scGIST: gene panel design for spatial transcriptomics with prioritized gene sets [0.03%]
scGIST：基于优先基因集的空间转录组学基因panel设计
Mashrur Ahmed Yafi,Md Hasibul Husain Hisham,Francisco Grisanti et al.
Mashrur Ahmed Yafi et al.
A critical challenge of single-cell spatial transcriptomics (sc-ST) technologies is their panel size. Being based on fluorescence in situ hybridization, they are typically limited to panels of about a thousand genes. This constrains researc...
SHARE-Topic: Bayesian interpretable modeling of single-cell multi-omic data [0.03%]
分享主题：单细胞多组学数据的贝叶斯可解释建模
Nour El Kazwini,Guido Sanguinetti
Nour El Kazwini
Multi-omic single-cell technologies, which simultaneously measure the transcriptional and epigenomic state of the same cell, enable understanding epigenetic mechanisms of gene regulation. However, noisy and sparse data pose fundamental stat...
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods [0.03%]
基因组解读关键评估(CAGI)建立计算遗传变异解读方法的进展和前景
Critical Assessment of Genome Interpretation Consortium
Critical Assessment of Genome Interpretation Consortium
Background: The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete ed...
Tianru Zhang,Changhao Li,Jiaying Zhu et al.
Tianru Zhang et al.
Background: RNA secondary structure (RSS) can influence the regulation of transcription, RNA processing, and protein synthesis, among other processes. 3' untranslated regions (3' UTRs) of mRNA also hold the key for many a...
Undetectable off-target effects induced by FokI catalytic domain in mouse embryos [0.03%]
由FokI催化域在小鼠胚胎中诱导的无法检测到的脱靶效应
Long Xie,Hu Feng,Zhifang Li et al.
Long Xie et al.
The FokI catalytic domain can be fused to various DNA binding architectures to improve the precision of genome editing tools. However, evaluation of off-target effects is essential for developing these tools. We use Genome-wide Off-target a...
DNA satellite and chromatin organization at mouse centromeres and pericentromeres [0.03%]
小鼠着丝粒和近着丝粒的DNA卫星及染色质构象
Jenika Packiaraj,Jitendra Thakur
Jenika Packiaraj
Background: Centromeres are essential for faithful chromosome segregation during mitosis and meiosis. However, the organization of satellite DNA and chromatin at mouse centromeres and pericentromeres is poorly understood ...
Author Correction: Cross-phyla protein annotation by structural prediction and alignment [0.03%]
作者更正：通过结构预测和比对进行跨门蛋白注释
Fabian Ruperti,Nikolaos Papadopoulos,Jacob M Musser et al.
Fabian Ruperti et al.
Published Erratum
Genome biology. 2024 Feb 19;25(1):50. DOI:10.1186/s13059-024-03196-9 2024
RUBICON: a framework for designing efficient deep learning-based genomic basecallers [0.03%]
RUBICON：设计高效的基于深度学习的基因组碱基识别器的框架
Gagandeep Singh,Mohammed Alser,Kristof Denolf et al.
Gagandeep Singh et al.
Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The performance of basecalling has critical implications for all ...
Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species hybrids [0.03%]
通过种内和种间杂交剖析指导m6A沉积和演化的序列及结构因子
Ran Shachar,David Dierks,Miguel Angel Garcia-Campos et al.
Ran Shachar et al.
Background: N6-methyladenosine (m6A) is the most abundant mRNA modification, and controls mRNA stability. m6A distribution varies considerably between and within species. Yet, it is unclear to what extent this variability...
pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging [0.03%]
pyHiM：一个新的开源多平台软件包，基于多重DNA-FISH成像的空间基因组学技术
Xavier Devos,Jean-Bernard Fiche,Marion Bardou et al.
Xavier Devos et al.
Genome-wide ensemble sequencing methods improved our understanding of chromatin organization in eukaryotes but lack the ability to capture single-cell heterogeneity and spatial organization. To overcome these limitations, new imaging-based ...