Results 51 to 60 of about 672,449 (294)

Application of long-read sequencing to the detection of structural variants in human cancer genomes

Computational and Structural Biotechnology Journal, 2021
In recent years, the so-called long-read sequencing technology has had a substantial impact on various aspects of genome sciences. Here, we introduce recent studies of cancerous structural variants (SVs) using long-read sequencing technologies, namely ...
Yoshitaka Sakamoto, Suzuko Zaha, Yutaka Suzuki, Masahide Seki, Ayako Suzuki   +4 more
doaj   +1 more source

Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA. [PDF]

, 2018
High-throughput short-read sequencing has revolutionized how transcriptomes are quantified and annotated. However, while Illumina short-read sequencers can be used to analyze entire transcriptomes down to the level of individual splicing events with ...
Byrne, Ashley, Cole, Charles, Green, Richard E, Palmer, Theron, Schmitz, Robert J, Volden, Roger, Vollmers, Christopher   +6 more
core   +1 more source

SVIM: Structural Variant Identification using Mapped Long Reads

, 2019
Motivation: Structural variants are defined as genomic variants larger than 50bp. They have been shown to affect more bases in any given genome than SNPs or small indels. Additionally, they have great impact on human phenotype and diversity and have been
Heller, D., Vingron, M.
core   +1 more source

The hidden perils of read mapping as a quality assessment tool in genome sequencing [PDF]

, 2017
This article provides a comparative analysis of the various methods of genome sequencing focusing on verification of the assembly quality. The results of a comparative assessment of various de novo assembly tools, as well as sequencing technologies, are ...
A Bankevich, AV Karlyshev, D Antipov, EW Myers, HC Lin, IJ Tsai, J Parkhill, K Rutherford, M Hunt, M Land, MT Swain, S Lin, S Meader, TD Otto, TJ Carver   +14 more
core   +1 more source

Can long-read sequencing tackle the barriers, which the next-generation could not? A review

Pathology and Oncology Research
The large-scale heterogeneity of genetic diseases necessitated the deeper examination of nucleotide sequence alterations enhancing the discovery of new targeted drug attack points.
Nikolett Szakállas, Barbara K. Barták, Gábor Valcz, Gábor Valcz, Zsófia B. Nagy, István Takács, Béla Molnár   +6 more
doaj   +1 more source

By dawn or dusk—how circadian timing rewrites bacterial infection outcomes

FEBS Letters, EarlyView.
The circadian clock shapes immune function, yet its influence on infection outcomes is only beginning to be understood. This review highlights how circadian timing alters host responses to the bacterial pathogens Salmonella enterica, Listeria monocytogenes, and Streptococcus pneumoniae revealing that the effectiveness of immune defense depends not only
Devons Mo, Catherine S. Palmer, Jacqueline M. Kimmey   +2 more
wiley   +1 more source

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding [PDF]

