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Items: 1 to 50 of 131

1.

Thresher: determining the number of clusters while removing outliers.

Wang M, Abrams ZB, Kornblau SM, Coombes KR.

BMC Bioinformatics. 2018 Jan 8;19(1):9. doi: 10.1186/s12859-017-1998-9.

2.

The long noncoding RNA, treRNA, decreases DNA damage and is associated with poor response to chemotherapy in chronic lymphocytic leukemia.

Miller CR, Ruppert AS, Fobare S, Chen TL, Liu C, Lehman A, Blachly JS, Zhang X, Lucas DM, Grever MR, Tallman MS, Flinn IW, Rassenti LZ, Kipps TJ, Sampath D, Coombes KR, Hertlein EK.

Oncotarget. 2017 Apr 18;8(16):25942-25954. doi: 10.18632/oncotarget.15401.

3.

Low expression of ASH2L protein correlates with a favorable outcome in acute myeloid leukemia.

Butler JS, Qiu YH, Zhang N, Yoo SY, Coombes KR, Dent SY, Kornblau SM.

Leuk Lymphoma. 2017 May;58(5):1207-1218. doi: 10.1080/10428194.2016.1235272. Epub 2016 Oct 13.

PMID:
28185526
4.

Identification of proteasomal catalytic subunit PSMA6 as a therapeutic target for lung cancer.

Kakumu T, Sato M, Goto D, Kato T, Yogo N, Hase T, Morise M, Fukui T, Yokoi K, Sekido Y, Girard L, Minna JD, Byers LA, Heymach JV, Coombes KR, Kondo M, Hasegawa Y.

Cancer Sci. 2017 Apr;108(4):732-743. doi: 10.1111/cas.13185. Epub 2017 Apr 25.

5.

Risk Factors of 131I-Induced Salivary Gland Damage in Thyroid Cancer Patients.

Hollingsworth B, Senter L, Zhang X, Brock GN, Jarjour W, Nagy R, Brock P, Coombes KR, Kloos RT, Ringel MD, Sipos J, Lattimer I, Carrau R, Jhiang SM.

J Clin Endocrinol Metab. 2016 Nov;101(11):4085-4093. Epub 2016 Aug 17.

6.

Genetic variants in thyroid cancer distant metastases.

Justiniano SE, McElroy JP, Yu L, Yilmaz AS, Coombes KR, Senter L, Nagy R, Wakely P Jr, Volinia S, Vinco M, Giordano TJ, Croce CM, Saji M, Ringel MD.

Endocr Relat Cancer. 2016 Oct;23(10):L33-6. doi: 10.1530/ERC-16-0351. Epub 2016 Aug 19. No abstract available.

7.

Epidermal growth factor receptor is expressed and active in a subset of acute myeloid leukemia.

Mahmud H, Kornblau SM, Ter Elst A, Scherpen FJ, Qiu YH, Coombes KR, de Bont ES.

J Hematol Oncol. 2016 Aug 3;9(1):64. doi: 10.1186/s13045-016-0294-x.

8.

The BATTLE-2 Study: A Biomarker-Integrated Targeted Therapy Study in Previously Treated Patients With Advanced Non-Small-Cell Lung Cancer.

Papadimitrakopoulou V, Lee JJ, Wistuba II, Tsao AS, Fossella FV, Kalhor N, Gupta S, Byers LA, Izzo JG, Gettinger SN, Goldberg SB, Tang X, Miller VA, Skoulidis F, Gibbons DL, Shen L, Wei C, Diao L, Peng SA, Wang J, Tam AL, Coombes KR, Koo JS, Mauro DJ, Rubin EH, Heymach JV, Hong WK, Herbst RS.

J Clin Oncol. 2016 Aug 1. pii: JCO660084. [Epub ahead of print]

9.

Preclinical Evaluation of the Novel BTK Inhibitor Acalabrutinib in Canine Models of B-Cell Non-Hodgkin Lymphoma.

Harrington BK, Gardner HL, Izumi R, Hamdy A, Rothbaum W, Coombes KR, Covey T, Kaptein A, Gulrajani M, Van Lith B, Krejsa C, Coss CC, Russell DS, Zhang X, Urie BK, London CA, Byrd JC, Johnson AJ, Kisseberth WC.

