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List of works by Gary Siuzdak

A computational framework for proteome-wide pursuit and prediction of metalloproteins using ICP-MS and MS/MS data

scientific article

A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome

scientific article published on 25 September 2019

A mass spectrometry plate reader: monitoring enzyme activity and inhibition with a Desorption/Ionization on Silicon (DIOS) platform

scientific article

A nanostructure-initiator mass spectrometry-based enzyme activity assay

scientific article

A view from above: cloud plots to visualize global metabolomic data

scientific article

ABHD12 controls brain lysophosphatidylserine pathways that are deregulated in a murine model of the neurodegenerative disease PHARC

scientific journal article

Acoustic deposition with NIMS as a high-throughput enzyme activity assay

scientific article

Acylcarnitines are anticoagulants that inhibit factor Xa and are reduced in venous thrombosis, based on metabolomics data

scientific article

Affinity mass spectrometry from a tailored porous silicon surface

scientific article

Alterations in Spinal Cord Metabolism during Treatment of Neuropathic Pain

scientific article

An Interactive Cluster Heat Map to Visualize and Explore Multidimensional Metabolomic Data

scientific article

An accelerated workflow for untargeted metabolomics using the METLIN database

scientific article

An assembly landscape for the 30S ribosomal subunit

scientific article

An automated MALDI mass spectrometry approach for optimizing cyclosporin extraction and quantitation.

scientific article published on September 1997

Annotation: A Computational Solution for Streamlining Metabolomics Analysis.

scientific article published on 17 October 2017

Antioxidant or neurotrophic factor treatment preserves function in a mouse model of neovascularization-associated oxidative stress

scientific article published on 02 February 2009

Antiviral agent blocks breathing of the common cold virus.

scientific article

Arteriovenous Blood Metabolomics: A Readout of Intra-Tissue Metabostasis

scientific article published on 5 August 2015

Assignment of endogenous substrates to enzymes by global metabolite profiling

scientific article

Atmospheric pressure desorption/ionization on silicon ion trap mass spectrometry applied to the quantitation of midazolam in rat plasma and determination of midazolam 1'-hydroxylation kinetics in human liver microsomes

scientific article

Autonomous METLIN-Guided In-source Fragment Annotation for Untargeted Metabolomics

scientific article published on 25 January 2019

Autonomous metabolomics for rapid metabolite identification in global profiling

scientific article

Bioinformatics: the next frontier of metabolomics

scientific article

Biomarkers for neuroAIDS: the widening scope of metabolomics

scientific article published on 10 October 2006

Brain region mapping using global metabolomics

scientific article

Cationic drug analysis using matrix-assisted laser desorption/ionization mass spectrometry: application to influx kinetics, multidrug resistance, and intracellular chemical change

scientific article published on November 1993

Cationization of organometallo carbonyl compounds by fast ion bombardment

Cerebrospinal fluid proteomics reveals potential pathogenic changes in the brains of SIV-infected monkeys

scientific article published on May 2009

Chemoenzymatic Preparation of Novel Cyclic Imine Sugars and Rapid Biological Activity Evaluation Using Electrospray Mass Spectrometry and Kinetic Analysis

article

Clathrate nanostructures for mass spectrometry

scientific article

Cleavable Linkers for Porous Silicon-Based Mass Spectrometry

Cloud‐based archived metabolomics data: A resource for in‐source fragmentation/annotation, meta‐analysis and systems biology

scientific article published on 13 June 2020

Coagulation and Complement Protein Differences Between Septic and Uninfected Systemic Inflammatory Response Syndrome Patients

article

Cognitive analysis of metabolomics data for systems biology

scientific article published in 2021

Combined immunocapture and laser desorption/ionization mass spectrometry on porous silicon.

scientific article

Comprehensive bioimaging with fluorinated nanoparticles using breathable liquids

scientific article published on 20 January 2015

Correlating the transcriptome, proteome, and metabolome in the environmental adaptation of a hyperthermophile.

scientific article published on 2 February 2008

Corrigendum to “Maturation of a tetravirus capsid alters the dynamic properties and creates a metastable complex” [Virology 334 (2005) 17–27]

scholarly article by Brian Bothner published in August 2005

Crystallographically identical virus capsids display different properties in solution.

scientific article

Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online.

