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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. 2020 Jan 3;19(1):161-173. doi: 10.1021/acs.jproteome.9b00478. Epub 2019 Dec 20.


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.


In vitro characterization and preclinical immunogenicity of Typhax, a typhoid fever protein capsular matrix vaccine candidate.

Griffin TJ 4th, Thanawastien A, Cartee RT, Mekalanos JJ, Killeen KP.

Hum Vaccin Immunother. 2019;15(6):1310-1316. doi: 10.1080/21645515.2019.1599674. Epub 2019 May 28.


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.


Distinct Cancer-Promoting Stromal Gene Expression Depending on Lung Function.

Sandri BJ, Masvidal L, Murie C, Bartish M, Avdulov S, Higgins L, Markowski T, Peterson M, Bergh J, Yang P, Rolny C, Limper AH, Griffin TJ, Bitterman PB, Wendt CH, Larsson O.

Am J Respir Crit Care Med. 2019 Aug 1;200(3):348-358. doi: 10.1164/rccm.201801-0080OC.


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.


Plasma lipoproteome in Alzheimer's disease: a proof-of-concept study.

Li D, Huang F, Zhao Y, Villata PW, Griffin TJ, Zhang L, Li L, Yu F.

Clin Proteomics. 2018 Sep 20;15:31. doi: 10.1186/s12014-018-9207-z. eCollection 2018.


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.


AAP President's Address.

Griffin TJ.

J Periodontol. 2018 Sep;89(9):1011-1014. doi: 10.1002/JPER.18-0476. No abstract available.


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.


Periodontal health and gingival diseases and conditions on an intact and a reduced periodontium: Consensus report of workgroup 1 of the 2017 World Workshop on the Classification of Periodontal and Peri-Implant Diseases and Conditions.

Chapple ILC, Mealey BL, Van Dyke TE, Bartold PM, Dommisch H, Eickholz P, Geisinger ML, Genco RJ, Glogauer M, Goldstein M, Griffin TJ, Holmstrup P, Johnson GK, Kapila Y, Lang NP, Meyle J, Murakami S, Plemons J, Romito GA, Shapira L, Tatakis DN, Teughels W, Trombelli L, Walter C, Wimmer G, Xenoudi P, Yoshie H.

J Periodontol. 2018 Jun;89 Suppl 1:S74-S84. doi: 10.1002/JPER.17-0719.


Periodontal health and gingival diseases and conditions on an intact and a reduced periodontium: Consensus report of workgroup 1 of the 2017 World Workshop on the Classification of Periodontal and Peri-Implant Diseases and Conditions.

Chapple ILC, Mealey BL, Van Dyke TE, Bartold PM, Dommisch H, Eickholz P, Geisinger ML, Genco RJ, Glogauer M, Goldstein M, Griffin TJ, Holmstrup P, Johnson GK, Kapila Y, Lang NP, Meyle J, Murakami S, Plemons J, Romito GA, Shapira L, Tatakis DN, Teughels W, Trombelli L, Walter C, Wimmer G, Xenoudi P, Yoshie H.

J Clin Periodontol. 2018 Jun;45 Suppl 20:S68-S77. doi: 10.1111/jcpe.12940.


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.


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.


Salivary proteomics of healthy dogs: An in depth catalog.

Torres SMF, Furrow E, Souza CP, Granick JL, de Jong EP, Griffin TJ, Wang X.

PLoS One. 2018 Jan 12;13(1):e0191307. doi: 10.1371/journal.pone.0191307. eCollection 2018.


Increased Indoleamine-2,3-Dioxygenase Activity Is Associated With Poor Clinical Outcome in Adults Hospitalized With Influenza in the INSIGHT FLU003Plus Study.

Pett SL, Kunisaki KM, Wentworth D, Griffin TJ, Kalomenidis I, Nahra R, Montejano Sanchez R, Hodgson SW, Ruxrungtham K, Dwyer D, Davey RT, Wendt CH; INSIGHT FLU003 Plus Study Group .

Open Forum Infect Dis. 2017 Oct 25;5(1):ofx228. doi: 10.1093/ofid/ofx228. eCollection 2018 Jan.


ULK1 phosphorylates Ser30 of BECN1 in association with ATG14 to stimulate autophagy induction.

Park JM, Seo M, Jung CH, Grunwald D, Stone M, Otto NM, Toso E, Ahn Y, Kyba M, Griffin TJ, Higgins L, Kim DH.

Autophagy. 2018;14(4):584-597. doi: 10.1080/15548627.2017.1422851. Epub 2018 Feb 21.


Normalization of mass spectrometry data (NOMAD).

Murie C, Sandri B, Sandberg AS, Griffin TJ, Lehtiö J, Wendt C, Larsson O.

Adv Biol Regul. 2018 Jan;67:128-133. doi: 10.1016/j.jbior.2017.11.005. Epub 2017 Nov 20.


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.


Plasma sphingolipids in HIV-associated chronic obstructive pulmonary disease.

Hodgson S, Griffin TJ, Reilly C, Harvey S, Witthuhn BA, Sandri BJ, Kunisaki KM, Wendt CH.

BMJ Open Respir Res. 2017 Apr 3;4(1):e000180. doi: 10.1136/bmjresp-2017-000180. eCollection 2017.


Use of Allograft with Platelet Concentrate in the Treatment of Multiple Miller Class III Gingival Recession Defects: Report of Three Cases.

Ogata Y, Bui M, Griffin TJ, Hur Y.

Int J Periodontics Restorative Dent. 2017 May/Jun;37(3):339-344. doi: 10.11607/prd.2673.


Tryptophan catabolism in acute exacerbations of chronic obstructive pulmonary disease.