PLoS One. 2016 Jul 19;11(7):e0159607. doi: 10.1371/journal.pone.0159607. eCollection 2016.

10.

Selecting Reliable mRNA Expression Measurements Across Platforms Improves Downstream Analysis.

Tong P, Diao L, Shen L, Li L, Heymach JV, Girard L, Minna JD, Coombes KR, Byers LA, Wang J.

Cancer Inform. 2016 May 10;15:81-9. doi: 10.4137/CIN.S38590. eCollection 2016.

11.

MLL-Rearranged Acute Lymphoblastic Leukemias Activate BCL-2 through H3K79 Methylation and Are Sensitive to the BCL-2-Specific Antagonist ABT-199.

Benito JM, Godfrey L, Kojima K, Hogdal L, Wunderlich M, Geng H, Marzo I, Harutyunyan KG, Golfman L, North P, Kerry J, Ballabio E, Chonghaile TN, Gonzalo O, Qiu Y, Jeremias I, Debose L, O'Brien E, Ma H, Zhou P, Jacamo R, Park E, Coombes KR, Zhang N, Thomas DA, O'Brien S, Kantarjian HM, Leverson JD, Kornblau SM, Andreeff M, Müschen M, Zweidler-McKay PA, Mulloy JC, Letai A, Milne TA, Konopleva M.

Cell Rep. 2015 Dec 29;13(12):2715-27. doi: 10.1016/j.celrep.2015.12.003. Epub 2015 Dec 17.

12.

Phosphorylation of GSK3α/β correlates with activation of AKT and is prognostic for poor overall survival in acute myeloid leukemia patients.

Ruvolo PP, Qiu Y, Coombes KR, Zhang N, Neeley ES, Ruvolo VR, Hail N Jr, Borthakur G, Konopleva M, Andreeff M, Kornblau SM.

BBA Clin. 2015 Jul 23;4:59-68. doi: 10.1016/j.bbacli.2015.07.001. eCollection 2015 Dec.

13.

A Patient-Derived, Pan-Cancer EMT Signature Identifies Global Molecular Alterations and Immune Target Enrichment Following Epithelial-to-Mesenchymal Transition.

Mak MP, Tong P, Diao L, Cardnell RJ, Gibbons DL, William WN, Skoulidis F, Parra ER, Rodriguez-Canales J, Wistuba II, Heymach JV, Weinstein JN, Coombes KR, Wang J, Byers LA.

Clin Cancer Res. 2016 Feb 1;22(3):609-20. doi: 10.1158/1078-0432.CCR-15-0876. Epub 2015 Sep 29.

14.

Patterns of CTCF and ZFHX3 Mutation and Associated Outcomes in Endometrial Cancer.

Walker CJ, Miranda MA, O'Hern MJ, McElroy JP, Coombes KR, Bundschuh R, Cohn DE, Mutch DG, Goodfellow PJ.

J Natl Cancer Inst. 2015 Sep 1;107(11). pii: djv249. doi: 10.1093/jnci/djv249. Print 2015 Nov.

15.

Latent Feature Decompositions for Integrative Analysis of Multi-Platform Genomic Data.

Gregory KB, Momin AA, Coombes KR, Baladandayuthapani V.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Nov-Dec;11(6):984-94. doi: 10.1109/TCBB.2014.2325035. Epub 2014 May 19.

16.

Erk Negative Feedback Control Enables Pre-B Cell Transformation and Represents a Therapeutic Target in Acute Lymphoblastic Leukemia.

Shojaee S, Caeser R, Buchner M, Park E, Swaminathan S, Hurtz C, Geng H, Chan LN, Klemm L, Hofmann WK, Qiu YH, Zhang N, Coombes KR, Paietta E, Molkentin J, Koeffler HP, Willman CL, Hunger SP, Melnick A, Kornblau SM, Müschen M.

Cancer Cell. 2015 Jul 13;28(1):114-28. doi: 10.1016/j.ccell.2015.05.008. Epub 2015 Jun 11.

17.