scientific article published in March 2018

Desorption/ionization on silicon (DIOS) mass spectrometry: background and applications

scholarly article by Warren G. Lewis et al published March 2003 in International Journal of Mass Spectrometry

Desorption/ionization on silicon (DIOS): a diverse mass spectrometry platform for protein characterization

scientific article

Desorption/ionization on silicon nanowires

scientific article (publication date: 15 March 2005)

Desorption/ionization on silicon time-of-flight/time-of-flight mass spectrometry

scientific article

Desorption–ionization on silicon mass spectrometry: an application in forensics

article

Detection of carbohydrates and steroids by cation-enhanced nanostructure-initiator mass spectrometry (NIMS) for biofluid analysis and tissue imaging

scientific article

Determining conserved metabolic biomarkers from a million database queries

scientific article published on 13 August 2015

Differential macrophage polarization promotes tissue remodeling and repair in a model of ischemic retinopathy

scientific article published on 30 August 2011

Direct characterization of solid phase resin-bound molecules by mass spectrometry

article by Michael C. Fitzgerald et al published April 1996 in Bioorganic & Medicinal Chemistry Letters

Discriminating precursors of common fragments for large-scale metabolite profiling by triple quadrupole mass spectrometry

scientific article published on 16 February 2015

Dissection of an antibody-catalyzed reaction

scientific article published on August 1994

Electrospray ionization of a whole virus: analyzing mass, structure, and viability

scientific article published in March 2004

Endothelial targeting of cowpea mosaic virus (CPMV) via surface vimentin

scientific article

Enhanced in-Source Fragmentation Annotation Enables Novel Data Independent Acquisition and Autonomous METLIN Molecular Identification

scientific article published on 10 April 2020

Examination of the sialyl lewis X - calcium complex by electrospray mass spectrometry

article

Expanding coverage of the metabolome for global metabolite profiling

scientific article published on 17 February 2011

Exposome-Scale Investigations Guided by Global Metabolomics, Pathway Analysis, and Cognitive Computing.

scientific article published on 25 September 2017

Fluorinated Gold Nanoparticles for Nanostructure Imaging Mass Spectrometry

From exogenous to endogenous: the inevitable imprint of mass spectrometry in metabolomics

scientific article published on February 2007

Gas-Phase Micelles

Generation of Induced Pluripotent Stem Cells Using Recombinant Proteins

Generation of retinal pigment epithelial cells from small molecules and OCT4 reprogrammed human induced pluripotent stem cells

scientific article published in February 2012

Global Isotope Metabolomics Reveals Adaptive Strategies for Nitrogen Assimilation

scientific article published on 5 April 2016

Global metabolomics reveals metabolic dysregulation in ischemic retinopathy

scientific article

Guiding the choice of informatics software and tools for lipidomics research applications

scientific article published on 21 December 2022

High sensitivity and analyte capture with desorption/ionization mass spectrometry on silylated porous silicon

scientific article

High surface area of porous silicon drives desorption of intact molecules

scientific article

High-temperature protein mass mapping using a thermophilic protease.

scientific article

Human rhinovirus capsid dynamics is controlled by canyon flexibility

scientific article published in September 2003

Hypoxia-induced metabolic stress in retinal pigment epithelial cells is sufficient to induce photoreceptor degeneration

scientific article published on 15 March 2016

Identification of Modified Tryptophan Residues in Apolipoprotein B-100 Derived from Copper Ion-Oxidized Low-Density Lipoprotein†

scientific article published on 01 November 1999

Identification of a new endogenous metabolite and the characterization of its protein interactions through an immobilization approach ⬇️

scientific article published on January 2009

Identification of bioactive metabolites using activity metabolomics

scientific article published on 01 June 2019

Identification of viral mutants by mass spectrometry.

scientific article

Innovation: Metabolomics: the apogee of the omics trilogy

scientific article published on 22 March 2012

Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses

scientific article

Investigating Molecular Recognition by Mass Spectrometry: Characterization of Calixarene-Based Self-Assembling Capsule Hosts with Charged Guests

scientific article published in 1999

Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis

scientific article

Liquid chromatography mass spectrometry of antisense oligonucleotides

scientific article published in 1995

Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database

scientific article (publication date: March 2013)

Luciferase does not Alter Metabolism in Cancer Cells

scientific article published on June 2014

METLIN MS2 molecular standards database: a broad chemical and biological resource

scientific article published on 24 August 2020

METLIN: A Technology Platform for Identifying Knowns and Unknowns.

