AIMC Topic: Evolution, Molecular
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Systematic Analysis and Prediction of In Situ Cross Talk of O-GlcNAcylation and Phosphorylation.
BioMed research international
Oct 27, 2015
Reversible posttranslational modification (PTM) plays a very important role in biological process by changing properties of proteins. As many proteins are multiply modified by PTMs, cross talk of PTMs is becoming an intriguing topic and draws much at...
Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning.
Bioinformatics (Oxford, England)
Aug 14, 2015
MOTIVATION: Protein contact prediction is important for protein structure and functional study. Both evolutionary coupling (EC) analysis and supervised machine learning methods have been developed, making use of different information sources. However...
Better prediction of functional effects for sequence variants.
BMC genomics
Jun 18, 2015
Elucidating the effects of naturally occurring genetic variation is one of the major challenges for personalized health and personalized medicine. Here, we introduce SNAP2, a novel neural network based classifier that improves over the state-of-the-a...
Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework.
PloS one
Apr 20, 2015
The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation o...
Bridging scales in cancer progression: mapping genotype to phenotype using neural networks.
Seminars in cancer biology
May 12, 2014
In this review we summarise our recent efforts in trying to understand the role of heterogeneity in cancer progression by using neural networks to characterise different aspects of the mapping from a cancer cells genotype and environment to its pheno...
Comprehensive Characterization of Somatic Mutation Timing Reveals the Evolutionary Trajectory of Lung Adenocarcinoma in Chinese Patients.
Cancer research
Aug 1, 2025
UNLABELLED: Lung adenocarcinoma (LUAD) is a heterogeneous disease with substantial genomic differences between individuals of Chinese and European ancestries. Deciphering the timing of driver mutations may lead to insights into tumor evolution that c...
SARS-CoV-2: lessons in virus mutation prediction and pandemic preparedness.
Current opinion in immunology
Aug 1, 2025
The COVID-19 pandemic has prompted an unprecedented global response. In particular, extraordinary efforts have been dedicated toward monitoring and predicting variant emergence due to its huge impact, particularly for vaccine escape. Broadly, we clas...
Evolutionary accumulation modeling in AMR: machine learning to infer and predict evolutionary dynamics of multi-drug resistance.
mBio
Jun 11, 2025
Can we understand and predict the evolutionary pathways by which bacteria acquire multi-drug resistance (MDR)? These questions have substantial potential impact in basic biology and in applied approaches to address the global health challenge of anti...
Computationally designed proteins mimic antibody immune evasion in viral evolution.
Immunity
Jun 10, 2025
Recurrent waves of viral infection necessitate vaccines and therapeutics that remain effective against emerging viruses. Our ability to evaluate interventions is currently limited to assessments against past or circulating variants, which likely diff...
MEGA-GPT: Artificial Intelligence Guidance and Building Analytical Protocols Using MEGA Software.
Molecular biology and evolution
Jun 4, 2025
Over the past three decades, the Molecular Evolutionary Genetics Analysis (MEGA) software has evolved into a powerful tool with an ever-expanding suite of functionalities. Yet, despite its user-friendly design and widespread adoption by researchers a...
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