, 2016
We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish ...
A Bairoch, A Christoffels, A Gurevich, A Kozomara, A McKenna, A Mitchell, A Morgulis, A Morgulis, A Pradhan, A Reiner, A Rodriguez-Mari, A Stamatakis, A Yates, AI Makunin, AJ Enright, AL Price, AL Price, Alan Christoffels, Aleksey Komissarov, Alexey Tupikin, Amy Hin Yan Tong, Andrey A. Yurchenko, AR Quinlan, B Langmead, B Star, C Berthelot, C Camacho, C Holt, C Wang, Chen-Shan Chin, CS Chin, D Brawand, D Ellinghaus, DA Benson, Darrell Green, DC Hardie, Dean R. Jerry, DH Alexander, Doreen Lau, DR Kelley, DRS-K, C. Jerry, E Casacuberta, E. TG Staristina, EW Myers, F Abascal, F Chen, F Yang, FC Jones, FJ Krsticevic, Fritz J. Sedlazeck, G Abrusan, G Benson, G Lin, G Marcais, G Parra, G Parra, G Tamazian, GH Yue, GH Yue, Gopikrishna Gopalapillai, Gregory W. Vurture, GS Slater, GT Valente, H Li, H Saiga, Heiner Kuhl, HH Kazazian Jr., I Braasch, Inna S. Kuznetsova, IS Kuznetsova, J Castresana, J Eid, J Huerta-Cepas, J Jurka, J Lin, James P. Drake, JG Ruby, JN Volff, JN Volff, Jolly M. Saju, Jonas Korlach, JS Chew, Junhui Jiang, K Howe, K Katoh, K Prufer, Kathiresan Purushothaman, KD Pruitt, KJ Hoff, KP Koepfli, KW Tzung, Lawrence S. Hon, László Orbán, M Blanchette, M Kanehisa, M Kasahara, M Kolmogorov, M Krzywinski, M Martin, M Schartl, M Tarailoâ-Graovac, M Tine, MA Larkin, Mario Jonas, Marsel Kabilov, Matthew Boitano, MB Stocks, MG Grabherr, Michael C. Schatz, MJ Chaisson, MR Friedlander, N Siegel, Natascha M. Thevasagayam, NM Thevasagayam, O Jaillon, O Otero, P Cingolani, P Ravi, P Schattner, P Shannon, P Xu, Paul M. Richardson, PE Warburton, Peter Van Heusden, R Kajitani, R Lorenz, R Luo, R Moore, R Pethiyagoda, R Poulter, R She, R Sreenivasan, Ramkumar Lachumanan, RD Ward, RD Ward, Richard Hall, RJ Roberts, S Chen, S Guindon, S Hoegg, S Hoegg, S Koren, S Vij, S Zhou, Sai Rama Sridatta Prakki, Sarah Mwangi, SF Altschul, Shubha Vij, Si Lok, Si Yan Ngoh, Siddharth Singh, Simon Moxon, SM Kielbasa, Sridhar Sivasubbu, Stanley Kimbung Mbandi, Stephen J. O'Brien, Stephen W. Turner, T Anantharaman, Tamás Dalmay, Tansyn H. Noble, TD Wu, TF DeLuca, TH O'Hare, TLO Davis, TS Anantharaman, Tyler Garvin, U Consortium, U Grimholt, V Douard, V Ravi, Vinaya Kumar Katneni, Vinod Scaria, Vladimir Trifonov, W Xue, WC Liew, Woei Chang Liew, WS Davidson, X Huang, X Zheng, XG Wang, XG Wang, Xueyan Shen, Y Guiguen, Y Han, Y Hashiguchi, Y Moriya, Y Sato, Y Sato, Y Sato, Z Lai, Ø Hammer   +190 more
core   +5 more sources

Interplay between circadian and other transcription factors—Implications for cycling transcriptome reprogramming

FEBS Letters, EarlyView.
This perspective highlights emerging insights into how the circadian transcription factor CLOCK:BMAL1 regulates chromatin architecture, cooperates with other transcription factors, and coordinates enhancer dynamics. We propose an updated framework for how circadian transcription factors operate within dynamic and multifactorial chromatin landscapes ...
Xinyu Y. Nie, Jerome S. Menet
wiley   +1 more source

Haplotype‐Resolved Genotyping and Association Analysis of 1,020 β‐Thalassemia Patients by Targeted Long‐Read Sequencing

Advanced Science
Despite the well‐documented mutation spectra of β‐thalassemia, the genetic variants and haplotypes of globin gene clusters modulating its clinical heterogeneity remain incompletely illustrated.
Yuhua Ye, Chao Niu, Aiping Mao, Lang Qin, Jiahan Zhan, Weijie Chen, Zhentian Liu, Tiantian Xie, Qianqian Zhang, Jiaqi Li, Li Huang, Wanli Meng, Yumeng Liu, Liuhua Liao, Junqin Cai, Riyang Liu, Xinhua Zhang, Lihong Zeng, Yaoyun Li, Bin Lin, Kui Li, Xiaoyun Hua, Binbin Huang, Honggui Qin, Yueyan Huang, Zhijing Huang, Jinquan Lao, Xiang Qu, Juanjuan Chen, Xiaoqin Feng, Qiujun Liu, Wanying Lin, Xiaoman Zhou, Yidan Liang, Xingjiang Long, Jiaofeng Qin, Lixiang Yan, Weijian Zhu, Lian Yu, Chengwu Fan, Deguo Tang, Tianyu Zhong, Jufang Tan, Zhilin Ren, Xiangmin Xu   +44 more
doaj   +1 more source

Real‐time assay of ribonucleotide reductase activity with a fluorescent RNA aptamer

FEBS Letters, EarlyView.
Ribonucleotide reductases (RNR) synthesize DNA building blocks de novo, making them crucial in DNA replication and drug targeting. FLARE introduces the first single‐tube real‐time coupled RNR assay, which enables isothermal tracking of RNR activity at nanomolar enzyme levels and allows the reconstruction of allosteric regulatory patterns and rapid ...
Jacopo De Capitani, Noemi E. Nwosu, Viktoria Gocke, Müge Kasanmascheff, Hannes Mutschler   +4 more
wiley   +1 more source