scientific article published on 30 January 2018

METLIN: a metabolite mass spectral database

scientific article (publication date: December 2005)

Maintaining retinal astrocytes normalizes revascularization and prevents vascular pathology associated with oxygen-induced retinopathy

scientific article

Mass spectrometry in viral proteomics.

scientific article

Mass spectrometry reveals specific and global molecular transformations during viral infection.

scientific article published on September 2006

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

scientific article published in 2021

Maturation of a tetravirus capsid alters the dynamic properties and creates a metastable complex

scientific article published on March 2005

Membrane cofactor protein is a receptor for adenoviruses associated with epidemic keratoconjunctivitis

scientific article published on April 2004

Meta-analysis of global metabolomic data identifies metabolites associated with life-span extension

scientific article

Meta-analysis of untargeted metabolomic data from multiple profiling experiments

scientific article

Metabolic adaptation to calorie restriction

scientific article published on 08 September 2020

Metabolic oxidation regulates embryonic stem cell differentiation

scientific article

Metabolic rewiring of the hypertensive kidney

scientific article published on 10 December 2019

Metabolism links bacterial biofilms and colon carcinogenesis

scientific article published on 7 May 2015

Metabolite and Microbiome Interplay in Cancer Immunotherapy

scientific article published on 11 October 2016

Metabolizing Data in the Cloud

scientific article

Metabolomic data streaming for biology-dependent data acquisition

scientific article

Metabolomics activity screening for identifying metabolites that modulate phenotype.

scientific article

Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites

scientific article (publication date: 10 March 2009)

Metabolomics annotates ABHD3 as a physiologic regulator of medium-chain phospholipids

scientific article published in November 2011

Metabolomics identifies perturbations in human disorders of propionate metabolism

scientific article published on 19 October 2007

Metabolomics implicates altered sphingolipids in chronic pain of neuropathic origin.

scientific article

Metabolomics-based discovery of a metabolite that enhances oligodendrocyte maturation.

scientific article published on 13 November 2017

Metabolomics: beyond biomarkers and towards mechanisms

scientific article published on 16 March 2016

Microbial Metabolite 3-Indolepropionic Acid Mediates Immunosuppression

scientific article published in 2022

Microbial metalloproteomes are largely uncharacterized.

scientific article

Mobilization of pro-inflammatory lipids in obese Plscr3-deficient mice

scientific article published on January 2007

Molecular basis for the specificity of p27 toward cyclin-dependent kinases that regulate cell division

scientific article

Monitoring enzyme catalysis with mass spectrometry.

scientific article

Multiphoton ionization studies of amines with UV-VIS lasers

Multiphoton-induced chemistry of phenol in hexane at 266 nm

Multiple ionization mass spectrometry strategy used to reveal the complexity of metabolomics

scientific article

Multiple organic anion transporters contribute to net renal excretion of uric acid

scientific article

Nanostructure imaging mass spectrometry: the role of fluorocarbons in metabolite analysis and yoctomole level sensitivity

scientific article

Nanostructure initiator mass spectrometry: tissue imaging and direct biofluid analysis

scientific article published on April 2009

Nanostructure-initiator mass spectrometry (NIMS) imaging of brain cholesterol metabolites in Smith-Lemli-Opitz syndrome

scientific article

Nanostructure-initiator mass spectrometry metabolite analysis and imaging

scientific article

Nanostructure-initiator mass spectrometry: a protocol for preparing and applying NIMS surfaces for high-sensitivity mass analysis

scientific article

New catalysts for the asymmetric hydrosilylation of ketones discovered by mass spectrometry screening

scientific article published in April 2003

Nonlinear data alignment for UPLC-MS and HPLC-MS based metabolomics: quantitative analysis of endogenous and exogenous metabolites in human serum

scientific article

Novel multiprotein complexes identified in the hyperthermophilic archaeon Pyrococcus furiosus by non-denaturing fractionation of the native proteome

scientific article

Organic anion transporter 3 contributes to the regulation of blood pressure

scientific article published on 28 May 2008

Palbociclib and Fulvestrant Act in Synergy to Modulate Central Carbon Metabolism in Breast Cancer Cells

scientific article published on 02 January 2019

Phospholipid capture combined with non-linear chromatographic correction for improved serum metabolite profiling

article published in 2006

Phosphonium labeling for increasing metabolomic coverage of neutral lipids using electrospray ionization mass spectrometry

scientific article

Probing Protein/Protein Interactions with Mass Spectrometry and Isotopic Labeling: Analysis of the p21/Cdk2 Complex

article

Probing protein structure using biochemical and biophysical methods. Proteolysis, matrix-assisted laser desorption/ionization mass spectrometry, high-performance liquid chromatography and size-exclusion chromatography of p21Waf1/Cip1/Sdi1.

