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John  Koomen

John Koomen, PhD

Program: Molecular Oncology

Research Program: Molecular Medicine Program

Contact

  • Overview

    Our research projects share the common goal of changing the standard of patient assessment and care using mass spectrometry.

    Associations

    • Molecular Oncology
    • Pathology
    • Melanoma & Skin Cancer Center of Excellence
    • Pentecost Family Myeloma Research Center
    • Lung Cancer Center of Excellence
    • Systems Medicine Working Group
    • Molecular Medicine Program
    • Molecular Oncology & Drug Discovery Program

    Education & Training

    Graduate:

    • Texas A&M University, PhD - Chemistry
    • University of Texas at Houston Graduate School of Biomedical Science, MS - Biochemistry
  • Research Interest

    Research in the Koomen Laboratory focuses on analytical chemistry development, elucidation of biological processes, and implementation of clinical assays using proteomics and quantitative mass spectrometry.  Much of this work is performed using multiple reaction monitoring (MRM); three examples are detailed below.  In colon cancer, broad scale proteomics employing relative quantification techniques and gene expression profiles have determined candidate biomarkers related to the Adenomatous Polyposis Coli protein.  Targeted analysis of this panel of proteins coupled with the interrogation of protein expression in relevant signaling pathways, including Wnt, TGF/SMAD, and Notch, in tumors and adjacent normal tissue can be used to select and evaluate candidate biomarkers for predicting patient outcomes.   In multiple myeloma, the same techniques and technologies are being applied in cell lines to develop preclinical models that will provide a molecular basis for rational chemotherapy.  In these experiments, direct drug targets and apoptosis-related proteins are being monitored in parallel with specific signaling pathways, including NFkB.  These data will elucidate mechanisms of drug resistance and provide another method to evaluate combination therapy.   Finally, direct patient assessment is being performed in multiple myeloma using MRM.  Current clinical assays use gel or capillary electrophoresis to measure the antibody secreted by the myeloma, which is used to stage the patients and estimate tumor burden.  Quantitative mass spectrometry should be significantly more sensitive at detecting and quantifying these antibodies.  Improvements in the analytical technique would lead to earlier detection of disease relapse, more rapid intervention with second line therapies, and potentially improved patient outcomes. These projects share the common goal of changing the standard of patient assessment and care using mass spectrometry.    

