Michael R. Shortreed
Reproducibility track record
1
assessed papers
79/100
mean reproducibility
1
reproduced (C1–C2)
0
flagged
0
total citations
flag rate:
0%
(0/1)
The share of this author’s assessed papers carrying a ⚑ flag. A concentration is a prompt for expert review — never, on its own, a determination about the person.
Authorship role
first author: 0
last author: 0
Topics
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Funders
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Frequent co-authors
Christina Chatzipantsiou 1Ana Conesa 1Anne Deslattes Mays 1Madison Mehlferber 1Lloyd M. Smith 1Chance John Luckey 1Erin D. Jeffery 1Peter J. Castaldi 1Yunxiang Dai 1Simi Kaur 1
Institutions
University of Wisconsin–Madison 1University of Virginia 1SIB Swiss Institute of Bioinformatics 1University of Zurich 1Brigham and Women's Hospital 1Consejo Superior de Investigaciones Científicas 1
Geography (author institutions)
US 1CH 1ES 1
Co-author network
Collaborators, sized by shared output and coloured by their own reproducibility (green = high, red = low). Click a node to open their card. A pattern is a prompt for review, never a determination.
How this author’s assessed papers reproduced — the outcome of reproduction attempts, not a judgement of the person. Coverage is partial and grows over time.
Assessed papers (1)
Complete publication record (140)
Request a reproduction →1 assessed by us (1 reproduced) · 139 not yet assessed — every PubMed paper on record, linked below.
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Most-abundant isotopic peak precursor matching in MetaMorpheus: re-analysis results for the yeast top-down dataset MSV000081592 ↗Zenodo (CERN European Organization for Nuclear Research) · 2026not yet assessed
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Most-abundant isotopic peak precursor matching in MetaMorpheus: re-analysis results for the yeast top-down dataset MSV000081592 ↗Zenodo (CERN European Organization for Nuclear Research) · 2026not yet assessed
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Open-Source and FAIR Research Software for Proteomics ↗Journal of Proteome Research · 2025 · PMID 40267229not yet assessed
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IsoBayes: a Bayesian approach for single-isoform proteomics inference ↗Bioinformatics · 2025 · PMID 40796134not yet assessed
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Improved Detection of Differentially Abundant Proteins through FDR-Control of Peptide-Identity-Propagation ↗Journal of Proteome Research · 2025 · PMID 40736352not yet assessed
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A Fast Neural Network for Isotopic Charge State Assignment ↗Journal of the American Chemical Society · 2025 · PMID 40493377not yet assessed
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A Fast Neural Network for Isotopic Charge State Assignment ↗ChemRxiv · 2025not yet assessed
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A Fast Neural Network for Isotopic Charge State Assignment ↗ChemRxiv · 2025not yet assessed
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Quantitative proteome-wide O-glycoproteomics analysis with FragPipe ↗Analytical and Bioanalytical Chemistry · 2024 · PMID 38877149not yet assessed
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Dehydroamino acids and their crosslinks in Alzheimer’s disease aggregates ↗Brain Communications · 2024 · PMID 39882022not yet assessed
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Open-source and FAIR Research Software for Proteomics ↗ChemRxiv · 2024not yet assessed
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Discovery of dehydroamino acids and their crosslinks in Tau and other aggregating proteins of Alzheimer’s disease ↗bioRxiv (Cold Spring Harbor Laboratory) · 2024not yet assessed
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Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet ↗iScience · 2023 · PMID 38188515not yet assessed
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Enhanced protein isoform characterization through long-read proteogenomicsGenome biology · 2022 · PMID 35241129L1 79/100
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MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses ↗Journal of Proteome Research · 2022 · PMID 35073098not yet assessed
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A Hybrid Spectral Library and Protein Sequence Database Search Strategy for Bottom-Up and Top-Down Proteomic Data Analysis ↗Journal of Proteome Research · 2022 · PMID 36206157not yet assessed
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Evaluation of Variant-Specific Peptides for Detection of SARS-CoV-2 Variants of Concern ↗Journal of Proteome Research · 2022 · PMID 36108102not yet assessed
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Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1 ↗Journal of Proteome Research · 2022 · PMID 35192358not yet assessed
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Enhanced Protein Isoform Characterization Through Long-Read Proteogenomics - Workflow Results ↗Zenodo (CERN European Organization for Nuclear Research) · 2022not yet assessed
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Enhanced Protein Isoform Characterization Through Long-Read Proteogenomics - Workflow Results ↗Zenodo (CERN European Organization for Nuclear Research) · 2022not yet assessed
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Proteoform Analysis and Construction of Proteoform Families in Proteoform Suite ↗Methods in molecular biology · 2022 · PMID 35657588not yet assessed
