Gilbert S. Omenn

VO: The Vaccine Ontology

The paper introduces the Vaccine Ontology (VO), a standardized framework for representing vaccines and related data, enhancing data integration and AI research.

Predicting the Structural Impact of Human Alternative Splicing

The paper predicts the structural impact of human alternative splicing using AlphaFold2 on over 11,000 isoforms and identifies structural changes across multiple metrics.

De Novo Protein Fold Design Through Sequence-Independent Fragment Assembly Simulations

This paper introduces FoldDesign, a method for de novo protein fold design that creates novel structures from secondary structure assignments, achieving high fidelity and stability.

De Novo RNA Tertiary Structure Prediction at Atomic Resolution Using Geometric Potentials from Deep Learning

DeepFoldRNA couples deep self-attention neural networks with gradient-based folding simulations to predict atomic-resolution RNA tertiary structures from sequence in ~1 minute with 2.69 A average RMSD.

TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for High-Accuracy Gene Function Annotations

TripletGO improves gene function annotations by integrating transcript expression, sequence alignment, and probability models across multiple species and proteins.

Functional Organization of the Maternal and Paternal Human 4D Nucleome

The paper investigates allele-specific relationships between gene expression and genome structure in human cells using integrated haplotype-resolved data.

Identifying zoonotic origin of SARS-CoV-2 by modeling the binding affinity between Spike receptor-binding domain and host ACE2

This study identifies potential intermediate hosts of SARS-CoV-2 by modeling Spike-RBD binding affinity to ACE2 proteins across multiple species.

ClusterMine: a Knowledge-integrated Clustering Approach based on Expression Profiles of Gene Sets

ClusterMine integrates biological knowledge to cluster samples based on gene set expression profiles, improving interpretability of clusters.

Measurement of organ-specific and acute-phase blood protein levels in early Lyme disease

The paper identifies 10 blood proteins with altered serum levels in early Lyme disease patients, developing a 10-protein panel for potential diagnostic use.

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0

The paper updates the HPP MS Data Interpretation Guidelines to improve accuracy and address new workflows and data standards.

Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data

The paper provides considerations and recommendations for designing and analyzing plasma proteomics studies to improve translational applications in clinical settings.

Blood metabolome signature predicts gut microbiome α-diversity in health and disease

The paper identifies a blood metabolome signature that robustly predicts gut microbiome α-diversity across health and disease conditions.

Chromosome 17: neXt-MP50 C-HPP Challenge Completed

The paper reports a 50% reduction in PE2,3,4 missing proteins on Chromosome 17 using protein-level evidence from proteomics data.

Modeling the functional relationship network at the splice isoform level through heterogeneous data integration

This paper develops a probabilistic method to model functional relationships at the splice isoform level by integrating heterogeneous genomic data in mice, revealing isoform-specific interactions and functional diversity.