Results 41 to 50 of about 23,440 (247)

Single‐cell DNA methylation profiling: Technologies, computation, and applications in precision oncology

Molecular Oncology, EarlyView.
Single‐cell DNA methylation (scDNAme) profiling maps epimutational clonal evolution, revealing mechanisms of malignancy and therapeutic resistance across diverse cancer types. By providing a high‐resolution landscape of intratumoral heterogeneity, these technologies empower precise patient stratification, guide the development of enhanced ...
Ik Soo Kim
wiley   +1 more source

High resolution long-read telomere sequencing reveals dynamic mechanisms in aging and cancer

Nature Communications
Telomeres are the protective nucleoprotein structures at the end of linear eukaryotic chromosomes. Telomeres’ repetitive nature and length have traditionally challenged the precise assessment of the composition and length of individual human telomeres ...
Tobias T. Schmidt, Carly Tyer, Preeyesh Rughani, Candy Haggblom, Jeffrey R. Jones, Xiaoguang Dai, Kelly A. Frazer, Fred H. Gage, Sissel Juul, Scott Hickey, Jan Karlseder   +10 more
doaj   +1 more source

Somatostatin receptor 4 (SSTR4) is a tumor suppressor in cutaneous and head & neck squamous cell carcinomas

Molecular Oncology, EarlyView.
This study identifies somatostatin receptor 4 (Sstr4) as a critical tumor suppressor against skin and head/neck cancers (HNSCC, cSCC, and BCC). The loss of Sstr4 removes a check on cell growth, causing hyperactivation of the MAPK‐ERK signaling pathway (↑).
Ali Taqvi, Tuan Khang Huynh, Adway Kadam, Zahra Kardan, Yue Yan, Amina Jamal Laham, Sampath Kumar Loganathan   +6 more
wiley   +1 more source

MethPhaser: methylation-based long-read haplotype phasing of human genomes

Nature Communications
The assignment of variants across haplotypes, phasing, is crucial for predicting the consequences, interaction, and inheritance of mutations and is a key step in improving our understanding of phenotype and disease.
Yilei Fu, Sergey Aganezov, Medhat Mahmoud, John Beaulaurier, Sissel Juul, Todd J. Treangen, Fritz J. Sedlazeck   +6 more
doaj   +1 more source

MagmaFlow: A desktop platform for artificial intelligence‐driven expression analysis

FEBS Open Bio, EarlyView.
MagmaFlow is a free, no‐code platform for gene expression analysis. It generates interactive volcano plots, links genes to literature, pathways, and diseases, prioritizes candidates using millions of publications, identifies affected biological processes, builds network diagrams, and exports publication‐ready figures and reports for macOS and Windows ...
Carlos E. Buss, Ao Li, Eduardo H. Gilglioni, Mayank Bansal, Sumeet Pal Singh, Latifa Bakiri, Alessandra K. Cardozo, Esteban N. Gurzov   +7 more
wiley   +1 more source

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Nature Communications
Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new genomes.
Marie C. Schoelmerich, Lynn Ly, Jacob West-Roberts, Ling-Dong Shi, Cong Shen, Nikhil S. Malvankar, Najwa Taib, Simonetta Gribaldo, Ben J. Woodcroft, Christopher W. Schadt, Basem Al-Shayeb, Xiaoguang Dai, Christopher Mozsary, Scott Hickey, Christine He, John Beaulaurier, Sissel Juul, Rohan Sachdeva, Jillian F. Banfield   +18 more
doaj   +1 more source

Consistent ultra-long DNA sequencing with automated slow pipetting

BMC Genomics, 2021
Background Oxford Nanopore Technologies’ instruments can sequence reads of great length. Long reads improve sequence assemblies by unambiguously spanning repetitive elements of the genome.
Trent M. Prall, Emma K. Neumann, Julie A. Karl, Cecilia G. Shortreed, David A. Baker, Hailey E. Bussan, Roger W. Wiseman, David H. O’Connor   +7 more
doaj   +1 more source

Compound Heterozygote Friedreich Ataxia Patients With Covert Proximal FXN Gene Deletions

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT We present Friedreich ataxia patients with frataxin gene deletions. Data and records were collected at the Children's Hospital of Philadelphia from patients enrolled in the FACOMS natural history study. Patients with proximal deletions initially diagnosed with only one GAA expanded allele had more severe disease than their homozygous expansion
Michael P. Lazaropoulos, Morgan C. Devore, Christina Lam, Courtney Park, Sanjay Bidichandani, David R. Lynch   +5 more
wiley   +1 more source

Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology

BMC Biology, 2022
Background Structural variants (SVs), including deletions, insertions, duplications, and inversions, are relatively long genomic variations implicated in a diverse range of processes from human disease to ecology and evolution.
Marc-André Lemay, Jonas A. Sibbesen, Davoud Torkamaneh, Jérémie Hamel, Roger C. Levesque, François Belzile   +5 more
doaj   +1 more source

Augmenting and Assaying Nav1.1 Protein Quantity for Dravet Syndrome Therapy

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Dravet Syndrome (DS) is a developmental and epileptic encephalopathy predominantly caused by heterozygous loss‐of‐function variants in SCN1A, which encodes Nav1.1. Conserved upstream open reading frames (uORFs) in SCN1A were validated to regulate translation in reporter assays, demonstrating the therapeutic viability of increasing Nav1.1 from ...
Aiswarya Saravanan, Jordan Safran, Anna Loughman, Grace Lin, Shivanshi Vaid, Dana Allababidi, Peter M. Tessier, Louis T. Dang   +7 more
wiley   +1 more source