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; et al. 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; et al. 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.

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

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.

Tan, AL M; Getzen, EJ; Hutch, MR; Strasser, ZH; Gutiérrez-Sacristán, A; Le, TT; Dagliati, A; Morris, M; Hanauer, DA; Moal, B; et al. Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record?. Journal of Biomedical Informatics. 2023; 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. 2023; 1-8.

Orieux, A; Ferté, T; Jouhet, V; Aaron, JR; Agapito, G; Albayrak, A; Albi, G; Alessiani, M; Alloni, A; Amendola, DF; et al. 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.

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; et al. Long-term kidney function recovery and mortality after COVID-19-associated acute kidney injury: An international multi-centre observational cohort study. EClinicalMedicine. 2023; 55.

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

Weber, GM; Hong, C; Xia, Z; Palmer, NP; L’Yi, S; Keller, MS; Murphy, SN; Gutiérrez-Sacristán, A; Bonzel, CL; Serret-Larmande, A; et al. International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality. npj Digital Medicine. 2022; 5.

Zhang, HG; Dagliati, A; Shakeri Hossein Abad, Z; Xiong, X; Bonzel, CL; Xia, Z; Tan, BW Q; Avillach, P; Brat, GA; Hong, C; et al. International electronic health record-derived post-acute sequelae profiles of COVID-19 patients. npj Digital Medicine. 2022; 5.

Gaddis, N; Fortriede, J; Guo, M; Bardes, EE; Kouril, M; Tabar, S; Burns, K; Ardini-Poleske, ME; Loos, S; Schnell, D; et al. LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung. American Journal of Respiratory Cell and Molecular Biology. 2022.

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.

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.

Barrila, J; Yang, J; Franco Meléndez, KP; Yang, S; Buss, K; Davis, TJ; Aronow, BJ; Bean, HD; Davis, RR; Forsyth, RJ; et al. 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.

Xu, X; Jin, K; Bais, AS; Zhu, W; Yagi, H; Feinstein, TN; Nguyen, PK; Criscione, JD; Liu, X; Beutner, G; et al. 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.

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

Karlebach, G; Aronow, B; Baylin, SB; Butler, D; Foox, J; Levy, S; Meydan, C; Mozsary, C; Saravia-Butler, AM; Taylor, DM; et al. Betacoronavirus-specific alternate splicing. Genomics. 2022; 114.

Ware, SM; Bhatnagar, S; Dexheimer, PJ; Wilkinson, JD; Sridhar, A; Fan, X; Shen, Y; Tariq, M; Schubert, JA; Colan, SD; et al. The genetic architecture of pediatric cardiomyopathy. 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.

Sun, X; Perl, AK; Li, R; Bell, SM; Sajti, E; Kalinichenko, VV; Kalin, TV; Misra, RS; Deshmukh, H; Clair, G; et al. 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; et al. Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images. BMC Bioinformatics. 2021; 22.

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.

Kerlavage, AR; Kirchhoff, AC; Guidry Auvil, JM; Sharpless, NE; Davis, KL; Reilly, K; Reaman, G; Penberthy, L; Deapen, D; Hwang, A; et al. 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.

Estiri, H; Strasser, ZH; Brat, GA; Semenov, YR; Aaron, JR; Agapito, G; Albayrak, A; Alessiani, M; Amendola, DF; Anthony, LL L J; et al. Evolving phenotypes of non-hospitalized patients that indicate long COVID. BMC Medicine. 2021; 19.

Le, TT; Gutiérrez-Sacristán, A; Son, J; Hong, C; South, AM; Beaulieu-Jones, BK; Loh, NH W; Luo, Y; Morris, M; Ngiam, KY; et al. Multinational characterization of neurological phenotypes in patients hospitalized with COVID-19. Scientific Reports. 2021; 11.

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.

