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Challenges in Peptide-Spectrum Matching: a Robust and Reproducible Statistical Framework for Removing Low-Accuracy, High-Scoring Hits.

Hubler SL, Kumar P, Mehta S, Easterly C, Johnson JE, Jagtap PD, Griffin TJ.

J Proteome Res. 2019 Dec 3. doi: 10.1021/acs.jproteome.9b00478. [Epub ahead of print]


Corrigendum: Selective Inhibitors of FKBP51 Employ Conformational Selection of Dynamic Invisible States.

Jagtap PKA, Asami S, Sippel C, Kaila VRI, Hausch F, Sattler M.

Angew Chem Int Ed Engl. 2019 Sep 23;58(39):13619. doi: 10.1002/anie.201908888. Epub 2019 Aug 20. No abstract available.


Levomilnacipran: More of the Same?

Gautam M, Kaur M, Jagtap P, Krayem B.

Prim Care Companion CNS Disord. 2019 Sep 5;21(5). pii: 19nr02475. doi: 10.4088/PCC.19nr02475.


Drumstick (Moringa oleifera) Flower as an Antioxidant Dietary Fibre in Chicken Meat Nuggets.

Madane P, Das AK, Pateiro M, Nanda PK, Bandyopadhyay S, Jagtap P, Barba FJ, Shewalkar A, Maity B, Lorenzo JM.

Foods. 2019 Aug 1;8(8). pii: E307. doi: 10.3390/foods8080307.


metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes.

Easterly CW, Sajulga R, Mehta S, Johnson J, Kumar P, Hubler S, Mesuere B, Rudney J, Griffin TJ, Jagtap PD.

Mol Cell Proteomics. 2019 Aug 9;18(8 suppl 1):S82-S91. doi: 10.1074/mcp.RA118.001240. Epub 2019 Jun 24.


Switching the Post-translational Modification of Translation Elongation Factor EF-P.

Volkwein W, Krafczyk R, Jagtap PKA, Parr M, Mankina E, Macošek J, Guo Z, Fürst MJLJ, Pfab M, Frishman D, Hennig J, Jung K, Lassak J.

Front Microbiol. 2019 May 24;10:1148. doi: 10.3389/fmicb.2019.01148. eCollection 2019.


Selective Inhibitors of FKBP51 Employ Conformational Selection of Dynamic Invisible States.

Jagtap PKA, Asami S, Sippel C, Kaila VRI, Hausch F, Sattler M.

Angew Chem Int Ed Engl. 2019 Jul 8;58(28):9429-9433. doi: 10.1002/anie.201902994. Epub 2019 Jun 5. Erratum in: Angew Chem Int Ed Engl. 2019 Sep 23;58(39):13619.


The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis.

Stewart PA, Kuenzi BM, Mehta S, Kumar P, Johnson JE, Jagtap P, Griffin TJ, Haura EB.

Methods Mol Biol. 2019;1977:249-261. doi: 10.1007/978-1-4939-9232-4_16.


Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.

Saito MA, Bertrand EM, Duffy ME, Gaylord DA, Held NA, Hervey WJ 4th, Hettich RL, Jagtap PD, Janech MG, Kinkade DB, Leary DH, McIlvin MR, Moore EK, Morris RM, Neely BA, Nunn BL, Saunders JK, Shepherd AI, Symmonds NI, Walsh DA.

J Proteome Res. 2019 Apr 5;18(4):1461-1476. doi: 10.1021/acs.jproteome.8b00761. Epub 2019 Mar 12.


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.


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 PD.

J Proteome Res. 2019 Feb 1;18(2):782-790. doi: 10.1021/acs.jproteome.8b00727. Epub 2019 Jan 4.


Update on the moFF Algorithm for Label-Free Quantitative Proteomics.

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

J Proteome Res. 2019 Feb 1;18(2):728-731. doi: 10.1021/acs.jproteome.8b00708. Epub 2018 Dec 14.


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.


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.


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 Dec 7;17(12):4329-4336. doi: 10.1021/acs.jproteome.8b00404. Epub 2018 Sep 5.


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.


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.


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.


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.


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]


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


Microbiomes - embracing complexity.

Jagtap P, Griffin T, Armengaud J.

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


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.

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