Biomedical Informatics

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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.

Bartram, J; Song, BA; Xu, J; Salomonis, N; Grimes, HL; Filippi, M. Divisional Memory Drives Hematopoietic Stem Cell Functional Diversity. Blood. 2021; 138:20-20.

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Bono, C; Guerrero, P; Jordán-Pla, A; Erades, A; Salomonis, N; Grimes, HL; Gil, ML; Yáñez, A. GM-CSF Programs Hematopoietic Stem and Progenitor Cells During Candida albicans Vaccination for Protection Against Reinfection. Frontiers in Immunology. 2021; 12.

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Chen, D; Wang, Y; Manakkat Vijay, GK; Fu, S; Nash, CW; Xu, D; He, D; Salomonis, N; Singh, H; Xu, H. Coupled analysis of transcriptome and BCR mutations reveals role of OXPHOS in affinity maturation. Nature Immunology. 2021; 22:904-913.

Chen, JA; Hou, Y; Roskin, KM; Arber, DA; Bangs, CD; Baughn, LB; Cherry, AM; Ewalt, MD; Fire, AZ; Fresard, L; et al. Lymphoid blast transformation in an MPN with BCR-JAK2 treated with ruxolitinib: putative mechanisms of resistance. Blood Advances. 2021; 5:3492-3496.

Chidambaran, V; Pilipenko, V; Jegga, AG; Geisler, K; Martin, LJ. Systems Biology Guided Gene Enrichment Approaches Improve Prediction of Chronic Post-surgical Pain After Spine Fusion. Frontiers in Genetics. 2021; 12.

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Damal Villivalam, S; Ebert, SM; Lim, HW; Kim, J; You, D; Jung, BC; Palacios, HH; Tcheau, T; Adams, CM; Kang, S. A necessary role of DNMT3A in endurance exercise by suppressing ALDH1L1-mediated oxidative stress. EMBO Journal. 2021; 40.

Davidson, WS; Cooke, AL; Swertfeger, DK; Shah, AS. The Difference Between High Density Lipoprotein Subfractions and Subspecies: an Evolving Model in Cardiovascular Disease and Diabetes. Current Atherosclerosis Reports. 2021; 23.

Desai, DA; Rao, V; Jegga, A; Dhandapany, P; Sadayappan, S. Abstract MP264: Heterogeneous Distribution Of Mutations In Myosin Binding Protein-c Paralogs. Circulation Research. 2021; 129.

Desprez, PY; Murase, R; Limbad, C; Woo, RW L; Adrados, I; Weitenthaler, K; Soroceanu, L; Salomonis, N; McAllister, SD. Cannabidiol Treatment Results in a Common Gene Expression Response Across Aggressive Cancer Cells from Various Origins. Cannabis and Cannabinoid Research. 2021; 6:148-155.

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Dighe, P; Woo, R; Salomonis, N; Bhattacharjee, A; Nosrati, M; Desprez, P; Dickinson, L; McAllister, S; Soroceanu, L. EXTH-62. COMBINATORIAL THERAPY TARGETING TRANSCIPTION AND IMMUNO-METABOLISM IN RECURRENT GLIOBLASTOMA. Neuro-Oncology. 2021; 23:vi177-vi177.

Dreskin, SC; Koppelman, SJ; Andorf, S; Nadeau, KC; Kalra, A; Braun, W; Negi, SS; Chen, X; Schein, CH. The importance of the 2S albumins for allergenicity and cross-reactivity of peanuts, tree nuts, and sesame seeds. Journal of Allergy and Clinical Immunology. 2021; 147:1154-1163.

Ebrahimpour, A; Wang, M; Li, L; Jegga, AG; Bonnen, MD; Eissa, NT; Raghu, G; Jyothula, S; Kheradmand, F; Hanania, NA; et al. Esomeprazole attenuates inflammatory and fibrotic response in lung cells through the MAPK/Nrf2/HO1 pathway. Journal of Inflammation. 2021; 18.

