-
Transposable Elements and the Emergence of Genomic Innovation
Analyzes thousands of genomic datasets to understand how transposable elements drive regulatory innovation. Nearly half of the human genome comprises these mobile sequences that... -
Intelligent Metadata Compilation to Enhance Synthesis of Mass...
Develops automated workflows extracting and standardizing proteomics metadata using bioinformatics and natural language processing. Enhances PRIDE repository accessibility for... -
Protein Misfolding, Mutations and the Emergence of Disease Phenotypes
Analyzes structural, sequence, and gene-disease data linking protein entanglement to disease. Explores previously unrecognized causes of disease through protein topology-disease... -
Identifying the Molecular Origins of Heat Resistance in Plants
Analyzes omics datasets comparing cytokinesis under normal and high-temperature conditions across species. Identifies genetic factors enabling heat tolerance relevant to... -
The Epigenetic Drivers of Neurodegenerative Processes in Human Brain Cells
Develops multimodal AI integrating single-cell genomic data to reveal genome architecture-expression relationships. Identifies epigenetic drivers of neurodegeneration in... -
Unraveling the Evolutionary Origin of Complex Topologies
Maps when topological entanglement (knots, slipknots, lasso motifs) emerged across protein families using sequence, structure, and phylogenetic data. Tests functional... -
Mapping Bacterial Cell States Across Environments and Evolution
Synthesizes bacterial gene expression data to create the first atlas of cell states including growth, starvation, biofilm formation, and dormancy across diverse environments.... -
Discovering New Protein-Protein Interactions Within Crosslinking Mass...
Integrates crosslinking mass spectrometry data from PRIDE with AlphaFold3 predictions to validate and map protein interactions. Delivers hybrid structural models integrated into... -
Learning Sequence Conservation from Functional Constraints in Intrinsically...
Links evolutionary conservation with structural and functional signatures in intrinsically disordered regions. Integrates sequence alignments, molecular simulations, and... -
Data-Driven Discovery of Regulatory Mechanisms and Cellular Resource...
Integrates multi-omics data from single-cell sequencing across well-characterized model cell lines. Creates a benchmarking resource for understanding regulatory mechanisms and... -
A Unified Framework for Analyses of Proteome Turnover Dynamics
Harmonizes fragmented protein turnover datasets across species (E. coli, yeast, mouse, human). Creates a standardized Protein Stability Database using consistent reanalysis... -
Protein Misfolding, Proteostasis, and Aging
Uses high-throughput mass spectrometry to investigate the prevalence and consequences of protein misfolding for protein homeostasis and aging-related structural changes across... -
Energetic Origins of Connectivity Within Protein Interaction Networks
Investigates how protein instability and disorder shape network architecture across organisms, revealing connections between biophysical properties and network topology across... -
Predicting Cell Fate and State from RNA and Protein Spatial Maps
Integrates high-resolution spatial transcriptomics and proteomics data to predict cellular fate. Develops computational frameworks for registering multi-modal spatial images,... -
Oceans of Disorder: Elucidating the Role of Disordered Proteins in Cellular...
Examines intrinsically disordered region evolution in deep-sea organisms using metagenomic datasets and bioinformatics. Creates the first comprehensive map of molecular... -
Mapping the Non-Canonical Human Translatome and Proteome
Resolves discrepancies between ribosomal translation detection and protein identification by synthesizing RNA-seq, ribosome profiling, and proteomics datasets. Quantifies... -
Emergent Order Parameters of Allostery: An AI Framework for Predicting and...
Integrates simulations, deep mutational scanning, and evolutionary data to quantify dynamic coupling in proteins. Develops allosteric order parameters and trains models... -
EntanGoPy: Python Tools for Protein Entanglement Analysis
Computational tools and datasets for analyzing protein topological entanglement, supporting NCEMS working groups studying protein misfolding, disease phenotypes, and structural...