John M. Koomen, Ph.D. - Publications

Affiliations: 
2002 Texas A & M University, College Station, TX, United States 
Area:
Biological Mass Spectrometry

123 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Sumi NJ, Ctortecka C, Hu Q, Bryant AT, Fang B, Remsing Rix LL, Ayaz M, Kinose F, Welsh EA, Eschrich SA, Lawrence HR, Koomen JM, Haura EB, Rix U. Divergent Polypharmacology-Driven Cellular Activity of Structurally Similar Multi-Kinase Inhibitors through Cumulative Effects on Individual Targets. Cell Chemical Biology. PMID 31257184 DOI: 10.1016/j.chembiol.2019.06.003  0.4
2019 Faião-Flores F, Emmons MF, Durante MA, Kinose F, Saha B, Fang B, Koomen JM, Chellappan SP, Maria-Engler SS, Rix U, Licht JD, Harbour JW, Smalley KSM. HDAC inhibition enhances the in vivo efficacy of MEK inhibitor therapy in uveal melanoma. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 31227503 DOI: 10.1158/1078-0432.CCR-18-3382  0.32
2019 Li Q, Fisher K, Meng W, Fang B, Welsh E, Haura EB, Koomen JM, Eschrich SA, Fridley BL, Chen YA. GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis. Bioinformatics (Oxford, England). PMID 31199438 DOI: 10.1093/bioinformatics/btz488  0.32
2019 Koomen DC, Guingab-Cagmat JD, Oliveira PS, Fang B, Liu M, Welsh EA, Meads MB, Nguyen T, Meke L, Eschrich SA, Shain KH, Garrett TJ, Koomen JM. Proteometabolomics of Melphalan Resistance in Multiple Myeloma. Methods in Molecular Biology (Clifton, N.J.). 1996: 273-296. PMID 31127562 DOI: 10.1007/978-1-4939-9488-5_21  0.32
2019 Zhao X, Ren Y, Lawlor M, Shah BD, Park PMC, Lwin T, Wang X, Liu K, Wang M, Gao J, Li T, Xu M, Silva AS, Lee K, Zhang T, ... Koomen JM, et al. BCL2 Amplicon Loss and Transcriptional Remodeling Drives ABT-199 Resistance in B Cell Lymphoma Models. Cancer Cell. 35: 752-766.e9. PMID 31085176 DOI: 10.1016/j.ccell.2019.04.005  0.32
2019 Yin Q, Han T, Fang B, Zhang G, Zhang C, Roberts ER, Izumi V, Zheng M, Jiang S, Yin X, Kim M, Cai J, Haura EB, Koomen JM, Smalley KSM, et al. K27-linked ubiquitination of BRAF by ITCH engages cytokine response to maintain MEK-ERK signaling. Nature Communications. 10: 1870. PMID 31015455 DOI: 10.1038/s41467-019-09844-0  0.32
2019 Ramello MC, Benzaïd I, Kuenzi BM, Lienlaf-Moreno M, Kandell WM, Santiago DN, Pabón-Saldaña M, Darville L, Fang B, Rix U, Yoder S, Berglund A, Koomen JM, Haura EB, Abate-Daga D. An immunoproteomic approach to characterize the CAR interactome and signalosome. Science Signaling. 12. PMID 30755478 DOI: 10.1126/scisignal.aap9777  0.32
2018 Hill KS, Roberts ER, Wang X, Marin E, Park TD, Son S, Ren Y, Fang B, Yoder S, Kim S, Wan L, Sarnaik AA, Koomen JM, Messina JL, Teer JK, et al. PTPN11 plays oncogenic roles and is a therapeutic target for BRAF wild-type melanomas. Molecular Cancer Research : McR. PMID 30355677 DOI: 10.1158/1541-7786.MCR-18-0777  0.4
2018 Ren Y, Bi C, Zhao X, Lwin T, Wang C, Yuan J, Silva AS, Shah BD, Fang B, Li T, Koomen JM, Jiang H, Chavez JC, Pham L, Sudalagunta PR, et al. PLK1 stabilizes a MYC-dependent kinase network in aggressive B cell lymphomas. The Journal of Clinical Investigation. PMID 30260324 DOI: 10.1172/JCI122533  0.32
2018 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, ... ... Koomen JM, et al. Combined BRAF and HSP90 inhibition in patients with unresectable V600E mutant melanoma. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 29674508 DOI: 10.1158/1078-0432.CCR-18-0565  0.32
2017 Hoffman MA, Fang B, Haura EB, Rix U, Koomen JM. Comparison of Quantitative Mass Spectrometry Platforms for Monitoring Kinase ATP Probe Uptake in Lung Cancer. Journal of Proteome Research. PMID 29164889 DOI: 10.1021/acs.jproteome.7b00329  0.32
2017 Kuenzi BM, Remsing Rix LL, Stewart PA, Fang B, Kinose F, Bryant AT, Boyle TA, Koomen JM, Haura EB, Rix U. Polypharmacology-based ceritinib repurposing using integrated functional proteomics. Nature Chemical Biology. PMID 28991240 DOI: 10.1038/nchembio.2489  0.32
2017 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, ... ... Koomen JM, et al. Unification of de novo and acquired ibrutinib resistance in mantle cell lymphoma. Nature Communications. 8: 14920. PMID 28416797 DOI: 10.1038/ncomms14920  0.32
