相关论文: SIREN Cytoscape plugin: Interaction Type Discrimin…

Background. Dynamical models of gene regulatory networks (GRNs) are highly effective in describing complex biological phenomena and processes, such as cell differentiation and cancer development. Yet, the topological and functional…

Living cells are the product of gene expression programs that involve the regulated transcription of thousands of genes. The elucidation of transcriptional regulatory networks in thus needed to understand the cell's working mechanism, and…

The increasing availability of sequencing data of cancer samples is fueling the development of algorithmic strategies to investigate tumor heterogeneity and infer reliable models of cancer evolution. We here build up on previous works on…

To provide the Cytoscape users the possibility of integrating ITM Probe into their workflows, we developed CytoITMprobe, a new Cytoscape plugin. CytoITMprobe maintains all the desirable features of ITM Probe and adds additional flexibility…

Motivation: Network visualizations of complex biological datasets usually result in 'hairball' images, which do not discriminate network modules. Results: We present the EntOptLayout Cytoscape plug-in based on a recently developed network…

HPC systems use monitoring and operational data analytics to ensure efficiency, performance, and orderly operations. Application-specific insights are crucial for analyzing the increasing complexity and diversity of HPC workloads,…

The emergent dynamics of complex gene regulatory networks govern various cellular processes. However, understanding these dynamics is challenging due to the difficulty of parameterizing the computational models for these networks,…

Detecting and discovering new gene interactions based on known gene expressions and gene interaction data presents a significant challenge. Various statistical and deep learning methods have attempted to tackle this challenge by leveraging…

Motivation: Identifying interaction clusters of large gene regulatory networks (GRNs) is critical for its further investigation, while this task is very challenging, attributed to data noise in experiment data, large scale of GRNs, and…

The diversity of expressed genes plays a critical role in cellular specialization, adaptation to environmental changes, and overall cell functionality. This diversity varies dramatically across cell types and is orchestrated by intricate,…

Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene…

Gene Regulatory Network (GRN) plays an important role in knowing insight of cellular life cycle. It gives information about at which different environmental conditions genes of particular interest get over expressed or under expressed.…

Accurately inferring Gene Regulatory Networks (GRNs) is a critical and challenging task in biology. GRNs model the activatory and inhibitory interactions between genes and are inherently causal in nature. To accurately identify GRNs,…

Software development is a complex process that includes many different tasks besides just writing code. One of the aspects of software engineering is selecting and managing licenses for the given project. In this paper, we present Sorrel -…

The software for chemical interaction networks (SCINE) project aims at pushing the frontier of quantum chemical calculations on molecular structures to a new level. While calculations on individual structures as well as on simple relations…

SIREN is a flexible, extensible, and customizable web-based general-purpose interface for auditory data display (sonification). Designed as a digital audio workstation for sonification, synthesizers written in JavaScript using the Web Audio…

Background. Biological networks have growing importance for the interpretation of high-throughput "omics" data. Statistical and combinatorial methods allow to obtain mechanistic insights through the extraction of smaller subnetwork modules.…

Sequential interaction networks (SIN) have been commonly adopted in many applications such as recommendation systems, search engines and social networks to describe the mutual influence between users and items/products. Efforts on…

Click-through rate (CTR) Prediction is a crucial task in personalized information retrievals, such as industrial recommender systems, online advertising, and web search. Most existing CTR Prediction models utilize explicit feature…

Text-to-image diffusion models are pushing the boundaries of what generative AI can achieve in our lives. Beyond their ability to generate general images, new personalization techniques have been proposed to customize the pre-trained base…