Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome
Kusebauch, Ulrike, Campbell, David S., Deutsch, Eric W., Chu, Caroline S., Spicer, Douglas A., Brusniak, Mi-Youn, Slagel, Joseph, Sun, Zhi, Stevens, Jeffrey, Grimes, Barbara, Shteynberg, David, Hoopmann, Michael R., Blattmann, Peter, Ratushny, Alexander V., Rinner, Oliver, Picotti, Paola, Carapito, Christine, Huang, Chung-Ying, Kapousouz, Meghan, Lam, Henry, Tran, Tommy, Demir, Emek, Aitchison, John D., Sander, Chris, Hood, Leroy, Aebersold, Ruedi, Moritz, Robert L.
Published in Cell (28.07.2016)
Published in Cell (28.07.2016)
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Journal Article
mProphet: automated data processing and statistical validation for large-scale SRM experiments
Reiter, Lukas, Rinner, Oliver, Picotti, Paola, Hüttenhain, Ruth, Beck, Martin, Brusniak, Mi-Youn, Hengartner, Michael O, Aebersold, Ruedi
Published in Nature methods (01.05.2011)
Published in Nature methods (01.05.2011)
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Journal Article
PASSEL: The PeptideAtlas SRMexperiment library
Farrah, Terry, Deutsch, Eric W., Kreisberg, Richard, Sun, Zhi, Campbell, David S., Mendoza, Luis, Kusebauch, Ulrike, Brusniak, Mi-Youn, Hüttenhain, Ruth, Schiess, Ralph, Selevsek, Nathalie, Aebersold, Ruedi, Moritz, Robert L.
Published in Proteomics (Weinheim) (01.04.2012)
Published in Proteomics (Weinheim) (01.04.2012)
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Journal Article
SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling
Mueller, Lukas N, Rinner, Oliver, Schmidt, Alexander, Letarte, Simon, Bodenmiller, Bernd, Brusniak, Mi-Youn, Vitek, Olga, Aebersold, Ruedi, Müller, Markus
Published in Proteomics (Weinheim) (01.10.2007)
Published in Proteomics (Weinheim) (01.10.2007)
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Journal Article
Mammalian display screening of diverse cystine-dense peptides for difficult to drug targets
Crook, Zachary R., Sevilla, Gregory P., Friend, Della, Brusniak, Mi-Youn, Bandaranayake, Ashok D., Clarke, Midori, Gewe, Mesfin, Mhyre, Andrew J., Baker, David, Strong, Roland K., Bradley, Philip, Olson, James M.
Published in Nature communications (21.12.2017)
Published in Nature communications (21.12.2017)
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Journal Article
Screening, large-scale production and structure-based classification of cystine-dense peptides
Correnti, Colin E., Gewe, Mesfin M., Mehlin, Christopher, Bandaranayake, Ashok D., Johnsen, William A., Rupert, Peter B., Brusniak, Mi-Youn, Clarke, Midori, Burke, Skyler E., De Van Der Schueren, Willem, Pilat, Kristina, Turnbaugh, Shanon M., May, Damon, Watson, Alex, Chan, Man Kid, Bahl, Christopher D., Olson, James M., Strong, Roland K.
Published in Nature structural & molecular biology (01.03.2018)
Published in Nature structural & molecular biology (01.03.2018)
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Journal Article
Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast
Bodenmiller, Bernd, Wanka, Stefanie, Kraft, Claudine, Urban, Jörg, Campbell, David, Pedrioli, Patrick G, Gerrits, Bertran, Picotti, Paola, Lam, Henry, Vitek, Olga, Brusniak, Mi-Youn, Roschitzki, Bernd, Zhang, Chao, Shokat, Kevan M, Schlapbach, Ralph, Colman-Lerner, Alejandro, Nolan, Garry P, Nesvizhskii, Alexey I, Peter, Matthias, Loewith, Robbie, von Mering, Christian, Aebersold, Ruedi
Published in Science signaling (21.12.2010)
Published in Science signaling (21.12.2010)
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Journal Article
ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry
Brusniak, Mi-Youn K, Kwok, Sung-Tat, Christiansen, Mark, Campbell, David, Reiter, Lukas, Picotti, Paola, Kusebauch, Ulrike, Ramos, Hector, Deutsch, Eric W, Chen, Jingchun, Moritz, Robert L, Aebersold, Ruedi
Published in BMC bioinformatics (18.03.2011)
Published in BMC bioinformatics (18.03.2011)
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Journal Article
Laboratory information management software for engineered mini-protein therapeutic workflow
Brusniak, Mi-Youn, Ramos, Hector, Lee, Bernard, Olson, James M
Published in BMC bioinformatics (17.06.2019)
Published in BMC bioinformatics (17.06.2019)
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Journal Article
ARTEMIS: A Novel Mass-Spec Platform for HLA-Restricted Self and Disease-Associated Peptide Discovery
Finton, Kathryn A K, Brusniak, Mi-Youn, Jones, Lisa A, Lin, Chenwei, Fioré-Gartland, Andrew J, Brock, Chance, Gafken, Philip R, Strong, Roland K
Published in Frontiers in immunology (23.04.2021)
Published in Frontiers in immunology (23.04.2021)
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Journal Article
Targeted Quantitative Analysis of Streptococcus pyogenes Virulence Factors by Multiple Reaction Monitoring
Lange, Vinzenz, Malmström, Johan A., Didion, John, King, Nichole L., Johansson, Björn P., Schäfer, Juliane, Rameseder, Jonathan, Wong, Chee-Hong, Deutsch, Eric W., Brusniak, Mi-Youn, Buühlmann, Peter, Björck, Lars, Domon, Bruno, Aebersold, Ruedi
Published in Molecular & cellular proteomics (01.08.2008)
Published in Molecular & cellular proteomics (01.08.2008)
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Journal Article
TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists
Deutsch, Eric W., Chambers, Matthew, Neumann, Steffen, Levander, Fredrik, Binz, Pierre-Alain, Shofstahl, Jim, Campbell, David S., Mendoza, Luis, Ovelleiro, David, Helsens, Kenny, Martens, Lennart, Aebersold, Ruedi, Moritz, Robert L., Brusniak, Mi-Youn
Published in Molecular & cellular proteomics (01.04.2012)
Published in Molecular & cellular proteomics (01.04.2012)
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Journal Article
An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology
Brusniak, Mi-Youn K., Chu, Caroline S., Kusebauch, Ulrike, Sartain, Mark J., Watts, Julian D., Moritz, Robert L.
