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...
H3K4me3 binding ALFIN-LIKE proteins recruit SWR1 for gene-body deposition of H2A.Z [0.03%]
带H3K4me3结合域的ALFIN-LIKE蛋白募集SWR1复合体并在基因体内沉积H2A.Z
Linhao Xu,Yafei Wang,Xueying Li et al.
Linhao Xu et al.
Background: The H2A.Z histone variant is highly enriched over gene bodies, playing an essential role in several genome-templated processes, including transcriptional regulation and epigenetic patterning across eukaryotes....
SMOPCA: spatially aware dimension reduction integrating multi-omics improves the efficiency of spatial domain detection [0.03%]
SMOPCA：整合多组学的空域感知降维可提高空间域检测效率
Mo Chen,Ruihua Cheng,Jianuo He et al.
Mo Chen et al.
Technological advances have enabled us to profile multiple omics layers with spatial information, significantly enhancing spatial domain detection and advancing a variety of biomedical research fields. Despite these advancements, there is a...
Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming [0.03%]
基于ipd修整的6mA图谱解析染色质空间构象及其原位DNA甲基化分布
Wentao Yang,Xue Qing Wang,Fan Wei et al.
Wentao Yang et al.
Enabled by long-read sequencing technologies, particularly Single Molecule, Real-Time sequencing, N6-methyladenine (6mA) footprinting is a transformative methodology for revealing the heterogenous and dynamic distribution of nucleosomes and...
CloseRead: a tool for assessing assembly errors in immunoglobulin loci applied to vertebrate long-read genome assemblies [0.03%]
CloseRead：一种用于评估免疫球蛋白系装配错误的工具，并将其应用于脊椎动物长读长基因组装配中
Yixin Zhu,Corey Watson,Yana Safonova et al.
Yixin Zhu et al.
Despite tremendous advances in long-read sequencing, some structurally complex and repeat-rich genomic regions remain challenging to assemble. Furthermore, we lack tools to assess local assembly quality, making it hard to identify problems ...
Evaluating topography of mutational signatures with SigProfilerTopography [0.03%]
利用SigProfilerTopography评估突变特征的地形学分布特征
Burçak Otlu,Ludmil B Alexandrov
Burçak Otlu
The mutations found in a cancer genome are shaped by diverse processes, each displaying a characteristic mutational signature that may be influenced by the genome's architecture. While prior analyses have evaluated the effect of topographic...