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Items: 1 to 50 of 100

1.

Improve your Galaxy text life: The Query Tabular Tool.

Johnson JE, Kumar P, Easterly C, Esler M, Mehta S, Eschenlauer AC, Hegeman AD, Jagtap PD, Griffin TJ.

Version 2. F1000Res. 2018 Oct 5 [revised 2019 Jan 1];7:1604. doi: 10.12688/f1000research.16450.2. eCollection 2018.

2.

QuanTP: A software resource for quantitative proteo-transcriptomic comparative data analysis and informatics.

Kumar P, Panigrahi P, Johnson J, Weber WJ, Mehta S, Sajulga R, Easterly C, Crooker BA, Heydarian M, Anamika K, Griffin TJ, Jagtap P.

J Proteome Res. 2018 Dec 24. doi: 10.1021/acs.jproteome.8b00727. [Epub ahead of print]

PMID:
30582332
3.

An update on the moFF Algorithm for label-free quantitative proteomics.

Argentini A, Staes A, Grüning BA, Mehta S, Easterly C, Griffin TJ, Jagtap P, Impens F, Martens L.

J Proteome Res. 2018 Dec 4. doi: 10.1021/acs.jproteome.8b00708. [Epub ahead of print]

PMID:
30511867
4.

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
5.

Mechanistic Evaluation of Lipopolysaccharide-Alexidine Interaction Using Spectroscopic and in Silico Approaches.

Jagtap P, Mishra R, Khanna S, Kumari P, Mittal B, Kashyap HK, Gupta S.

ACS Infect Dis. 2018 Nov 9;4(11):1546-1552. doi: 10.1021/acsinfecdis.8b00087. Epub 2018 Oct 11.

PMID:
30226750
6.

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
7.
8.

Comparative Evaluation of Cytotoxicity of Root Canal Sealers on Cultured Human Periodontal Fibroblasts: In vitro Study.

Jagtap P, Shetty R, Agarwalla A, Wani P, Bhargava K, Martande S.

J Contemp Dent Pract. 2018 Jul 1;19(7):847-852.

PMID:
30066690
9.

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.

10.

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.

11.

A Flowthrough Assay for Rapid Bedside Stratification of Bloodstream Bacterial Infection in Critically Ill Patients: a Pilot Study.

Jagtap P, Singh R, Deepika K, Sritharan V, Gupta S.

J Clin Microbiol. 2018 Aug 27;56(9). pii: e00408-18. doi: 10.1128/JCM.00408-18. Print 2018 Sep.

PMID:
29925639
12.

Enantioselective Synthesis of All-Carbon Quaternary Centers Structurally Related to Amaryllidaceae Alkaloids.

Mikušek J, Jansa P, Jagtap PR, Vašíček T, Císařová I, Matoušová E.

Chemistry. 2018 May 18. doi: 10.1002/chem.201802493. [Epub ahead of print]

PMID:
29775495
13.

Chylothorax as a Risk Factor for Thrombosis in Adults: A Proof-of-Concept Study.

Hoskote SS, Yadav H, Jagtap P, Wigle DA, Daniels CE.

Ann Thorac Surg. 2018 Apr;105(4):1065-1070. doi: 10.1016/j.athoracsur.2017.11.011. Epub 2018 Feb 14.

PMID:
29452999
14.

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.

15.

Pharmacokinetic determination and analysis of nortriptyline based on GC-MS coupled with hollow-fiber drop-to-drop solvent microextraction technique.

Jagtap PK, Tapadia K.

Bioanalysis. 2018 Feb;10(3):143-152. doi: 10.4155/bio-2017-0207. Epub 2018 Jan 15.

PMID:
29333862
16.
17.

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.

18.

Structural Basis for EarP-Mediated Arginine Glycosylation of Translation Elongation Factor EF-P.

Krafczyk R, Macošek J, Jagtap PKA, Gast D, Wunder S, Mitra P, Jha AK, Rohr J, Hoffmann-Röder A, Jung K, Hennig J, Lassak J.

MBio. 2017 Sep 26;8(5). pii: e01412-17. doi: 10.1128/mBio.01412-17.

19.

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.

20.