Published in Proteomics (Weinheim) (01.04.2012)
Published in Proteomics (Weinheim) (01.04.2012)
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Journal Article
Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics
Brusniak, Mi-Youn, Bodenmiller, Bernd, Campbell, David, Cooke, Kelly, Eddes, James, Garbutt, Andrew, Lau, Hollis, Letarte, Simon, Mueller, Lukas N, Sharma, Vagisha, Vitek, Olga, Zhang, Ning, Aebersold, Ruedi, Watts, Julian D
Published in BMC bioinformatics (16.12.2008)
Published in BMC bioinformatics (16.12.2008)
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Journal Article
jTraML: An Open Source Java API for TraML, the PSI Standard for Sharing SRM Transitions
Helsens, Kenny, Brusniak, Mi-Youn, Deutsch, Eric, Moritz, Robert L, Martens, Lennart
Published in Journal of proteome research (04.11.2011)
Published in Journal of proteome research (04.11.2011)
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Journal Article
The Protein Information and Property Explorer 2: Gaggle-like exploration of biological proteomic data within one webpage
Ramos, Hector, Shannon, Paul, Brusniak, Mi-Youn, Kusebauch, Ulrike, Moritz, Robert L., Aebersold, Ruedi
Published in Proteomics (Weinheim) (01.01.2011)
Published in Proteomics (Weinheim) (01.01.2011)
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Journal Article
A cross-platform toolkit for mass spectrometry and proteomics
Chambers, Matthew C, Maclean, Brendan, Burke, Robert, Amodei, Dario, Ruderman, Daniel L, Neumann, Steffen, Gatto, Laurent, Fischer, Bernd, Pratt, Brian, Egertson, Jarrett, Hoff, Katherine, Kessner, Darren, Tasman, Natalie, Shulman, Nicholas, Frewen, Barbara, Baker, Tahmina A, Brusniak, Mi-Youn, Paulse, Christopher, Creasy, David, Flashner, Lisa, Kani, Kian, Moulding, Chris, Seymour, Sean L, Nuwaysir, Lydia M, Lefebvre, Brent, Kuhlmann, Frank, Roark, Joe, Rainer, Paape, Detlev, Suckau, Hemenway, Tina, Huhmer, Andreas, Langridge, James, Connolly, Brian, Chadick, Trey, Holly, Krisztina, Eckels, Josh, Deutsch, Eric W, Moritz, Robert L, Katz, Jonathan E, Agus, David B, MacCoss, Michael, Tabb, David L, Mallick, Parag
Published in Nature biotechnology (01.10.2012)
Published in Nature biotechnology (01.10.2012)
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Journal Article
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)
Kinsinger, Christopher R., Apffel, James, Baker, Mark, Bian, Xiaopeng, Borchers, Christoph H., Bradshaw, Ralph, Brusniak, Mi-Youn, Chan, Daniel W., Deutsch, Eric W., Domon, Bruno, Gorman, Jeff, Grimm, Rudolf, Hancock, William, Hermjakob, Henning, Horn, David, Hunter, Christie, Kolar, Patrik, Kraus, Hans-Joachim, Langen, Hanno, Linding, Rune, Moritz, Robert L., Omenn, Gilbert S., Orlando, Ron, Pandey, Akhilesh, Ping, Peipei, Rahbar, Amir, Rivers, Robert, Seymour, Sean L., Simpson, Richard J., Slotta, Douglas, Smith, Richard D., Stein, Stephen E., Tabb, David L., Tagle, Danilo, Yates, John R., Rodriguez, Henry
Published in Proteomics (01.01.2012)
Published in Proteomics (01.01.2012)
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Journal Article
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