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 …
we examine the relationship between histone modifications and transcription using …
Identification of regulatory elements from nascent transcription using dREG
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 …
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 …
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 …
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
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 …
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 …
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 …
endothelial origin that closely resembles visceral angiosarcoma in humans, both clinically and …
Rgtsvm: support vector machines on a GPU in R
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 …
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…
germline disorders. GS library preparation typically involves mechanical DNA fragmentation…
A novel substitution of proline (P32L) destabilises β2-microglobulin inducing hereditary systemic amyloidosis
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 …
deposition disease associated with long-term haemodialysis. More recently, two inherited forms …