2017 Stewart PA, Fang B, Slebos RJ, Zhang G, Borne AL, Fellows K, Teer JK, Chen YA, Welsh E, Eschrich SA, Haura EB, Koomen JM. Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms. Proteomics. PMID 28195392 DOI: 10.1002/pmic.201600300  0.32
2016 Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura EB. Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer. Proteomes. 4. PMID 28248226 DOI: 10.3390/proteomes4020016  0.32
2016 Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura EB. Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer. Proteomes. 4: 16. PMID 28154798 DOI: 10.3390/proteomes4020016  0.32
2016 Knezevic CE, Wright G, Remsing Rix LL, Kim W, Kuenzi BM, Luo Y, Watters JM, Koomen JM, Haura EB, Monteiro AN, Radu C, Lawrence HR, Rix U. Proteome-wide Profiling of Clinical PARP Inhibitors Reveals Compound-Specific Secondary Targets. Cell Chemical Biology. PMID 27866910 DOI: 10.1016/j.chembiol.2016.10.011  0.4
2016 Kim JY, Welsh EA, Fang B, Bai Y, Kinose F, Eschrich SA, Koomen JM, Haura EB. Phosphoproteomics reveals MAPK inhibitors enhance MET- and EGFR-driven AKT signaling in KRAS-mutant lung cancer. Molecular Cancer Research : McR. PMID 27422710 DOI: 10.1158/1541-7786.MCR-15-0506  0.32
2016 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. Tyrosine Kinase Signaling in Clear Cell and Papillary Renal Cell Carcinoma Revealed by Mass Spectrometry-Based Phosphotyrosine Proteomics. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 27220961 DOI: 10.1158/1078-0432.CCR-15-1673  0.32
2016 Li J, Fang B, Kinose F, Bai Y, Kim JY, Chen YA, Rix U, Koomen JM, Haura EB. Target identification in small cell lung cancer via integrated phenotypic screening and activity-based protein profiling. Molecular Cancer Therapeutics. PMID 26772203 DOI: 10.1158/1535-7163.MCT-15-0444  0.96
2015 Stewart PA, Parapatics K, Welsh EA, Müller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB. A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma. Plos One. 10: e0142162. PMID 26539827 DOI: 10.1371/journal.pone.0142162  0.96
2015 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. Targeting PYK2 mediates microenvironment-specific cell death in multiple myeloma. Oncogene. PMID 26387544 DOI: 10.1038/onc.2015.334  0.96
2015 Greer T, Hao L, Nechyporenko A, Lee S, Vezina CM, Ricke WA, Marker PC, Bjorling DE, Bushman W, Li L. Custom 4-Plex DiLeu Isobaric Labels Enable Relative Quantification of Urinary Proteins in Men with Lower Urinary Tract Symptoms (LUTS). Plos One. 10: e0135415. PMID 26267142 DOI: 10.1371/journal.pone.0135415  0.96
2015 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, et al. Fibronectin induction abrogates the BRAF inhibitor response of BRAF V600E/PTEN-null melanoma cells. Oncogene. PMID 26073081 DOI: 10.1038/onc.2015.188  0.96
2015 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. Evaluating kinase ATP uptake and tyrosine phosphorylation using multiplexed quantification of chemically labeled and post-translationally modified peptides. Methods (San Diego, Calif.). 81: 41-9. PMID 25782629 DOI: 10.1016/j.ymeth.2015.03.006  0.96
2015 Schneeberger VE, Ren Y, Luetteke N, Huang Q, Chen L, Lawrence HR, Lawrence NJ, Haura EB, Koomen JM, Coppola D, Wu J. Inhibition of Shp2 suppresses mutant EGFR-induced lung tumors in transgenic mouse model of lung adenocarcinoma. Oncotarget. 6: 6191-202. PMID 25730908  0.4
2015 Peng L, Yuan Z, Li Y, Ling H, Izumi V, Fang B, Fukasawa K, Koomen J, Chen J, Seto E. Ubiquitinated sirtuin 1 (SIRT1) function is modulated during DNA damage-induced cell death and survival. The Journal of Biological Chemistry. 290: 8904-12. PMID 25670865 DOI: 10.1074/jbc.M114.612796  0.96
2015 Yuan W, Sanda M, Wu J, Koomen J, Goldman R. Quantitative analysis of immunoglobulin subclasses and subclass specific glycosylation by LC-MS-MRM in liver disease. Journal of Proteomics. 116: 24-33. PMID 25582524 DOI: 10.1016/j.jprot.2014.12.020  0.96
2015 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, et al. Ligand-independent EPHA2 signaling drives the adoption of a targeted therapy-mediated metastatic melanoma phenotype. Cancer Discovery. 5: 264-73. PMID 25542447 DOI: 10.1158/2159-8290.CD-14-0293  0.96
2015 Fedorenko IV, Fang B, Munko AC, Gibney GT, Koomen JM, Smalley KS. Phosphoproteomic analysis of basal and therapy-induced adaptive signaling networks in BRAF and NRAS mutant melanoma. Proteomics. 15: 327-39. PMID 25339196 DOI: 10.1002/pmic.201400200  0.96
