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Author Details

Mark Scalf
University of Wisconsin-Madison College of Letters and Sciences
1997
66
27
Leah V Schaffer (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
38043095Defining Distinct RNA-Protein Interactomes of SARS-CoV-2 Genomic and Subgenomic RNAs.J Proteome Res2024
36308694Fast, Free, and Flexible Peptide and Protein Quantification with FlashLFQ.Methods Mol Biol2023
37039476Axon guidance genes modulate neurotoxicity of ALS-associated UBQLN2.Elife2023
37093976Elucidating the RNA-Protein Interactomes of Target RNAs in Tissue.Anal Chem2023
37293069Defining distinct RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs.bioRxiv2023
34694612Identifying Protein Interactomes of Target RNAs Using HyPR-MS.Methods Mol Biol2022
35192358Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1.J Proteome Res2022
35073098MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses.J Proteome Res2022
35055128Towards an Ideal <i>In Cell</i> Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules.Int J Mol Sci2022
34375640Fused in sarcoma regulates DNA replication timing and kinetics.J Biol Chem2021
33629952Identification of host proteins differentially associated with HIV-1 RNA splice variants.Elife2021
33754701Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics.J Am Soc Mass Spectrom2021
32243168A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics.J Proteome Res2020
32584579Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data.J Proteome Res2020
30765479HDA9-PWR-HOS15 Is a Core Histone Deacetylase Complex Regulating Transcription and Development.Plant Physiol2019
31562246Proteomic analysis of affinity-purified 26S proteasomes identifies a suite of assembly chaperones in <i>Arabidopsis</i>.J Biol Chem2019
31296583Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS.RNA2019
31479276Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database.J Proteome Res2019
29161404Mutation-dependent aggregation and toxicity in a Drosophila model for UBQLN2-associated ALS.Hum Mol Genet2018
30082787EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis.Nat Genet2018
29972301HyPR-MS for Multiplexed Discovery of MALAT1, NEAT1, and NORAD lncRNA Protein Interactomes.J Proteome Res2018
30180576Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy.J Proteome Res2018
29588388SUMOylome Profiling Reveals a Diverse Array of Nuclear Targets Modified by the SUMO Ligase SIZ1 during Heat Stress.Plant Cell2018
29358085Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance.Stem Cell Reports2018
29793340Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus.J Proteome Res2018
29227670Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families.Anal Chem2018
29195273Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.J Proteome Res2018
29343504Canonical and Noncanonical Actions of Arabidopsis Histone Deacetylases in Ribosomal RNA Processing.Plant Cell2018
28654248Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins.Anal Chem2017
28461270Mass Spectrometric Analyses Reveal a Central Role for Ubiquitylation in Remodeling the Arabidopsis Proteome during Photomorphogenesis.Mol Plant2017
28248113Global Post-Translational Modification Discovery.J Proteome Res2017
29208937Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry.Sci Rep2017
28968100Elucidating Escherichia coli Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database.J Proteome Res2017
28704058Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry.J Proteome Res2017
28608680Correction to "Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements".J Proteome Res2017
26791624Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus search engine.Proteomics2016
26476196Proteomic analysis of naturally-sourced biological scaffolds.Biomaterials2016
27873573POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in <i>Arabidopsis</i>.Elife2016
27184763HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae.Genomics2016
26941048Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements.J Proteome Res2016
26418581Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search.J Proteome Res2015
24175627Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences.J Proteome Res2014
24999558Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae.J Proteome Res2014
24486316Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions.Biochem Biophys Res Commun2014
23197790Quantitative proteomics reveals factors regulating RNA biology as dynamic targets of stress-induced SUMOylation in Arabidopsis.Mol Cell Proteomics2013
23667124Advanced proteomic analyses yield a deep catalog of ubiquitylation targets in Arabidopsis.Plant Cell2013
23536786Characterization and quantification of intact 26S proteasome proteins by real-time measurement of intrinsic fluorescence prior to top-down mass spectrometry.PLoS One2013
21172464Quantitative proteomic analysis of the chemolithoautotrophic bacterium Nitrosomonas europaea: comparison of growing- and energy-starved cells.J Proteomics2011
21806063A mechanical nanomembrane detector for time-of-flight mass spectrometry.Nano Lett2011
21314137Parallel detection of intrinsic fluorescence from peptides and proteins for quantification during mass spectrometric analysis.Anal Chem2011
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Collaborators

Lloyd M Smith
University of Wisconsin-Madison College of Letters and Sciences
Co-authored papers 65
Michael R Shortreed
University of Wisconsin-Madison
Co-authored papers 24
Brian L Frey
University of Wisconsin-Madison, 1101 University Ave
Co-authored papers 16
Rachel A Knoener
University of Wisconsin-Madison College of Letters and Sciences
Co-authored papers 10
Anthony J Cesnik
University of Wisconsin-Madison
Co-authored papers 10
Leah V Schaffer (CM4AI)
University of California San Diego
Co-authored papers 8
Robert J Millikin
Morgridge Institute for Research
Co-authored papers 6
Michael Olivier
Co-authored papers 5
Yunxiang Dai
University of Wisconsin-Madison
Co-authored papers 4
Stefan K Solntsev
University of Wisconsin-Madison
Co-authored papers 4
Audrey P Gasch
University of Wisconsin-Madison
Co-authored papers 4
Katherine E Buxton
University of Wisconsin , 1101 University Avenue
Co-authored papers 3
Rupa Sridharan
Wisconsin Institute for Discovery, University of Wisconsin-Madison
Co-authored papers 2
Yoshihiro Kawaoka
Influenza Research Institute, University of Wisconsin
Co-authored papers 2
Zach Rolfs
University of Wisconsin-Madison
Co-authored papers 2
Andrew S Greene
Co-authored papers 2
Craig D Wenger
University of Wisconsin
Co-authored papers 2
Nur Zafirah Zaidan
Wisconsin Institute for Discovery, University of Wisconsin-Madison
Co-authored papers 2
Gloria M Sheynkman (CM4AI)
University of Virginia
Co-authored papers 2
Ji Eun Lee
Soonchunhyang University College of Medicine, Bucheon Hospital
Co-authored papers 2
Qiyao Li
The Second Hospital of Hebei Medical University
Co-authored papers 2
Gopal Iyer
University of Wisconsin School of Medicine and Public Health, University of Wisconsin
Co-authored papers 1
Jaime E Brown
Wisconsin Institute for Discovery, University of Wisconsin-Madison
Co-authored papers 1
Christina Kendziorski
University of Wisconsin-Madison
Co-authored papers 1
Kolin J Walker
Wisconsin Institute for Discovery, University of Wisconsin-Madison
Co-authored papers 1
Jarred W Rensvold
Washington University School of Medicine
Co-authored papers 1
Jiani Chen
Co-authored papers 1
Michael F Moran
Hospital for Sick Children, University of Toronto
Co-authored papers 1
Adam Jochem
Morgridge Institute for Research
Co-authored papers 1
Rachel M Miller
University of Wisconsin , 1101 University Avenue
Co-authored papers 1
Release 1.2