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Items: 1 to 50 of 75

1.

Integration of Multiple Data Sources for Gene Network Inference Using Genetic Perturbation Data.

Liang X, Young WC, Hung LH, Raftery AE, Yeung KY.

J Comput Biol. 2019 Apr 22. doi: 10.1089/cmb.2019.0036. [Epub ahead of print]

PMID:
31009236
2.

Holistic optimization of an RNA-seq workflow for multi-threaded environments.

Hung LH, Lloyd W, Agumbe Sridhar R, Devi Athmalingam Ravishankar S, Xiong Y, Sobie E, Yeung KY.

Bioinformatics. 2019 Mar 11. pii: btz169. doi: 10.1093/bioinformatics/btz169. [Epub ahead of print]

PMID:
30859176
3.

A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection.

Fourati S, Talla A, Mahmoudian M, Burkhart JG, Klén R, Henao R, Yu T, Aydın Z, Yeung KY, Ahsen ME, Almugbel R, Jahandideh S, Liang X, Nordling TEM, Shiga M, Stanescu A, Vogel R; Respiratory Viral DREAM Challenge Consortium, Pandey G, Chiu C, McClain MT, Woods CW, Ginsburg GS, Elo LL, Tsalik EL, Mangravite LM, Sieberts SK.

Nat Commun. 2018 Oct 24;9(1):4418. doi: 10.1038/s41467-018-06735-8.

4.

Hot-starting software containers for STAR aligner.

Zhang P, Hung LH, Lloyd W, Yeung KY.

Gigascience. 2018 Aug 1;7(8). doi: 10.1093/gigascience/giy092.

5.

Reproducible Bioconductor workflows using browser-based interactive notebooks and containers.

Almugbel R, Hung LH, Hu J, Almutairy A, Ortogero N, Tamta Y, Yeung KY.

J Am Med Inform Assoc. 2018 Jan 1;25(1):4-12. doi: 10.1093/jamia/ocx120.

6.

fastBMA: scalable network inference and transitive reduction.

Hung LH, Shi K, Wu M, Young WC, Raftery AE, Yeung KY.

Gigascience. 2017 Oct 1;6(10):1-10. doi: 10.1093/gigascience/gix078.

7.

GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software.

Mittal V, Hung LH, Keswani J, Kristiyanto D, Lee SB, Yeung KY.

Gigascience. 2017 Apr 1;6(4):1-6. doi: 10.1093/gigascience/giw013.

8.

A prospective interventional study to examine the effect of a silver alloy and hydrogel-coated catheter on the incidence of catheter-associated urinary tract infection.

Chung PH, Wong CW, Lai CK, Siu HK, Tsang DN, Yeung KY, Ip DK, Tam PK.

Hong Kong Med J. 2017 Jun;23(3):239-45. doi: 10.12809/hkmj164906. Epub 2017 Feb 17.

9.

A posterior probability approach for gene regulatory network inference in genetic perturbation data.

Young WC, Raftery AE, Yeung KY.

Math Biosci Eng. 2016 Dec 1;13(6):1241-1251.

PMID:
27775378
10.

Mitochondrial DNA plasticity is an essential inducer of tumorigenesis.

Lee WT, Cain JE, Cuddihy A, Johnson J, Dickinson A, Yeung KY, Kumar B, Johns TG, Watkins DN, Spencer A, St John JC.

Cell Death Discov. 2016 Apr 4;2:16016. doi: 10.1038/cddiscovery.2016.16. eCollection 2016.

11.

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.

Hung LH, Kristiyanto D, Lee SB, Yeung KY.

PLoS One. 2016 Apr 5;11(4):e0152686. doi: 10.1371/journal.pone.0152686. eCollection 2016.

12.

Model-Based Clustering With Data Correction For Removing Artifacts In Gene Expression Data.

Young WC, Raftery AE, Yeung KY.

Ann Appl Stat. 2016 Feb;11(4):1998-2026. doi: 10.1214/17-AOAS1051. Epub 2017 Dec 28.

13.

Sustainable development of tyre char-based activated carbons with different textural properties for value-added applications.

Hadi P, Yeung KY, Guo J, Wang H, McKay G.

J Environ Manage. 2016 Apr 1;170:1-7. doi: 10.1016/j.jenvman.2016.01.005. Epub 2016 Jan 14.

PMID:
26775155
14.

Analysis of Mitochondrial DNA in Induced Pluripotent and Embryonic Stem Cells.

Lee W, Kelly RD, Yeung KY, Cagnone G, McKenzie M, St John JC.

Methods Mol Biol. 2015;1330:219-52. doi: 10.1007/978-1-4939-2848-4_18.

PMID:
26621601
15.

CyNetworkBMA: a Cytoscape app for inferring gene regulatory networks.

Fronczuk M, Raftery AE, Yeung KY.

Source Code Biol Med. 2015 Nov 11;10:11. doi: 10.1186/s13029-015-0043-5. eCollection 2015.

16.

Symmetry Engineering of Graphene Plasmonic Crystals.