2015 Schneeberger VE, Ren Y, Luetteke N, Huang Q, Chen L, Lawrence HR, Lawrence NJ, Haura EB, Koomen JM, Coppola D, Wu J. Inhibition of Shp2 suppresses mutant EGFR-induced lung tumors in transgenic mouse model of lung adenocarcinoma Oncotarget. 6: 6191-6202.  0.96
2014 Bai Y, Kim JY, Watters JM, Fang B, Kinose F, Song L, Koomen JM, Teer JK, Fisher K, Chen YA, Rix U, Haura EB. Adaptive responses to dasatinib-treated lung squamous cell cancer cells harboring DDR2 mutations. Cancer Research. 74: 7217-28. PMID 25348954 DOI: 10.1158/0008-5472.CAN-14-0505  0.96
2014 Fedorenko IV, Fang B, Koomen JM, Gibney GT, Smalley KS. Amuvatinib has cytotoxic effects against NRAS-mutant melanoma but not BRAF-mutant melanoma. Melanoma Research. 24: 448-53. PMID 24950457 DOI: 10.1097/CMR.0000000000000103  0.96
2014 Koomen JM. Immunoglobulins: expanding the role for mass spectrometry in protein biomarker quantification. Clinical Chemistry. 60: 1034-5. PMID 24938750 DOI: 10.1373/clinchem.2014.226035  0.96
2014 Yoshida T, Zhang G, Smith MA, Lopez AS, Bai Y, Li J, Fang B, Koomen J, Rawal B, Fisher KJ, Chen AY, Kitano M, Morita Y, Yamaguchi H, Shibata K, et al. Tyrosine phosphoproteomics identifies both codrivers and cotargeting strategies for T790M-related EGFR-TKI resistance in non-small cell lung cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 20: 4059-74. PMID 24919575 DOI: 10.1158/1078-0432.CCR-13-1559  0.96
2014 Zhang M, Xiang S, Joo HY, Wang L, Williams KA, Liu W, Hu C, Tong D, Haakenson J, Wang C, Zhang S, Pavlovicz RE, Jones A, Schmidt KH, Tang J, ... ... Koomen J, et al. HDAC6 deacetylates and ubiquitinates MSH2 to maintain proper levels of MutSα. Molecular Cell. 55: 31-46. PMID 24882211 DOI: 10.1016/j.molcel.2014.04.028  0.96
2014 Rebecca VW, Wood E, Fedorenko IV, Paraiso KH, Haarberg HE, Chen Y, Xiang Y, Sarnaik A, Gibney GT, Sondak VK, Koomen JM, Smalley KS. Evaluating melanoma drug response and therapeutic escape with quantitative proteomics. Molecular & Cellular Proteomics : McP. 13: 1844-54. PMID 24760959 DOI: 10.1074/mcp.M113.037424  0.96
2014 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. Quantification of peptides from immunoglobulin constant and variable regions by LC-MRM MS for assessment of multiple myeloma patients. Proteomics. Clinical Applications. 8: 783-95. PMID 24723328 DOI: 10.1002/prca.201300077  0.96
2014 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, et al. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Molecular & Cellular Proteomics : McP. 13: 907-17. PMID 24443746 DOI: 10.1074/mcp.M113.036095  0.96
2014 Remsing Rix LL, Kuenzi BM, Luo Y, Remily-Wood E, Kinose F, Wright G, Li J, Koomen JM, Haura EB, Lawrence HR, Rix U. GSK3 alpha and beta are new functionally relevant targets of tivantinib in lung cancer cells Acs Chemical Biology. 9: 353-358. PMID 24215125 DOI: 10.1021/cb400660a  0.96
2014 Zheng XQ, Guo JP, Yang H, Kanai M, He LL, Li YY, Koomen JM, Minton S, Gao M, Ren XB, Coppola D, Cheng JQ. Aurora-A is a determinant of tamoxifen sensitivity through phosphorylation of ERα in breast cancer. Oncogene. 33: 4985-96. PMID 24166501 DOI: 10.1038/onc.2013.444  0.96
2013 Li J, Bennett K, Stukalov A, Fang B, Zhang G, Yoshida T, Okamoto I, Kim JY, Song L, Bai Y, Qian X, Rawal B, Schell M, Grebien F, Winter G, ... ... Koomen J, et al. Perturbation of the mutated EGFR interactome identifies vulnerabilities and resistance mechanisms. Molecular Systems Biology. 9: 705. PMID 24189400 DOI: 10.1038/msb.2013.61  0.96
2013 Pierce Campbell CM, Guan W, Sprung R, Koomen JM, O'Keefe MT, Ingles DJ, Abrahamsen M, Giuliano AR. Quantification of secretory leukocyte protease inhibitor (SLPI) in oral gargle specimens collected using mouthwash. Journal of Immunological Methods. 400: 117-21. PMID 24140751 DOI: 10.1016/j.jim.2013.10.005  0.96
2013 Zheng H, Yang L, Peng L, Izumi V, Koomen J, Seto E, Chen J. hMOF acetylation of DBC1/CCAR2 prevents binding and inhibition of SirT1. Molecular and Cellular Biology. 33: 4960-70. PMID 24126058 DOI: 10.1128/MCB.00874-13  0.96
2013 He G, Kuang J, Koomen J, Kobayashi R, Khokhar AR, Siddik ZH. Recruitment of trimeric proliferating cell nuclear antigen by G1-phase cyclin-dependent kinases following DNA damage with platinum-based antitumour agents. British Journal of Cancer. 109: 2378-88. PMID 24104967 DOI: 10.1038/bjc.2013.613  0.96
