Publications

Aaij, R; Abellán Beteta, C; Ackernley, T; Adeva, B; Adinolfi, M; Afsharnia, H; Aidala, CA; Aiola, S; Ajaltouni, Z; Akar, S; et al. Searches for low-mass dimuon resonances. Journal of High Energy Physics. 2020; 2020.

Aaij, R; Beteta, CA; Ackernley, T; Adeva, B; Adinolfi, M; Afsharnia, H; Aidala, CA; Aiola, S; Ajaltouni, Z; Akar, S; et al. Search for CP violation in Ξc+→pK-π+ decays using model-independent techniques. Nuovo Cimento A. 2020; 80.

Aaij, R; Beteta, CA; Adeva, B; Adinolfi, M; Aidala, CA; Ajaltouni, Z; Akar, S; Albicocco, P; Albrecht, J; Alessio, F; et al. Measurement of the branching fraction of the decay Bs0 → K S0 K S0. Physical Review D. 2020; 102.

Alexandrou, E; Cabrera-Salcedo, C; Labilloy, G; Tyzinski, L; Smolarek, TA; Andrew, M; Huang, Y; Backeljauw, P; Dauber, A. (2020) Algorithm-Driven Electronic Health Record Notification Enhances the Detection of Turner Syndrome. Elsevier BV. 216:227-231.

Andorf, S; Bunning, B; Tupa, D; Cao, S; Long, AJ; Borres, MP; Galli, SJ; Chinthrajah, RS; Nadeau, KC. Trends in egg specific immunoglobulin levels during natural tolerance and oral immunotherapy. Allergy: European Journal of Allergy and Clinical Immunology. 2020; 75:1454-1456.

Angueira, AR; Shapira, SN; Ishibashi, J; Sampat, S; Sostre-Colon, J; Emmett, MJ; Titchenell, PM; Lazar, MA; Lim, H; Seale, P. Early B Cell Factor Activity Controls Developmental and Adaptive Thermogenic Gene Programming in Adipocytes. Cell Reports. 2020; 30:2869-2878.e4.

Bidani, S; Priya, RP; Vijayarajan, V; Prasath, VB S. Automatic body mass index detection using correlation of face visual cues. Technology and health care : official journal of the European Society for Engineering and Medicine. 2020; 28:107-112.

Bunning, BJ; Contrepois, K; Lee-McMullen, B; Dhondalay, GK R; Zhang, W; Tupa, D; Raeber, O; Desai, M; Nadeau, KC; Snyder, MP; et al. Global metabolic profiling to model biological processes of aging in twins. Aging Cell. 2020; 19.

Cabrera-Salcedo, C; Hawkes, CP; Tyzinski, L; Andrew, M; Labilloy, G; Campos, D; Feld, A; Deodati, A; Hwa, V; Hirschhorn, JN; et al. Targeted Searches of the Electronic Health Record and Genomics Identify an Etiology in Three Patients with Short Stature and High IGF-I Levels. Hormone Research in Paediatrics: from developmental endocrinology to clinical research. 2020; 92:186-195.

Chen, J; Bacelis, J; Sole-Navais, P; Srivastava, A; Juodakis, J; Rouse, A; Hallman, M; Teramo, K; Melbye, M; Feenstra, B; et al. Dissecting maternal and fetal genetic effects underlying the associations between maternal phenotypes, birth outcomes, and adult phenotypes: A mendelian-randomization and haplotype-based genetic score analysis in 10,734 mother–infant pairs. PLoS Medicine. 2020; 17:e1003305-e1003305.

Chidambaran, V; Ashton, M; Martin, LJ; Jegga, AG. Systems biology-based approaches to summarize and identify novel genes and pathways associated with acute and chronic postsurgical pain. Journal of Clinical Anesthesia. 2020; 62:109738-109738.

Chinthrajah, RS; Purington, N; Andorf, S; Long, A; O'Laughlin, KL; Lyu, SC; Manohar, M; Boyd, SD; Tibshirani, R; Maecker, H; et al. Sustained outcomes in oral immunotherapy for peanut allergy (POISED study): a large, randomised, double-blind, placebo-controlled, phase 2 study (vol 394, pg 1437, 2019). The Lancet. 2020; 396:380-380.

