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In the last ten years, the field of proteomics has expanded at a rapid rate. A range of exciting new technology has been developed and enthusiastically applied to an enormous variety of biological questions. However, the degree of…
Mass spectrometry (MS) plays a critical role in molecular identification, significantly advancing scientific discovery. However, structure elucidation from MS data remains challenging due to the scarcity of annotated spectra. While…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…
The selection, development, or comparison of machine learning methods in data mining can be a difficult task based on the target problem and goals of a particular study. Numerous publicly available real-world and simulated benchmark…
Magnetic resonance imaging (MRI) is indispensable for diagnosing and planning treatment in various medical conditions due to its ability to produce multi-series images that reveal different tissue characteristics. However, integrating these…
Link prediction is an open problem in the complex network, which attracts much research interest currently. However, little attention has been paid to the relation between network structure and the performance of prediction methods. In…
The past two decades have witnessed the rapid development of personalized recommendation techniques. Despite significant progress made in both research and practice of recommender systems, to date, there is a lack of a widely-recognized…
The customers and users need for new products and services according to high-quality standards have increased in the last time. In that sense, the production processes must be aligned with the organization and development process in order…
Mass spectrometry-based metabolomic analysis depends upon the identification of spectral peaks by their mass and retention time. Statistical analysis that follows the identification currently relies on one main peak of each compound.…
In cancer therapeutics, protein-metal binding mechanisms critically govern the pharmacokinetics and targeting efficacy of drugs, thereby fundamentally shaping the rational design of anticancer metallodrugs. While conventional laboratory…
Large Language Models (LLMs) have demonstrated their transformative potential across numerous disciplinary studies, reshaping the existing research methodologies and fostering interdisciplinary collaboration. However, a systematic…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by…
Mass spectrometry (MS) based single-cell proteomics (SCP) explores cellular heterogeneity by focusing on the functional effectors of the cells - proteins. However, extracting meaningful biological information from MS data is far from…
Many proteins carry out their biological functions by forming the characteristic tertiary structures. Therefore, the search of the stable states of proteins by molecular simulations is important to understand their functions and…
Complex networks considering both positive and negative links have gained considerable attention during the past several years. Community detection is one of the main challenges for complex network analysis. Most of the existing algorithms…
Protein footprinting is a new methodology that is based on probing, typically with the use of mass spectrometry, of reactivity of different aminoacid residues to a modifying reagent. Data thus obtained allow one to make inferences about…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
Over the last decade, proteomic analysis of single cells by mass spectrometry transitioned from an uncertain possibility to a set of robust and rapidly advancing technologies supporting the accurate quantification of thousands of proteins.…
Machine learning (ML) is increasingly adopted in scientific research, yet the quality and reliability of results often depend on how experiments are designed and documented. Poor baselines, inconsistent preprocessing, or insufficient…