Aronow Lab

Publications

Ding, J; Aronow, BJ; Kaminski, N; Kitzmiller, J; Whitsett, JA; Bar-Joseph, Z. Reconstructing differentiation networks and their regulation from time series single-cell expression data. Genome research. 2018; 28:383-395.

Marigorta, UM; Denson, LA; Hyams, JS; Mondal, K; Prince, J; Walters, TD; Griffiths, A; Noe, JD; Crandall, WV; Rosh, JR; Cho, J; Aronow, BJ; Kugathasan, S; Gibson, G. Transcriptional risk scores link GWAS to eQTLs and predict complications in Crohn's disease. Nature Genetics. 2017; 49:1517-1521.

Liu, X; Yagi, H; Saeed, S; Bais, AS; Gabriel, GC; Chen, Z; Peterson, KA; Li, Y; Schwartz, MC; Reynolds, WT; Martin, LJ; Benson, DW; Aronow, BJ; Lo, CW. The complex genetics of hypoplastic left heart syndrome. Nature Genetics. 2017; 49:1152-1159.

Olsson, A; Venkatasubramanian, M; Chaudhri, VK; Aronow, BJ; Salomonis, N; Singh, H; Grimes, HL. Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. Nature. 2016; 537:698-702.

Sarangdhar, M; Tabar, S; Schmidt, C; Kushwaha, A; Shah, K; Dahlquist, JE; Jegga, AG; Aronow, BJ. Data mining differential clinical outcomes associated with drug regimens using adverse event reporting data. Nature Biotechnology. 2016; 34:697-700.

Salomonis, N; Dexheimer, PJ; Omberg, L; Schroll, R; Bush, S; Huo, J; Schriml, L; Sui, SH; Keddache, M; Mayhew, C; Malik, P; Cancelas, JA; Aronow, BJ; Lutzko, C. Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium. Stem Cell Reports. 2016; 7:110-125.

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

Debsarkar, SS; Aronow, B; Prasath, VB S. 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.

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

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; 37:37-44.

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

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

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; 34:268-277.

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

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.

Rajdeo, P; Aronow, B; Surya Prasath, VB. Deep learning-based multimodal spatial transcriptomics analysis for cancer. Cutting Edge Artificial Intelligence, Spatial Transcriptomics and Proteomics Approaches to Analyze Cancer. : Elsevier; Elsevier; 2024.

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:e2422202.

SUMI, G; KITAJIMA, T; KAWANAKA, H; IYER, B; SURYA PRASATH, VB; 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; 36:527-531.

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; 46:723-730.

銀河, 鷲; 普晴, 川; 巧海, 北; Prasath, VB S; 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. 2024; 345-348.

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; 70:129-139.

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

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

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; 14:1975.

Sperotto, F; Gutiérrez-Sacristán, A; Makwana, S; Li, X; Rofeberg, VN; Cai, T; Bourgeois, FT; Omenn, GS; Hanauer, DA; Sáez, C; Daniel, C; Das, P; Devkota, B; Duan, R. 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.

Dagliati, A; Strasser, ZH; Hossein Abad, ZS; Klann, JG; Wagholikar, KB; Mesa, R; Visweswaran, S; Morris, M; Luo, Y; Henderson, DW; Hanauer, DA; Haverkamp, C; Hazard, DY; He, B. Characterization of long COVID temporal sub-phenotypes by distributed representation learning from electronic health record data: a cohort study. EClinicalMedicine. 2023; 64:102210.

Zhang, HG; Honerlaw, JP; Maripuri, M; Samayamuthu, MJ; Beaulieu-Jones, BR; Baig, HS; L’Yi, S; Ho, YL; Morris, M; Panickan, VA; Grisel, O; Gutiérrez-Sacristán, A; Han, L; Hanauer, DA. Potential pitfalls in the use of real-world data for studying long COVID. Nature Medicine. 2023; 29:1040-1043.

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. Editor, Byrne R; Gaebler-Spira D; Green M; Kim H. Journal of Pediatric Rehabilitation Medicine. 2023; 16:139-148.

Tan, AL M; 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.

Orieux, A; Ferté, T; Jouhet, V; Aaron, JR; Agapito, G; Albayrak, A; Albi, G; Alessiani, M; Alloni, A; Amendola, DF; Henderson, DW; Hilka, M; Ho, YL; Holmes, JH. 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. Editor, Chen RJ. PloS one. 2023; 18:e0266985.

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; 65:100-106.

Tan, BW L; Tan, BW Q; Tan, AL M; Schriver, ER; Gutiérrez-Sacristán, A; Das, P; Yuan, W; Hutch, MR; García Barrio, N; Pedrera Jimenez, M; Cimino, JJ; Colicchio, TK; Cormont, S; Cossin, S. 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.

