Biomedical Informatics


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Clarkston, K; Karns, R; Jegga, AG; Sharma, M; Fox, S; Ojo, BA; Minar, P; Walters, TD; Griffiths, AM; Mack, DR; et al. Targeted Assessment of Mucosal Immune Gene Expression Predicts Clinical Outcomes in Children with Ulcerative Colitis. Journal of Crohn's and Colitis. 2022; 16:1735-1750.

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Dedhia, PH; Chen, K; Song, Y; Larose, E; Imbus, JR; Peissig, PL; Mendonca, EA; Schneider, DF. Ambiguous and Incomplete: Natural Language Processing Reveals Problematic Reporting Styles in Thyroid Ultrasound Reports. Methods of Information in Medicine: journal of methodology in medical research, information and documentation. 2022; 61:11-18.

Desai, DA; Rao, VJ; Jegga, AG; Dhandapany, PS; Sadayappan, S. Heterogeneous Distribution of Genetic Mutations in Myosin Binding Protein-C Paralogs. Frontiers in Genetics. 2022; 13:896117.

Díaz, PC; Chou, C; Mistry, J; Khan, MD; Salomonis, N; Grimes, HL; Trowbridge, J. 3055 – METALLOTHIONEIN 1 (MT1) AS A TARGETABLE DEPENDENCY IN ACUTE MYELOID LEUKEMIA. Experimental Hematology. 2022; 111:s72.

Diop, EH S; Burdin, V; Prasath, VB S. Note on the Existence of Minimizers for Variational Geometric Active Contours. 2022.

Ebrahimpour, A; Ahir, M; Wang, M; Jegga, AG; Bonnen, MD; Eissa, NT; Montesi, SB; Raghu, G; Ghebre, YT. Combination of esomeprazole and pirfenidone enhances antifibrotic efficacy in vitro and in a mouse model of TGFβ-induced lung fibrosis. Scientific Reports. 2022; 12:20668.

Ehrman, JM; Merchan-Sala, P; Ehrman, LA; Chen, B; Lim, HW; Waclaw, RR; Campbell, K. Formation of the Mouse Internal Capsule and Cerebral Peduncle: A Pioneering Role for Striatonigral Axons as Revealed in Isl1 Conditional Mutants. The Journal of neuroscience : the official journal of the Society for Neuroscience. 2022; 42:3344-3364.

Feng, Y; Cai, L; Hong, W; Zhang, C; Tan, N; Wang, M; Wang, C; Liu, F; Wang, X; Ma, J; et al. Rewiring of 3D Chromatin Topology Orchestrates Transcriptional Reprogramming and the Development of Human Dilated Cardiomyopathy. Circulation. 2022; 145:1663-1683.

Feria, MG; Chang, C; Ticona, E; Moussa, A; Zhang, B; Ballena, I; Azañero, R; Ticona, C; De Cecco, CN; Fichtenbaum, CJ; et al. Pro-Inflammatory Alterations of Circulating Monocytes in Latent Tuberculosis Infection. Open Forum Infectious Diseases. 2022; 9:ofac629.

Fitzsimmons, L; Dewan, M; Dexheimer, JW. Diversity in Machine Learning: A Systematic Review of Text-Based Diagnostic Applications. Applied Clinical Informatics - ACI. 2022; 13:569-582.

Garrett, MC; Albano, R; Carnwath, T; Shah, S; Woo, D; Lamba, M; Plas, DR; Paranjpe, A; Roskin, K; Zhao, C; et al. Chromatin structure predicts survival in glioma patients. Scientific Reports. 2022; 12:8221.

Ghandikota, S; Jegga, AG. gene2gauss: A multi-view gaussian gene embedding learner for analyzing transcriptomic networks. AMIA Joint Summits on Translational Science proceedings AMIA Summit on Translational Science. 2022; 2022:206-215.

Ghandikota, S; Sharma, M; Ediga, HH; Madala, SK; Jegga, AG. Consensus Gene Co-Expression Network Analysis Identifies Novel Genes Associated with Severity of Fibrotic Lung Disease. International Journal of Molecular Sciences. 2022; 23:5448.

