A5052364640- Genomics and Rare Diseases
- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Marine and fisheries research
- Fish Ecology and Management Studies
- Genomics and Phylogenetic Studies
- Genetic factors in colorectal cancer
- Biomedical Text Mining and Ontologies
- PARP inhibition in cancer therapy
- BRCA gene mutations in cancer
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- Machine Learning in Bioinformatics
- Fetal and Pediatric Neurological Disorders
- Innovative Teaching Methods
- Topic Modeling
- Colorectal Cancer Treatments and Studies
- DNA Repair Mechanisms
- Mycorrhizal Fungi and Plant Interactions
- Environmental Justice and Health Disparities
- Aquatic Ecosystems and Phytoplankton Dynamics
- Soil Carbon and Nitrogen Dynamics
- Antimicrobial Resistance in Staphylococcus
- Pneumonia and Respiratory Infections
- Aquatic Ecosystems and Biodiversity
Invitae (United States)
2022-2024
University of Washington Bothell
2023
Northwestern University
2023
Canada's Michael Smith Genome Sciences Centre
2016-2021
University of Regina
2011-2020
BC Cancer Agency
2016-2019
Christ Hospital
1940
University of Cincinnati
1940
Ectomycorrhizal fungi (EMF) provide nutrients to their hosts by means of hyphae that extend beyond nutrient-depleted rhizosphere soil. Soil bacteria may compete with EMF for or act synergistically enhance nutrient supply hosts. To assess the interactions between and bacteria, two types small, sand-filled mesh bags were incubated in a Pseudotsuga menziesii/Betula papyrifera forest. The allowed ingrowth (35-μm mesh) excluded (0.5-μm mesh), while allowing migration soil bacteria. After...
PURPOSE Homologous recombination deficiency (HRD) assays measure DNA damage repair dysfunction to identify patients with high-grade serous ovarian cancer (HGSOC) who may benefit from poly ADP-ribose polymerase inhibitors (PARPis). Numerous are available, but only two have undergone prospective clinical validation. Assay variability can affect patient and provider treatment choices; however, the level of assay across laboratory developed tests is unknown. METHODS Friends Cancer Research...
The anticipated impacts of climate change on aquatic biota are difficult to evaluate because potentially contrasting effects temperature and hydrology lake ecosystems, particularly those closed-basin lakes within semiarid regions. To address this shortfall, we quantified decade-scale changes in chemical biological properties 20 endorheic central North America response a pronounced transition from drought pluvial period during the early 21st century. Lakes exhibited marked temporal...
Journal Article The Response of Different Types and Strains Pneumococcus to Sulfapyridine Get access L. H. Schmidt, Schmidt From the Christ Hospital Research Institute Department Biochemistry, College Medicine, University Cincinnati,Cincinnati, Ohio Search for other works by this author on: Oxford Academic PubMed Google Scholar Carolyn Hilles, Hilles A. Dettwiler, Dettwiler Effie Starks Infectious Diseases, Volume 67, Issue 3, November 1940, Pages 232–242,...
Nearly 14% of disease-causing germline variants result from the disruption mRNA splicing. Most (67%) DNA predicted in silico to disrupt splicing are classified as uncertain significance. An analytic workflow-splice effect event resolver (SPEER)-was developed and validated use sequencing reveal significant deviations splicing, pinpoint potentially involved, measure deleterious effects altered on transcripts, providing evidence for assessing pathogenicity variant. SPEER was used analyze...
Formalin fixation is the standard method for preservation of tissue diagnostic purposes, including pathologic review and molecular assays. However, this known to cause artifacts that can affect accuracy genetic test results. We assessed applicability alternative fixatives determine whether these perform significantly better on next-generation sequencing assays, adequate morphology retained primary diagnosis, in a prospective study using clinical-grade, laboratory-developed targeted...
The rapidly growing biomedical literature has been a challenging target for natural language processing algorithms.One of the tasks these algorithms focus on is called named entity recognition (NER), often employed to tag gene mentions.Here we describe new approach this task, an that uses graphbased semi-supervised learning train Conditional Random Field (CRF) model.Benchmarking it BioCreative II Gene Mention tagging achieved statistically significant improvements in Fmeasure over BANNER,...
The rapidly growing amount of research papers in computational biology makes it difficult for researchers to keep up date on new results. motivation behind this paper is use natural language processing automatically understand relevant concepts from the large text data published biology. As a proof-of-concept, we focus gene mention detection task, which allows us identify genes that are being discussed papers, making possible search like rather than searching words. In introduce GraphNER,...
Abstract Homologous recombination deficiency (HRD) assays determine patient eligibility for treatment with PARP inhibitors and other DNA repair targeting drugs; therefore, understanding variability in how these measure report HRD is critical patients providers. various factors to status including causes (i.e., inactivation HR pathway genes) consequences genomic scarring). Methodological across has led a suggestion that the may not agree on per basis. An empirical assessment of assay guide...
ABSTRACT Nearly 14% of disease-causing germline variants result from disruption mRNA splicing. Most (67%) DNA predicted in silico to disrupt splicing end up classified as uncertain significance (VUS). We developed and validated an analytic workflow — Sp lice E ffect vent R esolver (SPEER) that uses sequencing reveal significant deviations splicing, pinpoints the potentially responsible, measures deleterious effect altered on transcripts, providing evidence assess pathogenicity variant. SPEER...
Abstract Introduction: NGS-based tests that include biomarkers such as microsatellite instability (MSI) and tumor mutational burden (TMB) increase patient access to immune checkpoint inhibitors improve the personalization of cancer care. Tumor-only NGS typically rely on germline reference sets in order subtract variants from biomarker scores. Many lack sufficient population diversity ensure consistent test quality for all patients. Informatic strategies somatic/germline zygosity prediction...
Abstract This study evaluated the status of native and stocked fish species in 13 prairie lakes central Canada over eight years (2007–14) using three metrics: resource‐use (benthic versus pelagic carbon via stable isotopes); body condition (relative weight index W r ); parasite load (cestode gut enumerations). Analyses included game non‐game fishes, like naturally occurring northern pike, Esox lucius L., yellow perch, Perca flavescens Mitchill, but focused on walleye, Sander vitreus...
1582 Background: ctDNA is a potentially superior means of classifying tumor genotype but predictors Con with atDNA are not well established. We conducted prospective multicenter study to determine the feasibility genotyping on Next-Generation Sequencing (NSG) platform and among patients advanced solid malignancies. was concurrently performed variables associated were investigated. Methods: Patients at 5 BC Cancer Agency Centers enrolled over 14 months. using NSG high-throughput multiplex...
Postsecondary science education has been shaped by Eurocentric ideologies that center as a set of culturally neutral, color-blind, and meritocratic systems designed to exclude underrepresented groups from positions power knowledge production.Nationally, white faculty still predominate senior positions, resulting in few opportunities for students color take courses who share their racial or cultural backgrounds (Haynes & Patton, 2019).At the same time, there is need diversify predominantly...
Abstract Objectives Non-invasive prenatal testing requires the presence of fetal DNA in maternal plasma. Understanding how preexamination conditions affect integrity cell-free (cfDNA) and fraction (FF) are a prerequisite for test implementation. Therefore, we examined adjusted effect that EDTA Streck tubes have on cfDNA quantity FF. Methods A total 3,568 blood samples across Canada were collected either EDTA, or tubes, processing metrics, body mass index (BMI), gestational age karyotype sex...