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Items: 30

1.

Validation of Microsatellite Instability Detection Using a Comprehensive Plasma-Based Genotyping Panel.

Willis J, Lefterova MI, Artyomenko A, Kasi PM, Nakamura Y, Mody K, Catenacci DVT, Fakih M, Barbacioru C, Zhao J, Sikora M, Fairclough SR, Lee H, Kim KM, Kim ST, Kim J, Gavino D, Benavides M, Peled N, Nguyen T, Cusnir M, Eskander RN, Azzi G, Yoshino T, Banks KC, Raymond VM, Lanman RB, Chudova DI, Talasaz A, Kopetz S, Lee J, Odegaard JI.

Clin Cancer Res. 2019 Aug 4. doi: 10.1158/1078-0432.CCR-19-1324. [Epub ahead of print]

PMID:
31383735
2.

Rare autosomal trisomies, revealed by maternal plasma DNA sequencing, suggest increased risk of feto-placental disease.

Pertile MD, Halks-Miller M, Flowers N, Barbacioru C, Kinnings SL, Vavrek D, Seltzer WK, Bianchi DW.

Sci Transl Med. 2017 Aug 30;9(405). pii: eaan1240. doi: 10.1126/scitranslmed.aan1240.

PMID:
28855395
3.

Does addition of BRAF V600E mutation testing modify sensitivity or specificity of the Afirma Gene Expression Classifier in cytologically indeterminate thyroid nodules?

Kloos RT, Reynolds JD, Walsh PS, Wilde JI, Tom EY, Pagan M, Barbacioru C, Chudova DI, Wong M, Friedman L, LiVolsi VA, Rosai J, Lanman RB, Kennedy GC.

J Clin Endocrinol Metab. 2013 Apr;98(4):E761-8. doi: 10.1210/jc.2012-3762. Epub 2013 Mar 8.

PMID:
23476074
4.

Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities.

Craig DW, O'Shaughnessy JA, Kiefer JA, Aldrich J, Sinari S, Moses TM, Wong S, Dinh J, Christoforides A, Blum JL, Aitelli CL, Osborne CR, Izatt T, Kurdoglu A, Baker A, Koeman J, Barbacioru C, Sakarya O, De La Vega FM, Siddiqui A, Hoang L, Billings PR, Salhia B, Tolcher AW, Trent JM, Mousses S, Von Hoff D, Carpten JD.

Mol Cancer Ther. 2013 Jan;12(1):104-16. doi: 10.1158/1535-7163.MCT-12-0781. Epub 2012 Nov 19.

5.

RNA-Seq mapping and detection of gene fusions with a suffix array algorithm.

Sakarya O, Breu H, Radovich M, Chen Y, Wang YN, Barbacioru C, Utiramerur S, Whitley PP, Brockman JP, Vatta P, Zhang Z, Popescu L, Muller MW, Kudlingar V, Garg N, Li CY, Kong BS, Bodeau JP, Nutter RC, Gu J, Bramlett KS, Ichikawa JK, Hyland FC, Siddiqui AS.

PLoS Comput Biol. 2012;8(4):e1002464. doi: 10.1371/journal.pcbi.1002464. Epub 2012 Apr 5.

6.

MicroRNAs and their isomiRs function cooperatively to target common biological pathways.

Cloonan N, Wani S, Xu Q, Gu J, Lea K, Heater S, Barbacioru C, Steptoe AL, Martin HC, Nourbakhsh E, Krishnan K, Gardiner B, Wang X, Nones K, Steen JA, Matigian NA, Wood DL, Kassahn KS, Waddell N, Shepherd J, Lee C, Ichikawa J, McKernan K, Bramlett K, Kuersten S, Grimmond SM.

Genome Biol. 2011 Dec 30;12(12):R126. doi: 10.1186/gb-2011-12-12-r126.

7.

Next-generation sequencing identifies novel microRNAs in peripheral blood of lung cancer patients.

Keller A, Backes C, Leidinger P, Kefer N, Boisguerin V, Barbacioru C, Vogel B, Matzas M, Huwer H, Katus HA, Stähler C, Meder B, Meese E.

