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Proteogenomic landscape of squamous cell lung cancer.

Stewart PA, Welsh EA, Slebos RJC, Fang B, Izumi V, Chambers M, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Fellows KM, Francis JM, Saller JJ, Mesa T, Zhang C, Yoder S, DeNicola GM, Beg AA, Boyle TA, Teer JK, Ann Chen Y, Koomen JM, Eschrich SA, Haura EB.

Nat Commun. 2019 Aug 8;10(1):3578. doi: 10.1038/s41467-019-11452-x.


lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNA.

Li Q, Yu X, Chaudhary R, Slebos RJC, Chung CH, Wang X.

BMC Genomics. 2019 Jul 2;20(1):539. doi: 10.1186/s12864-019-5926-4.


Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities.

Vasaikar S, Huang C, Wang X, Petyuk VA, Savage SR, Wen B, Dou Y, Zhang Y, Shi Z, Arshad OA, Gritsenko MA, Zimmerman LJ, McDermott JE, Clauss TR, Moore RJ, Zhao R, Monroe ME, Wang YT, Chambers MC, Slebos RJC, Lau KS, Mo Q, Ding L, Ellis M, Thiagarajan M, Kinsinger CR, Rodriguez H, Smith RD, Rodland KD, Liebler DC, Liu T, Zhang B; Clinical Proteomic Tumor Analysis Consortium.

Cell. 2019 May 2;177(4):1035-1049.e19. doi: 10.1016/j.cell.2019.03.030. Epub 2019 Apr 25.


Human Papillomavirus Genotype Detection in Oral Gargle Samples Among Men With Newly Diagnosed Oropharyngeal Squamous Cell Carcinoma.

Martin-Gomez L, Giuliano AR, Fulp WJ, Caudell J, Echevarria M, Sirak B, Abrahamsen M, Isaacs-Soriano KA, Hernandez-Prera JC, Wenig BM, Vorwald K, McMullen CP, Wadsworth JT, Slebos RJ, Chung CH.

JAMA Otolaryngol Head Neck Surg. 2019 May 1;145(5):460-466. doi: 10.1001/jamaoto.2019.0119.


Identification of Proteomic Features To Distinguish Benign Pulmonary Nodules from Lung Adenocarcinoma.

Codreanu SG, Hoeksema MD, Slebos RJC, Zimmerman LJ, Rahman SMJ, Li M, Chen SC, Chen H, Eisenberg R, Liebler DC, Massion PP.

J Proteome Res. 2017 Sep 1;16(9):3266-3276. doi: 10.1021/acs.jproteome.7b00245. Epub 2017 Aug 8.


Colorectal Cancer Cell Line Proteomes Are Representative of Primary Tumors and Predict Drug Sensitivity.

Wang J, Mouradov D, Wang X, Jorissen RN, Chambers MC, Zimmerman LJ, Vasaikar S, Love CG, Li S, Lowes K, Leuchowius KJ, Jousset H, Weinstock J, Yau C, Mariadason J, Shi Z, Ban Y, Chen X, Coffey RJC, Slebos RJC, Burgess AW, Liebler DC, Zhang B, Sieber OM.

Gastroenterology. 2017 Oct;153(4):1082-1095. doi: 10.1053/j.gastro.2017.06.008. Epub 2017 Jun 16.


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.


The airway epithelium undergoes metabolic reprogramming in individuals at high risk for lung cancer.

Rahman SMJ, Ji X, Zimmerman LJ, Li M, Harris BK, Hoeksema MD, Trenary IA, Zou Y, Qian J, Slebos RJ, Beane J, Spira A, Shyr Y, Eisenberg R, Liebler DC, Young JD, Massion PP.

JCI Insight. 2016 Nov 17;1(19):e88814. doi: 10.1172/jci.insight.88814.


Oncogenic KRAS and BRAF Drive Metabolic Reprogramming in Colorectal Cancer.

Hutton JE, Wang X, Zimmerman LJ, Slebos RJ, Trenary IA, Young JD, Li M, Liebler DC.

