Results 111 to 120 of about 152,624 (261)

De novo transcriptome assembly

, 2015
In this thesis, a de novo transcriptome assembler was implemented based on the overlap-layout-consensus paradigm. It was written in the C++ programming language and was named Ra which is short for RNA assembler. Its overlap phase relies on the enhanced suffix arrays and reproduces exact overlaps between input reads.
openaire   +1 more source

De Novo Design of Membrane‐Targeting Antimicrobial Peptides Against Gram‐Negative Bacteria Using a Generative Artificial Intelligence Framework

Advanced Science, EarlyView.
Antimicrobial resistance caused by Gram‐negative bacteria remains difficult to overcome due to the protective outer membrane. To address this challenge, a multi‐condition constrained generative AI framework, GenMTAMP is proposed for de novo membrane‐targeting antimicrobial peptide design by integrating physicochemical and spatial structure descriptors.
Jingxiao Yu, Da‐Wen Sun, QingYi Wei, Yibing Zhang, Jidong Tang, Hongbin Pu   +5 more
wiley   +1 more source

Introduction to de novo genome assembly

, 2017
Beginners introduction to the use of de novo assembly of genomic sequences.
openaire   +1 more source

Hair Follicle Seedling Cryomicroneedles from Hierarchical Microfluidic Organoid on a Chip

Advanced Science, EarlyView.
In this paper, a hierarchical microfluidic chip is developed to produce uniform hair follicle organoids (HFOs) in cryomicroneedles. Cryopreservation agents encapsulate HFOs, preserving viability and hair growth potential. The cryomicroneedles enable simple intradermal transplantation with good skin penetration.
Xinyue Cao, Dongyu Xu, Minhui Lu, Yuanjin Zhao   +3 more
wiley   +1 more source

Generation of Self‐Organizing Macrovascular Constructs by Bioprinting Human iPSC‐Derived Mesodermal Progenitor Cells

Advanced Science, EarlyView.
ABSTRACT Vascularization remains a major obstacle in tissue engineering. Here, we introduce a bioprinting strategy to generate centimeter‐scale, self‐organizing “mother vessel” constructs from iPSC‐derived hiMPCs. By optimizing bioink composition, printing was accomplished in a single‐step approach. Within one week, hiMPCs differentiated into both CD31+
Leyla E. Dogan, Nathaly A. Chicaiza‐Cabezas, Florian Kleefeldt, Philipp Wörsdörfer, Jürgen Groll, Süleyman Ergün   +5 more
wiley   +1 more source

ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs

BMC Bioinformatics
Background Transcriptome assembly from RNA-sequencing data in species without a reliable reference genome has to be performed de novo, but studies have shown that de novo methods often have inadequate ability to reconstruct transcript isoforms.
Karl Johan Westrin, Warren W. Kretzschmar, Olof Emanuelsson   +2 more
doaj   +1 more source

PRMT9 Aggravated Dopaminergic Neurodegeneration in Parkinson's Disease Model by Facilitating the Degradation of DUSP26 and Inducing Mitochondrial Dysfunction

Advanced Science, EarlyView.
In the pathological state of PD induced by MPP+, the upregulated PRMT9 in dopaminergic neurons translocates into mitochondrion and interacts with DUSP26 and catalyzes its arginine methylation, leading to the ubiquitin‐proteasomal degradation of DUSP26 mediated by Trim32.
Tengfei Liu, Xiaomeng Song, Xin Guo, Rui Xiao, Ru Sun, Qiuran Ji, Lu Yu, Yiquan Li, Qingyi Fu, Qidi Xue, Lingjun Kong, Lin Chen, Chengjiang Gao, Huiqing Liu   +13 more
wiley   +1 more source

Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing

BMC Genomics
Long-read sequencing is revolutionizing de-novo genome assemblies, with continued advancements making it more readily available for previously understudied, non-model organisms.
Benjamin D. Young, Olivia M. Williamson, Nicholas S. Kron, Natalia Andrade Rodriguez, Lys M. Isma, Nicholas J. MacKnight, Erinn M. Muller, Stephanie M. Rosales, Stephanie M. Sirotzke, Nikki Traylor-Knowles, Sara D. Williams, Michael S. Studivan   +11 more
doaj   +1 more source

CREAT: A CRISPR‐Based Genome Trimming Strategy for Systematic Identification of Dispensable Regions and Rapid Genome Reduction

Advanced Science, EarlyView.
Current genome‐reduction methods work in a trial‐and‐error fashion, constituting a long‐standing bottleneck in the research. We developed CREAT (CRISPR‐based genome trimming with a multi‐homology‐arm template), a CRISPR‐based genetic approach that enables systematically classifying essential versus non‐essential genomic regions and subsequently ...
Guanhua Yuan, Zhe Gao, Yingxuan Qi, Yang Zhang, Xuhui Tian, Pengpeng Zhao, Xu Feng, Qunxin She   +7 more
wiley   +1 more source

Synergistic HMGN1 and VP64 Fusions Potentiate High‐Precision and PAM‐Flexible Base Editing

Advanced Science, EarlyView.
A novel CDA1Δ‐SpRY architecture fused with HMGN1 and VP64 yields a nearly PAM‐less base editing platform. By focusing cytosine conversion predominantly at position −18, this synergistic complex ensures highly precise targeting. Demonstrating enhanced efficiency across diverse models, including yeast and rice, the platform offers a robust solution for ...
Xi Luo, Yuyao Qu, Zhengyan Ye, Zheng Li, Yuanyan Zhang, Longjiong Luo, Shaokang Li, Wei Zhao, Ming Wang, Ralph Bock, Jianmin Wan, Junjie Tan   +11 more
wiley   +1 more source