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How many post-translationally proteasomal spliced HLA-I peptides can be confidently identified in large scale MS/MS data? ↗Molecular Immunology · 2022not yet assessed
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Enhanced Protein Isoform Characterization Through Long-Read Proteogenomics - Workflow Results ↗Zenodo (CERN European Organization for Nuclear Research) · 2022not yet assessed
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Additional file 5 of Enhanced protein isoform characterization through long-read proteogenomics ↗Figshare · 2022not yet assessed
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Additional file 4 of Enhanced protein isoform characterization through long-read proteogenomics ↗Figshare · 2022not yet assessed
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Additional file 7 of Enhanced protein isoform characterization through long-read proteogenomics ↗Figshare · 2022not yet assessed
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Additional file 3 of Enhanced protein isoform characterization through long-read proteogenomics ↗Figshare · 2022not yet assessed
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Additional file 8 of Enhanced protein isoform characterization through long-read proteogenomics ↗Figshare · 2022not yet assessed
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Additional file 6 of Enhanced protein isoform characterization through long-read proteogenomics ↗Figshare · 2022not yet assessed
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Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet ↗iScience · 2021 · PMID 34622154not yet assessed
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Advanced Strategies for Proton-Transfer Reactions Coupled with Parallel Ion Parking on a 21 T FT-ICR MS for Intact Protein Analysis ↗Analytical Chemistry · 2021 · PMID 34165955not yet assessed
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Enhanced Proteomic Data Analysis with MetaMorpheus ↗Methods in molecular biology · 2021 · PMID 36308684not yet assessed
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Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics ↗Journal of the American Society for Mass Spectrometry · 2021 · PMID 33754701not yet assessed
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Fast, Free, and Flexible Peptide and Protein Quantification with FlashLFQ ↗Methods in molecular biology · 2021 · PMID 36308694not yet assessed
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Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus ↗Journal of Proteome Research · 2021 · PMID 33683901not yet assessed
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Enhanced Protein Isoform Characterization Through Long-Read Proteogenomics - Jurkat Samples and Reference Data ↗Zenodo (CERN European Organization for Nuclear Research) · 2021not yet assessed
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Enhanced protein isoform characterization through long-read proteogenomics ↗Zenodo (CERN European Organization for Nuclear Research) · 2021not yet assessed
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Enhanced protein isoform characterization through long-read proteogenomics ↗Zenodo (CERN European Organization for Nuclear Research) · 2021not yet assessed
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Enhanced protein isoform characterization through long-read proteogenomics ↗Zenodo (CERN European Organization for Nuclear Research) · 2021not yet assessed
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Enhanced protein isoform characterization through long-read proteogenomics ↗Zenodo (CERN European Organization for Nuclear Research) · 2021not yet assessed
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Enhanced protein isoform characterization through long-read proteogenomics ↗Zenodo (CERN European Organization for Nuclear Research) · 2021not yet assessed
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O-Pair Search with MetaMorpheus for O-glycopeptide characterization ↗Nature Methods · 2020 · PMID 33106676not yet assessed
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Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry ↗Journal of the American Society for Mass Spectrometry · 2020 · PMID 32812765not yet assessed
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Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data ↗Journal of Proteome Research · 2020 · PMID 32584579not yet assessed
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Spritz: A Proteogenomic Database Engine ↗Journal of Proteome Research · 2020 · PMID 32967423not yet assessed
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Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform ↗Proteomes · 2020 · PMID 32650610not yet assessed
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Comprehensive Detection of Single Amino Acid Variants and Evaluation of Their Deleterious Potential in a PANC-1 Cell Line ↗Journal of Proteome Research · 2020 · PMID 32058723not yet assessed
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Construction of Human Proteoform Families from 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Top-Down Proteomic Data ↗Journal of Proteome Research · 2020 · PMID 33074679not yet assessed
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A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics ↗Journal of Proteome Research · 2020 · PMID 32243168not yet assessed