Cohen, J; Wright-Berryman, J; Rohlfs, L; Wright, D; Campbell, M; Gingrich, D; Santel, D; Pestian, J. A feasibility study using a machine learning suicide risk prediction model based on open-ended interview language in adolescent therapy sessions. International journal of environmental research and public health. 2020; 17:8187-8187.

de Semir, D; Bezrookove, V; Nosrati, M; Scanlon, KR; Singer, E; Judkins, J; Rieken, C; Wu, C; Shen, J; Schmudermayer, C; et al. PHIP drives glioblastoma motility and invasion by regulating the focal adhesion complex. Proceedings of the National Academy of Sciences of USA. 2020; 117:9064-9073.

Deng, S; Essandoh, K; Wang, X; Li, Y; Huang, W; Chen, J; Peng, J; Jiang, D; Mu, X; Wang, C; et al. Tsg101 positively regulates P62-Keap1-Nrf2 pathway to protect hearts against oxidative damage. Redox Biology. 2020; 32:101453-101453.

DePasquale, E; Schnell, D; Chetal, K; Salomonisi, N. Identification and Removal of Doublets with DoubletDecon. 2020.

DePasquale, EA K; Schnell, D; Chetal, K; Salomonis, N. Protocol for Identification and Removal of Doublets with DoubletDecon. 2020; 1:100085-100085.

DeWire, M; Fuller, C; Hummel, TR; Chow, LM L; Salloum, R; de Blank, P; Pater, L; Lawson, S; Zhu, X; Dexheimer, P; et al. A phase I/II study of ribociclib following radiation therapy in children with newly diagnosed diffuse intrinsic pontine glioma (DIPG). Journal of Neuro-Oncology. 2020; 149:511-522.

Dhondalay, GK R; Bunning, B; Bauer, RN; Barnathan, ES; Maniscalco, C; Baribaud, F; Nadeau, KC; Andorf, S. Transcriptomic and methylomic features in asthmatic and nonasthmatic twins. Allergy: European Journal of Allergy and Clinical Immunology. 2020; 75:989-992.

Diop, EH S; Boudraa, A; Prasath, VB S. Optimal Nonlinear Signal Approximations Based on Piecewise Constant Functions. Circuits, Systems, and Signal Processing. 2020; 39:2673-2694.

Fortriede, JD; Pells, TJ; Chu, S; Chaturvedi, P; Wang, D; Fisher, ME; James-Zorn, C; Wang, Y; Nenni, MJ; Burns, KA; et al. Xenbase: Deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database. Nucleic Acids Research. 2020; 48:D776-D782.

Garvin, MR; Alvarez, C; Miller, JI; Prates, ET; Walker, AM; Amos, BK; Mast, AE; Justice, A; Aronow, B; Jacobson, D. A mechanistic model and therapeutic interventions for covid-19 involving a ras-mediated bradykinin storm. eLife. 2020; 9:1-16.

Ghandikota, S; Sharma, M; Jegga, A. Secondary analysis of transcriptomes of SARS-CoV-2 infection models to characterize COVID-19. 2020.

Glauser, T; Santel, D; DelBello, M; Faist, R; Toon, T; Clark, P; McCourt, R; Wissel, B; Pestian, J. Identifying epilepsy psychiatric comorbidities with machine learning. Acta Neurologica Scandinavica. 2020; 141:388-396.

Govindarajah, V; Lee, J; Solomon, M; Goddard, B; Nayak, R; Nattamai, K; Geiger, H; Salomonis, N; Cancelas, JA; Reynaud, D. FOXO activity adaptation safeguards the hematopoietic stem cell compartment in hyperglycemia. Blood Advances. 2020; 4:5512-5526.

Goyal, NK; Brown, CM; Folger, AT; Hall, ES; Van Ginkel, JB; Ammerman, RT. Adherence to Well-Child Care and Home Visiting Enrollment Associated with Increased Emergency Department Utilization. Maternal and Child Health Journal. 2020; 24:73-81.