Ghandikota, S; Yella, JK; Jegga, AG. (2022) Multimodal feature learning framework for disease biomarker discovery. Institute of Electrical and Electronics Engineers (IEEE). 00:3252-3259.

Gorski, JK; Mendonça, EA; Showalter, CD. The Impact of Diagnostic Decisions on Patient Experience in the Pediatric Emergency Department. Pediatric Emergency Care. 2022; 38:e644-e649.

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: the hematology journal. 2022; 107:803-815.

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:e2246548.

H. Tran, Y; Coven, SL; Park, S; Mendonca, EA. Social determinants of health and pediatric cancer survival: A systematic review. Pediatric Blood and Cancer. 2022; 69:e29546.

Jackson, CM; Demmert, M; Mukherjee, S; Isaacs, T; Thompson, R; Chastain, C; Gray, J; Senthamaraikannan, P; Presicce, P; Chetal, K; et al. A potent myeloid response is rapidly activated in the lungs of premature Rhesus macaques exposed to intra-uterine inflammation. Mucosal Immunology. 2022; 15:730-744.

Jee, JJ; Yang, L; Shivakumar, P; Xu, PP; Mourya, R; Thanekar, U; Yu, P; Zhu, Y; Pan, Y; Wang, H; et al. Maternal regulation of biliary disease in neonates via gut microbial metabolites. Nature Communications. 2022; 13:18.

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.

Jurickova, I; Bonkowski, E; Angerman, E; Novak, E; Huron, A; Akers, G; Iwasawa, K; Braun, T; Hadar, R; Hooker, M; et al. Eicosatetraynoic Acid and Butyrate Regulate Human Intestinal Organoid Mitochondrial and Extracellular Matrix Pathways Implicated in Crohn's Disease Strictures. Inflammatory Bowel Diseases. 2022; 28:988-1003.



Kadam, P; Pandya, S; Phansalkar, S; Sarangdhar, M; Petkar, N; Kotecha, K; Garg, D. FVEstimator: A novel food volume estimator Wellness model for calorie measurement and healthy living. Measurement. 2022; 198:111294.

Kalim, KW; Yang, JQ; Wunderlich, M; Modur, V; Nguyen, P; Li, Y; Wen, T; Davis, AK; Verma, R; Lu, QR; et al. Targeting of Cdc42 GTPase in regulatory T cells unleashes antitumor T-cell immunity. Journal for ImmunoTherapy of Cancer. 2022; 10:e004806.

Kanbar, L; Barzman, DH; Dexheimer, J; Osborn, A; Combs, JS; Diler, RS; Sorter, MT; Zhang, B; Hemphill, R; Decker, RM; et al. 2.7 Automated Detection of School Violence Using Linguistic Features. Journal of the American Academy of Child and Adolescent Psychiatry. 2022; 61:s184-s185.

Kanbar, LJ; Wissel, B; Ni, Y; Pajor, N; Glauser, T; Pestian, J; Dexheimer, JW. Implementation of Machine Learning Pipelines for Clinical Practice: Development and Validation Study. JMIR Medical Informatics. 2022; 10:e37833.

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; 114:110270.

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.

Kaushik, A; Dunham, D; Han, X; Do, E; Andorf, S; Gupta, S; Fernandes, A; Kost, LE; Sindher, SB; Yu, W; et al. CD8+ T cell differentiation status correlates with the feasibility of sustained unresponsiveness following oral immunotherapy. Nature Communications. 2022; 13:6646.

Kershner, LJ; Choi, K; Wu, J; Zhang, X; Perrino, M; Salomonis, N; Shern, JF; Ratner, N. Multiple Nf1 Schwann cell populations reprogram the plexiform neurofibroma tumor microenvironment. JCI insight. 2022; 7:e154513.

Kidwell, KM; Reiter-Purtill, J; Decker, K; Howarth, T; Doland, F; Zeller, MH. Stress and eating responses in adolescent females predisposed to obesity: A pilot and feasibility study. Appetite. 2022; 179:106308.

