Reconstructing differentiation networks and their regulation from time series single-cell expression data. Genome Research. 2018; 28:383-395..
Transcriptional risk scores link GWAS to eQTLs and predict complications in Crohn's disease. Nature Genetics. 2017; 49:1517-1521..
The complex genetics of hypoplastic left heart syndrome. Nature Genetics. 2017; 49:1152-1159..
Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. Nature. 2016; 537:698-702..
Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium. Stem Cell Reports. 2016; 7:110-125..
Data mining differential clinical outcomes associated with drug regimens using adverse event reporting data. Nature Biotechnology. 2016; 34:697-700..
Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record?. Journal of Biomedical Informatics. 2023; 139..
A big data approach to evaluate receipt of optimal care in childhood cerebral palsy. Disability and Rehabilitation. 2023; 1-8..
Acute respiratory distress syndrome after SARS-CoV-2 infection on young adult population: International observational federated study based on electronic health records through the 4CE consortium. PLoS ONE. 2023; 18..
Gross motor function prediction using natural language processing in cerebral palsy. Developmental Medicine and Child Neurology. 2023; 65:100-106..
Long-term kidney function recovery and mortality after COVID-19-associated acute kidney injury: An international multi-centre observational cohort study. EClinicalMedicine. 2023; 55..
Hospitalizations Associated With Mental Health Conditions Among Adolescents in the US and France During the COVID-19 Pandemic. JAMA Network Open. 2022; 5..
International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality. npj Digital Medicine. 2022; 5..
International electronic health record-derived post-acute sequelae profiles of COVID-19 patients. npj Digital Medicine. 2022; 5..
LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung. American Journal of Respiratory Cell and Molecular Biology. 2022..
CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons. iScience. 2022; 25..
CellDrift: inferring perturbation responses in temporally sampled single-cell data. Briefings in Bioinformatics. 2022; 23..
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..
Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease. Cell Stem Cell. 2022; 29:840-855.e7..
2022; 26:138-146.. Data Augmentation Using Generative Adversarial Networks for Multi-Class Segmentation of Lung Confocal IF Images. Journal of Advanced Computational Intelligence and Intelligent Informatics.
Endosomal Sequestration of TLR4 Antibody Induces Myeloid-Derived Suppressor Cells and Reverses Acute Type 1 Diabetes. Diabetes. 2022; 71:470-482..
Betacoronavirus-specific alternate splicing. Genomics. 2022; 114..
The genetic architecture of pediatric cardiomyopathy. American Journal of Human Genetics. 2022; 109:282-298..
Response to comment on 'SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung'. eLife. 2022; 11..
A census of the lung: CellCards from LungMAP. Developmental Cell. 2022; 57:112-145.e2..
Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images. BMC Bioinformatics. 2021; 22..
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..
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..
Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma. Communications Biology. 2021; 4..
Evolving phenotypes of non-hospitalized patients that indicate long COVID. BMC Medicine. 2021; 19..
Multinational characterization of neurological phenotypes in patients hospitalized with COVID-19. Scientific Reports. 2021; 11..
Electronic health record and patterns of care for children with cerebral palsy. Developmental Medicine and Child Neurology. 2021; 63:1337-1343..
An interactive single cell web portal identifies gene and cell networks in COVID-19 host responses. iScience. 2021; 24..
A roadmap for the Human Developmental Cell Atlas. Nature. 2021; 597:196-205..
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..
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..
Betacoronavirus-specific alternate splicing. 2021..
Implicating Gene and Cell Networks Responsible for Differential COVID-19 Host Responses via an Interactive Single Cell Web Portal. 2021..
International Analysis of Electronic Health Records of Children and Youth Hospitalized With COVID-19 Infection in 6 Countries. JAMA Network Open. 2021; 4..
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..
Genetic Causes of Cardiomyopathy in Children: First Results From the Pediatric Cardiomyopathy Genes Study. Journal of the American Heart Association. 2021; 10..
2021.. Integration of Molecular Analysis, Cutting-edge Mouse Genetic Models and Proton Therapy to Improve Outcomes for Glioma Patients. Gliomas.
Describing the Delivery of Evidence-Based Physical Therapy Intervention to Individuals With Cerebral Palsy. Pediatric Physical Therapy. 2021; 33:65-72..
SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung. eLife. 2021; 10..
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..
Therapeutic Opportunities for Intestinal Angioectasia- Targeting PPARγ and Oxidative Stress. Clinical and Translational Science. 2021; 14:518-528..