Eric, V; Yi, V; Murdock, D; Kalla, SE; Wu, TJ; Sabo, A; Li, S; Meng, Q; Tian, X; Murugan, M; et al. Neptune: an environment for the delivery of genomic medicine. Genetics in Medicine. 2021; 23:1838-1846.

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.

Fenix, AM; Miyaoka, Y; Bertero, A; Blue, SM; Spindler, MJ; Tan, KK B; Perez-Bermejo, JA; Chan, AH; Mayerl, SJ; Nguyen, TD; et al. Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. Nature Communications. 2021; 12.

Gajjala, PR; Kasam, RK; Soundararajan, D; Sinner, D; Huang, SK; Jegga, AG; Madala, SK. Dysregulated overexpression of Sox9 induces fibroblast activation in pulmonary fibrosis. JCI insight. 2021; 6.

Gao, DK; Salomonis, N; Henderlight, M; Woods, C; Thakkar, K; Grom, AA; Thornton, S; Jordan, MB; Wikenheiser-Brokamp, KA; Schulert, GS. IFN-γ is essential for alveolar macrophage-driven pulmonary inflammation in macrophage activation syndrome. JCI insight. 2021; 6.

Gecili, E; Brokamp, C; Palipana, A; Huang, R; Andrinopoulou, ER; Pestian, T; Rasnick, E; Keogh, RH; Ni, Y; Clancy, JP; et al. Seasonal variation of lung function in cystic fibrosis: Longitudinal modeling to compare a Midwest US cohort to international populations. Science of the Total Environment. 2021; 776.

Gecili, E; Palipana, A; Brokamp, C; Huang, R; Andrinopoulou, ER; Pestian, T; Rasnick, E; Keogh, RH; Ni, Y; Clancy, JP; et al. Seasonality, mediation and comparison (SMAC) methods to identify influences on lung function decline. MethodsX. 2021; 8.

Ghandikota, S; Sharma, M; Jegga, AG. Secondary analysis of transcriptomes of SARS-CoV-2 infection models to characterize COVID-19. Patterns. 2021; 2.

Ghandikota, S; Sharma, M; Jegga, AG. Computational workflow for functional characterization of COVID-19 through secondary data analysis. STAR Protocols. 2021; 2.

Gracia-Maldonado, G; Clark, J; Burwinkel, M; Greenslade, B; Wunderlich, M; Salomonis, N; Leone, D; Gatti, E; Pierre, P; Kumar, AR; et al. LAMP-5 is an essential inflammatory-signaling regulator and novel immunotherapy target for Mixed Lineage Leukemia-Rearranged acute leukemia. Haematologica. 2021.

Guarnieri, KM; Slack, IF; Gadoury-Lévesque, V; Eapen, AA; Andorf, S; Lierl, MB. Peanut oral immunotherapy in a pediatric allergy clinic: Patient factors associated with clinical outcomes. Annals of Allergy, Asthma and Immunology. 2021; 127:214-222.e4.

Haberman, Y; Iqbal, NT; Ghandikota, S; Mallawaarachchi, I; Tzipi Braun, ; Dexheimer, PJ; Rahman, N; Hadar, R; Sadiq, K; Ahmad, Z; et al. Mucosal Genomics Implicate Lymphocyte Activation and Lipid Metabolism in Refractory Environmental Enteric Dysfunction. Gastroenterology. 2021; 160:2055-2071.e0.

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.

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: New biology. 2021; 597:196-205.

Hartiala, JA; Han, Y; Jia, Q; Hilser, JR; Huang, P; Gukasyan, J; Schwartzman, WS; Cai, Z; Biswas, S; Trégouët, DA; et al. Genome-wide analysis identifies novel susceptibility loci for myocardial infarction. European Heart Journal. 2021; 42:919-933.

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.

