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Combined BRAF and HSP90 inhibition in patients with unresectable BRAF V600E mutant melanoma.

Eroglu Z, Chen YA, Gibney GT, Weber JS, Kudchadkar RR, Khushalani NI, Markowitz J, Brohl AS, Tetteh LF, Ramadan H, Arnone G, Li J, Zhao X, Sharma R, Darville LNF, Fang B, Smalley I, Messina JL, Koomen JM, Sondak VK, Smalley KSM.

Clin Cancer Res. 2018 Apr 19. pii: clincanres.0565.2018. doi: 10.1158/1078-0432.CCR-18-0565. [Epub ahead of print]


Quantification of Breast Cancer Protein Biomarkers at Different Expression Levels in Human Tumors.

Chen Y, Britton D, Wood ER, Brantley S, Fournier M, Wloch M, Williams VL, Johnson J, Magliocco A, Pike I, Koomen JM.

Methods Mol Biol. 2017 Dec 15. doi: 10.1007/7651_2017_113. [Epub ahead of print]


Comparison of Quantitative Mass Spectrometry Platforms for Monitoring Kinase ATP Probe Uptake in Lung Cancer.

Hoffman MA, Fang B, Haura EB, Rix U, Koomen JM.

J Proteome Res. 2018 Jan 5;17(1):63-75. doi: 10.1021/acs.jproteome.7b00329. Epub 2017 Nov 22.


Polypharmacology-based ceritinib repurposing using integrated functional proteomics.

Kuenzi BM, Remsing Rix LL, Stewart PA, Fang B, Kinose F, Bryant AT, Boyle TA, Koomen JM, Haura EB, Rix U.

Nat Chem Biol. 2017 Dec;13(12):1222-1231. doi: 10.1038/nchembio.2489. Epub 2017 Oct 9.


Multiplexed Liquid Chromatography-Multiple Reaction Monitoring Mass Spectrometry Quantification of Cancer Signaling Proteins.

Chen Y, Fisher KJ, Lloyd M, Wood ER, Coppola D, Siegel E, Shibata D, Chen YA, Koomen JM.

Methods Mol Biol. 2017;1647:19-45. doi: 10.1007/978-1-4939-7201-2_2.


Unification of de novo and acquired ibrutinib resistance in mantle cell lymphoma.

Zhao X, Lwin T, Silva A, Shah B, Tao J, Fang B, Zhang L, Fu K, Bi C, Li J, Jiang H, Meads MB, Jacobson T, Silva M, Distler A, Darville L, Zhang L, Han Y, Rebatchouk D, Di Liberto M, Moscinski LC, Koomen JM, Dalton WS, Shain KH, Wang M, Sotomayor E, Tao J.

Nat Commun. 2017 Apr 18;8:14920. doi: 10.1038/ncomms14920.


Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer.

Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura EB.

Proteomes. 2016 Apr 27;4(2). pii: E16. doi: 10.3390/proteomes4020016.


Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms.

Stewart PA, Fang B, Slebos RJ, Zhang G, Borne AL, Fellows K, Teer JK, Chen YA, Welsh E, Eschrich SA, Haura EB, Koomen JM.

Proteomics. 2017 Mar;17(6). doi: 10.1002/pmic.201600300.


Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer.

Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura EB.

Proteomes. 2016 Apr 27;4(2):16. doi: 10.3390/proteomes4020016. eCollection 2016 Jun.


Quantitative proteomics of breast tumors: Tissue quality assessment to clinical biomarkers.

Chen Y, Britton D, Wood ER, Brantley S, Magliocco A, Pike I, Koomen JM.

Proteomics. 2017 Mar;17(6). doi: 10.1002/pmic.201600335.


Activity-Based Protein Profiling Shows Heterogeneous Signaling Adaptations to BRAF Inhibition.

Sharma R, Fedorenko I, Spence PT, Sondak VK, Smalley KS, Koomen JM.