  • Publications

    • Jimenez J, Dubey P, Carter B, Koomen J, Markowitz J. A metabolic perspective on nitric oxide function in melanoma. BBA. Reviews on cancer. 2024 Jan.1879(1):189038. Pubmedid: 38061664.
    • Zheng XQ, Guo JP, Yang H, Kanai M, He LL, Li YY, Koomen JM, Minton S, Gao M, Ren XB, Coppola D, Cheng JQ. Retraction Note: Aurora-A is a determinant of tamoxifen sensitivity through phosphorylation of ERα in breast cancer. Oncogene. 2024 Feb. Pubmedid: 38396296.
    • Liao Y, Remsing Rix LL, Li X, Fang B, Izumi V, Welsh EA, Monastyrskyi A, Haura EB, Koomen JM, Doebele RC, Rix U. Differential network analysis of ROS1 inhibitors reveals lorlatinib polypharmacology through co-targeting PYK2. Cell Chem Biol. 2024 Feb.31(2):284-297.e10. Pubmedid: 37848034. Pmcid: PMC10922442.
    • Peak T, Tian Y, Patel A, Shaw T, Obermayer A, Laborde J, Kim Y, Johnson J, Stewart P, Fang B, Teer JK, Koomen J, Berglund A, Marchion D, Francis N, Echevarria PR, Dhillon J, Clark N, Chang A, Sexton W, Zemp L, Chahoud J, Wang L, Manley B. Pathogenic Roles for RNASET2 in Clear Cell Renal Cell Carcinoma. Lab Invest. 2024 Feb.102041. Pubmedid: 38431116.
    • Liu Q, Adhikari E, Lester DK, Fang B, Johnson JO, Tian Y, Mockabee-Macias AT, Izumi V, Guzman KM, White MG, Koomen JM, Wargo JA, Messina JL, Qi J, Lau EK. Androgen drives melanoma invasiveness and metastatic spread by inducing tumorigenic fucosylation. Nat Commun. 2024 Feb.15(1):1148. Pubmedid: 38326303. Pmcid: PMC10850104.
    • Elmarsafawi AG, Hesterberg RS, Fernandez MR, Yang C, Darville LN, Liu M, Koomen JM, Phanstiel Iv O, Atkins R, Mullinax JE, Pilon-Thomas SA, Locke FL, Epling-Burnette PK, Cleveland JL. Modulating the polyamine/hypusine axis controls generation of CD8+ tissue-resident memory T cells. JCI Insight. 2023 Sep.8(18). Pubmedid: 37581943. Pmcid: PMC10561731.
    • Nguyen T, Sridaran D, Chouhan S, Weimholt C, Wilson A, Luo J, Li T, Koomen J, Fang B, Putluri N, Sreekumar A, Feng FY, Mahajan K, Mahajan NP. Author Correction: Histone H2A Lys130 acetylation epigenetically regulates androgen production in prostate cancer. Nat Commun. 2023 Sep.14(1):6022. Pubmedid: 37758702. Pmcid: PMC10533897.
    • Yaghjyan L, Mai V, Darville LNF, Cline J, Wang X, Ukhanova M, Tagliamonte MS, Martinez YC, Rich SN, Koomen JM, Egan KM. Associations of gut microbiome with endogenous estrogen levels in healthy postmenopausal women. Cancer Causes Control. 2023 Oct.34(10):873-881. Pubmedid: 37286847.
    • Emmons MF, Bennett RL, Riva A, Gupta K, Carvalho LADC, Zhang C, Macaulay R, Dupéré-Richér D, Fang B, Seto E, Koomen JM, Li J, Chen YA, Forsyth PA, Licht JD, Smalley KSM. HDAC8-mediated inhibition of EP300 drives a transcriptional state that increases melanoma brain metastasis. Nat Commun. 2023 Nov.14(1):7759. Pubmedid: 38030596. Pmcid: PMC10686983.
    • Ross KE, Zhang G, Akcora C, Lin Y, Fang B, Koomen J, Haura EB, Grimes M. Network models of protein phosphorylation, acetylation, and ubiquitination connect metabolic and cell signaling pathways in lung cancer. PLoS Comput Biol. 2023 Mar.19(3):e1010690. Pubmedid: 36996232. Pmcid: PMC10089347.
    • Hu Q, Liao Y, Cao J, Fang B, Yun S, Kinose F, Haura E, Lawrence H, Doebele R, Koomen J, Rix U. Differential Chemoproteomics Reveals MARK2/3 as Cell Migration-Relevant Targets of the ALK Inhibitor Brigatinib. Chembiochem. 2023 Jun.24(11):e202200766. Pubmedid: 36922348. Pmcid: PMC10413441.
    • Putty Reddy S, Alontaga AY, Welsh EA, Haura EB, Boyle TA, Eschrich SA, Koomen JM. Deciphering Phenotypes from Protein Biomarkers for Translational Research with PIPER. J Proteome Res. 2023 Jun.22(6):2055-2066. Pubmedid: 37171072.
    • Nguyen T, Sridaran D, Chouhan S, Weimholt C, Wilson A, Luo J, Li T, Koomen J, Fang B, Putluri N, Sreekumar A, Feng FY, Mahajan K, Mahajan NP. Histone H2A Lys130 acetylation epigenetically regulates androgen production in prostate cancer. Nat Commun. 2023 Jun.14(1):3357. Pubmedid: 37296155. Pmcid: PMC10256812.
    • Mooradian MJ, Cleary JM, Giobbie-Hurder A, Darville LNF, Parikh A, Buchbinder EI, Cohen JV, Lawrence DP, Shapiro GI, Keer H, Chen HX, Ivy SP, Smalley KSM, Koomen JM, Sullivan RJ. Dose-escalation trial of combination dabrafenib, trametinib, and AT13387 in patients with BRAF-mutant solid tumors. Cancer. 2023 Jun.129(12):1904-1918. Pubmedid: 37042037.
    • Soupir AC, Tian Y, Stewart PA, Nunez-Lopez YO, Manley BJ, Pellini B, Bloomer AM, Zhang J, Mo Q, Marchion DC, Liu M, Koomen JM, Siegel EM, Wang L. Detectable Lipidomes and Metabolomes by Different Plasma Exosome Isolation Methods in Healthy Controls and Patients with Advanced Prostate and Lung Cancer. Int J Mol Sci. 2023 Jan.24(3). Pubmedid: 36768152. Pmcid: PMC9916336.
    • Lester DK, Burton C, Gardner A, Innamarato P, Kodumudi K, Liu Q, Adhikari E, Ming Q, Williamson DB, Frederick DT, Sharova T, White MG, Markowitz J, Cao B, Nguyen J, Johnson J, Beatty M, Mockabee-Macias A, Mercurio M, Watson G, Chen PL, McCarthy S, MoranSegura C, Messina J, Thomas KL, Darville L, Izumi V, Koomen JM, Pilon-Thomas SA, Ruffell B, Luca VC, Haltiwanger RS, Wang X, Wargo JA, Boland GM, Lau EK. Fucosylation of HLA-DRB1 regulates CD4+ T cell-mediated anti-melanoma immunity and enhances immunotherapy efficacy. Nat Cancer. 2023 Feb.4(2):222-239. Pubmedid: 36690875. Pmcid: PMC9970875.
    • Liao Y, Chin Chan S, Welsh EA, Fang B, Sun L, Schönbrunn E, Koomen JM, Duckett DR, Haura EB, Monastyrskyi A, Rix U. Chemical Proteomics with Novel Fully Functionalized Fragments and Stringent Target Prioritization Identifies the Glutathione-Dependent Isomerase GSTZ1 as a Lung Cancer Target. Acs Chem Biol. 2023 Feb.18(2):251-264. Pubmedid: 36630201.
    • Adhikari E, Liu Q, Johnson J, Stewart P, Marusyk V, Fang B, Izumi V, Bowers K, Guzman KM, Koomen JM, Marusyk A, Lau EK. Brain metastasis-associated fibroblasts secrete fucosylated PVR/CD155 that induces breast cancer invasion. Cell Rep. 2023 Dec.42(12):113463. Pubmedid: 37995180.
    • Burger KL, Fernandez MR, Meads MB, Sudalagunta PR, Oliveira PS, Renatino Canevarolo R, Alugubelli RR, Tungsevik A, De Avila G, Silva M, Graeter AI, Dai H, Vincelette ND, Prabhu A, Magaletti D, Yang C, Li W, Kulkarni A, Hampton OA, Koomen JM, Roush WR, Monastyrskyi A, Berglund AE, Silva AS, Cleveland JL, Shain KH. CK1δ and CK1ε Signaling Sustains Mitochondrial Metabolism and Cell Survival in Multiple Myeloma. Cancer Res. 2023 Dec.83(23):3901-3919. Pubmedid: 37702657. Pmcid: PMC10690099.
