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Items: 44

1.

Matrisome-Associated Gene Expression Patterns Correlating with TIMP2 in Cancer.

Peeney D, Fan Y, Nguyen T, Meerzaman D, Stetler-Stevenson WG.

Sci Rep. 2019 Dec 27;9(1):20142. doi: 10.1038/s41598-019-56632-3.

2.

The Bromodomain Protein 4 Contributes to the Regulation of Alternative Splicing.

Uppal S, Gegonne A, Chen Q, Thompson PS, Cheng D, Mu J, Meerzaman D, Misra HS, Singer DS.

Cell Rep. 2019 Nov 19;29(8):2450-2460.e5. doi: 10.1016/j.celrep.2019.10.066.

3.

Comprehensive Transcriptome Profiling of Cryptic CBFA2T3-GLIS2 Fusion-Positive AML Defines Novel Therapeutic Options: A COG and TARGET Pediatric AML Study.

Smith JL, Ries RE, Hylkema T, Alonzo TA, Gerbing RB, Santaguida MT, Eidenschink Brodersen L, Pardo L, Cummings CL, Loeb KR, Le Q, Imren S, Leonti AR, Gamis AS, Aplenc R, Kolb EA, Farrar JE, Triche TJ Jr, Nguyen C, Meerzaman D, Loken MR, Oehler VG, Bolouri H, Meshinchi S.

Clin Cancer Res. 2020 Feb 1;26(3):726-737. doi: 10.1158/1078-0432.CCR-19-1800. Epub 2019 Nov 12.

PMID:
31719049
4.

Adrenocortical tumors have a distinct, long, non-coding RNA expression profile and LINC00271 is downregulated in malignancy.

Buishand FO, Liu-Chittenden Y, Fan Y, Tirosh A, Gara SK, Patel D, Meerzaman D, Kebebew E.

Surgery. 2020 Jan;167(1):224-232. doi: 10.1016/j.surg.2019.04.067. Epub 2019 Sep 13.

PMID:
31522749
5.

Value of Collaboration among Multi-Domain Experts in Analysis of High-Throughput Genomics Data.

Meerzaman D, Dunn BK.

Cancer Res. 2019 Oct 15;79(20):5140-5145. doi: 10.1158/0008-5472.CAN-19-0769. Epub 2019 Jul 23. Review.

PMID:
31337654
6.

Predicting Complete Remission of Acute Myeloid Leukemia: Machine Learning Applied to Gene Expression.

Gal O, Auslander N, Fan Y, Meerzaman D.

Cancer Inform. 2019 Mar 15;18:1176935119835544. doi: 10.1177/1176935119835544. eCollection 2019.

7.

Comparing the performance of selected variant callers using synthetic data and genome segmentation.

Bian X, Zhu B, Wang M, Hu Y, Chen Q, Nguyen C, Hicks B, Meerzaman D.

BMC Bioinformatics. 2018 Nov 19;19(1):429. doi: 10.1186/s12859-018-2440-7.

8.

Immature CD8 Single-Positive Thymocytes Are a Molecularly Distinct Subpopulation, Selectively Dependent on BRD4 for Their Differentiation.

Gegonne A, Chen QR, Dey A, Etzensperger R, Tai X, Singer A, Meerzaman D, Ozato K, Singer DS.

Cell Rep. 2018 Jul 3;24(1):117-129. doi: 10.1016/j.celrep.2018.06.007.

9.

Chromatic: WebAssembly-Based Cancer Genome Viewer.

Finney R, Meerzaman D.

Cancer Inform. 2018 Apr 27;17:1176935118771972. doi: 10.1177/1176935118771972. eCollection 2018. Review.

10.

A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor.

Gadd S, Huff V, Walz AL, Ooms AHAG, Armstrong AE, Gerhard DS, Smith MA, Auvil JMG, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Hermida LC, Davidsen T, Gesuwan P, Ma Y, Zong Z, Mungall AJ, Moore RA, Marra MA, Dome JS, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Ross N, Gastier-Foster JM, Arold ST, Perlman EJ.

Nat Genet. 2017 Oct;49(10):1487-1494. doi: 10.1038/ng.3940. Epub 2017 Aug 21.

11.

Erratum: BRD4 is a histone acetyltransferase that evicts nucleosomes from chromatin.

Devaiah BN, Case-Borden C, Gegonne A, Hsu CH, Chen Q, Meerzaman D, Dey A, Ozato K, Singer DS.

Nat Struct Mol Biol. 2017 Feb 6;24(2):194. doi: 10.1038/nsmb0217-194c. No abstract available.

PMID:
28169998
12.

Somatic Genomics and Clinical Features of Lung Adenocarcinoma: A Retrospective Study.