He, Z; Vadali, VL G; Szabady, RL; Zhang, W; Norman, JM; Roberts, B; Tibshirani, R; Desai, M; Chinthrajah, RS; Galli, SJ; et al. Increased diversity of gut microbiota during active oral immunotherapy in peanut-allergic adults. Allergy: European Journal of Allergy and Clinical Immunology. 2021; 76:927-930.

Hunter, LL; Blankenship, CM; Lin, L; Sloat, NT; Perdew, A; Stewart, H; Moore, DR. Peripheral Auditory Involvement in Childhood Listening Difficulty. Ear and Hearing. 2021; 42:29-41.

Huynh, VN; Wang, S; Ouyang, X; Wani, WY; Johnson, MS; Chacko, BK; Jegga, AG; Qian, W; Chatham, JC; Darley-Usmar, VM; et al. Defining the Dynamic Regulation of O-GlcNAc Proteome in the Mouse Cortex---the O-GlcNAcylation of Synaptic and Trafficking Proteins Related to Neurodegenerative Diseases. 2021; 2.

Jarmas, AE; Brunskill, EW; Chaturvedi, P; Salomonis, N; Kopan, R. Progenitor translatome changes coordinated by Tsc1 increase perception of Wnt signals to end nephrogenesis. Nature Communications. 2021; 12.

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.

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.

Kaushik, A; Dunham, D; He, Z; Manohar, M; Desai, M; Nadeau, KC; Andorf, S. CyAnno: A semi-automated approach for cell type annotation of mass cytometry datasets. Computer Applications in the Biosciences. 2021.

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.

Kim, KB; Soroceanu, L; de Semir, D; Millis, SZ; Ross, J; Vosoughi, E; Dar, AA; Nosrati, M; Desprez, PY; Ice, R; et al. Prevalence of Homologous Recombination Pathway Gene Mutations in Melanoma: Rationale for a New Targeted Therapeutic Approach. Journal of Investigative Dermatology. 2021; 141:2028-2036.e2.

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.

Kolega, J; Poppenberg, KE; Lim, HW; Gutierrez, LC; Veeturi, SS; Siddiqui, AH; Rajabzadeh-Oghaz, H; Tutino, VM. Identification of intima-to-media signals for flow-induced vascular remodeling using correlative gene expression analysis. Scientific Reports. 2021; 11.

Kumar, A; Elko, E; Bruno, SR; Mark, ZF; Chamberlain, N; Mihavics, BK; Chandrasekaran, R; Walzer, J; Ruban, M; Gold, C; et al. Inhibition of PDIA3 in club cells attenuates osteopontin production and lung fibrosis. Thorax. 2021.

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.

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.

Lee, M; Hall, ES; Taylor, M; DeFranco, EA. Regional Contribution of Previable Infant Deaths to Infant Mortality Rates in the United States. American Journal of Perinatology. 2021; 38:158-165.

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.

Li, G; Iyer, B; Prasath, VB S; Ni, Y; Salomonis, N. DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity. Briefings in Bioinformatics. 2021; 22.

Li, Y; Deng, S; Wang, X; Huang, W; Chen, J; Robbins, N; Mu, X; Essandoh, K; Peng, T; Jegga, AG; et al. Sectm1a deficiency aggravates inflammation-triggered cardiac dysfunction through disruption of LXRα signalling in macrophages. Cardiovascular Research. 2021; 117:890-902.

Liu, H; Xu, J; Lan, Y; Lim, HW; Jiang, R. The Scleraxis Transcription Factor Directly Regulates Multiple Distinct Molecular and Cellular Processes During Early Tendon Cell Differentiation. Frontiers in Cell and Developmental Biology. 2021; 9.

Liu, L; Ni, Y; Beck, AF; Brokamp, C; Ramphul, RC; Highfield, LD; Kanjia, MK; Pratap, J. Understanding Pediatric Surgery Cancellation: Geospatial Analysis. Journal of Medical Internet Research. 2021; 23.

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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.

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