Results 71 to 80 of about 7,946,195 (290)

SMURF-seq: efficient copy number profiling on long-read sequencers

Genome Biology, 2019
We present SMURF-seq, a protocol to efficiently sequence short DNA molecules on a long-read sequencer by randomly ligating them to form long molecules. Applying SMURF-seq using the Oxford Nanopore MinION yields up to 30 fragments per read, providing an ...
Rishvanth K. Prabakar, Liya Xu, James Hicks, Andrew D. Smith   +3 more
doaj   +1 more source

Epigenetic reprogramming of lineage switching in cancer

FEBS Letters, EarlyView.
Cancer cells rarely commit to a single identity. Epigenetic mechanisms and tumor microenvironment cues push epithelial cells toward flexible, hybrid states that can shift into mesenchymal, neuroendocrine, or stem‐like fates, driving metastasis, drug resistance, and tumor heterogeneity. Targeting the epigenetic regulators behind these transitions, using
Ezgi Boyvatlı, Burcu Akman, Ezgi Bağırsakçı, Nese Atabey, Serap Erkek‐Ozhan   +4 more
wiley   +1 more source

cnvCapSeq: detecting copy number variation in long-range targeted resequencing data. [PDF]

, 2014
Targeted resequencing technologies have allowed for efficient and cost-effective detection of genomic variants in specific regions of interest. Although capture sequencing has been primarily used for investigating single nucleotide variants and indels ...
Bellos, Evangelos; https://orcid.org/, Bellos, Evangelos, Kumar, Vikrant, Cheng, C-Y, Cheng, CY, Wong, TYI, Davila, S, Bellos, E, Phua, ZYA, Maggi, Jordi; https://orcid.org/, Lin, C, Phua, Zai Yang, Coin, Lachlan J M, Coin, LJM, Hibberd, ML, Hibberd, Martin L., Wong, TY, Cheng, Ching-Yu, Gemmy Cheung, CM, Cheung, CMIG, Coin, Lachlan JM, Yang Phua, Z, Lin, Clarabelle, Maggi, Jordi, Kumar, V, Cheng, Ching Yu, Maggi, J, Hibberd, Martin L, Coin, Lachlan J.M., Cheung, Chui Ming Gemmy, Davila, Sonia, Wong, Tien Yin   +31 more
core   +1 more source

Benchmarking datasets for assembly-based variant calling using high-fidelity long reads

BMC Genomics, 2023
Background Recent advances in long-read sequencing technologies have enabled accurate identification of all genetic variants in individuals or cells; this procedure is known as variant calling.
Hyunji Lee, Jun Kim, Junho Lee
doaj   +1 more source

Partial depletion of plasminogen activator inhibitor‐1 decreases subcutaneous fat cell hypertrophy and liver cholesterol in high‐fat‐fed female mice

FEBS Letters, EarlyView.
Obesity raises blood levels of PAI‐1, a protein linked to metabolic dysfunction‐associated steatotic liver disease in people with obesity. In female mice fed a high‐fat diet, partially lowering PAI‐1 led to smaller subcutaneous fat cells and lower liver cholesterol, without changing body weight or insulin sensitivity.
Claudia E. Ramirez Bustamante, Robert Sharp, Pradip K. Saha, Elizabeth S. Anaya, Elizabeth L. Lieu, Evelyn L. de Groot, Pooja Patel, Mi Jeong Heo, Aaron R. Cox, Kang Ho Kim, Sean M. Hartig   +10 more
wiley   +1 more source

Reply to: "A global survey of alternative splicing of HBV transcriptome using long-read sequencing" (Letter)

, 2022
We read with delight and great interest the latest work by Professors Chen, Lu and their colleagues that confirmed some of the major findings reported in our recently published article, in which multiomics approaches were applied to study HBV-host ...
Yuan, Shilin, Hu, Ronggui, Yang, Yuedong
core   +1 more source

Long‐read sequencing for biodiversity analyses—A comprehensive guide

Methods in Ecology and Evolution
DNA‐based monitoring of biodiversity has revolutionised our ability to describe communities and rapidly assess anthropogenic impacts on biodiversity.
Iliana Bista, Alexandra Lino
doaj   +1 more source

LongReadSum: A fast and flexible quality control and signal summarization tool for long-read sequencing data

Computational and Structural Biotechnology Journal
While several well-established quality control (QC) tools exist for short-read sequencing data, there is a general paucity of computational tools that efficiently deliver comprehensive metrics across a wide range of long-read sequencing data formats ...
Jonathan Elliot Perdomo, Mian Umair Ahsan, Qian Liu, Li Fang, Kai Wang   +4 more
doaj   +1 more source

Synergistic perspectives—How single‐molecule biophysics complement biochemical understanding

FEBS Letters, EarlyView.
In this review, we discuss how ensemble biochemistry and single‐molecule approaches are complementary, outline commonly used single‐molecule techniques, and illustrate their relevance through two representative case studies: chromatin organization by SMC complexes and pathway choice during DNA double‐strand break repair.
Sara De Bragança, Eline L. Jansen, Jorine M. Eeftens   +2 more
wiley   +1 more source

Long-Read Annotation: Automated Eukaryotic Genome Annotation Based on Long-Read cDNA Sequencing [PDF]

Plant Physiology, 2018
Single-molecule full-length complementary DNA (cDNA) sequencing can aid genome annotation by revealing transcript structure and alternative splice forms, yet current annotation pipelines do not incorporate such information. Here we present long-read annotation (LoReAn) software, an automated annotation pipeline utilizing short- and long-read cDNA ...
David E. Cook, Jose Espejo Valle-Inclan, Alice Pajoro, Hanna Rovenich, Bart P.H.J. Thomma, Luigi Faino   +5 more
openaire   +2 more sources