Mol Cell Proteomics. 2016 Sep;15(9):2924-38. doi: 10.1074/mcp.M116.058925. Epub 2016 Jun 23.


proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data.

Wang X, Slebos RJ, Chambers MC, Tabb DL, Liebler DC, Zhang B.

Mol Cell Proteomics. 2016 Mar;15(3):1164-75. doi: 10.1074/mcp.M115.052860. Epub 2015 Dec 11.


Corrigendum: Proteomic analysis of colon and rectal carcinoma using standard and customized databases.

Slebos RJ, Wang X, Wang X, Zhang B, Tabb DL, Liebler DC.

Sci Data. 2015 Jul 21;2:150037. doi: 10.1038/sdata.2015.37. eCollection 2015. No abstract available.


Phenotype-Driven Plasma Biobanking Strategies and Methods.

Bowton EA, Collier SP, Wang X, Sutcliffe CB, Van Driest SL, Couch LJ, Herrera M, Jerome RN, Slebos RJ, Alborn WE, Liebler DC, McNaughton CD, Mernaugh RL, Wells QS, Brown NJ, Roden DM, Pulley JM.

J Pers Med. 2015 May 14;5(2):140-52. doi: 10.3390/jpm5020140.


Proteomic analysis of colon and rectal carcinoma using standard and customized databases.

Slebos RJ, Wang X, Wang X, Zhang B, Tabb DL, Liebler DC.

Sci Data. 2015 Jun 23;2:150022. doi: 10.1038/sdata.2015.22. eCollection 2015. Erratum in: Sci Data. 2015;2:150037. Wang, Xaojing [corrected to Wang, Xiaojing].


Phosphotyrosine signaling analysis in human tumors is confounded by systemic ischemia-driven artifacts and intra-specimen heterogeneity.

Gajadhar AS, Johnson H, Slebos RJ, Shaddox K, Wiles K, Washington MK, Herline AJ, Levine DA, Liebler DC, White FM; Clinical Proteomic Tumor Analysis Consortium.

Cancer Res. 2015 Apr 1;75(7):1495-503. doi: 10.1158/0008-5472.CAN-14-2309. Epub 2015 Feb 10.


A 3'-UTR KRAS-variant is associated with cisplatin resistance in patients with recurrent and/or metastatic head and neck squamous cell carcinoma.

Chung CH, Lee JW, Slebos RJ, Howard JD, Perez J, Kang H, Fertig EJ, Considine M, Gilbert J, Murphy BA, Nallur S, Paranjape T, Jordan RC, Garcia J, Burtness B, Forastiere AA, Weidhaas JB.

Ann Oncol. 2014 Nov;25(11):2230-6. doi: 10.1093/annonc/mdu367. Epub 2014 Jul 31. Erratum in: Ann Oncol. 2015 May;26(5):1038-9.


Proteogenomic characterization of human colon and rectal cancer.

Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC; NCI CPTAC.

Nature. 2014 Sep 18;513(7518):382-7. doi: 10.1038/nature13438. Epub 2014 Jul 20.


Proteogenomic analysis reveals unanticipated adaptations of colorectal tumor cells to deficiencies in DNA mismatch repair.

Halvey PJ, Wang X, Wang J, Bhat AA, Dhawan P, Li M, Zhang B, Liebler DC, Slebos RJ.

Cancer Res. 2014 Jan 1;74(1):387-97. doi: 10.1158/0008-5472.CAN-13-2488. Epub 2013 Nov 18.


Comparison of protein immunoprecipitation-multiple reaction monitoring with ELISA for assay of biomarker candidates in plasma.

Lin D, Alborn WE, Slebos RJ, Liebler DC.

J Proteome Res. 2013 Dec 6;12(12):5996-6003. doi: 10.1021/pr400877e. Epub 2013 Nov 19.


Integrative omics analysis reveals the importance and scope of translational repression in microRNA-mediated regulation.

Liu Q, Halvey PJ, Shyr Y, Slebos RJ, Liebler DC, Zhang B.