Haniffa, M; Taylor, D; Linnarsson, S; Aronow, BJ; Bader, GD; Barker, RA; Camara, PG; Camp, JG; Chédotal, A; Copp, A; et al. 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; et al. Stratification of risk of progression to colectomy in ulcerative colitis via measured and predicted gene expression. 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; et al. 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.

Karlebach, G; Aronow, B; Baylin, SB; Butler, D; Foox, J; Levy, S; Meydan, C; Mozsary, C; Saravia-Butler, AM; Taylor, DM; et al. Betacoronavirus-specific alternate splicing. 2021.

Jin, K; Bardes, EE; Mitelpunkt, A; Wang, JY; Bhatnagar, S; Sengupta, S; Krummel, DP; Rothenberg, ME; Aronow, BJ. Implicating Gene and Cell Networks Responsible for Differential COVID-19 Host Responses via an Interactive Single Cell Web Portal. 2021.

Bourgeois, FT; Gutiérrez-Sacristán, A; Keller, MS; Liu, M; Hong, C; Bonzel, CL; Tan, AL M; Aronow, BJ; Boeker, M; Booth, J; et al. International Analysis of Electronic Health Records of Children and Youth Hospitalized With COVID-19 Infection in 6 Countries. JAMA Network Open. 2021; 4.

Pak, CH; Danko, T; Mirabella, VR; Wang, J; Liu, Y; Vangipuram, M; Grieder, S; Zhang, X; Ward, T; Huang, YW A; et al. Cross-platform validation of neurotransmitter release impairments in schizophrenia patient-derived NRXN1-mutant neurons. Proceedings of the National Academy of Sciences of the United States of America. 2021; 118.

Ware, SM; Wilkinson, JD; Tariq, M; Schubert, JA; Sridhar, A; Colan, SD; Shi, L; Canter, CE; Hsu, DT; Webber, SA; et al. Genetic Causes of Cardiomyopathy in Children: First Results From the Pediatric Cardiomyopathy Genes Study. Journal of the American Heart Association. 2021; 10.

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. 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.

Kohane, IS; Aronow, BJ; Avillach, P; Beaulieu-Jones, BK; Bellazzi, R; Bradford, RL; Brat, GA; Cannataro, M; Cimino, JJ; García-Barrio, N; et al. 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.

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.

Weber, GM; Hong, C; Palmer, NP; Avillach, P; Murphy, SN; Gutiérrez-Sacristán, A; Xia, Z; Serret-Larmande, A; Neuraz, A; Omenn, GS; et al. International Comparisons of Harmonized Laboratory Value Trajectories to Predict Severe COVID-19: Leveraging the 4CE Collaborative Across 342 Hospitals and 6 Countries: A Retrospective Cohort Study. 2021.

Haberman, Y; Minar, P; Karns, R; Dexheimer, PJ; Ghandikota, S; Tegge, S; Shapiro, D; Shuler, B; Venkateswaran, S; Braun, T; et al. 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.

Füllgrabe, A; George, N; Green, M; Nejad, P; Aronow, B; Fexova, SK; Fischer, C; Freeberg, MA; Huerta, L; Morrison, N; et al. Guidelines for reporting single-cell RNA-seq experiments. Nature Biotechnology. 2020; 38:1384-1386.

Saito, D; Kawanaka, H; Surya Prasath, VB; Aronow, BJ. CNNを用いたGliomaの疾患進行度評価における形状特徴量に関する一検討. IEEJ Transactions on Electronics, Information and Systems. 2020; 140:1367-1368.

Haniffa, M; Taylor, D; Linnarsson, S; Aronow, B; Bader, G; Camara, P; Camp, G; Chédotal, A; Copp, A; Etchevers, H; et al. Human Developmental Cell Atlas: milestones achieved and the roadmap ahead. 2020.

Riccetti, M; Gokey, JJ; Aronow, B; Perl, AT. The elephant in the lung: Integrating lineage-tracing, molecular markers, and single cell sequencing data to identify distinct fibroblast populations during lung development and regeneration. Matrix Biology. 2020; 91-92:51-74.

