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Gender-specific changes in energy metabolism and protein degradation as major pathways affected in livers of mice treated with ibuprofen.

Tiwari S, Mishra M, Salemi MR, Phinney BS, Newens JL, Gomes AV.

Sci Rep. 2020 Feb 25;10(1):3386. doi: 10.1038/s41598-020-60053-y.


Prioritization of metabolic genes as novel therapeutic targets in estrogen-receptor negative breast tumors using multi-omics data and text mining.

Barupal DK, Gao B, Budczies J, Phinney BS, Perroud B, Denkert C, Fiehn O.

Oncotarget. 2019 Jun 11;10(39):3894-3909. doi: 10.18632/oncotarget.26995. eCollection 2019 Jun 11.


AtTRAPPC11/ROG2: A Role for TRAPPs in Maintenance of the Plant Trans-Golgi Network/Early Endosome Organization and Function.

Rosquete MR, Worden N, Ren G, Sinclair RM, Pfleger S, Salemi M, Phinney BS, Domozych D, Wilkop T, Drakakaki G.

Plant Cell. 2019 Aug;31(8):1879-1898. doi: 10.1105/tpc.19.00110. Epub 2019 Jun 7.


Proteomic manifestations of genetic defects in autosomal recessive congenital ichthyosis.

Karim N, Durbin-Johnson B, Rocke DM, Salemi M, Phinney BS, Naeem M, Rice RH.

J Proteomics. 2019 Jun 15;201:104-109. doi: 10.1016/j.jprot.2019.04.007. Epub 2019 Apr 10.


Physiological profile of undifferentiated bovine blastocyst-derived trophoblasts.

Pillai VV, Siqueira LG, Das M, Kei TG, Tu LN, Herren AW, Phinney BS, Cheong SH, Hansen PJ, Selvaraj V.

Biol Open. 2019 May 1;8(5). pii: bio037937. doi: 10.1242/bio.037937.


Comparison of protein expression levels and proteomically-inferred genotypes using human hair from different body sites.

Milan JA, Wu PW, Salemi MR, Durbin-Johnson BP, Rocke DM, Phinney BS, Rice RH, Parker GJ.

Forensic Sci Int Genet. 2019 Jul;41:19-23. doi: 10.1016/j.fsigen.2019.03.009. Epub 2019 Mar 11.


Human stratum corneum proteomics reveals cross-linking of a broad spectrum of proteins in cornified envelopes.

Karim N, Phinney BS, Salemi M, Wu PW, Naeem M, Rice RH.

Exp Dermatol. 2019 May;28(5):618-622. doi: 10.1111/exd.13925.


Cornification of nail keratinocytes requires autophagy for bulk degradation of intracellular proteins while sparing components of the cytoskeleton.

Jaeger K, Sukseree S, Zhong S, Phinney BS, Mlitz V, Buchberger M, Narzt MS, Gruber F, Tschachler E, Rice RH, Eckhart L.

Apoptosis. 2019 Feb;24(1-2):62-73. doi: 10.1007/s10495-018-1505-4.


Corneocyte proteomics: Applications to skin biology and dermatology.

Rice RH, Durbin-Johnson BP, Mann SM, Salemi M, Urayama S, Rocke DM, Phinney BS, Sundberg JP.

Exp Dermatol. 2018 Aug;27(8):931-938. doi: 10.1111/exd.13756. Review.


Glaucomatous cell derived matrices differentially modulate non-glaucomatous trabecular meshwork cellular behavior.

Raghunathan VK, Benoit J, Kasetti R, Zode G, Salemi M, Phinney BS, Keller KE, Staverosky JA, Murphy CJ, Acott T, Vranka J.

Acta Biomater. 2018 Apr 15;71:444-459. doi: 10.1016/j.actbio.2018.02.037. Epub 2018 Mar 7.


A functional link between NAD+ homeostasis and N-terminal protein acetylation in Saccharomyces cerevisiae.

Croft T, James Theoga Raj C, Salemi M, Phinney BS, Lin SJ.

J Biol Chem. 2018 Feb 23;293(8):2927-2938. doi: 10.1074/jbc.M117.807214. Epub 2018 Jan 9.


Profiling of proteins secreted in the bovine oviduct reveals diverse functions of this luminal microenvironment.

Pillai VV, Weber DM, Phinney BS, Selvaraj V.

PLoS One. 2017 Nov 20;12(11):e0188105. doi: 10.1371/journal.pone.0188105. eCollection 2017.


Proteomes of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5 Incubated in Milk at Optimal and Low Temperatures.

Yin X, Salemi MR, Phinney BS, Gotcheva V, Angelov A, Marco ML.

mSystems. 2017 Sep 19;2(5). pii: e00027-17. doi: 10.1128/mSystems.00027-17. eCollection 2017 Sep-Oct.