Gutiérrez-Sacristán, A; Serret-Larmande, A; Hutch, MR; Sáez, C; Aronow, BJ; Bhatnagar, S; Bonzel, CL; Cai, T; Devkota, B; Hanauer, DA; González, TG; Gradinger, T; Gramfort, A; Griffier, R. Hospitalizations Associated With Mental Health Conditions Among Adolescents in the US and France During the COVID-19 Pandemic. JAMA Network Open. 2022; 5:e2246548.

Zhang, HG; Dagliati, A; Shakeri Hossein Abad, Z; Xiong, X; Bonzel, CL; Xia, Z; Tan, BW Q; 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; 5:81.

Weber, GM; Hong, C; Xia, Z; Palmer, NP; Avillach, P; L’Yi, S; Keller, MS; Murphy, SN; Gutiérrez-Sacristán, A; Bonzel, CL; Caucheteux, C; Champ, J; Chen, KY; Chen, J. International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality. npj Digital Medicine. 2022; 5:74.

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

Jin, K; Schnell, D; Li, G; Salomonis, N; Prasath, VB S; Szczesniak, R; Aronow, BJ. CellDrift: inferring perturbation responses in temporally sampled single-cell data. Briefings in Bioinformatics. 2022; 23:bbac324.

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.

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

Katsuma, D; Kawanaka, H; Prasath, VB S; 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; 26:138-146.

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; 114:110270.

Locker, KC S; 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; 71:470-482.

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. The American Journal of Human Genetics. 2022; 109:282-298.

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:e74951.

Sun, X; Perl, AK; 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; 57:112-145.e2.

Masci, AM; White, S; Neely, B; Ardini-Polaske, M; Hill, CB; Misra, RS; Aronow, B; Gaddis, N; Yang, L; Wert, SE; Palmer, SM; Chan, C. Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images. BMC Bioinformatics. 2021; 22:82.

Singh, U; Hernandez, KM; Aronow, BJ; Wurtele, ES. African Americans and European Americans exhibit distinct gene expression patterns across tissues and tumors associated with immunologic functions and environmental exposures. Scientific Reports. 2021; 11:9905.

Kerlavage, AR; Kirchhoff, AC; Auvil, JM G; Sharpless, NE; Davis, KL; Reilly, K; Reaman, G; Penberthy, L; Deapen, D; Hwang, A; Resnick, AC; Shalley, ER; Nadaf, S; Kibbe, WA. Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer. JCO clinical cancer informatics. 2021; 5:881-896.

Bondoc, A; Glaser, K; Jin, K; Lake, C; Cairo, S; Geller, J; Tiao, G; Aronow, B. Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma. Communications Biology. 2021; 4:1049.

Estiri, H; Strasser, ZH; Brat, GA; Semenov, YR; Aaron, JR; Agapito, G; Albayrak, A; Alessiani, M; Amendola, DF; Anthony, LL L J; Le, TT; Leblanc, J; Leite, AR R; Lemaitre, G. Evolving phenotypes of non-hospitalized patients that indicate long COVID. BMC Medicine. 2021; 19:249.

Le, TT; Gutiérrez-Sacristán, A; Son, J; Hong, C; South, AM; Beaulieu-Jones, BK; Loh, NH W; Luo, Y; Morris, M; Ngiam, KY; Jouhet, V; Kavuluru, R; Keller, MS; Kirchoff, K. Multinational characterization of neurological phenotypes in patients hospitalized with COVID-19. Scientific Reports. 2021; 11:20238.

Kurowski, BG; Greve, K; Bailes, AF; Zahner, J; Vargus-Adams, J; Mcmahon, MA; Aronow, BJ; Mitelpunkt, A. Electronic health record and patterns of care for children with cerebral palsy. Developmental Medicine and Child Neurology. 2021; 63:1337-1343.

Jin, K; Bardes, EE; Mitelpunkt, A; Wang, JY; Bhatnagar, S; Sengupta, S; Krummel, DP; Rothenberg, ME; Aronow, BJ. An interactive single cell web portal identifies gene and cell networks in COVID-19 host responses. iScience. 2021; 24:103115.

Haniffa, M; Taylor, D; Linnarsson, S; Aronow, BJ; Bader, GD; Barker, RA; Camara, PG; Camp, JG; Chédotal, A; Copp, A; Souyri, M; Sundström, E; Zaffran, S; Zilbauer, M. A roadmap for the Human Developmental Cell Atlas. Nature. 2021; 597:196-205.

Mo, A; Nagpal, S; Gettler, K; Haritunians, T; Giri, M; Haberman, Y; Karns, R; Prince, J; Arafat, D; Hsu, NY; Kugathasan, S; Cho, JH; Denson, LA; Gibson, G. Stratification of risk of progression to colectomy in ulcerative colitis via measured and predicted gene expression. The American Journal of Human Genetics. 2021; 108:1765-1779.