Shi J, Hua X, Zhu B, Ravichandran S, Wang M, Nguyen C, Brodie SA, Palleschi A, Alloisio M, Pariscenti G, Jones K, Zhou W, Bouk AJ, Boland J, Hicks B, Risch A, Bennett H, Luke BT, Song L, Duan J, Liu P, Kohno T, Chen Q, Meerzaman D, Marconett C, Laird-Offringa I, Mills I, Caporaso NE, Gail MH, Pesatori AC, Consonni D, Bertazzi PA, Chanock SJ, Landi MT.

PLoS Med. 2016 Dec 6;13(12):e1002162. doi: 10.1371/journal.pmed.1002162. eCollection 2016 Dec.

13.

Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group.

Ooms AH, Gadd S, Gerhard DS, Smith MA, Guidry Auvil JM, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Ma Y, Zong Z, Mungall AJ, Moore RA, Marra MA, Huff V, Dome JS, Chi YY, Tian J, Geller JI, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Walz AL, van den Heuvel-Eibrink MM, de Krijger RR, Ross N, Gastier-Foster JM, Perlman EJ.

Clin Cancer Res. 2016 Nov 15;22(22):5582-5591. doi: 10.1158/1078-0432.CCR-16-0985. Epub 2016 Oct 4.

14.

Rare Germline Copy Number Variations and Disease Susceptibility in Familial Melanoma.

Shi J, Zhou W, Zhu B, Hyland PL, Bennett H, Xiao Y, Zhang X, Burke LS, Song L, Hsu CH, Yan C, Chen Q, Meerzaman D, Dagnall CL, Burdette L, Hicks B, Freedman ND, Chanock SJ, Yeager M, Tucker MA, Goldstein AM, Yang XR.

J Invest Dermatol. 2016 Dec;136(12):2436-2443. doi: 10.1016/j.jid.2016.07.023. Epub 2016 Jul 29.

15.

BRD4 is a histone acetyltransferase that evicts nucleosomes from chromatin.

Devaiah BN, Case-Borden C, Gegonne A, Hsu CH, Chen Q, Meerzaman D, Dey A, Ozato K, Singer DS.

Nat Struct Mol Biol. 2016 Jun;23(6):540-8. doi: 10.1038/nsmb.3228. Epub 2016 May 9. Erratum in: Nat Struct Mol Biol. 2017 Feb 6;24(2):194.

16.

The promise of omics-based approaches to cancer prevention.

Meerzaman D, Dunn BK, Lee M, Chen Q, Yan C, Ross S.

Semin Oncol. 2016 Feb;43(1):36-48. doi: 10.1053/j.seminoncol.2015.09.004. Epub 2015 Sep 8. Review.

PMID:
26970123
17.

A function-blocking CD47 antibody suppresses stem cell and EGF signaling in triple-negative breast cancer.

Kaur S, Elkahloun AG, Singh SP, Chen QR, Meerzaman DM, Song T, Manu N, Wu W, Mannan P, Garfield SH, Roberts DD.

Oncotarget. 2016 Mar 1;7(9):10133-52. doi: 10.18632/oncotarget.7100.

18.

MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours.

Perlman EJ, Gadd S, Arold ST, Radhakrishnan A, Gerhard DS, Jennings L, Huff V, Guidry Auvil JM, Davidsen TM, Dome JS, Meerzaman D, Hsu CH, Nguyen C, Anderson J, Ma Y, Mungall AJ, Moore RA, Marra MA, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Gastier-Foster JM, Ross N, Smith MA.

Nat Commun. 2015 Dec 4;6:10013. doi: 10.1038/ncomms10013.

19.

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.

Finney RP, Chen QR, Nguyen CV, Hsu CH, Yan C, Hu Y, Abawi M, Bian X, Meerzaman DM.

Cancer Inform. 2015 Sep 13;14:105-7. doi: 10.4137/CIN.S26470. eCollection 2015. Review.

20.

Transcriptome Profiling of Pediatric Core Binding Factor AML.

Hsu CH, Nguyen C, Yan C, Ries RE, Chen QR, Hu Y, Ostronoff F, Stirewalt DL, Komatsoulis G, Levy S, Meerzaman D, Meshinchi S.

PLoS One. 2015 Sep 23;10(9):e0138782. doi: 10.1371/journal.pone.0138782. eCollection 2015.

21.

TCF21 hypermethylation in genetically quiescent clear cell sarcoma of the kidney.

Gooskens SL, Gadd S, Guidry Auvil JM, Gerhard DS, Khan J, Patidar R, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Mullighan CG, Ma J, Jennings LJ, de Krijger RR, van den Heuvel-Eibrink MM, Smith MA, Ross N, Gastier-Foster JM, Perlman EJ.

Oncotarget. 2015 Jun 30;6(18):15828-41.

22.

Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.

