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Publications (since 1998)

 
 
| 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005  
2014
  • Xin Ma, Luo Xiao and Wing Hung Wong (2014)
    Learning regulatory programs by threshold SVD regression.
    Proceedings of the National Academy of Sciences, 111:15675–15680, doi: 10.1073/pnas.1417808111 [online]
  • Tsai C.-H., Wu T.-Y., Hsu S.-Y., Chu C.-C., Ku F.-J., Laio Y.-S., Chen C.-L., Wong W.-H., Chang, H.-C., Lee C.-Y. (2014)
    A 7.11mJ/Gb/query data-driven machine learning processor (D2MLP) for big data analysis and applications.
    IEEE Symposium on VLSI Circuits, Digest of Technical Papers, art. no. 6858422
  • Wing-Sze Lo, Elisabeth Gardiner, Zhiwen Xu, Ching-Fun Lau, Feng Wang, Jie J. Zhou, John D. Mendlein, Leslie A. Nangle, Kyle P. Chiang, Xiang-Lei Yang, Kin-Fai Au, Wing Hung Wong, Min Guo, Mingjie Zhang, and Paul Schimmel (2014)
    Human tRNA synthetase catalytic nulls with diverse functions.
    Science, July 2014: 345 (6194), 328-332. doi:10.1126/science.1252943 [online]
  • Arwen Meister, Chao Du, Ye Henry Li, Wing Hung Wong (2014)
    Modeling stochastic noise in gene regulatory systems.
    Quantitative Biology, March 2014, Volume 2, Issue 1, pp 1-29 [online]
  • Linxi Liu and Wing Hung Wong (2014)
    Multivariate Density Estimation Based on Adaptive Partitioning: Convergence Rate, Variable Selection and Spatial Adaptation.
    arXiv:1401.2597 [math.ST] [arxiv]
  • Kun Yang and Wing Hung Wong (2014)
    Discovering and Visualizing Hierarchy in the Data.
    arXiv:1403.4370 [stat.AP] [arxiv]
2013
  • Brady, J. J., Li M., Suthram S., Jiang H., Wong W. H., Blau H. M. (2013)
    Early role for IL-6 signalling during generation of induced pluripotent stem cells revealed by heterokaryon RNA-Seq.
    Nature Cell Biology, 15 (10): 1244-1252 [online]
  • Kin Fai Au, Vittorio Sebastiano, Pegah Tootoonchi Afshar, Jens Durruthy Durruthy, Lawrence Lee, Brian A. Williams, Harm van Bakel, Eric E. Schadt, Renee A. Reijo-Pera, Jason G. Underwood, and Wing Hung Wong (2013)
    Characterization of the human ESC transcriptome by hybrid sequencing.
    PNAS 2013, 110(50), E4821-E4830, doi:10.1073/pnas.1320101110 [online]
  • Luo Lu, Hui Jiang and Wing H. Wong (2013)
    Multivariate Density Estimation by Bayesian Sequential Partitioning.
    Journal of the American Statistical Association 2013, 108(504), 1402-1410 [free e-print] [online]
  • Nicholas A Johnson, Stephanie J. London, Isabelle Romieu, Wing H. Wong, Hua Tang (2013)
    Accurate construction of long range haplotype in unrelated individuals.
    Statistica Sinica 23 (2013), 1441-1461 [online]
  • Junhee Seok, Lu Tian and Wing H. Wong (2013)
    Density estimation on multivariate censored data with optional Polya tree.
    Biostatistics 2013, doi:10.1093/biostatistics/kxt025 [online]
  • Feng Z, Fang G, Korlach J, Clark T, Luong K, Zhang X, Wong W, Schadt E (2013)
    Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic.
    PLoS Comput Biol 2013, 9(3), doi:10.1371/journal.pcbi.1002935 [online]
  • Arwen Meister, Ye Henry Li, Bokyung Choi, and Wing Hung Wong (2013)
    Learning a Nonlinear Dynamical System Model of Gene Regulation: A Perturbed Steady-State Approach
    Annals of Applied Statistics 2013, 7(3), 1311-1333. doi:10.1214/13-AOAS645 [online]
  • Bokyung Choi, Ernesto Bosch, Benjamin M. Lannon, Marie-Claude Leveille, Wing H. Wong, Arthur Leader, Antonio Pellicer, Alan S. Penzias, Mylene W.M. Yao (2013)
    Personalized prediction of first-cycle in vitro fertilization success
    Fertility and Sterility 25 March 2013, doi:10.1016/j.fertnstert.2013.02.016 [online]
  • Meng How Tan, Kin Fai Au, Denise E Leong, Kira Foygel, Wing H Wong and Mylene WM Yao (2013)
    An Oct4-Sall4-Nanog network controls developmental progression in the pre-implantation mouse embryo
    Molecular Systems Biology 9(632) doi:10.1038/msb.2012.65 [online]
2012
  • Ma L, Wong WH, and Owen AB. (2012)
    A sparse transmission disequilibrium test for haplotypes based on Bradley-Terry graphs.
