Biomedical Informatics

Avellino, R; Mulet-Lazaro, R; Havermans, M; Hoogenboezem, R; Smeenk, L; Salomonis, N; Schneider, RK; Rombouts, E; Bindels, E; Grimes, L; et al. Induced cell-autonomous neutropenia systemically perturbs hematopoiesis in Cebpa enhancer-null mice. Blood Advances. 2022; 6:1406-1419.

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.

Bayram, U; Lee, W; Santel, D; Minai, A; Clark, P; Glauser, T; Pestian, J. Toward Suicidal Ideation Detection with Lexical Network Features and Machine Learning. 2022; 4.

Bradford, L; Ross, MK; Minso, J; Cernelc-Kohan, M; Shayan, K; Wong, SS; Li, X; Rivier, L; Jegga, AG; Deutsch, GH; et al. Interstitial lung disease in children with Rubinstein-Taybi syndrome. Pediatric Pulmonology. 2022; 57:264-272.

Chen, J; Navais, PS; Xu, H; Flatley, C; Bacelis, J; Monangi, N; Kacerovsky, M; Hallman, M; Teramo, K; Lawlor, D; et al. Interrogating the causal effects of maternal circulating CRP on gestational duration and birth weight. 2022.

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.

Dar, AA; Bezrookove, V; Nosrati, M; Ice, R; Patino, JM; Vaquero, EM; Parrett, B; Leong, SP; Kim, KB; Debs, RJ; et al. Bromodomain inhibition overcomes treatment resistance in distinct molecular subtypes of melanoma. Proceedings of the National Academy of Sciences of the United States of America. 2022; 119.

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. 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.

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. Journal of 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.

Ghandikota, S; Jegga, AG. gene2gauss: A multi-view gaussian gene embedding learner for analyzing transcriptomic networks. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium. 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.

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. 2022; 107:803-815.

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. 2022.

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.

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.

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.

Jin, K; Schnell, D; Li, G; Salomonis, N; Surya Prasath, VB; Szczesniak, R; Aronow, B. CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data. 2022.

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: Journal of the International Measurement Confederation. 2022; 198.

Kanbar, L; Wissel, B; Ni, Y; Pajor, N; Glauser, T; Pestian, J; Dexheimer, J. Implementation of Machine Learning Pipelines for Clinical Practice (Preprint). JMIR Medical Informatics. 2022.

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.

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.

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.

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.

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.

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. 2022; 4.

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.

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.

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.

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. 2022; 5.

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; 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.

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.

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.

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. 2022; 67:976-984.

Santoleri, D; Lim, HW; Emmett, MJ; Stoute, J; Gavin, MJ; Sostre-Colón, J; Uehara, K; Welles, JE; Liu, KF; Lazar, MA; et al. Global-run on sequencing identifies Gm11967 as an Akt-dependent long noncoding RNA involved in insulin sensitivity. iScience. 2022; 25.

Schmidt, AF; Schnell, DJ; Eaton, KP; Chetal, K; Kannan, PS; Miller, LA; Chougnet, CA; Swarr, DT; Jobe, AH; Salomonis, N; et al. Fetal maturation revealed by amniotic fluid cell-free transcriptome in rhesus macaques. JCI insight. 2022; 7.

Severance, TS; Milgrom, Z; Carson, A; Scanlon, CM; Chauhan O’Brien, R; Anderson, B; Robertson, M; Janota, A; Coven, SL; Mendonca, EA; et al. Cancer prevention, screening, and survivorship ECHO: A pilot experience with an educational telehealth program. Cancer Medicine. 2022; 11:238-244.

Siegel, R; Khoury, P; Spooner, SA; Stackpole, K; Allen, N; Kirk, S; Kharofa, R. Body Mass Index Increased at a Large Midwestern Children's Hospital during the COVID-19 Pandemic. Childhood Obesity. 2022.