Mol Cell Proteomics. 2013 Jul;12(7):1900-11. doi: 10.1074/mcp.M112.025783. Epub 2013 Apr 2.


In-depth proteomic analysis of nonsmall cell lung cancer to discover molecular targets and candidate biomarkers.

Kikuchi T, Hassanein M, Amann JM, Liu Q, Slebos RJ, Rahman SM, Kaufman JM, Zhang X, Hoeksema MD, Harris BK, Li M, Shyr Y, Gonzalez AL, Zimmerman LJ, Liebler DC, Massion PP, Carbone DP.

Mol Cell Proteomics. 2012 Oct;11(10):916-32. Epub 2012 Jul 3.


Proteomic analysis of oropharyngeal carcinomas reveals novel HPV-associated biological pathways.

Slebos RJ, Jehmlich N, Brown B, Yin Z, Chung CH, Yarbrough WG, Liebler DC.

Int J Cancer. 2013 Feb 1;132(3):568-79. doi: 10.1002/ijc.27699. Epub 2012 Jul 20.


A Reporter System for Translational Readthrough of Stop Codons in Human Cells.

Halvey PJ, Liebler DC, Slebos RJ.

FEBS Open Bio. 2012 Dec;2:56-59. Epub 2012 Apr 17.


Global stability of plasma proteomes for mass spectrometry-based analyses.

Zimmerman LJ, Li M, Yarbrough WG, Slebos RJ, Liebler DC.

Mol Cell Proteomics. 2012 Jun;11(6):M111.014340. doi: 10.1074/mcp.M111.014340. Epub 2012 Feb 1.


Glucose-independent glutamine metabolism via TCA cycling for proliferation and survival in B cells.

Le A, Lane AN, Hamaker M, Bose S, Gouw A, Barbi J, Tsukamoto T, Rojas CJ, Slusher BS, Zhang H, Zimmerman LJ, Liebler DC, Slebos RJ, Lorkiewicz PK, Higashi RM, Fan TW, Dang CV.

Cell Metab. 2012 Jan 4;15(1):110-21. doi: 10.1016/j.cmet.2011.12.009.


Protein identification using customized protein sequence databases derived from RNA-Seq data.

Wang X, Slebos RJ, Wang D, Halvey PJ, Tabb DL, Liebler DC, Zhang B.

J Proteome Res. 2012 Feb 3;11(2):1009-17. doi: 10.1021/pr200766z. Epub 2011 Dec 14. Erratum in: J Proteome Res. 2012 Sep 7;11(9):4764.


Proteomic consequences of a single gene mutation in a colorectal cancer model.

Halvey PJ, Zhang B, Coffey RJ, Liebler DC, Slebos RJ.

J Proteome Res. 2012 Feb 3;11(2):1184-95. doi: 10.1021/pr2009109. Epub 2011 Dec 13.


Analysis of microsatellite mutations in buccal cells from a case-control study for lung cancer.

Baumann JL, Li M, Poulsen A, Chadwick NS, Cai Q, Chung CH, Shyr Y, Olsen JH, Zheng W, Slebos RJ.

Cancer Epidemiol. 2012 Feb;36(1):e33-9. doi: 10.1016/j.canep.2011.06.003. Epub 2011 Nov 6.


Phase 2 trial of oxaliplatin and pemetrexed as an induction regimen in locally advanced head and neck cancer.

Gilbert J, Murphy B, Dietrich MS, Henry E, Jordan R, Counsell A, Wirth P, Yarbrough WG, Slebos RJ, Chung CH.

Cancer. 2012 Feb 15;118(4):1007-13. doi: 10.1002/cncr.26364. Epub 2011 Jul 15.


A bioinformatics workflow for variant peptide detection in shotgun proteomics.

Li J, Su Z, Ma ZQ, Slebos RJ, Halvey P, Tabb DL, Liebler DC, Pao W, Zhang B.

Mol Cell Proteomics. 2011 May;10(5):M110.006536. doi: 10.1074/mcp.M110.006536. Epub 2011 Mar 9.


