Results 111 to 120 of about 60,554,138 (296)

DOGMA: de novo assembly of densely labelled optical DNA maps using a matrix profile approach.

PLoS ONE
In optical genome mapping (OGM), large numbers of individual DNA maps-sequence-specific data series along single DNA molecules-are produced. Such individual maps have to be stitched together in a process called de novo OGM assembly in order to create ...
Albertas Dvirnas, Luis Mario Leal-Garza, Zahra Abbaspour, Erik Fröbrant, Karolin Frykholm, Marie Wrande, Linus Sandegren, Fredrik Westerlund, Tobias Ambjörnsson   +8 more
doaj   +1 more source

The effect of variant interference on de novo assembly for viral deep sequencing

BMC Genomics, 2020
Background Viruses have high mutation rates and generally exist as a mixture of variants in biological samples. Next-generation sequencing (NGS) approaches have surpassed Sanger for generating long viral sequences, yet how variants affect NGS de novo ...
Christina J. Castro, Rachel L. Marine, Edward Ramos, Terry Fei Fan Ng   +3 more
doaj   +1 more source

SOX5 Orchestrates Malignant Evolution via Promoter‐Centric Chromatin Remodeling in MYC‐Driven B‐Cell Lymphoma

Advanced Science, EarlyView.
In MYC‐enforced B‐cell lymphoma, SOX5 occupies promoter‐proximal regulatory regions and is associated with reduced chromatin accessibility at the PCNP locus. PCNP repression promotes proliferative remodeling by limiting apoptosis and cell‐cycle restraint.
Yiyou Mao, Zhenyuan Jia, Xiao‐Qin Mu, Ruilin Wang, Jianli Ma, Qingyuan Zhang, Yuwei Deng   +6 more
wiley   +1 more source

AI‐Assisted Engineering of Glycyrrhizic Acid/Simvastatin Nanocrystals for Multifunctional Treatment of Bacterial Osteomyelitis

Advanced Science, EarlyView.
Through AI‐assisted screening from FDA‐approved API to overcome the limitations of bacterial osteomyelitis treatment, glycyrrhizic acid and simvastatin are identified as a multifunctional combination capable of self‐assembling into mechanism‐targeting nanocrystals that effectively neutralize reactive oxygen species, suppress M1 macrophage polarization,
Yu Han, Yao Zhao, Chengbo Yang, Miao Niu, Jun Dai, Quanxin Ning, Kai Xiao, Jinzheng Liang, Wensheng Zhang, Liang Wang, Dan Shao, Dongsong Li   +11 more
wiley   +1 more source

Leveraging the Assembly of the Durum Wheat Genome cv. Svevo

, 2017
Tetraploid wheat species, with his two wild and cultivated subspecies T. turgidum ssp. dicoccoides and ssp. durum, is a cornerstone of the wheat polyploidy complex.
The International Durum wheat Genome Sequencing Consortium, L. Cattivelli, M. Maccaferri   +2 more
core   +1 more source

PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Burkholderia pseudomallei Two-Chromosome Genome

Frontiers in Microbiology, 2017
Although PacBio third-generation sequencers have improved the read lengths of genome sequencing which facilitates the assembly of complete genomes, no study has reported success in using PacBio data alone to completely sequence a two-chromosome bacterial
Jade L. L. Teng, Jade L. L. Teng, Jade L. L. Teng, Jade L. L. Teng, Man Lung Yeung, Man Lung Yeung, Man Lung Yeung, Man Lung Yeung, Elaine Chan, Lilong Jia, Chi Ho Lin, Yi Huang, Herman Tse, Herman Tse, Herman Tse, Herman Tse, Samson S. Y. Wong, Samson S. Y. Wong, Samson S. Y. Wong, Samson S. Y. Wong, Pak Chung Sham, Pak Chung Sham, Susanna K. P. Lau, Susanna K. P. Lau, Susanna K. P. Lau, Susanna K. P. Lau, Susanna K. P. Lau, Patrick C. Y. Woo, Patrick C. Y. Woo, Patrick C. Y. Woo, Patrick C. Y. Woo, Patrick C. Y. Woo   +31 more
doaj   +1 more source

Transposable Element–Driven PIEZO Mutation Enhances Locust Flight in Plateau Hypoxia

Advanced Science, EarlyView.
Why transposable elements (TEs) persisted or expanded in genomes remains a mystery. Using integrated analysis of TE macro‐ and microevolution in locusts, our results showed that thousands of TE insertions promoted widespread adaptive variation. Subfamilies of candidate adaptive TEs amplified and reshaped species‐level genomic architecture.
Xuanzhao Li, Ying Liu, Longsheng Xing, Xianliang Huang, Yingming Sun, Lei Yue, Yuze Zhang, Huilong Du, Bing Chen   +8 more
wiley   +1 more source

Integrated Single‐Cell and TCR Profiling Reveals Protection‐Associated CD8+ T Cell Subsets Linked to Viral Control in PRRSV

Advanced Science, EarlyView.
PRRSV vaccine‐mediated protection is associated with clonally expanded cytotoxic CD8+ T cell subsets driven by viral structural proteins and supported by innate TLR4/TLR8 signaling and CD4+ T cell help, whereas non‐protective responses are characterized by dysfunctional exhausted‐like CD8+ T cells linked to poor viral control.
Can Kong, Siang Chen, Maolin Li, Meng Wang, Hailin Zhang, Bolun Zhou, Zhenhua Xie, Chen Wang, Peng Gao, Jianjun Luo, Hanchun Yang, Runsheng Chen, Dongdong Zhang, Jie Li, Jun Han   +14 more
wiley   +1 more source

Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs [PDF]

, 2017
Leishmania parasites are the causative of leishmaniasis, a group of potentially fatal human diseases. Control strategies for leishmaniasis can be enhanced by genome based investigations.
Requena, Jose M, Javier Moreno, González-de la Fuente, Sandra, Jose M. Requena, Moreno, Javier, Fernando Carrasco-Ramiro, Requena, José María, Requena Rolania, José María, Begoña Aguado, Carrasco-Ramiro, Fernando, Alberto Rastrojo, Ramón Peiró-Pastor, Rastrojo Lastras, Alberto, Aguado, Begoña, Rastrojo, Alberto, Peiró-Pastor, Ramón, Sandra González-de la Fuente   +16 more
core   +1 more source

A Personalized Haplotype‐Resolved Near‐Gapless Genome Framework for Somatic Variant Discovery in Hepatocellular Carcinoma

Advanced Science, EarlyView.
A patient‐specific, haplotype‐resolved genome framework improves detection and interpretation of somatic variants in hepatocellular carcinoma. Using multi‐platform sequencing, the personalized assembly resolves complex regions including centromeres and MHC/HLA loci, enhances structural variant discovery, and links regulatory alterations to allele ...
Jiazheng Lin, Yao Xiao, Shuangzi Luo, Yifan Li, Wenfei Zhang, Xiaoyu Zhang, Xinyi Wang, Di Wu, Jieru Hong, Yongkun Luan, Xun Huang, Yixiu Wang, Ningbo Wu, Xiaoxiao Hu, Fei Zhao, Wei Li, Xiao Luo, Bi Shi   +17 more
wiley   +1 more source