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..
Mucosal Inflammatory and Wound Healing Gene Programs Reveal Targets for Stricturing Behavior in Pediatric Crohn's Disease. Journal of Crohn's and Colitis. 2021; 15:273-286..
2021; 28:1-13.. Computational Nuclei Segmentation Methods in Digital Pathology: A Survey. Archives of Computational Methods in Engineering.
Guidelines for reporting single-cell RNA-seq experiments. Nature Biotechnology. 2020; 38:1384-1386..
2020; 140:1367-1368.. CNNを用いたGliomaの疾患進行度評価における形状特徴量に関する一検討. IEEJ Transactions on Electronics, Information and Systems.
2020.. Human Developmental Cell Atlas: milestones achieved and the roadmap ahead.
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..
A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm. eLife. 2020; 9..
2020; 38:e17078-e17078.. TCGA Kidney Cell Atlas: A differential gene expression database for the dissection of tumor-specific gene modules. Journal of Clinical Oncology.
AB569, a nontoxic chemical tandem that kills major human pathogenic bacteria. Proceedings of the National Academy of Sciences of the United States of America. 2020; 117:4921-4930..
Proteasomal adaptations underlying carfilzomib-resistance in human bone marrow plasma cells. American Journal of Transplantation. 2020; 20:399-410..
Identification of a Sacral, Visceral Sensory Transcriptome in Embryonic and Adult Mice. eNeuro. 2020; 7..
2020; 14:s127-s127.. DOP89 Pre-treatment mucosal inflammatory and wound healing gene programmes reveal mechanisms associated with future stricturing behaviour during 5-year follow-up in paediatric Crohn’s disease. Journal of Crohn's and Colitis.
(2020) Development of a Web Based Image Annotation Tool for Lung Immunofluorescent Confocal Images. ISASE2018:1-5..
Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response. Nature Communications. 2019; 10..
(2019) Multi-Class Segmentation of Lung Immunofluorescence Confocal Images Using Deep Learning. 00:2362-2368..
Synergistic effects of common schizophrenia risk variants. Nature Genetics. 2019; 51:1475-1485..
2019; 125.. Abstract 837: Different Disease States in Heart Have Distinct Cardiac Interstitial Cells Contributing to Fibrosis. Circulation Research.
Elimination of the fibrinogen integrin αMβ2-binding motif improves renal pathology in mice with sickle cell anemia. Blood Advances. 2019; 3:1519-1532..
Single-Cell Transcriptomics Uncovers Glial Progenitor Diversity and Cell Fate Determinants during Development and Gliomagenesis. Cell Stem Cell. 2019; 24:707-723.e8..
Single-cell RNA sequencing identifies inflammatory tissue T cells in eosinophilic esophagitis. Journal of Clinical Investigation. 2019; 129:2014-2028..
Single cell RNA sequencing reveals regional heterogeneity of hepatobiliary innate lymphoid cells in a tissue-enriched fashion. PLoS ONE. 2019; 14..
The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Developmental Cell. 2019; 49:10-29..
Age-of-diagnosis dependent ileal immune intensification and reduced alpha-defensin in older versus younger pediatric Crohn Disease patients despite already established dysbiosis. Mucosal Immunology. 2019; 12:491-502..
Genetic and Transcriptomic Variation Linked to Neutrophil Granulocyte-Macrophage Colony-Stimulating Factor Signaling in Pediatric Crohn's Disease. Inflammatory Bowel Diseases. 2019; 25:547-560..
(2019) Glioma Subtypes Clustering Method using Histopathological Image Analysis. 00:442-446..
Genetic variants and pathways implicated in a pediatric inflammatory bowel disease cohort. Genes and Immunity. 2019; 20:131-142..
Discovery of SERPINA3 as a candidate urinary biomarker of lupus nephritis activity. Rheumatology. 2019; 58:321-330..
Spatial distribution of marker gene activity in the mouse lung during alveolarization. Data in Brief. 2019; 22:365-372..
mTOR kinase inhibition reduces tissue factor expression and growth of pancreatic neuroendocrine tumors. Journal of Thrombosis and Haemostasis. 2019; 17:169-182..
Expression Profiling of Fibroblasts in Chronic and Acute Disease Models Reveals Novel Pathways in Kidney Fibrosis. Journal of the American Society of Nephrology : JASN. 2019; 30:80-94..
Division of Biomedical Informatics
3333 Burnet Ave
Cincinnati, OH 45229