Start & Stop: a PhysiCell and PhysiBoSS 2.0 add-on for interactive simulation control [0.03%]
启动与停止：一个用于生理细胞和生理.BOSS 2.0的交互式模拟控制插件
Riccardo Smeriglio,Roberta Bardini,Alessandro Savino et al.
Riccardo Smeriglio et al.
In computational biology, in silico simulators are vital for exploring and understanding the behavior of complex biological systems. Hybrid multi-level simulators, such as PhysiCell and PhysiBoSS 2.0, integrate multiple layers of biological...
SCATrans: semantic cross-attention transformer for drug-drug interaction predication through multimodal biomedical data [0.03%]
基于多模态生物医学数据的药物相互作用预测的语义交叉注意变压器(SCATrans)
Shanwen Zhang,Changqing Yu,Chuanlei Zhang
Shanwen Zhang
Predicting potential drug-drug interactions (DDIs) from biomedical data plays a critical role in drug therapy, drug development, drug regulation, and public health. However, it remains challenging due to the large number of possible drug co...
SEQSIM: A novel bioinformatics tool for comparisons of promoter regions-a case study of calcium binding protein spermatid associated 1 (CABS1) [0.03%]
SEQSIM：一种新的转录起始位点上游区域生物信息学比较工具——以钙结合蛋白精子细胞相关蛋白1（CABSA）为例
Joy Ramielle L Santos,Weijie Sun,A Dean Befus et al.
Joy Ramielle L Santos et al.
Background: Understanding transcriptional regulation requires an in-depth analysis of promoter regions, which house vital cis-regulatory elements such as core promoters, enhancers, and silencers. Despite the significance ...
Bigpicc: a graph-based approach to identifying carcinogenic gene combinations from mutation data [0.03%]
基于图形的癌症驱动基因组合识别方法BigPicc研究
Vladyslav Oles,Sajal Dash,Ramu Anandakrishnan
Vladyslav Oles
Genome data from cancer patients represents relationships between the presence of a gene mutation and cancer occurrence in a patient. Different types of cancer in human are thought to be caused by combinations of two to nine gene mutations....
'gitana' (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures [0.03%]
'Gitana'（系发生像工具，用于调整节点和其他布局），一个将系谱树绘制为可发布图形的工具
Cristina Galisteo,Rafael R de la Haba
Cristina Galisteo
Background: Phylogenetic trees are essential diagrams used in different sciences, such as evolutionary biology or taxonomy, and they depict the relationships between a given set of taxa sharing a common ancestor. So far, ...
GNNMutation: a heterogeneous graph-based framework for cancer detection [0.03%]
基于异构图的癌症检测框架GNNMutation
Nuriye Özlem Özcan Şimşek,Arzucan Özgür,Fikret Gürgen
Nuriye Özlem Özcan Şimşek
Background: When genes are translated into proteins, mutations in the gene sequence can lead to changes in protein structure and function as well as in the interactions between proteins. These changes can disrupt cell fun...
HLN-DDI: hierarchical molecular representation learning with co-attention mechanism for drug-drug interaction prediction [0.03%]
基于协同注意机制的分层分子表示学习方法用于药物相互作用预测
Yue Luo,Lei Deng,Zhijian Huang
Yue Luo
Background: Accurate identification of drug-drug interactions (DDIs) is critical in pharmacology, as DDIs can either enhance therapeutic efficacy or trigger adverse reactions when multiple medications are administered con...
Pytrf: a python package for finding tandem repeats from genomic sequences [0.03%]
Pytrf：一个从基因组序列中识别串联重复的Python包
Lianming Du,Dalin Sun,Jiahao Chen et al.
Lianming Du et al.
Background: Tandem repeats (TRs) are major sources of genetic variation and important genetic markers. Their expansions are not only involved in gene expression regulation but also associated with many nervous system dise...
Efficient structure learning of gene regulatory networks with Bayesian active learning [0.03%]
基于贝叶斯主动学习的基因调控网络有效结构学习方法研究
Dániel Sándor,Péter Antal
Dániel Sándor
Background: Gene regulatory network modeling is a complex structure learning problem that involves both observational data analysis and experimental interventions. Bayesian causal discovery provides a principled framework...
Universal multilayer network embedding reveals a causal link between GABA neurotransmitter and cancer [0.03%]
泛化多层网络嵌入发现了GABA神经递质与癌症之间的因果关系
Léo Pio-Lopez,Michael Levin
Léo Pio-Lopez
Background: The volume and complexity of biological data have significantly increased in recent years, often represented as network models continue to increase at a rapid pace. However, drug discovery in the context of co...