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O-Pair Search with MetaMorpheus for O-glycopeptide Characterization ↗bioRxiv (Cold Spring Harbor Laboratory) · 2020not yet assessed
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Spritz: A Proteogenomic Database Engine ↗bioRxiv (Cold Spring Harbor Laboratory) · 2020not yet assessed
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Precursor intensity-based label-free quantification software tools for proteomic and multiomic analysis within the Galaxy Platform ↗bioRxiv (Cold Spring Harbor Laboratory) · 2020not yet assessed
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Identification and Quantification of Proteoforms by Mass Spectrometry ↗PROTEOMICS · 2019 · PMID 31050378not yet assessed
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Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS ↗RNA · 2019 · PMID 31296583not yet assessed
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Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data ↗Journal of Proteome Research · 2019 · PMID 31378069not yet assessed
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Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database ↗Journal of Proteome Research · 2019 · PMID 31479276not yet assessed
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Intact-Mass Analysis Facilitating the Identification of Large Human Heart Proteoforms ↗Analytical Chemistry · 2019 · PMID 31393705not yet assessed
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Identification and Quantification of Proteoforms by Mass SpectrometryPMC · 2019not yet assessed
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Comment on “A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands” ↗Science Immunology · 2019 · PMID 31420320not yet assessed
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Back Cover: Identification and Quantification of Proteoforms by Mass Spectrometry ↗PROTEOMICS · 2019not yet assessed
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Enhanced Global Post-translational Modification Discovery with MetaMorpheus ↗Journal of Proteome Research · 2018 · PMID 29578715not yet assessed
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Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus ↗Journal of Proteome Research · 2018 · PMID 29793340not yet assessed
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Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance ↗Stem Cell Reports · 2018 · PMID 29358085not yet assessed
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ProForma: A Standard Proteoform Notation ↗Journal of Proteome Research · 2018 · PMID 29397739not yet assessed
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Global Identification of Post-Translationally Spliced Peptides with Neo-Fusion ↗Journal of Proteome Research · 2018 · PMID 30346791not yet assessed
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Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy ↗Journal of Proteome Research · 2018 · PMID 30180576not yet assessed
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Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers ↗Translational Oncology · 2018 · PMID 29723810not yet assessed
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Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells ↗Journal of Visualized Experiments · 2018 · PMID 29912191not yet assessed
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Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells ↗Journal of Visualized Experiments · 2018not yet assessed
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PD60-09 DISCOVERY AND VALIDATION OF NOVEL LONG NONCODING RNAS THAT DIFFERENTIATE AGGRESSIVE AND INDOLENT PROSTATE CANCER ↗The Journal of Urology · 2018not yet assessed
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Evaluation of moFF and FlashLFQ for label free peptide quantification in proteomic workflows within Galaxy-P framework. ↗Faculty of 1000 Research Ltd · 2018not yet assessed
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Ultrafast Peptide Label-Free Quantification with FlashLFQ ↗Journal of Proteome Research · 2017 · PMID 29083185not yet assessed
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Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families ↗Journal of Proteome Research · 2017 · PMID 29195273not yet assessed
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Elucidating <i>Escherichia coli</i> Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database ↗Journal of Proteome Research · 2017 · PMID 28968100not yet assessed
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Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families ↗Analytical Chemistry · 2017 · PMID 29227670not yet assessed
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Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys ↗BMC Genomics · 2017 · PMID 29132314not yet assessed
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Elucidating Protein–DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry ↗Journal of Proteome Research · 2017 · PMID 28704058not yet assessed
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Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins ↗Analytical Chemistry · 2017 · PMID 28654248not yet assessed
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Correction to “Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements” ↗Journal of Proteome Research · 2017 · PMID 28608680not yet assessed
