J. C. Smith

TCR-H: Machine Learning Prediction of T-cell Receptor Epitope Binding on Unseen Datasets

TCR-H is a SVM model trained on experimentally validated non-binders to predict TCR epitope binding, achieving high AUC on unseen test sets.

A drug's most potent target is not necessarily the source of its anti-cancer activity

This study shows that ralimetinib's anti-cancer effect is due to EGFR inhibition, not p38, and highlights the need for comprehensive profiling to determine drug mechanisms.

Tailoring Tfh Profiles Enhances Antibody Persistence to a Clade C HIV-1 Vaccine in Rhesus Macaques

This study shows that inducing GC Tfh1 cells with MPLA+QS-21 adjuvant leads to higher and longer-lasting HIV-1 Env antibodies in rhesus macaques compared to CAF01.

MCAK Inhibitors Induce Aneuploidy in Triple Negative Breast Cancer Models

This study identifies three MCAK inhibitors that induce aneuploidy in TNBC cells, reduce clonogenic survival, and sensitize cells to paclitaxel.

Pose prediction accuracy in ligand docking to RNA

This study evaluates pose prediction accuracy of docking protocols for RNA-small molecule complexes, finding rDock slightly better than Vina for known structures but both underperform compared to protein targets.

Oncogene-like addiction to aneuploidy in human cancers

This study demonstrates that trisomy of chromosome 1q is essential for malignant growth in cancers and shows that TP53 mutations are mutually exclusive with 1q aneuploidy.

Differential Boric Acid and Water Transport in Type I and Type II Pores of Arabidopsis Nodulin 26-Intrinsic Protein

This study compares boric acid and water transport in Arabidopsis NIP I and II proteins, showing differences linked to the ar/R filter's helix 2 amino acid.

Microstructures of Ant Chemosensory Sensilla Support a Dual Function in Detecting Both Volatile and Contact-Mediated Cues

The paper examines the microstructure of ant chemosensory sensilla, finding they have features supporting both volatile and contact-mediated cue detection.

Genome-wide identification and analysis of prognostic features in human cancers

The paper constructs genome-wide survival models using multi-omics data from 10,884 cancer patients to identify prognostic biomarkers and reveals that adverse biomarkers are not enriched for oncogenes or therapeutic targets.

Salmonella enterica serovar Typhimurium from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type

This study sequenced S. Typhimurium strains from wild birds in the U.S. and identified three distinct lineages associated with different bird types, improving source attribution and outbreak investigation.

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

This study uses molecular dynamics simulations to investigate how inhibitor binding affects the protonation states of histidines in SARS-CoV-2 main protease, showing their impact on structural stability and inhibitor binding.

Small molecule FGF23 inhibitors increase serum phosphate and improve skeletal abnormalities in Hyp mice

Mesophilic enzyme function at high temperature: moleculardynamics of hyperthermophilic and mesophilicpyrophosphatases

This study compares the molecular dynamics of mesophilic and hyperthermophilic pyrophosphatases to explain their differing thermal stability and function.

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

This study uses enhanced molecular dynamics simulations to generate accurate structural ensembles of intrinsically disordered proteins, validating results against experimental data.

Immune Selection Pressure Contributes to Pancreatic Cancer Immune Evasion

This study shows immune selection pressure in pancreatic cancer drives myeloid mimicry and immune evasion, which can be counteracted by JAK/STAT pathway inhibition to enhance immunotherapy.

FAM83F regulates canonical Wnt signalling through an interaction with CK1α

This study identifies FAM83F as a regulator of canonical Wnt signaling through its interaction with CK1α, showing it enhances signaling in Xenopus embryos and human colorectal cancer cells.

Cigarette smoke exposure and inflammatory signaling increase the expression of the SARS-CoV-2 receptor ACE2 in the respiratory tract

This study shows cigarette smoke increases ACE2 expression in lung cells, making smokers more susceptible to severe SARS-CoV-2 infections.

Structure based virtual screening identifies novel competitive inhibitors for the sialoglycan binding protein Hsa

The paper identifies nine novel competitive inhibitors of the sialoglycan binding protein Hsa using structure-based virtual screening and in vitro validation.

Single chromosome gains can function as metastasis suppressors and metastasis promoters

The paper investigates how single chromosome gains can either suppress or promote metastasis in cancer, showing that specific aneuploidies are linked to distinct clinical outcomes.

Combining CRISPR/Cas9 mutagenesis and a small-molecule inhibitor to probe the function of MELK in cancer

This study uses CRISPR/Cas9 and a MELK inhibitor to show that MELK knockout cancer cells grow normally, suggesting anti-MELK therapies may not be effective as monotherapies.

An integrated analysis of the epigenetic, genetic, and transcriptional patterns associated with outcome across cancer types

The paper analyzes genomic data from 33,036 tumors to identify prognostic patterns, finding that copy number changes and methylation are more predictive of survival than mutations.

FAM83G/PAWS1 controls cytoskeletal dynamics and cell migration through association with the SH3 adaptor CD2AP

The paper shows PAWS1/FAM83G regulates cell migration by controlling F-actin organization and focal adhesion dynamics through its interaction with CD2AP.