SCICONE: Single-Cell Copy Number Calling and Event History Reconstruction

Information Science, Computer Science, Medicine, Oncology, Life Sciences, Cell Biology, Bioengineering, Genetics,
single-cell sequencing   copy number variation   tumor evolution   SCICONE model   low-depth sequencing  

During tumor development, copy number alterations (CNAs) are key drivers of tumor heterogeneity and evolution. Understanding these variations is crucial for developing personalized cancer diagnostics and therapies. Single-cell sequencing technology offers the highest resolution for copy number analysis, down to the individual cell level. However, l...

GCLink: A Graph Contrastive Link Prediction Framework for Gene Regulatory Network Inference

Information Science, Computer Science, Artificial Intelligence, Life Sciences, Bioengineering, Genetics,
Gene Regulatory Networks   Single-cell RNA Sequencing   Graph Contrastive Learning   Link Prediction   Machine Learning  

Research Background Gene Regulatory Networks (GRNs) are crucial tools for understanding the complex biological processes within cells. They reveal the interactions between Transcription Factors (TFs) and target genes, thereby controlling gene transcription and regulating cellular behavior. With the advancement of single-cell RNA sequencing (scRNA-s...

Trajectory Alignment of Gene Expression Dynamics

Medicine, Life Sciences, Cell Biology, Biochemistry, Bioengineering, Immunology, Genetics, Microbiology,
gene expression   single-cell transcriptomics   trajectory alignment   bioinformatics   differentially expressed genes  

The advent of single-cell RNA sequencing (scRNA-seq) technology has provided unprecedented resolution for studying gene expression dynamics during cell development and differentiation. However, due to the complexity of biological processes, cell developmental trajectories under different conditions are often asymmetric, posing challenges for data i...

Efficient Storage and Regression Computation for Population-Scale Genome Sequencing Studies

Information Science, Computer Science, Life Sciences, Bioengineering, Genetics,
genome sequencing   data compression   regression analysis   computational efficiency   rare variants  

With the increasing availability of large-scale population biobanks, the potential of Whole Genome Sequencing (WGS) data in human health and disease research has been significantly enhanced. However, the massive computational and storage demands of WGS data pose significant challenges to research institutions, especially those with limited funding ...

Clinical and Genetic Markers of Vascular Toxicity in Glioblastoma Patients: Insights from NRG Oncology RTOG-0825

Medicine, Neurology, Oncology, Life Sciences, Genetics,
Glioblastoma   Vascular Toxicity   Genetic Markers   Hypertension   Thrombosis   Clinical Prediction Model   Genome-Wide Association Study  

Clinical and Genetic Markers of Vascular Toxicity in Glioblastoma Patients: Insights from NRG Oncology RTOG-0825 Academic Background Glioblastoma (GBM) is a highly aggressive form of brain cancer, accounting for nearly 80% of malignant primary brain tumors. Despite standard treatments including surgical resection, radiotherapy, and chemotherapy, th...

Genomic Reanalysis of a Pan-European Rare-Disease Resource Yields New Diagnoses

Medicine, Life Sciences, Genetics,
rare diseases   genomic reanalysis   European collaboration   diagnostic yield   genetic variants  

European Genomic Reanalysis of Rare Diseases: New Diagnoses and Future Blueprint Academic Background Rare diseases are defined as conditions affecting a very small proportion of the population, with the European Union setting the threshold at fewer than 50 individuals per 100,000. Despite the vast diversity of rare diseases (over 6,000 types), more...