    • Khaled ML, Ren Y, Kundalia R, Alhaddad H, Chen Z, Wallace GC, Evernden B, Ospina OE, Hall M, Liu M, Darville LNF, Izumi V, Chen YA, Pilon-Thomas S, Stewart PA, Koomen JM, Corallo SA, Jain MD, Robinson TJ, Locke FL, Forsyth PA, Smalley I. Branched-chain keto acids promote an immune-suppressive and neurodegenerative microenvironment in leptomeningeal disease. bioRxiv. 2023 Dec. Pubmedid: 38187773. Pmcid: PMC10769272.
    • Madanayake TW, Welsh EA, Darville LNF, Koomen JM, Chalfant CE, Haura EB, Robinson TJ. Inhibition of Epidermal Growth Factor Receptor Signaling by Antisense Oligonucleotides as a Novel Approach to Epidermal Growth Factor Receptor Inhibition. Nucleic Acid Ther. 2022 Oct.32(5):391-400. Pubmedid: 35861718. Pmcid: PMC9595651.
    • Hesterberg RS, Liu M, Elmarsafawi AG, Koomen JM, Welsh EA, Hesterberg SG, Ranatunga S, Yang C, Li W, Lawrence HR, Rodriguez PC, Berglund AE, Cleveland JL. TCR-Independent Metabolic Reprogramming Precedes Lymphoma-Driven Changes in T-cell Fate. Cancer Immunol Res. 2022 Oct.10(10):1263-1279. Pubmedid: 35969234. Pmcid: PMC9662872.
    • Chang A, Chakiryan NH, Du D, Stewart PA, Zhang Y, Tian Y, Soupir AC, Bowers K, Fang B, Morganti A, Teer JK, Kim Y, Spiess PE, Chahoud J, Noble JD, Putney RM, Berglund AE, Robinson TJ, Koomen JM, Wang L, Manley BJ. Proteogenomic, Epigenetic, and Clinical Implications of Recurrent Aberrant Splice Variants in Clear Cell Renal Cell Carcinoma. Eur Urol. 2022 Oct.82(4):354-362. Pubmedid: 35718636.
    • Deng O, Dash S, Nepomuceno TC, Fang B, Yun SY, Welsh EA, Lawrence HR, Marchion D, Koomen JM, Monteiro AN, Rix U. Integrated proteomics identifies PARP inhibitor-induced prosurvival signaling changes as potential vulnerabilities in ovarian cancer. J Biol Chem. 2022 Nov.298(11):102550. Pubmedid: 36183837. Pmcid: PMC9636579.
    • Li J, Smalley I, Chen Z, Wu JY, Phadke MS, Teer JK, Nguyen T, Karreth FA, Koomen JM, Sarnaik AA, Zager JS, Khushalani NI, Tarhini AA, Sondak VK, Rodriguez PC, Messina JL, Chen YA, Smalley KSM. Single-cell Characterization of the Cellular Landscape of Acral Melanoma Identifies Novel Targets for Immunotherapy. Clin Cancer Res. 2022 May.28(10):2131-2146. Pubmedid: 35247927. Pmcid: PMC9106889.
    • Palve V, Knezevic CE, Bejan DS, Luo Y, Li X, Novakova S, Welsh EA, Fang B, Kinose F, Haura EB, Monteiro AN, Koomen JM, Cohen MS, Lawrence HR, Rix U. The non-canonical target PARP16 contributes to polypharmacology of the PARP inhibitor talazoparib and its synergy with WEE1 inhibitors. Cell Chem Biol. 2022 Feb.29(2):202-214.e7. Pubmedid: 34329582. Pmcid: PMC8782927.
    • Yaghjyan L, Darville LNF, Cline J, Martinez YC, Rich S, Austin-Datta RJ, Koomen JM, Tworoger SS, Egan KM. Associations of established breast cancer risk factors with urinary estrogens in postmenopausal women. Cancer Causes Control. 2022 Feb.33(2):279-291. Pubmedid: 34988766.
    • Sarcar B, Fang B, Izumi V, Nunez-Lopez Y, Tassielli A, Pratley R, Jeong D, Permuth JB, Koomen JM, Fleming JB, Stewart PA. A comparative Proteomics Analysis Identified Differentially Expressed Proteins in Pancreatic Cancer-Associated Stellate Cell Small Extracellular Vesicles. Mol Cell Proteomics. 2022 Dec.21(12):100438. Pubmedid: 36332889. Pmcid: PMC9792568.
    • Remsing Rix LL, Sumi NJ, Hu Q, Desai B, Bryant AT, Li X, Welsh EA, Fang B, Kinose F, Kuenzi BM, Chen YA, Antonia SJ, Lovly CM, Koomen JM, Haura EB, Marusyk A, Rix U. IGF-binding proteins secreted by cancer-associated fibroblasts induce context-dependent drug sensitization of lung cancer cells. Sci Signal. 2022 Aug.15(747):eabj5879. Pubmedid: 35973030. Pmcid: PMC9528501.
    • Fernandez MR, Schaub FX, Yang C, Li W, Yun S, Schaub SK, Dorsey FC, Liu M, Steeves MA, Ballabio A, Tzankov A, Chen Z, Koomen JM, Berglund AE, Cleveland JL. Disrupting the MYC-TFEB Circuit Impairs Amino Acid Homeostasis and Provokes Metabolic Anergy. Cancer Res. 2022 Apr.82(7):1234-1250. Pubmedid: 35149590. Pmcid: PMC9004540.
    • Mahajan S, Majumder A, Stewart PA, Chen YA, Adhikari E, Fang B, Yang Y, Lawrence H, Kinose F, Koomen JM, Haura EB. Deubiquitinase Vulnerabilities Identified through Activity-Based Protein Profiling in Non-Small Cell Lung Cancer. Acs Chem Biol. 2022 Apr.17(4):776-784. Pubmedid: 35311290.
    • Majumder A, Hosseinian S, Stroud M, Adhikari E, Saller JJ, Smith MA, Zhang G, Agarwal S, Creixell M, Meyer BS, Kinose F, Bowers K, Fang B, Stewart PA, Welsh EA, Boyle TA, Meyer AS, Koomen JM, Haura EB. Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration. Mol Cancer Res. 2022 Apr.20(4):542-555. Pubmedid: 35022314. Pmcid: PMC8983558.
    • Ampomah PB, Cai B, Sukka SR, Gerlach BD, Yurdagul A, Wang X, Kuriakose G, Darville LNF, Sun Y, Sidoli S, Koomen JM, Tall AR, Tabas I. Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution. Nat Metab. 2022 Apr.4(4):444-457. Pubmedid: 35361955. Pmcid: PMC9050866.
    • El-Kenawi A, Dominguez-Viqueira W, Liu M, Awasthi S, Abraham-Miranda J, Keske A, Steiner KK, Noel L, Serna AN, Dhillon J, Gillies RJ, Yu X, Koomen JM, Yamoah K, Gatenby RA, Ruffell B. Macrophage-Derived Cholesterol Contributes to Therapeutic Resistance in Prostate Cancer. Cancer Res. 2021 Nov.81(21):5477-5490. Pubmedid: 34301759. Pmcid: PMC8563406.
    • Solanki HS, Welsh EA, Fang B, Izumi V, Darville LNF, Stone B, Franzese R, Chavan S, Kinose F, Imbody D, Koomen JM, Rix U, Haura EB. Cell Type-specific Adaptive Signaling Responses to KRASG12C Inhibition. Clin Cancer Res. 2021 May.27(9):2533-2548. Pubmedid: 33619172.
    • Watson G, Lester D, Ren H, Forsyth CM, Medina E, Gonzalez Perez D, Darville L, Yao J, Luca V, Koomen J, Cen L, Lau E. Fucosylated Proteome Profiling Identifies a Fucosylated, Non-Ribosomal, Stress-Responsive Species of Ribosomal Protein S3. Cells. 2021 May.10(6). Pubmedid: 34070332. Pmcid: PMC8228307.
    • Koomen DC, Meads MB, Magaletti DM, Guingab-Cagmat JD, Oliveira PS, Fang B, Liu M, Welsh EA, Meke LE, Jiang Z, Hampton OA, Tungesvik A, De Avila G, Alugubelli RR, Nishihori T, Silva AS, Eschrich SA, Garrett TJ, Koomen JM, Shain KH. Metabolic Changes Are Associated with Melphalan Resistance in Multiple Myeloma. J Proteome Res. 2021 Jun.20(6):3134-3149. Pubmedid: 34014671.
