M. Shortreed

发表

Thermodynamically based DNA strand design

Lloyd M. Smith, S. B. Chang, H. Hoos, 2005, Nucleic acids research.

Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS

Anthony J. Cesnik, Lloyd M. Smith, M. Scalf, 2019, RNA.

Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.

Anthony J. Cesnik, Lloyd M. Smith, Gloria M. Sheynkman, 2016, Annual review of analytical chemistry.

Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements

Anthony J. Cesnik, Brian L. Frey, Lloyd M. Smith, 2016, Journal of proteome research.

Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search

Brian L. Frey, Lloyd M. Smith, Gloria M. Sheynkman, 2015, Journal of proteome research.

Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq*

Brian L. Frey, Lloyd M. Smith, Gloria M. Sheynkman, 2013, Molecular & Cellular Proteomics.

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

James E. Johnson, Brian L. Frey, Lloyd M. Smith, 2014, BMC Genomics.

Global Post-Translational Modification Discovery

Brian L. Frey, Lloyd M. Smith, M. Scalf, 2016, Journal of proteome research.

Ultrafast Peptide Label-Free Quantification with FlashLFQ.

Michael R. Shortreed, Robert J. Millikin, Lloyd M. Smith, 2018, Journal of proteome research.

Identification and Quantification of Proteoforms by Mass Spectrometry

Liangliang Sun, Zhijie Wu, Ying Ge, 2019, Proteomics.

Miniature sodium-selective ion-exchange optode with fluorescent pH chromoionophores and tunable dynamic range.

M. Shortreed, E. Bakker, R. Kopelman, 1996, Analytical chemistry.

Utilization of lipophilic ionic additives in liquid polymer film optodes for selective anion activity measurements.

M. Shortreed, R. Kopelman, S. Barker, 1997, Analytical chemistry.

Development of a fluorescent optical potassium-selective ion sensor with ratiometric response for intracellular applications

Michael R. Shortreed, Raoul Kopelman, Sunil Dourado, 1997 .

Molecular nano-lenses: Directed energy migration and back-transfer in dendrimeric antenna supermolecules

Jeffrey S. Moore, C. Devadoss, M. Shortreed, 1998 .

Dendrimeric Antenna Supermolecules with Multistep Directed Energy Transfer

Jeffrey S. Moore, M. Shortreed, R. Kopelman, 1998 .

Supermolecular Excitation Antenna: Ordered Energy Funnel

M. Shortreed, R. Kopelman, Z. Shi, 1996 .

Chapter 7 Novel NMR and MS Approaches to Metabolomics

J. Markley, M. Shortreed, I. Lewis, 2012 .

Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry.

Lloyd M. Smith, M. Olivier, M. Scalf, 2017, Journal of proteome research.

Global Identification of Post-Translationally Spliced Peptides with Neo-Fusion.

Brian L. Frey, Lloyd M. Smith, Stefan K Solntsev, 2018, Journal of proteome research.

High-throughput single-molecule DNA screening based on electrophoresis.

E. Yeung, M. Shortreed, Weihua Huang, 2000 .

Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global PTM Discovery Database.

Michael R. Shortreed, Robert J. Millikin, Brian L. Frey, 2019, Journal of proteome research.

Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families.

Anthony J. Cesnik, Brian L. Frey, Lloyd M. Smith, 2018, Analytical chemistry.

In Situ and In Vivo Molecular Analysis by Coherent Raman Scattering Microscopy

Michael G. Roper, Anthony J. Cesnik, Lloyd M. Smith, 2016 .

Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys

Anthony J. Cesnik, Lloyd M. Smith, M. Olivier, 2017, BMC Genomics.

Lifetime enhancement of ultrasmall fluorescent liquid polymeric film based optodes by diffusion-induced self-recovery after photobleaching.

M. Shortreed, R. Kopelman, E. Monson, 1996, Analytical chemistry.

Anion-selective liquid-polymer optodes with fluorescent pH chromoionophores, tunable dynamic range and diffusion enhanced lifetimes

M. Shortreed, R. Kopelman, S. Barker, 1996 .

O-Pair Search with MetaMorpheus for O-glycopeptide Characterization

Lloyd M. Smith, C. Bertozzi, M. Shortreed, 2020, Nature Methods.

Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers

Anthony J. Cesnik, Brian L. Frey, Lloyd M. Smith, 2018, Translational oncology.

Intact-Mass Analysis Facilitates the Identification of Large Human Heart Proteoforms.

Lloyd M. Smith, M. Shortreed, Ying Ge, 2019, Analytical chemistry.

Carbon-on-metal films for surface plasmon resonance detection of DNA arrays.

Lloyd M. Smith, R. Hamers, R. Corn, 2008, Journal of the American Chemical Society.

Construction of Human Proteoform Families from 21 Tesla FT-ICR Mass Spectrometry Top-Down Proteomic Data

Lloyd M. Smith, M. Shortreed, D. Butcher, 2021 .

Comment on “A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands”

Lloyd M. Smith, Markus Müller, M. Shortreed, 2019, Science Immunology.

Relative quantification of carboxylic acid metabolites by liquid chromatography-mass spectrometry using isotopic variants of cholamine.

Brian L. Frey, Lloyd M. Smith, P. J. Belshaw, 2007, Analytical chemistry.

A Hybrid Spectral Library and Protein Sequence Database Search Strategy for Bottom-Up and Top-Down Proteomic Data Analysis.

Lloyd M. Smith, M. Shortreed, Zach Rolfs, 2022, Journal of proteome research.

Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus.

Brian L. Frey, Lloyd M. Smith, M. Shortreed, 2021, Journal of proteome research.

Evaluation of Variant-Specific Peptides for Detection of SARS-CoV-2 Variants of Concern.

M. Shortreed, A. Timperman, Kantaphon Suddhapas, 2022, Journal of proteome research.

Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus.

Lloyd M. Smith, Stefan K Solntsev, M. Scalf, 2018, Journal of proteome research.

Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database global PTM discovery; multi-protease;

Brian L. Frey, Lloyd M. Smith, M. Scalf, 2019 .

Revealing the role of phosphatidylserine in shear stress-mediated protection in endothelial cells.

Lloyd M. Smith, Julie K. Freed, M. Shortreed, 2008, Endothelium : journal of endothelial cell research.

Ionizable isotopic labeling reagent for relative quantification of amine metabolites by mass spectrometry.

Brian L. Frey, Lloyd M. Smith, P. J. Belshaw, 2006, Analytical chemistry.

Fluorescent fiber-optic calcium sensor for physiological measurements.

M. Shortreed, R. Kopelman, M Shortreed, 1996, Analytical chemistry.

Real-time dynamics of single-DNA molecules undergoing adsorption and desorption at liquid-solid interfaces.

E. Yeung, M. Shortreed, E S Yeung, 2001, Analytical chemistry.

Anion selective optodes: development of a fluorescent fiber optic sensor for the determination of nitrite activity

Michael R. Shortreed, Susan L. R. Barker, Raoul Kopelman, 1996, Optics & Photonics.

In situ oligonucleotide synthesis on carbon materials: stable substrates for microarray fabrication

Lloyd M. Smith, F. Cerrina, M. Rodesch, 2007, Nucleic acids research.

Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences.

Michael R. Shortreed, Brian L. Frey, Lloyd M. Smith, 2014, Journal of proteome research.

Sequence-Specific Capture of Protein-DNA Complexes for Mass Spectrometric Protein Identification

Brian L. Frey, Lloyd M. Smith, M. Olivier, 2011, PloS one.

Sirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction.

Lloyd M. Smith, Brian C. Smith, James J. Ellinger, 2011, Molecular cell.

Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry.

Lloyd M. Smith, Norelle C. Wildburger, Anton N. Kozhinov, 2020, Journal of the American Society for Mass Spectrometry.

Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae

Brian L. Frey, Lloyd M. Smith, A. Gasch, 2014, Journal of proteome research.

HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae.

Anthony J. Cesnik, Lloyd M. Smith, Eugene I. Drigalenko, 2016, Genomics.

Advanced methods for the analysis of chromatin-associated proteins.