Haniffa, M; Taylor, D; Linnarsson, S; Aronow, B; Bader, G; Camara, P; Camp, G; Chédotal, A; Copp, A; Etchevers, H; et al. Human Developmental Cell Atlas: milestones achieved and the roadmap ahead. 2020.

He, Z; Dongre, P; Lyu, S; Manohar, M; Chinthrajah, RS; Galli, SJ; DeKruyff, RH; Nadeau, KC; Andorf, S. Identification of cross-reactive allergens in cashew- and pistachio-allergic children during oral immunotherapy. Pediatric Allergy and Immunology. 2020; 31:709-714.

Hinge, A; He, J; Bartram, J; Javier, J; Xu, J; Fjellman, E; Sesaki, H; Li, T; Yu, J; Wunderlich, M; et al. Asymmetrically Segregated Mitochondria Provide Cellular Memory of Hematopoietic Stem Cell Replicative History and Drive HSC Attrition. Cell Stem Cell. 2020; 26:420-430.e6.

Hoh, RA; Joshi, SA; Lee, J; Martin, BA; Varma, S; Kwok, S; Nielsen, SC A; Nejad, P; Haraguchi, E; Dixit, PS; et al. Origins and clonal convergence of gastrointestinal IgE+ B cells in human peanut allergy. Science Immunology. 2020; 5:eaay4209-eaay4209.

Holowiecki, A; Linstrum, K; Ravisankar, P; Chetal, K; Salomonis, N; Waxman, JS. Pbx4 limits heart size and fosters arch artery formation by partitioning second heart field progenitors and restricting proliferation. Development (Cambridge). 2020; 147:dev185652-dev185652.

Hortells, L; Valiente-Alandi, I; Thomas, ZM; Agnew, EJ; Schnell, DJ; York, AJ; Vagnozzi, RJ; Meyer, EC; Molkentin, JD; Yutzey, KE. A specialized population of Periostin-expressing cardiac fibroblasts contributes to postnatal cardiomyocyte maturation and innervation. Proceedings of the National Academy of Sciences of USA. 2020; 117:21469-21479.

Isaka, S; Kawanaka, H; Prasath, VB S; Aronow, BJ; Tsuruoka, S. (2020) Development of a web based image annotation tool for lung immunofluorescent confocal images.

Itskovich, SS; Gurunathan, A; Clark, J; Burwinkel, M; Wunderlich, M; Berger, MR; Kulkarni, A; Chetal, K; Venkatasubramanian, M; Salomonis, N; et al. MBNL1 regulates essential alternative RNA splicing patterns in MLL-rearranged leukemia. Nature Communications. 2020; 11.

Kasam, RK; Gajjala, PR; Jegga, AG; Courtney, JA; Randell, SH; Kramer, EL; Clancy, JP; Madala, SK. Fibrocyte accumulation in the lungs of cystic fibrosis patients. Journal of Cystic Fibrosis. 2020; 19:815-822.

Kasam, RK; Ghandikota, S; Soundararajan, D; Reddy, GB; Huang, SK; Jegga, AG; Madala, SK. Inhibition of Aurora Kinase B attenuates fibroblast activation and pulmonary fibrosis. EMBO Molecular Medicine. 2020; 12.

Kwok, I; Becht, E; Xia, Y; Ng, M; Teh, YC; Tan, L; Evrard, M; Li, JL Y; Tran, HT N; Tan, Y; et al. Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor. Journal of Cleaner Production. 2020; 53:303-318.e5.

Lazow, MA; Johnson, SL; Johnson, ND; Breneman, JC; Dexheimer, PJ; Szabo, S; Pressey, JG. Genome-driven therapy for chemotherapy-resistant metastatic CDK6-amplified osteosarcoma. JCO Precision Oncology. 2020; 4:498-504.

Lucas, D; Salomonis, N; Grimes, HL. Unraveling bone marrow architecture. Nature Cell Biology. 2020; 22:5-6.

Mandl, KD; Glauser, T; Krantz, ID; Avillach, P; Bartels, A; Beggs, AH; Biswas, S; Bourgeois, FT; Corsmo, J; Dauber, A; et al. The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system. Genetics in Medicine. 2020; 22:371-380.

