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Developmental subtypes assessed by DNA methylation-iPLEX forecast the natural history of chronic lymphocytic leukemia.

Giacopelli B, Zhao Q, Ruppert AS, Agyeman A, Weigel C, Wu YZ, Gerber MM, Rabe KG, Larson MC, Lu J, Blachly JS, Rogers KA, Wierda WG, Brown JR, Rai KR, Keating M, Rassenti LZ, Kipps TJ, Zenz T, Shanafelt TD, Kay NE, Abruzzo LV, Coombes KR, Woyach JA, Byrd JC, Oakes CC.

Blood. 2019 Aug 22;134(8):688-698. doi: 10.1182/blood.2019000490. Epub 2019 Jul 10.


CytoGPS: A Web-Enabled Karyotype Analysis Tool for Cytogenetics.

Abrams ZB, Zhang L, Abruzzo LV, Heerema NA, Li S, Dillon T, Rodriguez R, Coombes KR, Payne PRO.

Bioinformatics. 2019 Jul 2. pii: btz520. doi: 10.1093/bioinformatics/btz520. [Epub ahead of print]


Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing.

Zucker MR, Abruzzo LV, Herling CD, Barron LL, Keating MJ, Abrams ZB, Heerema N, Coombes KR.

Bioinformatics. 2019 Sep 1;35(17):3216. doi: 10.1093/bioinformatics/btz243. No abstract available.


LGALS3 is connected to CD74 in a previously unknown protein network that is associated with poor survival in patients with AML.

Ruvolo PP, Hu CW, Qiu Y, Ruvolo VR, Go RL, Hubner SE, Coombes KR, Andreeff M, Qutub AA, Kornblau SM.

EBioMedicine. 2019 Jun;44:126-137. doi: 10.1016/j.ebiom.2019.05.025. Epub 2019 May 16.


A quantitative analysis of heterogeneities and hallmarks in acute myelogenous leukaemia.

Hu CW, Qiu Y, Ligeralde A, Raybon AY, Yoo SY, Coombes KR, Qutub AA, Kornblau SM.

Nat Biomed Eng. 2019 Apr 15. doi: 10.1038/s41551-019-0387-2. [Epub ahead of print]


Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing.

Zucker MR, Abruzzo LV, Herling CD, Barron LL, Keating MJ, Abrams ZB, Heerema N, Coombes KR.

Bioinformatics. 2019 Sep 1;35(17):2924-2931. doi: 10.1093/bioinformatics/btz057.


Human papillomavirus and the landscape of secondary genetic alterations in oral cancers.

Gillison ML, Akagi K, Xiao W, Jiang B, Pickard RKL, Li J, Swanson BJ, Agrawal AD, Zucker M, Stache-Crain B, Emde AK, Geiger HM, Robine N, Coombes KR, Symer DE.

Genome Res. 2019 Jan;29(1):1-17. doi: 10.1101/gr.241141.118. Epub 2018 Dec 18.


Co-Expression Analysis Reveals Mechanisms Underlying the Varied Roles of NOTCH1 in NSCLC.

Sinicropi-Yao SL, Amann JM, Lopez DLY, Cerciello F, Coombes KR, Carbone DP.

J Thorac Oncol. 2019 Feb;14(2):223-236. doi: 10.1016/j.jtho.2018.10.162. Epub 2018 Nov 5.


Thirty biologically interpretable clusters of transcription factors distinguish cancer type.

Abrams ZB, Zucker M, Wang M, Asiaee Taheri A, Abruzzo LV, Coombes KR.

BMC Genomics. 2018 Oct 11;19(1):738. doi: 10.1186/s12864-018-5093-z.


Proteogenomic Analysis of Surgically Resected Lung Adenocarcinoma.

Sharpnack MF, Ranbaduge N, Srivastava A, Cerciello F, Codreanu SG, Liebler DC, Mascaux C, Miles WO, Morris R, McDermott JE, Sharpnack JL, Amann J, Maher CA, Machiraju R, Wysocki VH, Govindan R, Mallick P, Coombes KR, Huang K, Carbone DP.

J Thorac Oncol. 2018 Oct;13(10):1519-1529. doi: 10.1016/j.jtho.2018.06.025. Epub 2018 Jul 11.


Trisomy 12 chronic lymphocytic leukemia expresses a unique set of activated and targetable pathways.

Abruzzo LV, Herling CD, Calin GA, Oakes C, Barron LL, Banks HE, Katju V, Keating MJ, Coombes KR.

Haematologica. 2018 Dec;103(12):2069-2078. doi: 10.3324/haematol.2018.190132. Epub 2018 Jul 5.


Decomposing the Apoptosis Pathway Into Biologically Interpretable Principal Components.

Wang M, Kornblau SM, Coombes KR.

Cancer Inform. 2018 May 9;17:1176935118771082. doi: 10.1177/1176935118771082. eCollection 2018.


Chemistry-First Approach for Nomination of Personalized Treatment in Lung Cancer.

McMillan EA, Ryu MJ, Diep CH, Mendiratta S, Clemenceau JR, Vaden RM, Kim JH, Motoyaji T, Covington KR, Peyton M, Huffman K, Wu X, Girard L, Sung Y, Chen PH, Mallipeddi PL, Lee JY, Hanson J, Voruganti S, Yu Y, Park S, Sudderth J, DeSevo C, Muzny DM, Doddapaneni H, Gazdar A, Gibbs RA, Hwang TH, Heymach JV, Wistuba I, Coombes KR, Williams NS, Wheeler DA, MacMillan JB, Deberardinis RJ, Roth MG, Posner BA, Minna JD, Kim HS, White MA.

Cell. 2018 May 3;173(4):864-878.e29. doi: 10.1016/j.cell.2018.03.028. Epub 2018 Apr 19.


eIF2β, a subunit of translation-initiation factor EIF2, is a potential therapeutic target for non-small cell lung cancer.

Tanaka I, Sato M, Kato T, Goto D, Kakumu T, Miyazawa A, Yogo N, Hase T, Morise M, Sekido Y, Girard L, Minna JD, Byers LA, Heymach JV, Coombes KR, Kondo M, Hasegawa Y.

Cancer Sci. 2018 Jun;109(6):1843-1852. doi: 10.1111/cas.13602. Epub 2018 May 25.


IntLIM: integration using linear models of metabolomics and gene expression data.

Siddiqui JK, Baskin E, Liu M, Cantemir-Stone CZ, Zhang B, Bonneville R, McElroy JP, Coombes KR, Mathé EA.

BMC Bioinformatics. 2018 Mar 5;19(1):81. doi: 10.1186/s12859-018-2085-6.


Histone Modification Patterns Using RPPA-Based Profiling Predict Outcome in Acute Myeloid Leukemia Patients.

van Dijk AD, Hu CW, de Bont ESJM, Qiu Y, Hoff FW, Yoo SY, Coombes KR, Qutub AA, Kornblau SM.

Proteomics. 2018 Apr;18(8):e1700379. doi: 10.1002/pmic.201700379. Epub 2018 Apr 2.


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.


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.


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.


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.


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.


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.


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.


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 Oct 20;34(30):3638-3647. doi: 10.1200/JCO.2015.66.0084.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.



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

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


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.


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.


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.


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.


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.


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.

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