Lloyd M. Smith, M. Olivier, M. Shortreed, 2014, Physiological genomics.

To understand the whole, you must know the parts: unraveling the roles of protein-DNA interactions in genome regulation.

Lloyd M. Smith, M. Olivier, M. Shortreed, 2011, The Analyst.

Enhanced protein isoform characterization through long-read proteogenomics

Lloyd M. Smith, Gloria M. Sheynkman, A. Conesa, 2022, Genome Biology.

Specific capture of mammalian cells by cell surface receptor binding to ligand immobilized on gold thin films.

Michael R Shortreed, Lloyd M Smith, Lloyd M. Smith, 2006, Journal of proteome research.

Single‐molecule immunoassay and DNA diagnosis

E. Yeung, M. Shortreed, Yinfa Ma, 2001, Electrophoresis.

Elucidating Escherichia coli Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database.

Leah V Schaffer, Michael R Shortreed, Lloyd M Smith, 2017, Journal of proteome research.

Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins.

Lloyd M. Smith, A. Gasch, M. Scalf, 2017, Analytical chemistry.

Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy

Michael R. Shortreed, Anthony J. Cesnik, Brian L. Frey, 2015, Journal of proteome research.

Enhanced Global Post-translational Modification Discovery with MetaMorpheus.

Michael R Shortreed, Lloyd M Smith, Brian L. Frey, 2018, Journal of proteome research.

Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet

Lloyd M. Smith, Sean J. Humphrey, D. James, 2021, iScience.

Comprehensive Detection of Single Amino Acid Variants and Evaluation of Their Deleterious Potential in a PANC-1 Cell Line.

Michael R Shortreed, Liangliang Sun, Anthony J Cesnik, 2020, Journal of proteome research.

Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data.

Michael R. Shortreed, Robert J. Millikin, Lloyd M. Smith, 2019, Journal of proteome research.

Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data.

Leah V Schaffer, Robert J Millikin, Michael R Shortreed, 2020, Journal of proteome research.

High-throughput single-molecule DNA screening based on electrophoresis

Michael R. Shortreed, Hanlin Li, Edward S. Yeung, 2000, Photonics West - Biomedical Optics.

Directed Energy Transfer Funnels in Dendrimeric Antenna Supermolecules

Michael R. Shortreed, Raoul Kopelman, Zhong You Shi, 1997 .

A surface invasive cleavage assay for highly parallel SNP analysis

Lloyd M. Smith, M. Shortreed, P. W. Stevens, 2002, Human mutation.

Structure-specific DNA cleavage on surfaces.

Lloyd M. Smith, M. Shortreed, P. W. Stevens, 2002, Journal of the American Chemical Society.

A five-level classification system for proteoform identifications

Lloyd M. Smith, N. Kelleher, H. Schlüter, 2019, Nature Methods.

Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance

Lloyd M. Smith, M. Scalf, M. Shortreed, 2018, Stem cell reports.

High-throughput single-molecule spectroscopy in free solution.

E. Yeung, M. Shortreed, Y. Ma, 2000, Analytical chemistry.

ProForma: A Standard Proteoform Notation.

Michael R Shortreed, Lloyd M Smith, Jared B Shaw, 2018, Journal of proteome research.

Evaluation of moFF and FlashLFQ for label free peptide quantification in proteomic workflows within Galaxy-P framework.

Lennart Martens, Andrea Argentini, Praveen Kumar, 2018 .

MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses.

Anthony J. Cesnik, Brian L. Frey, Lloyd M. Smith, 2022, Journal of proteome research.

Spectroscopic Evidence for Excitonic Localization in Fractal Antenna Supermolecules

Michael R. Shortreed, Raoul Kopelman, Joseph Klafter, 1997 .

Alpha-Ketoisocaproate-induced hypersecretion of insulin by islets from diabetes-susceptible mice.

Brian L. Frey, Lloyd M. Smith, A. Attie, 2005, American journal of physiology. Endocrinology and metabolism.

Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform

Lennart Martens, Robert J Millikin, Michael R Shortreed, 2020, Proteomes.

Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform

Lennart Martens, Praveen Kumar, Andrea Argentini, 2020, bioRxiv.

Molecular beacon-style hybridization assay for quantitative analysis of surface invasive cleavage reactions.

Lloyd M. Smith, M. Shortreed, Matthew R. Lockett, 2007, Analytical chemistry.

Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1.

Brian L. Frey, Lloyd M. Smith, M. Scalf, 2022, Journal of proteome research.

A thermodynamic approach to designing structure-free combinatorial DNA word sets

Anne Condon, Holger H. Hoos, Michael R. Shortreed, 2005, Nucleic acids research.

A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics.

Robert J Millikin, Michael R Shortreed, Mark Scalf, 2020, Journal of proteome research.

Analysis of cell surface carbohydrate expression patterns in normal and tumorigenic human breast cell lines using lectin arrays.

Lloyd M. Smith, M. Shortreed, Siyuan Chen, 2007, Analytical chemistry.

Novel NMR and MS Approaches to Metabolomics

J. Markley, M. Shortreed, I. Lewis, 2012 .

Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys

Anthony J. Cesnik, Lloyd M. Smith, M. Olivier, 2017, BMC Genomics.

Construction of Human Proteoform Families from 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Top-Down Proteomic Data.

Leah V Schaffer, Michael R Shortreed, Lloyd M Smith, 2020, Journal of proteome research.

Multiplexed Analysis of Cage and Cage Free Chicken Egg Fatty Acids Using Stable Isotope Labeling and Mass Spectrometry

Lloyd M. Smith, M. Shortreed, A. J. Therrien, 2013, Molecules.

Parallel detection of intrinsic fluorescence from peptides and proteins for quantification during mass spectrometric analysis.

Lloyd M. Smith, M. Scalf, J. Coon, 2011, Analytical chemistry.

Spritz: A Proteogenomic Database Engine

Lei Lu, Michael R. Shortreed, Anthony J. Cesnik, 2020, bioRxiv.

Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells.

Lloyd M. Smith, M. Olivier, Prahlad K Rao, 2018, Journal of Visualized Experiments.

Multiplexed Programmable Release of Captured DNA

Lloyd M. Smith, J. Kennedy-Darling, M. Shortreed, 2014, Chembiochem : a European journal of chemical biology.

Advanced Strategies for Proton-Transfer Reactions Coupled with Parallel Ion Parking on a 21 T FT-ICR MS for Intact Protein Analysis.

Lloyd M. Smith, Chad R. Weisbrod, J. Shabanowitz, 2021, Analytical chemistry.

Sirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction.

Lloyd M. Smith, Brian C. Smith, James J. Ellinger, 2011, Molecular cell.

Carbon-on-metal films for surface plasmon resonance detection of DNA arrays.

Lloyd M. Smith, R. Hamers, R. Corn, 2008, Journal of the American Chemical Society.

Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy.

Leah V Schaffer, Michael R Shortreed, Lloyd M Smith, 2018, Journal of proteome research.

Revealing the role of phosphatidylserine in shear stress-mediated protection in endothelial cells.

Lloyd M. Smith, Julie K. Freed, M. Shortreed, 2008, Endothelium : journal of endothelial cell research.

Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq*

Brian L. Frey, Lloyd M. Smith, Gloria M. Sheynkman, 2013, Molecular & Cellular Proteomics.

Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance

Lloyd M. Smith, M. Scalf, M. Shortreed, 2018, Stem cell reports.

Enhanced Global Post-translational Modification Discovery with MetaMorpheus.

Brian L. Frey, Lloyd M. Smith, Stefan K Solntsev, 2018, Journal of proteome research.

Fast, Free, and Flexible Peptide and Protein Quantification with FlashLFQ.

M. Scalf, M. Shortreed, R. Millikin, 2023, Methods in molecular biology.

Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.

Leah V Schaffer, Michael R Shortreed, Lloyd M Smith, 2018, Journal of proteome research.

IsoBayes: a Bayesian approach for single-isoform proteomics inference

M. Shortreed, Rachel M. Miller, Simone Tiberi, 2024, bioRxiv.