McDaniel, CT; Panmanee, W; Winsor, GL; Gill, E; Bertelli, C; Schurr, MJ; Dongare, P; Paul, AT; Ko, SB; Lau, GW; et al. AB569, a nontoxic chemical tandem that kills major human pathogenic bacteria. Proceedings of the National Academy of Sciences of USA. 2020; 117:4921-4930.

Mitelpunkt, A; Galili, T; Kozlovski, T; Bregman, N; Shachar, N; Markus-Kalish, M; Benjamini, Y. Novel Alzheimer’s disease subtypes identified using a data and knowledge driven strategy. Scientific Reports. 2020; 10.

Moore, C; Gao, B; Roskin, KM; Vasilescu, EM; Addonizio, L; Givertz, MM; Madsen, JC; Zorn, E. B cell clonal expansion within immune infiltrates in human cardiac allograft vasculopathy. American Journal of Transplantation. 2020; 20:1431-1438.

Moore, DR; Hugdahl, K; Stewart, HJ; Vannest, J; Perdew, AJ; Sloat, NT; Cash, EK; Hunter, LL. Listening Difficulties in Children: Behavior and Brain Activation Produced by Dichotic Listening of CV Syllables. Frontiers in Psychology. 2020; 11.

Muench, DE; Olsson, A; Ferchen, K; Pham, G; Serafin, RA; Chutipongtanate, S; Dwivedi, P; Song, B; Hay, S; Chetal, K; et al. Mouse models of neutropenia reveal progenitor-stage-specific defects. Nature. 2020; 582:109-114.

Nair, N; Merhar, S; Wessel, J; Hall, E; Kingma, PS. Factors that Influence Longitudinal Growth from Birth to 18 Months of Age in Infants with Gastroschisis. American Journal of Perinatology: neonatal and maternal-fetal medicine. 2020; 37:1438-1445.

Neeland, MR; Andorf, S; Manohar, M; Dunham, D; Lyu, S; Dang, TD; Peters, RL; Perrett, KP; Tang, ML K; Saffery, R; et al. Mass cytometry reveals cellular fingerprint associated with IgE plus peanut tolerance and allergy in early life. Nature Communications. 2020; 11.

Ni, Y; Barzman, D; Bachtel, A; Griffey, M; Osborn, A; Sorter, M. Finding warning markers: Leveraging natural language processing and machine learning technologies to detect risk of school violence. International Journal of Medical Informatics. 2020; 139:104137-104137.

Ni, Y; Lingren, T; Huth, H; Timmons, K; Melton, K; Kirkendall, E. Integrating and Evaluating the Data Quality and Utility of Smart Pump Information in Detecting Medication Administration Errors: Evaluation Study. JMIR Medical Informatics. 2020; 8:e19774-e19774.

Niederkorn, M; Hueneman, K; Choi, K; Varney, ME; Romano, L; Pujato, MA; Greis, KD; Inoue, J; Meetei, R; Starczynowski, DT. TIFAB Regulates USP15-Mediated p53 Signaling during Stressed and Malignant Hematopoiesis. Cell Reports. 2020; 30:2776-2790.e6.

Ouyang, X; Ahmad, I; Johnson, MS; Redmann, M; Craver, J; Wani, WY; Benavides, GA; Chacko, B; Li, P; Young, M; et al. Nuclear receptor binding factor 2 (NRBF2) is required for learning and memory. Laboratory Investigation. 2020; 100:1238-1251.

Pestian, J; Santel, D; Sorter, M; Bayram, U; Connolly, B; Glauser, T; DelBello, M; Tamang, S; Cohen, K. A Machine Learning Approach to Identifying Changes in Suicidal Language. Suicide and Life-Threatening Behavior. 2020; 50:939-947.

Petrany, M; Swoboda, C; Sun, C; Chetal, K; Chen, X; Weirauch, M; Salomonis, N; Millay, D. Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers. 2020.

Rai, MA; Hammonds, J; Pujato, M; Mayhew, C; Roskin, K; Spearman, P. Comparative analysis of human microglial models for studies of HIV replication and pathogenesis. Retrovirology. 2020; 17.

