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Items: 1 to 50 of 181

1.

Exposure-response relationships of the sodium-glucose co-transporter 2 inhibitor dapagliflozin for renal risk markers.

Kroonen MYAM, Koomen JV, Petrykiv SI, Laverman GD, Heerspink HJL, Stevens J.

Diabetes Obes Metab. 2020 Jan 27. doi: 10.1111/dom.13976. [Epub ahead of print]

PMID:
31984620
2.

Network of Interactions between ZIKA Virus Non-Structural Proteins and Human Host Proteins.

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.

Cells. 2020 Jan 8;9(1). pii: E153. doi: 10.3390/cells9010153.

3.

Proteomic analysis of CSF from patients with leptomeningeal melanoma metastases identifies signatures associated with disease progression and therapeutic resistance.

Smalley I, Law V, Wyatt C, Evernden B, Fang B, Koomen JM, Welsh EA, Macaulay RJB, Forsyth PA, Smalley KSM.

Clin Cancer Res. 2020 Jan 10. pii: clincanres.2840.2019. doi: 10.1158/1078-0432.CCR-19-2840. [Epub ahead of print]

PMID:
31924735
4.

HDAC11 deficiency disrupts oncogene-induced hematopoiesis in myeloproliferative neoplasms.

Yue L, Sharma V, Horvat NP, Akuffo AA, Beatty MS, Murdun C, Colin C, Billington JMR, Goodheart WE, Sahakian E, Zhang L, Powers JJ, Amin NE, Lambert-Showers QT, Darville LN, Pinilla-Ibarz J, Reuther GW, Wright KL, 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.

Blood. 2020 Jan 16;135(3):191-207. doi: 10.1182/blood.2019895326.

PMID:
31750881
5.

Translational pathology, genomics and the development of systemic therapies for acral melanoma.

Chen YA, Teer JK, Eroglu Z, Wu JY, Koomen JM, Karreth FA, Messina JL, Smalley KSM.

Semin Cancer Biol. 2019 Nov 2. pii: S1044-579X(19)30343-8. doi: 10.1016/j.semcancer.2019.10.017. [Epub ahead of print] Review.

PMID:
31689494
6.

The mitochondrial deoxyguanosine kinase is required for cancer cell stemness in lung adenocarcinoma.

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.

EMBO Mol Med. 2019 Dec;11(12):e10849. doi: 10.15252/emmm.201910849. Epub 2019 Oct 21.

7.

Fascin Controls Metastatic Colonization and Mitochondrial Oxidative Phosphorylation by Remodeling Mitochondrial Actin Filaments.

Lin S, Huang C, Gunda V, Sun J, Chellappan SP, Li Z, Izumi V, Fang B, Koomen J, Singh PK, Hao J, Yang S.

Cell Rep. 2019 Sep 10;28(11):2824-2836.e8. doi: 10.1016/j.celrep.2019.08.011.

8.

Exposure and response analysis of aleglitazar on cardiovascular risk markers and safety outcomes: An analysis of the AleCardio trial.

Koomen JV, Heerspink HJL, Schrieks IC, Schwartz GG, Lincoff AM, Nicholls SJ, Svensson A, Wedel H, Weichert A, Grobbee DE, Stevens J.

Diabetes Obes Metab. 2020 Jan;22(1):30-38. doi: 10.1111/dom.13862. Epub 2019 Oct 1.

9.

Proteogenomic landscape of squamous cell lung cancer.

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

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

10.

Divergent Polypharmacology-Driven Cellular Activity of Structurally Similar Multi-Kinase Inhibitors through Cumulative Effects on Individual Targets.

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.

Cell Chem Biol. 2019 Sep 19;26(9):1240-1252.e11. doi: 10.1016/j.chembiol.2019.06.003. Epub 2019 Jun 27.

PMID:
31257184
11.

HDAC Inhibition Enhances the In Vivo Efficacy of MEK Inhibitor Therapy in Uveal Melanoma.

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.

Clin Cancer Res. 2019 Sep 15;25(18):5686-5701. doi: 10.1158/1078-0432.CCR-18-3382. Epub 2019 Jun 21.

PMID:
31227503
12.

GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis.

Li Q, Fisher K, Meng W, Fang B, Welsh E, Haura EB, Koomen JM, Eschrich SA, Fridley BL, Chen YA.

Bioinformatics. 2020 Jan 1;36(1):257-263. doi: 10.1093/bioinformatics/btz488.

13.

Proteometabolomics of Melphalan Resistance in Multiple Myeloma.

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.

Methods Mol Biol. 2019;1996:273-296. doi: 10.1007/978-1-4939-9488-5_21.

PMID:
31127562
14.

BCL2 Amplicon Loss and Transcriptional Remodeling Drives ABT-199 Resistance in B Cell Lymphoma Models.

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, Jiang H, Sudalagunta PR, Meads MB, Cheng F, Bi C, Fu K, Fan H, Dalton WS, Moscinski LC, Shain KH, Sotomayor EM, Wang GG, Gray NS, Cleveland JL, Qi J, Tao J.

Cancer Cell. 2019 May 13;35(5):752-766.e9. doi: 10.1016/j.ccell.2019.04.005.

15.

K27-linked ubiquitination of BRAF by ITCH engages cytokine response to maintain MEK-ERK signaling.

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.

Nat Commun. 2019 Apr 23;10(1):1870. doi: 10.1038/s41467-019-09844-0.

16.

