D. McCloskey

发表

Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics.

Daniel C. Zielinski, B. Palsson, A. Bordbar, 2015, Cell systems.

RapidRIP quantifies the intracellular metabolome of 7 industrial strains of E. coli.

Markus J. Herrgård, D. McCloskey, Julia Xu, 2018, Metabolic engineering.

Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism

Adam M. Feist, Troy E. Sandberg, B. Palsson, 2018, Nature Communications.

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

Jason H. Yang, J. Collins, B. Palsson, 2019, Cell.

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

Jason H. Yang, J. Collins, B. Palsson, 2019, Cell.

Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale.

Adam M. Feist, Jamey D. Young, B. Palsson, 2016, Analytical chemistry.

A model‐driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K‐12 MG1655 that is biochemically and thermodynamically consistent

Adam M. Feist, Zachary A. King, B. Palsson, 2014, Biotechnology and bioengineering.

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

Adam M. Feist, B. Palsson, A. Feist, 2013, Molecular systems biology.

Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.

Edward J. O'Brien, Adam M. Feist, Jonathan M. Monk, 2016, Cell systems.

Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution.

Ke Chen, Edward J. O'Brien, Adam M. Feist, 2016, Cell systems.

Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System.

Elizabeth Brunk, Richard Szubin, Bernhard O Palsson, 2018, Metabolic engineering.

Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes.

Elizabeth Brunk, Richard Szubin, Adam M. Feist, 2018, Metabolic engineering.

Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts Saccharomyces cerevisiae and Yarrowia lipolytica

Markus J. Herrgård, Ulf W. Liebal, L. Blank, 2019, Front. Genet..

MID Max: LC-MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications.

Adam M. Feist, Bernhard O. Palsson, Douglas McCloskey, 2016, Analytical chemistry.

Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase in Escherichia coli.

Adam M. Feist, Daniel C. Zielinski, A. Feist, 2014, Microbiology.

Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions

Adam M. Feist, Troy E. Sandberg, B. Palsson, 2018, Applied and Environmental Microbiology.

Global Rebalancing of Cel lular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution Graphical

Edward J. O'Brien, Adam M. Feist, B. Palsson, 2016 .

A pH and solvent optimized reverse-phase ion-paring-LC–MS/MS method that leverages multiple scan-types for targeted absolute quantification of intracellular metabolites

Adam M. Feist, B. Palsson, A. Feist, 2015, Metabolomics.

Precision diagnostic approach to predict 5-year risk for microvascular complications in type 1 diabetes

T. Suvitaival, F. Pociot, D. McCloskey, 2022, EBioMedicine.

High-resolution scanning of optimal biosensor reporter promoters in yeast.

J. Keasling, D. McCloskey, M. K. Jensen, 2020, ACS synthetic biology.

An automated workflow for multi-omics screening of microbial model organisms

Markus J. Herrgård, L. Nielsen, D. McCloskey, 2022, bioRxiv.

Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function.

Jason H. Yang, J. Collins, B. Palsson, 2017, Cell host & microbe.

Automating the design-build-test-learn cycle towards next-generation bacterial cell factories.

D. McCloskey, D. Volke, P. Nikel, 2023, New biotechnology.

Tracing compartmentalized NADPH metabolism in the cytosol and mitochondria of mammalian cells.

Adam M. Feist, Christian M. Metallo, A. Feist, 2014, Molecular cell.

AMPD2 Regulates GTP Synthesis and Is Mutated in a Potentially Treatable Neurodegenerative Brainstem Disorder

S. Gabriel, E. Nickerson, R. Naviaux, 2013, Cell.

SmartPeak Automates Targeted and Quantitative Metabolomics Data Processing.

Markus J. Herrgård, O. Kohlbacher, L. Nielsen, 2020, Analytical Chemistry.

SmartPeak automates targeted and quantitative metabolomics data processing

Timo Sachsenberg, Oliver Kohlbacher, Svetlana Kutuzova, 2020, bioRxiv.

A pH and solvent optimized reverse-phase ion-paring-LC–MS/MS method that leverages multiple scan-types for targeted absolute quantification of intracellular metabolites

Adam M. Feist, A. Feist, D. McCloskey, 2015, Metabolomics.

A Machine Learning Approach to Predict 5-year Risk for Complications in Type 1 Diabetes

T. Suvitaival, D. McCloskey, P. Rossing, 2021, medRxiv.

Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome

Adam M. Feist, Troy E. Sandberg, B. Palsson, 2018, bioRxiv.

Oral supplementation of nicotinamide riboside alters intestinal microbial composition in rats and mice, but not humans

Markus J. Herrgård, M. Arumugam, M. Gillum, 2023, npj Aging.

Fast Swinnex filtration (FSF): a fast and robust sampling and extraction method suitable for metabolomics analysis of cultures grown in complex media

Adam M. Feist, B. Palsson, A. Feist, 2015, Metabolomics.

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

Edward J. O'Brien, Adam M. Feist, Bernhard O. Palsson, 2018, bioRxiv.

Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism

Troy E. Sandberg, A. Feist, D. McCloskey, 2018, Nature Communications.

A Comprehensive Evaluation of Metabolomics Data Preprocessing Methods for Deep Learning

D. McCloskey, K. Abram, 2022, Metabolites.

In Search of Disentanglement in Tandem Mass Spectrometry Datasets

D. McCloskey, K. Abram, 2023, bioRxiv.

Bi-modal Variational Autoencoders for Metabolite Identification Using Tandem Mass Spectrometry

C. Igel, D. McCloskey, S. Kutuzova, 2021, bioRxiv.

Multimodal Variational Autoencoders for Semi-Supervised Learning: In Defense of Product-of-Experts pdf

Oswin Krause, Christian Igel, Mads Nielsen, 2021, ArXiv.

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

Adam M. Feist, B. Palsson, D. McCloskey, 2013, Molecular systems biology.

Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution.

Edward J. O'Brien, Adam M. Feist, D. McCloskey, 2016, Cell systems.

MID Max: LC-MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications.

Adam M. Feist, D. McCloskey, Sibei Xu, 2016, Analytical chemistry.

Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes.

Adam M. Feist, Troy E. Sandberg, B. Palsson, 2018, Metabolic engineering.

Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution.

Edward J. O'Brien, Adam M. Feist, D. McCloskey, 2016, Cell systems.

RapidRIP quantifies the intracellular metabolome of 7 industrial strains of E. coli.

Markus J. Herrgård, D. McCloskey, Julia Xu, 2018, Metabolic engineering.

Quantifying the Metabolome of Pseudomonas taiwanensis VLB120: Evaluation of Hot and Cold Combined Quenching/Extraction Approaches.

D. McCloskey, Lars Schrübbers, Konstantin Schneider, 2017, Analytical chemistry.

Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System.

Adam M. Feist, Troy E. Sandberg, B. Palsson, 2018, Metabolic engineering.

Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome

Adam M. Feist, Troy E. Sandberg, B. Palsson, 2018, bioRxiv.