iIMPACT: integrating image and molecular profiles for spatial transcriptomics analysis [0.03%]
IIMPACT：整合图像和分子特征进行空间转录组分析
Xi Jiang,Shidan Wang,Lei Guo et al.
Xi Jiang et al.
Current clustering analysis of spatial transcriptomics data primarily relies on molecular information and fails to fully exploit the morphological features present in histology images, leading to compromised accuracy and interpretability. T...
Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios [0.03%]
系统评估多种场景下单细胞和空间解析转录组数据模拟的实用指南
Hongrui Duo,Yinghong Li,Yang Lan et al.
Hongrui Duo et al.
Background: Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have led to groundbreaking advancements in life sciences. To develop bioinformatics tools for scRNA-seq and SRT data and perf...
Predicting gene expression state and prioritizing putative enhancers using 5hmC signal [0.03%]
基于5hmC信号预测基因表达状态和筛选潜在增强子元件
Edahi Gonzalez-Avalos,Atsushi Onodera,Daniela Samaniego-Castruita et al.
Edahi Gonzalez-Avalos et al.
Background: Like its parent base 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) is a direct epigenetic modification of cytosines in the context of CpG dinucleotides. 5hmC is the most abundant oxidized form of 5mC,...
Sequential drug treatment targeting cell cycle and cell fate regulatory programs blocks non-genetic cancer evolution in acute lymphoblastic leukemia [0.03%]
针对细胞周期和细胞命运调控程序的序贯药物治疗可阻断急性淋巴细胞白血病中的非遗传性癌变进化
Alena Malyukova,Mari Lahnalampi,Ton Falqués-Costa et al.
Alena Malyukova et al.
Background: Targeted therapies exploiting vulnerabilities of cancer cells hold promise for improving patient outcome and reducing side-effects of chemotherapy. However, efficacy of precision therapies is limited in part b...
X-chromosome inactivation in human iPSCs provides insight into X-regulated gene expression in autosomes [0.03%]
人诱导多能干细胞中的X染色体失活为常染色体上的X连锁调节基因表达提供了见解
Hande Topa,Clara Benoit-Pilven,Taru Tukiainen et al.
Hande Topa et al.
Background: Variation in X chromosome inactivation (XCI) in human-induced pluripotent stem cells (hiPSCs) can impact their ability to model biological sex biases. The gene-wise landscape of X chromosome gene dosage remain...
Sophie Hawkins,Alexandre Mondaini,Seema C Namboori et al.
Sophie Hawkins et al.
RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions, such as CLIP, rely on purif...
Reproductive isolation arises during laboratory adaptation to a novel hot environment [0.03%]
实验室适应新温度环境的繁殖隔离产生机制
Sheng-Kai Hsu,Wei-Yun Lai,Johannes Novak et al.
Sheng-Kai Hsu et al.
Background: Reproductive isolation can result from adaptive processes (e.g., ecological speciation and mutation-order speciation) or stochastic processes such as "system drift" model. Ecological speciation predicts barrie...
Current status of community resources and priorities for weed genomics research [0.03%]
关于杂草基因组研究的现状及优先事项
Jacob Montgomery,Sarah Morran,Dana R MacGregor et al.
Jacob Montgomery et al.
Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of genomic information precludes resea...
Clarice K Y Hong,Avinash Ramu,Siqi Zhao et al.
Clarice K Y Hong et al.
Background: Individual cells from isogenic populations often display large cell-to-cell differences in gene expression. This "noise" in expression derives from several sources, including the genomic and cellular environme...
Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage [0.03%]
Rosace：一种稳健的深层突变扫描分析框架，采用位置和均值方差收缩法
Jingyou Rao,Ruiqi Xin,Christian Macdonald et al.
Jingyou Rao et al.
Deep mutational scanning (DMS) measures the effects of thousands of genetic variants in a protein simultaneously. The small sample size renders classical statistical methods ineffective. For example, p-values cannot be correctly calibrated ...