Methods for peptide and protein quantitation by liquid chromatography-multiple reaction monitoring mass spectrometry.

Zhang H, Liu Q, Zimmerman LJ, Ham AJ, Slebos RJ, Rahman J, Kikuchi T, Massion PP, Carbone DP, Billheimer D, Liebler DC.

Mol Cell Proteomics. 2011 Jun;10(6):M110.006593. doi: 10.1074/mcp.M110.006593. Epub 2011 Feb 27.


Regulation of heparin-binding EGF-like growth factor by miR-212 and acquired cetuximab-resistance in head and neck squamous cell carcinoma.

Hatakeyama H, Cheng H, Wirth P, Counsell A, Marcrom SR, Wood CB, Pohlmann PR, Gilbert J, Murphy B, Yarbrough WG, Wheeler DL, Harari PM, Guo Y, Shyr Y, Slebos RJ, Chung CH.

PLoS One. 2010 Sep 13;5(9):e12702. doi: 10.1371/journal.pone.0012702.


Cysteinyl peptide capture for shotgun proteomics: global assessment of chemoselective fractionation.

Lin D, Li J, Slebos RJ, Liebler DC.

J Proteome Res. 2010 Oct 1;9(10):5461-72. doi: 10.1021/pr1007015.


Depletion of abundant plasma proteins and limitations of plasma proteomics.

Tu C, Rudnick PA, Martinez MY, Cheek KL, Stein SE, Slebos RJ, Liebler DC.

J Proteome Res. 2010 Oct 1;9(10):4982-91. doi: 10.1021/pr100646w.


Comparative shotgun proteomics using spectral count data and quasi-likelihood modeling.

Li M, Gray W, Zhang H, Chung CH, Billheimer D, Yarbrough WG, Liebler DC, Shyr Y, Slebos RJ.

J Proteome Res. 2010 Aug 6;9(8):4295-305. doi: 10.1021/pr100527g. Erratum in: J Proteome Res. 2010 Nov 5;9(11):6090.


Efficacy of cetuximab in the treatment of Menetrier's disease.

Fiske WH, Tanksley J, Nam KT, Goldenring JR, Slebos RJ, Liebler DC, Abtahi AM, La Fleur B, Ayers GD, Lind CD, Washington MK, Coffey RJ.

Sci Transl Med. 2009 Nov 25;1(8):8ra18. doi: 10.1126/scitranslmed.3000320.


TagRecon: high-throughput mutation identification through sequence tagging.

Dasari S, Chambers MC, Slebos RJ, Zimmerman LJ, Ham AJ, Tabb DL.

J Proteome Res. 2010 Apr 5;9(4):1716-26. doi: 10.1021/pr900850m.


Nuclear factor-kappa B pathway and response in a phase II trial of bortezomib and docetaxel in patients with recurrent and/or metastatic head and neck squamous cell carcinoma.

Chung CH, Aulino J, Muldowney NJ, Hatakeyama H, Baumann J, Burkey B, Netterville J, Sinard R, Yarbrough WG, Cmelak AJ, Slebos RJ, Shyr Y, Parker J, Gilbert J, Murphy BA.

Ann Oncol. 2010 Apr;21(4):864-70. doi: 10.1093/annonc/mdp390. Epub 2009 Oct 22.


Human papillomavirus in early laryngeal carcinoma.

Baumann JL, Cohen S, Evjen AN, Law JH, Vadivelu S, Attia A, Schindler JS, Chung CH, Wirth PS, Meijer CJ, Snijders PJ, Yarbrough WG, Slebos RJ.

Laryngoscope. 2009 Aug;119(8):1531-7. doi: 10.1002/lary.20509.


Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis.

Sprung RW Jr, Brock JW, Tanksley JP, Li M, Washington MK, Slebos RJ, Liebler DC.

Mol Cell Proteomics. 2009 Aug;8(8):1988-98. doi: 10.1074/mcp.M800518-MCP200. Epub 2009 May 24.


Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry.

