MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments
Choi, Meena, Chang, Ching-Yun, Clough, Timothy, Broudy, Daniel, Killeen, Trevor, MacLean, Brendan, Vitek, Olga
Published in Bioinformatics (Oxford, England) (01.09.2014)
Published in Bioinformatics (Oxford, England) (01.09.2014)
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Journal Article
MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets
Choi, Meena, Carver, Jeremy, Chiva, Cristina, Tzouros, Manuel, Huang, Ting, Tsai, Tsung-Heng, Pullman, Benjamin, Bernhardt, Oliver M, Hüttenhain, Ruth, Teo, Guo Ci, Perez-Riverol, Yasset, Muntel, Jan, Müller, Maik, Goetze, Sandra, Pavlou, Maria, Verschueren, Erik, Wollscheid, Bernd, Nesvizhskii, Alexey I, Reiter, Lukas, Dunkley, Tom, Sabidó, Eduard, Bandeira, Nuno, Vitek, Olga
Published in Nature methods (01.10.2020)
Published in Nature methods (01.10.2020)
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Journal Article
A proteomics sample metadata representation for multiomics integration and big data analysis
Dai, Chengxin, Füllgrabe, Anja, Pfeuffer, Julianus, Solovyeva, Elizaveta M, Deng, Jingwen, Moreno, Pablo, Kamatchinathan, Selvakumar, Kundu, Deepti Jaiswal, George, Nancy, Fexova, Silvie, Grüning, Björn, Föll, Melanie Christine, Griss, Johannes, Vaudel, Marc, Audain, Enrique, Locard-Paulet, Marie, Turewicz, Michael, Eisenacher, Martin, Uszkoreit, Julian, Van Den Bossche, Tim, Schwämmle, Veit, Webel, Henry, Schulze, Stefan, Bouyssié, David, Jayaram, Savita, Duggineni, Vinay Kumar, Samaras, Patroklos, Wilhelm, Mathias, Choi, Meena, Wang, Mingxun, Kohlbacher, Oliver, Brazma, Alvis, Papatheodorou, Irene, Bandeira, Nuno, Deutsch, Eric W, Vizcaíno, Juan Antonio, Bai, Mingze, Sachsenberg, Timo, Levitsky, Lev I, Perez-Riverol, Yasset
Published in Nature communications (06.10.2021)
Published in Nature communications (06.10.2021)
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Journal Article
Prediction of colorectal cancer diagnosis based on circulating plasma proteins
Surinova, Silvia, Choi, Meena, Tao, Sha, Schüffler, Peter J, Chang, Ching‐Yun, Clough, Timothy, Vysloužil, Kamil, Khoylou, Marta, Srovnal, Josef, Liu, Yansheng, Matondo, Mariette, Hüttenhain, Ruth, Weisser, Hendrik, Buhmann, Joachim M, Hajdúch, Marián, Brenner, Hermann, Vitek, Olga, Aebersold, Ruedi
Published in EMBO molecular medicine (01.09.2015)
Published in EMBO molecular medicine (01.09.2015)
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Journal Article
Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry
Caron, Etienne, Roncagalli, Romain, Hase, Takeshi, Wolski, Witold E., Choi, Meena, Menoita, Marisa G., Durand, Stephane, García-Blesa, Antonio, Fierro-Monti, Ivo, Sajic, Tatjana, Heusel, Moritz, Weiss, Tobias, Malissen, Marie, Schlapbach, Ralph, Collins, Ben C., Ghosh, Samik, Kitano, Hiroaki, Aebersold, Ruedi, Malissen, Bernard, Gstaiger, Matthias
Published in Cell reports (Cambridge) (28.03.2017)
Published in Cell reports (Cambridge) (28.03.2017)
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Journal Article
ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments
Choi, Meena, Eren-Dogu, Zeynep F, Colangelo, Christopher, Cottrell, John, Hoopmann, Michael R, Kapp, Eugene A, Kim, Sangtae, Lam, Henry, Neubert, Thomas A, Palmblad, Magnus, Phinney, Brett S, Weintraub, Susan T, MacLean, Brendan, Vitek, Olga
Published in Journal of proteome research (03.02.2017)
Published in Journal of proteome research (03.02.2017)
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Journal Article
New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins
Abbatiello, Susan, Ackermann, Bradley L., Borchers, Christoph, Bradshaw, Ralph A., Carr, Steven A., Chalkley, Robert, Choi, Meena, Deutsch, Eric, Domon, Bruno, Hoofnagle, Andrew N., Keshishian, Hasmik, Kuhn, Eric, Liebler, Daniel C., MacCoss, Michael, MacLean, Brendan, Mani, DR, Neubert, Hendrik, Smith, Derek, Vitek, Olga, Zimmerman, Lisa
Published in Molecular & cellular proteomics (01.03.2017)
Published in Molecular & cellular proteomics (01.03.2017)
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Journal Article
Genetic inactivation of RIP1 kinase activity in rats protects against ischemic brain injury
Stark, Kimberly, Goncharov, Tatiana, Varfolomeev, Eugene, Xie, Luke, Ngu, Hai, Peng, Ivan, Anderson, Keith R, Verschueren, Erik, Choi, Meena, Kirkpatrick, Donald S, Easton, Amy, Webster, Joshua D, McKenzie, Brent S, Vucic, Domagoj, Bingol, Baris
Published in Cell death & disease (07.04.2021)
Published in Cell death & disease (07.04.2021)
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Journal Article
Multiplexed proteomics of autophagy-deficient murine macrophages reveals enhanced antimicrobial immunity via the oxidative stress response
Maculins, Timurs, Verschueren, Erik, Hinkle, Trent, Choi, Meena, Chang, Patrick, Chalouni, Cecile, Rao, Shilpa, Kwon, Youngsu, Lim, Junghyun, Katakam, Anand Kumar, Kunz, Ryan C, Erickson, Brian K, Huang, Ting, Tsai, Tsung-Heng, Vitek, Olga, Reichelt, Mike, Senbabaoglu, Yasin, Mckenzie, Brent, Rohde, John R, Dikic, Ivan, Kirkpatrick, Donald S, Murthy, Aditya
Published in eLife (04.06.2021)
Published in eLife (04.06.2021)
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Journal Article
Gene Expression and Metabolomics Profiling of the Common Wheat Obtaining Leaf Rust Resistance by Salicylic or Jasmonic Acid through a Novel Detached Leaf Rust Assay
Kim, Minseo, Lee, Aro, Roh, Yeon Jin, Lee, Hae Min, Jo, Youngho, Cho, Hwayeon, Choi, Dong Wook, Choi, Meena, Eyun, Seong-il, Choi, Changhyun, Chung, Namhyun, Lee, Hojoung, Lee, Byung Cheon
Published in Agronomy (Basel) (29.10.2020)
Published in Agronomy (Basel) (29.10.2020)
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Journal Article
MSstatsTMT: Statistical Detection of Differentially Abundant Proteins in Experiments with Isobaric Labeling and Multiple Mixtures
Huang, Ting, Choi, Meena, Tzouros, Manuel, Golling, Sabrina, Pandya, Nikhil Janak, Banfai, Balazs, Dunkley, Tom, Vitek, Olga
Published in Molecular & cellular proteomics (01.10.2020)
Published in Molecular & cellular proteomics (01.10.2020)
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Journal Article
MSstatsPTM: Statistical Relative Quantification of Posttranslational Modifications in Bottom-Up Mass Spectrometry-Based Proteomics
Kohler, Devon, Tsai, Tsung-Heng, Verschueren, Erik, Huang, Ting, Hinkle, Trent, Phu, Lilian, Choi, Meena, Vitek, Olga
Published in Molecular & cellular proteomics (01.01.2023)
Published in Molecular & cellular proteomics (01.01.2023)
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Journal Article
MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments
Kohler, Devon, Kaza, Maanasa, Pasi, Cristina, Huang, Ting, Staniak, Mateusz, Mohandas, Dhaval, Sabido, Eduard, Choi, Meena, Vitek, Olga
Published in Journal of proteome research (03.02.2023)
Published in Journal of proteome research (03.02.2023)
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Journal Article
Increasing the Throughput and Reproducibility of Activity-Based Proteome Profiling Studies with Hyperplexing and Intelligent Data Acquisition
Budayeva, Hanna G., Ma, Taylur P., Wang, Shuai, Choi, Meena, Rose, Christopher M.
