David W. Hall
YOU?
Author Swipe
View article: Phlorest phylogeny derived from Chang et al. 2015 'Ancestry-constrained phylogenetic analysis supports the Indo-European steppe hypothesis'
Phlorest phylogeny derived from Chang et al. 2015 'Ancestry-constrained phylogenetic analysis supports the Indo-European steppe hypothesis' Open
Cite the source of the dataset as: Chang W, Cathcart C, Hall D, & Garrett A. 2015. Ancestry-constrained phylogenetic analysis supports the Indo-European steppe hypothesis. Language, 91(1):194-244.
View article: Comprehensive genomic profiling of over 10,000 advanced solid tumors
Comprehensive genomic profiling of over 10,000 advanced solid tumors Open
The broad capabilities of the OncoExTra assay detected therapeutically actionable and other clinically relevant genomic events that can inform clinical decision-making for patients with advanced solid tumors.
View article: Costs and Benefits of Whole-Exome, Whole-Transcriptome Sequencing in Patients With Advanced Non–Small Cell Lung Cancer
Costs and Benefits of Whole-Exome, Whole-Transcriptome Sequencing in Patients With Advanced Non–Small Cell Lung Cancer Open
PURPOSE With an increase in approved targeted therapies for non–small cell lung cancer (NSCLC), tumor profiling that maximizes identification of patients eligible for these treatments is essential. In this study, we compare testing approac…
View article: Neural ODE Transformers: Analyzing Internal Dynamics and Adaptive Fine-tuning
Neural ODE Transformers: Analyzing Internal Dynamics and Adaptive Fine-tuning Open
Recent advancements in large language models (LLMs) based on transformer architectures have sparked significant interest in understanding their inner workings. In this paper, we introduce a novel approach to modeling transformer architectu…
View article: Circulating Tumor DNA as a Marker of Recurrence Risk in Stage III Colorectal Cancer: The α‐CORRECT Study
Circulating Tumor DNA as a Marker of Recurrence Risk in Stage III Colorectal Cancer: The α‐CORRECT Study Open
Background and Objectives Identification of colorectal cancer (CRC) patients at high risk of recurrence could be of substantial clinical use. We evaluated the association of ctDNA status, using a tumor‐informed assay, with recurrence‐free …
View article: Spontaneous single-nucleotide substitutions and microsatellite mutations have distinct distributions of fitness effects
Spontaneous single-nucleotide substitutions and microsatellite mutations have distinct distributions of fitness effects Open
The fitness effects of new mutations determine key properties of evolutionary processes. Beneficial mutations drive evolution, yet selection is also shaped by the frequency of small-effect deleterious mutations, whose combined effect can b…
View article: Associations with other cancer-related biomarkers might contribute to poor outcomes in <i>RAS</i>-altered, younger patients with colorectal cancer
Associations with other cancer-related biomarkers might contribute to poor outcomes in <i>RAS</i>-altered, younger patients with colorectal cancer Open
Colorectal cancer (CRC) is a common cancer in younger adults. In patients undergoing liver resection with RAS-altered CRCs, there is evidence suggesting younger patients have worse outcomes than older patients. To explain this pattern, dif…
View article: Value of next generation sequencing (NGS) testing in advanced cancer patients
Value of next generation sequencing (NGS) testing in advanced cancer patients Open
Compared to single-gene testing, results indicate that using next generation sequencing test such as OncoExTra identified more actionable alterations, leading to improved outcomes and reduced costs.
View article: Phlorest phylogeny derived from Chang et al. 2015 'Ancestry-constrained phylogenetic analysis supports the Indo-European steppe hypothesis'
Phlorest phylogeny derived from Chang et al. 2015 'Ancestry-constrained phylogenetic analysis supports the Indo-European steppe hypothesis' Open
Cite the source of the dataset as: Chang W, Cathcart C, Hall D, & Garrett A. 2015. Ancestry-constrained phylogenetic analysis supports the Indo-European steppe hypothesis. Language, 91(1):194-244.
View article: 219 Prevalence of genomic alterations in Xerna<sup>TM</sup> tumor microenvironment subtypes in colorectal cancer patients
219 Prevalence of genomic alterations in Xerna<sup>TM</sup> tumor microenvironment subtypes in colorectal cancer patients Open
Background In advanced colorectal cancer (CRC), analysis of the tumor microenvironment (TME) may be useful as a predictive biomarker, particularly supporting the use of immunotherapies and anti-angiogenic therapies.1 The XernaTM TME Panel …
View article: Phlorest phylogeny derived from Chang et al. 2015 'Ancestry-constrained phylogenetic analysis supports the Indo-European steppe hypothesis'
Phlorest phylogeny derived from Chang et al. 2015 'Ancestry-constrained phylogenetic analysis supports the Indo-European steppe hypothesis' Open
Cite the source of the dataset as: Chang W, Cathcart C, Hall D, & Garrett A. 2015. Ancestry-constrained phylogenetic analysis supports the Indo-European steppe hypothesis. Language, 91(1):194-244.