Yeung KY, Chee J, Song Y, Kong J, Ham D.

Nano Lett. 2015 Aug 12;15(8):5001-9. doi: 10.1021/acs.nanolett.5b00970. Epub 2015 Jul 13.

PMID:
26154440
17.

Analysis of the Mitochondrial DNA and Its Replicative Capacity in Induced Pluripotent Stem Cells.

Cagnone G, Vaghjiani V, Lee W, Sun C, Johnson J, Yeung KY, St John JC.

Methods Mol Biol. 2016;1357:231-67. doi: 10.1007/7651_2014_156.

PMID:
25646603
18.

Electrophoretic and field-effect graphene for all-electrical DNA array technology.

Xu G, Abbott J, Qin L, Yeung KY, Song Y, Yoon H, Kong J, Ham D.

Nat Commun. 2014 Sep 5;5:4866. doi: 10.1038/ncomms5866.

PMID:
25189574
19.

Fast Bayesian inference for gene regulatory networks using ScanBMA.

Young WC, Raftery AE, Yeung KY.

BMC Syst Biol. 2014 Apr 17;8:47. doi: 10.1186/1752-0509-8-47.

20.

Far-infrared graphene plasmonic crystals for plasmonic band engineering.

Yeung KY, Chee J, Yoon H, Song Y, Kong J, Ham D.

Nano Lett. 2014 May 14;14(5):2479-84. doi: 10.1021/nl500158y. Epub 2014 Apr 6.

21.

Plasmonics with two-dimensional conductors.

Yoon H, Yeung KY, Kim P, Ham D.

Philos Trans A Math Phys Eng Sci. 2014 Feb 24;372(2012):20130104. doi: 10.1098/rsta.2013.0104. Print 2014 Mar 28.

22.

The identification of mitochondrial DNA variants in glioblastoma multiforme.

Yeung KY, Dickinson A, Donoghue JF, Polekhina G, White SJ, Grammatopoulos DK, McKenzie M, Johns TG, St John JC.

Acta Neuropathol Commun. 2014 Jan 2;2:1. doi: 10.1186/2051-5960-2-1.

23.

The regulation of mitochondrial DNA copy number in glioblastoma cells.

Dickinson A, Yeung KY, Donoghue J, Baker MJ, Kelly RD, McKenzie M, Johns TG, St John JC.

Cell Death Differ. 2013 Dec;20(12):1644-53. doi: 10.1038/cdd.2013.115. Epub 2013 Aug 30.

24.

Integrating external biological knowledge in the construction of regulatory networks from time-series expression data.

Lo K, Raftery AE, Dombek KM, Zhu J, Schadt EE, Bumgarner RE, Yeung KY.

BMC Syst Biol. 2012 Aug 16;6:101. doi: 10.1186/1752-0509-6-101.

25.

A Newtonian approach to extraordinarily strong negative refraction.

Yoon H, Yeung KY, Umansky V, Ham D.

Nature. 2012 Aug 2;488(7409):65-9. doi: 10.1038/nature11297.

PMID:
22859202
26.

Ultra-subwavelength two-dimensional plasmonic circuits.

Andress WF, Yoon H, Yeung KY, Qin L, West K, Pfeiffer L, Ham D.

Nano Lett. 2012 May 9;12(5):2272-7. doi: 10.1021/nl300046g. Epub 2012 Apr 18.

PMID:
22494364
27.

Predicting relapse prior to transplantation in chronic myeloid leukemia by integrating expert knowledge and expression data.

Yeung KY, Gooley TA, Zhang A, Raftery AE, Radich JP, Oehler VG.

Bioinformatics. 2012 Mar 15;28(6):823-30. doi: 10.1093/bioinformatics/bts059. Epub 2012 Jan 31.

28.

Fast Inference for the Latent Space Network Model Using a Case-Control Approximate Likelihood.

Raftery AE, Niu X, Hoff PD, Yeung KY.

J Comput Graph Stat. 2012;21(4):901-919. Epub 2012 Apr 4.

29.

Construction of regulatory networks using expression time-series data of a genotyped population.

Yeung KY, Dombek KM, Lo K, Mittler JE, Zhu J, Schadt EE, Bumgarner RE, Raftery AE.

Proc Natl Acad Sci U S A. 2011 Nov 29;108(48):19436-41. doi: 10.1073/pnas.1116442108. Epub 2011 Nov 14.

30.

An exploration of factors affecting Hong Kong ICU nurses in providing oral care.

Yeung KY, Chui YY.

J Clin Nurs. 2010 Nov;19(21-22):3063-72. doi: 10.1111/j.1365-2702.2010.03344.x.

PMID:
21040012
31.

The vanishing zero revisited: thresholds in the age of genomics.

Zarbl H, Gallo MA, Glick J, Yeung KY, Vouros P.

Chem Biol Interact. 2010 Mar 19;184(1-2):273-8. doi: 10.1016/j.cbi.2010.01.031. Epub 2010 Jan 28.

