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Author Details

Michael Riffle
University of Washington
2003
42
23
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36629399Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline.J Proteome Res2023
37683181Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data-Independent Acquisition.J Proteome Res2023
37398334Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data Independent Acquisition.bioRxiv2023
35184559Discovery and Visualization of Uncharacterized Drug-Protein Adducts Using Mass Spectrometry.Anal Chem2022
35353161Three interacting regions of the Ndc80 and Dam1 complexes support microtubule tip-coupling under load.J Cell Biol2022
35716664Cullin-independent recognition of HHARI substrates by a dynamic RBR catalytic domain.Structure2022
31492961Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes.ISME J2020
33170893Survey of metaproteomics software tools for functional microbiome analysis.PLoS One2020
30525651Proxl (Protein Cross-Linking Database): A Public Server, QC Tools, and Other Major Updates.J Proteome Res2019
31796751Growth phase proteomics of the heterotrophic marine bacterium Ruegeria pomeroyi.Sci Data2019
29487209Human Ska complex and Ndc80 complex interact to form a load-bearing assembly that strengthens kinetochore-microtubule attachments.Proc Natl Acad Sci U S A2018
29903865Novel phosphorylation states of the yeast spindle pole body.Biol Open2018
27824341Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.ISME J2017
28191870The Ndc80 complex bridges two Dam1 complex rings.Elife2017
28331072Direct measurement of the strength of microtubule attachment to yeast centrosomes.Mol Biol Cell2017
29280960MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data.Proteomes2017
28730805Integrating Discovery-driven Proteomics and Selected Reaction Monitoring To Develop a Noninvasive Assay for Geoduck Reproductive Maturation.J Proteome Res2017
27302480ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data.J Proteome Res2016
25812159Kojak: efficient analysis of chemically cross-linked protein complexes.J Proteome Res2015
26430240Regulation of outer kinetochore Ndc80 complex-based microtubule attachments by the central kinetochore Mis12/MIND complex.Proc Natl Acad Sci U S A2015
26560693The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling.Nat Commun2015
26163422Genetic Regulation of Dna2 Localization During the DNA Damage Response.G3 (Bethesda)2015
26133526Visualization and dissemination of multidimensional proteomics data comparing protein abundance during Caenorhabditis elegans development.J Am Soc Mass Spectrom2015
25884379Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences.BMC Res Notes2015
25662576Integrated RNA- and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development.J Proteomics2015
25139910Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data.Mol Cell Proteomics2014
25230952Kinetochore biorientation in Saccharomyces cerevisiae requires a tightly folded conformation of the Ndc80 complex.Genetics2014
25056180SnipViz: a compact and lightweight web site widget for display and dissemination of multiple versions of gene and protein sequences.BMC Res Notes2014
23720455Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast.Genome Res2013
22611296A mass spectrometry proteomics data management platform.Mol Cell Proteomics2012
22846423JobCenter: an open source, cross-platform, and distributed job queue management system optimized for scalability and versatility.Source Code Biol Med2012
22842922Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress.Nat Cell Biol2012
21824995The Proteome Folding Project: proteome-scale prediction of structure and function.Genome Res2011
20298601Large-scale prediction of protein-protein interactions from structures.BMC Bioinformatics2010
20482811The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images.BMC Bioinformatics2010
19056681Bir1 is required for the tension checkpoint.Mol Biol Cell2009
19795424Proteomics data repositories.Proteomics2009
18989393Transmembrane topology and signal peptide prediction using dynamic bayesian networks.PLoS Comput Biol2008
17373854Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology.PLoS Biol2007
15608220The Yeast Resource Center Public Data Repository.Nucleic Acids Res2005
15282802Localization of proteins that are coordinately expressed with Cln2 during the cell cycle.Yeast2004
14690591Assigning function to yeast proteins by integration of technologies.Mol Cell2003
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Collaborators

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University of Washington
Co-authored papers 27
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University of Washington
Co-authored papers 15
Alex Zelter
University of Washington
Co-authored papers 13
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University of Washington
Co-authored papers 12
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Co-authored papers 7
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University of Washington-Genome Sciences
Co-authored papers 6
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Institute for Systems Biology
Co-authored papers 5
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Institute for Systems Biology
Co-authored papers 5
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Co-authored papers 4
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Co-authored papers 4
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University of Washington
Co-authored papers 3
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University of Washington
Co-authored papers 2
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Institut Pasteur, Universite Paris Cite, CNRS UMR 8
Co-authored papers 2
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University of Toronto, 1 King's College Circle
Co-authored papers 2
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Co-authored papers 2
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TheScripps Research Institute
Co-authored papers 2
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University of Washington
Co-authored papers 2
Richard Bonneau
Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation
Co-authored papers 2
Jimmy K Eng
University of Washington
Co-authored papers 2
Brendan MacLean
Co-authored papers 2
David Baker
University of Washington
Co-authored papers 2
Dennis Shasha
Courant Institute of Mathematical Sciences, New York University
Co-authored papers 1
Timothy J Griffin
University of Minnesota
Co-authored papers 1
David A Agard
University of California, USA Quantitative Biosciences Institute (QBI) san francisco
Co-authored papers 1
Jeff A Bilmes
Co-authored papers 1
Pratik D Jagtap
University of Minnesota
Co-authored papers 1
Brian E Snydsman
Co-authored papers 1
Anna Y Lee
Ontario Institute for Cancer Research
Co-authored papers 1
Riccardo Pellarin
CNRS UMR 5086 and Universite Claude Bernard Lyon 1
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Michael Costanzo
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Release 1.2