Biochemical and biomechanical properties of the pacemaking sinoatrial node extracellular matrix are distinct from contractile left ventricular matrix.

Gluck JM, Herren AW, Yechikov S, Kao HKJ, Khan A, Phinney BS, Chiamvimonvat N, Chan JW, Lieu DK.

PLoS One. 2017 Sep 21;12(9):e0185125. doi: 10.1371/journal.pone.0185125. eCollection 2017.


Absolute Quantification of Human Milk Caseins and the Whey/Casein Ratio during the First Year of Lactation.

Liao Y, Weber D, Xu W, Durbin-Johnson BP, Phinney BS, Lönnerdal B.

J Proteome Res. 2017 Nov 3;16(11):4113-4121. doi: 10.1021/acs.jproteome.7b00486. Epub 2017 Oct 9.


The Metalloprotease, Mpr1, Engages AnnexinA2 to Promote the Transcytosis of Fungal Cells across the Blood-Brain Barrier.

Na Pombejra S, Salemi M, Phinney BS, Gelli A.

Front Cell Infect Microbiol. 2017 Jun 30;7:296. doi: 10.3389/fcimb.2017.00296. eCollection 2017.


Proteomic profiling of Pachyonychia congenita plantar callus.

Rice RH, Durbin-Johnson BP, Salemi M, Schwartz ME, Rocke DM, Phinney BS.

J Proteomics. 2017 Aug 8;165:132-137. doi: 10.1016/j.jprot.2017.06.017. Epub 2017 Jun 23.


Proteomic analysis of hair shafts from monozygotic twins: Expression profiles and genetically variant peptides.

Wu PW, Mason KE, Durbin-Johnson BP, Salemi M, Phinney BS, Rocke DM, Parker GJ, Rice RH.

Proteomics. 2017 Jul;17(13-14). doi: 10.1002/pmic.201600462. Epub 2017 Jun 23.


Integrated Metabolomics and Proteomics Highlight Altered Nicotinamide- and Polyamine Pathways in Lung Adenocarcinoma.

Fahrmann JF, Grapov DD, Wanichthanarak K, DeFelice BC, Salemi MR, Rom WN, Gandara DR, Phinney BS, Fiehn O, Pass H, Miyamoto S.

Carcinogenesis. 2017 Mar;38(3):271-280. doi: 10.1093/carcin/bgw205. Epub 2017 Jan 3. Review.


ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments.

Choi M, Eren-Dogu ZF, Colangelo C, Cottrell J, Hoopmann MR, Kapp EA, Kim S, Lam H, Neubert TA, Palmblad M, Phinney BS, Weintraub ST, MacLean B, Vitek O.

J Proteome Res. 2017 Feb 3;16(2):945-957. doi: 10.1021/acs.jproteome.6b00881. Epub 2017 Jan 3.


In vivo digestomics of milk proteins in human milk and infant formula using a suckling rat pup model.

Wada Y, Phinney BS, Weber D, Lönnerdal B.

Peptides. 2017 Feb;88:18-31. doi: 10.1016/j.peptides.2016.11.012. Epub 2016 Dec 13.


Proteomic profiling of lung adenocarcinoma indicates heightened DNA repair, antioxidant mechanisms and identifies LASP1 as a potential negative predictor of survival.

Fahrmann JF, Grapov D, Phinney BS, Stroble C, DeFelice BC, Rom W, Gandara DR, Zhang Y, Fiehn O, Pass H, Miyamoto S.

Clin Proteomics. 2016 Oct 27;13:31. doi: 10.1186/s12014-016-9132-y. eCollection 2016.


The Secreted Protease PrtA Controls Cell Growth, Biofilm Formation and Pathogenicity in Xylella fastidiosa.

Gouran H, Gillespie H, Nascimento R, Chakraborty S, Zaini PA, Jacobson A, Phinney BS, Dolan D, Durbin-Johnson BP, Antonova ES, Lindow SE, Mellema MS, Goulart LR, Dandekar AM.

Sci Rep. 2016 Aug 5;6:31098. doi: 10.1038/srep31098.


Proteomic Analysis of Loricrin Knockout Mouse Epidermis.

Rice RH, Durbin-Johnson BP, Ishitsuka Y, Salemi M, Phinney BS, Rocke DM, Roop DR.

J Proteome Res. 2016 Aug 5;15(8):2560-6. doi: 10.1021/acs.jproteome.6b00108. Epub 2016 Jul 26.


Using LC-MS Based Methods for Testing the Digestibility of a Nonpurified Transgenic Membrane Protein in Simulated Gastric Fluid.

Skinner WS, Phinney BS, Herren A, Goodstal FJ, Dicely I, Facciotti D.

