Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet [0.03%]
中国四胞胎的单倍体型解析基因组和变异基准
Peng Jia,Lianhua Dong,Xiaofei Yang et al.
Peng Jia et al.
Background: Recent state-of-the-art sequencing technologies enable the investigation of challenging regions in the human genome and expand the scope of variant benchmarking datasets. Herein, we sequence a Chinese Quartet,...
A large-scale genomically predicted protein mass database enables rapid and broad-spectrum identification of bacterial and archaeal isolates by mass spectrometry [0.03%]
基于基因组预测蛋白质质量的大规模数据库可快速、广泛地通过质谱技术鉴定细菌和古菌的分离株
Yuji Sekiguchi,Kanae Teramoto,Dieter M Tourlousse et al.
Yuji Sekiguchi et al.
MALDI-TOF MS-based microbial identification relies on reference spectral libraries, which limits the screening of diverse isolates, including uncultured lineages. We present a new strategy for broad-spectrum identification of bacterial and ...
TargetRNA3: predicting prokaryotic RNA regulatory targets with machine learning [0.03%]
TargetRNA3：使用机器学习预测原核生物的RNA调控靶点
Brian Tjaden
Brian Tjaden
Small regulatory RNAs pervade prokaryotes, with the best-studied family of these non-coding genes corresponding to trans-acting regulators that bind via base pairing to their message targets. Given the increasing frequency with which these ...
Xiongbin Kang,Jialu Xu,Xiao Luo et al.
Xiongbin Kang et al.
Although generally superior, hybrid approaches for correcting errors in third-generation sequencing (TGS) reads, using next-generation sequencing (NGS) reads, mistake haplotype-specific variants for errors in polyploid and mixed samples. We...
Comparing methods for constructing and representing human pangenome graphs [0.03%]
比较构建和表示人类泛基因组图的方法
Francesco Andreace,Pierre Lechat,Yoann Dufresne et al.
Francesco Andreace et al.
Background: As a single reference genome cannot possibly represent all the variation present across human individuals, pangenome graphs have been introduced to incorporate population diversity within a wide range of genom...
ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model [0.03%]
基于拷贝数约束的肿瘤演化树推理模型ConDoR
Palash Sashittal,Haochen Zhang,Christine A Iacobuzio-Donahue et al.
Palash Sashittal et al.
A tumor contains a diverse collection of somatic mutations that reflect its past evolutionary history and that range in scale from single nucleotide variants (SNVs) to large-scale copy-number aberrations (CNAs). However, no current single-c...
STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer [0.03%]
STmut：用于可视化空间转录组数据中癌症体细胞改变的框架
Limin Chen,Darwin Chang,Bishal Tandukar et al.
Limin Chen et al.
Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues. Here, we describe new software, STmut, to visualize somatic point mutations, allelic imbalance, and copy number alter...
Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance [0.03%]
全面评估胚系变异呼叫性能的 Quartet DNA 参考材料和数据集
Luyao Ren,Xiaoke Duan,Lianhua Dong et al.
Luyao Ren et al.
Background: Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results...
Cooperation of MLL1 and Jun in controlling H3K4me3 on enhancers in colorectal cancer [0.03%]
MLL1和Jun在结直肠癌增强子上控制H3K4me3的协作作用
Xiang Lin,Ji-Dong Chen,Chen-Yu Wang et al.
Xiang Lin et al.
Background: Enhancer dysregulation is one of the important features for cancer cells. Enhancers enriched with H3K4me3 have been implicated to play important roles in cancer. However, their detailed features and regulatory...
Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation [0.03%]
人类视网膜单细胞多组学揭示了转录因子在介导基因变异对基因调控的类型特异性效应中的层次合作关系
Jun Wang,Xuesen Cheng,Qingnan Liang et al.
Jun Wang et al.
Background: Systematic characterization of how genetic variation modulates gene regulation in a cell type-specific context is essential for understanding complex traits. To address this question, we profile gene expressio...