Cas12f1 gene drives propagate efficiently in herpesviruses and induce minimal resistance [0.03%]
高效的Cas12f1基因驱动在疱疹病毒中传播并产生最小的抗性
Zhuangjie Lin,Qiaorui Yao,Keyuan Lai et al.
Zhuangjie Lin et al.
Background: Synthetic CRISPR-Cas9 gene drive has been developed to control harmful species. However, resistance to Cas9 gene drive can be acquired easily when DNA repair mechanisms patch up the genetic insults introduced ...
TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies [0.03%]
基于时间信息的降维方法在纵向微生物组研究中的应用
Pixu Shi,Cameron Martino,Rungang Han et al.
Pixu Shi et al.
Longitudinal studies are crucial for understanding complex microbiome dynamics and their link to health. We introduce TEMPoral TEnsor Decomposition (TEMPTED), a time-informed dimensionality reduction method for high-dimensional longitudinal...
SyntheVAEiser: augmenting traditional machine learning methods with VAE-based gene expression sample generation for improved cancer subtype predictions [0.03%]
基于变分自编码器的基因表达样本生成增强传统机器学习方法以提高癌症亚型预测性能
Brian Karlberg,Raphael Kirchgaessner,Jordan Lee et al.
Brian Karlberg et al.
The accuracy of machine learning methods is often limited by the amount of training data that is available. We proposed to improve machine learning training regimes by augmenting datasets with synthetically generated samples. We present a m...
GenomeDelta: detecting recent transposable element invasions without repeat library [0.03%]
基因组进化中转座元件的新插入位点的识别和注释
Riccardo Pianezza,Anna Haider,Robert Kofler
Riccardo Pianezza
We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-quality assemblies with short-read data to det...
HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling [0.03%]
HIPSD&R-seq 实现了可扩展的基因组拷贝数和转录组分析
Jan Otoničar,Olga Lazareva,Jan-Philipp Mallm et al.
Jan Otoničar et al.
Single-cell DNA sequencing (scDNA-seq) enables decoding somatic cancer variation. Existing methods are hampered by low throughput or cannot be combined with transcriptome sequencing in the same cell. We propose HIPSD&R-seq (HIgh-throughPut ...
EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics [0.03%]
EpiGePT：一种基于预训练变换器的组学语言模型用于人类表观基因调控区域预测
Zijing Gao,Qiao Liu,Wanwen Zeng et al.
Zijing Gao et al.
The inherent similarities between natural language and biological sequences have inspired the use of large language models in genomics, but current models struggle to incorporate chromatin interactions or predict in unseen cellular contexts...
Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references [0.03%]
评估高质量 phased 基因组的数据需求，以创建稳健的泛基因组参考序列
Prasad Sarashetti,Josipa Lipovac,Filip Tomas et al.
Prasad Sarashetti et al.
Background: Long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ultra-long ONT. Despite...
Transcriptional regulatory network reveals key transcription factors for regulating agronomic traits in soybean [0.03%]
转录调控网络揭示了大豆中控制农艺性状的关键转录因子
Wu Jiao,Mangmang Wang,Yijian Guan et al.
Wu Jiao et al.
Background: Transcription factors (TFs) bind regulatory genomic regions to orchestrate spatio-temporal expression of target genes. Global dissection of the cistrome is critical for elucidating transcriptional networks und...
Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment [0.03%]
免疫抵抗性透明细胞肾细胞癌肿瘤微环境中的整联蛋白和IV型胶原的空间耦合度增加
Alex C Soupir,Mitchell T Hayes,Taylor C Peak et al.
Alex C Soupir et al.
Background: Immunotherapy has improved survival for patients with advanced clear cell renal cell carcinoma (ccRCC), but resistance to therapy develops in most patients. We use cellular-resolution spatial transcriptomics i...
Systemic evaluation of various CRISPR/Cas13 orthologs for knockdown of targeted transcripts in plants [0.03%]
植物中靶向转录本降解的多种CRISPR / Cas13同源物的系统评价
Lu Yu,Jiawei Zou,Amjad Hussain et al.
Lu Yu et al.
Background: CRISPR/Cas13 system, recognized for its compact size and specificity in targeting RNA, is currently employed for RNA degradation. However, the potential of various CRISPR/Cas13 subtypes, particularly concernin...