Slebos RJ, Brock JW, Winters NF, Stuart SR, Martinez MA, Li M, Chambers MC, Zimmerman LJ, Ham AJ, Tabb DL, Liebler DC.

J Proteome Res. 2008 Dec;7(12):5286-94. doi: 10.1021/pr8004666.


Global impact of oncogenic Src on a phosphotyrosine proteome.

Luo W, Slebos RJ, Hill S, Li M, Brábek J, Amanchy R, Chaerkady R, Pandey A, Ham AJ, Hanks SK.

J Proteome Res. 2008 Aug;7(8):3447-60. doi: 10.1021/pr800187n. Epub 2008 Jun 19.


Update on molecular diagnostic tests in head and neck cancer.

Palka KT, Slebos RJ, Chung CH.

Semin Oncol. 2008 Jun;35(3):198-210. doi: 10.1053/j.seminoncol.2008.03.002. Review.


Cetuximab-induced anaphylaxis and IgE specific for galactose-alpha-1,3-galactose.

Chung CH, Mirakhur B, Chan E, Le QT, Berlin J, Morse M, Murphy BA, Satinover SM, Hosen J, Mauro D, Slebos RJ, Zhou Q, Gold D, Hatley T, Hicklin DJ, Platts-Mills TA.

N Engl J Med. 2008 Mar 13;358(11):1109-17. doi: 10.1056/NEJMoa074943.


Microsatellite mutations in buccal cells are associated with aging and head and neck carcinoma.

Slebos RJ, Li M, Vadivelu S, Burkey BB, Netterville JL, Sinard R, Gilbert J, Murphy B, Chung CH, Shyr Y, Yarbrough WG.

Br J Cancer. 2008 Feb 12;98(3):619-26. doi: 10.1038/sj.bjc.6604198. Epub 2008 Jan 22.


Gene expression profiles as markers of aggressive disease-EGFR as a factor.

Chung CH, Parker J, Levy S, Slebos RJ, Dicker AP, Rodeck U.

Int J Radiat Oncol Biol Phys. 2007;69(2 Suppl):S102-5. No abstract available.


Detection of pre-invasive lung cancer: technical aspects of the LIFE project.

Flake GP, Rivera MP, Funkhouser WK, Maygarden SJ, Meadows KL, Long EH, Stockton PS, Jones TC, Yim HW, Slebos RJ, Taylor JA.

Toxicol Pathol. 2007 Jan;35(1):65-74.


Mutagenic effect of cadmium on tetranucleotide repeats in human cells.

Slebos RJ, Li M, Evjen AN, Coffa J, Shyr Y, Yarbrough WG.

Mutat Res. 2006 Dec 1;602(1-2):92-9. Epub 2006 Sep 20.


Increased epidermal growth factor receptor gene copy number is associated with poor prognosis in head and neck squamous cell carcinomas.

Chung CH, Ely K, McGavran L, Varella-Garcia M, Parker J, Parker N, Jarrett C, Carter J, Murphy BA, Netterville J, Burkey BB, Sinard R, Cmelak A, Levy S, Yarbrough WG, Slebos RJ, Hirsch FR.

J Clin Oncol. 2006 Sep 1;24(25):4170-6.


Gene expression profiles identify epithelial-to-mesenchymal transition and activation of nuclear factor-kappaB signaling as characteristics of a high-risk head and neck squamous cell carcinoma.

Chung CH, Parker JS, Ely K, Carter J, Yi Y, Murphy BA, Ang KK, El-Naggar AK, Zanation AM, Cmelak AJ, Levy S, Slebos RJ, Yarbrough WG.

Cancer Res. 2006 Aug 15;66(16):8210-8.


Smoking is associated with increased telomerase activity in short-term cultures of human bronchial epithelial cells.

Yim HW, Slebos RJ, Randell SH, Umbach DM, Parsons AM, Rivera MP, Detterbeck FC, Taylor JA.

Cancer Lett. 2007 Feb 8;246(1-2):24-33. Epub 2006 Mar 6.


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