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...
New insights into the cold tolerance of upland switchgrass by integrating a haplotype-resolved genome and multi-omics analysis [0.03%]
通过整合单倍型解析基因组和多组学分析深入研究高梁的耐冷性
Bingchao Wu,Dan Luo,Yuesen Yue et al.
Bingchao Wu et al.
Background: Switchgrass (Panicum virgatum L.) is a bioenergy and forage crop. Upland switchgrass exhibits superior cold tolerance compared to the lowland ecotype, but the underlying molecular mechanisms remain unclear. ...
Deciphering the role of RNA in regulating CTCF's DNA binding affinity in leukemia cells [0.03%]
解密RNA在白血病细胞中对CTCFDNA结合亲和力调节的作用
Judith Hyle,Wenjie Qi,Mohamed Nadhir Djekidel et al.
Judith Hyle et al.
Background: CTCF, a highly studied transcription factor, is essential for chromatin interaction maintenance. Several independent studies report that CTCF interacts with RNAs in vitro and in cells. Yet continuous debates a...
Endometrial tumorigenesis involves epigenetic plasticity demarcating non-coding somatic mutations and 3D-genome alterations [0.03%]
子宫肿瘤发生涉及表观遗传塑性、非编码体细胞突变和三维基因组改变之间的分界线
Sebastian Gregoricchio,Aleksandar Kojic,Marlous Hoogstraat et al.
Sebastian Gregoricchio et al.
Background: The incidence and mortality of endometrial cancer (EC) is on the rise. Eighty-five percent of ECs depend on estrogen receptor alpha (ERα) for proliferation, but little is known about its transcriptional regul...
ChromActivity: integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types [0.03%]
ChromActivity：基于多种人类细胞类型调控活性的表观基因组和功能特征注释整合分析方法
Tevfik Umut Dincer,Jason Ernst
Tevfik Umut Dincer
We introduce ChromActivity, a computational framework for predicting and annotating regulatory activity across the genome through integration of multiple epigenomic maps and various functional characterization datasets. ChromActivity genera...
Parent-of-origin regulation by maternal auts2 shapes neurodevelopment and behavior in fish [0.03%]
鱼的母源AUTS2调节影响神经发育和行为的父系基因表达
Antoine Emile Clément,Constance Merdrignac,Sergi Roig Puiggros et al.
Antoine Emile Clément et al.
Background: Parental experience can influence progeny behavior through gamete-mediated non-genetic inheritance, that is, mechanisms that do not involve changes in inherited DNA sequence. However, underlying mechanisms rem...