Michael Riffle
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Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress
JM Tkach, A Yimit, AY Lee, M Riffle, M Costanzo, D Jaschob, JA Hendry, ...
Nature cell biology 14 (9), 966-976, 2012
Assigning function to yeast proteins by integration of technologies
TR Hazbun, L Malmström, S Anderson, BJ Graczyk, B Fox, M Riffle, ...
Molecular cell 12 (6), 1353-1365, 2003
Transmembrane topology and signal peptide prediction using dynamic bayesian networks
SM Reynolds, L Käll, ME Riffle, JA Bilmes, WS Noble
PLoS computational biology 4 (11), e1000213, 2008
Kojak: efficient analysis of chemically cross-linked protein complexes
MR Hoopmann, A Zelter, RS Johnson, M Riffle, MJ MacCoss, TN Davis, ...
Journal of proteome research 14 (5), 2190-2198, 2015
Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast
DA Skelly, GE Merrihew, M Riffle, CF Connelly, EO Kerr, M Johansson, ...
Genome research 23 (9), 1496-1504, 2013
Large-scale prediction of protein-protein interactions from structures
M Hue, M Riffle, JP Vert, WS Noble
BMC bioinformatics 11 (1), 1-9, 2010
Human Ska complex and Ndc80 complex interact to form a load-bearing assembly that strengthens kinetochore–microtubule attachments
LA Helgeson, A Zelter, M Riffle, MJ MacCoss, CL Asbury, TN Davis
Proceedings of the National Academy of Sciences 115 (11), 2740-2745, 2018
Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns
E Timmins-Schiffman, DH May, M Mikan, M Riffle, C Frazar, HR Harvey, ...
The ISME journal 11 (2), 309-314, 2017
Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology
L Malmström, M Riffle, CEM Strauss, D Chivian, TN Davis, R Bonneau, ...
PLoS biology 5 (4), e76, 2007
The Ndc80 complex bridges two Dam1 complex rings
J Kim, A Zelter, NT Umbreit, A Bollozos, M Riffle, R Johnson, MJ MacCoss, ...
Elife 6, e21069, 2017
The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling
A Zelter, M Bonomi, JO Kim, NT Umbreit, MR Hoopmann, R Johnson, ...
Nature communications 6 (1), 8673, 2015
ProXL (protein cross-linking database): a platform for analysis, visualization, and sharing of protein cross-linking mass spectrometry data
M Riffle, D Jaschob, A Zelter, TN Davis
Journal of Proteome Research 15 (8), 2863-2870, 2016
MetaGOmics: a web-based tool for peptide-centric functional and taxonomic analysis of metaproteomics data
M Riffle, DH May, E Timmins-Schiffman, MP Mikan, D Jaschob, WS Noble, ...
Proteomes 6 (1), 2, 2017
Regulation of outer kinetochore Ndc80 complex-based microtubule attachments by the central kinetochore Mis12/MIND complex
EM Kudalkar, EA Scarborough, NT Umbreit, A Zelter, DR Gestaut, M Riffle, ...
Proceedings of the National Academy of Sciences 112 (41), E5583-E5589, 2015
The Proteome Folding Project: proteome-scale prediction of structure and function
K Drew, P Winters, GL Butterfoss, V Berstis, K Uplinger, J Armstrong, ...
Genome research 21 (11), 1981-1994, 2011
The yeast resource center public image repository: a large database of fluorescence microscopy images
M Riffle, TN Davis
BMC bioinformatics 11 (1), 1-9, 2010
Bir1 is required for the tension checkpoint
MM Shimogawa, PO Widlund, M Riffle, M Ess, TN Davis
Molecular biology of the cell 20 (3), 915-923, 2009
The yeast resource center public data repository
M Riffle, L Malmström, TN Davis
Nucleic acids research 33 (suppl_1), D378-D382, 2005
Proteomics data repositories
M Riffle, JK Eng
Proteomics 9 (20), 4653-4663, 2009
Survey of metaproteomics software tools for functional microbiome analysis
R Sajulga, C Easterly, M Riffle, B Mesuere, T Muth, S Mehta, P Kumar, ...
PLoS One 15 (11), e0241503, 2020
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