A5079734791- Antifungal resistance and susceptibility
- Fungal Infections and Studies
- Medical Imaging and Pathology Studies
- Occupational and environmental lung diseases
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- Gene expression and cancer classification
- Single-cell and spatial transcriptomics
- Nail Diseases and Treatments
- Cancer Immunotherapy and Biomarkers
- Ferroptosis and cancer prognosis
- Cancer Research and Treatments
- Radiomics and Machine Learning in Medical Imaging
- Congenital Diaphragmatic Hernia Studies
- Cancer Cells and Metastasis
- Plant Pathogens and Fungal Diseases
- Genetics, Bioinformatics, and Biomedical Research
- Gastric Cancer Management and Outcomes
- Gene Regulatory Network Analysis
- Tracheal and airway disorders
- Cell Image Analysis Techniques
- Neonatal Respiratory Health Research
- Helicobacter pylori-related gastroenterology studies
- Computational Drug Discovery Methods
- Medical Coding and Health Information
Institute for Systems Biology
2016-2025
Environment Canterbury
2023-2024
Center for Systems Biology
2023
Harvard University
2023
Massachusetts General Hospital
2023
Children's Hospital of Orange County
2022
Texas State University
2017-2021
North Seattle College
2020-2021
Baylor University
2019
InSysBio (Russia)
2019
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled TCGA. Across types, we identified six immune subtypes—wound healing, IFN-γ dominant, inflammatory, lymphocyte depleted, immunologically quiet, and TGF-β dominant—characterized differences in macrophage or signatures, Th1:Th2 cell ratio, extent intratumoral heterogeneity, aneuploidy, neoantigen load, overall proliferation, expression immunomodulatory genes,...
Fluconazole in vitro susceptibility test results for 256,882 isolates of Candida spp. were collected from 142 sites 41 countries June 1997 to December 2007. Data 197,619 tested with voriconazole 2001 A total 31 different species isolated. Increased rates isolation the common non-albicans C. glabrata (10.2% 11.7%), tropicalis (5.4% 8.0%), and parapsilosis (4.8% 5.6%) noted when time periods 2000 2005 2007 compared. Investigators clinical by CLSI M44-A disk diffusion method. Overall, 90.2%...
Abstract Malignant pleural mesothelioma (MPM) is a highly lethal cancer of the lining chest cavity. To expand our understanding MPM, we conducted comprehensive integrated genomic study, including most detailed analysis BAP1 alterations to date. We identified histology-independent molecular prognostic subsets, and defined novel subtype with TP53 SETDB1 mutations extensive loss heterozygosity. also report strong expression immune-checkpoint gene VISTA in epithelioid strikingly higher than...
Fluconazole in vitro susceptibility test results for 205,329 yeasts were collected from 134 study sites 40 countries June 1997 through December 2005. Data 147,776 yeast isolates tested with voriconazole 2001 All investigators clinical by the CLSI M44-A disk diffusion method. Test plates automatically read and recorded a BIOMIC image analysis system. Species, drug, zone diameter, category, quality control quarterly. Duplicate (same patient, same species, susceptible-resistant biotype profile...
Highlights•An overview of PanCancer Atlas analyses on oncogenic molecular processes•Germline genome affects somatic genomic landscape in a pathway-dependent fashion•Genome mutations impact expression, signaling, and multi-omic profiles•Mutation burdens drivers influence immune-cell composition microenvironmentSummaryThe Cancer Genome (TCGA) has catalyzed systematic characterization diverse alterations underlying human cancers. At this historic junction marking the completion over 11,000...
ABSTRACT Fluconazole in vitro susceptibility test results for 205,329 yeasts were collected from 134 study sites 40 countries June 1997 through December 2005. Data 147,776 yeast isolates tested with voriconazole 2001 All investigators clinical by the CLSI M44-A disk diffusion method. Test plates automatically read and recorded a BIOMIC image analysis system. Species, drug, zone diameter, category, quality control quarterly. Duplicate (same patient, same species, susceptible-resistant biotype...
Candida krusei is well known as a fungal pathogen for patients with hematologic malignancies and transplant recipients. Using the ARTEMIS Antifungal Surveillance Program database, we describe geographic temporal trends in isolation of C. from clinical specimens vitro susceptibilities 3,448 isolates to voriconazole determined by CLSI (formerly NCCLS) disk diffusion testing. In addition, report bloodstream infection amphotericin B (304 isolates), flucytosine (254 anidulafungin (121 caspofungin...
ABSTRACT Fluconazole in vitro susceptibility test results for 140,767 yeasts were collected from 127 participating investigators 39 countries June 1997 through December 2003. Data on 79,343 yeast isolates tested with voriconazole 2001 All clinical by the CLSI (formerly NCCLS) M44-A disk diffusion method. Test plates automatically read and recorded BIOMIC Vision Image Analysis System. Species, drug, zone diameter, category, quality control quarterly via e-mail analysis. Duplicate (the same...
