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Integrative meta-omics in Galaxy and beyond.
Published in:
Environmental Microbiome, 2023, v. 18, n. 1, p. 1, doi. 10.1186/s40793-023-00514-9
By:
- Schiml, Valerie C.;
- Delogu, Francesco;
- Kumar, Praveen;
- Kunath, Benoit;
- Batut, Bérénice;
- Mehta, Subina;
- Johnson, James E.;
- Grüning, Björn;
- Pope, Phillip B.;
- Jagtap, Pratik D.;
- Griffin, Timothy J.;
- Arntzen, Magnus Ø.
Publication type:
Article
Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.
Published in:
Microbiome, 2015, v. 3, p. 1, doi. 10.1186/s40168-015-0136-z
By:
- Rudney, Joel D.;
- Jagtap, Pratik D.;
- Reilly, Cavan S.;
- Ruoqiong Chen;
- Markowski, Todd W.;
- Higgins, LeeAnn;
- Johnson, James E.;
- Griffin, Timothy J.
Publication type:
Article
Multi-omic data analysis using Galaxy.
Published in:
Nature Biotechnology, 2015, v. 33, n. 2, p. 137, doi. 10.1038/nbt.3134
By:
- Boekel, Jorrit;
- Chilton, John M;
- Cooke, Ira R;
- Horvatovich, Peter L;
- Jagtap, Pratik D;
- Käll, Lukas;
- Lehtiö, Janne;
- Lukasse, Pieter;
- Moerland, Perry D;
- Griffin, Timothy J
Publication type:
Article
Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration.
Published in:
GigaScience, 2020, v. 9, n. 4, p. N.PAG, doi. 10.1093/gigascience/giaa025
By:
- McGowan, Thomas;
- Johnson, James E;
- Kumar, Praveen;
- Sajulga, Ray;
- Mehta, Subina;
- Jagtap, Pratik D;
- Griffin, Timothy J
Publication type:
Article
Proteomic Profiles in Acute Respiratory Distress Syndrome Differentiates Survivors from Non-Survivors.
Published in:
PLoS ONE, 2014, v. 9, n. 10, p. 1, doi. 10.1371/journal.pone.0109713
By:
- Bhargava, Maneesh;
- Becker, Trisha L.;
- Viken, Kevin J.;
- Jagtap, Pratik D.;
- Dey, Sanjoy;
- Steinbach, Michael S.;
- Wu, Baolin;
- Kumar, Vipin;
- Bitterman, Peter B.;
- Ingbar, David H.;
- Wendt, Christine H.
Publication type:
Article
Metaproteomic analysis using the Galaxy framework.
Published in:
Proteomics, 2015, v. 15, n. 20, p. 3553, doi. 10.1002/pmic.201500074
By:
- Jagtap, Pratik D.;
- Blakely, Alan;
- Murray, Kevin;
- Stewart, Shaun;
- Kooren, Joel;
- Johnson, James E.;
- Rhodus, Nelson L.;
- Rudney, Joel;
- Griffin, Timothy J.
Publication type:
Article
Survey of metaproteomics software tools for functional microbiome analysis.
Published in:
PLoS ONE, 2020, v. 15, n. 11, p. 1, doi. 10.1371/journal.pone.0241503
By:
- 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.
Publication type:
Article
BAL Fluid Metaproteome in Acute Respiratory Failure.
Published in:
2018
By:
- Jagtap, Pratik D.;
- Viken, Kevin J.;
- Johnson, James;
- McGowan, Thomas;
- Pendleton, Kathryn M.;
- Griffin, Timothy J.;
- Hunter, Ryan C.;
- Rudney, Joel D.;
- Bhargava, Maneesh
Publication type:
Letter to the Editor
Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: 1 Effects of LC-MS Acquisition and Data Analysis Procedures.
Published in:
Biogeosciences Discussions, 2024, p. 1, doi. 10.5194/egusphere-2023-3148
By:
- 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
Publication type:
Article
Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow.
Published in:
Proteomes, 2022, v. 10, n. 2, p. N.PAG, doi. 10.3390/proteomes10020011
By:
- Rajczewski, Andrew T.;
- Han, Qiyuan;
- Mehta, Subina;
- Kumar, Praveen;
- Jagtap, Pratik D.;
- Knutson, Charles G.;
- Fox, James G.;
- Tretyakova, Natalia Y.;
- Griffin, Timothy J.
Publication type:
Article
Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform.
Published in:
Proteomes, 2020, v. 8, n. 3, p. 15, doi. 10.3390/proteomes8030015
By:
- Mehta, Subina;
- Easterly, Caleb W.;
- Sajulga, Ray;
- Millikin, Robert J.;
- Argentini, Andrea;
- Eguinoa, Ignacio;
- Martens, Lennart;
- Shortreed, Michael R.;
- Smith, Lloyd M.;
- McGowan, Thomas;
- Kumar, Praveen;
- Johnson, James E.;
- Griffin, Timothy J.;
- Jagtap, Pratik D.
Publication type:
Article
Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.
Published in:
Proteomes, 2018, v. 6, n. 1, p. 7, doi. 10.3390/proteomes6010007
By:
- Blank, Clemens;
- Easterly, Caleb;
- Gruening, Bjoern;
- Johnson, James;
- Kolmeder, Carolin A.;
- Kumar, Praveen;
- May, Damon;
- Mehta, Subina;
- Mesuere, Bart;
- Brown, Zachary;
- Elias, Joshua E.;
- Hervey, W. Judson;
- McGowan, Thomas;
- Muth, Thilo;
- Nunn, Brook L.;
- Rudney, Joel;
- Tanca, Alessandro;
- Griffin, Timothy J.;
- Jagtap, Pratik D.
Publication type:
Article
Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations.
Published in:
Viruses (1999-4915), 2022, v. 14, n. 10, p. N.PAG, doi. 10.3390/v14102205
By:
- Mehta, Subina;
- Carvalho, Valdemir M.;
- Rajczewski, Andrew T.;
- Pible, Olivier;
- Grüning, Björn A.;
- Johnson, James E.;
- Wagner, Reid;
- Armengaud, Jean;
- Griffin, Timothy J.;
- Jagtap, Pratik D.
Publication type:
Article
The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020).
Published in:
Journal of Biomolecular Techniques, 2023, v. 34, n. 3, p. 1, doi. 10.7171/3fc1f5fe.a058bad4
By:
- Jagtap, Pratik D.;
- Hoopmann, Michael R.;
- Neely, Benjamin A.;
- Harvey, Antony;
- Käll, Lukas;
- Perez-Riverol, Yasset;
- Abajorga, Milky K.;
- Thomas, Julie A.;
- Weintraub, Susan T.;
- Palmblad, Magnus
Publication type:
Article
2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Proteomics Study.
Published in:
Journal of Biomolecular Techniques, 2023, v. 34, n. 2, p. 1, doi. 10.7171/3fc1f5fe.9b78d780
By:
- Kirkpatrick, Joanna;
- Stemmer, Paul M.;
- Searle, Brian C.;
- Herring, Laura E.;
- Martin, LeRoy;
- Midha, Mukul K.;
- Phinney, Brett S.;
- Shan, Baozhen;
- Palmblad, Magnus;
- Yan Wang;
- Jagtap, Pratik D.;
- Neely, Benjamin A.
Publication type:
Article
Galaxy Training: A powerful framework for teaching!
Published in:
PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010752
By:
- Hiltemann, Saskia;
- Rasche, Helena;
- Gladman, Simon;
- Hotz, Hans-Rudolf;
- Larivière, Delphine;
- Blankenberg, Daniel;
- Jagtap, Pratik D.;
- Wollmann, Thomas;
- Bretaudeau, Anthony;
- Goué, Nadia;
- Griffin, Timothy J.;
- Royaux, Coline;
- Le Bras, Yvan;
- Mehta, Subina;
- Syme, Anna;
- Coppens, Frederik;
- Droesbeke, Bert;
- Soranzo, Nicola;
- Bacon, Wendi;
- Psomopoulos, Fotis
Publication type:
Article
Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations.
Published in:
BMC Genomics, 2014, v. 15, n. 1, p. 703, doi. 10.1186/1471-2164-15-703
By:
- Sheynkman, Gloria M;
- Johnson, James E;
- Jagtap, Pratik D;
- Shortreed, Michael R;
- Onsongo, Getiria;
- Frey, Brian L;
- Griffin, Timothy J;
- Smith, Lloyd M
Publication type:
Article
The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes.
Published in:
2021
By:
- Van Den Bossche, Tim;
- Arntzen, Magnus Ø.;
- Becher, Dörte;
- Benndorf, Dirk;
- Eijsink, Vincent G. H.;
- Henry, Céline;
- Jagtap, Pratik D.;
- Jehmlich, Nico;
- Juste, Catherine;
- Kunath, Benoit J.;
- Mesuere, Bart;
- Muth, Thilo;
- Pope, Phillip B.;
- Seifert, Jana;
- Tanca, Alessandro;
- Uzzau, Sergio;
- Wilmes, Paul;
- Hettich, Robert L.;
- Armengaud, Jean
Publication type:
Letter
An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples.
Published in:
Clinical Proteomics, 2023, v. 20, n. 1, p. 1, doi. 10.1186/s12014-023-09404-1
By:
- Weise, Danielle O.;
- Kruk, Monica E.;
- Higgins, LeeAnn;
- Markowski, Todd W.;
- Jagtap, Pratik D.;
- Mehta, Subina;
- Mickelson, Alan;
- Parker, Laurie L.;
- Wendt, Christine H.;
- Griffin, Timothy J.
Publication type:
Article
A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).
Published in:
Clinical Proteomics, 2021, v. 18, n. 1, p. 1, doi. 10.1186/s12014-021-09321-1
By:
- Rajczewski, Andrew T.;
- Mehta, Subina;
- Nguyen, Dinh Duy An;
- Grüning, Björn;
- Johnson, James E.;
- McGowan, Thomas;
- Griffin, Timothy J.;
- Jagtap, Pratik D.
Publication type:
Article
Novel approach to exploring protease activity and targets in HIV-associated obstructive lung disease using combined proteomic-peptidomic analysis.
Published in:
Respiratory Research, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12931-024-02933-9
By:
- Samorodnitsky, Sarah;
- Kruk, Monica;
- Lock, Eric F.;
- Kunisaki, Ken M.;
- Morris, Alison;
- Leung, Janice M.;
- Weise, Danielle;
- Mehta, Subina;
- Parker, Laurie L.;
- Jagtap, Pratik D.;
- Griffin, Timothy J.;
- Wendt, Chris H.
Publication type:
Article

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