Kovaleski, C; Courter, JD; Ghulam, E; Hagedorn, PA; Haslam, DB; Kurowski, EM; Rudloff, J; Szczesniak, R; Dexheimer, JW. Aligning Provider Prescribing With Guidelines for Soft Tissue Infections. Pediatric Emergency Care. 2022; 38:e1063-e1068.

Krietsch, KN; Duraccio, KM; Zhang, N; Saelens, BE; Howarth, T; Combs, A; Beebe, DW. Earlier bedtimes and more sleep displace sedentary behavior but not moderate-to-vigorous physical activity in adolescents. Sleep Health. 2022; 8:270-276.

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. 2022; 77:669-678.


Ley, SL; Kidwell, KM; Van Dyk, TR; Orkin, S; Odar Stough, C; Howarth, T; Goetz, AR; Xanthakos, SA; Bramlage, K; Mouzaki, M; et al. Insight Into the Adolescent Patient Experience With Nonalcoholic Fatty Liver Disease. Journal of Pediatric Gastroenterology and Nutrition. 2022; 75:88-96.

Li, Q; Li, Y; Huang, W; Wang, X; Liu, Z; Chen, J; Fan, Y; Peng, T; Sadayappan, S; Wang, Y; et al. Loss of Lipocalin 10 Exacerbates Diabetes-Induced Cardiomyopathy via Disruption of Nr4a1-Mediated Anti-Inflammatory Response in Macrophages. Frontiers in Immunology. 2022; 13:930397.

Li, S; Rajapuri, AS; Felix Gomez, GG; Schleyer, T; Mendonca, EA; Thyvalikakath, TP. How Do Dental Clinicians Obtain Up-To-Date Patient Medical Histories? Modeling Strengths, Drawbacks, and Proposals for Improvements. Frontiers in Digital Health. 2022; 4:847080.

Liu, L; Wu, DT Y; Spooner, SA; Ni, Y. Development and Evaluation of an Automated Approach to Detect Weight Abnormalities in Pediatric Weight Charts. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium. 2022; 2021:783-792.

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.

Lozano, PM; Lane-Fall, M; Franklin, PD; Rothman, RL; Gonzales, R; Ong, MK; Gould, MK; Beebe, TJ; Roumie, CL; Guise, JM; et al. Training the next generation of learning health system scientists. Learning Health Systems. 2022; 6:e10342.

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.

McDaniel, MM; Chawla, AS; Jain, A; Meibers, HE; Saha, I; Gao, Y; Jain, V; Roskin, K; Way, SS; Pasare, C. Effector memory CD4+ T cells induce damaging innate inflammation and autoimmune pathology by engaging CD40 and TNFR on myeloid cells. Science Immunology. 2022; 7:eabk0182.

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.

Mendonca, EA; Richesson, RL; Hochheiser, H; Cooper, DM; Bruck, MN; Berner, ES. Informatics education for translational research teams: An unrealized opportunity to strengthen the national research infrastructure. Journal of Clinical and Translational Science. 2022; 6:e130.

Milgrom, ZZ; Severance, TS; Scanlon, CM; Carson, AT; Janota, AD; Burns, JL; Vik, TA; Duwve, JM; Dixon, BE; Mendonca, EA. Enhancing cancer prevention and survivorship care with a videoconferencing model for continuing education: a mixed-methods study to identify barriers and incentives to participation. JAMIA Open. 2022; 5:ooac004.

Milgrom, ZZ; Severance, TS; Scanlon, CM; Carson, AT; Janota, AD; Vik, TA; Duwve, JM; Dixon, BE; Mendonca, EA. An evaluation of an Extension for Community Healthcare Outcomes (ECHO) intervention in cancer prevention and survivorship care. BMC Medical Informatics and Decision Making. 2022; 22:135.

Milgrom, ZZ; Severance, TS; Scanlon, CM; Carson, AT; Janota, AD; Vik, TA; Duwve, JM; Dixon, BE; Mendonca, EA. Building Cancer Control Capacity in Health Professionals Through Telementoring: A Survey Study of a Cancer Prevention and Survivorship Care ECHO Program. Studies in Health Technology and Informatics. 2022; 290:1122-1123.

