Biomedical Informatics

Publications

Avelino, R; Mulet-Lazaro, R; Havermans, M; Hoogenboezem, R; Smeenk, L; Salomonis, N; Schneider, RK; Rombouts, EJ C; Bindels, E; Grimes, HL; et al. Induced cell-autonomous neutropenia systemically perturbs hematopoiesis in Cebpa enhancer-null mice. Blood Advances. 2021.

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.

Bondoc, A; Glaser, K; Jin, K; Lake, C; Cairo, S; Geller, J; Tiao, G; Aronow, B. Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma. Communications Biology. 2021; 4.

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.

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.

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.

Choi, KM; Kim, JH; Kong, X; Isik, M; Zhang, J; Lim, HW; Yoon, JC. Defective brown adipose tissue thermogenesis and impaired glucose metabolism in mice lacking Letmd1. Cell Reports. 2021; 37.

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.

Devonshire, AL; Fan, H; Pujato, M; Paranjpe, A; Gursel, D; Schipma, M; Dunn, JM; Andorf, S; Pongracic, JA; Kottyan, LC; et al. Whole blood transcriptomics identifies gene expression associated with peanut allergy in infants at high risk. Clinical and Experimental Allergy. 2021; 51:1396-1400.

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.

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; 76:2809-2826.

Masci, AM; White, S; Neely, B; Ardini-Polaske, M; Hill, CB; Misra, RS; Aronow, B; Gaddis, N; Yang, L; Wert, SE; et al. Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images. BMC Bioinformatics. 2021; 22.

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.

Melchior, JT; Swertfeger, DK; Morris, J; Street, SE; Warshak, CR; Welge, JA; Remaley, AT; Catov, JM; Davidson, WS; Woollett, LA. Pregnancy is accompanied by larger high density lipoprotein particles and compositionally distinct subspecies. Journal of Lipid Research. 2021; 62.

Mo, A; Nagpal, S; Gettler, K; Haritunians, T; Giri, M; Haberman, Y; Karns, R; Prince, J; Arafat, D; Hsu, NY; et al. Stratification of risk of progression to colectomy in ulcerative colitis via measured and predicted gene expression. American Journal of Human Genetics. 2021; 108:1765-1779.

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.

Niklinska-Schirtz, BJ; Venkateswaran, S; Anbazhagan, M; Kolachala, VL; Prince, J; Dodd, A; Chinnadurai, R; Gibson, G; Denson, LA; Cutler, DJ; et al. Ileal Derived Organoids From Crohn's Disease Patients Show Unique Transcriptomic and Secretomic Signatures. CMGH Cellular and Molecular Gastroenterology and Hepatology. 2021; 12:1267-1280.

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. 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.

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.

Petley, L; Hunter, LL; Zadeh, LM; Stewart, HJ; Sloat, NT; Perdew, A; Lin, L; Moore, DR. Listening Difficulties in Children With Normal Audiograms: Relation to Hearing and Cognition. Ear and Hearing. 2021; 42:1640-1655.

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.

Prozan, L; Shusterman, E; Ablin, J; Mitelpunkt, A; Weiss-Meilik, A; Adler, A; Choshen, G; Kehat, O. Prognostic value of neutrophil-to-lymphocyte ratio in COVID-19 compared with Influenza and respiratory syncytial virus infection. Scientific Reports. 2021; 11.

Purington, N; Andorf, S; Bunning, B; Chinthrajah, S; Nadeau, K; Desai, M. Novel application of a discrete time-to-event model for randomized oral immunotherapy clinical trials with repeat food challenges. Statistics in Medicine. 2021; 40:4136-4149.

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.

Shi, T; Roskin, K; Baker, BM; Woodle, ES; Hildeman, D. Advanced Genomics-Based Approaches for Defining Allograft Rejection With Single Cell Resolution. Frontiers in Immunology. 2021; 12.

Singh, U; Hernandez, KM; Aronow, BJ; Wurtele, ES. African Americans and European Americans exhibit distinct gene expression patterns across tissues and tumors associated with immunologic functions and environmental exposures. Scientific Reports. 2021; 11.

Surumbayeva, A; Kotliar, M; Gabitova-Cornell, L; Kartashov, A; Peri, S; Salomonis, N; Barski, A; Astsaturov, I. Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data. STAR Protocols. 2021; 2.

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; 27:1707-1718.

Tokatly Latzer, I; Senderowich, N; Fattal-Valevski, A; Mitelpunkt, A; Uliel-Sibony, S; Hausman-Kedem, M. Disordered Eating Behaviors in Young Individuals With Idiopathic Intracranial Hypertension. Pediatric Neurology. 2021; 125:1-8.

Vaughn, S; Sarangdhar, M; Poweleit, E; Strawn, J; Ramsey, L. 32.5 The Combination of CYP2C19 Metabolized Antidepressants and Cannabinoids Presents Elevated Risk of Antidepressant-Related Side Effects. Journal of the American Academy of Child and Adolescent Psychiatry. 2021; 60:s215-s216.

Vaughn, SE; Strawn, JR; Poweleit, EA; Sarangdhar, M; Ramsey, LB. The Impact of Marijuana on Antidepressant Treatment in Adolescents: Clinical and Pharmacologic Considerations. Journal of Personalized Medicine. 2021; 11.

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.

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; 144:41-50.

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.

Wu, Q; Zhang, J; Johnson, C; Weinhaus, B; Slaughter, A; Valladares-Nuñez, A; Sherman, A; Filippi, M; Vellai Badradoss, SP; Way, SS; et al. A Durable Anatomy with Local Plasticity Enables Normal and Stress Hematopoiesis. Blood. 2021; 138:297-297.

Yan, Z; Maecker, HT; Brodin, P; Nygaard, UC; Lyu, SC; Davis, MM; Nadeau, KC; Andorf, S. Aging and CMV discordance are associated with increased immune diversity between monozygotic twins. Immunity and Ageing. 2021; 18.

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.

Yella, JK; Jegga, AG. Magic bullets: Drug repositioning and drug combinations. Reference Module in Biomedical Sciences. 2021.

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.

Zhu, X; Lazow, MA; Schafer, A; Bartlett, A; Senthil Kumar, S; Mishra, DK; Dexheimer, P; DeWire, M; Fuller, C; Leach, JL; et al. A pilot radiogenomic study of DIPG reveals distinct subgroups with unique clinical trajectories and therapeutic targets. Acta neuropathologica communications. 2021; 9.