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While most studies emphasize on certain aspects of Pathogen-Host Interactions (PHI), such as the preferential attachment of bacteria or virus to its human receptor homolog, studies have attempted to methodically classify interactions among…

Molecular Networks · Quantitative Biology 2016-09-13 S. Chatterjee , B. S. Sanjeev

The development of therapeutic targets for COVID-19 treatment is based on the understanding of the molecular mechanism of pathogenesis. The identification of genes and proteins involved in the infection mechanism is the key to shed out…

Biomolecules · Quantitative Biology 2021-05-19 Jayanta Kumar Das , Swarup Roy , Pietro Hiram Guzzi

Endeavoring toward a transferable, predictive coarse-grained explicit-chain model for biomolecular condensates underlain by liquid-liquid phase separation (LLPS), we conducted multiple-chain simulations of the N-terminal intrinsically…

Biomolecules · Quantitative Biology 2020-12-10 Suman Das , Yi-Hsuan Lin , Robert M. Vernon , Julie D. Forman-Kay , Hue Sun Chan

The strategic induction of cell death serves as a crucial immune defense mechanism for the eradication of pathogenic infections within host cells. Investigating the molecular mechanisms underlying immunogenic cell pathways has significantly…

Molecular Networks · Quantitative Biology 2024-02-08 Chuang Li , Yichen Wei , Chao Qin , Shifan Chen , Xiaolong Shao

Bacteria produce a range of proteolytic enzymes, for which a number human equivalent or structurally similar examples exist and the primary focus of this study was to analyse the published literature to find proteolytic enzymes,…

Biomolecules · Quantitative Biology 2014-06-06 Maria Antony Dhivyan JE

Antimicrobial peptides (AMPs) have intrigued researchers for decades due to the contradiction between their high potential against resistant bacteria and the inability to find a structure-function relationship for the development of an…

Soft Condensed Matter · Physics 2025-02-14 Marta V. Volovik , Zaret G. Denieva , Oleg V. Kondrashov , Sergey A. Akimov , Oleg V. Batishchev

Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection…

Machine Learning · Computer Science 2021-11-30 Thi Ngan Dong , Graham Brogden , Gisa Gerold , Megha Khosla

Antimicrobial peptides (AMPs) are anti-infectives that have potential as a novel and untapped class of biotherapeutics. Modes of action of antimicrobial peptides imply interaction with cell envelope. Comprehensive understanding of…

Biomolecules · Quantitative Biology 2020-05-11 Malak Pirtskhalava , Boris Vishnepolsky , Maya Grigolava

Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…

Molecular Networks · Quantitative Biology 2023-10-05 Rodrigo Henrique Ramos , Cynthia de Oliveira Lage Ferreira , Adenilso Simao

The innate immune system is vital to rapidly responding to pathogens and Toll-like receptors (TLRs) are a critical component of this response. Nanovesicular exosomes play a role in immunity, but to date their exact contribution to the…

Characterization of host responses associated with severe malaria through an integrative approach is necessary to understand the dynamics of a \textit{Plasmodium cynomolgi} infection. In this study, we conducted temporal immune profiling,…

Tissues and Organs · Quantitative Biology 2017-07-03 Yi H. Yan , Diego M. Moncada , Elizabeth D. Trippe , Juan B. Gutierrez

Infections depend on interactions between pathogen and host proteins, but comprehensively mapping these interactions is challenging and labor intensive. Many biological networks have hierarchical, scale-free structure, so we developed a…

Molecular Networks · Quantitative Biology 2025-11-19 Xiaoqiong Xia , Cesar de la Fuente-Nunez

Current CoVID-19 pandemic is spreading rapidly worldwide, and it may become one of the largest pandemic events in modern history if out of control. It appears most of the SARS-CoV2 virus infection resulted deaths are mainly due to…

Other Quantitative Biology · Quantitative Biology 2020-09-28 Sam-Shajing Sun

Air pollution, particularly airborne particulate matter (PM), poses a significant threat to public health globally. It is crucial to comprehend the association between PM-associated toxic components and their cellular targets in humans to…

Machine Learning · Computer Science 2024-12-24 Yan Zhu , Shihao Wang , Yong Han , Yao Lu , Shulan Qiu , Ling Jin , Xiangdong Li , Weixiong Zhang

The initial reaction of the body to pathogenic microbial infection or severe tissue trauma is an acute inflammatory response. The magnitude of such a response is of critical importance, since an uncontrolled response can cause further…

Pattern analysis of tandem repeats in gene is an indispensable computational approach to the understanding of the gene expression and pathogenesis of diseases. This research applied a computational motif model and database techniques to…

Genomics · Quantitative Biology 2013-02-11 Sim-Hui Tee

The innate immune system, acting as the first line of host defense, senses and adapts to foreign challenges through complex intracellular and intercellular signaling networks. Endotoxin tolerance and priming elicited by macrophages are…

Molecular Networks · Quantitative Biology 2017-08-23 Yan Fu , Trevor Glaros , Meng Zhu , Ping Wang , Zhanghan Wu , John J Tyson , Liwu Li , Jianhua Xing

Uncontrolled, excessive production of pro-inflammatory mediators from immune cells and traumatized tissues can cause systemic inflammatory issues like sepsis, one of the ten leading causes of death in the United States and one of the three…

Tissues and Organs · Quantitative Biology 2019-08-22 Atanaska Dobreva , Renee Brady , Kamila Larripa , Charles Puelz , Jesper Mehlsen , Mette S. Olufsen

The rapid evolution and global impact of coronaviruses, notably SARS-CoV-1 and SARS-CoV-2, underscore the importance of understanding their molecular mechanisms in detail. This study focuses on the receptor-binding motif (RBM) within the…

Biological Physics · Physics 2026-03-16 Rafael B. Frigori

Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…

Computation and Language · Computer Science 2025-04-24 Gilchan Park , Byung-Jun Yoon , Xihaier Luo , Vanessa López-Marrero , Shinjae Yoo , Shantenu Jha
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