Ying Zhang

Publications

• Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.)
• FindPrimaryPairs: An efficient algorithm for predicting element-transferring reactant/product pairs in metabolic networks
• Using PSAMM for the curation and analysis of genome-scale metabolic models
• Addendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) [Front. Microbiol., 8, (2017), (682)] doi: 10.3389/fmicb.2017.00682
• Deep learning for neural decoding in motor cortex
• A Genome-Scale Model of Shewanella piezotolerans Simulates Mechanisms of Metabolic Diversity and Energy Conservation
• A Simple In Vitro Gut Model for Studying the Interaction between Escherichia coli and the Intestinal Commensal Microbiota in Cecal Mucus
• From the raw bar to the bench: Bivalves as models for human health
• Evolution of the Natural Transformation Protein, ComEC, in Bacteria
• Variation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100
• Two canonically aerobic foraminifera express distinct peroxisomal and mitochondrial metabolisms
• Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme Thermophile Caldicellulosiruptor bescii.
• Genome-Scale Metabolic Model of Caldicellulosiruptor bescii Reveals Optimal Metabolic Engineering Strategies for Bio-based Chemical Production.
• The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest
• Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria
• Diversity and Function of the Eastern Oyster (Crassostrea virginica) Microbiome
• Reconstruction and analysis of thermodynamically-constrained models reveal metabolic responses of a deep-sea bacterium to temperature perturbations
• FARCI: Fast and Robust Connectome Inference
• Reconstruction and Analysis of Thermodynamically Constrained Models Reveal Metabolic Responses of a Deep-Sea Bacterium to Temperature Perturbations
• Durable changes in the gut microbiome in survivors of childhood acute lymphoblastic leukemia
• Biochemical and Regulatory Analyses of Xylanolytic Regulons in Caldicellulosiruptor bescii Reveal Genus-Wide Features of Hemicellulose Utilization
• FARCI: Fast and Robust Connectome Inference
• Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core
• A Mollicutes Metagenome-Assembled Genome from the Gut of the Pteropod Limacina rangii
• Structural Determinants of Limited Proteolysis
• The FGGY Carbohydrate Kinase Family: Insights into the Evolution of Functional Specificities
• Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure
• Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure (vol 106, pg 10505, 2009)
• PMAP: databases for analyzing proteolytic events and pathways
• Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima
• Between order and disorder in protein structures: Analysis of "dual personality" fragments in proteins
• CutDB: a proteolytic event database
• PSAMM: A Portable System for the Analysis of Metabolic Models
• Microbiome Analysis Reveals Diversity and Function of Mollicutes Associated with the Eastern Oyster, Crassostrea virginica
• Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments
• Erratum: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest (BMC Biology (2020) 18 (90) DOI: 10.1186/s12915-020-00820-5)
• Rewiring Dynamics of Functional Connectome in Motor Cortex during Motor Skill Learning
• DL-TODA: A Deep Learning Tool for Omics Data Analysis
• Manipulating Fermentation Pathways in the Hyperthermophilic Archaeon Pyrococcus furiosus for Ethanol Production up to 95°C Driven by Carbon Monoxide Oxidation
• Manipulating Fermentation Pathways in the Hyperthermophilic Archaeon Pyrococcus furiosus for Ethanol Production up to 95°C Driven by Carbon Monoxide Oxidation
• A predicted CRISPR-mediated symbiosis between uncultivated archaea
• Optimizing Strategies for Bio-Based Ethanol Production Using Genome-Scale Metabolic Modeling of the Hyperthermophilic Archaeon, Pyrococcus furiosus
• Rewiring Dynamics of Functional Connectomes during Motor-Skill Learning
• Metabolic engineering of Caldicellulosiruptor bescii for 2,3-butanediol production from unpretreated lignocellulosic biomass and metabolic strategies for improving yields and titers
• Divergent learning-related transcriptional states of cortical glutamatergic neurons
• Engineering ethanologenicity into the extremely thermophilic bacterium Anaerocellum (f. Caldicellulosiriuptor) bescii
• Morphological responses of a temperate salt marsh foraminifer, Haynesina sp., to coastal acidification
• Array of metabolic pathways in a kleptoplastidic foraminiferan protist supports chemoautotrophy in dark, euxinic seafloor sediments
• Engineering the hyperthermophilic archaeon Pyrococcus furiosus for 1-propanol production