Transmembrane topology and signal peptide prediction using dynamic bayesian networks von Reynolds, Sheila M, Käll, Lukas, Riffle, Michael E, Bilmes, Jeff A, Noble, William Stafford

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Kojak: Efficient Analysis of Chemically Cross-Linked Protein Complexes von Hoopmann, Michael R, Zelter, Alex, Johnson, Richard S, Riffle, Michael, MacCoss, Michael J, Davis, Trisha N, Moritz, Robert L

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Large-scale prediction of protein-protein interactions from structures von Hue, Martial, Riffle, Michael, Vert, Jean-Philippe, Noble, William S

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Survey of metaproteomics software tools for functional microbiome analysis von Sajulga, Ray, Easterly, Caleb, Riffle, Michael, Mesuere, Bart, Muth, Thilo, Mehta, Subina, Kumar, Praveen, Johnson, James, Gruening, Bjoern Andreas, Schiebenhoefer, Henning, Kolmeder, Carolin A., Fuchs, Stephan, Nunn, Brook L., Rudney, Joel, Griffin, Timothy J., Jagtap, Pratik D.

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Integrating Discovery-driven Proteomics and Selected Reaction Monitoring To Develop a Noninvasive Assay for Geoduck Reproductive Maturation von Timmins-Schiffman, Emma B, Crandall, Grace A, Vadopalas, Brent, Riffle, Michael E, Nunn, Brook L, Roberts, Steven B

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Regulation of outer kinetochore Ndc80 complex-based microtubule attachments by the central kinetochore Mis12/MIND complex von Kudalkar, Emily M., Scarborough, Emily A., Umbreit, Neil T., Zelter, Alex, Gestaut, Daniel R., Riffle, Michael, Johnson, Richard S., MacCoss, Michael J., Asbury, Charles L., Davis, Trisha N.

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The Ndc80 complex bridges two Dam1 complex rings von Kim, Jae Ook, Zelter, Alex, Umbreit, Neil T, Bollozos, Athena, Riffle, Michael, Johnson, Richard, MacCoss, Michael J, Asbury, Charles L, Davis, Trisha N

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The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images von Riffle, Michael, Davis, Trisha N

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MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data von Riffle, Michael, May, Damon H, Timmins-Schiffman, Emma, Mikan, Molly P, Jaschob, Daniel, Noble, William Stafford, Nunn, Brook L

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Assigning Function to Yeast Proteins by Integration of Technologies von Hazbun, Tony R, Malmström, Lars, Anderson, Scott, Graczyk, Beth J, Fox, Bethany, Riffle, Michael, Sundin, Bryan A, Aranda, J.Derringer, McDonald, W.Hayes, Chiu, Chun-Hwei, Snydsman, Brian E, Bradley, Phillip, Muller, Eric G.D, Fields, Stanley, Baker, David, Yates, John R, Davis, Trisha N

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SnipViz: a compact and lightweight web site widget for display and dissemination of multiple versions of gene and protein sequences von Jaschob, Daniel, Davis, Trisha N, Riffle, Michael

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Novel phosphorylation states of the yeast spindle pole body von Fong, Kimberly K, Zelter, Alex, Graczyk, Beth, Hoyt, Jill M, Riffle, Michael, Johnson, Richard, MacCoss, Michael J, Davis, Trisha N

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Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology von Malmström, Lars, Riffle, Michael, Strauss, Charlie E M, Chivian, Dylan, Davis, Trisha N, Bonneau, Richard, Baker, David

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Human Ska complex and Ndc80 complex interact to form a load-bearing assembly that strengthens kinetochore–microtubule attachments von Helgeson, Luke A., Zelter, Alex, Riffle, Michael, MacCoss, Michael J., Asbury, Charles L., Davis, Trisha N.

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ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data von Riffle, Michael, Jaschob, Daniel, Zelter, Alex, Davis, Trisha N

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Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress von Tkach, Johnny M., Yimit, Askar, Lee, Anna Y., Riffle, Michael, Costanzo, Michael, Jaschob, Daniel, Hendry, Jason A., Ou, Jiongwen, Moffat, Jason, Boone, Charles, Davis, Trisha N., Nislow, Corey, Brown, Grant W.

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Three interacting regions of the Ndc80 and Dam1 complexes support microtubule tip-coupling under load von Flores, Rachel L, Peterson, Zachary E, Zelter, Alex, Riffle, Michael, Asbury, Charles L, Davis, Trisha N

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Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data-Independent Acquisition von Heil, Lilian R., Damoc, Eugen, Arrey, Tabiwang N., Pashkova, Anna, Denisov, Eduard, Petzoldt, Johannes, Peterson, Amelia C., Hsu, Chris, Searle, Brian C., Shulman, Nicholas, Riffle, Michael, Connolly, Brian, MacLean, Brendan X., Remes, Philip M., Senko, Michael W., Stewart, Hamish I., Hock, Christian, Makarov, Alexander A., Hermanson, Daniel, Zabrouskov, Vlad, Wu, Christine C., MacCoss, Michael J.

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Discovery and Visualization of Uncharacterized Drug–Protein Adducts Using Mass Spectrometry von Riffle, Michael, Hoopmann, Michael R, Jaschob, Daniel, Zhong, Guo, Moritz, Robert L, MacCoss, Michael J, Davis, Trisha N, Isoherranen, Nina, Zelter, Alex

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A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline von Rojas Echeverri, Juan Camilo, Hause, Frank, Iacobucci, Claudio, Ihling, Christian H., Tänzler, Dirk, Shulman, Nicholas, Riffle, Michael, MacLean, Brendan X., Sinz, Andrea

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