ABSTRACT Although a rare cause of invasive candidiasis, Candida guilliermondii has been reported to exhibit decreased susceptibility antifungal agents. Aside from case reports and small surveys, there is little information regarding the epidemiology profile C. . We report geographic temporal trends in isolation susceptibilities 1,029 clinical isolates collected 127 medical centers as part ARTEMIS DISK Antifungal Surveillance Program. In addition, we vitro 132 bloodstream caspofungin....
The purpose of this study was to correlate inhibition zone diameters, in millimeters (agar diffusion disk method), with the broth dilution MICs or minimum effective concentrations (MECs) (CLSI M38-A method) five antifungal agents identify optimal testing guidelines for mold testing. following parameters were evaluated 555 isolates molds Absidia corymbifera, Aspergillus sp. (five species), Alternaria sp., Bipolaris spicifera, Fusarium (three Mucor (two Paecilomyces lilacinus, Rhizopus and...
Combining P-values from multiple statistical tests is a common exercise in bioinformatics. However, this procedure non-trivial for dependent P-values. Here, we discuss an empirical adaptation of Brown's method (an extension Fisher's method) combining which appropriate the large and correlated datasets found high-throughput biology.We show that Empirical (EBM) outperforms as well alternative approaches using both noisy simulated data gene expression The Cancer Genome Atlas.The available...
Elements of field cancerization, including atrophic gastritis, metaplasia, and dysplasia, promote gastric cancer development in association with chronic inflammation. However, it remains unclear how stroma changes during carcinogenesis the contributes to progression preneoplasia. Here we investigated heterogeneity fibroblasts, one most important elements stroma, their roles neoplastic transformation metaplasia.We used single-cell transcriptomics evaluate cellular mucosal cells from patients...
Background: Previous studies have described sex-specific patient subtyping in glioblastoma. The cluster labels associated with these “legacy data” were used to train a predictive model capable of recapitulating this clustering contemporary contexts. Methods: We robust ensemble machine learning using gene microarray data perform multi-platform predictions including RNA-seq and potentially scRNA-seq. Results: engineered feature set was composed many previously reported genes that are...
ABSTRACT We examined data from the ARTEMIS DISK Antifungal Surveillance Program to describe geographic and temporal trends in isolation of Candida parapsilosis clinical specimens vitro susceptibilities 9,371 isolates fluconazole voriconazole. also report susceptibility bloodstream infection (BSI) C. echinocandins, anidulafungin, caspofungin, micafungin. represented 6.6% 141,383 collected 2001 2005 was most common among North America (14.3%) Latin (9.9%). High levels both (90.8 95.8%)...
Preterm birth (PTB) complications are the leading cause of long-term morbidity and mortality in children. By using whole blood samples, we integrated whole-genome sequencing (WGS), RNA (RNA-seq), DNA methylation data for 270 PTB 521 control families. We analyzed this combined dataset to identify genomic variants associated with secondary analyses very early (VEPTB) as well other subcategories disease that may contribute PTB. identified differentially expressed genes (DEGs) methylated loci...
<ns4:p>The Cancer Research Institute (CRI) iAtlas is an interactive web platform for data exploration and discovery in the context of tumors their interactions with immune microenvironment. allows researchers to study response characterizations patterns individual tumor types, subtypes, subtypes. supports computation visualization correlations statistics among features related microenvironment, cell composition, expression signatures, mutation burden, cancer driver mutations, adaptive...
Background & Aims Isthmic progenitors, tissue-specific stem cells in the stomach corpus, maintain mucosal homeostasis by balancing between proliferation and differentiation to gastric epithelial lineages. The progenitor rapidly adopt an active state response injury. However, it remains unclear how isthmic cell niche is controlled during regeneration of damaged epithelium. Methods We recapitulated tissue recovery process after acute injury mouse stomach. BrdU incorporation was utilized trace...
Congenital diaphragmatic defects (CDDs) may occur in malformation syndromes of varied causes. Syndromic cases CDDs due to chromosomal defects, autosomal recessive, dominant, or X-linked inheritance have been described. In order determine the frequency and nature syndromes, malformations, chromosome abnormalities associated with CDDs, we reviewed records all patients evaluated over a 4-year period. During interval, total 60 was evaluated. Of these, 29 had therapeutic spontaneous abortion, 31...
ABSTRACT From June 1997 to December 2001, results of in vitro susceptibility tests yeast isolates from 35 countries were collected. For 2001 alone, fluconazole reported for 22,111 77 institutions 30 countries. Of these isolates, 18,569 also tested voriconazole. All study sites clinical by recently endorsed NCCLS disk diffusion method M44-P. Disk test plates automatically read and recorded with the BIOMIC Image Analysis System. Species, drug, zone diameter, category, MIC, quality control...
ABSTRACT Candida rugosa is a fungus that appears to be emerging as cause of infection in some geographic regions. We utilized the extensive database ARTEMIS DISK Antifungal Surveillance Program describe and temporal trends isolation C. from clinical specimens vitro susceptibilities 452 isolates fluconazole voriconazole. accounted for 0.4% 134,715 , frequency increased 0.03% over 6.5-year study period (1997 2003). was most common Latin American region (2.7% versus 0.1 0.4%). Decreased...