microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis [0.03%]
MicrobeTag：通过注释、丰富性检验和代谢互补性分析简化微生物网络解释
Haris Zafeiropoulos,Ermis Ioannis Michail Delopoulos,Andi Erega et al.
Haris Zafeiropoulos et al.
Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to annotate microbial networks. Nodes, representing taxa, are enriched wit...
Topsicle: a method for estimating telomere length from whole genome long-read sequencing data [0.03%]
一种从全基因组长读段测序数据估计端粒长度的方法
Linh Nguyen,Jae Young Choi
Linh Nguyen
Telomeres protect chromosome ends and their length varies significantly between organisms. Because telomere length variation is associated with various biomedical and eco-evolutionary phenotypes, many biological fields are interested in und...
Bruce Budowle,Kristen Mittelman,David Mittelman
Bruce Budowle
Dense single nucleotide polymorphism testing has revolutionized forensic science, helping solve decadesold, current and future cases by overcoming the limitations of traditional short tandem repeat profiling. By embracing innovations from f...
ScIsoX: a multidimensional framework for measuring isoform-level transcriptomic complexity in single cells [0.03%]
ScIsoX：单细胞中测量转录本异构体水平转录组复杂度的多维框架
Siyuan Wu,Ulf Schmitz
Siyuan Wu
Single-cell isoform analysis enables high-resolution characterization of transcript expression, yet analytical frameworks to systematically measure transcriptomic complexity are lacking. Here, we introduce ScIsoX, a computational framework ...
Jonas Scheid,Steffen Lemke,Naomi Hoenisch-Gravel et al.
Jonas Scheid et al.
Confident identification of human leukocyte antigen (HLA)-presented peptides is crucial for advancing cancer immunotherapy. We present MHCquant2, a scalable and modular Nextflow pipeline integrated into nf-core as a reproducible, portable, ...
Deciphering the sequence basis and application of transcriptional initiation regulation in plant genomes through deep learning [0.03%]
基于深度学习的植物基因组转录起始调控的序列解析及应用研究
Pengfei Gao,Lijie Lian,Wanjie Feng et al.
Pengfei Gao et al.
Background: Transcription initiation is a key checkpoint in plant gene regulation, yet the DNA features that determine where and the frequency of the genes start transcription remain unclear. ...
SIGEL: a context-aware genomic representation learning framework for spatial genomics analysis [0.03%]
SIGEL：一种用于空间组学分析的上下文感知基因组表示学习框架
Wenlin Li,Maocheng Zhu,Yucheng Xu et al.
Wenlin Li et al.
Spatial transcriptomics (ST) integrates spatial information into genomics, yet methods for generating spatially-informed gene representations are limited and computationally intensive. We present SIGEL, a cost-effective framework that deriv...
A compendium of synthetic lethal gene pairs defined by extensive combinatorial pan-cancer CRISPR screening [0.03%]
大规模泛癌种CRISPR筛选鉴定合成致死基因对汇编
Victoria Harle,Victoria Offord,Birkan Gökbağ et al.
Victoria Harle et al.
Background: Synthetic lethal interactions are attractive therapeutic candidates as they enable selective targeting of cancer cells in which somatic alterations have disrupted one member of a synthetic lethal gene pair whi...
The 5-methylcytosine DNA glycosylase ROS1 prevents paternal genome hypermethylation in Arabidopsis endosperm [0.03%]
拟南芥胚乳中ROS1甲基胞嘧啶DNA糖基化酶可防止父本基因组高甲基化现象
Elizabeth A Hemenway,Mary Gehring
Elizabeth A Hemenway
Background: DNA methylation patterning is a consequence of opposing activities of DNA methyltransferases and DNA demethylases. In many plant and animal species, reproduction is a period of significant epigenome lability. ...
Systematic benchmarking of computational methods to identify spatially variable genes [0.03%]
系统评估计算方法识别空间可变性基因的能力
Zhijian Li,Zain M Patel,Dongyuan Song et al.
Zhijian Li et al.
Background: Spatially resolved transcriptomics offers unprecedented insight by enabling the profiling of gene expression within the intact spatial context of cells, effectively adding a new and essential dimension to data...