Co-occurring genomic alterations define major subsets of KRAS-mutant lung adenocarcinoma with distinct biology, immune profiles, and therapeutic vulnerabilities.

Skoulidis F, Byers LA, Diao L, Papadimitrakopoulou VA, Tong P, Izzo J, Behrens C, Kadara H, Parra ER, Canales JR, Zhang J, Giri U, Gudikote J, Cortez MA, Yang C, Fan Y, Peyton M, Girard L, Coombes KR, Toniatti C, Heffernan TP, Choi M, Frampton GM, Miller V, Weinstein JN, Herbst RS, Wong KK, Zhang J, Sharma P, Mills GB, Hong WK, Minna JD, Allison JP, Futreal A, Wang J, Wistuba II, Heymach JV.

Cancer Discov. 2015 Aug;5(8):860-77. doi: 10.1158/2159-8290.CD-14-1236. Epub 2015 Jun 11.

18.

drexplorer: A tool to explore dose-response relationships and drug-drug interactions.

Tong P, Coombes KR, Johnson FM, Byers LA, Diao L, Liu DD, Lee JJ, Heymach JV, Wang J.

Bioinformatics. 2015 May 15;31(10):1692-4. doi: 10.1093/bioinformatics/btv028. Epub 2015 Jan 18.

19.

Biological properties of ligand-dependent activation of the MET receptor kinase in acute myeloid leukemia.

McGee SF, Kornblau SM, Qiu Y, Look AT, Zhang N, Yoo SY, Coombes KR, Kentsis A.

Leukemia. 2015 May;29(5):1218-21. doi: 10.1038/leu.2014.348. Epub 2014 Dec 26. No abstract available.

20.

Genes suppressed by DNA methylation in non-small cell lung cancer reveal the epigenetics of epithelial-mesenchymal transition.

Lin SH, Wang J, Saintigny P, Wu CC, Giri U, Zhang J, Menju T, Diao L, Byers L, Weinstein JN, Coombes KR, Girard L, Komaki R, Wistuba II, Date H, Minna JD, Heymach JV.

BMC Genomics. 2014 Dec 8;15:1079. doi: 10.1186/1471-2164-15-1079.

21.

Development of a robust classifier for quality control of reverse-phase protein arrays.

Ju Z, Liu W, Roebuck PL, Siwak DR, Zhang N, Lu Y, Davies MA, Akbani R, Weinstein JN, Mills GB, Coombes KR.

Bioinformatics. 2015 Mar 15;31(6):912-8. doi: 10.1093/bioinformatics/btu736. Epub 2014 Nov 6.

22.

Loss of TRIM62 expression is an independent adverse prognostic factor in acute myeloid leukemia.

Quintás-Cardama A, Zhang N, Qiu YH, Post S, Creighton CJ, Cortes J, Coombes KR, Kornblau SM.

Clin Lymphoma Myeloma Leuk. 2015 Feb;15(2):115-127.e15. doi: 10.1016/j.clml.2014.07.011. Epub 2014 Aug 12.

23.

The protein phosphatase 2A regulatory subunit B55α is a modulator of signaling and microRNA expression in acute myeloid leukemia cells.

Ruvolo PP, Ruvolo VR, Jacamo R, Burks JK, Zeng Z, Duvvuri SR, Zhou L, Qiu Y, Coombes KR, Zhang N, Yoo SY, Pan R, Hail N Jr, Konopleva M, Calin G, Kornblau SM, Andreeff M.

Biochim Biophys Acta. 2014 Sep;1843(9):1969-77. doi: 10.1016/j.bbamcr.2014.05.006. Epub 2014 May 21.

24.

VEGF/VEGFR-2 upregulates EZH2 expression in lung adenocarcinoma cells and EZH2 depletion enhances the response to platinum-based and VEGFR-2-targeted therapy.

Riquelme E, Suraokar M, Behrens C, Lin HY, Girard L, Nilsson MB, Simon G, Wang J, Coombes KR, Lee JJ, Hong WK, Heymach J, Minna JD, Wistuba II.

Clin Cancer Res. 2014 Jul 15;20(14):3849-61. doi: 10.1158/1078-0432.CCR-13-1916. Epub 2014 May 21.

25.