J Proteome Res. 2016 Dec 2;15(12):4476-4489. Epub 2016 Nov 17.


Proteome-wide Profiling of Clinical PARP Inhibitors Reveals Compound-Specific Secondary Targets.

Knezevic CE, Wright G, Rix LLR, Kim W, Kuenzi BM, Luo Y, Watters JM, Koomen JM, Haura EB, Monteiro AN, Radu C, Lawrence HR, Rix U.

Cell Chem Biol. 2016 Dec 22;23(12):1490-1503. doi: 10.1016/j.chembiol.2016.10.011. Epub 2016 Nov 17.


IKKϵ phosphorylation of estrogen receptor α Ser-167 and contribution to tamoxifen resistance in breast cancer.

Guo JP, Shu SK, Esposito NN, Coppola D, Koomen JM, Cheng JQ.

J Biol Chem. 2016 Oct 21;291(43):22857. No abstract available.


APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data.

Kuenzi BM, Borne AL, Li J, Haura EB, Eschrich SA, Koomen JM, Rix U, Stewart PA.

J Proteome Res. 2016 Dec 2;15(12):4747-4754. Epub 2016 Oct 21.


Phosphoproteomics Reveals MAPK Inhibitors Enhance MET- and EGFR-Driven AKT Signaling in KRAS-Mutant Lung Cancer.

Kim JY, Welsh EA, Fang B, Bai Y, Kinose F, Eschrich SA, Koomen JM, Haura EB.

Mol Cancer Res. 2016 Oct;14(10):1019-1029. Epub 2016 Jul 15.


Inhibition of PI3K/Akt/mTOR signaling in PI3KR2-overexpressing colon cancer stem cells reduces tumor growth due to apoptosis.

Chen S, Fisher RC, Signs S, Molina LA, Shenoy AK, Lopez MC, Baker HV, Koomen JM, Chen Y, Gittleman H, Barnholtz-Sloan J, Berg A, Appelman HD, Huang EH.

Oncotarget. 2016 Jun 8;8(31):50476-50488. doi: 10.18632/oncotarget.9919. eCollection 2017 Aug 1.


Tyrosine Kinase Signaling in Clear Cell and Papillary Renal Cell Carcinoma Revealed by Mass Spectrometry-Based Phosphotyrosine Proteomics.

Haake SM, Li J, Bai Y, Kinose F, Fang B, Welsh EA, Zent R, Dhillon J, Pow-Sang JM, Chen YA, Koomen JM, Rathmell WK, Fishman M, Haura EB.

Clin Cancer Res. 2016 Nov 15;22(22):5605-5616. doi: 10.1158/1078-0432.CCR-15-1673. Epub 2016 May 24.


PAXIP1 Potentiates the Combination of WEE1 Inhibitor AZD1775 and Platinum Agents in Lung Cancer.

Jhuraney A, Woods NT, Wright G, Rix L, Kinose F, Kroeger JL, Remily-Wood E, Cress WD, Koomen JM, Brantley SG, Gray JE, Haura EB, Rix U, Monteiro AN.

Mol Cancer Ther. 2016 Jul;15(7):1669-81. doi: 10.1158/1535-7163.MCT-15-0182. Epub 2016 May 11.


Target Identification in Small Cell Lung Cancer via Integrated Phenotypic Screening and Activity-Based Protein Profiling.

Li J, Fang B, Kinose F, Bai Y, Kim JY, Chen YA, Rix U, Koomen JM, Haura EB.

Mol Cancer Ther. 2016 Feb;15(2):334-42. doi: 10.1158/1535-7163.MCT-15-0444. Epub 2016 Jan 15.


Chronic acidosis in the tumour microenvironment selects for overexpression of LAMP2 in the plasma membrane.

Damaghi M, Tafreshi NK, Lloyd MC, Sprung R, Estrella V, Wojtkowiak JW, Morse DL, Koomen JM, Bui MM, Gatenby RA, Gillies RJ.