Lewis, CS; Karve, A; Matiash, K; Stone, T; Li, J; Wang, JK; Versteeg, HH; Aronow, BJ; Ahmad, SA; Desai, PB; Bogdanov, VY. A First-In-Class, Humanized Antibody Targeting Alternatively Spliced Tissue Factor: Preclinical Evaluation in an Orthotopic Model of Pancreatic Ductal Adenocarcinoma. Frontiers in Oncology. 2021; 11:691685.

Bourgeois, FT; Gutiérrez-Sacristán, A; Keller, MS; Liu, M; Hong, C; Bonzel, CL; Tan, AL M; Aronow, BJ; Boeker, M; Booth, J; Weber, GM; Kohane, IS; Cai, T; Avillach, P. International Analysis of Electronic Health Records of Children and Youth Hospitalized With COVID-19 Infection in 6 Countries. JAMA Network Open. 2021; 4:e2112596.

Pak, CH; Danko, T; Mirabella, VR; Wang, J; Liu, Y; Vangipuram, M; Grieder, S; Zhang, X; Ward, T; Huang, YW A; Pang, ZP; Levinson, DF; Wernig, M; Südhof, TC. Cross-platform validation of neurotransmitter release impairments in schizophrenia patient-derived NRXN1-mutant neurons. Proceedings of the National Academy of Sciences of USA. 2021; 118:e2025598118.

Ware, SM; Wilkinson, JD; Tariq, M; Schubert, JA; Sridhar, A; Colan, SD; Shi, L; Canter, CE; Hsu, DT; Webber, SA; Sleeper, LA; Razoky, H; Czachor, J; Lipshultz, SE. Genetic Causes of Cardiomyopathy in Children: First Results From the Pediatric Cardiomyopathy Genes Study. Journal of the American Heart Association: Cardiovascular and Cerebrovascular Disease. 2021; 10:e017731.

Sengupta, S; Pater, LE; Krummel, DP; Aronow, BJ; Hirota, Y; Phoenix, TN; Sasaki, AT. Integration of Molecular Analysis, Cutting-edge Mouse Genetic Models and Proton Therapy to Improve Outcomes for Glioma Patients. Gliomas. : Exon Publications; Exon Publications; 2021.

Bailes, AF; Greve, K; Long, J; Kurowski, BG; Vargus-Adams, J; Aronow, B; Mitelpunkt, A. Describing the Delivery of Evidence-Based Physical Therapy Intervention to Individuals With Cerebral Palsy. Pediatric Physical Therapy. 2021; 33:65-72.

Mast, AE; Wolberg, AS; Gailani, D; Garvin, MR; Alvarez, C; Izaak Miller, J; Aronow, B; Jacobson, D. SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung. eLife. 2021; 10:e64330.

Kohane, IS; Aronow, BJ; Avillach, P; Beaulieu-Jones, BK; Bellazzi, R; Bradford, RL; Brat, GA; Cannataro, M; Cimino, JJ; García-Barrio, N; Kraska, D; Krishnamurthy, AK; L'Yi, S; Le, TT. What Every Reader Should Know About Studies Using Electronic Health Record Data but May Be Afraid to Ask. Journal of Medical Internet Research. 2021; 23:e22219.

Elbert, GN; Valentine, C; Aronow, B; Hovey, R; Trott, J; Wagner, E; Karns, R; Riddle, S; Thompson, A; Ward, LP; Nommsen-Rivers, L. Expression Of Inflammation Associated Genes In The Mammary Gland Of Lactating Women With Elevated Plasma Triglycerides. Pediatrics. 2021; 147:315-316.

Sarangdhar, M; Yacyshyn, MB; Gruenzel, AR; Engevik, MA; Harris, NL; Aronow, BJ; Yacyshyn, BR. Therapeutic Opportunities for Intestinal Angioectasia- Targeting PPARγ and Oxidative Stress. Clinical and Translational Science. 2021; 14:518-528.

Haberman, Y; Minar, P; Karns, R; Dexheimer, PJ; Ghandikota, S; Tegge, S; Shapiro, D; Shuler, B; Venkateswaran, S; Braun, T; Hyams, JS; Kugathasan, S; Jegga, AG; Denson, LA. Mucosal Inflammatory and Wound Healing Gene Programs Reveal Targets for Stricturing Behavior in Pediatric Crohn's Disease. Journal of Crohn's and Colitis. 2021; 15:273-286.

Hayakawa, T; Prasath, VB S; Kawanaka, H; Aronow, BJ; Tsuruoka, S. Computational Nuclei Segmentation Methods in Digital Pathology: A Survey. Archives of Computational Methods in Engineering. 2021; 28:1-13.