The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI, and G4 sequencers [0.03%]
PCR复制对使用NovaSeq 6000、NovaSeq X、AVITI和G4测序仪生成的RNAseq数据的影响
Natalia Zajac,Ioannis S Vlachos,Sija Sajibu et al.
Natalia Zajac et al.
Background: Transcriptome sequencing (RNA-seq) is a powerful technology for gene expression profiling. Selection of optimal parameters for cDNA library generation is crucial for acquisition of high-quality data. In this s...
Rapid reprogramming and stabilization of homoeolog expression bias in hexaploid wheat biparental populations [0.03%]
六倍体小麦杂种群体中的基因表达偏向快速重塑及稳定化现象研究
Marek Glombik,Ramesh Arunkumar,Samuel Burrows et al.
Marek Glombik et al.
Background: Differences in the relative level of expression of homoeologs, known as homoeolog expression bias, are widely observed in allopolyploids. While the evolution of homoeolog expression bias through hybridization ...
Non-cyanobacterial diazotrophs support the survival of marine microalgae in nitrogen-depleted environment [0.03%]
固氮非蓝藻菌在氮耗尽的环境中支持海洋微藻的存活
Udita Chandola,Marinna Gaudin,Camille Trottier et al.
Udita Chandola et al.
Background: Non-cyanobacteria diazotrophs (NCDs) are shown to dominate in surface waters shifting the long-held paradigm of cyanobacteria dominance. This raises fundamental questions on how these putative heterotrophic ba...
Linda Shearwin-Whyatt,Jane Fenelon,Hongshi Yu et al.
Linda Shearwin-Whyatt et al.
Background: Egg-laying mammals (monotremes) evolved multiple sex chromosomes independently of therian mammals and lack the sex-determining gene SRY. The Y-localized anti-Müllerian hormone gene (AMHY) is the candidate sex...
Author Correction: Efficient precise knockin with a double cut HDR donor after CRISPR/Cas9-mediated double-stranded DNA cleavage [0.03%]
作者更正：CRISPR/Cas9介导的双链DNA断裂后的双重切割HDR供体的有效精准敲入
Jian-Ping Zhang,Xiao-Lan Li,Guo-Hua Li et al.
Jian-Ping Zhang et al.
Published Erratum
Genome biology. 2025 May 27;26(1):143. DOI:10.1186/s13059-025-03629-z 2025
Precise measurement of molecular phenotypes with barcode-based CRISPRi systems [0.03%]
条形码引导的CRISPRi系统实现分子表型的精确测量
Joseph H Lobel,Nicholas T Ingolia
Joseph H Lobel
Genome-wide CRISPR-Cas9 screens have untangled regulatory networks driving diverse biological processes. Their success relies on interrogating specific molecular phenotypes and distinguishing key regulators from background effects. Here, we...
A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data [0.03%]
一种从无细胞DNA测序数据中稳健提取片段组学特征的标准框架
Haichao Wang,Paulius D Mennea,Yu Kiu Elkie Chan et al.
Haichao Wang et al.
Fragmentomics features of cell-free DNA represent promising non-invasive biomarkers for cancer diagnosis. A lack of systematic evaluation of biases in feature quantification hinders the adoption of such applications. We compare features der...
Analyzing the relationship of RNA and DNA methylation with gene expression [0.03%]
分析RNA和DNA甲基化与基因表达的关系
Shangqian Xie,Darren Hagen,Gabrielle M Becker et al.
Shangqian Xie et al.
Background: DNA 5-methylcytosine (5mC) and RNA N6-methyladenosine (m6A) methylation are prevalent modifications in eukaryotes, both playing crucial roles in gene regulation. Recent studies have explored their crosstalk an...
Yingbo Cui,Chenchen Peng,Zeyu Xia et al.
Yingbo Cui et al.
A pangenome can reveal the genetic diversity across different individuals simultaneously. It offers a more comprehensive reference for genome analysis compared to a single linear genome that may introduce allele bias. Pangenomes are often r...
Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization [0.03%]
在微生物组和基因表达分析中将尺度不确定性作为归一化的扩展来纳入考虑
Michelle Pistner Nixon,Gregory B Gloor,Justin D Silverman
Michelle Pistner Nixon
Statistical normalizations are used in differential analyses to address sample-to-sample variation in sequencing depth. Yet normalizations make strong, implicit assumptions about the scale of biological systems, such as microbial load, lead...