2013 Williams KA, Zhang M, Xiang S, Hu C, Wu JY, Zhang S, Ryan M, Cox AD, Der CJ, Fang B, Koomen J, Haura E, Bepler G, Nicosia SV, Matthias P, et al. Extracellular signal-regulated kinase (ERK) phosphorylates histone deacetylase 6 (HDAC6) at serine 1035 to stimulate cell migration. The Journal of Biological Chemistry. 288: 33156-70. PMID 24089523 DOI: 10.1074/jbc.M113.472506  0.96
2013 Gebhard AW, Jain P, Nair RR, Emmons MF, Argilagos RF, Koomen JM, McLaughlin ML, Hazlehurst LA. MTI-101 (cyclized HYD1) binds a CD44 containing complex and induces necrotic cell death in multiple myeloma. Molecular Cancer Therapeutics. 12: 2446-58. PMID 24048737 DOI: 10.1158/1535-7163.MCT-13-0310  0.96
2013 Yang L, Song T, Chen L, Kabra N, Zheng H, Koomen J, Seto E, Chen J. Regulation of SirT1-nucleomethylin binding by rRNA coordinates ribosome biogenesis with nutrient availability. Molecular and Cellular Biology. 33: 3835-48. PMID 23897426 DOI: 10.1128/MCB.00476-13  0.96
2013 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. Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells. Proceedings of the National Academy of Sciences of the United States of America. 110: 12414-9. PMID 23836654 DOI: 10.1073/pnas.1220674110  0.96
2013 Song T, Yang L, Kabra N, Chen L, Koomen J, Haura EB, Chen J. The NAD+ synthesis enzyme nicotinamide mononucleotide adenylyltransferase (NMNAT1) regulates ribosomal RNA transcription. The Journal of Biological Chemistry. 288: 20908-17. PMID 23737528 DOI: 10.1074/jbc.M113.470302  0.96
2013 Martyniuk CJ, Feswick A, Fang B, Koomen JM, Barber DS, Gavin T, Lopachin RM. Protein targets of acrylamide adduct formation in cultured rat dopaminergic cells. Toxicology Letters. 219: 279-87. PMID 23566896 DOI: 10.1016/j.toxlet.2013.03.031  0.96
2013 Ozcan S, Kazi A, Marsilio F, Fang B, Guida WC, Koomen J, Lawrence HR, Sebti SM. Oxadiazole-isopropylamides as potent and noncovalent proteasome inhibitors Journal of Medicinal Chemistry. 56: 3783-3805. PMID 23547706 DOI: 10.1021/jm400221d  0.96
2013 Haarberg HE, Paraiso KH, Wood E, Rebecca VW, Sondak VK, Koomen JM, Smalley KS. Inhibition of Wee1, AKT, and CDK4 underlies the efficacy of the HSP90 inhibitor XL888 in an in vivo model of NRAS-mutant melanoma. Molecular Cancer Therapeutics. 12: 901-12. PMID 23538902 DOI: 10.1158/1535-7163.MCT-12-1003  0.96
2012 Woods NT, Mesquita RD, Sweet M, Carvalho MA, Li X, Liu Y, Nguyen H, Thomas CE, Iversen ES, Marsillac S, Karchin R, Koomen J, Monteiro AN. Charting the landscape of tandem BRCT domain-mediated protein interactions. Science Signaling. 5: rs6. PMID 22990118 DOI: 10.1126/scisignal.2002255  0.96
2012 Boucher K, Parquet N, Widen R, Shain K, Baz R, Alsina M, Koomen J, Anasetti C, Dalton W, Perez LE. Stemness of B-cell progenitors in multiple myeloma bone marrow. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 18: 6155-68. PMID 22988056 DOI: 10.1158/1078-0432.CCR-12-0531  0.96
2012 Mahajan K, Fang B, Koomen JM, Mahajan NP. H2B Tyr37 phosphorylation suppresses expression of replication-dependent core histone genes. Nature Structural & Molecular Biology. 19: 930-7. PMID 22885324 DOI: 10.1038/nsmb.2356  0.96
2012 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. GSK3β inhibition blocks melanoma cell/host interactions by downregulating N-cadherin expression and decreasing FAK phosphorylation. The Journal of Investigative Dermatology. 132: 2818-27. PMID 22810307 DOI: 10.1038/jid.2012.237  0.96
2012 Peng L, Ling H, Yuan Z, Fang B, Bloom G, Fukasawa K, Koomen J, Chen J, Lane WS, Seto E. SIRT1 negatively regulates the activities, functions, and protein levels of hMOF and TIP60. Molecular and Cellular Biology. 32: 2823-36. PMID 22586264 DOI: 10.1128/MCB.00496-12  0.96
2012 Wilson DS, Fang B, Dalton WS, Meade CD, Koomen JM. An ET-CURE pilot project supporting undergraduate training in cancer research, emerging technology, and health disparities. Journal of Cancer Education : the Official Journal of the American Association For Cancer Education. 27: 418-27. PMID 22528637 DOI: 10.1007/s13187-012-0362-z  0.96