    • Smalley KSM, Teer JK, Chen YA, Wu JY, Yao J, Koomen JM, Chen WS, Rodriguez-Waitkus P, Karreth FA, Messina JL. A Mutational Survey of Acral Nevi. JAMA Dermatol. 2021 Jul.157(7):831-835. Pubmedid: 33978681. Pmcid: PMC8117064.
    • Kazi A, Chen L, Xiang S, Vangipurapu R, Yang H, Beato F, Fang B, Williams TM, Husain K, Underwood PW, Fleming JB, Malafa MP, Welsh EA, Koomen JM, Trevino JG, Sebti SM. Global Phosphoproteomics Reveal CDK Suppression as a Vulnerability to KRas Addiction in Pancreatic Cancer. Clin Cancer Res. 2021 Jul.27(14):4012-4024. Pubmedid: 33879459. Pmcid: PMC8493485.
    • Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Cell Rep Methods. 2021 Jul.1(3). Pubmedid: 34671754. Pmcid: PMC8525888.
    • Mostofa A, Distler A, Meads MB, Sahakian E, Powers JJ, Achille A, Noyes D, Wright G, Fang B, Izumi V, Koomen J, Rampakrishnan R, Nguyen TP, De Avila G, Silva AS, Sudalagunta P, Canevarolo RR, Siqueira Silva MDC, Alugubelli RR, Dai HA, Kulkarni A, Dalton WS, Hampton OA, Welsh EA, Teer JK, Tungesvik A, Wright KL, Pinilla-Ibarz J, Sotomayor EM, Shain KH, Brayer J. Plasma cell dependence on histone/protein deacetylase 11 reveals a therapeutic target in multiple myeloma. JCI Insight. 2021 Dec.6(24). Pubmedid: 34793338. Pmcid: PMC8783683.
    • Creelan BC, Wang C, Teer JK, Toloza EM, Yao J, Kim S, Landin AM, Mullinax JE, Saller JJ, Saltos AN, Noyes DR, Montoya LB, Curry W, Pilon-Thomas SA, Chiappori AA, Tanvetyanon T, Kaye FJ, Thompson ZJ, Yoder SJ, Fang B, Koomen JM, Sarnaik AA, Chen DT, Conejo-Garcia JR, Haura EB, Antonia SJ. Tumor-infiltrating lymphocyte treatment for anti-PD-1-resistant metastatic lung cancer: a phase 1 trial. Nat Med. 2021 Aug.27(8):1410-1418. Pubmedid: 34385708. Pmcid: PMC8509078.
    • Hajiran A, Chakiryan N, Aydin AM, Zemp L, Nguyen J, Laborde JM, Chahoud J, Spiess PE, Zaman S, Falasiri S, Fournier M, Teer JK, Dhillon J, McCarthy S, Moran-Segura C, Katende EN, Sexton WJ, Koomen JM, Mulé J, Kim Y, Manley B. Reconnaissance of tumor immune microenvironment spatial heterogeneity in metastatic renal cell carcinoma and correlation with immunotherapy response. Clin Exp Immunol. 2021 Apr.204(1):96-106. Pubmedid: 33346915. Pmcid: PMC7944355.
    • Zhang C, Smalley I, Emmons MF, Sharma R, Izumi V, Messina J, Koomen JM, Pasquale EB, Forsyth PA, Smalley KSM. Noncanonical EphA2 Signaling Is a Driver of Tumor-Endothelial Cell Interactions and Metastatic Dissemination in BRAF Inhibitor‒Resistant Melanoma. J Invest Dermatol. 2021 Apr.141(4):840-851.e4. Pubmedid: 32890629. Pmcid: PMC7921215.
    • Hamaidi I, Zhang L, Kim N, Wang MH, Iclozan C, Fang B, Liu M, Koomen JM, Berglund AE, Yoder SJ, Yao J, Engelman RW, Creelan BC, Conejo-Garcia JR, Antonia SJ, Mulé JJ, Kim S. Sirt2 Inhibition Enhances Metabolic Fitness and Effector Functions of Tumor-Reactive T Cells. Cell Metab. 2020 Sep.32(3):420-436.e12. Pubmedid: 32768387. Pmcid: PMC7484212.
    • Stewart PA, Welsh EA, Fang B, Izumi V, Mesa T, Zhang C, Yoder S, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Avedon M, Wloch M, Fournier M, Fellows KM, Francis JM, Saller JJ, Boyle TA, Chen YA, Haura EB, Teer JK, Eschrich SA, Koomen JM. Managing a Large-Scale Multiomics Project: A Team Science Case Study in Proteogenomics. Methods Mol Biol. 2020 Sep.2194:187-221. Pubmedid: 32926368. Pmcid: PMC7771375.
    • Taylor NJ, Gaynanova I, Eschrich SA, Welsh EA, Garrett TJ, Beecher C, Sharma R, Koomen JM, Smalley KSM, Messina JL, Kanetsky PA. Metabolomics of primary cutaneous melanoma and matched adjacent extratumoral microenvironment. PLoS One. 2020 Oct.15(10):e0240849. Pubmedid: 33108391. Pmcid: PMC7591037.
    • Darville LNF, Cline JK, Rozmeski C, Martinez YC, Rich S, Eschrich SA, Egan KM, Yaghjyan L, Koomen JM. LC-HRMS of derivatized urinary estrogens and estrogen metabolites in postmenopausal women. J Chromatogr B Analyt Technol Biomed Life Sci. 2020 Oct.1154:122288. Pubmedid: 32769047. Pmcid: PMC7882395.
    • Garg SK, Welsh EA, Fang B, Hernandez YI, Rose T, Gray J, Koomen JM, Berglund A, Mulé JJ, Markowitz J. Multi-Omics and Informatics Analysis of FFPE Tissues Derived from Melanoma Patients with Long/Short Responses to Anti-PD1 Therapy Reveals Pathways of Response. Cancers (Basel). 2020 Nov.12(12). Pubmedid: 33255891. Pmcid: PMC7768436.
    • Smalley I, Law V, Wyatt C, Evernden B, Fang B, Koomen JM, Welsh EA, Macaulay RJB, Forsyth PA, Smalley KSM. Proteomic Analysis of CSF from Patients with Leptomeningeal Melanoma Metastases Identifies Signatures Associated with Disease Progression and Therapeutic Resistance. Clin Cancer Res. 2020 May.26(9):2163-2175. Pubmedid: 31924735. Pmcid: PMC7196498.
    • Yurdagul A, Subramanian M, Wang X, Crown SB, Ilkayeva OR, Darville L, Kolluru GK, Rymond CC, Gerlach BD, Zheng Z, Kuriakose G, Kevil CG, Koomen JM, Cleveland JL, Muoio DM, Tabas I. Macrophage Metabolism of Apoptotic Cell-Derived Arginine Promotes Continual Efferocytosis and Resolution of Injury. Cell Metab. 2020 Mar.31(3):518-533.e10. Pubmedid: 32004476. Pmcid: PMC7173557.
    • Sadeghi M, Ordway B, Rafiei I, Borad P, Fang B, Koomen JL, Zhang C, Yoder S, Johnson J, Damaghi M. Integrative Analysis of Breast Cancer Cells Reveals an Epithelial-Mesenchymal Transition Role in Adaptation to Acidic Microenvironment. Front Oncol. 2020 Mar.10:304. Pubmedid: 32211331. Pmcid: PMC7076123.
    • 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. 2020 Jan.36(1):257-263. Pubmedid: 31199438. Pmcid: PMC6956786.
    • Yue L, Sharma V, Horvat NP, Akuffo AA, Beatty MS, Murdun C, Colin C, Billington J, Goodheart WE, Sahakian E, Zhang L, Powers JJ, Amin NE, Lambert-Showers QT, Darville LN, Pinilla-Ibarz J, Reuther G, Wright K, Conti C, Lee JY, Zheng X, Ng PY, Martin MW, Marshall CG, Koomen JM, Levine RL, Verma A, Grimes HL, Sotomayor EM, Shao Z, Epling-Burnette PK. HDAC11 deficiency disrupts oncogene-induced hematopoiesis in myeloproliferative neoplasms. Blood. 2020 Jan.135(3):191-207. Pubmedid: 31750881. Pmcid: PMC6966930.
    • Golubeva VA, Nepomuceno TC, Gregoriis G, Mesquita RD, Li X, Dash S, Garcez PP, Suarez-Kurtz G, Izumi V, Koomen J, Carvalho MA, Monteiro ANA. Network of Interactions between ZIKA Virus Non-Structural Proteins and Human Host Proteins. Cells. 2020 Jan.9(1). Pubmedid: 31936331. Pmcid: PMC7016862.
