Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2 [0.03%]
利用Cuttlefish 2进行可扩展的、超快的和低内存的紧凑de Bruijn图构建
Jamshed Khan,Marek Kokot,Sebastian Deorowicz et al.
Jamshed Khan et al.
The de Bruijn graph is a key data structure in modern computational genomics, and construction of its compacted variant resides upstream of many genomic analyses. As the quantity of genomic data grows rapidly, this often forms a computation...
Abnormal molecular signatures of inflammation, energy metabolism, and vesicle biology in human Huntington disease peripheral tissues [0.03%]
亨廷顿舞蹈病外周组织炎症、能量代谢和囊泡生物学的分子特征异常
Andreas Neueder,Kerstin Kojer,Tanja Hering et al.
Andreas Neueder et al.
Background: A major challenge in neurodegenerative diseases concerns identifying biological disease signatures that track with disease progression or respond to an intervention. Several clinical trials in Huntington disea...
Genomic insights into the evolutionary history and diversification of bulb traits in garlic [0.03%]
基因组学见解揭示了大蒜的进化史及鳞茎性状多样化情况
Ningyang Li,Xueyu Zhang,Xiudong Sun et al.
Ningyang Li et al.
Background: Garlic is an entirely sterile crop with important value as a vegetable, condiment, and medicine. However, the evolutionary history of garlic remains largely unknown. ...
The histone modification reader ZCWPW1 promotes double-strand break repair by regulating cross-talk of histone modifications and chromatin accessibility at meiotic hotspots [0.03%]
组蛋白修饰阅读器ZCWPW1通过调节重组热点位点处的组蛋白修饰交流和染色质可及性促进同源重组修复
Shenli Yuan,Tao Huang,Ziyou Bao et al.
Shenli Yuan et al.
Background: The PRDM9-dependent histone methylation H3K4me3 and H3K36me3 function in assuring accurate homologous recombination at recombination hotspots in mammals. Beyond histone methylation, H3 lysine 9 acetylation (H3...
Integrating temporal single-cell gene expression modalities for trajectory inference and disease prediction [0.03%]
整合时间单细胞基因表达模式以进行轨迹推理和疾病预测
Jolene S Ranek,Natalie Stanley,Jeremy E Purvis
Jolene S Ranek
Background: Current methods for analyzing single-cell datasets have relied primarily on static gene expression measurements to characterize the molecular state of individual cells. However, capturing temporal changes in c...
Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize [0.03%]
基于基因组注释预测进化约束可改善玉米基因组变异的功能优先级划分
Guillaume P Ramstein,Edward S Buckler
Guillaume P Ramstein
Background: Crop improvement through cross-population genomic prediction and genome editing requires identification of causal variants at high resolution, within fewer than hundreds of base pairs. Most genetic mapping stu...
CTCF and cohesin promote focal detachment of DNA from the nuclear lamina [0.03%]
CTCF和粘连素促使DNA从核小体上局部脱落
Tom van Schaik,Ning Qing Liu,Stefano G Manzo et al.
Tom van Schaik et al.
Background: Lamina-associated domains (LADs) are large genomic regions that are positioned at the nuclear lamina. It has remained largely unclear what drives the positioning and demarcation of LADs. Because the insulator ...
MIRTH: Metabolite Imputation via Rank-Transformation and Harmonization [0.03%]
基于等级转换和协整的代谢物填充（MIRTH）
Benjamin A Freeman,Sophie Jaro,Tricia Park et al.
Benjamin A Freeman et al.
Out of the thousands of metabolites in a given specimen, most metabolomics experiments measure only hundreds, with poor overlap across experimental platforms. Here, we describe Metabolite Imputation via Rank-Transformation and Harmonization...
Multiple genome alignment in the telomere-to-telomere assembly era [0.03%]
全基因组多倍体_alignment在端到端序列组装时代的发展
Bryce Kille,Advait Balaji,Fritz J Sedlazeck et al.
Bryce Kille et al.
With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the computational challenge of efficiently and accurately constructing multiple genome alignments at an unprecedented scale. By identifying nucleotides acro...
The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants [0.03%]
拟南芥APOLO和人类UPAT两个序列不相关长非编码RNA可以调控植物的DNA甲基化和组蛋白甲基化修饰机器
Camille Fonouni-Farde,Aurélie Christ,Thomas Blein et al.
Camille Fonouni-Farde et al.
Background: RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO), are emerging as important regulators of three-dimensional chromatin con...