Wu TJ, Schriml LM, Chen QR, Colbert M, Crichton DJ, Finney R, Hu Y, Kibbe WA, Kincaid H, Meerzaman D, Mitraka E, Pan Y, Smith KM, Srivastava S, Ward S, Yan C, Mazumder R.

Database (Oxford). 2015 Apr 4;2015:bav032. doi: 10.1093/database/bav032. Print 2015.

23.

Recurrent DGCR8, DROSHA, and SIX homeodomain mutations in favorable histology Wilms tumors.

Walz AL, Ooms A, Gadd S, Gerhard DS, Smith MA, Guidry Auvil JM, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Bowlby R, Brooks D, Ma Y, Mungall AJ, Moore RA, Schein J, Marra MA, Huff V, Dome JS, Chi YY, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Jafari N, Ross N, Gastier-Foster JM, Perlman EJ.

Cancer Cell. 2015 Feb 9;27(2):286-97. doi: 10.1016/j.ccell.2015.01.003. Erratum in: Cancer Cell. 2015 Mar 9;27(3):426. Guidry Auvil, Jamie M [corrected to Guidry Auvil, Jaime M].

24.

Systematic genetic analysis identifies Cis-eQTL target genes associated with glioblastoma patient survival.

Chen QR, Hu Y, Yan C, Buetow K, Meerzaman D.

PLoS One. 2014 Aug 18;9(8):e105393. doi: 10.1371/journal.pone.0105393. eCollection 2014.

25.

Addition of MR imaging features and genetic biomarkers strengthens glioblastoma survival prediction in TCGA patients.

Nicolasjilwan M, Hu Y, Yan C, Meerzaman D, Holder CA, Gutman D, Jain R, Colen R, Rubin DL, Zinn PO, Hwang SN, Raghavan P, Hammoud DA, Scarpace LM, Mikkelsen T, Chen J, Gevaert O, Buetow K, Freymann J, Kirby J, Flanders AE, Wintermark M; TCGA Glioma Phenotype Research Group.

J Neuroradiol. 2015 Jul;42(4):212-21. doi: 10.1016/j.neurad.2014.02.006. Epub 2014 Jul 2.

26.

Systems analysis utilising pathway interactions identifies sonic hedgehog pathway as a primary biomarker and oncogenic target in hepatocellular carcinoma.

Efroni S, Meerzaman D, Schaefer CF, Greenblum S, Soo-Lyu M, Hu Y, Cultraro C, Meshorer E, Buetow KH.

IET Syst Biol. 2013 Dec;7(6):243-51.

PMID:
24712101
27.

Genome-wide transcriptional sequencing identifies novel mutations in metabolic genes in human hepatocellular carcinoma.

Meerzaman DM, Yan C, Chen QR, Edmonson MN, Schaefer CF, Clifford RJ, Dunn BK, Dong L, Finney RP, Cultraro CM, Hu Y, Yang Z, Nguyen CV, Kelley JM, Cai S, Zhang H, Zhang J, Wilson R, Messmer L, Chung YH, Kim JA, Park NH, Lyu MS, Song IH, Komatsoulis G, Buetow KH.

Cancer Genomics Proteomics. 2014 Jan-Feb;11(1):1-12.

PMID:
24633315
28.

OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data.

Hu Y, Yan C, Hsu CH, Chen QR, Niu K, Komatsoulis GA, Meerzaman D.

Cancer Inform. 2014 Jan 16;13:13-20. doi: 10.4137/CIN.S13495. eCollection 2014.

29.

Multi-SNP analysis of GWAS data identifies pathways associated with nonalcoholic fatty liver disease.

Chen QR, Braun R, Hu Y, Yan C, Brunt EM, Meerzaman D, Sanyal AJ, Buetow K.

PLoS One. 2013 Jul 19;8(7):e65982. doi: 10.1371/journal.pone.0065982. Print 2013.

30.

Discovery analysis of TCGA data reveals association between germline genotype and survival in ovarian cancer patients.

Braun R, Finney R, Yan C, Chen QR, Hu Y, Edmonson M, Meerzaman D, Buetow K.

PLoS One. 2013;8(3):e55037. doi: 10.1371/journal.pone.0055037. Epub 2013 Mar 21.

31.

The general transcription factor TAF7 is essential for embryonic development but not essential for the survival or differentiation of mature T cells.

Gegonne A, Tai X, Zhang J, Wu G, Zhu J, Yoshimoto A, Hanson J, Cultraro C, Chen QR, Guinter T, Yang Z, Hathcock K, Singer A, Rodriguez-Canales J, Tessarollo L, Mackem S, Meerzaman D, Buetow K, Singer DS.

Mol Cell Biol. 2012 May;32(10):1984-97. doi: 10.1128/MCB.06305-11. Epub 2012 Mar 12.

32.

Frequent homozygous deletion of the LKB1/STK11 gene in non-small cell lung cancer.