    • Fang B, Izumi V, Rix LLR, Welsh E, Pike I, Reuther GW, Haura EB, Rix U, Koomen JM. Lowering Sample Requirements to Study Tyrosine Kinase Signaling Using Phosphoproteomics with the TMT Calibrator Approach. Proteomics. 2020 Dec.20(24):e2000116. Pubmedid: 32865326. Pmcid: PMC7771371.
    • Hesterberg RS, Beatty MS, Han Y, Fernandez MR, Akuffo AA, Goodheart WE, Yang C, Chang S, Colin C, Alontaga AY, McDaniel J, Mailloux AW, Billington JMR, Yue L, Russell S, Gillies RJ, Yun SY, Ayaz M, Lawrence NJ, Lawrence H, Yu XZ, Fu J, Darville LN, Koomen JM, Ren X, Messina J, Jiang K, Garrett TJ, Rajadhyaksha A, Cleveland JL, Epling-Burnette PK. Cereblon harnesses Myc-dependent bioenergetics and activity of CD8+ T lymphocytes. Blood. 2020 Aug.136(7):857-870. Pubmedid: 32403132. Pmcid: PMC7426646.
    • Chen YA, Teer JK, Eroglu Z, Wu JY, Koomen JM, Karreth FA, Messina JL, Smalley KSM. Translational pathology, genomics and the development of systemic therapies for acral melanoma. Semin Cancer Biol. 2020 Apr.61:149-157. Pubmedid: 31689494. Pmcid: PMC7771370.
    • 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 Chem Biol. 2019 Sep.26(9):1240-1252.e11. Pubmedid: 31257184. Pmcid: PMC6754293.
    • 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. Clin Cancer Res. 2019 Sep.25(18):5686-5701. Pubmedid: 31227503. Pmcid: PMC6744978.
    • Lin S, Huang C, Gunda V, Sun J, Chellappan SP, Li Z, Izumi V, Fang B, Koomen J, Singh PK, Hao J, Yang S. Fascin Controls Metastatic Colonization and Mitochondrial Oxidative Phosphorylation by Remodeling Mitochondrial Actin Filaments. Cell Rep. 2019 Sep.28(11):2824-2836.e8. Pubmedid: 31509745. Pmcid: PMC6759858.
    • 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 Mol Biol. 2019 May.1996:273-296. Pubmedid: 31127562. Pmcid: PMC7771550.
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    • 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, Kim Y, Wu J, Chalfant CE, Kim M. PTPN11 Plays Oncogenic Roles and Is a Therapeutic Target for BRAF Wild-Type Melanomas. Mol Cancer Res. 2019 Feb.17(2):583-593. Pubmedid: 30355677. Pmcid: PMC6386183.
    • Lin S, Huang C, Sun J, Bollt O, Wang X, Martine E, Kang J, Taylor MD, Fang B, Singh PK, Koomen J, Hao J, Yang S. The mitochondrial deoxyguanosine kinase is required for cancer cell stemness in lung adenocarcinoma. EMBO Mol Med. 2019 Dec.11(12):e10849. Pubmedid: 31633874. Pmcid: PMC6895611.
    • 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. Proteogenomic landscape of squamous cell lung cancer. Nat Commun. 2019 Aug.10(1):3578. Pubmedid: 31395880. Pmcid: PMC6687710.
    • 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, Wan L. K27-linked ubiquitination of BRAF by ITCH engages cytokine response to maintain MEK-ERK signaling. Nat Commun. 2019 Apr.10(1):1870. Pubmedid: 31015455. Pmcid: PMC6478693.
    • Pérez-Morales J, Mejías-Morales D, Rivera-Rivera S, González-Flores J, González-Loperena M, Cordero-Báez FY, Pedreira-García WM, Chardón-Colón C, Cabán-Rivera J, Cress WD, Gordian ER, Muñoz-Antonia T, Cabrera-Ríos M, Isidro A, Coppola D, Rosa M, Boyle TA, Izumi V, Koomen JM, Santiago-Cardona PG. Hyper-phosphorylation of Rb S249 together with CDK5R2/p39 overexpression are associated with impaired cell adhesion and epithelial-to-mesenchymal transition: Implications as a potential lung cancer grading and staging biomarker. PLoS One. 2018 Nov.13(11):e0207483. Pubmedid: 30452490. Pmcid: PMC6242691.
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    • Guo D, Xu Q, Pabla S, Koomen J, Biddinger P, Sharma A, Pabla S, Pacholczyk R, Chang CC, Friedrich K, Mohammed K, Smallridge RC, Copland JA, She JX, Weinberger PM. Cytokeratin-8 in Anaplastic Thyroid Carcinoma: More Than a Simple Structural Cytoskeletal Protein. Int J Mol Sci. 2018 Feb.19(2). Pubmedid: 29443941. Pmcid: PMC5855799.
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    • 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. 2017 Mar.17(6). Pubmedid: 28195392. Pmcid: PMC5606153.
    • Chen Y, Britton D, Wood ER, Brantley S, Magliocco A, Pike I, Koomen JM. Quantitative proteomics of breast tumors: Tissue quality assessment to clinical biomarkers. Proteomics. 2017 Mar.17(6). Pubmedid: 28127872. Pmcid: PMC5996774.
    • Chen Y, Fisher KJ, Lloyd M, Wood ER, Coppola D, Siegel E, Shibata D, Chen YA, Koomen JM. Multiplexed Liquid Chromatography-Multiple Reaction Monitoring Mass Spectrometry Quantification of Cancer Signaling Proteins. Methods Mol Biol. 2017 Dec.1647:19-45. Pubmedid: 28808993. Pmcid: PMC5729929.
    • 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. Nat Chem Biol. 2017 Dec.13(12):1222-1231. Pubmedid: 28991240. Pmcid: PMC5909815.
    • Chen Y, Britton D, Wood ER, Brantley S, Fournier M, Wloch M, Williams VL, Johnson J, Magliocco A, Pike I, Koomen JM. Quantification of Breast Cancer Protein Biomarkers at Different Expression Levels in Human Tumors. Methods Mol Biol. 2017 Dec.1788:251-268. Pubmedid: 29243084. Pmcid: PMC7771335.
    • Frieling JS, Shay G, Izumi V, Aherne ST, Saul RG, Budzevich M, Koomen J, Lynch CC. Matrix metalloproteinase processing of PTHrP yields a selective regulator of osteogenesis, PTHrP1-17. Oncogene. 2017 Aug.36(31):4498-4507. Pubmedid: 28368420. Pmcid: PMC7771297.
    • 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. Inhibition of PI3K/Akt/mTOR signaling in PI3KR2-overexpressing colon cancer stem cells reduces tumor growth due to apoptosis. Oncotarget. 2017 Aug.8(31):50476-50488. Pubmedid: 28881576. Pmcid: PMC5584153.
    • 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. Unification of de novo and acquired ibrutinib resistance in mantle cell lymphoma. Nat Commun. 2017 Apr.8:14920. Pubmedid: 28416797. Pmcid: PMC5399304.
    • Guo JP, Shu SK, Esposito NN, Coppola D, Koomen JM, Cheng JQ. IKKϵ phosphorylation of estrogen receptor α Ser-167 and contribution to tamoxifen resistance in breast cancer. J Biol Chem. 2016 Oct.291(43):22857. Pubmedid: 27825095. Pmcid: PMC5077232.
    • 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. Mol Cancer Res. 2016 Oct.14(10):1019-1029. Pubmedid: 27422710. Pmcid: PMC5065770.
    • Zhang G, Scarborough H, Kim J, Rozhok AI, Chen YA, Zhang X, Song L, Bai Y, Fang B, Liu RZ, Koomen J, Tan AC, Degregori J, Haura EB. Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors. Sci Signal. 2016 Oct.9(450):rs12. Pubmedid: 27811184. Pmcid: PMC5377910.