View article: Spontaneous single-nucleotide substitutions and microsatellite mutations have distinct distributions of fitness effects
Spontaneous single-nucleotide substitutions and microsatellite mutations have distinct distributions of fitness effects Open
The fitness effects of new mutations determine key properties of evolutionary processes. Beneficial mutations drive evolution, yet selection is also shaped by the frequency of small-effect deleterious mutations, whose combined effect can b…
View article: Comprehensive Review on the Clinical Impact of Next-Generation Sequencing Tests for the Management of Advanced Cancer
Comprehensive Review on the Clinical Impact of Next-Generation Sequencing Tests for the Management of Advanced Cancer Open
PURPOSE This review summarizes the published evidence on the clinical impact of using next-generation sequencing (NGS) tests to guide management of patients with cancer in the United States. METHODS We performed a comprehensive literature …
View article: Tumor-Type Agnostic, Targeted Therapies: BRAF Inhibitors Join the Group
Tumor-Type Agnostic, Targeted Therapies: BRAF Inhibitors Join the Group Open
In the present review, we briefly discuss the breakthrough advances in precision medicine using a tumor-agnostic approach and focus on BRAF treatment modalities, the mechanisms of resistance and the diagnostic approach in cancers with BRAF…
View article: The 17-gene Genomic Prostate Score assay as a predictor of biochemical recurrence in men with intermediate and high-risk prostate cancer
The 17-gene Genomic Prostate Score assay as a predictor of biochemical recurrence in men with intermediate and high-risk prostate cancer Open
The validated 17-gene Oncotype DX Genomic Prostate Score® (GPS™) assay risk-stratifies prostate-cancer patients with localized disease. The assay has primarily been utilized in lower risk patients deciding between active surveillance versu…
View article: Genome Assembly of the Ty1-Less Saccharomyces paradoxus Strain DG1768
Genome Assembly of the Ty1-Less Saccharomyces paradoxus Strain DG1768 Open
Here, we report an essentially complete genome assembly for the Ty1-less Saccharomyces paradoxus strain DG1768 (derivative of strain 337) based on PacBio and Illumina shotgun sequence data. We also document the genetic alterations that mak…
View article: Living with the Lab: A Project-Based Curriculum for First-Year Engineering Students
Living with the Lab: A Project-Based Curriculum for First-Year Engineering Students Open
The freshman engineering course sequence has been completely revised with support from an NSF CCLI grant.The mission of the curriculum is to instill the attributes of "The Engineer of 2020" in our students.We have structured the content ti…
View article: Enhancing thermally activated delayed fluorescence by fine-tuning the dendron donor strength
Enhancing thermally activated delayed fluorescence by fine-tuning the dendron donor strength Open
Thermally activated delayed fluorescence (TADF) relies on a small energy gap between the emissive singlet and the non-emissive triplet state, obtained by reducing the wavefunction overlap between donor and acceptor moieties. Efficient emis…
View article: No evidence for whole-chromosome dosage compensation or global transcriptomic expression differences in spontaneously-aneuploid mutation accumulation lines of<i>Saccharomyces cerevisiae</i>
No evidence for whole-chromosome dosage compensation or global transcriptomic expression differences in spontaneously-aneuploid mutation accumulation lines of<i>Saccharomyces cerevisiae</i> Open
Aneuploidy, the state in which an organism’s genome contains one or more missing or additional chromosomes, often causes widespread genotypic and phenotypic effects. Most often, aneuploidies are deleterious; the most common examples in hum…
View article: First Year Design Experience: Assembling The “Big Picture” Through Innovative Product Design
First Year Design Experience: Assembling The “Big Picture” Through Innovative Product Design Open
NOTE: The first page of text has been automatically extracted and included below in lieu of an abstract First-Year Design Experience: Assembling the “Big Picture” Through Innovative Product Design Abstract As part of the freshmen engineeri…
View article: Fitness consequences of a non-recombining<i>sex-ratio</i>drive chromosome can explain its prevalence in the wild
Fitness consequences of a non-recombining<i>sex-ratio</i>drive chromosome can explain its prevalence in the wild Open
Understanding the pleiotropic consequences of gene drive systems on host fitness is essential to predict their spread through a host population. Here, we study sex-ratio (SR) X-chromosome drive in the fly Drosophila recens , where SR cause…
View article: The somatic genetic and epigenetic mutation rate in a wild long-lived perennial<i>Populus trichocarpa</i>
The somatic genetic and epigenetic mutation rate in a wild long-lived perennial<i>Populus trichocarpa</i> Open
Background Plants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development contributes to local a…
View article: Higher-Level Phylogeny and Reclassification of Lampyridae (Coleoptera: Elateroidea)
Higher-Level Phylogeny and Reclassification of Lampyridae (Coleoptera: Elateroidea) Open
Fireflies (Lampyridae Rafinesque) are a diverse family of beetles which exhibit an array of morphologies including varying antennal and photic organ features. Due in part to their morphological diversity, the classification within the Lamp…
View article: Supplementary material from "Fitness consequences of a non-recombining <i>sex-ratio</i> drive chromosome can explain its prevalence in the wild"
Supplementary material from "Fitness consequences of a non-recombining <i>sex-ratio</i> drive chromosome can explain its prevalence in the wild" Open
Understanding the pleiotropic consequences of gene drive systems on host fitness is essential to predict their spread through a host population. Here, we study sex-ratio (SR) X-chromosome drive in the fly Drosophila recens, where SR causes…
View article: Firefly genomes illuminate parallel origins of bioluminescence in beetles
Firefly genomes illuminate parallel origins of bioluminescence in beetles Open
Fireflies and their luminous courtships have inspired centuries of scientific study. Today firefly luciferase is widely used in biotechnology, but the evolutionary origin of bioluminescence within beetles remains unclear. To shed light on …
View article: Molecular variation across populations of a widespread North American firefly, Photinus pyralis, reveals that coding changes do not underlie flash color variation or associated visual sensitivity
Molecular variation across populations of a widespread North American firefly, Photinus pyralis, reveals that coding changes do not underlie flash color variation or associated visual sensitivity Open
The absence of protein variation at both loci challenges the paradigm that variation in signal color and visual sensitivity in fireflies is exclusively due to coding variation in luciferase and opsin genes. Instead, flash color variation w…