Transcriptomic architecture of the adjacent airway field cancerization in non-small cell lung cancer.

Kadara H, Fujimoto J, Yoo SY, Maki Y, Gower AC, Kabbout M, Garcia MM, Chow CW, Chu Z, Mendoza G, Shen L, Kalhor N, Hong WK, Moran C, Wang J, Spira A, Coombes KR, Wistuba II.

J Natl Cancer Inst. 2014 Mar;106(3):dju004. doi: 10.1093/jnci/dju004. Epub 2014 Feb 22.

26.

Synergistic targeting of AML stem/progenitor cells with IAP antagonist birinapant and demethylating agents.

Carter BZ, Mak PY, Mak DH, Shi Y, Qiu Y, Bogenberger JM, Mu H, Tibes R, Yao H, Coombes KR, Jacamo RO, McQueen T, Kornblau SM, Andreeff M.

J Natl Cancer Inst. 2014 Feb;106(2):djt440. doi: 10.1093/jnci/djt440.

27.

BCL-2 family proteins as 5-Azacytidine-sensitizing targets and determinants of response in myeloid malignancies.

Bogenberger JM, Kornblau SM, Pierceall WE, Lena R, Chow D, Shi CX, Mantei J, Ahmann G, Gonzales IM, Choudhary A, Valdez R, Camoriano J, Fauble V, Tiedemann RE, Qiu YH, Coombes KR, Cardone M, Braggio E, Yin H, Azorsa DO, Mesa RA, Stewart AK, Tibes R.

Leukemia. 2014 Aug;28(8):1657-65. doi: 10.1038/leu.2014.44. Epub 2014 Jan 23.

28.

BAYESIAN SPARSE GRAPHICAL MODELS FOR CLASSIFICATION WITH APPLICATION TO PROTEIN EXPRESSION DATA.

Baladandayuthapani V, Talluri R, Ji Y, Coombes KR, Lu Y, Hennessy BT, Davies MA, Mallick BK.

Ann Appl Stat. 2014;8(3):1443-1468.

29.

Proteomic profiling identifies distinct protein patterns in acute myelogenous leukemia CD34+CD38- stem-like cells.

Kornblau SM, Qutub A, Yao H, York H, Qiu YH, Graber D, Ravandi F, Cortes J, Andreeff M, Zhang N, Coombes KR.

PLoS One. 2013 Oct 24;8(10):e78453. doi: 10.1371/journal.pone.0078453. eCollection 2013.

30.

targetHub: a programmable interface for miRNA-gene interactions.

Manyam G, Ivan C, Calin GA, Coombes KR.

Bioinformatics. 2013 Oct 15;29(20):2657-8. doi: 10.1093/bioinformatics/btt439. Epub 2013 Sep 6.

31.

Independent validation of a model using cell line chemosensitivity to predict response to therapy.

Wang W, Baggerly KA, Knudsen S, Askaa J, Mazin W, Coombes KR.

J Natl Cancer Inst. 2013 Sep 4;105(17):1284-91. doi: 10.1093/jnci/djt202. Epub 2013 Aug 20.

32.

Transglutaminase 2 expression in acute myeloid leukemia: association with adhesion molecule expression and leukemic blast motility.

Pierce A, Whetton AD, Meyer S, Ravandi-Kashani F, Borthakur G, Coombes KR, Zhang N, Kornblau S.

Proteomics. 2013 Jul;13(14):2216-2224. doi: 10.1002/pmic.201200471. Epub 2013 Jun 6.

33.

Prognostic impact and targeting of CRM1 in acute myeloid leukemia.

Kojima K, Kornblau SM, Ruvolo V, Dilip A, Duvvuri S, Davis RE, Zhang M, Wang Z, Coombes KR, Zhang N, Qiu YH, Burks JK, Kantarjian H, Shacham S, Kauffman M, Andreeff M.

Blood. 2013 May 16;121(20):4166-74. doi: 10.1182/blood-2012-08-447581. Epub 2013 Apr 5.

34.

Sources of variation in false discovery rate estimation include sample size, correlation, and inherent differences between groups.

Zhang J, Coombes KR.