Garvin, MR; Alvarez, C; Miller, JI; Prates, ET; Walker, AM; Amos, BK; Mast, AE; Justice, A; Aronow, B; Jacobson, D. A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm. eLife. 2020; 9.

Alimohamed, S; Geller, JI; Aronow, B. TCGA Kidney Cell Atlas: A differential gene expression database for the dissection of tumor-specific gene modules. Journal of Clinical Oncology. 2020; 38:e17078-e17078.

McDaniel, CT; Panmanee, W; Winsor, GL; Gill, E; Bertelli, C; Schurr, MJ; Dongare, P; Paul, AT; Ko, SB; Lau, GW; et al. AB569, a nontoxic chemical tandem that kills major human pathogenic bacteria. Proceedings of the National Academy of Sciences of the United States of America. 2020; 117:4921-4930.

Woodle, ES; Tremblay, S; Brailey, P; Girnita, A; Alloway, RR; Aronow, B; Dasgupta, N; Ebstein, F; Kloetzel, P; Lee, MJ; et al. Proteasomal adaptations underlying carfilzomib-resistance in human bone marrow plasma cells. American Journal of Transplantation. 2020; 20:399-410.

Smith-Anttila, CJ A; Mason, EA; Wells, CA; Aronow, BJ; Osborne, PB; Keast, JR. Identification of a Sacral, Visceral Sensory Transcriptome in Embryonic and Adult Mice. eNeuro. 2020; 7.

Haberman Ziv, Y; Minar, P; Karns, R; Dexheimer, P; Ghandikota, S; Tegge, S; Shapiro, D; Shuler, B; Venkateswaran, S; Braun, T; et al. DOP89 Pre-treatment mucosal inflammatory and wound healing gene programmes reveal mechanisms associated with future stricturing behaviour during 5-year follow-up in paediatric Crohn’s disease. Journal of Crohn's and Colitis. 2020; 14:s127-s127.

Isaka, S; Kawanaka, H; Prasath, VB S; Aronow, BJ; Tsuruoka, S. (2020) Development of a Web Based Image Annotation Tool for Lung Immunofluorescent Confocal Images. ISASE2018:1-5.

Haberman, Y; Karns, R; Dexheimer, PJ; Schirmer, M; Somekh, J; Jurickova, I; Braun, T; Novak, E; Bauman, L; Collins, MH; et al. Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response. Nature Communications. 2019; 10.

Isaka, S; Kawanaka, H; Aronow, BJ; Prasath, VB S. (2019) Multi-Class Segmentation of Lung Immunofluorescence Confocal Images Using Deep Learning. 00:2362-2368.

Schrode, N; Ho, S; Yamamuro, K; Dobbyn, A; Huckins, L; Matos, MR; Cheng, E; Deans, PJ M; Flaherty, E; Barretto, N; et al. Synergistic effects of common schizophrenia risk variants. Nature Genetics. 2019; 51:1475-1485.

Khalil, H; Jones, SM; Alam, P; Aronow, BJ; Molkentin, JD; Kanisicak, O. Abstract 837: Different Disease States in Heart Have Distinct Cardiac Interstitial Cells Contributing to Fibrosis. Circulation Research. 2019; 125.

Nasimuzzaman, M; Arumugam, PI; Mullins, ES; James, JM; VandenHeuvel, K; Narciso, MG; Shaw, MA; McGraw, S; Aronow, BJ; Malik, P. Elimination of the fibrinogen integrin αMβ2-binding motif improves renal pathology in mice with sickle cell anemia. Blood Advances. 2019; 3:1519-1532.