HDAC8 Regulates a Stress Response Pathway in Melanoma to Mediate Escape from BRAF Inhibitor Therapy.

Emmons MF, Faião-Flores F, Sharma R, Thapa R, Messina JL, Becker JC, Schadendorf D, Seto E, Sondak VK, Koomen JM, Chen YA, Lau EK, Wan L, Licht JD, Smalley KSM.

Cancer Res. 2019 Jun 1;79(11):2947-2961. doi: 10.1158/0008-5472.CAN-19-0040. Epub 2019 Apr 15.

PMID:
30987999
17.

An immunoproteomic approach to characterize the CAR interactome and signalosome.

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.

Sci Signal. 2019 Feb 12;12(568). pii: eaap9777. doi: 10.1126/scisignal.aap9777.

18.

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.

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.

PLoS One. 2018 Nov 19;13(11):e0207483. doi: 10.1371/journal.pone.0207483. eCollection 2018.

19.

PTPN11 Plays Oncogenic Roles and Is a Therapeutic Target for BRAF Wild-Type Melanomas.

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.

Mol Cancer Res. 2019 Feb;17(2):583-593. doi: 10.1158/1541-7786.MCR-18-0777. Epub 2018 Oct 24.

PMID:
30355677
20.

PLK1 stabilizes a MYC-dependent kinase network in aggressive B cell lymphomas.

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 LV, Sudalagunta PR, Wan L, Wang X, Dalton WS, Moscinski LC, Shain KH, Vose J, Cleveland JL, Sotomayor EM, Fu K, Tao J.

J Clin Invest. 2018 Dec 3;128(12):5517-5530. doi: 10.1172/JCI122533. Epub 2018 Nov 5.

21.

Functional Proteomics and Deep Network Interrogation Reveal a Complex Mechanism of Action of Midostaurin in Lung Cancer Cells.

Ctortecka C, Palve V, Kuenzi BM, Fang B, Sumi NJ, Izumi V, Novakova S, Kinose F, Remsing Rix LL, Haura EB, Koomen JM, Rix U.

Mol Cell Proteomics. 2018 Dec;17(12):2434-2447. doi: 10.1074/mcp.RA118.000713. Epub 2018 Sep 14.

22.

Gene profiling-based phenotyping for identification of cellular parameters that contribute to fitness, stress-tolerance and virulence of Listeria monocytogenes variants.

Koomen J, den Besten HMW, Metselaar KI, Tempelaars MH, Wijnands LM, Zwietering MH, Abee T.

Int J Food Microbiol. 2018 Oct 20;283:14-21. doi: 10.1016/j.ijfoodmicro.2018.06.003. Epub 2018 Jun 7.

23.

Combined BRAF and HSP90 Inhibition in Patients with Unresectable BRAF V600E-Mutant Melanoma.

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

Clin Cancer Res. 2018 Nov 15;24(22):5516-5524. doi: 10.1158/1078-0432.CCR-18-0565. Epub 2018 Apr 19.

24.

Determining the optimal dose of atrasentan by evaluating the exposure-response relationships of albuminuria and bodyweight.

Koomen JV, Stevens J, Mostafa NM, Parving HH, de Zeeuw D, Heerspink HJL.

Diabetes Obes Metab. 2018 Aug;20(8):2019-2022. doi: 10.1111/dom.13312. Epub 2018 May 1.

25.

Cytokeratin-8 in Anaplastic Thyroid Carcinoma: More Than a Simple Structural Cytoskeletal Protein.

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.

Int J Mol Sci. 2018 Feb 14;19(2). pii: E577. doi: 10.3390/ijms19020577.

26.

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

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

Methods Mol Biol. 2018;1788:251-268. doi: 10.1007/7651_2017_113.

PMID:
29243084
27.

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

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

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

28.

Adaptive benefits from small mutation supplies in an antibiotic resistance enzyme.

Salverda MLM, Koomen J, Koopmanschap B, Zwart MP, de Visser JAGM.

Proc Natl Acad Sci U S A. 2017 Nov 28;114(48):12773-12778. doi: 10.1073/pnas.1712999114. Epub 2017 Nov 13.

29.

Polypharmacology-based ceritinib repurposing using integrated functional proteomics.

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

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

30.

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

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

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

31.

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

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

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

32.

Matrix metalloproteinase processing of PTHrP yields a selective regulator of osteogenesis, PTHrP1-17.

Frieling JS, Shay G, Izumi V, Aherne ST, Saul RG, Budzevich M, Koomen J, Lynch CC.

Oncogene. 2017 Aug;36(31):4498-4507. doi: 10.1038/onc.2017.70. Epub 2017 Apr 3.

PMID:
28368420
33.

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

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

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

34.

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

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

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

35.

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

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

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

36.

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

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

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

37.

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

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

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

38.

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

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

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

39.

Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors.

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.

Sci Signal. 2016 Oct 18;9(450):rs12.

40.

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

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

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

41.

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

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

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

42.

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

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

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

43.

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

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

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

44.

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

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

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

45.

Impact of Pathogen Population Heterogeneity and Stress-Resistant Variants on Food Safety.

Abee T, Koomen J, Metselaar KI, Zwietering MH, den Besten HM.

Annu Rev Food Sci Technol. 2016;7:439-56. doi: 10.1146/annurev-food-041715-033128. Epub 2016 Jan 11. Review.

PMID:
26772414
46.

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

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

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

47.

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

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

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

48.

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

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

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

49.

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

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

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

50.

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

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

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

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