32.

The derivation of diagnostic markers of chronic myeloid leukemia progression from microarray data.

Oehler VG, Yeung KY, Choi YE, Bumgarner RE, Raftery AE, Radich JP.

Blood. 2009 Oct 8;114(15):3292-8. doi: 10.1182/blood-2009-03-212969. Epub 2009 Aug 4.

33.

Methods for the inference of biological pathways and networks.

Bumgarner RE, Yeung KY.

Methods Mol Biol. 2009;541:225-45. doi: 10.1007/978-1-59745-243-4_11. Review.

PMID:
19381545
34.

Iterative Bayesian Model Averaging: a method for the application of survival analysis to high-dimensional microarray data.

Annest A, Bumgarner RE, Raftery AE, Yeung KY.

BMC Bioinformatics. 2009 Feb 26;10:72. doi: 10.1186/1471-2105-10-72.

35.

MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis.

Chu VT, Gottardo R, Raftery AE, Bumgarner RE, Yeung KY.

Genome Biol. 2008;9(7):R118. doi: 10.1186/gb-2008-9-7-r118. Epub 2008 Jul 24.

36.

Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset.

Liu X, Sivaganesan S, Yeung KY, Guo J, Bumgarner RE, Medvedovic M.

Bioinformatics. 2006 Jul 15;22(14):1737-44. Epub 2006 May 18.

37.

Bayesian robust inference for differential gene expression in microarrays with multiple samples.

Gottardo R, Raftery AE, Yeung KY, Bumgarner RE.

Biometrics. 2006 Mar;62(1):10-8.

PMID:
16542223
38.

Donuts, scratches and blanks: robust model-based segmentation of microarray images.

Li Q, Fraley C, Bumgarner RE, Yeung KY, Raftery AE.

Bioinformatics. 2005 Jun 15;21(12):2875-82. Epub 2005 Apr 21.

PMID:
15845656
39.

Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data.

Yeung KY, Bumgarner RE, Raftery AE.

Bioinformatics. 2005 May 15;21(10):2394-402. Epub 2005 Feb 15.

PMID:
15713736
40.

Bcl-2 overexpression leads to increases in suppressor of cytokine signaling-3 expression in B cells and de novo follicular lymphoma.

Vanasse GJ, Winn RK, Rodov S, Zieske AW, Li JT, Tupper JC, Tang J, Raines EW, Peters MA, Yeung KY, Harlan JM.

Mol Cancer Res. 2004 Nov;2(11):620-31.

41.

From co-expression to co-regulation: how many microarray experiments do we need?

Yeung KY, Medvedovic M, Bumgarner RE.

Genome Biol. 2004;5(7):R48. Epub 2004 Jun 28.

42.

Bayesian mixture model based clustering of replicated microarray data.

Medvedovic M, Yeung KY, Bumgarner RE.

Bioinformatics. 2004 May 22;20(8):1222-32. Epub 2004 Feb 10.

PMID:
14871871
43.

Multiclass classification of microarray data with repeated measurements: application to cancer.

Yeung KY, Bumgarner RE.

Genome Biol. 2003;4(12):R83. Epub 2003 Nov 24. Erratum in: Genome Biol. 2005;6(13):405-405.4.

44.

Screening for mutations in a novel retinal-specific gene among Chinese patients with retinitis pigmentosa.

Xiaoli Z, Weiling F, Pang CP, Yeung KY.

Chin Med Sci J. 2002 Dec;17(4):225-30.

PMID:
12901510
45.

Clustering gene-expression data with repeated measurements.

Yeung KY, Medvedovic M, Bumgarner RE.

Genome Biol. 2003;4(5):R34. Epub 2003 Apr 25.

46.

[Screening for point mutations in rhodopsin gene among one hundred Chinese patients with retinitis pigmentosa].

Zhang X, Fu W, Pang CP, Yeung KY.

Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2002 Dec;19(6):463-6. Chinese.

PMID:
12476415
47.

[Mutation analysis of retinitis pigmentosa 1 gene in Chinese with retinitis pigmentosa].

Zhang X, Yeung KY, Pang CP, Fu W.

Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2002 Jun;19(3):194-7. Chinese.

PMID:
12048676
48.

Transcriptional analyses of Barrett's metaplasia and normal upper GI mucosae.

Barrett MT, Yeung KY, Ruzzo WL, Hsu L, Blount PL, Sullivan R, Zarbl H, Delrow J, Rabinovitch PS, Reid BJ.

Neoplasia. 2002 Mar-Apr;4(2):121-8.

49.

Molecular diagnostics for retinitis pigmentosa.

Yeung KY, Baum L, Chan WM, Lam DS, Kwok AK, Pang CP.

Clin Chim Acta. 2001 Nov;313(1-2):209-15.

PMID:
11694261
50.

Model-based clustering and data transformations for gene expression data.

Yeung KY, Fraley C, Murua A, Raftery AE, Ruzzo WL.

Bioinformatics. 2001 Oct;17(10):977-87.

PMID:
11673243

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