Song Feng

Integrative Multi-PTM Profiling by an Automated Shotgun Proteomics Coupled with Top-down Proteomics

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Tong Zhang

Project type

Contracted Time

To use PTM data to understand cell signaling and profile molecular phenotypes, PNNL has made substantial strides in advancing phosphoproteome and thiol redox proteome profiling. However, the current…

Enhancing biopreparedness through a model system to understand the molecular mechanisms that lead to pathogenesis and disease transmission

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Margaret Cheung-Wyker

The science of biopreparedness to counter biological threats hinges on understanding the fundamental principles and molecular mechanisms that lead to pathogenesis and disease transmission. Our vision…

Integrative Multi-PTM Profiling by an Automated Shotgun Proteomics Coupled with Top-down Proteomics

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Tong Zhang

To use PTM data to understand cell signaling and profile molecular phenotypes, PNNL has made substantial strides in advancing phosphoproteome and thiol redox proteome profiling. However, the current…

AlphaEnzyme: predicting enzyme functions directly from AlphaFold encoding

Lead Institution

Kent State University

Principal Investigator

Qiang Guan

Project type

Exploratory Research

Predicting the function of enzyme (represented as an enzyme commission number, or EC number) is one of the central tasks in annotating genomes and metagenomes. It is crucial for understanding the…

Inferring Kinetic Models for Large-Scale Biochemical Networks

Lead Institution

University of Washington

Principal Investigator

Herbert Sauro

Project type

Large-Scale EMSL Research

Mechanistic models of cell networks that accurately predict changes in input-output dynamics and outcomes upon perturbation have the potential to facilitate a greater understanding of the…

Determination of the Molecular Architecture and Temporal Dynamics that Drive Microbial Lignocellulose Degradation

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Song Feng

Project type

Large-Scale EMSL Research

In order to link phenotypic outcomes to molecular determinants, we have developed an integrated functional profiling platform, PhenoProfiling, that pairs activity-based probes (ABPs) with…

Moisture and seasonal drivers of Inter-Kingdom metabolic interaction in a marginal soil rhizosphere

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

William Nelson

Project type

FICUS Research

Soil is a complex environment with numerous competing and cooperating populations contributing to overall ecosystem services. Plants provide most of the fresh organic carbon inputs through growth and…

Prediction of response in soil microbiome carbon utilization to changing moisture conditions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jason McDermott

Project type

FICUS Research

The goal of this project is to attain a systems level understanding of the soil microbiome and its phenotypic response to changing moisture through a tractable, spatially explicit examination of the…

Prediction of soil microbiome phenotypic responses to changing moisture conditions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jason McDermott

The goal of this project is to attain a systems level understanding of the soil microbiome and its phenotypic response to changing moisture through a tractable, spatially explicit examination of the…

Structural profiling of the molecular interactome to define phenotype

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Melchior

The functional pathways that define phenotype are reflected by protein quinary structure; the transient encounters of proteins with other proteins, molecules, cofactors, and nucleic acids that…

EMSL Science Overview

Song Feng

Projects

Integrative Multi-PTM Profiling by an Automated Shotgun Proteomics Coupled with Top-down Proteomics

Enhancing biopreparedness through a model system to understand the molecular mechanisms that lead to pathogenesis and disease transmission

Integrative Multi-PTM Profiling by an Automated Shotgun Proteomics Coupled with Top-down Proteomics

AlphaEnzyme: predicting enzyme functions directly from AlphaFold encoding

Inferring Kinetic Models for Large-Scale Biochemical Networks

Determination of the Molecular Architecture and Temporal Dynamics that Drive Microbial Lignocellulose Degradation

Moisture and seasonal drivers of Inter-Kingdom metabolic interaction in a marginal soil rhizosphere

Prediction of response in soil microbiome carbon utilization to changing moisture conditions

Prediction of soil microbiome phenotypic responses to changing moisture conditions

Structural profiling of the molecular interactome to define phenotype