Nat Commun. 2015 Dec 10;6:8752. doi: 10.1038/ncomms9752.


A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma.

Stewart PA, Parapatics K, Welsh EA, Müller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB.

PLoS One. 2015 Nov 5;10(11):e0142162. doi: 10.1371/journal.pone.0142162. eCollection 2015.


Targeting PYK2 mediates microenvironment-specific cell death in multiple myeloma.

Meads MB, Fang B, Mathews L, Gemmer J, Nong L, Rosado-Lopez I, Nguyen T, Ring JE, Matsui W, MacLeod AR, Pachter JA, Hazlehurst LA, Koomen JM, Shain KH.

Oncogene. 2016 May;35(21):2723-34. doi: 10.1038/onc.2015.334. Epub 2015 Sep 21.


Fibronectin induction abrogates the BRAF inhibitor response of BRAF V600E/PTEN-null melanoma cells.

Fedorenko IV, Abel EV, Koomen JM, Fang B, Wood ER, Chen YA, Fisher KJ, Iyengar S, Dahlman KB, Wargo JA, Flaherty KT, Sosman JA, Sondak VK, Messina JL, Gibney GT, Smalley KS.

Oncogene. 2016 Mar 10;35(10):1225-35. doi: 10.1038/onc.2015.188. Epub 2015 Jun 15.


MPP8 and SIRT1 crosstalk in E-cadherin gene silencing and epithelial-mesenchymal transition.

Sun L, Kokura K, Izumi V, Koomen JM, Seto E, Chen J, Fang J.

EMBO Rep. 2015 Jun;16(6):689-99. doi: 10.15252/embr.201439792. Epub 2015 Apr 13.


Evaluating kinase ATP uptake and tyrosine phosphorylation using multiplexed quantification of chemically labeled and post-translationally modified peptides.

Fang B, Hoffman MA, Mirza AS, Mishall KM, Li J, Peterman SM, Smalley KS, Shain KH, Weinberger PM, Wu J, Rix U, Haura EB, Koomen JM.

Methods. 2015 Jun 15;81:41-9. doi: 10.1016/j.ymeth.2015.03.006. Epub 2015 Mar 14.


Inhibition of Shp2 suppresses mutant EGFR-induced lung tumors in transgenic mouse model of lung adenocarcinoma.

Schneeberger VE, Ren Y, Luetteke N, Huang Q, Chen L, Lawrence HR, Lawrence NJ, Haura EB, Koomen JM, Coppola D, Wu J.

Oncotarget. 2015 Mar 20;6(8):6191-202.


Ligand-independent EPHA2 signaling drives the adoption of a targeted therapy-mediated metastatic melanoma phenotype.

Paraiso KH, Das Thakur M, Fang B, Koomen JM, Fedorenko IV, John JK, Tsao H, Flaherty KT, Sondak VK, Messina JL, Pasquale EB, Villagra A, Rao UN, Kirkwood JM, Meier F, Sloot S, Gibney GT, Stuart D, Tawbi H, Smalley KS.

Cancer Discov. 2015 Mar;5(3):264-73. doi: 10.1158/2159-8290.CD-14-0293. Epub 2014 Dec 26.


Adaptive responses to dasatinib-treated lung squamous cell cancer cells harboring DDR2 mutations.

Bai Y, Kim JY, Watters JM, Fang B, Kinose F, Song L, Koomen JM, Teer JK, Fisher K, Chen YA, Rix U, Haura EB.

Cancer Res. 2014 Dec 15;74(24):7217-7228. doi: 10.1158/0008-5472.CAN-14-0505. Epub 2014 Oct 27.


Phosphoproteomic analysis of basal and therapy-induced adaptive signaling networks in BRAF and NRAS mutant melanoma.

Fedorenko IV, Fang B, Munko AC, Gibney GT, Koomen JM, Smalley KS.

Proteomics. 2015 Jan;15(2-3):327-39. doi: 10.1002/pmic.201400200. Epub 2014 Dec 17.