J Agric Food Chem. 2016 Jun 29;64(25):5251-9. doi: 10.1021/acs.jafc.6b01829. Epub 2016 Jun 15.


The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses.

Bennett KL, Wang X, Bystrom CE, Chambers MC, Andacht TM, Dangott LJ, Elortza F, Leszyk J, Molina H, Moritz RL, Phinney BS, Thompson JW, Bunger MK, Tabb DL.

Mol Cell Proteomics. 2015 Dec;14(12):3299-309. doi: 10.1074/mcp.O115.051888. Epub 2015 Oct 4.


Anopheles stephensi p38 MAPK signaling regulates innate immunity and bioenergetics during Plasmodium falciparum infection.

Wang B, Pakpour N, Napoli E, Drexler A, Glennon EK, Surachetpong W, Cheung K, Aguirre A, Klyver JM, Lewis EE, Eigenheer R, Phinney BS, Giulivi C, Luckhart S.

Parasit Vectors. 2015 Aug 19;8:424. doi: 10.1186/s13071-015-1016-x.


Dexamethasone Stiffens Trabecular Meshwork, Trabecular Meshwork Cells, and Matrix.

Raghunathan VK, Morgan JT, Park SA, Weber D, Phinney BS, Murphy CJ, Russell P.

Invest Ophthalmol Vis Sci. 2015 Jul;56(8):4447-59. doi: 10.1167/iovs.15-16739.


Lactobacillus casei Low-Temperature, Dairy-Associated Proteome Promotes Persistence in the Mammalian Digestive Tract.

Lee B, Tachon S, Eigenheer RA, Phinney BS, Marco ML.

J Proteome Res. 2015 Aug 7;14(8):3136-47. doi: 10.1021/acs.jproteome.5b00387. Epub 2015 Jul 24.


CaMKII Phosphorylation of Na(V)1.5: Novel in Vitro Sites Identified by Mass Spectrometry and Reduced S516 Phosphorylation in Human Heart Failure.

Herren AW, Weber DM, Rigor RR, Margulies KB, Phinney BS, Bers DM.

J Proteome Res. 2015 May 1;14(5):2298-311. doi: 10.1021/acs.jproteome.5b00107. Epub 2015 Apr 13.


Comparative Proteomics of Human and Macaque Milk Reveals Species-Specific Nutrition during Postnatal Development.

Beck KL, Weber D, Phinney BS, Smilowitz JT, Hinde K, Lönnerdal B, Korf I, Lemay DG.

J Proteome Res. 2015 May 1;14(5):2143-57. doi: 10.1021/pr501243m. Epub 2015 Apr 6.


Gene expression profiling in pachyonychia congenita skin.

Cao YA, Hickerson RP, Seegmiller BL, Grapov D, Gross MM, Bessette MR, Phinney BS, Flores MA, Speaker TJ, Vermeulen A, Bravo AA, Bruckner AL, Milstone LM, Schwartz ME, Rice RH, Kaspar RL.

J Dermatol Sci. 2015 Mar;77(3):156-65. doi: 10.1016/j.jdermsci.2015.01.001. Epub 2015 Jan 14.


The human colostrum whey proteome is altered in gestational diabetes mellitus.

Grapov D, Lemay DG, Weber D, Phinney BS, Azulay Chertok IR, Gho DS, German JB, Smilowitz JT.

J Proteome Res. 2015 Jan 2;14(1):512-20. doi: 10.1021/pr500818d. Epub 2014 Dec 1.


Human hair shaft proteomic profiling: individual differences, site specificity and cuticle analysis.

Laatsch CN, Durbin-Johnson BP, Rocke DM, Mukwana S, Newland AB, Flagler MJ, Davis MG, Eigenheer RA, Phinney BS, Rice RH.

PeerJ. 2014 Aug 5;2:e506. doi: 10.7717/peerj.506. eCollection 2014.


Shotgun proteomic analysis unveils survival and detoxification strategies by Caulobacter crescentus during exposure to uranium, chromium, and cadmium.

Yung MC, Ma J, Salemi MR, Phinney BS, Bowman GR, Jiao Y.

J Proteome Res. 2014 Apr 4;13(4):1833-47. doi: 10.1021/pr400880s. Epub 2014 Mar 7.


Mitochondrial proteome remodeling in ischemic heart failure.

Liu T, Chen L, Kim E, Tran D, Phinney BS, Knowlton AA.

Life Sci. 2014 Apr 17;101(1-2):27-36. doi: 10.1016/j.lfs.2014.02.004. Epub 2014 Feb 16.


Distinguishing ichthyoses by protein profiling.

Rice RH, Bradshaw KM, Durbin-Johnson BP, Rocke DM, Eigenheer RA, Phinney BS, Schmuth M, Gruber R.