Gulcev M, Reilly C, Griffin TJ, Broeckling CD, Sandri BJ, Witthuhn BA, Hodgson SW, Woodruff PG, Wendt CH.

Int J Chron Obstruct Pulmon Dis. 2016 Sep 29;11:2435-2446. eCollection 2016.


RIPPER: a framework for MS1 only metabolomics and proteomics label-free relative quantification.

Van Riper SK, Higgins L, Carlis JV, Griffin TJ.

Bioinformatics. 2016 Jul 1;32(13):2035-7. doi: 10.1093/bioinformatics/btw091. Epub 2016 Feb 18.


Slx5/Slx8 Promotes Replication Stress Tolerance by Facilitating Mitotic Progression.

Thu YM, Van Riper SK, Higgins L, Zhang T, Becker JR, Markowski TW, Nguyen HD, Griffin TJ, Bielinsky AK.

Cell Rep. 2016 May 10;15(6):1254-65. doi: 10.1016/j.celrep.2016.04.017. Epub 2016 Apr 28.


AminoxyTMT: A novel multi-functional reagent for characterization of protein carbonylation.

Afiuni-Zadeh S, Rogers JC, Snovida SI, Bomgarden RD, Griffin TJ.

Biotechniques. 2016 Apr 1;60(4):186-8, 190, 192-6. doi: 10.2144/000114402. eCollection 2016 Apr.


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.


Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to detect monoclonal immunoglobulin light chains in serum and urine.

Barnidge DR, Krick TP, Griffin TJ, Murray DL.

Rapid Commun Mass Spectrom. 2015 Nov 15;29(21):2057-60. doi: 10.1002/rcm.7314.


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.


mRNA 3'-UTR shortening is a molecular signature of mTORC1 activation.

Chang JW, Zhang W, Yeh HS, de Jong EP, Jun S, Kim KH, Bae SS, Beckman K, Hwang TH, Kim KS, Kim DH, Griffin TJ, Kuang R, Yong J.

Nat Commun. 2015 Jun 15;6:7218. doi: 10.1038/ncomms8218.


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.


Quetiapine-induced hypertriglyceridaemia causing acute pancreatitis.

Franco JM, Vallabhajosyula S, Griffin TJ.

BMJ Case Rep. 2015 May 14;2015. pii: bcr2015209571. doi: 10.1136/bcr-2015-209571.


Conjugate-like immunogens produced as protein capsular matrix vaccines.

Thanawastien A, Cartee RT, Griffin TJ 4th, Killeen KP, Mekalanos JJ.

Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):E1143-51. doi: 10.1073/pnas.1425005112. Epub 2015 Feb 19.


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.


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.


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.


A feasibility study to identify proteins in the residual Pap test fluid of women with normal cytology by mass spectrometry-based proteomics.

Boylan KL, Afiuni-Zadeh S, Geller MA, Hickey K, Griffin TJ, Pambuccian SE, Skubitz AP.

Clin Proteomics. 2014 Jul 14;11(1):30. doi: 10.1186/1559-0275-11-30. eCollection 2014.


Quantitative proteomic analysis of oral brush biopsies identifies secretory leukocyte protease inhibitor as a promising, mechanism-based oral cancer biomarker.

Yang Y, Rhodus NL, Ondrey FG, Wuertz BR, Chen X, Zhu Y, Griffin TJ.

PLoS One. 2014 Apr 18;9(4):e95389. doi: 10.1371/journal.pone.0095389. eCollection 2014.


Improved intensity-based label-free quantification via proximity-based intensity normalization (PIN).

Van Riper SK, de Jong EP, Higgins L, Carlis JV, Griffin TJ.

J Proteome Res. 2014 Mar 7;13(3):1281-92. doi: 10.1021/pr400866r. Epub 2014 Feb 26.


Salivary proteomics in bisphosphonate-related osteonecrosis of the jaw.

Thumbigere-Math V, Michalowicz BS, de Jong EP, Griffin TJ, Basi DL, Hughes PJ, Tsai ML, Swenson KK, Rockwell L, Gopalakrishnan R.

Oral Dis. 2015 Jan;21(1):46-56. doi: 10.1111/odi.12204. Epub 2013 Nov 29.


Restoration of gingival and esthetic deformities following flap advancement: the physiologically pigmented gingival graft--a case report.

Marcuschamer E, Tsukiyama T, Moroi H, Hawley CE, Griffin TJ.

Int J Periodontics Restorative Dent. 2013 Sep-Oct;33(5):591-7. doi: 10.11607/prd.1252.


Comparison of double-flap incision to periosteal releasing incision for flap advancement: a prospective clinical trial.

Ogata Y, Griffin TJ, Ko AC, Hur Y.

Int J Oral Maxillofac Implants. 2013 Mar-Apr;28(2):597-604. doi: 10.11607/jomi.2714.


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.


Mass spectrometry-based proteomics: basic principles and emerging technologies and directions.

Van Riper SK, de Jong EP, Carlis JV, Griffin TJ.

Adv Exp Med Biol. 2013;990:1-35. doi: 10.1007/978-94-007-5896-4_1. Review.


Trap door: an alternative procedure to the triangular distal wedge for the elimination of distal periodontal pockets adjacent to edentulous areas.

Singh M, Stark PC, Damoulis PD, Levi P, Griffin TJ.

Compend Contin Educ Dent. 2012 Feb;33(2):e38-44.


Early bone healing around 2 different experimental, HA grit-blasted, and dual acid-etched titanium implant surfaces. A pilot study in rabbits.

Gobbato L, Arguello E, Martin IS, Hawley CE, Griffin TJ.

Implant Dent. 2012 Dec;21(6):454-60. doi: 10.1097/ID.0b013e3182611cd7.


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