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Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation ↗Annual Review of Analytical Chemistry · 2016 · PMID 27049631not yet assessed
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Global Post-Translational Modification Discovery ↗Journal of Proteome Research · 2016 · PMID 28248113not yet assessed
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Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements ↗Journal of Proteome Research · 2016 · PMID 26941048not yet assessed
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HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae ↗Genomics · 2016 · PMID 27184763not yet assessed
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Recent developments and new directions for the Galaxy-P project ↗Faculty of 1000 Research Ltd · 2016not yet assessed
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Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search ↗Journal of Proteome Research · 2015 · PMID 26418581not yet assessed
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Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy ↗Journal of Proteome Research · 2015 · PMID 26704769not yet assessed
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Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations ↗BMC Genomics · 2014 · PMID 25149441not yet assessed
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Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in <i>Saccharomyces cerevisiae</i> ↗Journal of Proteome Research · 2014 · PMID 24999558not yet assessed
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Multiplexed Programmable Release of Captured DNA ↗ChemBioChem · 2014 · PMID 25157426not yet assessed
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Advanced methods for the analysis of chromatin-associated proteins ↗Physiological Genomics · 2014 · PMID 24803678not yet assessed
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Inside Cover: Multiplexed Programmable Release of Captured DNA (ChemBioChem 16/2014) ↗ChemBioChem · 2014not yet assessed
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Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq ↗Molecular & Cellular Proteomics · 2013 · PMID 23629695not yet assessed
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Large-Scale Mass Spectrometric Detection of Variant Peptides Resulting from Nonsynonymous Nucleotide Differences ↗Journal of Proteome Research · 2013 · PMID 24175627not yet assessed
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Multiplexed Analysis of Cage and Cage Free Chicken Egg Fatty Acids Using Stable Isotope Labeling and Mass Spectrometry ↗Molecules · 2013 · PMID 24317525not yet assessed
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Novel NMR and MS Approaches to Metabolomics ↗Methods in pharmacology and toxicology · 2012not yet assessed
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Sirt3 Promotes the Urea Cycle and Fatty Acid Oxidation during Dietary Restriction ↗Molecular Cell · 2011 · PMID 21255725not yet assessed
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Sequence-Specific Capture of Protein-DNA Complexes for Mass Spectrometric Protein Identification ↗PLoS ONE · 2011 · PMID 22028835not yet assessed
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Sirt3 Promotes the Urea Cycle and Fatty Acid Oxidation during Dietary Restriction ↗Molecular Cell · 2011not yet assessed
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Parallel Detection of Intrinsic Fluorescence from Peptides and Proteins for Quantification during Mass Spectrometric Analysis ↗Analytical Chemistry · 2011 · PMID 21314137not yet assessed
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To understand the whole, you must know the parts: unraveling the roles of protein–DNA interactions in genome regulation ↗The Analyst · 2011 · PMID 21629937not yet assessed
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Carbon-on-Metal Films for Surface Plasmon Resonance Detection of DNA Arrays ↗Journal of the American Chemical Society · 2008 · PMID 18597426not yet assessed
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Aldehyde-Terminated Amorphous Carbon Substrates for the Fabrication of Biomolecule Arrays ↗Langmuir · 2008 · PMID 18672922not yet assessed
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Revealing the Role of Phosphatidylserine in Shear Stress–Mediated Protection in Endothelial Cells ↗Endothelium · 2008 · PMID 18663626not yet assessed
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Analysis of Cell Surface Carbohydrate Expression Patterns in Normal and Tumorigenic Human Breast Cell Lines Using Lectin Arrays ↗Analytical Chemistry · 2007 · PMID 17580952not yet assessed
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Relative Quantification of Carboxylic Acid Metabolites by Liquid Chromatography−Mass Spectrometry Using Isotopic Variants of Cholamine ↗Analytical Chemistry · 2007 · PMID 17563114not yet assessed
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Molecular Beacon-Style Hybridization Assay for Quantitative Analysis of Surface Invasive Cleavage Reactions ↗Analytical Chemistry · 2007 · PMID 17595056not yet assessed
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Ionizable Isotopic Labeling Reagent for Relative Quantification of Amine Metabolites by Mass Spectrometry ↗Analytical Chemistry · 2006 · PMID 16970314not yet assessed
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Quantitative Detection of Individual Cleaved DNA Molecules on Surfaces Using Gold Nanoparticles and Scanning Electron Microscope Imaging ↗Analytical Chemistry · 2006 · PMID 16503604not yet assessed
