A brief review and comparative analysis of RNA secondary structure prediction tools [0.03%]
RNA二级结构预测工具简评及比较分析
Pranav Ballaney,Gourav Saha,Vaibhav Kulshrestha et al.
Pranav Ballaney et al.
Ribonucleic acid (RNA) lies at the heart of the central dogma. It spans the breadth of biological functions, from information storage to gene regulation and catalysis. RNA molecules must attain specific structures to perform these functions...
An algorithm for peptide de novo sequencing from a group of SILAC labeled MS/MS spectra [0.03%]
一种从一组SILAC标记的MS/MS谱图中进行肽从头测序的新算法
Fang Han,Kaizhong Zhang
Fang Han
Shotgun proteomics coupled with high-performance liquid chromatography and mass spectrometry has been instrumental in identifying proteins in complex mixtures. Effective computational approaches are required to automate the spectra interpre...
Subhash Kak
Subhash Kak
The helical coil is ubiquitous in biological and natural systems, and it is often the basic form in complex structures. This paper considers the question of its dimensionality, D, in biological information as the helical coil goes through r...
M3-20M: A large-scale multi-modal molecule dataset for AI-driven drug design and discovery [0.03%]
大规模的多模态分子数据集M3-20M用于人工智能驱动的药物设计与发现
Siyuan Guo,Lexuan Wang,Chang Jin et al.
Siyuan Guo et al.
This paper introduces M3-20M, a large-scale Multi-Modal Molecule dataset that contains over 20 million molecules, with the data mainly being integrated from existing databases and partially generated by large language models. Designed to su...
Prediction and annotation of alternative transcription starts and promoter shift in the chicken genome [0.03%]
鸡基因组中可变转录起始和启动子转换的预测及注释
Valentina A Grushina,Ivan S Yevshin,Oleg A Gusev et al.
Valentina A Grushina et al.
Promoter shifting, characterized by alterations in Transcription Start Site (TSS) coordinates, is a well-documented phenomenon. The impact and statistical significance of promoter shifting can be assessed through analysis of Cap Analysis of...
Computational modeling and dynamical analysis for B. subtilis competence genic regulation circuit with multiple time delays and external noisy regulation [0.03%]
具有多个时间延迟和外部噪声调控的枯草芽孢杆菌（B. subtilis）受性基因调控回路的计算建模与动力学分析
Na Zhao,Haihong Liu,Fang Yan
Na Zhao
Bacillus subtilis (B. subtilis), a bacterium known to enter a competent state spontaneously, has garnered significant attention due to its intricate internal regulatory mechanisms. This study proposes a six-dimensional continuous delay diff...
Paulo Henrique Ribeiro,Adenilso Simao
Paulo Henrique Ribeiro
Cancer is a complex disease that progresses through Darwinian evolution in cells with genetic mutations, leading to the development of multiple distinct cell populations within tumors, a process known as clonal evolution. While computationa...
Cross-cellular analysis of chromatin accessibility markers H3K4me3 and DNase in the context of detecting cell-identity genes: An "all-or-nothing" approach [0.03%]
染色体可访问性标记H3K4me3和DNase的跨细胞分析：在检测细胞身份基因背景下的“全部或无”的方法
Boon How Low,Kaushal Krishna Kaliskar,Stefano Perna et al.
Boon How Low et al.
Cell identity is often associated to a subset of highly-expressed genes that define the cell processes, as opposed to essential genes that are always active. Cell-specific genes may be defined in opposition to essential genes, or via experi...
DDINet: Drug-drug interaction prediction network based on multi-molecular fingerprint features and multi-head attention centered weighted autoencoder [0.03%]
基于多分子指纹特征和多头注意力集中式自编码器的药物相互作用预测网络
K Soni Sharmila,Thanga Revathi S,Pokkuluri Kiran Sree
K Soni Sharmila
Drug-drug interactions (DDIs) pose a major concern in polypharmacy due to their potential to cause unexpected side effects that can adversely affect a patient's health. Therefore, it is crucial to identify DDIs effectively during the early ...
Computation and analysis of stationary and periodic solutions of the COVID-19 infection dynamics model [0.03%]
COVID-19感染动力学模型的平稳和周期解的计算与分析
Michael Khristichenko,Yuri Nechepurenko,Dmitry Grebennikov et al.
Michael Khristichenko et al.
In this work, we search for the conditions for the occurrence of long COVID using the recently developed COVID-19 disease dynamics model which is a system of delay differential equations. To do so, we search for stable stationary or periodi...