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Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome Rajczewski, Andrew T.; Blakeley-Ruiz, J. Alfredo; Meyer, Annaliese; Vintila, Simina; Mcilvin, Matthew R.; van den Bossche, Tim; Searle, Brian C.; Griffin, Timothy J.; Saito, Mak A.; Kleiner, Manuel; Jagtap, Pratik D. Share Save
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Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer Perez, Jesenia M.; Duda, Jolene M.; Ryu, Joohyun; Shetty, Mihir; Mehta, Subina; Jagtap, Pratik D.; Nelson, Andrew C.; Winterhoff, Boris; Griffin, Timothy J.; Starr, Timothy K.; Thomas, Stefani N. Share Save
Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures Saito, Mak A.; Saunders, Jaclyn K.; McIlvin, Matthew R.; Bertrand, Erin M.; Breier, John A.; Brisbin, Margaret Mars; Colston, Sophie M.; Compton, Jaimee R.; Griffin, Tim J.; Hervey, W. Judson; Hettich, Robert L.; Jagtap, Pratik D.; Janech, Michael; Johnson, Rod; Keil, Rick; Kleikamp, Hugo; Leary, Dagmar; Martens, Lennart; McCain, J. Scott P.; Moore, Eli; Mehta, Subina; Moran, Dawn M.; Neibauer, Jaqui; Neely, Benjamin A.; Jakuba, Michael V.; Johnson, Jim; Duffy, Megan; Herndl, Gerhard J.; Giannone, Richard; Mueller, Ryan; Nunn, Brook L.; Pabst, Martin; Peters, Samantha; Rajczewski, Andrew; Rowland, Elden; Searle, Brian; Van Den Bossche, Tim; Vora, Gary J.; Waldbauer, Jacob R.; Zheng, Haiyan; Zhao, Zihao Share Save
Dichotomous intronic polyadenylation profiles reveal multifaceted gene functions in the pan-cancer transcriptome Sun, Jiao; Kim, Jin-Young; Jun, Semo; Park, Meeyeon; de Jong, Ebbing; Chang, Jae-Woong; Cheng, Sze; Fan, Deliang; Chen, Yue; Griffin, Timothy J.; Lee, Jung-Hee; You, Ho Jin; Zhang, Wei; Yong, Jeongsik Share Save
The lung proteome in HIV-associated obstructive lung disease Samorodnitsky, Sarah; Weise, Danielle; Lock, Eric F.; Kunisaki, Ken M.; Morris, Alison; Leung, Janice M.; Kruk, Monica; Parker, Laurie; Jagtap, Pratik; Griffin, Timothy J.; Wendt, Chris H. Share Save
An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease Kruk, Monica E.; Mehta, Subina; Murray, Kevin; Higgins, LeeAnn; Do, Katherine; Johnson, James E.; Wagner, Reid; Wendt, Chris H.; O'Connor, John B.; Harris, J. Kirk; Laguna, Theresa A.; Jagtap, Pratik D.; Griffin, Timothy J. Share Save
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A Galaxy of informatics resources for MS-based proteomics Mehta, Subina; Bernt, Matthias; Chambers, Matthew; Fahrner, Matthias; Foell, Melanie Christine; Gruening, Bjoern; Horro, Carlos; Johnson, James E.; Loux, Valentin; Rajczewski, Andrew T.; Schilling, Oliver; Vandenbrouck, Yves; Gustafsson, Ove Johan Ragnar; Thang, W. C. Mike; Hyde, Cameron; Price, Gareth; Jagtap, Pratik D.; Griffin, Timothy J. Share Save
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Integrative meta-omics in Galaxy and beyond Schiml, Valerie C.; Delogu, Francesco; Kumar, Praveen; Kunath, Benoit; Batut, Berenice; Mehta, Subina; Johnson, James E.; Gruening, Bjoern; Pope, Phillip B.; Jagtap, Pratik D.; Griffin, Timothy J.; Arntzen, Magnus O. Share Save
Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations Mehta, Subina; Carvalho, Valdemir M.; Rajczewski, Andrew T.; Pible, Olivier; Gruening, Bjoern A.; Johnson, James E.; Wagner, Reid; Armengaud, Jean; Griffin, Timothy J.; Jagtap, Pratik D. Share Save
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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update Ostrovsky, Alexander E.; Mahmoud, Alexandru; Lonie, Andrew J.; Syme, Anna; Fouilloux, Anne; Bretaudeau, Anthony; Nekrutenko, Anton; Kumar, Anup; Eschenlauer, Arthur C.; DeSanto, Assunta D.; Guerler, Aysam; Serrano-Solano, Beatriz; Batut, Berenice; Gruening, Bjoern A.; Langhorst, Bradley W.; Carr, Bridget; Raubenolt, Bryan A.; Hyde, Cameron J.; Bromhead, Catherine J.; Barnett, Christopher B.; Royaux, Coline; Gallardo, Cristobal; Blankenberg, Daniel; Fornika, Daniel J.; Baker, Dannon; Bouvier, Dave; Clements, Dave; Morais, David A. de Lima; Tabernero, David Lopez; Lariviere, Delphine; Nasr, Engy; Afgan, Enis; Zambelli, Federico; Heyl, Florian; Psomopoulos, Fotis; Coppens, Frederik; Price, Gareth R.; Cuccuru, Gianmauro; Le Corguille, Gildas; Von Kuster, Greg; Akbulut, Gulsum Gudukbay; Rasche, Helena; Hans-Rudolf, Hotz; Eguinoa, Ignacio; Makunin, Igor; Ranawaka, Isuru J.; Taylor, James P.; Joshi, Jayadev; Hillman-Jackson, Jennifer; Goecks, Jeremy; Chilton, John M.; Kamali, Kaivan; Suderman, Keith; Poterlowicz, Krzysztof; Yvan, Le Bras; Lopez-Delisle, Lucille; Sargent, Luke; Bassetti, Madeline E.; Tangaro, Marco Antonio; van den Beek, Marius; Cech, Martin; Bernt, Matthias; Fahrner, Matthias; Tekman, Mehmet; Foell, Melanie C.; Schatz, Michael C.; Crusoe, Michael R.; Roncoroni, Miguel; Kucher, Natalie; Coraor, Nate; Stoler, Nicholas; Rhodes, Nick; Soranzo, Nicola; Pinter, Niko; Goonasekera, Nuwan A.; Moreno, Pablo A.; Videm, Pavankumar; Melanie, Petera; Mandreoli, Pietro; Jagtap, Pratik D.; Gu, Qiang; Weber, Ralf J. M.; Lazarus, Ross; Vorderman, Ruben H. P.; Hiltemann, Saskia; Golitsynskiy, Sergey; Garg, Shilpa; Bray, Simon A.; Gladman, Simon L.; Leo, Simone; Mehta, Subina P.; Griffin, Timothy J.; Jalili, Vahid; Yves, Vandenbrouck; Wen, Victor; Nagampalli, Vijay K.; Bacon, Wendi A.; de Koning, Willem; Maier, Wolfgang; Briggs, Peter J. Share Save
Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow Rajczewski, Andrew T.; Han, Qiyuan; Mehta, Subina; Kumar, Praveen; Jagtap, Pratik D.; Knutson, Charles G.; Fox, James G.; Tretyakova, Natalia Y.; Griffin, Timothy J. Share Save
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