Y. Yue

Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models

This study analyzes transfer learning in protein language models, finding that downstream task performance often relies on early pretraining features rather than scaling with pretraining duration.

DeCOIL: Optimization of Degenerate Codon Libraries for Machine Learning-Assisted Protein Engineering

DeCOIL optimizes degenerate codon libraries for ML-assisted protein engineering to generate diverse and high-fitness protein variants.

Farnesoid X receptor agonism prevents neutrophil extracellular traps via reduced sphingosine-1-phosphate in chronic kidney disease

This study shows FXR agonism reduces kidney NETosis in male mice by inhibiting S1P signaling, but not in females.

Redefining hematopoietic progenitor cells and reforming the hierarchy of hematopoiesis

This study redefines hematopoietic progenitor cells and reformulates the hematopoiesis hierarchy using a transcriptional atlas, identifying key transcription factors and distinct lineage commitment processes.

Autoinhibited kinesin-1 adopts a hierarchical folding pattern

This study determines the structure of autoinhibited kinesin-1 using XL-MS, EM, and AlphaFold, showing how light chains stabilize the inhibited state and how activation requires disrupting multiple domain interactions.

TRPV1-mediated sonogenetic neuromodulation of motor cortex in freely moving mice

This study demonstrates that TRPV1-mediated sonogenetics can safely modulate motor cortex activity in mice, inducing behavioral changes without significant tissue damage.

Chromosome-level genome assembly of Euphorbia peplus, a model system for plant latex, reveals that relative lack of Ty3 transposons contributed to its small genome size

This paper presents a chromosome-level genome assembly of Euphorbia peplus, identifies a gene cluster for ingenol mebutate biosynthesis, and explains its small genome size through restricted Ty3 transposon expansion.

Long-term passaging of replication competent pseudo-typed SARS-CoV-2 reveals the antiviral breadth of monoclonal and bispecific antibody cocktails

This study evaluates the antiviral breadth of monoclonal and bispecific antibody cocktails against SARS-CoV-2 variants using a replication competent VSV-SARS-CoV-2 model, showing resistance to mutation in two cocktails.

Efficient Neutralization of SARS-CoV-2 Omicron and Other VOCs by a Broad Spectrum Antibody 8G3

This study evaluates the neutralization efficacy of antibodies against SARS-CoV-2 Omicron and other variants, finding that antibody 8G3 maintains broad neutralizing activity while EUA antibodies lose effectiveness.

Comprehensive Evaluation of ACE2-Fc Combination with Neutralization Antibody on Broad Protection against SARS-CoV-2 and Its Variants

This study evaluates ACE2-Fc combined with neutralizing antibodies against SARS-CoV-2 variants, showing enhanced neutralization and resistance to escape mutations.

A kinesin-1 variant reveals motor-induced microtubule damage in cells

This study shows a kinesin-1 variant causes microtubule damage in cells, leading to breakage and fragmentation, suggesting evolutionary pressure against such variants.

Broad ultra-potent neutralization of SARS-CoV-2 variants by monoclonal antibodies specific to the tip of RBD

This paper identifies a monoclonal antibody, 2G1, that neutralizes all SARS-CoV-2 variants with high potency and describes its mechanism of action and therapeutic efficacy in animal models.

Mycobacteria tuberculosis PPE36 modulates host inflammation by promoting E3 ligase Smurf1-mediated MyD88 degradation

This study identifies PPE36 as a Mycobacterium tuberculosis protein that modulates host inflammation by promoting Smurf1-mediated MyD88 degradation, enhancing bacterial survival.

A simple Agrobacterium-mediated stable transformation technique for the hornwort model Anthoceros agrestis

This paper develops a stable transformation technique for the hornwort Anthoceros agrestis using Agrobacterium, enabling genetic studies of molecular mechanisms in land plants.

In vitro and in vivo characterization of a recombinant rhesus cytomegalovirus containing a complete genome

This paper constructs a full-length rhesus cytomegalovirus (RhCMV) by repairing mutations in the 68-1 strain and shows it replicates more effectively in vivo compared to the passaged strain.

Forkhead box O1-mediated ubiquitination suppresses RIG-I-mediated antiviral immune responses via its DNA binding domain

The paper withdraws its manuscript due to the need for further experiments to validate conclusions.

The YdiU Domain Modulates Bacterial Stress Signaling through Mn2+-dependent UMPylation

This paper identifies YdiU as a Mn2+-dependent UMPylase in Salmonella that modulates chaperone function through UMPylation, enhancing stress resistance.

Late-life restoration of mitochondrial function reverses cardiac dysfunction in old mice

This study shows that treating old mice with SS-31 improves cardiac diastolic function by reducing mitochondrial oxidative stress and restoring redox balance.

Microtubule binding of the kinesin-4 KIF7 and its regulation by autoinhibition

This study shows that KIF7, an atypical kinesin, is autoinhibited to prevent microtubule binding and microtubule dynamics alteration in cells.

Autoinhibition of kinesin-1 is essential to the dendrite-specific localization of Golgi outposts

The paper shows that autoinhibition of kinesin-1 is crucial for dendrite-specific Golgi outpost localization, preventing their mislocalization to axons.