Sole-Navais, P; Flatley, C; Steinthorsdottir, V; Vaudel, M; Juodakis, J; Chen, J; Laisk, T; LaBella, A; Westergaard, D; Bacelis, J; et al. Genetic effects on the timing of parturition and links to fetal birth weight. 2022.

Stevens, J; Steinmeyer, S; Bonfield, M; Peterson, L; Wang, T; Gray, J; Lewkowich, I; Xu, Y; Du, Y; Guo, M; et al. The balance between protective and pathogenic immune responses to pneumonia in the neonatal lung is enforced by gut microbiota. Science Translational Medicine. 2022; 14.

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.

Toth, A; Steinmeyer, S; Kannan, P; Gray, J; Jackson, CM; Mukherjee, S; Demmert, M; Sheak, JR; Benson, D; Kitzmiller, J; et al. Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates. Science Translational Medicine. 2022; 14.

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.

Weaver, KN; Chen, J; Shikany, A; White, PS; Prada, CE; Gelb, BD; Cnota, JF. Prevalence of Genetic Diagnoses in a Cohort With Valvar Pulmonary Stenosis. Circulation: Genomic and Precision Medicine. 2022; 15.

Whitacre, BE; Howles, P; Street, S; Morris, J; Swertfeger, D; Davidson, WS. Apolipoprotein E content of VLDL limits LPL-mediated triglyceride hydrolysis. Journal of Lipid Research. 2022; 63.

Wiley, K; Findley, L; Goldrich, M; Rakhra-Burris, TK; Stevens, A; Williams, P; Bult, CJ; Chisholm, R; Deverka, P; Ginsburg, GS; et al. A research agenda to support the development and implementation of genomics-based clinical informatics tools and resources. Journal of the American Medical Informatics Association : JAMIA. 2022; 29:1342-1349.

Wu, DT Y; Van Camp, PJ; Kim, A; Parikh, M; Liu, L; Mahdi, M; Ni, Y; Spooner, SA. User-Centered Evaluation of a Visual Annotation Tool for Rapid Assessment of Pediatric Weight Entry Errors. . 2022.

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.

Yang, Z; Shikany, A; Ni, Y; Zhang, G; Weaver, KN; Chen, J. Using deep learning and electronic health records to detect Noonan syndrome in pediatric patients. Genetics in Medicine. 2022.

Yella, J; Ghandikota, S; Jegga, A. GraMDTA: Multimodal Graph Neural Networks for Predicting Drug-Target Associations. 2022.

Yella, JK; Jegga, AG. 2.32 Magic bullets: Drug repositioning and drug combinations. Comprehensive Pharmacology. 2022.

You, D; Jung, BC; Villivalam, SD; Lim, HW; Kang, S. JMJD8 is a Novel Molecular Nexus Between Adipocyte-Intrinsic Inflammation and Insulin Resistance. Diabetes. 2022.

Zanobetti, A; Ryan, PH; Coull, B; Brokamp, C; Datta, S; Blossom, J; Lothrop, N; Miller, RL; Beamer, PI; Visness, CM; et al. Childhood Asthma Incidence, Early and Persistent Wheeze, and Neighborhood Socioeconomic Factors in the ECHO/CREW Consortium. JAMA Pediatrics. 2022; 176:759-767.

Zhang, W; Dhondalay, GK; Liu, TA; Kaushik, A; Hoh, R; Kwok, S; Kambham, N; Fernandez-Becker, NQ; Andorf, S; Desai, M; et al. Gastrointestinal γδ T cells reveal differentially expressed transcripts and enriched pathways during peanut oral immunotherapy. Allergy: European Journal of Allergy and Clinical Immunology. 2022; 77:1606-1610.

Zoubovsky, SP; Williams, MT; Hoseus, S; Tumukuntala, S; Riesenberg, A; Schulkin, J; Vorhees, CV; Campbell, K; Lim, H; Muglia, LJ. Neurobehavioral abnormalities following prenatal psychosocial stress are differentially modulated by maternal environment. Translational Psychiatry. 2022; 12.