2012 Bai Y, Li J, Fang B, Edwards A, Zhang G, Bui M, Eschrich S, Altiok S, Koomen J, Haura EB. Phosphoproteomics identifies driver tyrosine kinases in sarcoma cell lines and tumors. Cancer Research. 72: 2501-11. PMID 22461510 DOI: 10.1158/0008-5472.CAN-11-3015  0.96
2012 Remily-Wood ER, Koomen JM. Evaluation of protein quantification using standard peptides containing single conservative amino acid replacements. Journal of Mass Spectrometry : Jms. 47: 188-94. PMID 22359328 DOI: 10.1002/jms.2053  0.96
2012 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. The HSP90 inhibitor XL888 overcomes BRAF inhibitor resistance mediated through diverse mechanisms. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 18: 2502-14. PMID 22351686 DOI: 10.1158/1078-0432.CCR-11-2612  0.96
2012 Xiang Y, Koomen JM. Evaluation of direct infusion-multiple reaction monitoring mass spectrometry for quantification of heat shock proteins. Analytical Chemistry. 84: 1981-6. PMID 22293045 DOI: 10.1021/ac203011j  0.96
2012 An Z, Chen Y, Koomen JM, Merkler DJ. A mass spectrometry-based method to screen for α-amidated peptides. Proteomics. 12: 173-82. PMID 22106059 DOI: 10.1002/pmic.201100327  0.96
2011 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. MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a. Nature Communications. 2: 533. PMID 22086334 DOI: 10.1038/ncomms1549  0.96
2011 Martyniuk CJ, Fang B, Koomen JM, Gavin T, Zhang L, Barber DS, Lopachin RM. Molecular mechanism of glyceraldehyde-3-phosphate dehydrogenase inactivation by α,β-unsaturated carbonyl derivatives. Chemical Research in Toxicology. 24: 2302-11. PMID 22084934 DOI: 10.1021/tx200437y  0.96
2011 Peng L, Yuan Z, Ling H, Fukasawa K, Robertson K, Olashaw N, Koomen J, Chen J, Lane WS, Seto E. SIRT1 deacetylates the DNA methyltransferase 1 (DNMT1) protein and alters its activities. Molecular and Cellular Biology. 31: 4720-34. PMID 21947282 DOI: 10.1128/MCB.06147-11  0.96
2011 Xiang Y, Remily-Wood ER, Oliveira V, Yarde D, He L, Cheng JQ, Mathews L, Boucher K, Cubitt C, Perez L, Gauthier TJ, Eschrich SA, Shain KH, Dalton WS, Hazlehurst L, ... Koomen JM, et al. Monitoring a nuclear factor-κB signature of drug resistance in multiple myeloma. Molecular & Cellular Proteomics : McP. 10: M110.005520. PMID 21846842 DOI: 10.1074/mcp.M110.005520  0.96
2011 Remily-Wood ER, Liu RZ, Xiang Y, Chen Y, Thomas CE, Rajyaguru N, Kaufman LM, Ochoa JE, Hazlehurst L, Pinilla-Ibarz J, Lancet J, Zhang G, Haura E, Shibata D, Yeatman T, ... ... Koomen JM, et al. A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. Proteomics. Clinical Applications. 5: 383-96. PMID 21656910 DOI: 10.1002/prca.201000115  0.96
2011 Koomen JM, Smalley KS. Using quantitative proteomic analysis to understand genotype specific intrinsic drug resistance in melanoma. Oncotarget. 2: 329-35. PMID 21505227  0.96
2011 Wong PG, Winter SL, Zaika E, Cao TV, Oguz U, Koomen JM, Hamlin JL, Alexandrow MG. Cdc45 limits replicon usage from a low density of preRCs in mammalian cells. Plos One. 6: e17533. PMID 21390258 DOI: 10.1371/journal.pone.0017533  0.96
2011 Paraiso KH, Xiang Y, Rebecca VW, Abel EV, Chen YA, Munko AC, Wood E, Fedorenko IV, Sondak VK, Anderson AR, Ribas A, Palma MD, Nathanson KL, Koomen JM, Messina JL, et al. PTEN loss confers BRAF inhibitor resistance to melanoma cells through the suppression of BIM expression. Cancer Research. 71: 2750-60. PMID 21317224 DOI: 10.1158/0008-5472.CAN-10-2954  0.96
2011 Zhang G, Fang B, Liu RZ, Lin H, Kinose F, Bai Y, Oguz U, Remily-Wood ER, Li J, Altiok S, Eschrich S, Koomen J, Haura EB. Mass spectrometry mapping of epidermal growth factor receptor phosphorylation related to oncogenic mutations and tyrosine kinase inhibitor sensitivity Journal of Proteome Research. 10: 305-319. PMID 21080693 DOI: 10.1021/pr1006203  0.96
2010 Ren Y, Chen Z, Chen L, Fang B, Win-Piazza H, Haura E, Koomen JM, Wu J. Critical role of Shp2 in tumor growth involving regulation of c-Myc. Genes & Cancer. 1: 994-1007. PMID 21442024 DOI: 10.1177/1947601910395582  0.96
2010 Machida K, Eschrich S, Li J, Bai Y, Koomen J, Mayer BJ, Haura EB. Characterizing tyrosine phosphorylation signaling in lung cancer using SH2 profiling Plos One. 5. PMID 20976048 DOI: 10.1371/journal.pone.0013470  0.96
