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2024
Facilitating pathway and network based analysis of RNA-Seq data with pathlinkR
PLOS Computational Biology
2024
Extracellular Matrix Remodeling in Atopic Dermatitis Harnesses the Onset of an Asthmatic Phenotype and Is a Potential Contributor to the Atopic March
Journal of Investigative Dermatology
2024
Colocalization analysis of 3′ UTR alternative polyadenylation quantitative trait loci reveals novel mechanisms underlying associations with lung function
Human Molecular Genetics
2024
Gene Expression Profiling in Pediatric Appendicitis
JAMA Pediatrics
2024
Predictive gene expression signature diagnoses neonatal sepsis before clinical presentation
eBioMedicine
2023
Post-COVID symptoms are associated with endotypes reflecting poor inflammatory and hemostatic modulation
Frontiers in Immunology
2023
Facilitating systems-level analyses of all-cause and Covid-mediated sepsis through SeptiSearch, a manually-curated compendium of dysregulated gene sets
Frontiers in Immunology
2023
Placental Inflammation Leads to Abnormal Embryonic Heart Development
Circulation
2023
Blood Gene Expression and Immune Cell Subtypes Associated with Chronic Obstructive Pulmonary Disease Exacerbations
American Journal of Respiratory and Critical Care Medicine
2022
Host Response of Human Epidermis to Methicillin-Resistant Staphylococcus aureus Biofilm Infection and Synthetic Antibiofilm Peptide Treatment
Cells
2022
Detecting genetic epistasis by differential departure from independence
Molecular Genetics and Genomics
2022
Gene Expression Profiling: Identification of Novel Pathways and Potential Biomarkers in Severe Acute Pancreatitis
Journal of the American College of Surgeons
2022
Subcutaneous adipose tissue splice quantitative trait loci reveal differences in isoform usage associated with cardiometabolic traits
The American Journal of Human Genetics
2022
Development of a Blood-based Transcriptional Risk Score for Chronic Obstructive Pulmonary Disease
American Journal of Respiratory and Critical Care Medicine
2022
Blood gene expression risk profiles and interstitial lung abnormalities: COPDGene and ECLIPSE cohort studies
Respiratory Research
2022
A transcriptomic analysis of the effects of macrophage polarization and endotoxin tolerance on the response to Salmonella
PLOS ONE
2021
Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria
BMC Genomics
2021
Fundamental gene network rewiring at the second order within and across mammalian systems
Bioinformatics
2020
Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis B Vaccine Response in a Small Cohort
Frontiers in Immunology
2020
Systems Biology Approaches to Understanding the Human Immune System
Frontiers in Immunology
2020
Immunomodulatory function of the cystic fibrosis modifier gene BPIFA1
PLOS ONE
2020
Rhinovirus Infection Drives Complex Host Airway Molecular Responses in Children With Cystic Fibrosis
Frontiers in Immunology
2020
Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults
Frontiers in Immunology
2020
DNA Methylation Events in Transcription Factors and Gene Expression Changes in Colon Cancer
Epigenomics
2020
Whole blood transcriptional responses of very preterm infants during late-onset sepsis
PLOS ONE
2019
A Genome-Wide Knockout Screen in Human Macrophages Identified Host Factors Modulating Salmonella Infection
mBio
2019
Analysis of genetically driven alternative splicing identifies FBXO38 as a novel COPD susceptibility gene
PLOS Genetics
2019
Characterization of Host Responses during Pseudomonas aeruginosa Acute Infection in the Lungs and Blood and after Treatment with the Synthetic Immunomodulatory Peptide IDR-1002
Infection and Immunity
2019
Dynamic molecular changes during the first week of human life follow a robust developmental trajectory
Nature Communications
2018
Experimental infection of cattle with Mycobacterium tuberculosis isolates shows the attenuation of the human tubercle bacillus for cattle
Scientific Reports
2018
Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli
Microbial Genomics
2018
Gene Pathways Analysis of the Effects of Suspension Culture on Primary Human Renal Proximal Tubular Cells
Microgravity Science and Technology
2018
LPRP: A Gene–Gene Interaction Network Construction Algorithm and Its Application in Breast Cancer Data Analysis
Interdisciplinary Sciences: Computational Life Sciences
2018
Systems analysis of key genes and pathways in the progression of hepatocellular carcinoma
Medicine
2017
Comprehensive analysis of copy number aberrations in microsatellite stable colon cancer in view of stromal component
British Journal of Cancer
2017
Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis
Nature Communications
2017
Mechanisms of the Innate Defense Regulator Peptide-1002 Anti-Inflammatory Activity in a Sterile Inflammation Mouse Model
The Journal of Immunology
2017
Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics
2016
Using biological networks to integrate, visualize and analyze genomics data
Genetics Selection Evolution
2015
Bioinformatics approaches for the functional interpretation of protein lists: From ontology term enrichment to network analysis
PROTEOMICS
2014
Aberrant gene expression in mucosa adjacent to tumor reveals a molecular crosstalk in colon cancer
Molecular Cancer
2014
Large differences in global transcriptional regulatory programs of normal and tumor colon cells
BMC Cancer
2012
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