Mullins, N; Kang, JE; Campos, AI; Coleman, JR I; Edwards, AC; Galfalvy, H; Levey, DF; Lori, A; Shabalin, A; Starnawska, A; et al. Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors. Biological Psychiatry. 2022; 91:313-327.

Mun, KS; Nathan, JD; Jegga, AG; Wikenheiser-Brokamp, KA; Abu-El-Haija, M; Naren, AP. Personalized medicine approaches in cystic fibrosis related pancreatitis. American Journal of Translational Research. 2022; 14:7612-7620.

Mun, KS; Nathan, JD; Lin, TK; Elder, DA; Jegga, AG; Naren, AP; Abu-El-Haija, M. Is There a Benefit From Islet Autotransplantation in Patients With Type 1 Diabetes Mellitus Undergoing Total Pancreatectomy?. Pancreas. 2022; 51:399-403.

Nayak, RC; Chang, KH; Singh, AK; Kotliar, M; Desai, M; Wellendorf, AM; Wunderlich, M; Bartram, J; Mizukawa, B; Cuadrado, M; et al. Nuclear Vav3 is required for polycomb repression complex-1 activity in B-cell lymphoblastic leukemogenesis. Nature Communications. 2022; 13:3056.

Noll, JG; Haag, AC; Shenk, CE; Wright, MF; Barnes, JE; Kohram, M; Malgaroli, M; Foley, DJ; Kouril, M; Bonanno, GA. An observational study of Internet behaviours for adolescent females following sexual abuse. Nature Human Behaviour. 2022; 6:74-87.

Pilarczyk, M; Fazel-Najafabadi, M; Kouril, M; Shamsaei, B; Vasiliauskas, J; Niu, W; Mahi, N; Zhang, L; Clark, NA; Ren, Y; et al. Connecting omics signatures and revealing biological mechanisms with iLINCS. Nature Communications. 2022; 13:4678.

Rochman, M; Wen, T; Kotliar, M; Dexheimer, PJ; Morgenstern, NB B; Caldwell, JM; Lim, HW; Rothenberg, ME. Single-cell RNA-Seq of human esophageal epithelium in homeostasis and allergic inflammation. JCI insight. 2022; 7:e159093.

Rogerson, C; He, T; Rowan, C; Tu, W; Mendonca, E. Ten year trends in hospital encounters for pediatric asthma: an Indiana experience. Journal of Asthma (Informa). 2022; 59:2421-2430.

Rogerson, CM; Carroll, AE; Tu, W; He, T; Schleyer, TK; Rowan, CM; Owora, AH; Mendonca, EA. Frequency and Correlates of Pediatric High-Flow Nasal Cannula Use for Bronchiolitis, Asthma, and Pneumonia. Respiratory Care: a monthly science journal. 2022; 67:976-984.

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Sveen, W; Dewan, M; Dexheimer, JW. The Risk of Coding Racism into Pediatric Sepsis Care: The Necessity of Antiracism in Machine Learning. The Journal of Pediatrics. 2022; 247:129-132.

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Wiley, KK; Mendonca, E; Blackburn, J; Menachemi, N; Groot, MD; Vest, JR. Quantifying Electronic Health Record Data Quality in Telehealth and Office-Based Diabetes Care. Applied Clinical Informatics - ACI. 2022; 13:1172-1180.

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Wunderlich, M; Chen, J; Sexton, C; Manning, N; Byerly, L; O’Brien, E; Perentesis, J; Mulloy, J; Mizukawa, B. PDX models of relapsed pediatric AML preserve global gene expression patterns and reveal therapeutic targets. 2022; 2022.01.31.478534.

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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.

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Yella, JK; Jegga, AG. MGATRx: Discovering Drug Repositioning Candidates Using Multi-View Graph Attention. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2022; 19:2596-2604.

Yella, JK; Jegga, AG. 2.32 Magic bullets: Drug repositioning and drug combinations. In: Mitchell R; Bradshaw R; McManus L, Ed. Comprehensive Pharmacology. New York: Elsevier; 2022.

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