Amuvatinib has cytotoxic effects against NRAS-mutant melanoma but not BRAF-mutant melanoma.

Fedorenko IV, Fang B, Koomen JM, Gibney GT, Smalley KS.

Melanoma Res. 2014 Oct;24(5):448-53. doi: 10.1097/CMR.0000000000000103.


Immunoglobulins: expanding the role for mass spectrometry in protein biomarker quantification.

Koomen JM.

Clin Chem. 2014 Aug;60(8):1034-5. doi: 10.1373/clinchem.2014.226035. Epub 2014 Jun 17. No abstract available.


Evaluating melanoma drug response and therapeutic escape with quantitative proteomics.

Rebecca VW, Wood E, Fedorenko IV, Paraiso KH, Haarberg HE, Chen Y, Xiang Y, Sarnaik A, Gibney GT, Sondak VK, Koomen JM, Smalley KS.

Mol Cell Proteomics. 2014 Jul;13(7):1844-54. doi: 10.1074/mcp.M113.037424. Epub 2014 Apr 23.


Quantification of peptides from immunoglobulin constant and variable regions by LC-MRM MS for assessment of multiple myeloma patients.

Remily-Wood ER, Benson K, Baz RC, Chen YA, Hussein M, Hartley-Brown MA, Sprung RW, Perez B, Liu RZ, Yoder SJ, Teer JK, Eschrich SA, Koomen JM.

Proteomics Clin Appl. 2014 Oct;8(9-10):783-95. doi: 10.1002/prca.201300077. Epub 2014 Sep 15.


Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach.

Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee JS, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S.

Mol Cell Proteomics. 2014 Mar;13(3):907-17. doi: 10.1074/mcp.M113.036095. Epub 2014 Jan 17.


GSK3 alpha and beta are new functionally relevant targets of tivantinib in lung cancer cells.

Remsing Rix LL, Kuenzi BM, Luo Y, Remily-Wood E, Kinose F, Wright G, Li J, Koomen JM, Haura EB, Lawrence HR, Rix U.

ACS Chem Biol. 2014 Feb 21;9(2):353-8. doi: 10.1021/cb400660a. Epub 2013 Nov 20.


Aurora-A is a determinant of tamoxifen sensitivity through phosphorylation of ERα in breast cancer.

Zheng XQ, Guo JP, Yang H, Kanai M, He LL, Li YY, Koomen JM, Minton S, Gao M, Ren XB, Coppola D, Cheng JQ.

Oncogene. 2014 Oct 16;33(42):4985-96. doi: 10.1038/onc.2013.444. Epub 2013 Oct 28.


Quantification of secretory leukocyte protease inhibitor (SLPI) in oral gargle specimens collected using mouthwash.

Pierce Campbell CM, Guan W, Sprung R, Koomen JM, O'Keefe MT, Ingles DJ, Abrahamsen M, Giuliano AR.

J Immunol Methods. 2013 Dec 31;400-401:117-21. doi: 10.1016/j.jim.2013.10.005. Epub 2013 Oct 17.


MTI-101 (cyclized HYD1) binds a CD44 containing complex and induces necrotic cell death in multiple myeloma.

Gebhard AW, Jain P, Nair RR, Emmons MF, Argilagos RF, Koomen JM, McLaughlin ML, Hazlehurst LA.

Mol Cancer Ther. 2013 Nov;12(11):2446-58. doi: 10.1158/1535-7163.MCT-13-0310. Epub 2013 Sep 18.


Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells.

Kim JY, Welsh EA, Oguz U, Fang B, Bai Y, Kinose F, Bronk C, Remsing Rix LL, Beg AA, Rix U, Eschrich SA, Koomen JM, Haura EB.

Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12414-9. doi: 10.1073/pnas.1220674110. Epub 2013 Jul 8.


Protein targets of acrylamide adduct formation in cultured rat dopaminergic cells.