Riccetti, M; Gokey, JJ; Aronow, B; Perl, AT. The elephant in the lung: Integrating lineage-tracing, molecular markers, and single cell sequencing data to identify distinct fibroblast populations during lung development and regeneration. Matrix Biology. 2020; 91-92:51-74.

Roskin, K; Spearman, P. HIV-1 Broadly Neutralizing Antibodies Take the Road Less Traveled, and That Makes All the Difference. Cell Host and Microbe. 2020; 27:487-488.

Roskin, KM; Jackson, KJ L; Lee, J; Hoh, RA; Joshi, SA; Hwang, K; Bonsignori, M; Pedroza-Pacheco, I; Liao, H; Moody, MA; et al. Aberrant B cell repertoire selection associated with HIV neutralizing antibody breadth. Nature Immunology. 2020; 21:199-209.

Rossi, RM; Brady, MJ; Hall, ES; Warshak, CR. Effect of Needle Exchange Program on Maternal Hepatitis C Virus Prevalence. American Journal of Perinatology: neonatal and maternal-fetal medicine. 2020; 37:881-889.

Rossi, RM; Requarth, E; Warshak, CR; Dufendach, KR; Hall, ES; DeFranco, EA. Risk Calculator to Predict Cesarean Delivery Among Women Undergoing Induction of Labor. Obstetrics and Gynecology. 2020; 135:559-568.

Rossi, RM; Wolfe, C; Brokamp, R; McAllister, JM; Wexelblatt, S; Warshak, CR; Hall, ES. Reported Prevalence of Maternal Hepatitis C Virus Infection in the United States. Obstetrics and Gynecology. 2020; Publish Ahead of Print:387-395.

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. 2020; 48:W85-W93.

Singh, U; Hernandez, K; Aronow, B; Wurtele, E. African Americans and European Americans exhibit distinct gene expression patterns across tissues and tumors that are associated with immunologic and infectious functions and environmental exposures. 2020.

Sirvent, S; Vallejo, AF; Davies, J; Clayton, K; Wu, Z; Woo, J; Riddell, J; Chaudhri, VK; Stumpf, P; Nazlamova, LA; et al. Genomic programming of IRF4-expressing human Langerhans cells. Nature Communications. 2020; 11.

Smith-Anttila, CJ A; Mason, EA; Wells, CA; Aronow, BJ; Osborne, PB; Keast, JR. Identification of a sacral, visceral sensory transcriptome in embryonic and adult mice. eNeuro. 2020; 7:ENEURO.0397-19.2019.

Sonnet, F; Namork, E; Stylianou, E; Gaare-Olstad, I; Huse, K; Andorf, S; Mjaaland, S; Dirven, H; Nygaard, U. Reduced polyfunctional T cells and increased cellular activation markers in adult allergy patients reporting adverse reactions to food. BMC Immunology. 2020; 21.

Srinivasan, S; Ravi, V; Sowmya, V; Krichen, M; Ben Noureddine, D; Anivilla, S; Soman, KP. (2020) Deep Convolutional Neural Network Based Image Spam Classification. IEEE. 112-117.

Stewart, HJ; Martinez, JL; Perdew, A; Green, CS; Moore, DR. Auditory cognition and perception of action video game players. Scientific Reports. 2020; 10.

Sung, JY; Lim, HW; Joung, JG; Park, WY. Pan-cancer analysis of alternative lengthening of telomere activity. Cancers. 2020; 12:2207-2207.

Szczesniak, R; Rice, JL; Brokamp, C; Ryan, P; Pestian, T; Ni, Y; Andrinopoulou, E; Keogh, RH; Gecili, E; Huang, R; et al. Influences of environmental exposures on individuals living with cystic fibrosis. Expert Review of Respiratory Medicine. 2020; 14:737-748.

Szczesniak, RD; Su, W; Brokamp, C; Keogh, RH; Pestian, JP; Seid, M; Diggle, PJ; Clancy, JP. Dynamic predictive probabilities to monitor rapid cystic fibrosis disease progression. Statistics in Medicine. 2020; 39:740-756.