Weng, Q; Wang, J; Wang, J; He, D; Cheng, Z; Zhang, F; Verma, R; Xu, L; Dong, X; Liao, Y; et al. Single-Cell Transcriptomics Uncovers Glial Progenitor Diversity and Cell Fate Determinants during Development and Gliomagenesis. Cell Stem Cell. 2019; 24:707-723.e8.

Wen, T; Aronow, BJ; Rochman, Y; Rochman, M; Kiran, KC; Dexheimer, PJ; Putnam, P; Mukkada, V; Foote, H; Rehn, K; et al. Single-cell RNA sequencing identifies inflammatory tissue T cells in eosinophilic esophagitis. Journal of Clinical Investigation. 2019; 129:2014-2028.

Peters, AL; Luo, Z; Li, J; Mourya, R; Wang, Y; Dexheimer, P; Shivakumar, P; Aronow, B; Bezerra, JA. Single cell RNA sequencing reveals regional heterogeneity of hepatobiliary innate lymphoid cells in a tissue-enriched fashion. PLoS ONE. 2019; 14.

Taylor, DM; Aronow, BJ; Tan, K; Bernt, K; Salomonis, N; Greene, CS; Frolova, A; Henrickson, SE; Wells, A; Pei, L; et al. The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Developmental Cell. 2019; 49:10-29.

Haberman, Y; Schirmer, M; Dexheimer, PJ; Karns, R; Braun, T; Kim, M; Walters, TD; Baldassano, RN; Noe, JD; Rosh, J; et al. Age-of-diagnosis dependent ileal immune intensification and reduced alpha-defensin in older versus younger pediatric Crohn Disease patients despite already established dysbiosis. Mucosal Immunology. 2019; 12:491-502.

Denson, LA; Jurickova, I; Karns, R; Shaw, KA; Cutler, DJ; Okou, D; Valencia, CA; Dodd, A; Mondal, K; Aronow, BJ; et al. Genetic and Transcriptomic Variation Linked to Neutrophil Granulocyte-Macrophage Colony-Stimulating Factor Signaling in Pediatric Crohn's Disease. Inflammatory Bowel Diseases. 2019; 25:547-560.

Yonekura, A; Kawanaka, H; Prasath, VB S; Aronow, BJ; Tsuruoka, S; IEEE, . (2019) Glioma Subtypes Clustering Method using Histopathological Image Analysis. 00:442-446.

Shaw, KA; Cutler, DJ; Okou, D; Dodd, A; Aronow, BJ; Haberman, Y; Stevens, C; Walters, TD; Griffiths, A; Baldassano, RN; et al. Genetic variants and pathways implicated in a pediatric inflammatory bowel disease cohort. Genes and Immunity. 2019; 20:131-142.

Turnier, JL; Brunner, HI; Bennett, M; Aleed, A; Gulati, G; Haffey, WD; Thornton, S; Wagner, M; Devarajan, P; Witte, D; et al. Discovery of SERPINA3 as a candidate urinary biomarker of lupus nephritis activity. Rheumatology. 2019; 58:321-330.

Ljungberg, MC; Sadi, M; Wang, Y; Aronow, BJ; Xu, Y; Kao, RJ; Liu, Y; Gaddis, N; Ardini-Poleske, ME; Umrod, T; et al. Spatial distribution of marker gene activity in the mouse lung during alveolarization. Data in Brief. 2019; 22:365-372.

Lewis, CS; Thomas, HE; Orr-Asman, MA; Green, LC; Boody, RE; Matiash, K; Karve, A; Hisada, YM; Davis, HW; Qi, X; et al. mTOR kinase inhibition reduces tissue factor expression and growth of pancreatic neuroendocrine tumors. Journal of Thrombosis and Haemostasis. 2019; 17:169-182.

Higashi, AY; Aronow, BJ; Dressler, GR. Expression Profiling of Fibroblasts in Chronic and Acute Disease Models Reveals Novel Pathways in Kidney Fibrosis. Journal of the American Society of Nephrology : JASN. 2019; 30:80-94.

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