BMC Bioinformatics. 2012;13 Suppl 13:S1. doi: 10.1186/1471-2105-13-S13-S1. Epub 2012 Aug 24.

35.

SIBER: systematic identification of bimodally expressed genes using RNAseq data.

Tong P, Chen Y, Su X, Coombes KR.

Bioinformatics. 2013 Mar 1;29(5):605-13. doi: 10.1093/bioinformatics/bts713. Epub 2013 Jan 9.

36.

Genomic variation by whole-genome SNP mapping arrays predicts time-to-event outcome in patients with chronic lymphocytic leukemia: a comparison of CLL and HapMap genotypes.

Schweighofer CD, Coombes KR, Majewski T, Barron LL, Lerner S, Sargent RL, O'Brien S, Ferrajoli A, Wierda WG, Czerniak BA, Medeiros LJ, Keating MJ, Abruzzo LV.

J Mol Diagn. 2013 Mar;15(2):196-209. doi: 10.1016/j.jmoldx.2012.09.006. Epub 2012 Dec 27.

37.

An epithelial-mesenchymal transition gene signature predicts resistance to EGFR and PI3K inhibitors and identifies Axl as a therapeutic target for overcoming EGFR inhibitor resistance.

Byers LA, Diao L, Wang J, Saintigny P, Girard L, Peyton M, Shen L, Fan Y, Giri U, Tumula PK, Nilsson MB, Gudikote J, Tran H, Cardnell RJ, Bearss DJ, Warner SL, Foulks JM, Kanner SB, Gandhi V, Krett N, Rosen ST, Kim ES, Herbst RS, Blumenschein GR, Lee JJ, Lippman SM, Ang KK, Mills GB, Hong WK, Weinstein JN, Wistuba II, Coombes KR, Minna JD, Heymach JV.

Clin Cancer Res. 2013 Jan 1;19(1):279-90. doi: 10.1158/1078-0432.CCR-12-1558. Epub 2012 Oct 22.

38.

Characterizing the molecular spatial and temporal field of injury in early-stage smoker non-small cell lung cancer patients after definitive surgery by expression profiling.

Kadara H, Shen L, Fujimoto J, Saintigny P, Chow CW, Lang W, Chu Z, Garcia M, Kabbout M, Fan YH, Behrens C, Liu DA, Mao L, Lee JJ, Gold KA, Wang J, Coombes KR, Kim ES, Hong WK, Wistuba II.

Cancer Prev Res (Phila). 2013 Jan;6(1):8-17. doi: 10.1158/1940-6207.CAPR-12-0290. Epub 2012 Oct 19.

39.

integIRTy: a method to identify genes altered in cancer by accounting for multiple mechanisms of regulation using item response theory.

Tong P, Coombes KR.

Bioinformatics. 2012 Nov 15;28(22):2861-9. doi: 10.1093/bioinformatics/bts561. Epub 2012 Sep 26.

40.

Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1.

Byers LA, Wang J, Nilsson MB, Fujimoto J, Saintigny P, Yordy J, Giri U, Peyton M, Fan YH, Diao L, Masrorpour F, Shen L, Liu W, Duchemann B, Tumula P, Bhardwaj V, Welsh J, Weber S, Glisson BS, Kalhor N, Wistuba II, Girard L, Lippman SM, Mills GB, Coombes KR, Weinstein JN, Minna JD, Heymach JV.

Cancer Discov. 2012 Sep;2(9):798-811. doi: 10.1158/2159-8290.CD-12-0112. Epub 2012 Sep 6.

41.

Concomitant inhibition of DNA methyltransferase and BCL-2 protein function synergistically induce mitochondrial apoptosis in acute myelogenous leukemia cells.

Tsao T, Shi Y, Kornblau S, Lu H, Konoplev S, Antony A, Ruvolo V, Qiu YH, Zhang N, Coombes KR, Andreeff M, Kojima K, Konopleva M.

Ann Hematol. 2012 Dec;91(12):1861-70. doi: 10.1007/s00277-012-1537-8. Epub 2012 Aug 15.

42.

Functional characterization of CLPTM1L as a lung cancer risk candidate gene in the 5p15.33 locus.

