Epistasis and co-adaptation in bacterial genome evolution - Nature Reviews Genetics Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic interactions into population-...

#Epistasis and co-adaptation in bacterial genome #evolution

#evoSky #mevoSky #microSky

www.nature.com/articles/s41...

Epistasis and co-adaptation in bacterial genome evolution - Nature Reviews Genetics Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic interactions into population-...

Epistasis and co-adaptation in bacterial genome evolution www.nature.com/articles/s41... #epistasis #microbiology #evolution #genomics

🔬 Paper: doi.org/10.1038/s414...

Check out the code and data: 💻 GitHub: github.com/Xavier-Caste...

#ComputationalBiology #Epistasis #OpenScience

PNAS Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

Predicting epistasis across proteins by structural logic - PNAS www.pnas.org/doi/10.1073/... #epistasis

Unraveling Epistatic Interactions Between Sites Under Drug-Dependent Selection in the Mycobacterium tuberculosis Genome Abstract. Many Mycobacterium tuberculosis genome sites experience different selective forces depending on whether a patient is treated with antibiotics. He

Popova et al. studied the evolution of M. tuberculosum under drug pressure using a unified phylogeny-based approach to reveal both drug-dependent evolution and epistatic interactions between sites.

🔗 doi.org/10.1093/molbev/msaf264

#evobio #molbio #epistasis

Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis Epistasis plays an important role in the genetic architecture of common human diseases and can be viewed from two perspectives, biological and statistical, each derived from and leading to different ...

I very much enjoyed writing this paper 20 years ago. One of my favorites & still very relevant to embracing the complexity of genetic architecture that is widely ignored onlinelibrary.wiley.com/doi/abs/10.1... #genetics #complexity #epistasis

Widespread epistasis shapes RNA polymerase II active site function and evolution - Nature Communications The active site of RNA Polymerase II is highly conserved. Here the authors show that mutations can propagate effects across the enzyme and alter genetic behavior of distal residues, demonstrating plas...

Final version of Bingbing Duan’s main thesis work is out now now in Nature Communications @natureportfolio.nature.com www.nature.com/articles/s41... I’m so pleased with this study that we’ve been working on for so long #epistasis #transcription #geneexpression 1/

Intramolecular Epistatic Interactions in Genetic Diseases onlinelibrary.wiley.com/doi/10.1002/... #epistasis #genetics

n summary:
Cryptic genetic variation — both regulatory and coding variation— biases the future of redundant gene duplicates by altering the effects of new mutations (12/12) #evolution #epistasis #genetics

How Computational Experiments Can Improve Our Understanding of the Genetic Architecture of Common Human Diseases Abstract. Susceptibility to common human diseases such as cancer is influenced by many genetic and environmental factors that work together in a complex manner. The state of the art is to perform a ge...

One of my favorite research projects (2020) direct.mit.edu/artl/article... #epistasis #bioinformatics

A genotype-phenotype transformer to assess and explain polygenic risk Genome-wide association studies have linked millions of genetic variants to biomedical phenotypes, but their utility has been limited by lack of mechanistic understanding and widespread epistatic inte...

A genotype-phenotype transformer to assess and explain polygenic risk www.biorxiv.org/content/10.1... #genetics #genomics #bioinformatics #gwas #prs #epistasis

Bring back the phenotype When thinking about evolutionary change, many practicing biologists will focus on changes in allele frequencies over time. This gene-centric view of evolution has strongly impacted how evolution (and...

"In this viewpoint, we join recent criticisms of the gene-centric view & call for reinstalling a phenotypic view of evolution" nph.onlinelibrary.wiley.com/doi/10.1111/... #genetics #genomics #evolution #epistasis

🧩 We made two key observations for the mechanism:
(1) NUDT5 binds to and oligomerizes with #PPAT, the first and rate-limiting enzyme in purine synthesis
(2) PPAT depletion rescues pyrimidine synthesis in NUDT5-KO cells #epistasis

But why pyrimidines?!?

5/9

Studying the genetic basis of ecological interactions with intergenomic epistasis

https://doi.org/10.1111/oik.10835

#GxGInteractions #SpeciesInteractions #CoEvolution #HostPathogenInteractions #Epistasis #EcoEvolutionaryDynamics

Join us tomorrow 👇
#Genetics #Omics #Parkinsons #Epistasis

Epistatic hotspots organize antibody fitness landscape and boost evolvability - PubMed The course of evolution is strongly shaped by interaction between mutations. Such epistasis can yield rugged sequence-function maps and constrain the availability of adaptive paths. While theoretical ...

Epistatic hotspots organize antibody fitness landscape and boost evolvability pubmed.ncbi.nlm.nih.gov/39773024/ #epistasis

PNAS Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

A combinatorially complete epistatic fitness landscape in an enzyme active site www.pnas.org/doi/10.1073/... #epistasis

Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis BioEssays is a review-and-discussion journal renowned for its collection of contemporary and forward-looking reviews on molecular, genetic and cellular biology.

Our TBT 2005 paper on "Traversing the conceptual divide between biological & statistical epistasis: systems biology & a more modern synthesis" onlinelibrary.wiley.com/doi/10.1002/... #epistasis #genetics #complexity #TBT

BridGE: a pathway-based analysis tool for detecting genetic interactions from GWAS - Nature Protocols Genetic interactions have been found to influence phenotypes in a variety of systems, yet their specific contribution to complex diseases remains unclear. This protocol describes Bridging Gene sets wi...

BridGE: a pathway-based analysis tool for detecting genetic interactions from GWAS www.nature.com/articles/s41... #epistasis #genetics #gwas #bioinformatics

Next-Gen GWAS: full 2D epistatic interaction maps retrieve part of missing heritability and improve phenotypic prediction - Genome Biology The problem of missing heritability requires the consideration of genetic interactions among different loci, called epistasis. Current GWAS statistical models require years to assess the entire combin...

Next-Gen GWAS: full 2D epistatic interaction maps retrieve part of missing heritability and improve phenotypic prediction genomebiology.biomedcentral.com/articles/10.... #gwas #epistasis #genetics #bioinformatics

Epistasis arises from shifting the rate-limiting step during enzyme evolution of a β-lactamase Nature Catalysis - The reasons for epistasis, wherein mutations interact non-additively, are often not fully understood. Now it is found that shifting the rate-limiting step from substrate binding...

Are you interested in how #epistasis shapes the AMR evolution?

We showed that epistasis can be caused by independently modulating substrate binding and the chemical step ultimately changing the rate-limiting step in the catalytic cycle. @NatureCatalysis

Full read: rdcu.be/dzqjk

Redirecting

Factorizing polygenic epistasis improves prediction and uncovers biological pathways in complex traits - AJHG linkinghub.elsevier.com/retrieve/pii... #epistasis #gwas

Pairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis Cancer occurs as a consequence of multiple somatic mutations that lead to uncontrolled cell growth. Mutual exclusivity and co-occurrence of mutations …

Pairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis www.sciencedirect.com/science/arti... #epistasis #cancer

Multiple genes in a single GWAS risk locus synergistically mediate aberrant synaptic development and... The mechanistic tie between genome-wide association study (GWAS)-implicated risk variants and disease-relevant cellular phenotypes remains largely unk…

Multiple genes in a single GWAS risk locus synergistically mediate aberrant synaptic development and function in human neurons www.sciencedirect.com/science/arti... #gwas #epistasis #schizophrenia