2010 Chen Y, Gruidl M, Remily-Wood E, Liu RZ, Eschrich S, Lloyd M, Nasir A, Bui MM, Huang E, Shibata D, Yeatman T, Koomen JM. Quantification of beta-catenin signaling components in colon cancer cell lines, tissue sections, and microdissected tumor cells using reaction monitoring mass spectrometry. Journal of Proteome Research. 9: 4215-27. PMID 20590165 DOI: 10.1021/pr1005197  0.96
2010 Chen L, Li Z, Zwolinska AK, Smith MA, Cross B, Koomen J, Yuan ZM, Jenuwein T, Marine JC, Wright KL, Chen J. MDM2 recruitment of lysine methyltransferases regulates p53 transcriptional output. The Embo Journal. 29: 2538-52. PMID 20588255 DOI: 10.1038/emboj.2010.140  0.96
2010 Shin H, Sampat MP, Koomen JM, Markey MK. Wavelet-based adaptive denoising and baseline correction for MALDI TOF MS. Omics : a Journal of Integrative Biology. 14: 283-95. PMID 20455751 DOI: 10.1089/omi.2009.0119  0.96
2010 Fang B, Haura EB, Smalley KS, Eschrich SA, Koomen JM. Methods for investigation of targeted kinase inhibitor therapy using chemical proteomics and phosphorylation profiling. Biochemical Pharmacology. 80: 739-47. PMID 20361944 DOI: 10.1016/j.bcp.2010.03.027  0.96
2010 Mahajan K, Coppola D, Challa S, Fang B, Chen YA, Zhu W, Lopez AS, Koomen J, Engelman RW, Rivera C, Muraoka-Cook RS, Cheng JQ, Schönbrunn E, Sebti SM, Earp HS, et al. Ack1 mediated AKT/PKB tyrosine 176 phosphorylation regulates its activation. Plos One. 5: e9646. PMID 20333297 DOI: 10.1371/journal.pone.0009646  0.96
2010 Thomas CE, Sexton W, Benson K, Sutphen R, Koomen J. Urine collection and processing for protein biomarker discovery and quantification. Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. 19: 953-9. PMID 20332277 DOI: 10.1158/1055-9965.EPI-10-0069  0.96
2010 Li J, Rix U, Fang B, Bai Y, Edwards A, Colinge J, Bennett KL, Gao J, Song L, Eschrich S, Superti-Furga G, Koomen J, Haura EB. A chemical and phosphoproteomic characterization of dasatinib action in lung cancer Nature Chemical Biology. 6: 291-299. PMID 20190765 DOI: 10.1038/nchembio.332  0.96
2010 Kahali S, Sarcar B, Fang B, Williams ES, Koomen JM, Tofilon PJ, Chinnaiyan P. Activation of the unfolded protein response contributes toward the antitumor activity of vorinostat. Neoplasia (New York, N.Y.). 12: 80-6. PMID 20072656 DOI: 10.1593/neo.91422  0.96
2010 Guo JP, Shu SK, Esposito NN, Coppola D, Koomen JM, Cheng JQ. IKKepsilon phosphorylation of estrogen receptor alpha Ser-167 and contribution to tamoxifen resistance in breast cancer. The Journal of Biological Chemistry. 285: 3676-84. PMID 19940156 DOI: 10.1074/jbc.M109.078212  0.96
2009 Remily-Wood E, Dirscherl H, Koomen JM. Acid hydrolysis of proteins in matrix assisted laser desorption ionization matrices. Journal of the American Society For Mass Spectrometry. 20: 2106-15. PMID 19679491 DOI: 10.1016/j.jasms.2009.07.007  0.96
2008 Lu D, Liu RZ, Izumi V, Fenstermacher D, Haura EB, Koomen J, Eschrich SA. IPEP: An in silico tool to examine proteolytic peptides for mass spectrometry Bioinformatics. 24: 2801-2802. PMID 18842605 DOI: 10.1093/bioinformatics/btn511  0.96
2008 Koomen JM, Haura EB, Bepler G, Sutphen R, Remily-Wood ER, Benson K, Hussein M, Hazlehurst LA, Yeatman TJ, Hildreth LT, Sellers TA, Jacobsen PB, Fenstermacher DA, Dalton WS. Proteomic contributions to personalized cancer care. Molecular & Cellular Proteomics : McP. 7: 1780-94. PMID 18664563 DOI: 10.1074/mcp.R800002-MCP200  0.96
2007 Shin H, Mutlu M, Koomen JM, Markey MK. Parametric power spectral density analysis of noise from instrumentation in MALDI TOF mass spectrometry. Cancer Informatics. 3: 219-30. PMID 19455245  0.96
2007 Zhang X, Yuan Z, Zhang Y, Yong S, Salas-Burgos A, Koomen J, Olashaw N, Parsons JT, Yang XJ, Dent SR, Yao TP, Lane WS, Seto E. HDAC6 Modulates Cell Motility by Altering the Acetylation Level of Cortactin Molecular Cell. 27: 197-213. PMID 17643370 DOI: 10.1016/j.molcel.2007.05.033  0.96
2007 Ohshiro K, Rosenthal DI, Koomen JM, Streckfus CF, Chambers M, Kobayashi R, El-Naggar AK. Pre-analytic saliva processing affect proteomic results and biomarker screening of head and neck squamous carcinoma. International Journal of Oncology. 30: 743-9. PMID 17273777  0.96
2007 Coussot G, Hawke DH, Mularz A, Koomen JM, Kobayashi R. A method for the isolation of blocked N-terminal peptides. Analytical Biochemistry. 361: 302-4. PMID 17188638 DOI: 10.1016/j.ab.2006.11.024  0.96
