Selected publications using Galaxy-P

Below is a selection of publications describing the development and application of the Galaxy-P platform.  For an updated list of all publications describing work enabled by the Galaxy-P platform, see this link.

Improve your Galaxy text life: The Query tabular tool. James E. Johnson , Praveen Kumar , Caleb Easterly , Mark Esler , Subina Mehta , Arthur C. Eschenlauer , Adrian D. Hegeman , Pratik D. Jagtap , Timothy J. Griffin. https://doi.org/10.12688/ f1000research.16450.1

Bridging the Chromosome-Centric and Biology and Disease Human Proteome Projects: Accessible and automated tools for interpreting biological and pathological impact of protein sequence variants detected via proteogenomics. Ray Sajulga, Subina Mehta, Praveen Kumar, James E. Johnson, Candace R. Guerrero, Michael C. Ryan, Rachel Karchin, Pratik D. Jagtap, and Timothy J. Griffin. doi: 10.1021/acs.jproteome.8b00404 PMID: 30130115

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework. Clemens Blank, Caleb Easterly, Bjoern Gruening, James Johnson, Carolin A. Kolmeder, Praveen Kumar, Damon May, Subina Mehta, Bart Mesuere, Zachary Brown, Joshua E. Elias, W. Judson Hervey, Thomas McGowan , Thilo Muth, Brook Nunn, Joel Rudney, Alessandro Tanca, Timothy J. Griffin and Pratik D. Jagtap. doi: 110.3390/proteomes6010007 PMID:29385081

Comparative Metaproteomics to Study Environmental Changes. Sabine Matallana-Surget, Pratik D. Jagtap, Timothy J. Griffin, Mélanie Beraud, Ruddy Wattiez. https://doi.org/10.1016/B978-0-08-102268-9.00017-3

An Accessible Proteogenomics Informatics Resource for Cancer Researchers. Matthew C. Chambers, Pratik D. Jagtap, James E. Johnson, Thomas McGowan, Praveen Kumar, Getiria Onsongo, Candace R. Guerrero, Harald Barsnes, Marc Vaudel, Lennart Martens, Björn Grüning, Ira R. Cooke, Mohammad Heydarian, Karen L. Reddy and Timothy J. Griffin. doi: 10.1158/0008-5472.CAN-17-0331 PMID:29092937

Bronchoalveolar Lavage Fluid Protein Expression in Acute Respiratory Distress Syndrome Provides Insights into Pathways Activated in Subjects with Different Outcomes. Bhargava M, Viken K, Wang Q, Jagtap P, Bitterman P, Ingbar D, Wendt C. Sci Rep. 2017 Aug 7;7(1):7464. doi: 10.1038/s41598-017-07791-8. PMID: 28785034 Free PMC Article

Proteome Profiling in Lung Injury after Hematopoietic Stem Cell Transplantation. Bhargava M, Viken KJ, Dey S, Steinbach MS, Wu B, Jagtap PD, Higgins L, Panoskaltsis-Mortari A, Weisdorf DJ, Kumar V, Arora M, Bitterman PB, Ingbar DH, Wendt CH. Biol Blood Marrow Transplant. 2016 Aug;22(8):1383-1390. doi: 10.1016/j.bbmt.2016.04.021. Epub 2016 May 5. PMID: 27155584 Free PMC Article

Proteogenomic Analysis of a Hibernating Mammal Indicates Contribution of Skeletal Muscle Physiology to the Hibernation Phenotype.  Anderson KJ, Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT.  J Proteome Res. (2016) 15:1253-61.

Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.  Rudney JD, Jagtap PD, Reilly CS, Chen R, Markowski TW, Higgins L, Johnson JE, Griffin TJ. Microbiome. (2015) 3:69.

Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics.  Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT. J Proteome Res. (2015) 14:4792-804. (see also this  commentary in Chemical and Engineering News)

Metaproteomic analysis using the Galaxy framework. Jagtap PD, Blakely A, Murray K, Stewart S, Kooren J, Johnson JE, Rhodus NL, Rudney J, Griffin TJ.  Proteomics. (2015) 15:3553-65.

Multi-omic data analysis using Galaxy. Boekel J, Chilton JM, Cooke IR, Horvatovich PL, Jagtap PD, Käll L, Lehtiö J, Lukasse P, Moerland PD, Griffin TJ. Nat Biotechnol. (2015) 33:137-9.

Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. Jagtap PD, Johnson JE, Onsongo G, Sadler FW, Murray K, Wang Y, Shenykman GM, Bandhakavi S, Smith LM, Griffin TJ. J Proteome Res. (2014) 13:5898-908.

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations. Sheynkman GM, Johnson JE, Jagtap PD, Shortreed MR, Onsongo G, Frey BL, Griffin TJ, Smith LM. BMC Genomics. (2014) 15:703.