6 Aug 2023

Some papers and resources from the past couple of weeks! Big backlog here, something for everyone here:

Genetic effects on molecular network states explain complex traits. Molecular Systems Biology papers are usually fun (imo). Here, the authors show how mutations result in system-level homeostatic adjustments that can actually be described in terms of PKA and TOR signaling. It’s an interesting exploration into how exactly genotype manifests into phenotype.

https://www.embopress.org/doi/full/10.15252/msb.202211493

https://twitter.com/AndreasBeyer012/status/1683417817666732035

 

Evolutionary histories of breast cancer and related clones. A tour de force where the authors apply phylogenomics to reconstruct the evolution of breast cancer cell lineages over the lifetime (!) of human patients. What surprised and interested me (a non-cancer biologist) the most was that although all cancer cells descended from a common ancestor with certain driver mutations, that common ancestor was non-cancerous, so the cancer cells comprising the malignancy actually evolved in multiple independent instances of parallel evolution. This leads to tumor heterogeneity.

https://www.nature.com/articles/s41586-023-06333-9

 

Potent pan huACE2-dependent sarbecovirus neutralizing monoclonal antibodies isolated from a BNT162b2-vaccinated SARS survivor. A single monoclonal antibody capable of hitting the RBD of SARS, MERS, and COVID-19 viruses! And it binds to a motif that seems involved in quaternary structure interactions, so is probably mutationally constrained holy shit holy shit

https://www.science.org/doi/10.1126/sciadv.ade3470

 

Inference of infectious disease transmission using multiple genomes per host. Thanks Alyssa for sharing this one! The authors build on existing approaches for inferring pathogen (or I suppose just generally endosymbiont) transmission networks from microbial sequencing data. Their innovations consist of using a model that accounts for unseen intrahost and inter-host evolution as well as strong transmission bottlenecks. Definitely relevant to some of my current work.

https://www.biorxiv.org/content/10.1101/2023.07.28.550949v1

 

Preventing antimalarial drug resistance with triple artemisinin-based combination therapies. I’ve kept an eye on Maciej Boni’s work for a while, big fan. Here, they use stochastic agent-based models to show how triple-combination therapies can slow the spread of artemisinin resistance in malaria parasites. I got to meet Maciek recently and he showed me work where they’re actually applying this in a real context, with colleagues in Rwanda.

https://www.nature.com/articles/s41467-023-39914-3

Tweetorial: https://twitter.com/maciekboni/status/1687289671724777472

 

Towards a post-pandemic future for global pathogen genome sequencing. A nice review on the post-covid emergence state of genomic epidemiology.

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002225

 

Shiny apps for teaching evolution. A collection of useful tools for classes, definitely hope to use these in the future!

https://bolnicklabresources.wordpress.com/2023/08/04/shiny-apps-for-teaching-evolution/

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