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...
Tumor ploidy determination in low-pass whole genome sequencing and allelic copy number visualization using the Constellation Plot [0.03%]
低覆盖全基因组测序中的肿瘤倍体测定及等位基因拷贝数的Constellation图可视化方法
Sarah H Johnson,James B Smadbeck,Roman M Zenka et al.
Sarah H Johnson et al.
Ploidy determination across the genome has been challenging for low-pass-WGS tumor-only samples. We present BACDAC, a method that calculates tumor ploidy down to 1.2X effective tumor coverage. Allele fraction patterns displayed in the Const...
CMImpute: cross-species and tissue imputation of species-level DNA methylation samples across mammalian species [0.03%]
跨物种和组织的哺乳动物DNA甲基化样本填补算法（CMImpute）
Emily Maciejewski,Steve Horvath,Jason Ernst
Emily Maciejewski
The large-scale application of the mammalian methylation array has substantially expanded the availability of DNA methylation data in mammalian species. However, this data captures only a small portion of species-tissue combinations. To add...
RobusTAD: reference panel based annotation of nested topologically associating domains [0.03%]
基于参考面板的嵌套拓扑关联区注释
Yanlin Zhang,Rola Dali,Mathieu Blanchette
Yanlin Zhang
Topologically associating domains (TADs) are fundamental units of 3D genomes and play essential roles in gene regulation. Hi-C data suggests a hierarchical organization of TADs. Accurately annotating nested TADs from Hi-C data remains chall...
Urbanization and genetic homogenization in the medieval Low Countries revealed through a ten-century paleogenomic study of the city of Sint-Truiden [0.03%]
基于圣特鲁伊登千年古基因组的中世纪低地国家城市化及遗传同质化的研究
Owyn Beneker,Ludovica Molinaro,Meriam Guellil et al.
Owyn Beneker et al.
Background: Processes shaping the formation of the present-day population structure in highly urbanized Northern Europe are still poorly understood. Gaps remain in our understanding of when and how currently observable re...
The gene regulatory mechanisms shaping the heterogeneity of venom production in the Cape coral snake [0.03%]
调节毒液产生的基因调控机制：开普珊瑚蛇为例
Pedro G Nachtigall,Brett R Hamilton,Taline D Kazandjian et al.
Pedro G Nachtigall et al.
Background: Venoms and their associated glands and delivery structures have evolved numerous times among animals. Within these venom systems, the molecular, cellular, and morphological components interact and co-evolve to...