scientific article

Quantitative ESI-TOF analysis of macromolecular assembly kinetics

scientific article

Quantitative analysis with desorption/ionization on silicon mass spectrometry using electrospray deposition

scientific article

Quantitative metabolomics of photoreceptor degeneration and the effects of stem cell-derived retinal pigment epithelium transplantation

scientific article published on October 2016

Quantitative plasma proteomic profiling identifies the vitamin E binding protein afamin as a potential pathogenic factor in SIV induced CNS disease

scientific article

Reactivity-Based One-Pot Synthesis of the Tumor-Associated Antigen N3 Minor Octasaccharide for the Development of a Photocleavable DIOS-MS Sugar Array

article

Response and recovery in the plasma metabolome tracks the acute LCMV-induced immune response

scientific article (publication date: July 2009)

Rice tungro bacilliform virus open reading frame 3 encodes a single 37-kDa coat protein.

scientific article

Selective metabolite and peptide capture/mass detection using fluorous affinity tags.

scientific article published on 8 March 2007

Sepsis plasma protein profiling with immunodepletion, three-dimensional liquid chromatography tandem mass spectrometry, and spectrum counting

scientific article

Short communication: quantitative proteomic plasma profiling reveals activation of host defense to oxidative stress in chronic SIV and methamphetamine comorbidity

scientific article published on 7 October 2010

Small-Molecule Desorption/Ionization Mass Analysis

article

Smartphone Analytics: Mobilizing the Lab into the Cloud for Omic-Scale Analyses

scientific article

Solvent-dependent metabolite distribution, clustering, and protein extraction for serum profiling with mass spectrometry

scientific article published in February 2006

Staying Alive: Measuring Intact Viable Microbes with Electrospray Ionization Mass Spectrometry

scientific article published on 25 July 2016

Surface modification and laser pulse length effects on internal energy transfer in DIOS.

scientific article published in December 2005

Surfactant-enhanced desorption/ionization on silicon mass spectrometry

scientific article

The METLIN small molecule dataset for machine learning-based retention time prediction

scientific article published on 20 December 2019

The Role of Metabolomics in Brain Metabolism Research

scientific article published on 23 July 2015

The emergence of mass spectrometry in biochemical research

scientific article published in November 1994

The expanding role of mass spectrometry in metabolite profiling and characterization

scientific article

The glycerophospho metabolome and its influence on amino acid homeostasis revealed by brain metabolomics of GDE1(-/-) mice

scientific article published on August 2010

The identification of an adenovirus receptor by using affinity capture and mass spectrometry.

scientific article

The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming

scientific article published on 8 November 2011

The structure of apo human glutamate dehydrogenase details subunit communication and allostery

scientific article

Thermal Degradation of Small Molecules: A Global Metabolomic Investigation.

scientific article

Toward 'omic scale metabolite profiling: a dual separation-mass spectrometry approach for coverage of lipid and central carbon metabolism

scientific article published on 03 July 2013

Type I signal peptidase and protein secretion in Staphylococcus epidermidis.

scientific article

Variability analysis of human plasma and cerebral spinal fluid reveals statistical significance of changes in mass spectrometry-based metabolomics data

scientific article

Viral capsid mobility: a dynamic conduit for inactivation.

scholarly article

Warfarin untargeted metabolomics study identifies novel procoagulant ethanolamide plasma lipids.

scientific article published on 23 January 2014

XCMS Online: a web-based platform to process untargeted metabolomic data

scientific article

XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules

scientific article published on 27 August 2018

XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization

scientific article

XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification

scientific article (publication date: February 2006)

isoMETLIN: a database for isotope-based metabolomics

scientific article published on 19 September 2014

metaXCMS: second-order analysis of untargeted metabolomics data

scientific article

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