SwitchTFI: identifying transcription factors driving cell differentiation [0.03%]
SwitchTFI：识别驱动细胞分化的转录因子
Paul Martini,Anne Hartebrodt,Gustavo P de Almeida et al.
Paul Martini et al.
Many methods exist that infer cell differentiation trajectories from single-cell RNA sequencing data, but only few determine which mechanisms drive the inferred differentiation dynamics. To close this gap, we developed the algorithm and Pyt...
Evaluation of false positive and false negative errors in targeted next generation sequencing [0.03%]
目标下一代测序假阳性和假阴性错误的评估
Youngbeen Moon,Young-Ho Kim,Jong-Kwang Kim et al.
Youngbeen Moon et al.
Background: Next-generation sequencing (NGS) has become an indispensable diagnostic tool across various diseases. However, sequencing and analysis errors remain major barriers to clinical implementation. In cancer diagnos...
Holotype genome of the lesula provides insights into demography and evolution of a threatened primate lineage [0.03%]
莱苏拉模式标本基因组揭示了一个受威胁灵长类谱系的人口动态及进化情况
Axel Jensen,Emma R Horton,Mardoché B Koko et al.
Axel Jensen et al.
Background: The development of genome sequencing techniques has revolutionized evolutionary biology, facilitating the study of adaptation and speciation at the genome level. Genomic data has also become a cornerstone in c...
A scalable equivariant graph network framework for precise protein function prediction [0.03%]
一种用于精确蛋白质功能预测的可扩展等变图网络框架
Zixu Ran,Xudong Guo,Tong Pan et al.
Zixu Ran et al.
Background: Protein function research helps in understanding the complex biological processes that occur within cells. However, the intricate nature of protein structures and functions, along with the rapid growth of prot...
HAlign-G: rapid and low-memory multiple-genome aligner for large-scale closely related genomes [0.03%]
HAlign-G：一种快速且低内存的大规模密切相关基因组对齐工具
Pinglu Zhang,Tong Zhou,Yanming Wei et al.
Pinglu Zhang et al.
HAlign-G is a fast and memory-efficient tool for large-scale multiple genome alignment. Using BWT-FM-LIS with an optimized K-band algorithm and star alignment strategy, it supports intra-species (HAlign-G1) and cross-species (HAlign-G2) ali...
Mitochondrial diversity of Bwindi Impenetrable National Park Mountain Gorillas [0.03%]
布恩迪姆森林国家公园山地大猩猩的线粒体多样性研究
Matthew A Knox,Valter Almeida,Gladys Kalema-Zikusoka et al.
Matthew A Knox et al.
Background: Mitochondrial DNA is a key marker for assessing genetic diversity, critical for the conservation of endangered species. This study investigates the mitochondrial diversity of the Bwindi Impenetrable National P...
Loss of IDH1 and IDH2 mutations during the evolution of metastatic chondrosarcoma [0.03%]
IDH1和IDH2在软骨肉瘤演变为转移性肿瘤过程中发生失活
William Cross,Iben Lyskjær,Christopher Davies et al.
William Cross et al.
Driver mutations in IDH1 and IDH2 are initiating events in the evolution of chondrosarcoma and several other cancer types. Here, we present evidence that mutant IDH1 is recurrently lost in metastatic central chondrosarcoma. This may reflect...
Ming-Ching C Wen,Joshua D Welch
Ming-Ching C Wen
Transposable elements (TEs) are often epigenetically repressed in eukaryotic cells, but still affect the molecular state of the cell in certain contexts. A flurry of recent studies have elucidated new effects of TE sequences in eukaryotic c...
scKGBERT: a knowledge-enhanced foundation model for single-cell transcriptomics [0.03%]
基于知识增强的单细胞转录组基础模型 scKGBERT
Yang Li,Guanyu Qiao,Hongli Du et al.
Yang Li et al.
Single-cell transcriptomics enables precise characterization of cellular heterogeneity, but current pre-trained models relying solely on expression data fail to capture gene associations. We present scKGBERT, a knowledge-enhanced foundation...
A reinforcement learning-based approach for dynamic privacy protection in genomic data sharing beacons [0.03%]
基于强化学习的基因组数据分享灯塔中的动态隐私保护方法
Masoud Poorghaffar Aghdam,Sobhan Shukueian Tabrizi,Kerem Ayöz et al.
Masoud Poorghaffar Aghdam et al.
The rise of genomic sequencing raises privacy concerns due to the identifiable nature of genomic data. The GA4GH Beacon Project enables privacy-preserving data sharing but is vulnerable to membership inference attacks that reveal individual...