James MA, Wen W, Wang Y, Byers LA, Heymach JV, Coombes KR, Girard L, Minna J, You M.

PLoS One. 2012;7(6):e36116. doi: 10.1371/journal.pone.0036116. Epub 2012 Jun 4.

43.

Survivin is highly expressed in CD34(+)38(-) leukemic stem/progenitor cells and predicts poor clinical outcomes in AML.

Carter BZ, Qiu Y, Huang X, Diao L, Zhang N, Coombes KR, Mak DH, Konopleva M, Cortes J, Kantarjian HM, Mills GB, Andreeff M, Kornblau SM.

Blood. 2012 Jul 5;120(1):173-80. doi: 10.1182/blood-2012-02-409888. Epub 2012 May 29.

44.

Relax with CouchDB--into the non-relational DBMS era of bioinformatics.

Manyam G, Payton MA, Roth JA, Abruzzo LV, Coombes KR.

Genomics. 2012 Jul;100(1):1-7. doi: 10.1016/j.ygeno.2012.05.006. Epub 2012 May 17.

45.

Perifosine plus docetaxel in patients with platinum and taxane resistant or refractory high-grade epithelial ovarian cancer.

Fu S, Hennessy BT, Ng CS, Ju Z, Coombes KR, Wolf JK, Sood AK, Levenback CF, Coleman RL, Kavanagh JJ, Gershenson DM, Markman M, Dice K, Howard A, Li J, Li Y, Stemke-Hale K, Dyer M, Atkinson E, Jackson E, Kundra V, Kurzrock R, Bast RC Jr, Mills GB.

Gynecol Oncol. 2012 Jul;126(1):47-53. doi: 10.1016/j.ygyno.2012.04.006. Epub 2012 Apr 6.

46.

Effect of KRAS oncogene substitutions on protein behavior: implications for signaling and clinical outcome.

Ihle NT, Byers LA, Kim ES, Saintigny P, Lee JJ, Blumenschein GR, Tsao A, Liu S, Larsen JE, Wang J, Diao L, Coombes KR, Chen L, Zhang S, Abdelmelek MF, Tang X, Papadimitrakopoulou V, Minna JD, Lippman SM, Hong WK, Herbst RS, Wistuba II, Heymach JV, Powis G.

J Natl Cancer Inst. 2012 Feb 8;104(3):228-39. doi: 10.1093/jnci/djr523. Epub 2012 Jan 13.

47.

A two-gene signature, SKI and SLAMF1, predicts time-to-treatment in previously untreated patients with chronic lymphocytic leukemia.

Schweighofer CD, Coombes KR, Barron LL, Diao L, Newman RJ, Ferrajoli A, O'Brien S, Wierda WG, Luthra R, Medeiros LJ, Keating MJ, Abruzzo LV.

PLoS One. 2011;6(12):e28277. doi: 10.1371/journal.pone.0028277. Epub 2011 Dec 14.

48.

Abnormal expression of FLI1 protein is an adverse prognostic factor in acute myeloid leukemia.

Kornblau SM, Qiu YH, Zhang N, Singh N, Faderl S, Ferrajoli A, York H, Qutub AA, Coombes KR, Watson DK.

Blood. 2011 Nov 17;118(20):5604-12. doi: 10.1182/blood-2011-04-348052. Epub 2011 Sep 13.

49.

Functional proteomics can define prognosis and predict pathologic complete response in patients with breast cancer.

Gonzalez-Angulo AM, Hennessy BT, Meric-Bernstam F, Sahin A, Liu W, Ju Z, Carey MS, Myhre S, Speers C, Deng L, Broaddus R, Lluch A, Aparicio S, Brown P, Pusztai L, Symmans WF, Alsner J, Overgaard J, Borresen-Dale AL, Hortobagyi GN, Coombes KR, Mills GB.

Clin Proteomics. 2011 Jul 8;8(1):11. doi: 10.1186/1559-0275-8-11.

50.

Use of reverse phase protein microarrays to study protein expression in leukemia: technical and methodological lessons learned.

Kornblau SM, Coombes KR.

Methods Mol Biol. 2011;785:141-55. doi: 10.1007/978-1-61779-286-1_10. Review.

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