2006 Shin H, Sampat MP, Bish SF, Koomen JM, Markey MK. Statistical characterization of chemical noise in MALDI TOF MS by wavelet analysis of multiple noise realizations. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1092. PMID 17238711  0.96
2006 He G, Kuang J, Huang Z, Koomen J, Kobayashi R, Khokhar AR, Siddik ZH. Upregulation of p27 and its inhibition of CDK2/cyclin e activity following DNA damage by a novel platinum agent are dependent on the expression of p21 British Journal of Cancer. 95: 1514-1524. PMID 17088910 DOI: 10.1038/sj.bjc.6603448  0.96
2006 Pan S, Wang R, Zhou X, He G, Koomen J, Kobayashi R, Sun L, Corvera J, Gallick GE, Kuang J. Involvement of the conserved adaptor protein Alix in actin cytoskeleton assembly Journal of Biological Chemistry. 281: 34640-34650. PMID 16966331 DOI: 10.1074/jbc.M602263200  0.96
2006 Koomen JM, Wilson CR, Guthrie P, Androlewicz MJ, Kobayashi R, Taegtmeyer H. Proteome analysis of isolated perfused organ effluent as a novel model for protein biomarker discovery. Journal of Proteome Research. 5: 177-82. PMID 16396509 DOI: 10.1021/pr050170g  0.96
2005 Coombes KR, Koomen JM, Baggerly KA, Morris JS, Kobayashi R. Understanding the characteristics of mass spectrometry data through the use of simulation. Cancer Informatics. 1: 41-52. PMID 19305631  0.96
2005 Chu F, Koomen JM, Kobayashi R, O'Brian CA. Identification of an inactivating cysteine switch in protein kinase Cepsilon, a rational target for the design of protein kinase Cepsilon-inhibitory cancer therapeutics. Cancer Research. 65: 10478-85. PMID 16288040 DOI: 10.1158/0008-5472.CAN-05-1989  0.96
2005 Yokoi K, Shih LCN, Kobayashi R, Koomen J, Hawke D, Li D, Hamilton SR, Abbruzzese JL, Coombes KR, Fidler IJ. Serum amyloid A as a tumor marker in sera of nude mice with orthotopic human pancreatic cancer and in plasma of patients with pancreatic cancer International Journal of Oncology. 27: 1361-1369. PMID 16211233  0.96
2005 Campos-Fernández CS, Schottel BL, Chifotides HT, Bera JK, Bacsa J, Koomen JM, Russell DH, Dunbar KR. Anion template effect on the self-assembly and interconversion of metallacyclophanes. Journal of the American Chemical Society. 127: 12909-23. PMID 16159285 DOI: 10.1021/ja052108q  0.96
2005 Koomen JM, Li D, Xiao LC, Liu TC, Coombes KR, Abbruzzese J, Kobayashi R. Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. Journal of Proteome Research. 4: 972-81. PMID 15952745 DOI: 10.1021/pr050046x  0.96
2005 Koomen JM, Zhao H, Li D, Nasser W, Hawke DH, Abbruzzese JL, Baggerly KA, Kobayashi R. Diagnostic protein discovery using liquid chromatography/mass spectrometry for proteolytic peptide targeting. Rapid Communications in Mass Spectrometry : Rcm. 19: 1624-36. PMID 15915451 DOI: 10.1002/rcm.1963  0.96
2005 Koomen J, Hawke D, Kobayashi R. Developing an understanding of proteomics: An introduction to biological mass spectrometry Cancer Investigation. 23: 47-59. PMID 15779868 DOI: 10.1081/CNV-200046344  0.96
2005 He G, Siddik ZH, Huang Z, Wang R, Koomen J, Kobayashi R, Khokhar AR, Kuang J. Induction of p21 by p53 following DNA damage inhibits both Cdk4 and Cdk2 activities Oncogene. 24: 2929-2943. PMID 15735718 DOI: 10.1038/sj.onc.1208474  0.96
2005 Koomen JM, Shih LN, Coombes KR, Li D, Xiao LC, Fidler IJ, Abbruzzese JL, Kobayashi R. Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 11: 1110-8. PMID 15709178  0.96
2005 Morris JS, Coombes KR, Koomen J, Baggerly KA, Kobayashi R. Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum. Bioinformatics (Oxford, England). 21: 1764-75. PMID 15673564 DOI: 10.1093/bioinformatics/bti254  0.96
2004 Koomen JM, Zhao H, Li D, Abbruzzese J, Baggerly K, Kobayashi R. Diagnostic protein discovery using proteolytic peptide targeting and identification. Rapid Communications in Mass Spectrometry : Rcm. 18: 2537-48. PMID 15468157 DOI: 10.1002/rcm.1657  0.96
2004 Chifotides HT, Koomen JM, Kang M, Tichy SE, Dunbar KR, Russell DH. Binding of DNA purine sites to dirhodium compounds probed by mass spectrometry. Inorganic Chemistry. 43: 6177-87. PMID 15446862 DOI: 10.1021/ic040040u  0.96
2004 Bresalier RS, Byrd JC, Tessler D, Lebel J, Koomen J, Hawke D, Half E, Liu KF, Mazurek N. A circulating ligand for galectin-3 is a haptoglobin-related glycoprotein elevated in individuals with colon cancer. Gastroenterology. 127: 741-8. PMID 15362030 DOI: 10.1053/j.gastro.2004.06.016  0.96
