Biomedical Informatics

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Jin, K; Bardes, EE; Mitelpunkt, A; Wang, JY; Bhatnagar, S; Sengupta, S; Krummel, DP; Rothenberg, ME; Aronow, BJ. A Web Portal and Workbench for Biological Dissection of Single Cell COVID-19 Host Responses. 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.

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.

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.

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.

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.

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.

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.

Manohar, M; Dunham, D; Gupta, S; Yan, Z; Zhang, W; Minnicozzi, S; Kirkey, M; Bunning, B; Roy Chowdhury, R; Galli, SJ; et al. Immune changes beyond Th2 pathways during rapid multifood immunotherapy enabled with omalizumab. Allergy: European Journal of Allergy and Clinical Immunology. 2021.

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.

Moreno-Fernandez, ME; Giles, DA; Oates, JR; Chan, CC; Damen, MS M A; Doll, JR; Stankiewicz, TE; Chen, X; Chetal, K; Karns, R; et al. PKM2-dependent metabolic skewing of hepatic Th17 cells regulates pathogenesis of non-alcoholic fatty liver disease. Cell Metabolism. 2021; 33:1187-1204.e9.

Mu, X; Fan, H; Wang, P; Li, Y; Domenico, K; Li, Q; Wang, X; Essandoh, K; Chen, J; Peng, T; et al. Sectm1a Facilitates Protection against Inflammation-Induced Organ Damage through Promoting TRM Self-Renewal. Molecular Therapy. 2021; 29:1294-1311.

Namjou, B; Stanaway, IB; Lingren, T; Mentch, FD; Benoit, B; Dikilitas, O; Niu, X; Shang, N; Shoemaker, AH; Carey, DJ; et al. Evaluation of the MC4R gene across eMERGE network identifies many unreported obesity-associated variants. International Journal of Obesity. 2021; 45:155-169.

Neeland, MR; Andorf, S; Dang, TD; McWilliam, VL; Perrett, KP; Koplin, JJ; Saffery, R. Altered immune cell profiles and impaired CD4 T-cell activation in single and multi-food allergic adolescents. Clinical and Experimental Allergy. 2021; 51:674-684.

Neeland, MR; Tursi, AR; Perrett, KP; Saffery, R; Koplin, JJ; Nadeau, KC; Andorf, S. Vitamin D insufficiency is associated with reduced regulatory T cell frequency in food-allergic infants. Pediatric Allergy and Immunology. 2021; 32:771-775.

Orlovsky, M; Meyer, J; Mitelpunkt, A; Weiss-Meilik, A. Patient monitoring as a predictor of blood culture results in a tertiary neonatal intensive care unit. Applied Ergonomics. 2021; 90.

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.

Porat Rein, A; Kramer, U; Hausman Kedem, M; Fattal-Valevski, A; Mitelpunkt, A. Early prediction of encephalopathic transformation in children with benign epilepsy with centro-temporal spikes. No To Hattatsu. 2021; 43:268-279.

Porat Rein, A; Kramer, U; Hausman Kedem, M; Fattal-Valevski, A; Mitelpunkt, A. Early risk factors for encephalopathic transformation in children with benign childhood epilepsy with centrotemporal spikes. No To Hattatsu. 2021; 43:603-604.

Reiman, D; Vijay, GK M; Xu, H; Sonin, A; Chen, D; Salomonis, N; Singh, H; Khan, AA. Pseudocell Tracer-A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination. PLoS Computational Biology. 2021; 17.

Salomone, J; Qin, S; Fufa, TD; Cain, B; Farrow, E; Guan, B; Hufnagel, RB; Nakafuku, M; Lim, HW; Campbell, K; et al. Conserved Gsx2/Ind homeodomain monomer versus homodimer DNA binding defines regulatory outcomes in flies and mice. Genes and Development. 2021; 35:157-174.

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.

Schuh, MP; Alkhudairy, L; Potter, A; Potter, SS; Chetal, K; Thakkar, K; Salomonis, N; Kopan, R. The Rhesus Macaque Serves As a Model for Human Lateral Branch Nephrogenesis. Journal of the American Society of Nephrology : JASN. 2021; 32:1097-1112.

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.

Sertorio, M; Nowrouzi, A; Akbarpour, M; Chetal, K; Salomonis, N; Brons, S; Mascia, A; Ionascu, D; McCauley, S; Kupneski, T; et al. Differential transcriptome response to proton versus X-ray radiation reveals novel candidate targets for combinatorial PT therapy in lymphoma. Radiotherapy and Oncology. 2021; 155:293-303.

Shamsaei, B; Chojnacki, S; Pilarczyk, M; Najafabadi, M; Niu, W; Chen, C; Ross, K; Matlock, A; Muhlich, J; Chutipongtanate, S; et al. piNET: a versatile web platform for downstream analysis and visualization of proteomics data. Nucleic Acids Research. 2021; 48:W85-W93.

Sherman, KE; Rouster, SD; Meeds, H; Tamargo, J; Chen, J; Ehman, R; Baum, M. PNPLA3 Single Nucleotide Polymorphism Prevalence and Association with Liver Disease in a Diverse Cohort of Persons Living with HIV. Biology. 2021; 10.

Ta, AD; Ollberding, NJ; Karns, R; Haberman, Y; Alazraki, AL; Hercules, D; Baldassano, R; Markowitz, J; Heyman, MB; Kim, S; et al. Association of Baseline Luminal Narrowing With Ileal Microbial Shifts and Gene Expression Programs and Subsequent Transmural Healing in Pediatric Crohn Disease. Inflammatory Bowel Diseases. 2021.

Wagar, LE; Salahudeen, A; Constantz, CM; Wendel, BS; Lyons, MM; Mallajosyula, V; Jatt, LP; Adamska, JZ; Blum, LK; Gupta, N; et al. Modeling human adaptive immune responses with tonsil organoids. Nature Medicine. 2021; 27:125-135.

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.

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.

Wu, G; Lee, YY; Gulla, EM; Potter, A; Kitzmiller, J; Ruben, MD; Salomonis, N; Whitsett, JA; Francey, LJ; Hogenesch, JB; et al. Short-term exposure to intermittent hypoxia leads to changes in gene expression seen in chronic pulmonary disease. eLife. 2021; 10.

Yang, F; Nielsen, SC A; Hoh, RA; Röltgen, K; Wirz, OF; Haraguchi, E; Jean, GH; Lee, JY; Pham, TD; Jackson, KJ L; et al. Shared B cell memory to coronaviruses and other pathogens varies in human age groups and tissues. The Scientific monthly. 2021; 372:738-741.

Yella, JK; Jegga, A. MGATRx: Discovering Drug Repositioning Candidates Using Multi-view Graph Attention. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2021; PP.

Yombo, DJ K; Odayar, V; Gupta, N; Jegga, AG; Madala, SK. The Protective Effects of IL-31RA Deficiency During Bleomycin-Induced Pulmonary Fibrosis. Frontiers in Immunology. 2021; 12.

Zhang, J; Wu, Q; Johnson, CB; Pham, G; Kinder, JM; Olsson, A; Slaughter, A; May, M; Weinhaus, B; D’Alessandro, A; et al. In situ mapping identifies distinct vascular niches for myelopoiesis. Nature: New biology. 2021; 590:457-462.