T. Okada

Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England

This paper develops a method to estimate genetic drift in SARS-CoV-2 transmission using lineage frequency time series and applies it to genomic data from England, finding consistently higher genetic drift than expected.

Actin dynamics switches two distinct modes of endosomal fusion in yolk sac visceral endoderm cells

Patterns of change in regulatory modules of chemical reaction systems induced by network modification

This paper develops a method to identify changes in buffering structures of chemical reaction networks caused by single degradation reactions, enabling prediction of regulatory changes without kinetic assumptions.

Evasion of APOBEC1-mediated Intrinsic Immunity by a Herpesvirus Uracil DNA Glycosylase Is a Determinant of Viral Encephalitis

This study shows that HSV-1's vUNG enzyme evades APOBEC1 immunity by preventing DNA editing, leading to more severe encephalitis in mice.

Engineering a highly durable adeno-associated virus receptor for analytical applications

The paper engineers a durable AAV receptor for analyzing AAV-AAVR interactions, showing diverse binding affinities among AAV serotypes and enabling quality checks and purification of AAV vectors.

Distance-based global analysis of consistent cis-bonds in protein backbones

The paper develops a method to detect and confirm cis-bonds in proteins using experimental coordinates, revealing trends in cis content and limits per polypeptide length.

Non-glycosylated Seipin to Cause a Motor Neuron Disease Induces ER stress and Apoptosis by Inactivating the ER Calcium Pump SERCA2b

Dynamic sampling bias and overdispersion induced by skewed offspring distributions

The paper analyzes how skewed offspring distributions affect allele frequency dynamics and shows that dynamic sampling bias leads to overdispersion in genetic data.

Repertoire of morphable proteins in an organism

The paper analyzes the structural variability of over a thousand E. coli proteins using a 'UnMorphness Factor' to understand the balance of rigidity and flexibility in an organism.

Evaluation of variability in high resolution protein structures by global distance scoring

This study evaluates variability in high-resolution protein structures using intramolecular distance scoring to enable global comparison of dynamics across proteins and species.