Paclitaxel-eluting stents versus everolimus-eluting coronary stents in a diabetic population: two-year follow-up of the TUXEDO-India trial.

Kaul U, Bhagwat A, Pinto B, Goel PK, Jagtap P, Sathe S, Wander GS, Arambam P, Bangalore S.

EuroIntervention. 2017 Nov 20;13(10):1194-1201. doi: 10.4244/EIJ-D-17-00333.

21.

Segmental, Domain-Selective Perdeuteration and Small-Angle Neutron Scattering for Structural Analysis of Multi-Domain Proteins.

Sonntag M, Jagtap PKA, Simon B, Appavou MS, Geerlof A, Stehle R, Gabel F, Hennig J, Sattler M.

Angew Chem Int Ed Engl. 2017 Aug 1;56(32):9322-9325. doi: 10.1002/anie.201702904. Epub 2017 Jul 5.

PMID:
28636238
22.

Rational Design of Cyclic Peptide Inhibitors of U2AF Homology Motif (UHM) Domains To Modulate Pre-mRNA Splicing.

Jagtap PK, Garg D, Kapp TG, Will CL, Demmer O, Lührmann R, Kessler H, Sattler M.

J Med Chem. 2016 Nov 23;59(22):10190-10197. Epub 2016 Nov 4.

PMID:
27753493
23.

Nanotheranostic approaches for management of bloodstream bacterial infections.

Jagtap P, Sritharan V, Gupta S.

Nanomedicine. 2017 Jan;13(1):329-341. doi: 10.1016/j.nano.2016.09.005. Epub 2016 Oct 1. Review.

PMID:
27702606
24.

Percutaneous Coronary Intervention in Patients With Insulin-Treated and Non-Insulin-Treated Diabetes Mellitus: Secondary Analysis of the TUXEDO Trial.

Bangalore S, Bhagwat A, Pinto B, Goel PK, Jagtap P, Sathe S, Arambam P, Kaul U.

JAMA Cardiol. 2016 Jun 1;1(3):266-73. doi: 10.1001/jamacardio.2016.0305.

PMID:
27438104
25.

Structural model of the dimeric Parkinson's protein LRRK2 reveals a compact architecture involving distant interdomain contacts.

Guaitoli G, Raimondi F, Gilsbach BK, Gómez-Llorente Y, Deyaert E, Renzi F, Li X, Schaffner A, Jagtap PK, Boldt K, von Zweydorf F, Gotthardt K, Lorimer DD, Yue Z, Burgin A, Janjic N, Sattler M, Versées W, Ueffing M, Ubarretxena-Belandia I, Kortholt A, Gloeckner CJ.

Proc Natl Acad Sci U S A. 2016 Jul 26;113(30):E4357-66. doi: 10.1073/pnas.1523708113. Epub 2016 Jun 29.

26.

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.

27.
28.

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
29.

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.

30.

Microbiomes - embracing complexity.

Jagtap P, Griffin T, Armengaud J.

Proteomics. 2015 Oct;15(20):3405-6. doi: 10.1002/pmic.201570183. No abstract available.

PMID:
26468045
31.

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
32.

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
33.

The significance of evalution of haematocrit in plateletpheresis donors.

Mane VB, Jagtap PE, Nagane NS, Dhonde SP, Belwalkar GJ, Mane VP.

J Clin Diagn Res. 2015 Apr;9(4):BC06-7. doi: 10.7860/JCDR/2015/8292.5746. Epub 2015 Apr 1.

34.

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
35.

Evaluating shock absorption behavior of small-sized systems under programmable electric field.

Jagtap P, Kumar P.

Rev Sci Instrum. 2014 Nov;85(11):113903. doi: 10.1063/1.4900842.

PMID:
25430120
36.

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.

37.

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.

38.

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 Aug 22;15:703. doi: 10.1186/1471-2164-15-703.

39.

Highly functionalized and potent antiviral cyclopentane derivatives formed by a tandem process consisting of organometallic, transition-metal-catalyzed, and radical reaction steps.

Jagtap PR, Ford L, Deister E, Pohl R, Císařová I, Hodek J, Weber J, Mackman R, Bahador G, Jahn U.

Chemistry. 2014 Aug 11;20(33):10298-304. doi: 10.1002/chem.201402595. Epub 2014 Jul 10.