Published in Journal of proteome research (02.08.2024)
Published in Journal of proteome research (02.08.2024)
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Journal Article
Antibody targeting of E3 ubiquitin ligases for receptor degradation
Marei, Hadir, Tsai, Wen-Ting K., Kee, Yee-Seir, Ruiz, Karen, He, Jieyan, Cox, Chris, Sun, Tao, Penikalapati, Sai, Dwivedi, Pankaj, Choi, Meena, Kan, David, Saenz-Lopez, Pablo, Dorighi, Kristel, Zhang, Pamela, Kschonsak, Yvonne T., Kljavin, Noelyn, Amin, Dhara, Kim, Ingrid, Mancini, Andrew G., Nguyen, Thao, Wang, Chunling, Janezic, Eric, Doan, Alexander, Mai, Elaine, Xi, Hongkang, Gu, Chen, Heinlein, Melanie, Biehs, Brian, Wu, Jia, Lehoux, Isabelle, Harris, Seth, Comps-Agrar, Laetitia, Seshasayee, Dhaya, de Sauvage, Frederic J., Grimmer, Matthew, Li, Jing, Agard, Nicholas J., de Sousa e Melo, Felipe
Published in Nature (London) (06.10.2022)
Published in Nature (London) (06.10.2022)
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Journal Article
MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale
Kohler, Devon, Staniak, Mateusz, Tsai, Tsung-Heng, Huang, Ting, Shulman, Nicholas, Bernhardt, Oliver M., MacLean, Brendan X., Nesvizhskii, Alexey I., Reiter, Lukas, Sabido, Eduard, Choi, Meena, Vitek, Olga
Published in Journal of proteome research (05.05.2023)
Published in Journal of proteome research (05.05.2023)
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Journal Article
Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments
Tsai, Tsung-Heng, Choi, Meena, Banfai, Balazs, Liu, Yansheng, MacLean, Brendan X., Dunkley, Tom, Vitek, Olga
Published in Molecular & cellular proteomics (01.06.2020)
Published in Molecular & cellular proteomics (01.06.2020)
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Journal Article
Statistical Detection of Differentially Abundant Proteins in Experiments with Repeated Measures Designs and Isobaric Labeling
Huang, Ting, Staniak, Mateusz, Veiga Leprevost, Felipe da, Figueroa-Navedo, Amanda M., Ivanov, Alexander R., Nesvizhskii, Alexey I., Choi, Meena, Vitek, Olga
Published in Journal of proteome research (04.08.2023)
Published in Journal of proteome research (04.08.2023)
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Journal Article
Non‐invasive prognostic protein biomarker signatures associated with colorectal cancer
Surinova, Silvia, Radová, Lenka, Choi, Meena, Srovnal, Josef, Brenner, Hermann, Vitek, Olga, Hajdúch, Marián, Aebersold, Ruedi
Published in EMBO molecular medicine (01.09.2015)
Published in EMBO molecular medicine (01.09.2015)
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Journal Article
A Targeted Mass Spectrometry Strategy for Developing Proteomic Biomarkers: A Case Study of Epithelial Ovarian Cancer[S]
Hüttenhain, Ruth, Choi, Meena, Martin de la Fuente, Laura, Oehl, Kathrin, Chang, Ching-Yun, Zimmermann, Anne-Kathrin, Malander, Susanne, Olsson, Håkan, Surinova, Silvia, Clough, Timothy, Heinzelmann-Schwarz, Viola, Wild, Peter J., Dinulescu, Daniela M., Niméus, Emma, Vitek, Olga, Aebersold, Ruedi
Published in Molecular & cellular proteomics (01.09.2019)
Published in Molecular & cellular proteomics (01.09.2019)
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