Daily Digest | February 25, 2023

Network expansion of genetic associations defines a pleiotropy map of human cell biology | Nature Genetics

Interacting proteins tend to have similar functions, influencing the same organismal traits. Interaction networks can be used to expand the list of candidate trait-associated genes from genome-wide association studies. Here, researchers performed network-based expansion of trait-associated genes for 1,002 human traits showing that this recovers known disease genes or drug targets.

Research paper

 

On the Effectiveness of Compact Biomedical Transformers | Bioinformatics

Language models pre-trained on biomedical corpora, such as BioBERT, have recently shown promising results on downstream biomedical tasks. In this paper researchers introduce six lightweight models, namely, BioDistilBERT, BioTinyBERT, BioMobileBERT, DistilBioBERT, TinyBioBERT, and CompactBioBERT which are obtained either by knowledge distillation from a biomedical teacher or continual learning on the Pubmed dataset. They evaluate all of our models on three biomedical tasks and compare them with BioBERT-v1.1 to create the best efficient lightweight models that perform on par with their larger counterparts.

Research paper

 

Protein complexes in cells by AI-assisted structural proteomics | Molecular Systems Biology

An integrative approach using crosslinking mass spectrometry (MS), co-fractionation MS and Alphafold-Multimer discovers novel protein complexes and their topologies in the model gram-positive bacterium Bacillus subtillis.

Research paper

 

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