2004 Pusztai L, Gregory BW, Baggerly KA, Peng B, Koomen J, Kuerer HM, Esteva FJ, Symmans WF, Wagner P, Hortobagyi GN, Laronga C, Semmes OJ, Wright GL, Drake RR, Vlahou A. Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma. Cancer. 100: 1814-22. PMID 15112261 DOI: 10.1002/cncr.20203  0.96
2004 Woods AS, Ugarov M, Egan T, Koomen J, Gillig KJ, Fuhrer K, Gonin M, Schultz JA. Lipid/peptide/nucleotide separation with MALDI-ion mobility-TOF MS. Analytical Chemistry. 76: 2187-95. PMID 15080727 DOI: 10.1021/ac035376k  0.96
2004 Gaertner TR, Kolodziej SJ, Wang D, Kobayashi R, Koomen JM, Stoops JK, Waxham MN. Comparative analyses of the three-dimensional structures and enzymatic properties of alpha, beta, gamma and delta isoforms of Ca2+-calmodulin-dependent protein kinase II. The Journal of Biological Chemistry. 279: 12484-94. PMID 14722083 DOI: 10.1074/jbc.M313597200  0.96
2003 Koomen JM, Lucas JE, Haneline MR, Beckwith King JD, Gabbai F, Russell DH. Nanoelectrospray MS and MS-MS investigation of two polydendate Lewis acids, (C6F4Hg)3 and o-C6F4(HgCl)2, characterization and halide binding selectivity International Journal of Mass Spectrometry. 225: 225-231. DOI: 10.1016/S1387-3806(02)01114-4  0.96
2002 Koomen JM, Ruotolo BT, Gillig KJ, McLean JA, Russell DH, Kang M, Dunbar KR, Fuhrer K, Gonin M, Schultz JA. Oligonucleotide analysis with MALDI-ion-mobility-TOFMS. Analytical and Bioanalytical Chemistry. 373: 612-7. PMID 12185573 DOI: 10.1007/s00216-002-1363-2  0.96
2002 Sulikowski GA, Agnelli F, Spencer P, Koomen JM, Russell DH. Studies on the biosynthesis of phomoidride B (CP-263,114): evidence for a decarboxylative homodimerization pathway. Organic Letters. 4: 1447-50. PMID 11975600 DOI: 10.1021/ol025594k  0.96
2002 Koomen JM, Russell WK, Tichy SE, Russell DH. Accurate mass measurement of DNA oligonucleotide ions using high-resolution time-of-flight mass spectrometry. Journal of Mass Spectrometry : Jms. 37: 357-71. PMID 11948842 DOI: 10.1002/jms.312  0.96
2002 Woods AS, Koomen JM, Ruotolo BT, Gillig KJ, Russel DH, Fuhrer K, Gonin M, Egan TF, Schultz JA. A study of peptide-peptide interactions using MALDI ion mobility o-TOF and ESI mass spectrometry. Journal of the American Society For Mass Spectrometry. 13: 166-9. PMID 11838019 DOI: 10.1016/S1044-0305(01)00348-8  0.96
2002 Koomen JM, Kang M, Chifotides H, Dunbar KR, Russell DH. A comparison of MALDI and ESI for analysis of dirhodium-DNA adducts Proceedings 50th Asms Conference On Mass Spectrometry and Allied Topics. 429-430.  0.96
2001 Campos-Fernández CS, Clérac R, Koomen JM, Russell DH, Dunbar KR. Fine-tuning the ring-size of metallacyclophanes: a rational approach to molecular pentagons. Journal of the American Chemical Society. 123: 773-4. PMID 11456607 DOI: 10.1021/ja002960r  0.96
2000 Koomen JM, Russell DH. Ultraviolet/matrix-assisted laser desorption/ionization mass spectrometric characterization of 2,5-dihydroxybenzoic acid-induced reductive hydrogenation of oligonucleotides on cytosine residues. Journal of Mass Spectrometry : Jms. 35: 1025-34. PMID 10973002 DOI: 10.1002/1096-9888(200008)35:8<1025::AID-JMS30>3.0.CO;2-9  0.96
2000 Koomen JM, Russell WK, Hettick JM, Russell DH. Improvement of resolution, mass accuracy, and reproducibility in reflected mode DE-MALDI-TOF analysis of DNA using fast evaporation--overlayer sample preparations. Analytical Chemistry. 72: 3860-6. PMID 10959974 DOI: 10.1021/ac0001941  0.96
2000 Botos I, Meyer E, Nguyen M, Swanson SM, Koomen JM, Russell DH, Meyer EF. The structure of an insect chymotrypsin. Journal of Molecular Biology. 298: 895-901. PMID 10801356 DOI: 10.1006/jmbi.2000.3699  0.96
2000 Koomen JM, Stoeckli M, Caprioli RM. Mapping of surrogate markers of cellular components and structures using laser desorption/ionization mass spectrometry. Journal of Mass Spectrometry : Jms. 35: 258-64. PMID 10679989 DOI: 10.1002/(SICI)1096-9888(200002)35:2<258::AID-JMS937>3.0.CO;2-Q  0.96
1997 Koomen JM, Lehre KP. The glycine transporter, GLYT 1, is localized to all amacrine cells but not coupled cone bipolar cells in the rabbit retina Investigative Ophthalmology and Visual Science. 38: S47.  0.96
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