen, EJ; Hutch, MR; Strasser, ZH; Gutiérrez-Sacristán, A; Le, TT; Dagliati, A; Morris, M; Hanauer, DA; Moal, B; Verdy, B; Long, Q; Mowery, DL; Holmes, JH. Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record? Journal of Biomedical Informatics. 2023; 139:104306.

Greve, K; Ni, Y; Bailes, AF; Vargus-Adams, J; Miley, AE; Aronow, B; Mcmahon, MM; Kurowski, BG; Mitelpunkt, A. Gross motor function prediction using natural language processing in cerebral palsy. Developmental Medicine and Child Neurology. 2023; 65(1):100-106.

Tan, BWL; Tan, BWQ; Tan, ALM; Schriver, ER; Gutiérrez-Sacristán, A; Das, P; Yuan, W; Hutch, MR; García Barrio, N; Pedrera Jimenez, M; Cai, T; Omenn, GS; Holmes, JH; Ngiam, KY. Long-term kidney function recovery and mortality after COVID-19-associated acute kidney injury: An international multi-centre observational cohort study. EClinicalMedicine. 2023; 55:101724.

Moal, B; Orieux, A; Ferté, T; Neuraz, A; Brat, GA; Avillach, P; Bonzel, C-L; Cai, T; Cho, K; Cossin, S; Zöller, D; Kohane, IS; Boyer, A; Jouhet, V. Acute respiratory distress syndrome after SARS-CoV-2 infection on young adult population: International observational federated study based on electronic health records through the 4CE consortium. PLoS ONE. 2023; 18(1):e0266985.

Greve, KR; Bailes, AF; Zhang, N; Long, J; Aronow, B; Mitelpunkt, A. Outpatient hospital utilization after single event multi-level surgery in children with cerebral palsy. Journal of Pediatric Rehabilitation Medicine. 2023; 16(1):139-148.

銀河, 鷲; 普晴, 川; 巧海, 北; Prasath, VBS; Aronow, BJ. Auto-Encoderを用いた脳性麻痺患者のための歩行機能評価手法に関する一検討. . 2023; 345-348.

Gutiérrez-Sacristán, A; Serret-Larmande, A; Hutch, MR; Sáez, C; Aronow, BJ; Bhatnagar, S; Bonzel, C-L; Cai, T; Devkota, B; Hanauer, DA; Xia, Z; Zahner, J; Avillach, P; Bourgeois, FT. Hospitalizations Associated With Mental Health Conditions Among Adolescents in the US and France During the COVID-19 Pandemic. JAMA Network Open. 2022; 5(12):e2246548.

Mcsweeney, D; Gabriel, R; Jin, K; Pang, ZP; Aronow, B; Pak, C. CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons. iScience. 2022; 25(10):105187.

Jin, K; Schnell, D; Li, G; Salomonis, N; Prasath, VBS; Szczesniak, R; Aronow, BJ. CellDrift: inferring perturbation responses in temporally sampled single-cell data. Briefings in Bioinformatics. 2022; 23(5).

Zhang, HG; Dagliati, A; Shakeri Hossein Abad, Z; Xiong, X; Bonzel, C-L; Xia, Z; Tan, BWQ; Avillach, P; Brat, GA; Hong, C; Cai, T; South, AM; Kohane, IS; Weber, GM. International electronic health record-derived post-acute sequelae profiles of COVID-19 patients. npj Digital Medicine. 2022; 5(1):81.

Weber, GM; Hong, C; Xia, Z; Palmer, NP; Avillach, P; L'yi, S; Keller, MS; Murphy, SN; Gutiérrez-Sacristán, A; Bonzel, C-L; Wang, X; Kohane, IS; Cai, T; Brat, GA. International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality. npj Digital Medicine. 2022; 5(1):74.

Xu, X; Jin, K; Bais, AS; Zhu, W; Yagi, H; Feinstein, TN; Nguyen, PK; Criscione, JD; Liu, X; Beutner, G; Porter, GA; Lin, J-HI; Aronow, B; Lo, CW. Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease. Cell Stem Cell. 2022; 29(5):840-855.e7.

Jin, K; Schnell, D; Li, G; Salomonis, N; Prasath, VBS; Szczesniak, R; Aronow, BJ. CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data. bioRxiv. 2022; 2022.04.13.488194.

Katsuma, D; Kawanaka, H; Prasath, VBS; Aronow, BJ. Data Augmentation Using Generative Adversarial Networks for Multi-Class Segmentation of Lung Confocal IF Images. Journal of Advanced Computational Intelligence and Intelligent Informatics. 2022; 26(2):138-146.

Locker, KCS; Kachapati, K; Wu, Y; Bednar, KJ; Adams, D; Patel, C; Tsukamoto, H; Heuer, LS; Aronow, BJ; Herr, AB; Ridgway, WM. Endosomal Sequestration of TLR4 Antibody Induces Myeloid-Derived Suppressor Cells and Reverses Acute Type 1 Diabetes. Diabetes. 2022; 71(3):470-482.

Karlebach, G; Aronow, B; Baylin, SB; Butler, D; Foox, J; Levy, S; Meydan, C; Mozsary, C; Saravia-Butler, AM; Taylor, DM; Wurtele, E; Mason, CE; Beheshti, A; Robinson, PN. Betacoronavirus-specific alternate splicing. Genomics. 2022; 114(2):110270.

Ware, SM; Bhatnagar, S; Dexheimer, PJ; Wilkinson, JD; Sridhar, A; Fan, X; Shen, Y; Tariq, M; Schubert, JA; Colan, SD; Miller, EM; Aronow, B; Martin, LJ; Lipshultz, SE. The genetic architecture of pediatric cardiomyopathy. American Journal of Human Genetics. 2022; 109(2):282-298.

Mast, AE; Wolberg, AS; Gailani, D; Garvin, MR; Alvarez, C; Miller, JI; Jones, P; Aronow, B; Jacobson, D. Response to comment on 'SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung'. eLife. 2022; 11.

Sun, X; Perl, A-K; Li, R; Bell, SM; Sajti, E; Kalinichenko, VV; Kalin, TV; Misra, RS; Deshmukh, H; Clair, G; Xu, Y; Pryhuber, G; Whitsett, J; Morrisey, EE. A census of the lung: CellCards from LungMAP. Developmental Cell. 2022; 57(1):112-145.e2.

Barrila, J; Yang, J; Franco Meléndez, KP; Yang, S; Buss, K; Davis, TJ; Aronow, BJ; Bean, HD; Davis, RR; Forsyth, RJ; Nauman, EA; Kong, W; Steel, J; Nickerson, CA. Spaceflight Analogue Culture Enhances the Host-Pathogen Interaction Between Salmonella and a 3-D Biomimetic Intestinal Co-Culture Model. Frontiers in Cellular and Infection Microbiology. 2022; 12:705647.