Biomedical Informatics

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.

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.

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.

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.

Kim, KB; Soroceanu, L; de Semir, D; Millis, SZ; Ross, J; Vosoughi, E; Dar, AA; Nosrati, M; Desprez, P; 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, 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.

Manohar, M; Dunham, D; Gupta, S; Yan, Z; Zhang, W; Minnicozzi, S; Kirkey, M; Bunning, B; Chowdhury, RR; 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.

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.

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.

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.

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.

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.

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.

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.

Varisco, B; Joshi, R; Jones, R; Paranjpe, A; Roskin, K; Yunger, T; Stoneman, E; Lahni, P; Wong, H; Williams, J. 1003: Nasal Transcriptomic and Serum Proteomic Identification of Three Pediatric ARDS Subtypes. Critical Care Medicine. 2021; 49:500-500.

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.

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.

Wissel, BD; Greiner, HM; Glauser, TA; Pestian, JP; Kemme, AJ; Santel, D; Ficker, DM; Mangano, FT; Szczesniak, RD; Dexheimer, JW. Early identification of epilepsy surgery candidates: A multicenter, machine learning study. Acta Neurologica Scandinavica. 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.

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.