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α-Ketoisocaproate-induced hypersecretion of insulin by islets from diabetes-susceptible mice ↗American Journal of Physiology-Endocrinology and Metabolism · 2005 · PMID 15741243not yet assessed
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Parallel Single Nucleotide Polymorphism Genotyping by Surface Invasive Cleavage with Universal Detection ↗Analytical Chemistry · 2005 · PMID 15828773not yet assessed
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Scoring Single-Nucleotide Polymorphisms at the Single-Molecule Level by Counting Individual DNA Cleavage Events on Surfaces ↗Analytical Chemistry · 2005 · PMID 16223245not yet assessed
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Surface Amplification of Invasive Cleavage Products ↗Journal of the American Chemical Society · 2004 · PMID 15012108not yet assessed
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Structure-Specific DNA Cleavage on Surfaces ↗Journal of the American Chemical Society · 2002 · PMID 12095336not yet assessed
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A surface invasive cleavage assay for highly parallel SNP analysis ↗Human Mutation · 2002 · PMID 11933196not yet assessed
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Real-Time Dynamics of Single-DNA Molecules Undergoing Adsorption and Desorption at Liquid−Solid Interfaces ↗Analytical Chemistry · 2001 · PMID 11305636not yet assessed
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Single-molecule immunoassay and DNA diagnosis ↗Electrophoresis · 2001 · PMID 11258749not yet assessed
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High-Throughput Single-Molecule Spectroscopy in Free Solution ↗Analytical Chemistry · 2000 · PMID 11028623not yet assessed
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High-Throughput Single-Molecule DNA Screening Based on Electrophoresis ↗Analytical Chemistry · 2000 · PMID 10905322not yet assessed
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<title>High-throughput single-molecule DNA screening based on electrophoresis</title> ↗Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · 2000not yet assessed
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Molecular Nano-Lenses: Directed Energy Migration and Back-Transfer in Dendrimeric Antenna Supermolecules ↗Molecular crystals and liquid crystals science technology. Section A, Molecular crystals and liquid crystals/Molecular crystals and liquid crystals science and technology. Section A, Molecular crystals and liquid crystals · 1998not yet assessed
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Directed Energy Transfer Funnels in Dendrimeric Antenna Supermolecules ↗The Journal of Physical Chemistry B · 1997not yet assessed
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Spectroscopic Evidence for Excitonic Localization in Fractal Antenna Supermolecules ↗Physical Review Letters · 1997not yet assessed
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Development of a fluorescent optical potassium-selective ion sensor with ratiometric response for intracellular applications ↗Sensors and Actuators B Chemical · 1997not yet assessed
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Utilization of Lipophilic Ionic Additives in Liquid Polymer Film Optodes for Selective Anion Activity Measurements ↗Analytical Chemistry · 1997 · PMID 9075401not yet assessed
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Fluorescent Fiber-Optic Calcium Sensor for Physiological Measurements ↗Analytical Chemistry · 1996 · PMID 8651501not yet assessed
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Miniature Sodium-Selective Ion-Exchange Optode with Fluorescent pH Chromoionophores and Tunable Dynamic Range ↗Analytical Chemistry · 1996 · PMID 8694263not yet assessed
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Anion-selective liquid-polymer optodes with fluorescent pH chromoionophores, tunable dynamic range and diffusion enhanced lifetimes ↗Sensors and Actuators B Chemical · 1996not yet assessed
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Supermolecular Excitation Antenna: Ordered Energy Funnel ↗Molecular crystals and liquid crystals science technology. Section A, Molecular crystals and liquid crystals/Molecular crystals and liquid crystals science and technology. Section A, Molecular crystals and liquid crystals · 1996not yet assessed
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<title>Anion selective optodes: development of a fluorescent fiber optic sensor for the determination of nitrite activity</title> ↗Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · 1996not yet assessed
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Lifetime Enhancement of Ultrasmall Fluorescent Liquid Polymeric Film Based Optodes by Diffusion-Induced Self-Recovery after Photobleaching ↗Analytical Chemistry · 1996 · PMID 8916453not yet assessed
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Development of ultrasmall ion optodes for physiological measurements and supermolecules for intramolecular energy transfer.Deep Blue (University of Michigan) · 1996not yet assessed
Full bibliography from OpenAlex; reproducibility verdicts matched by PMID.
Author attribution follows OpenAlex disambiguation, which is imperfect — a researcher's papers can be split across profiles or mixed with a namesake.
Merged across profiles sharing this ORCID where present. See every “Shortreed M” paper on PubMed ↗