Mol Biosyst. 2011 Dec;7(12):3187-99. doi: 10.1039/c1mb05353a. Epub 2011 Oct 25.

PMID:
22027949
8.

Deterministic and stochastic allele specific gene expression in single mouse blastomeres.

Tang F, Barbacioru C, Nordman E, Bao S, Lee C, Wang X, Tuch BB, Heard E, Lao K, Surani MA.

PLoS One. 2011;6(6):e21208. doi: 10.1371/journal.pone.0021208. Epub 2011 Jun 23.

9.

Small RNA profiling of Dengue virus-mosquito interactions implicates the PIWI RNA pathway in anti-viral defense.

Hess AM, Prasad AN, Ptitsyn A, Ebel GD, Olson KE, Barbacioru C, Monighetti C, Campbell CL.

BMC Microbiol. 2011 Feb 28;11:45. doi: 10.1186/1471-2180-11-45.

10.

Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis.

Tang F, Barbacioru C, Bao S, Lee C, Nordman E, Wang X, Lao K, Surani MA.

Cell Stem Cell. 2010 May 7;6(5):468-78. doi: 10.1016/j.stem.2010.03.015.

11.

RNA-Seq analysis to capture the transcriptome landscape of a single cell.

Tang F, Barbacioru C, Nordman E, Li B, Xu N, Bashkirov VI, Lao K, Surani MA.

Nat Protoc. 2010 Mar;5(3):516-35. doi: 10.1038/nprot.2009.236. Epub 2010 Feb 25.

12.

mRNA-sequencing whole transcriptome analysis of a single cell on the SOLiD system.

Lao KQ, Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Tuch B, Bodeau J, Siddiqui A, Surani MA.

J Biomol Tech. 2009 Dec;20(5):266-71.

13.

mRNA-Seq whole-transcriptome analysis of a single cell.

Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA.

Nat Methods. 2009 May;6(5):377-82. doi: 10.1038/nmeth.1315. Epub 2009 Apr 6.

PMID:
19349980
14.

The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies.

Shi L, Jones WD, Jensen RV, Harris SC, Perkins RG, Goodsaid FM, Guo L, Croner LJ, Boysen C, Fang H, Qian F, Amur S, Bao W, Barbacioru CC, Bertholet V, Cao XM, Chu TM, Collins PJ, Fan XH, Frueh FW, Fuscoe JC, Guo X, Han J, Herman D, Hong H, Kawasaki ES, Li QZ, Luo Y, Ma Y, Mei N, Peterson RL, Puri RK, Shippy R, Su Z, Sun YA, Sun H, Thorn B, Turpaz Y, Wang C, Wang SJ, Warrington JA, Willey JC, Wu J, Xie Q, Zhang L, Zhang L, Zhong S, Wolfinger RD, Tong W.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S10. doi: 10.1186/1471-2105-9-S9-S10.

15.

A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures.

Sharp AJ, Mefford HC, Li K, Baker C, Skinner C, Stevenson RE, Schroer RJ, Novara F, De Gregori M, Ciccone R, Broomer A, Casuga I, Wang Y, Xiao C, Barbacioru C, Gimelli G, Bernardina BD, Torniero C, Giorda R, Regan R, Murday V, Mansour S, Fichera M, Castiglia L, Failla P, Ventura M, Jiang Z, Cooper GM, Knight SJ, Romano C, Zuffardi O, Chen C, Schwartz CE, Eichler EE.

Nat Genet. 2008 Mar;40(3):322-8. doi: 10.1038/ng.93. Epub 2008 Feb 17.

16.

Hierarchical cluster analysis of myoepithelial/basal cell markers in adenoid cystic carcinoma and polymorphous low-grade adenocarcinoma.

Prasad ML, Barbacioru CC, Rawal YB, Husein O, Wen P.

Mod Pathol. 2008 Feb;21(2):105-14. Epub 2007 Dec 14.

17.

Gene expression signature in peripheral blood detects thoracic aortic aneurysm.

Wang Y, Barbacioru CC, Shiffman D, Balasubramanian S, Iakoubova O, Tranquilli M, Albornoz G, Blake J, Mehmet NN, Ngadimo D, Poulter K, Chan F, Samaha RR, Elefteriades JA.

PLoS One. 2007 Oct 17;2(10):e1050.

18.

Double immunohistochemical staining with MUC4/p53 is useful in the distinction of pancreatic adenocarcinoma from chronic pancreatitis: a tissue microarray-based study.

Bhardwaj A, Marsh WL Jr, Nash JW, Barbacioru CC, Jones S, Frankel WL.

Arch Pathol Lab Med. 2007 Apr;131(4):556-62.

PMID:
17425384
19.

Effect of various normalization methods on Applied Biosystems expression array system data.

Barbacioru CC, Wang Y, Canales RD, Sun YA, Keys DN, Chan F, Poulter KA, Samaha RR.

BMC Bioinformatics. 2006 Dec 15;7:533.

20.

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

MAQC Consortium, Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker W Jr.

Nat Biotechnol. 2006 Sep;24(9):1151-61.

21.

Evaluation of DNA microarray results with quantitative gene expression platforms.

Canales RD, Luo Y, Willey JC, Austermiller B, Barbacioru CC, Boysen C, Hunkapiller K, Jensen RV, Knight CR, Lee KY, Ma Y, Maqsodi B, Papallo A, Peters EH, Poulter K, Ruppel PL, Samaha RR, Shi L, Yang W, Zhang L, Goodsaid FM.

Nat Biotechnol. 2006 Sep;24(9):1115-22.

PMID:
16964225
22.

Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays.

Wang Y, Barbacioru C, Hyland F, Xiao W, Hunkapiller KL, Blake J, Chan F, Gonzalez C, Zhang L, Samaha RR.

BMC Genomics. 2006 Mar 21;7:59.

23.

Prediction of anticancer drug potency from expression of genes involved in growth factor signaling.

Dai Z, Barbacioru C, Huang Y, Sadée W.

Pharm Res. 2006 Feb;23(2):336-49. Epub 2006 Jan 26.

PMID:
16425089
24.

Cystine-glutamate transporter SLC7A11 in cancer chemosensitivity and chemoresistance.

Huang Y, Dai Z, Barbacioru C, Sadée W.

Cancer Res. 2005 Aug 15;65(16):7446-54.

25.

Correlating gene expression with chemical scaffolds of cytotoxic agents: ellipticines as substrates and inhibitors of MDR1.

Huang Y, Blower PE, Yang C, Barbacioru C, Dai Z, Zhang Y, Xiao JJ, Chan KK, Sadée W.

Pharmacogenomics J. 2005;5(2):112-25.

PMID:
15668728
26.

Membrane transporters and channels: role of the transportome in cancer chemosensitivity and chemoresistance.

Huang Y, Anderle P, Bussey KJ, Barbacioru C, Shankavaram U, Dai Z, Reinhold WC, Papp A, Weinstein JN, Sadée W.

Cancer Res. 2004 Jun 15;64(12):4294-301.

27.

CITED1 protein expression suggests Papillary Thyroid Carcinoma in high throughput tissue microarray-based study.

Prasad ML, Pellegata NS, Kloos RT, Barbacioru C, Huang Y, de la Chapelle A.

Thyroid. 2004 Mar;14(3):169-75.

PMID:
15072698
28.

Proteomic patterns analysis: a new era of screening cancers.

Kahwash EB, Barbacioru C, Cowden DJ, Saltz J.

AMIA Annu Symp Proc. 2003:885.

29.

Order sets utilization in a clinical order entry system.

Cowden D, Barbacioru C, Kahwash E, Saltz J.

AMIA Annu Symp Proc. 2003:819.

30.

Pharmacokinetic mapping of breast tumors: a new statistical analysis technique for dynamic magnetic resonance imaging.

Barbacioru C, Arunachalam A, Cowden D, Kahwash E, Saltz JH.

AMIA Annu Symp Proc. 2003:783.

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