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Items: 1 to 20 of 44

1.

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. 2019 Sep 12. pii: S0039-6060(19)30548-3. doi: 10.1016/j.surg.2019.04.067. [Epub ahead of print]

PMID:
31522749
2.

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
3.

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.

4.

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.

5.

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.

6.

Chromatic: WebAssembly-Based Cancer Genome Viewer.

Finney R, Meerzaman D.

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

7.

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.

8.

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
9.

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.

10.

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.

11.

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.

12.

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.

13.

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
14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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