Gill RK, Yang SH, Meerzaman D, Mechanic LE, Bowman ED, Jeon HS, Roy Chowdhuri S, Shakoori A, Dracheva T, Hong KM, Fukuoka J, Zhang JH, Harris CC, Jen J.

Oncogene. 2011 Sep 1;30(35):3784-91. doi: 10.1038/onc.2011.98. Epub 2011 May 2.

33.

Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format.

Edmonson MN, Zhang J, Yan C, Finney RP, Meerzaman DM, Buetow KH.

Bioinformatics. 2011 Mar 15;27(6):865-6. doi: 10.1093/bioinformatics/btr032. Epub 2011 Jan 28.

34.

Novel pathway analysis of genomic polymorphism-cancer risk interaction in the Breast Cancer Prevention Trial.

Dunn BK, Greene MH, Kelley JM, Costantino JP, Clifford RJ, Hu Y, Tang G, Kazerouni N, Rosenberg PS, Meerzaman DM, Buetow KH.

Int J Mol Epidemiol Genet. 2010;1(4):332-49. Epub 2010 Sep 5.

35.

Genetic variations at loci involved in the immune response are risk factors for hepatocellular carcinoma.

Clifford RJ, Zhang J, Meerzaman DM, Lyu MS, Hu Y, Cultraro CM, Finney RP, Kelley JM, Efroni S, Greenblum SI, Nguyen CV, Rowe WL, Sharma S, Wu G, Yan C, Zhang H, Chung YH, Kim JA, Park NH, Song IH, Buetow KH.

Hepatology. 2010 Dec;52(6):2034-43. doi: 10.1002/hep.23943.

PMID:
21105107
36.

Delineating genetic alterations for tumor progression in the MCF10A series of breast cancer cell lines.

Kadota M, Yang HH, Gomez B, Sato M, Clifford RJ, Meerzaman D, Dunn BK, Wakefield LM, Lee MP.

PLoS One. 2010 Feb 15;5(2):e9201. doi: 10.1371/journal.pone.0009201.

37.

SMAD6 contributes to patient survival in non-small cell lung cancer and its knockdown reestablishes TGF-beta homeostasis in lung cancer cells.

Jeon HS, Dracheva T, Yang SH, Meerzaman D, Fukuoka J, Shakoori A, Shilo K, Travis WD, Jen J.

Cancer Res. 2008 Dec 1;68(23):9686-92. doi: 10.1158/0008-5472.CAN-08-1083.

38.

Inactivation of LLC1 gene in nonsmall cell lung cancer.

Hong KM, Yang SH, Chowdhuri SR, Player A, Hames M, Fukuoka J, Meerzaman D, Dracheva T, Sun Z, Yang P, Jen J.

Int J Cancer. 2007 Jun 1;120(11):2353-8.

39.

Mutations in the tyrosine kinase domain of the epidermal growth factor receptor in non-small cell lung cancer.

Yang SH, Mechanic LE, Yang P, Landi MT, Bowman ED, Wampfler J, Meerzaman D, Hong KM, Mann F, Dracheva T, Fukuoka J, Travis W, Caporaso NE, Harris CC, Jen J.

Clin Cancer Res. 2005 Mar 15;11(6):2106-10. Erratum in: Clin Cancer Res. 2005 Nov 1;11(21):7960-1.

40.

Chromatin remodeling factors and BRM/BRG1 expression as prognostic indicators in non-small cell lung cancer.

Fukuoka J, Fujii T, Shih JH, Dracheva T, Meerzaman D, Player A, Hong K, Settnek S, Gupta A, Buetow K, Hewitt S, Travis WD, Jen J.

Clin Cancer Res. 2004 Jul 1;10(13):4314-24.

41.

Identification of TDE2 gene and its expression in non-small cell lung cancer.

Player A, Gillespie J, Fujii T, Fukuoka J, Dracheva T, Meerzaman D, Hong KM, Curran J, Attoh G, Travis W, Jen J.

Int J Cancer. 2003 Nov 1;107(2):238-43.

42.

Interaction and colocalization of PGP9.5 with JAB1 and p27(Kip1).

Caballero OL, Resto V, Patturajan M, Meerzaman D, Guo MZ, Engles J, Yochem R, Ratovitski E, Sidransky D, Jen J.

Oncogene. 2002 May 2;21(19):3003-10.

43.

Involvement of the MAP kinase ERK2 in MUC1 mucin signaling.

Meerzaman D, Shapiro PS, Kim KC.

Am J Physiol Lung Cell Mol Physiol. 2001 Jul;281(1):L86-91.

44.

Construction and characterization of a chimeric receptor containing the cytoplasmic domain of MUC1 mucin.

Meerzaman D, Xing PX, Kim KC.

Am J Physiol Lung Cell Mol Physiol. 2000 Mar;278(3):L625-9.

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