Metabolic signatures of regulation by phosphorylation and acetylation

Next-Generation Genome-Scale Metabolic Modeling through Integration of Regulatory Mechanisms

(2021) Carolina H. Chung et al.   Metabolites

Ferrochelatase regulates retinal neovascularization

(2020) Sardar Pasha Sheik Pran Babu et al.   FASEB JOURNAL

Enzyme capacity-based genome scale modelling of CHO cells

(2020) Hock Chuan Yeo et al.   METABOLIC ENGINEERING

Lysine is required for growth factor-induced mTORC1 activation

(2020) Se-Kyeong Jang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Systems Metabolic Engineering Strategies: Integrating Systems and Synthetic Biology with Metabolic Engineering

(2019) Kyeong Rok Choi et al.   TRENDS IN BIOTECHNOLOGY

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

(2019) Jason H. Yang et al.   CELL

Glioma Stem Cell Specific Super Enhancer Promotes Polyunsaturated Fatty Acid Synthesis to Support EGFR Signaling

(2019) Ryan C Gimple et al.   Cancer Discovery

Machine and deep learning meet genome-scale metabolic modeling

(2019) Guido Zampieri et al.   PLoS Computational Biology

Post-translational Protein Acetylation: An Elegant Mechanism for Bacteria to Dynamically Regulate Metabolic Functions

(2019) David G. Christensen et al.   Frontiers in Microbiology

ATP citrate lyase: A central metabolic enzyme in cancer

(2019) Philippe Icard et al.   CANCER LETTERS

Machine learning applications in systems metabolic engineering

(2019) Gi Bae Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Phosphoproteome dynamics during mitotic exit in budding yeast

(2018) Sandra A Touati et al.   EMBO JOURNAL

Explainable machine-learning predictions for the prevention of hypoxaemia during surgery

(2018) Scott M. Lundberg et al.   Nature Biomedical Engineering

Functions and mechanisms of non-histone protein acetylation

(2018) Takeo Narita et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

(2018) Elizabeth Brunk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

(2018) David Heckmann et al.   Nature Communications

Accurate Quantification of Site-specific Acetylation Stoichiometry Reveals the Impact of Sirtuin Deacetylase CobB on theE. coliAcetylome

(2017) Brian Tate Weinert et al.   MOLECULAR & CELLULAR PROTEOMICS

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

(2017) Benjamín J Sánchez et al.   Molecular Systems Biology

Proteomic and Metabolomic Characterization of a Mammalian Cellular Transition from Quiescence to Proliferation

(2017) Ho-Joon Lee et al.   Cell Reports

Comprehensive Mapping of Pluripotent Stem Cell Metabolism Using Dynamic Genome-Scale Network Modeling

(2017) Sriram Chandrasekaran et al.   Cell Reports

Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens

(2017) Traver Hart et al.   G3-Genes Genomes Genetics

Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal

(2017) Claus Jonathan Fritzemeier et al.   PLoS Computational Biology

Proteome-wide acetylation dynamics in human cells

(2017) Yekaterina Kori et al.   Scientific Reports

Systems-level analysis of mechanisms regulating yeast metabolic flux

(2016) S. R. Hackett et al.   SCIENCE

Investigating Conservation of the Cell-Cycle-Regulated Transcriptional Program in the Fungal Pathogen, Cryptococcus neoformans

(2016) Christina M. Kelliher et al.   PLoS Genetics

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

(2015) Traver Hart et al.   CELL

Posttranslational regulation of microbial metabolism

(2015) Karl Kochanowski et al.   CURRENT OPINION IN MICROBIOLOGY

Comprehensive Temporal Protein Dynamics during the Diauxic Shift inSaccharomyces cerevisiae

(2015) J. Patrick Murphy et al.   MOLECULAR & CELLULAR PROTEOMICS

Inferring causal metabolic signals that regulate the dynamic TORC1-dependent transcriptome

(2015) A. P. Oliveira et al.   Molecular Systems Biology

Acetylation site specificities of lysine deacetylase inhibitors in human cells

(2015) Christian Schölz et al.   NATURE BIOTECHNOLOGY

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins

(2015) Kai-Yao Huang et al.   NUCLEIC ACIDS RESEARCH

Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis

(2015) A. P. Oliveira et al.   Science Signaling

Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation

(2015) Sean J. Humphrey et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation

(2015) John R. Houser et al.   PLoS Computational Biology

The Roles of Post-translational Modifications in the Context of Protein Interaction Networks

(2015) Guangyou Duan et al.   PLoS Computational Biology

Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis

(2015) A. P. Oliveira et al.   Science Signaling

Oxidative stress response and nitrogen utilization are strongly variable in Saccharomyces cerevisiae wine strains with different fermentation performances

(2014) Laura Treu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Network Thermodynamic Curation of Human and Yeast Genome-Scale Metabolic Models

(2014) Verónica S. Martínez et al.   BIOPHYSICAL JOURNAL

Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae

(2014) B. T. Weinert et al.   Molecular Systems Biology

Coordination of microbial metabolism

(2014) Victor Chubukov et al.   NATURE REVIEWS MICROBIOLOGY

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

(2014) Kirti Sharma et al.   Cell Reports

Correction: Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

(2014) Jong Min Lee et al.   PLoS Computational Biology

Global Dynamics of the Escherichia coli Proteome and Phosphoproteome During Growth in Minimal Medium

(2013) Nelson C. Soares et al.   JOURNAL OF PROTEOME RESEARCH

Acetylation Stabilizes ATP-Citrate Lyase to Promote Lipid Biosynthesis and Tumor Growth

(2013) Ruiting Lin et al.   MOLECULAR CELL

Acetyl-Phosphate Is a Critical Determinant of Lysine Acetylation in E. coli

(2013) Brian T. Weinert et al.   MOLECULAR CELL

Evolution and functional cross-talk of protein post-translational modifications

(2013) Pedro Beltrao et al.   Molecular Systems Biology

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

Functioning of a metabolic flux sensor in Escherichia coli

(2013) K. Kochanowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Functional Prioritization of Protein Posttranslational Modifications

(2012) Pedro Beltrao et al.   CELL

Phosphorylation network dynamics in the control of cell cycle transitions

(2012) D. Fisher et al.   JOURNAL OF CELL SCIENCE

Regulation of yeast central metabolism by enzyme phosphorylation

(2012) Ana Paula Oliveira et al.   Molecular Systems Biology

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

Multidimensional Optimality of Microbial Metabolism

(2012) R. Schuetz et al.   SCIENCE

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

(2011) Jan Schellenberger et al.   BIOPHYSICAL JOURNAL

The importance of post-translational modifications in regulating Saccharomyces cerevisiae metabolism

(2011) Ana Paula Oliveira et al.   FEMS YEAST RESEARCH

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Systems biology of microbial metabolism

(2010) Matthias Heinemann et al.   CURRENT OPINION IN MICROBIOLOGY

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of Cellular Metabolism by Protein Lysine Acetylation

(2010) S. Zhao et al.   SCIENCE

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

(2010) J. V. Olsen et al.   Science Signaling

Posttranslational regulation impacts the fate of duplicated genes

(2009) G. D. Amoutzias et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA