Bronchoalveolar Lavage Fluid Protein Expression in Acute Respiratory Distress Syndrome Provides Insights into Pathways Activated in Subjects with Different Outcomes

por Bhargava, Maneesh, Viken, Kevin, Wang, Qi, Jagtap, Pratik, Bitterman, Peter, Ingbar, David, Wendt, Chris
Publicado 2017

Evaluating the potential of a novel oral lesion exudate collection method coupled with mass spectrometry-based proteomics for oral cancer biomarker discovery

por Kooren, Joel A, Rhodus, Nelson L, Tang, Chuanning, Jagtap, Pratik D, Horrigan, Bryan J, Griffin, Timothy J
Publicado 2011

Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration

por McGowan, Thomas, Johnson, James E, Kumar, Praveen, Sajulga, Ray, Mehta, Subina, Jagtap, Pratik D, Griffin, Timothy J
Publicado 2020

Iron-sparing Response of Mycobacterium avium subsp. paratuberculosis is strain dependent

por Janagama, Harish K, Senthilkumar, Bannantine, John P, Kugadas, Abirami, Jagtap, Pratik, Higgins, LeeAnn, Witthuhn, Bruce A, Sreevatsan, Srinand
Publicado 2010

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)

por Rajczewski, Andrew T., Mehta, Subina, Nguyen, Dinh Duy An, Grüning, Björn, Johnson, James E., McGowan, Thomas, Griffin, Timothy J., Jagtap, Pratik D.
Publicado 2021

Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries

por Rudney, Joel D., Jagtap, Pratik D., Reilly, Cavan S., Chen, Ruoqiong, Markowski, Todd W., Higgins, LeeAnn, Johnson, James E., Griffin, Timothy J.
Publicado 2015

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).

por Rajczewski, Andrew T., Mehta, Subina, Nguyen, Dinh Duy An, Grüning, Björn A., Johnson, James E., McGowan, Thomas, Griffin, Timothy J., Jagtap, Pratik D.
Publicado 2021

Novel In Situ Collection of Tumor Interstitial Fluid from a Head and Neck Squamous Carcinoma Reveals a Unique Proteome with Diagnostic Potential

por Stone, Matthew D., Odland, Rick M., McGowan, Thomas, Onsongo, Getiria, Tang, Chaunning, Rhodus, Nelson L., Jagtap, Pratik, Bandhakavi, Sricharan, Griffin, Timothy J.
Publicado 2010

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

por Sheynkman, Gloria M, Johnson, James E, Jagtap, Pratik D, Shortreed, Michael R, Onsongo, Getiria, Frey, Brian L, Griffin, Timothy J, Smith, Lloyd M
Publicado 2014

Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome

por Afiuni-Zadeh, Somaieh, Boylan, Kristin L. M., Jagtap, Pratik D., Griffin, Timothy J., Rudney, Joel D., Peterson, Marnie L., Skubitz, Amy P. N.
Publicado 2018

Improve your Galaxy text life: The Query Tabular Tool

por Johnson, James E., Kumar, Praveen, Easterly, Caleb, Esler, Mark, Mehta, Subina, Eschenlauer, Arthur C., Hegeman, Adrian D., Jagtap, Pratik D., Griffin, Timothy J.
Publicado 2019

Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow

por Rajczewski, Andrew T., Han, Qiyuan, Mehta, Subina, Kumar, Praveen, Jagtap, Pratik D., Knutson, Charles G., Fox, James G., Tretyakova, Natalia Y., Griffin, Timothy J.
Publicado 2022

Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations

por 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.
Publicado 2022

Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework

por Jagtap, Pratik D., Johnson, James E., Onsongo, Getiria, Sadler, Fredrik W., Murray, Kevin, Wang, Yuanbo, Shenykman, Gloria M., Bandhakavi, Sricharan, Smith, Lloyd M., Griffin, Timothy J.
Publicado 2014

An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples

por 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.
Publicado 2023

Proteomic Profiles in Acute Respiratory Distress Syndrome Differentiates Survivors from Non-Survivors

por 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.
Publicado 2014

Integrative meta-omics in Galaxy and beyond

por 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.
Publicado 2023

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework

por Mehta, Subina, Crane, Marie, Leith, Emma, Batut, Bérénice, Hiltemann, Saskia, Arntzen, Magnus Ø, Kunath, Benoit J., Pope, Phillip B., Delogu, Francesco, Sajulga, Ray, Kumar, Praveen, Johnson, James E., Griffin, Timothy J., Jagtap, Pratik D.
Publicado 2021

Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform

por 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.
Publicado 2020

Survey of metaproteomics software tools for functional microbiome analysis

por 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.
Publicado 2020