Fetal signatures in the 3D genome of iPSC-derived neurons and their implications for disease modeling [0.03%]
源自诱导多能干细胞神经元的三维基因组中的胎儿印记及其对疾病建模的意义
Diana Zagirova,Anna Kononkova,Kirill Morozov et al.
Diana Zagirova et al.
Induced pluripotent stem cells (iPSCs) have revolutionized neuroscience, providing an approach to generate patient-specific neurons for modeling of neurological diseases. However, it remains unclear how closely iPSC-derived neurons replicat...
Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments [0.03%]
在单细胞实验中， hashtag辅助池化可以平衡批次效应缓解和细胞损失的 moderated设计
Budha Chatterjee,Katrina Gorga,Carly Blair et al.
Budha Chatterjee et al.
Minimizing experimental noise is integral to robust data generation in single-cell omics. The current standard for avoiding batch effects during sample processing is barcode- or hashtag-assisted combining of different experimental treatment...
Cross-species variant-to-function analyses implicate MEIS1 in conferring sleep abnormalities and impaired cerebellar development [0.03%]
跨物种的变异到功能分析揭示了MEIS1基因在睡眠异常和小脑发育障碍中的作用
Amber Zimmerman,Erika Almeraya Del Valle,Matthew Pahl et al.
Amber Zimmerman et al.
Genome-wide association studies (GWAS) have identified numerous loci for insomnia, yet functional validation of effector genes remains limited because most risk variants lie in noncoding regions, and the true causal gene is not known. Here,...
Yan Ke,Tianwei Yu
Yan Ke
Analyzing omics data in the context of pathway knowledge is critical for understanding the molecular mechanisms underlying pathological changes. However, current pathway analysis methods do not model the detailed mechanistic nature of biolo...
Haodong Liu,Pinglu Zhang,Yanming Wei et al.
Haodong Liu et al.
Partial order alignment (POA) has emerged as a fundamental component in long-read error correction, assembly and pangenomics. However, conventional POA algorithms are limited by high time and memory requirements, making them inefficient for...
Mosaic integration of spatial multiomic data based on hierarchical graph contrastive learning with SpatialMOSI [0.03%]
基于层次图对比学习的SpatialMOSI空间多组学数据马赛克集成方法
Peimeng Zhen,Han Shu,Bingtao Wang et al.
Peimeng Zhen et al.
Spatial omic technologies have revolutionized tissue analysis by enabling multimodal molecular coprofiling within their native tissue context. Integrating multislice spatial multiomic data offers unprecedented opportunities to reconstruct t...
Multisource omic alignment and biological feature discovery with Performer encoder and triplet networks [0.03%]
基于Performer编码器和三元组网络的多源组学对齐与生物特征发现
Zihuan Du,Xiaoyu Zhang,Qiang Zhang et al.
Zihuan Du et al.
Advances in single-cell sequencing technologies greatly enhance our understanding of molecular and cellular features. However, effectively leveraging these data to uncover key biological factors remains a major challenge in integrative anal...
Identification of genomic features that uniquely impact estrogen receptor alpha binding and its effects on gene expression in endometrial cancer [0.03%]
识别影响雌激素受体α在子宫内膜癌中结合及效应的基因组特征
Alexandra Richey,Noel Kitchen,Craig M Rush et al.
Alexandra Richey et al.
Estrogen receptor 1 (ESR1) is an established oncogenic transcription factor in breast and endometrial cancer; however, more is known about the mechanisms controlling ESR1 behavior in breast cancer, and therapies targeting ESR1 have been muc...
Methylation variability and LINE-1 transcriptional activation in multiple myeloma [0.03%]
多发性骨髓瘤中的甲基化变异和LINE-1转录激活
Qianhui Wan,Amy Leung,Mahek Vinod Bhandari et al.
Qianhui Wan et al.
Multiple myeloma (MM) is a type of hematological cancer that arises from uncontrolled proliferation of plasma cells. In addition to frequent genetic mutations, malignant plasma cells are characterized by alterations to the epigenome. Myelom...
ComicGTN infers disease-associated rare cell states from single-cell multiomic data using DNA sequence-augmented graph transformer networks [0.03%]
基于DNA序列增强图变换器网络的ComicGTN方法从单细胞多组学数据中推断疾病相关罕见细胞状态
Boran Yang,Jiao Hua,Guanghua Zhou et al.
Boran Yang et al.
Single-cell multiomic technology makes it possible to profile both the transcriptome and epigenome within individual cells. The detection of rare cell states from such data is crucial for exploring novel disease biomarkers with clinical pot...