Zobrazeno 1 - 10
of 31
pro vyhledávání: '"David Yu Zhang"'
Autor:
Andrew T. Sullivan, Vibha Rao, Tyler Rockwood, Jahnavi Gandhi, Sarah Gruzka, Logan O’Connor, Bonnie Wang, Katherine B. Ragan, David Yu Zhang, Dmitriy Khodakov
Publikováno v:
Communications Biology, Vol 6, Iss 1, Pp 1-12 (2023)
Abstract Detection of RNA targets is typically achieved through RT-qPCR or RNAseq. RT-qPCR is rapid but limited in number and complexity of targets detected, while RNAseq is high-throughput but takes multiple days. We demonstrate simultaneous amplifi
Externí odkaz:
https://doaj.org/article/e2dc14ee5e3d42deb0fcb46faf914f07
Autor:
Nina G. Xie, Michael X. Wang, Ping Song, Shiqi Mao, Yifan Wang, Yuxia Yang, Junfeng Luo, Shengxiang Ren, David Yu Zhang
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-10 (2022)
The design of highly multiplex PCR primers to amplify and enrich many different DNA sequences is increasing in biomedical importance as new mutations and pathogens are identified. The authors present and experimentally validate Simulated Annealing De
Externí odkaz:
https://doaj.org/article/1916b170bab24fd2aaa4b697ee9a21da
Autor:
Lucia Ruojia Wu, Peng Dai, Michael Xiangjiang Wang, Sherry Xi Chen, Evan N. Cohen, Gitanjali Jayachandran, Jinny Xuemeng Zhang, Angela V. Serrano, Nina Guanyi Xie, Naoto T. Ueno, James M. Reuben, Carlos H. Barcenas, David Yu Zhang
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-9 (2022)
Highly multiplexed ddPCR for sensitive nucleic acid quantitation remains challenging due to limited fluorescence channels. Here the authors report quantitative amplicon sequencing (QASeq), a PCR-based molecular barcoding NGS approach which is compati
Externí odkaz:
https://doaj.org/article/4d7f4e4784404a73a971f604e13766e8
Autor:
Peng Dai, Lucia Ruojia Wu, Sherry Xi Chen, Michael Xiangjiang Wang, Lauren Yuxuan Cheng, Jinny Xuemeng Zhang, Pengying Hao, Weijie Yao, Jabra Zarka, Ghayas C. Issa, Lawrence Kwong, David Yu Zhang
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-9 (2021)
Quantification of rare somatic mutations is essential for basic research and translational applications. Here the authors present Quantitative Blocker Displacement Amplification allowing for accurate detection of mutations below 0.01% VAF.
Externí odkaz:
https://doaj.org/article/fa41048a06034246b3822d3ae3d81bf0
Autor:
Deepak Thirunavukarasu, Lauren Y. Cheng, Ping Song, Sherry X. Chen, Mitesh J. Borad, Lawrence Kwong, Phillip James, Daniel J. Turner, David Yu Zhang
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-17 (2021)
Abstract We develop the Oncogene Concatenated Enriched Amplicon Nanopore Sequencing (OCEANS) method, in which variants with low variant allele frequency (VAFs) are amplified and subsequently concatenated for Nanopore Sequencing. OCEANS allows accurat
Externí odkaz:
https://doaj.org/article/4bf551b9432b4350a7d2d7853a93be54
Publikováno v:
iScience, Vol 25, Iss 10, Pp 105046- (2022)
Summary: Cell-free DNA (cfDNA) has become the predominant analyte of liquid biopsy; however, recent studies suggest the presence of subnucleosomal-sized DNA fragments in circulation that are likely single-stranded. Here, we report a method called dir
Externí odkaz:
https://doaj.org/article/43d6c0b12503424abaa9c7b457a5e6b6
Autor:
Jinny X. Zhang, Boyan Yordanov, Alexander Gaunt, Michael X. Wang, Peng Dai, Yuan-Jyue Chen, Kerou Zhang, John Z. Fang, Neil Dalchau, Jiaming Li, Andrew Phillips, David Yu Zhang
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-10 (2021)
DNA probes used in next generation sequencing (NGS) have variable hybridisation kinetics, resulting in non-uniform coverage. Here, the authors develop a deep learning model to predict NGS depth using DNA probe sequences and apply to human and non-hum
Externí odkaz:
https://doaj.org/article/38cfd7ab6401440b9ae00deafd4781f0
Autor:
Yan Helen Yan, Sherry X. Chen, Lauren Y. Cheng, Alyssa Y. Rodriguez, Rui Tang, Karina Cabrera, David Yu Zhang
Publikováno v:
Scientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
Abstract Whole exome sequencing (WES) is used to identify mutations in a patient’s tumor DNA that are predictive of tumor behavior, including the likelihood of response or resistance to cancer therapy. WES has a mutation limit of detection (LoD) at
Externí odkaz:
https://doaj.org/article/27644cc07d57469489f2b52234db2f81
Autor:
Lauren Y. Cheng, Lauren E. Haydu, Ping Song, Jianyi Nie, Michael T. Tetzlaff, Lawrence N. Kwong, Jeffrey E. Gershenwald, Michael A. Davies, David Yu Zhang
Publikováno v:
Scientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
Abstract Mutations in the BRAF gene at or near the p. V600 locus are informative for therapy selection, but current methods for analyzing FFPE tissue DNA generally have a limit of detection of 5% variant allele frequency (VAF), or are limited to the
Externí odkaz:
https://doaj.org/article/a31f95e2d618422bb5e0d6e0b871a339
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-8 (2020)
The chemical stability of DNA makes complete erasure of DNA-encoded data difficult. Here the authors mix true and false messages, differentiated by whether a truth marker oligo is bound to it, and show that brief exposure to elevated temperatures ran
Externí odkaz:
https://doaj.org/article/521caa4ca79b45d38fd209aba923c447