Prediction of histone post-translational modification patterns based on nascent transcription data

Z Wang, AG Chivu, LA Choate, EJ Rice, DC Miller… - Nature …, 2022 - nature.com
The role of histone modifications in transcription remains incompletely understood. Here,
we examine the relationship between histone modifications and transcription using …

Identification of regulatory elements from nascent transcription using dREG

Z Wang, T Chu, LA Choate, CG Danko - Genome research, 2019 - genome.cshlp.org
Our genomes encode a wealth of transcription initiation regions (TIRs) that can be identified
by their distinctive patterns of actively elongating RNA polymerase. We previously …

Dynamic evolution of regulatory element ensembles in primate CD4+ T cells

CG Danko, LA Choate, BA Marks, EJ Rice… - Nature Ecology & …, 2018 - nature.com
How evolutionary changes at enhancers affect the transcription of target genes remains an
important open question. Previous comparative studies of gene expression have largely …

Genetic dissection of the RNA polymerase II transcription cycle

SP Chou, AK Alexander, EJ Rice, LA Choate… - Elife, 2022 - elifesciences.org
How DNA sequence affects the dynamics and position of RNA Polymerase II (Pol II) during
transcription remains poorly understood. Here, we used naturally occurring genetic variation …

[HTML][HTML] Multiple stages of evolutionary change in anthrax toxin receptor expression in humans

LA Choate, G Barshad, PW McMahon, I Said… - Nature …, 2021 - nature.com
The advent of animal husbandry and hunting increased human exposure to zoonotic
pathogens. To understand how a zoonotic disease may have influenced human evolution, we …

Confirmation of Insertion, Deletion, and Deletion-Insertion Variants Detected by Next-Generation Sequencing

LA Choate, A Koleilat, K Harris, N Vidal-Folch… - Clinical …, 2023 - academic.oup.com
Background Despite clinically demonstrated accuracy in next generation sequencing (NGS)
data, many clinical laboratories continue to confirm variants with Sanger sequencing, which …

[HTML][HTML] Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis

…, BA Marks, EJ Rice, Z Wang, LA Choate… - BMC veterinary …, 2020 - Springer
Background Canine visceral hemangiosarcoma (HSA) is a highly aggressive cancer of
endothelial origin that closely resembles visceral angiosarcoma in humans, both clinically and …

Rgtsvm: support vector machines on a GPU in R

Z Wang, T Chu, LA Choate, CG Danko - arXiv preprint arXiv:1706.05544, 2017 - arxiv.org
Rgtsvm provides a fast and flexible support vector machine (SVM) implementation for the R
language. The distinguishing feature of Rgtsvm is that support vector classification and …

Clinical Validation of Tagmentation-Based Genome Sequencing for Germline Disorders

W Shen, HL Sellers, LA Choate, MI Stein… - The Journal of Molecular …, 2023 - Elsevier
Genome sequencing (GS) is a powerful clinical tool used for the comprehensive diagnosis of
germline disorders. GS library preparation typically involves mechanical DNA fragmentation…

A novel substitution of proline (P32L) destabilises β2-microglobulin inducing hereditary systemic amyloidosis

…, JL Berk, SAM Cuddy, S Dasari, A Chiu, LA Choate… - Amyloid, 2022 - Taylor & Francis
Background β2-microglobulin amyloidosis was first described in the 1980s as a protein
deposition disease associated with long-term haemodialysis. More recently, two inherited forms …