Results 91 to 100 of about 283,388 (253)

Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

BMC Genomics, 2018
Background Chloroplasts are organelles that conduct photosynthesis in plant and algal cells. The information chloroplast genome contained is widely used in agriculture and studies of evolution and ecology.
Weiwen Wang, Miriam Schalamun, Alejandro Morales-Suarez, David Kainer, Benjamin Schwessinger, Robert Lanfear   +5 more
doaj   +1 more source

Spatial and single‐nuclei transcriptomics reveals idiosyncratic and generic patterns in papillary and anaplastic thyroid cancers

Molecular Oncology, EarlyView.
Matched spatial transcriptomics and single‐nuclei RNA‐seq were generated for anaplastic and BRAFV600E papillary thyroid cancers revealing generic and tumor‐specific states occurring in cancer cells and in the tumor microenvironment. In this context, cancer dedifferentiation mirrored organoid maturation through ordered thyroid marker gain/loss ...
Adrien Tourneur, Joel Rodrigues Vitória, Manuel Saiselet, Ligia Craciun, Denis Larsimont, Anne Lefort, Frédérick Libert, Carine Maenhaut, Sabine Costagliola, Maxime Tarabichi, Mirian Romitti, Vincent Detours   +11 more
wiley   +1 more source

Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies

GigaByte
Current microbial sequencing relies on short-read platforms like Illumina and DNBSEQ, which are cost-effective and accurate but often produce fragmented draft genomes.
Hewei Liang , Yuanqiang Zou , Mengmeng Wang , Tongyuan Hu , Haoyu Wang , Wenxin He , Yanmei Ju , Ruijin Guo , Junyi Chen , Fei Guo , Tao Zeng , Yuliang Dong , Yuning Zhang , Bo Wang , Chuanyu Liu , Xin Jin , Wenwei Zhang , Xun Xu , Liang Xiao   +18 more
doaj   +1 more source

Haplotype-phased synthetic long reads from short-read sequencing

PLOS ONE, 2015
Abstract Next-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences.
Stapleton, James A, Kim, Jeongwoon, Hamilton, John P, Wu, Ming, Irber, Luiz C, Maddamsetti, Rohan, Briney, Bryan, Newton, Linsey, Burton, Dennis R, Brown, C Titus, Chan, Christina, Buell, C Robin, Whitehead, Timothy A   +12 more
openaire   +6 more sources

Inhibition of cyclin‐dependent kinases 12/13 using CT7439 as a treatment for colorectal cancer with CDK12 upregulation

Molecular Oncology, EarlyView.
The proposed mechanism of action for the CDK12/13 inhibitor and cyclin K degrader, CT7439. CDK12/13 inhibition interrupts transcription elongation, leading to increased DNA damage that results in cell death. This agent is a potentially novel treatment option for patients with colorectal cancer. Created in BioRender. Cyclin‐dependent kinase (CDK) 12 and
Wylie K. Watlington, Divya L. Dayanidhi, Mohammad Zokaasadi, John B. Mantyh, Pelumi D. Olawuni, Gabrielle Rupprecht, Jeremy M. Force, Shannon McCall, Ashwani K. Bahl, David S. Hsu, Jason A. Somarelli   +10 more
wiley   +1 more source

In vitro and in silico modelling of ROS1‐positive non‐small cell lung cancer reveals fusion‐dependent tyrosine kinase inhibitor responses

Molecular Oncology, EarlyView.
Drug resistance limits treatment success in a subset of lung cancers driven by ROS1 gene alterations. Using patient‐derived cells and computer simulations, we studied three key mutations and how they affect five targeted drugs. The mutations reduced drug effectiveness in different ways by altering protein structure and behavior.
Farhan Ul Haq, Marc Terrones, Felicia Rodrigues Fortes, Anne Schepers, Alessia Denis, Christophe Deben, Ken Op de Beeck, Guy Van Camp, Geert Vandeweyer   +8 more
wiley   +1 more source

Epigenetic silencing of the liver‐specific lncRNA LUNAR promotes liver cancer progression via NOTCH activation

Molecular Oncology, EarlyView.
LUNAR is a liver‐specific long noncoding RNA (lncRNA) that is highly expressed in normal liver but becomes epigenetically silenced in hepatocellular carcinoma through promoter hypermethylation. Loss of LUNAR is associated with NOTCH activation, epithelial–mesenchymal transition, and metastasis, whereas restoring LUNAR restrains metastatic progression ...
Se Ha Jang, Hyung Seok Kim, Geum Ok Baek, Moon Gyeong Yoon, Su In Lee, Jee‐Yeong Jeong, Ji Eun Han, Soon Sun Kim, Jae Youn Cheong, Jung Woo Eun   +9 more
wiley   +1 more source

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

A sensitive short read homology search tool for paired-end read sequencing data

BMC Bioinformatics, 2017
Background Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species.
Prapaporn Techa-Angkoon, Yanni Sun, Jikai Lei   +2 more
doaj   +1 more source

CEACAM1 participation in breast cancer progression

Molecular Oncology, EarlyView.
In invasive breast cancer (BC), CEACAM1 shifts from an apical to a uniform membranous/cytoplasmic pattern, or is lost, as tumors dedifferentiate, inversely tracking the Ki‐67 proliferative index. In MCF‐7 cells, only CEACAM1‐4L suppresses proliferation, repressing cell cycle and growth factor genes.
Mykola Lyndin, Irina Kube‐Golovin, Anatolii Romaniuk, Gunther Wennemuth   +3 more
wiley   +1 more source