    • 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. Clin Cancer Res. 2016 Nov.22(22):5605-5616. Pubmedid: 27220961. Pmcid: PMC5122466.
    • 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. 2016 May.35(21):2723-2734. Pubmedid: 26387544. Pmcid: PMC4801703.
    • 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. Fibronectin induction abrogates the BRAF inhibitor response of BRAF V600E/PTEN-null melanoma cells. Oncogene. 2016 Mar.35(10):1225-1235. Pubmedid: 26073081. Pmcid: PMC4679729.
    • 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. 2016 Jun.4(2):16. Pubmedid: 28154798. Pmcid: PMC5217344.
    • 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. Inhibition of PI3K/Akt/mTOR signaling in PI3KR2-overexpressing colon cancer stem cells reduces tumor growth due to apoptosis. Oncotarget. 2016 Jun. Pubmedid: 27286264.
    • 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. PAXIP1 Potentiates the Combination of WEE1 Inhibitor AZD1775 and Platinum Agents in Lung Cancer. Mol Cancer Ther. 2016 Jul.15(7):1669-1681. Pubmedid: 27196765. Pmcid: PMC4936941.
    • 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. Mol Cancer Ther. 2016 Feb.15(2):334-342. Pubmedid: 26772203. Pmcid: PMC4747823.
    • 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 Chem Biol. 2016 Dec.23(12):1490-1503. Pubmedid: 27866910. Pmcid: PMC5182133.
    • Kuenzi BM, Borne AL, Li J, Haura EB, Eschrich SA, Koomen JM, Rix U, Stewart PA. APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data. J Proteome Res. 2016 Dec.15(12):4747-4754. Pubmedid: 27680298. Pmcid: PMC5231908.
    • Sharma R, Fedorenko I, Spence PT, Sondak VK, Smalley KS, Koomen JM. Activity-Based Protein Profiling Shows Heterogeneous Signaling Adaptations to BRAF Inhibition. J Proteome Res. 2016 Dec.15(12):4476-4489. Pubmedid: 27934295. Pmcid: PMC5642956.
    • 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. 2015 Nov.10(11):e0142162. Pubmedid: 26539827. Pmcid: PMC4634858.
    • 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. 2015 Mar.6(8):6191-6202. Pubmedid: 25730908. Pmcid: PMC4467431.
    • Paraiso KH, Thakur MD, 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. Ligand-independent EPHA2 signaling drives the adoption of a targeted therapy-mediated metastatic melanoma phenotype. Cancer Discov. 2015 Mar.5(3):264-273. Pubmedid: 25542447. Pmcid: PMC4355213.
    • 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. 2015 Jun.81:41-49. Pubmedid: 25782629. Pmcid: PMC4460980.
    • Sun L, Kokura K, Izumi V, Koomen JM, Seto E, Chen J, Fang J. MPP8 and SIRT1 crosstalk in E-cadherin gene silencing and epithelial-mesenchymal transition. EMBO Rep. 2015 Jun.16(6):689-699. Pubmedid: 25870236. Pmcid: PMC4467853.
    • 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. 2015 Jan.15(2-3):327-339. Pubmedid: 25339196. Pmcid: PMC4389901.
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    • Damaghi M, Tafreshi NK, Lloyd MC, Sprung R, Estrella V, Wojtkowiak JW, Morse DL, Koomen JM, Bui MM, Gatenby RA, Gillies RJ. Chronic acidosis in the tumour microenvironment selects for overexpression of LAMP2 in the plasma membrane. Nat Commun. 2015 Dec.6:8752. Pubmedid: 26658462. Pmcid: PMC4682176.
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    • 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. 2014 Oct.33(42):4985-4996. Pubmedid: 24166501. Pmcid: PMC4002670.
    • Remily-Wood ER, Benson K, Baz RC, Chen YA, Hussein M, Hartley-Brown MA, Sprung RW, Perez B, Liu RZ, Yoder S, Teer J, Eschrich SA, Koomen JM. Quantification of peptides from immunoglobulin constant and variable regions by LC-MRM MS for assessment of multiple myeloma patients. Proteom Clin Appl. 2014 Oct.8(9-10):783-795. Pubmedid: 24723328. Pmcid: PMC4302417.
    • Fedorenko IV, Fang B, Koomen JM, Gibney GT, Smalley KS. Amuvatinib has cytotoxic effects against NRAS-mutant melanoma but not BRAF-mutant melanoma. Melanoma Res. 2014 Oct.24(5):448-453. Pubmedid: 24950457. Pmcid: PMC4384823.
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    • Rebecca VW, Wood ER, 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. Mol Cell Proteomics. 2014 Jul.13(7):1844-1854. Pubmedid: 24760959. Pmcid: PMC4083119.
    • 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 Chem Biol. 2014 Feb.9(2):353-358. Pubmedid: 24215125. Pmcid: PMC3944088.
    • 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 Res. 2014 Dec.74(24):7217-7228. Pubmedid: 25348954. Pmcid: PMC4326029.
    • Yoshida T, Zhang G, Smith MA, Lopez AS, Bai Y, Li J, Fang B, Koomen JM, Rawal B, Fisher KJ, Chen YA, Kitano M, Morita Y, Yamaguchi H, Shibata K, Okabe T, Okamoto I, Nakagawa K, Haura EB. Tyrosine phosphoproteomics identifies both codrivers and cotargeting strategies for T790M-related EGFR-TKI resistance in non-small cell lung cancer. Clin Cancer Res. 2014 Aug.20(15):4059-4074. Pubmedid: 24919575. Pmcid: PMC4119578.
    • Koomen JM. Immunoglobulins: expanding the role for mass spectrometry in protein biomarker quantification. Clin Chem. 2014 Aug.60(8):1034-1035. Pubmedid: 24938750. Pmcid: PMC4674789.
    • 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. Mol Cell Biol. 2013 Oct.33(19):3835-3848. Pubmedid: 23897426. Pmcid: PMC3811878.
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    • 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, Wang C, Bai W, Zhang X. Extracellular signal-regulated kinase (ERK) phosphorylates histone deacetylase 6 (HDAC6) at serine 1035 to stimulate cell migration. J Biol Chem. 2013 Nov.288(46):33156-33170. Pubmedid: 24089523. Pmcid: PMC3829163.
    • 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. Mol Cancer Ther. 2013 Nov.12(11):2446-2458. Pubmedid: 24048737. Pmcid: PMC3859963.
    • Ozcan S, Kazi A, Marsilio F, Fang B, Guida WC, Koomen J, Lawrence HR, Sebti SM. Oxadiazole-isopropylamides as potent and noncovalent proteasome inhibitors. J Med Chem. 2013 May.56(10):3783-3805. Pubmedid: 23547706. Pmcid: PMC3774303.
    • 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. Mol Cancer Ther. 2013 Jun.12(6):901-912. Pubmedid: 23538902. Pmcid: PMC3683468.
    • 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. Toxicol Lett. 2013 Jun.219(3):279-287. Pubmedid: 23566896. Pmcid: PMC3707521.
