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Items: 1 to 20 of 21

1.

BAL Fluid Metaproteome in Acute Respiratory Failure.

Jagtap PD, Viken KJ, Johnson J, McGowan T, Pendleton KM, Griffin TJ, Hunter RC, Rudney JD, Bhargava M.

Am J Respir Cell Mol Biol. 2018 Nov;59(5):648-652. doi: 10.1165/rcmb.2018-0068LE. No abstract available.

PMID:
30382775
2.

Bridging the Chromosome-centric and Biology/Disease-driven Human Proteome Projects: Accessible and Automated Tools for Interpreting the Biological and Pathological Impact of Protein Sequence Variants Detected via Proteogenomics.

Sajulga R, Mehta S, Kumar P, Johnson JE, Guerrero CR, Ryan MC, Karchin R, Jagtap PD, Griffin TJ.

J Proteome Res. 2018 Sep 5. doi: 10.1021/acs.jproteome.8b00404. [Epub ahead of print]

PMID:
30130115
3.

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

Afiuni-Zadeh S, Boylan KLM, Jagtap PD, Griffin TJ, Rudney JD, Peterson ML, Skubitz APN.

Sci Rep. 2018 Jul 18;8(1):10868. doi: 10.1038/s41598-018-29092-4.

4.

Community-Driven Data Analysis Training for Biology.

Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz HR, Houwaart T, Jagtap P, Larivière D, Le Corguillé G, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D; Galaxy Training Network, Taylor J, Backofen R, Nekrutenko A, Grüning B.

Cell Syst. 2018 Jun 27;6(6):752-758.e1. doi: 10.1016/j.cels.2018.05.012.

PMID:
29953864
5.

Multi-omic molecular profiling of lung cancer in COPD.

Sandri BJ, Kaplan A, Hodgson SW, Peterson M, Avdulov S, Higgins L, Markowski T, Yang P, Limper AH, Griffin TJ, Bitterman P, Lock EF, Wendt CH.

Eur Respir J. 2018 Jul 4;52(1). pii: 1702665. doi: 10.1183/13993003.02665-2017. Print 2018 Jul.

PMID:
29794131
6.

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.

Blank C, Easterly C, Gruening B, Johnson J, Kolmeder CA, Kumar P, May D, Mehta S, Mesuere B, Brown Z, Elias JE, Hervey WJ, McGowan T, Muth T, Nunn B, Rudney J, Tanca A, Griffin TJ, Jagtap PD.

Proteomes. 2018 Jan 31;6(1). pii: E7. doi: 10.3390/proteomes6010007.

7.

An Accessible Proteogenomics Informatics Resource for Cancer Researchers.

Chambers MC, Jagtap PD, Johnson JE, McGowan T, Kumar P, Onsongo G, Guerrero CR, Barsnes H, Vaudel M, Martens L, Grüning B, Cooke IR, Heydarian M, Reddy KL, Griffin TJ.

Cancer Res. 2017 Nov 1;77(21):e43-e46. doi: 10.1158/0008-5472.CAN-17-0331.

8.

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.

9.

Seasonal changes in brown adipose tissue mitochondria in a mammalian hibernator: from gene expression to function.

Ballinger MA, Hess C, Napolitano MW, Bjork JA, Andrews MT.

Am J Physiol Regul Integr Comp Physiol. 2016 Aug 1;311(2):R325-36. doi: 10.1152/ajpregu.00463.2015. Epub 2016 May 25.

10.

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.

11.

Decreased Laminin Expression by Human Lung Epithelial Cells and Fibroblasts Cultured in Acellular Lung Scaffolds from Aged Mice.

Godin LM, Sandri BJ, Wagner DE, Meyer CM, Price AP, Akinnola I, Weiss DJ, Panoskaltsis-Mortari A.

PLoS One. 2016 Mar 8;11(3):e0150966. doi: 10.1371/journal.pone.0150966. eCollection 2016.

12.

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 Apr 1;15(4):1253-61. doi: 10.1021/acs.jproteome.5b01138. Epub 2016 Mar 3.

PMID:
26903422
13.

Proteome Scale-Protein Turnover Analysis Using High Resolution Mass Spectrometric Data from Stable-Isotope Labeled Plants.

Fan KT, Rendahl AK, Chen WP, Freund DM, Gray WM, Cohen JD, Hegeman AD.

J Proteome Res. 2016 Mar 4;15(3):851-67. doi: 10.1021/acs.jproteome.5b00772. Epub 2016 Jan 29.

14.

Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy.

Cesnik AJ, Shortreed MR, Sheynkman GM, Frey BL, Smith LM.

J Proteome Res. 2016 Mar 4;15(3):800-8. doi: 10.1021/acs.jproteome.5b00817. Epub 2016 Jan 12.

15.

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 Dec 19;3:69. doi: 10.1186/s40168-015-0136-z.

16.

Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics.

Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT.

J Proteome Res. 2015 Nov 6;14(11):4792-804. doi: 10.1021/acs.jproteome.5b00575. Epub 2015 Oct 23.

PMID:
26435507
17.

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 Oct;15(20):3553-65. doi: 10.1002/pmic.201500074. Epub 2015 Jul 24.

PMID:
26058579
18.

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 Feb;33(2):137-9. doi: 10.1038/nbt.3134. No abstract available.

PMID:
25658277
19.

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 Dec 5;13(12):5898-908. doi: 10.1021/pr500812t. Epub 2014 Oct 23.

20.

Proteomic profiles in acute respiratory distress syndrome differentiates survivors from non-survivors.

Bhargava M, Becker TL, Viken KJ, Jagtap PD, Dey S, Steinbach MS, Wu B, Kumar V, Bitterman PB, Ingbar DH, Wendt CH.

PLoS One. 2014 Oct 7;9(10):e109713. doi: 10.1371/journal.pone.0109713. eCollection 2014.

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