PMID:
25043655
40.

Leucine-rich repeat kinase 2 binds to neuronal vesicles through protein interactions mediated by its C-terminal WD40 domain.

Piccoli G, Onofri F, Cirnaru MD, Kaiser CJ, Jagtap P, Kastenmüller A, Pischedda F, Marte A, von Zweydorf F, Vogt A, Giesert F, Pan L, Antonucci F, Kiel C, Zhang M, Weinkauf S, Sattler M, Sala C, Matteoli M, Ueffing M, Gloeckner CJ.

Mol Cell Biol. 2014 Jun;34(12):2147-61. doi: 10.1128/MCB.00914-13. Epub 2014 Mar 31.

41.

Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1.

Wang I, Hennig J, Jagtap PK, Sonntag M, Valcárcel J, Sattler M.

Nucleic Acids Res. 2014 May;42(9):5949-66. doi: 10.1093/nar/gku193. Epub 2014 Mar 25.

42.

A study to compare the efficacy of corticosteroid therapy with platelet-rich plasma therapy in recalcitrant plantar fasciitis: a preliminary report.

Shetty VD, Dhillon M, Hegde C, Jagtap P, Shetty S.

Foot Ankle Surg. 2014 Mar;20(1):10-3. doi: 10.1016/j.fas.2013.08.002. Epub 2013 Aug 16.

PMID:
24480492
43.

Percutaneous dilational tracheostomy in patients receiving antiplatelet therapy: is it safe?

Abouzgheib W, Meena N, Jagtap P, Schorr C, Boujaoude Z, Bartter T.

J Bronchology Interv Pulmonol. 2013 Oct;20(4):322-5. doi: 10.1097/LBR.0000000000000023.

PMID:
24162115
44.

Emerging intra-articular causes of groin pain in athletes.

Jagtap P, Shetty G, Mane P, Shetty V.

Eur J Orthop Surg Traumatol. 2014 Dec;24(8):1331-9. doi: 10.1007/s00590-013-1325-8. Epub 2013 Oct 8. Review.

PMID:
24101188
45.

Crystal structures identify an atypical two-metal-ion mechanism for uridyltransfer in GlmU: its significance to sugar nucleotidyl transferases.

Jagtap PK, Verma SK, Vithani N, Bais VS, Prakash B.

J Mol Biol. 2013 May 27;425(10):1745-59. doi: 10.1016/j.jmb.2013.02.019. Epub 2013 Feb 26.

PMID:
23485416
46.

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.

Jagtap P, Goslinga J, Kooren JA, McGowan T, Wroblewski MS, Seymour SL, Griffin TJ.

Proteomics. 2013 Apr;13(8):1352-7. doi: 10.1002/pmic.201200352. Epub 2013 Mar 15.

47.

Substrate-bound crystal structures reveal features unique to Mycobacterium tuberculosis N-acetyl-glucosamine 1-phosphate uridyltransferase and a catalytic mechanism for acetyl transfer.

Jagtap PK, Soni V, Vithani N, Jhingan GD, Bais VS, Nandicoori VK, Prakash B.

J Biol Chem. 2012 Nov 16;287(47):39524-37. doi: 10.1074/jbc.M112.390765. Epub 2012 Sep 11.

48.

Workflow for analysis of high mass accuracy salivary data set using MaxQuant and ProteinPilot search algorithm.

Jagtap P, Bandhakavi S, Higgins L, McGowan T, Sa R, Stone MD, Chilton J, Arriaga EA, Seymour SL, Griffin TJ.

Proteomics. 2012 Jun;12(11):1726-30. doi: 10.1002/pmic.201100097.

49.

Deep metaproteomic analysis of human salivary supernatant.

Jagtap P, McGowan T, Bandhakavi S, Tu ZJ, Seymour S, Griffin TJ, Rudney JD.

Proteomics. 2012 Apr;12(7):992-1001. doi: 10.1002/pmic.201100503.

50.

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

Kooren JA, Rhodus NL, Tang C, Jagtap PD, Horrigan BJ, Griffin TJ.

Clin Proteomics. 2011 Sep 13;8:13. doi: 10.1186/1559-0275-8-13.

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