Taylor, ZL; Mizuno, T; Punt, NC; Baskaran, B; Sainz, AN; Shuman, W; Felicelli, N; Vinks, AA; Heldrup, J; Ramsey, LB. MTXPK.org: A Clinical Decision Support Tool Evaluating High-Dose Methotrexate Pharmacokinetics to Inform Post-Infusion Care and Use of Glucarpidase. Clinical Pharmacology and Therapeutics. 2020; 108:635-643.

Thanh, DN H; Thanh, LT; Hien, NN; Prasath, S. Adaptive total variation L1 regularization for salt and pepper image denoising. Optik. 2020; 208:163677-163677.

Treble-Barna, A; Pilipenko, V; Wade, SL; Jegga, AG; Yeates, KO; Taylor, HG; Martin, LJ; Kurowski, BG. Cumulative Influence of Inflammatory Response Genetic Variation on Long-Term Neurobehavioral Outcomes after Pediatric Traumatic Brain Injury Relative to Orthopedic Injury: An Exploratory Polygenic Risk Score. Journal of Neurotrauma. 2020; 37:1491-1503.

van Camp, PJ; Kirkendall, ES; Hagedorn, PA; Minich, T; Kouril, M; Spooner, SA; Gecili, E; Dexheimer, JW. Feedback at the Point of Care to Decrease Medication Alert Rates in an Electronic Health Record. Pediatric Emergency Care. 2020; 36:e417-e422.

Venkatasubramanian, M; Chetal, K; Schnell, DJ; Atluri, G; Salomonis, N. Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF. Bioinformatics. 2020; 36:3773-3780.

Villivalam, SD; You, D; Kim, J; Lim, HW; Xiao, H; Zushin, PH; Oguri, Y; Amin, P; Kang, S. TET1 is a beige adipocyte-selective epigenetic suppressor of thermogenesis. Nature Communications. 2020; 11.

Wang, W; Lyu, S; Ji, X; Gupta, S; Manohar, M; Dhondalay, GK R; Chinthrajah, S; Andorf, S; Boyd, SD; Tibshirani, R; et al. Transcriptional changes in peanut-specific CD4+ T cells over the course of oral immunotherapy. Clinical Immunology. 2020; 219:108568-108568.

Wang, Y; Yella, JK; Ghandikota, S; Cherukuri, TC; Ediga, HH; Madala, SK; Jegga, AG. Pan-transcriptome-based candidate therapeutic discovery for idiopathic pulmonary fibrosis. Therapeutic Advances in Respiratory Disease. 2020; 14:1753466620971143-175346662097114.

Wissel, BD; Greiner, HM; Glauser, TA; Holland-Bouley, KD; Mangano, FT; Santel, D; Faist, R; Zhang, N; Pestian, JP; Szczesniak, RD; et al. Prospective validation of a machine learning model that uses provider notes to identify candidates for resective epilepsy surgery. Epilepsia. 2020; 61:39-48.

Wissel, BD; Van Camp, PJ; Kouril, M; Weis, C; Glauser, TA; White, PS; Kohane, IS; Dexheimer, JW. An interactive online dashboard for tracking COVID-19 in U.S. counties, cities, and states in real time. Journal of the American Medical Informatics Association. 2020; 27:1121-1125.

Woodle, ES; Tremblay, S; Brailey, P; Girnita, A; Alloway, RR; Aronow, B; Dasgupta, N; Ebstein, F; Kloetzel, P; Lee, MJ; et al. Proteasomal adaptations underlying carfilzomib-resistance in human bone marrow plasma cells. American Journal of Transplantation. 2020; 20:399-410.

Woodle, ES; Tremblay, S; Rossi, A; Rojas, CC; Alloway, R; Roskin, K; Allman, D; Hildeman, D. Plasma cell targeting to prevent antibody-mediated rejection. American Journal of Transplantation. 2020; 20 Suppl 4:33-41.

Yella, JK; Jegga, A. MGATRx: Discovering Drug Repositioning Candidates Using Multi-view Graph Attention. 2020.

Yu, Y; Choi, K; Wu, J; Andreassen, PR; Dexheimer, PJ; Keddache, M; Brems, H; Spinner, RJ; Cancelas, JA; Martin, LJ; et al. NF1 patient missense variants predict a role for ATM in modifying neurofibroma initiation. Acta Neuropathologica. 2020; 139:157-174.