PLoS One. 2013 Oct 9;8(10):e75355. doi: 10.1371/journal.pone.0075355. eCollection 2013.


Proteomic analysis of human keratinocyte response to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure.

Hu Q, Rice RH, Qin Q, Phinney BS, Eigenheer RA, Bao W, Zhao B.

J Proteome Res. 2013 Nov 1;12(11):5340-7. doi: 10.1021/pr4006266. Epub 2013 Sep 16.


Cryptococcus neoformans promotes its transmigration into the central nervous system by inducing molecular and cellular changes in brain endothelial cells.

Vu K, Eigenheer RA, Phinney BS, Gelli A.

Infect Immun. 2013 Sep;81(9):3139-47. doi: 10.1128/IAI.00554-13. Epub 2013 Jun 17.


Sustained activation of Akt elicits mitochondrial dysfunction to block Plasmodium falciparum infection in the mosquito host.

Luckhart S, Giulivi C, Drexler AL, Antonova-Koch Y, Sakaguchi D, Napoli E, Wong S, Price MS, Eigenheer R, Phinney BS, Pakpour N, Pietri JE, Cheung K, Georgis M, Riehle M.

PLoS Pathog. 2013 Feb;9(2):e1003180. doi: 10.1371/journal.ppat.1003180. Epub 2013 Feb 28.


Interlaboratory studies and initiatives developing standards for proteomics.

Ivanov AR, Colangelo CM, Dufresne CP, Friedman DB, Lilley KS, Mechtler K, Phinney BS, Rose KL, Rudnick PA, Searle BC, Shaffer SA, Weintraub ST.

Proteomics. 2013 Mar;13(6):904-9. doi: 10.1002/pmic.201200532. Epub 2013 Feb 19.


Differentiating inbred mouse strains from each other and those with single gene mutations using hair proteomics.

Rice RH, Bradshaw KM, Durbin-Johnson BP, Rocke DM, Eigenheer RA, Phinney BS, Sundberg JP.

PLoS One. 2012;7(12):e51956. doi: 10.1371/journal.pone.0051956. Epub 2012 Dec 14.


Phosphorylation and activation of the plasma membrane Na+/H+ exchanger (NHE1) during osmotic cell shrinkage.

Rigor RR, Damoc C, Phinney BS, Cala PM.

PLoS One. 2011;6(12):e29210. doi: 10.1371/journal.pone.0029210. Epub 2011 Dec 28.


Label-free shotgun proteomics and metabolite analysis reveal a significant metabolic shift during citrus fruit development.

Katz E, Boo KH, Kim HY, Eigenheer RA, Phinney BS, Shulaev V, Negre-Zakharov F, Sadka A, Blumwald E.

J Exp Bot. 2011 Nov;62(15):5367-84. doi: 10.1093/jxb/err197. Epub 2011 Aug 12.


REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock.

Rawat R, Takahashi N, Hsu PY, Jones MA, Schwartz J, Salemi MR, Phinney BS, Harmer SL.

PLoS Genet. 2011 Mar;7(3):e1001350. doi: 10.1371/journal.pgen.1001350. Epub 2011 Mar 31.


ABRF-PRG07: advanced quantitative proteomics study.

Falick AM, Lane WS, Lilley KS, MacCoss MJ, Phinney BS, Sherman NE, Weintraub ST, Witkowska HE, Yates NA.

J Biomol Tech. 2011 Apr;22(1):21-6.


A label-free differential quantitative mass spectrometry method for the characterization and identification of protein changes during citrus fruit development.

Katz E, Fon M, Eigenheer RA, Phinney BS, Fass JN, Lin D, Sadka A, Blumwald E.

Proteome Sci. 2010 Dec 16;8:68. doi: 10.1186/1477-5956-8-68.


Proteomic analysis of human nail plate.

Rice RH, Xia Y, Alvarado RJ, Phinney BS.

J Proteome Res. 2010 Dec 3;9(12):6752-8. doi: 10.1021/pr1009349. Epub 2010 Nov 1.


A comparative study of in-gel digestions using microwave and pressure-accelerated technologies.

Alvarado R, Tran D, Ching B, Phinney BS.

J Biomol Tech. 2010 Sep;21(3):148-55.


The significance of protein maturation by plastidic type I signal peptidase 1 for thylakoid development in Arabidopsis chloroplasts.

Shipman-Roston RL, Ruppel NJ, Damoc C, Phinney BS, Inoue K.

Plant Physiol. 2010 Mar;152(3):1297-308. doi: 10.1104/pp.109.151977. Epub 2010 Jan 22. Erratum in: Plant Physiol. 2010 Dec;154(4):2008.

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