Daoud Meerzaman

DaoudMeerzaman
Title:
Adjunct Professor of Biology
Email:
[email protected]

Areas of Expertise

Bioinformatic analyses of cancer genomes

Current Research

Cancer genomics and bioinformatics analysis for life sciences, clinical and translational research.

Education

B.S. George Washington University

Doctorate: George Washington University

Fellowships: Children’s National Medical Center in Washington D.C., Joint program at the University of Maryland at Baltimore and Johns Hopkins University

Publications

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. PMID: 30453880 [PubMed - indexed for MEDLINE] 

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. PMID: 29972774 [PubMed - in process] 

Chromatic: WebAssembly-Based Cancer Genome Viewer. Finney R, Meerzaman D. Cancer Inform. 2018 Apr 27;17:1176935118771972. doi: 10.1177/1176935118771972. eCollection 2018. Review. PMID: 29881254 [PubMed] 

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. PMID: 28825729 [PubMed - indexed for MEDLINE] 

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 [PubMed] 

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. PMID: 27923066 [PubMed - indexed for MEDLINE] 

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. PMID: 27702824 [PubMed - indexed for MEDLINE] 

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. PMID: 27476724 [PubMed - indexed for MEDLINE] 

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. PMID: 27159561 [PubMed - indexed for MEDLINE] 

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 [PubMed - indexed for MEDLINE] 

Inferring causal molecular networks: empirical assessment through a community-based effort. Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S. Nat Methods. 2016 Apr;13(4):310-8. doi: 10.1038/nmeth.3773. Epub 2016 Feb 22. PMID: 26901648 [PubMed - indexed for MEDLINE] 

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. PMID: 26840086 [PubMed - indexed for MEDLINE]

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. PMID: 26635203 [PubMed - indexed for MEDLINE]

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. PMID: 26417198 [PubMed] 

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. PMID: 26397705 [PubMed - indexed for MEDLINE] 

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. PMID: 26158413 [PubMed - indexed for MEDLINE] 

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY; ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants, Kellen MR, Norman TC, Haussler D, Friend SH, Stolovitzky G, Margolin AA, Stuart JM, Boutros PC. Nat Methods. 2015 Jul;12(7):623-30. doi: 10.1038/nmeth.3407. Epub 2015 May 18. PMID: 25984700 [PubMed - indexed for MEDLINE] 

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. PMID: 25841438 [PubMed - indexed for MEDLINE] 

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]. PMID: 25670082 [PubMed - indexed for MEDLINE] 

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. PMID: 25133526 [PubMed - indexed for MEDLINE] 

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. PMID: 24997477 [PubMed - indexed for MEDLINE] 

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 [PubMed - indexed for MEDLINE] 

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 [PubMed - indexed for MEDLINE] 

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. PMID: 24526832 [PubMed]

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. PMID: 23894275 [PubMed - indexed for MEDLINE] 

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. PMID: 23555554 [PubMed - indexed for MEDLINE] 

Comprehensive molecular portraits of human breast tumours. Cancer Genome Atlas Network. Nature. 2012 Oct 4;490(7418):61-70. doi: 10.1038/nature11412. Epub 2012 Sep 23. PMID: 23000897 [PubMed - indexed for MEDLINE] 

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. PMID: 22411629 [PubMed - indexed for MEDLINE] 

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. PMID: 21278191 [PubMed - indexed for MEDLINE]

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. PMID: 21152245 [PubMed] 

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 [PubMed - indexed for MEDLINE] 

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. PMID: 20169162 [PubMed - indexed for MEDLINE] 

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. PMID: 19047146 [PubMed - indexed for MEDLINE] 

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. PMID: 17304513 [PubMed - indexed for MEDLINE] 

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. PMID: 15788655 [PubMed - indexed for MEDLINE] 

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. PMID: 15240517 [PubMed - indexed for MEDLINE] 

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. PMID: 12082530 [PubMed - indexed for MEDLINE]