    • 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. Proc Natl Acad Sci U S A. 2013 Jul.110(30):12414-12419. Pubmedid: 23836654. Pmcid: PMC3725062.
    • 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. J Biol Chem. 2013 Jul.288(29):20908-20917. Pubmedid: 23737528. Pmcid: PMC3774361.
    • 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. J Immunol Methods. 2013 Dec.400-401:117-121. Pubmedid: 24140751. Pmcid: PMC3990009.
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    • Mahajan K, Fang B, Koomen JM, Mahajan NP. H2B Tyr37 phosphorylation suppresses expression of replication-dependent core histone genes. Nat Struct Mol Biol. 2012 Sep.19(9):930-937. Pubmedid: 22885324. Pmcid: PMC4533924.
    • 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. Sci Signal. 2012 Sep.5(242):rs6. Pubmedid: 22990118. Pmcid: PMC4064718.
    • 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. Clin Cancer Res. 2012 Nov.18(22):6155-6168. Pubmedid: 22988056. Pmcid: PMC3500436.
    • 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 Res. 2012 May.72(10):2501-2511. Pubmedid: 22461510. Pmcid: PMC4641440.
    • 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. Clin Cancer Res. 2012 May.18(9):2502-2514. Pubmedid: 22351686. Pmcid: PMC3398738.
    • 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. J Cancer Educ. 2012 Jun.27(3):418-427. Pubmedid: 22528637. Pmcid: PMC3439555.
    • 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. Mol Cell Biol. 2012 Jul.32(14):2823-2836. Pubmedid: 22586264. Pmcid: PMC3416197.
    • An Z, Chen Y, Koomen JM, Merkler DJ. A mass spectrometry-based method to screen for α-amidated peptides. Proteomics. 2012 Jan.12(2):173-182. Pubmedid: 22106059. Pmcid: PMC3517110.
    • Xiang Y, Koomen JM. Evaluation of direct infusion-multiple reaction monitoring mass spectrometry for quantification of heat shock proteins. Anal Chem. 2012 Feb.84(4):1981-1986. Pubmedid: 22293045. Pmcid: PMC3332078.
    • Remily-Wood ER, Koomen JM. Evaluation of protein quantification using standard peptides containing single conservative amino acid replacements. J Mass Spectrom. 2012 Feb.47(2):188-194. Pubmedid: 22359328. Pmcid: PMC3465614.
    • 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. J Invest Dermatol. 2012 Dec.132(12):2818-2827. Pubmedid: 22810307. Pmcid: PMC3479306.
    • 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. Monitoring a nuclear factor-κB signature of drug resistance in multiple myeloma. Mol Cell Proteomics. 2011 Nov.10(11):M110.005520. Pubmedid: 21846842. Pmcid: PMC3226396.
    • 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. Nat Commun. 2011 Nov.2:533. Pubmedid: 22086334. Pmcid: PMC3286832.
    • 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. 2011 Mar.6(3):e17533. Pubmedid: 21390258. Pmcid: PMC3046982.
    • 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. J Proteome Res. 2011 Jan.10(1):305-319. Pubmedid: 21080693. Pmcid: PMC3050523.
    • 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. Mol Cell Biol. 2011 Dec.31(23):4720-4734. Pubmedid: 21947282. Pmcid: PMC3232929.
    • 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. Chem Res Toxicol. 2011 Dec.24(12):2302-2311. Pubmedid: 22084934. Pmcid: PMC3243798.
    • 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, Smalley KS, Dalton WS, Huang E, Scott E, Bloom GC, Eschrich SA, Koomen JM. A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. Proteom Clin Appl. 2011 Aug.5(7-8):383-396. Pubmedid: 21656910. Pmcid: PMC3530891.
    • 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, Smalley KS. PTEN loss confers BRAF inhibitor resistance to melanoma cells through the suppression of BIM expression. Cancer Res. 2011 Apr.71(7):2750-2760. Pubmedid: 21317224. Pmcid: PMC3070772.
    • Koomen JM, Smalley KS. Using quantitative proteomic analysis to understand genotype specific intrinsic drug resistance in melanoma. Oncotarget. 2011 Apr.2(4):329-335. Pubmedid: 21505227. Pmcid: PMC3248164.
    • Fang B, Haura EB, Smalley KS, Eschrich SA, Koomen JM. Methods for investigation of targeted kinase inhibitor therapy using chemical proteomics and phosphorylation profiling. Biochem Pharmacol. 2010 Sep.80(5):739-747. Pubmedid: 20361944. Pmcid: PMC2995952.
    • 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. 2010 Oct.1(10):994-1007. Pubmedid: 21442024. Pmcid: PMC3063420.
    • 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. 2010 Oct.5(10):e13470. Pubmedid: 20976048. Pmcid: PMC2957407.
    • 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, Mahajan NP. Ack1 mediated AKT/PKB tyrosine 176 phosphorylation regulates its activation. PLoS One. 2010 Mar.5(3):e9646. Pubmedid: 20333297. Pmcid: PMC2841635.
    • Shin H, Sampat MP, Koomen JM, Markey MK. Wavelet-Based Adaptive Denoising and Baseline Correction for MALDI TOF MS. OMICS. 2010 Jun.14(3):283-295. Pubmedid: 20455751.
    • 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. 2010 Jan.12(1):80-86. Pubmedid: 20072656. Pmcid: PMC2805886.
    • 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. J Biol Chem. 2010 Feb.285(6):3676-3684. Pubmedid: 19940156. Pmcid: PMC2823508.
    • 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. J Proteome Res. 2010 Aug.9(8):4215-4227. Pubmedid: 20590165. Pmcid: PMC2924816.
    • 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. Embo J. 2010 Aug.29(15):2538-2552. Pubmedid: 20588255. Pmcid: PMC2928696.
    • Thomas CE, Sexton W, Benson K, Sutphen R, Koomen J. Urine collection and processing for protein biomarker discovery and quantification. Cancer Epidemiol Biomarkers Prev. 2010 Apr.19(4):953-959. Pubmedid: 20332277. Pmcid: PMC2852495.
    • 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. Nat Chem Biol. 2010 Apr.6(4):291-299. Pubmedid: 20190765. Pmcid: PMC2842457.
    • Remily-Wood E, Dirscherl H, Koomen JM. Acid hydrolysis of proteins in matrix assisted laser desorption ionization matrices. J Am Soc Mass Spectrom. 2009 Nov.20(11):2106-2115. Pubmedid: 19679491.
    • 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. Mol Cell Proteomics. 2008 Oct.7(10):1780-1794. Pubmedid: 18664563. Pmcid: PMC2559938.
    • 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. 2008 Dec.24(23):2801-2802. Pubmedid: 18842605.