Martyniuk CJ, Feswick A, Fang B, Koomen JM, Barber DS, Gavin T, Lopachin RM.

Toxicol Lett. 2013 Jun 7;219(3):279-87. doi: 10.1016/j.toxlet.2013.03.031. Epub 2013 Apr 6.


Inhibition of Wee1, AKT, and CDK4 underlies the efficacy of the HSP90 inhibitor XL888 in an in vivo model of NRAS-mutant melanoma.

Haarberg HE, Paraiso KH, Wood E, Rebecca VW, Sondak VK, Koomen JM, Smalley KS.

Mol Cancer Ther. 2013 Jun;12(6):901-12. doi: 10.1158/1535-7163.MCT-12-1003. Epub 2013 Mar 28.


H2B Tyr37 phosphorylation suppresses expression of replication-dependent core histone genes.

Mahajan K, Fang B, Koomen JM, Mahajan NP.

Nat Struct Mol Biol. 2012 Sep;19(9):930-7. doi: 10.1038/nsmb.2356. Epub 2012 Aug 12.


GSK3β inhibition blocks melanoma cell/host interactions by downregulating N-cadherin expression and decreasing FAK phosphorylation.

John JK, Paraiso KH, Rebecca VW, Cantini LP, Abel EV, Pagano N, Meggers E, Mathew R, Krepler C, Izumi V, Fang B, Koomen JM, Messina JL, Herlyn M, Smalley KS.

J Invest Dermatol. 2012 Dec;132(12):2818-27. doi: 10.1038/jid.2012.237. Epub 2012 Jul 19.


An ET-CURE pilot project supporting undergraduate training in cancer research, emerging technology, and health disparities.

Wilson DS, Fang B, Dalton WS, Meade CD, Koomen JM.

J Cancer Educ. 2012 Jun;27(3):418-27. doi: 10.1007/s13187-012-0362-z.


Evaluation of protein quantification using standard peptides containing single conservative amino acid replacements.

Remily-Wood ER, Koomen JM.

J Mass Spectrom. 2012 Feb;47(2):188-94. doi: 10.1002/jms.2053.


The HSP90 inhibitor XL888 overcomes BRAF inhibitor resistance mediated through diverse mechanisms.

Paraiso KH, Haarberg HE, Wood E, Rebecca VW, Chen YA, Xiang Y, Ribas A, Lo RS, Weber JS, Sondak VK, John JK, Sarnaik AA, Koomen JM, Smalley KS.

Clin Cancer Res. 2012 May 1;18(9):2502-14. doi: 10.1158/1078-0432.CCR-11-2612. Epub 2012 Feb 20.


Evaluation of direct infusion-multiple reaction monitoring mass spectrometry for quantification of heat shock proteins.

Xiang Y, Koomen JM.

Anal Chem. 2012 Feb 21;84(4):1981-6. doi: 10.1021/ac203011j. Epub 2012 Jan 23.


A mass spectrometry-based method to screen for α-amidated peptides.

An Z, Chen Y, Koomen JM, Merkler DJ.

Proteomics. 2012 Jan;12(2):173-82. doi: 10.1002/pmic.201100327. Epub 2011 Dec 14.


MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a.

Chang Y, Sun L, Kokura K, Horton JR, Fukuda M, Espejo A, Izumi V, Koomen JM, Bedford MT, Zhang X, Shinkai Y, Fang J, Cheng X.

Nat Commun. 2011 Nov 15;2:533. doi: 10.1038/ncomms1549.


Molecular mechanism of glyceraldehyde-3-phosphate dehydrogenase inactivation by α,β-unsaturated carbonyl derivatives.

Martyniuk CJ, Fang B, Koomen JM, Gavin T, Zhang L, Barber DS, Lopachin RM.

Chem Res Toxicol. 2011 Dec 19;24(12):2302-11. doi: 10.1021/tx200437y. Epub 2011 Nov 29.

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