A5030699393- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Cancer Genomics and Diagnostics
- Microbial Community Ecology and Physiology
- RNA modifications and cancer
- Genomic variations and chromosomal abnormalities
- Oral Health Pathology and Treatment
- Otolaryngology and Infectious Diseases
- Genomics and Chromatin Dynamics
- Genomics and Rare Diseases
- Mosquito-borne diseases and control
- Reproductive tract infections research
- RNA and protein synthesis mechanisms
- Genetic Syndromes and Imprinting
- HIV Research and Treatment
- Insect symbiosis and bacterial influences
- Aquaculture disease management and microbiota
- Protist diversity and phylogeny
- Gut microbiota and health
- MicroRNA in disease regulation
- Genetic factors in colorectal cancer
- Malaria Research and Control
The University of Texas MD Anderson Cancer Center
2025
Fred Hutch Cancer Center
2008-2024
University of Washington
2004-2015
Rosetta Stone (United States)
2010-2011
Studies of the host response to virus infection typically focus on protein-coding genes. However, non-protein-coding RNAs (ncRNAs) are transcribed in mammalian cells, and roles many these ncRNAs remain enigmas. Using next-generation sequencing, we performed a whole-transcriptome analysis severe acute respiratory syndrome coronavirus (SARS-CoV) across four founder mouse strains Collaborative Cross. We observed differential expression approximately 500 annotated, long 1,000 nonannotated...
Abstract Fusobacterium nucleatum ( Fn ), a bacterium present in the human oral cavity and rarely found lower gastrointestinal tract of healthy individuals 1 , is enriched colorectal cancer (CRC) tumours 2–5 . High intratumoural loads are associated with recurrence, metastases poorer patient prognosis 5–8 Here, to delineate genetic factors facilitating tumour colonization, we generated closed genomes for 135 strains; 80 strains from without 55 unique cultured 51 patients CRC. Pangenomic...
Non-coding RNAs (ncRNAs) are an essential class of molecular species that have been difficult to monitor on high throughput platforms due frequent lack polyadenylation. Using a polyadenylation-neutral amplification protocol and next-generation sequencing, we explore ncRNA expression in eleven human tissues. ncRNAs 7SL, U2, 7SK, HBII-52 expressed at levels far exceeding mRNAs. C/D H/ACA box snoRNAs associated with rRNA methylation pseudouridylation, respectively: spleen expresses both,...
Malaria caused by Plasmodium falciparum results in approximately 1 million annual deaths worldwide, with young children and pregnant mothers at highest risk. Disease severity might be related to parasite virulence factors, but expression profiling studies of parasites test this hypothesis have been hindered extensive sequence variation putative genes a preponderance host RNA clinical samples. We report here the application sequencing isolates P. falciparum, using not-so-random (NSR) primers...
Abstract Bacterial vaginosis (BV) is a prevalent condition associated with an imbalance in the vaginal microbiota, often involving species of Gardnerella . The taxonomic complexity and inconsistent nomenclature have impeded progress understanding role specific health disease. In this study, we conducted comprehensive genomic pangenomic analysis to resolve ambiguities elucidate metabolic virulence potential across species. We obtained complete, closed genomes for 42 isolates from women BV...
DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform profile number.We developed a sequencing-based assay of nuclear, mitochondrial, telomeric that draws on the unbiased nature next-generation sequencing incorporates techniques for RNA expression profiling. To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads found tremendous variation, including...
Abstract The two main histological types of infiltrating breast cancer, lobular (ILC) and the more common ductal (IDC) carcinoma are morphologically clinically distinct. To assess molecular alterations associated with these cancer subtypes, we conducted a whole‐genome study 166 archival estrogen receptor (ER)‐positive tumors (89 IDC 77 ILC) using Affymetrix GeneChip® Mapping 10K Array to identify sites loss heterozygosity (LOH) that either distinguished, or were shared by, phenotypes. We...
Massively parallel sequencing (MPS) technologies, such as 454-pyrosequencing, allow for the identification of variants in sequence populations at lower levels than consensus and most single-template Sanger experiments. We sought to determine if greater depth population sampling attainable using MPS technology would detection minor HIV founder virus very early infection instances where detects only a single variant. compared nucleotide polymorphisms (SNPs) during acute HIV-1 from 32 subjects...
The genomes of representatives three bacterial phyla have been compared with the list 347 eukaryotic signature proteins (ESPs) derived by Hartman and Fedorov [Proc. Natl. Acad. Sci. USA 99 (2002) 1420]. species included Prosthecobacter dejongeii Verrucomicrobia phylum, Gemmata sp. Wa-1 Planctomycetes phylum Caulobacter crescentus Proteobacteria. protist Trypanosoma brucei was used as a control. P. had unique ERGO blast matches to alpha-, beta-, gamma-tubulin, Set2, transcriptional factor...
Massively-parallel DNA sequencing using the 454/pyrosequencing platform allows in-depth probing of diverse sequence populations, such as within an HIV-1 infected individual. Analysis this data, however, remains challenging due to shorter read lengths relative that obtained by Sanger well errors introduced during template amplification and pyrosequencing. The ability distinguish real variation from pyrosequencing with high sensitivity specificity is crucial interpreting data. We introduce a...