    • Shin H, Mutlu M, Koomen JM, Markey MK. Parametric power spectral density analysis of noise from instrumentation in MALDI TOF mass spectrometry. Cancer Inform. 2007 Sep.3:219-230. Pubmedid: 19455245. Pmcid: PMC2675828.
    • Ohshiro K, Rosenthal D, Koomen J, Streckfus C, Chambers M, Kobayashi R, El-Naggar A. Pre-analytic saliva processing affect proteomic results and biomarker screening of head and neck squamous carcinoma. Int J Oncol. 2007 Mar.30(3):743-749. Pubmedid: 17273777.
    • 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. Mol Cell. 2007 Jul.27(2):197-213. Pubmedid: 17643370. Pmcid: PMC2684874.
    • 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. J Biol Chem. 2006 Nov.281(45):34640-34650. Pubmedid: 16966331.
    • Koomen J, Wilson C, Guthrie P, Androlewicz M, Kobayashi R, Taegtmeyer H. Proteome analysis of isolated perfused organ effluent as a novel model for protein biomarker discovery. J Proteome Res. 2006 Jan.5(1):177-182. Pubmedid: 16396509.
    • Coussot G, Hawke D, Mularz A, Koomen J, Kobayashi R. A method for the isolation of blocked N-terminal peptides. Anal Biochem. 2006 Feb.361(2):302-4. Pubmedid: 17188638.
    • Shin H, Sampat M, Bish S, Koomen J, Markey M. Statistical characterization of chemical noise in MALDI TOF MS by wavelet analysis of multiple noise realizations. Amia Annu Symp Proc. 2006.1092. Pubmedid: 17238711. Pmcid: PMC1839299.
    • Campos-Fernandez C, Schottel B, Chifotides H, Bera J, Bacsa J, Koomen JM, Russell D, Dunbar K. Anion template effect on the self-assembly and interconversion of metallacyclophanes. J Am Chem Soc. 2005 Oct.127(37):12909-12923. Pubmedid: 16159285.
    • 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 Res. 2005 Nov.65(22):10478-10485. Pubmedid: 16288040.
    • Yokoi K, Shih LC, 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. Int J Oncol. 2005 Nov.27(5):1361-1369. Pubmedid: 16211233.
    • Koomen J, Li D, Xiao L, Liu T, Coombes K, Abbruzzese J, Kobayashi R. Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. J Proteome Res. 2005 May.4(3):972-981. Pubmedid: 15952745.
    • 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. 2005 May.21(9):1764-1775. Pubmedid: 15673564.
    • Koomen J, Shih L, Coombes K, Li D, Xiao L, Fidler I, Abbruzzese J, Kobayashi R. Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins. Clin Cancer Res. 2005 Feb.11(3):1110-1118. Pubmedid: 15709178.
    • 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. 2005 Apr.24(18):2929-2943. Pubmedid: 15735718.
    • Koomen J, Zhao H, Li D, Nasser W, Hawke D, Abbruzzese J, Baggerly K, Kobayashi R. Diagnostic protein discovery using liquid chromatography/mass spectrometry for proteolytic peptide targeting. Rapid Commun Mass Spectrom. 2005.19(12):1624-1636. Pubmedid: 15915451.
    • Coombes KR, Koomen JM, Baggerly KA, Morris JS, Kobayashi R. Understanding the characteristics of mass spectrometry data through the use of simulation. Cancer Inform. 2005.1:41-52. Pubmedid: 19305631. Pmcid: PMC2657656.
    • 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. 2004 Sep.127(3):741-748. Pubmedid: 15362030.
    • Chifotides H, Koomen J, Kang M, Tichy S, Dunbar K, Russell D. Binding of DNA purine sites to dirhodium compounds probed by mass spectrometry. Inorg Chem. 2004 Oct.43(20):6177-6187. Pubmedid: 15446862.
    • 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. 2004 May.100(9):1814-1822. Pubmedid: 15112261.
    • Gaertner T, Kolodziej S, Wang D, Kobayashi R, Koomen J, Stoops J, WaxhamMN. Comparative analyses of the three-dimensional structures and enzymatic properties of alpha, beta, gamma and delta isoforms of Ca2+-calmodulin-dependent protein kinase II. J Biol Chem. 2004 Mar.279(13):12484-12494. Pubmedid: 14722083.
    • Woods A, Ugarov M, Egan T, Koomen J, Gillig K, Fuhrer K, Gonin M, SchultzJA. Lipid/peptide/nucleotide separation with MALDI-ion mobility-TOF MS. Anal Chem. 2004 Apr.76(8):2187-2195. Pubmedid: 15080727.
    • Koomen J, Zhao H, Li D, Abbruzzese J, Baggerly K, Kobayashi R. Diagnostic protein discovery using proteolytic peptide targeting and identification. Rapid Commun Mass Spectrom. 2004.18(21):2537-2548. Pubmedid: 15468157.
    • Sulikowski G, Agnelli F, Spencer P, Koomen J, Russell D. Studies on the biosynthesis of phomoidride B (CP-263,114): evidence for a decarboxylative homodimerization pathway. Org Lett. 2002 May.4(9):1447-1450. Pubmedid: 11975600.
    • 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. J Am Soc Mass Spectrom. 2002 Feb.13(2):166-169. Pubmedid: 11838019.
    • Koomen J, Ruotolo B, Gillig K, McLean J, Russell D, Kang M, Dunbar K, Fuhrer K, Gonin M, Schultz J. Oligonucleotide analysis with MALDI-ion-mobility-TOFMS. Anal Bioanal Chem. 2002 Aug.373(7):612-617. Pubmedid: 12185573.
    • Koomen J, Russell W, Tichy S, Russell D. Accurate mass measurement of DNA oligonucleotide ions using high-resolution time-of-flight mass spectrometry. J Mass Spectrom. 2002.37(4):357-371. Pubmedid: 11948842.
    • Campos-Fernandez C, Clerac R, Koomen J, Russell D, Dunbar K. Fine-tuning the ring-size of metallacyclophanes: a rational approach to molecular pentagons. J Am Chem Soc. 2001.123(4):773-774. Pubmedid: 11456607.
    • Botos I, Meyer E, Nguyen M, Swanson S, Koomen J, Russell D, Meyer E. The structure of an insect chymotrypsin. J Mol Biol. 2000 May.298(5):895-901. Pubmedid: 10801356.
    • 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. Anal Chem. 2000 Aug.72(16):3860-3866. Pubmedid: 10959974.
    • 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. J Mass Spectrom. 2000 Aug.35(8):1025-1034. Pubmedid: 10973002.
  • Grants

    • Title: Developing a Proteomic Assay to Quantify Soluble B-cell Maturation Antigen and Determine the Effect of its Glycosylation on Targeted Immunotherapy
      Sponsor: Moffitt Cancer Center
      PI (Contact): Freeman, C., PI: Koomen, J.
    • Title: Identifying Metabolic Vulnerabilities in Lung Cancer
      Sponsor: Nat Institutes of Health
      PI (Contact): Flores, E., PI (MPI): Haura, E., Project PI: DeNicola, G., Project PI: Rodriguez, P., Project PI: Cleveland, J., Core PI/Director: Fridley, B., Core PI/Director: Cress, D., Core PI/Director: Koomen, J.
    • Title: CPTAC Phase III
      Sponsor: Nat Institutes of Health
      PI: Koomen, J.

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