A5051060627- RNA modifications and cancer
- Cancer Genomics and Diagnostics
- Immunotherapy and Immune Responses
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- T-cell and B-cell Immunology
- Cancer Immunotherapy and Biomarkers
- COVID-19 Clinical Research Studies
- Spectroscopy and Quantum Chemical Studies
- Quantum Mechanics and Applications
- SARS-CoV-2 and COVID-19 Research
- vaccines and immunoinformatics approaches
- Systemic Lupus Erythematosus Research
- Quantum Information and Cryptography
- Platelet Disorders and Treatments
- Lymphoma Diagnosis and Treatment
- Blood groups and transfusion
- Bladder and Urothelial Cancer Treatments
- Quantum optics and atomic interactions
- Complement system in diseases
- Molecular Biology Techniques and Applications
- Monoclonal and Polyclonal Antibodies Research
- Immune Cell Function and Interaction
- Renal cell carcinoma treatment
- SARS-CoV-2 detection and testing
Complete Genomics (United States)
2023
Oregon Health & Science University
2019-2022
University of Portland
2022
Oregon Medical Research Center
2020
Rhode Island Hospital
2012
Brown University
2012
The University of Texas at Austin
2008-2009
Hammersmith Hospital
1987
Individual genetic variation may help to explain different immune responses a virus across population. In particular, understanding how in HLA affect the course of COVID-19 could identify individuals at higher risk from disease. typing can be fast and inexpensive. Pairing with testing where feasible improve assessment severity viral disease Following development vaccine against SARS-CoV-2, that causes COVID-19, high-risk types prioritized for vaccination.
Tumor mutational burden (TMB; the quantity of aberrant nucleotide sequences a given tumor may harbor) has been associated with response to immune checkpoint inhibitor therapy and is gaining broad acceptance as result. However, TMB harbors intrinsic variability across cancer types, its assessment interpretation are poorly standardized.Using standardized approach, we quantify robustness metric potential predictor immunotherapy survival among diverse cohort patients. We also explore additive...
ABSTRACT Genetic variability across the three major histocompatibility complex (MHC) class I genes (human leukocyte antigen [HLA] A, B, and C) may affect susceptibility to severity of severe acute respiratory syndrome 2 (SARS-CoV-2), virus responsible for coronavirus disease 2019 (COVID-19). We execute a comprehensive in silico analysis viral peptide-MHC binding affinity 145 HLA -A, -B, -C genotypes all SARS-CoV-2 peptides. further explore potential cross-protective immunity conferred by...
Abstract There is a deficiency of complement receptor type 1 (CR1) on the erythrocytes patients with systemic lupus erythematosus (SLE). This involved in processing immune complexes. Whether inherited or acquired has been subject controversy. A restriction fragment length polymorphism (RFLP), identified using complementary DNA probe for CR1, correlated numeric expression CR1 normal erythrocytes. The gene frequency 2 alleles defined by this RFLP was compared 44 SLE (from 42 families), 43...
There is growing interest in retained introns a variety of disease contexts including cancer and aging. Many software tools have been developed to detect from short RNA-seq reads, but reliable detection complicated by overlapping genes transcripts as well the presence unprocessed or partially processed RNAs.We compared detected 8 using reads with observed long same biological specimens. We found significant disagreement among (Fleiss' [Formula: see text]) such that 47.7% all intron...
This study probes the distribution of putatively cancer-specific junctions across a broad set publicly available non-cancer human RNA sequencing (RNA-seq) datasets. We compared cancer and RNA-seq data from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx) Project Sequence Read Archive. found that (i) averaging types, 80.6% exon-exon thought to be based on comparison with tissue-matched samples (
To facilitate the search for isochrones when using complex-valued trajectory methods quantum barrier scattering calculations, structure and shape of in complex plane were studied. Isochrone segments categorized based on their distinguishing features, which are shared by each situation studied: High low energy wave packets, from both thick thin Gaussian Eckart barriers varying height. The characteristic isochrone is a trifurcated system: Trajectories that transmit launched lower branch (T),...
Abstract There is growing interest in retained introns a variety of disease contexts including cancer and aging. Many software tools have been developed to detect from short RNA-seq reads, but reliable detection complicated by overlapping genes transcripts as well the presence unprocessed or partially processed RNAs. We compared detected 5 using reads with observed long same biological specimens found: (1) significant disagreement among (Fleiss’ κ = 0.231 ) such that 52.4% all intron...
Abstract The major histocompatibility complex (MHC) is a region of the human genome that key to immune system function but sometimes refractory genomic analyses due extreme polymorphism and structural variation. We performed targeted long-read sequencing de novo assembly MHC create 246 highly accurate, fully contiguous, phased full-length sequences, mostly from data provided by Human Pangenome Reference Consortium (HPRC). identified alleles at high resolution across 39 loci including class I...
ABSTRACT Background Tumor mutational burden (TMB, the quantity of aberrant nucleotide sequences a given tumor may harbor) has been associated with response to immune checkpoint inhibitor therapy and is gaining broad acceptance as result. However, TMB harbors intrinsic variability across cancer types, its assessment interpretation are poorly standardized. Methods Using standardized approach, we quantify robustness metric potential predictor immunotherapy survival among diverse cohort...
ABSTRACT We compared cancer and non-cancer RNA sequencing (RNA-seq) data from The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) Project, Sequence Read Archive (SRA). found that: 1) averaging across types, 80.6% of exon-exon junctions thought to be cancer-specific based on comparison with tissue-matched samples are in fact present other adult tissues throughout body; 2) 30.8% not any GTEx or TCGA normal shared by multiple within at least one type cohort, 87.4% these...