    Human Heredity. Vol. 73, No. 1, 52-61, doi: 10.1159/000335937 [online]
  • Kevin A. Peterson, Yuichi Nishi, Wenxiu Ma, Anastasia Vedenko, Leila Shokri, Xiaoxiao Zhang, Matthew McFarlane, José-Manuel Baizabal, Jan Philipp Junker, Alexander van Oudenaarden, Tarjei Mikkelsen, Bradley E. Bernstein, Timothy L. Bailey, Martha L. Bulyk, Wing H. Wong and Andrew P. McMahon (2012)
    Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning
    Genes & Dev. 2012. 26:2802-2816, doi:10.1101/gad.207142.112 [online]
  • Eric E. Schadt, Onureena Banerjee, Gang Fang, Zhixing Feng, Wing H. Wong, Xuegong Zhang, Andrey Kislyuk, Tyson A. Clark, Khai Luong, Alona Keren-Paz, Andrew Chess, Vipin Kumar, Alice Chen-Plotkin, Neal Sondheimer, Jonas Korlach and Andrew Kasarskis (2012)
    Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases
    Genome Research Published in Advance October 23, 2012, doi:10.1101/gr.136739.111 [online, advance access]
  • Kin Fai Au, Jason G. Underwood, Lawrence Lee, Wing Hung Wong (2012)
    Improving PacBio Long Read Accuracy by Short Read Alignment
    PLoS ONE 2012. 7(10): e46679. doi:10.1371/journal.pone.0046679 [online, advance access]
  • Meng How Tan, Kin Fai Au, Arielle Yablonovitch, Andrea Wills, Jason Chuang, Julie Baker, Wing Hung Wong and Jin Billy Li (2012)
    RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development
    Genome Research 2012. doi:10.1101/gr.141424.112 [online, advance access]
  • Joo-Seop Park, Wenxiu Ma, Lori L. O'Brien, Eunah Chung, Jin-Jin Guo, Jr-Gang Cheng, M. Todd Valerius, Jill A. McMahon, Wing Hung Wong, Andrew P. McMahon (2012)
    Six2 and Wnt Regulate Self-Renewal and Commitment of Nephron Progenitors through Shared Gene Regulatory Networks
    Developmental Cell 2012. Volume 23, Issue 3, 11 September 2012, Pages 637–651, doi:10.1016/j.devcel.2012.07.008 [online]
  • John C. Mu, Hui Jiang, Amirhossein Kiani, Marghoob Mohiyuddin, Narges Bani Asadi and Wing H. Wong (2012)
    Fast and Accurate Read Alignment for Resequencing
    Bioinformatics 2012, 28 (18): 2366-2373, doi:10.1093/bioinformatics/bts450 [online]
  • David Hiller and Wing Hung Wong (2012)
    Simultaneous isoform discovery and quantification from RNA-seq.
    Stat Biosci. 2012, doi:10.1007/s12561-012-9069-2 [online]
  • Lannon BM, Choi B, Hacker MR, Dodge LE, Malizia BA, Barrett CB, Wong WH, Yao MW, Penzias AS (2012)
    Predicting personalized multiple birth risks after in vitro fertilization-double embryo transfer.
    Fertil Steril. July 2012, Volume 98, Issue 1, Pages 69–76, doi:10.1016/j.fertnstert.2012.04.011 [online]
  • Yichang Jia, John C. Mu, Susan L. Ackerman (2012)
    Mutation of a U2 snRNA Gene Causes Global Disruption of Alternative Splicing and Neurodegeneration
    Cell 2012, Vol. 148, Issue 1, 296-308. doi: 10.1016/j.cell.2011.11.057 [online]
2011
  • Li Ma and Wing Hung Wong (2011)
    Coupling optional Pólya trees and the two sample problem.
    Journal of the American Statistical Association December 1, 2011, 106(496): 1553-1565. doi:10.1198/jasa.2011.tm10003. [online]
  • Julia Salzman, Hui Jiang and Wing Hung Wong (2011)
    Statistical Modeling of RNA-Seq Data.
    Statistical Science 2011, Vol. 26, No. 1, 62-83. doi: 10.1214/10-STS343. [online] [arxiv]
  • Xu W, Seok J, Mindrinos MN, Schweitzer AC, Jiang H, Wilhelmy J, Clark TA, Kapur K, Xing Y, Faham M, Storey JD, Moldawer LL, Maier RV, Tompkins RG, Wong WH, Davis RW, Xiao W; Inflammation and Host Response to Injury Large-Scale Collaborative Research Program (2011)
    Human transcriptome array for high-throughput clinical studies.
    Proc. Natl. Acad. Sci. USA 2011 Mar 1;108(9):3707-12. Epub 2011 Feb 11. PMID: 21317363. doi: 10.1073/pnas.1019753108. [online]
  • Wenxiu Ma and Wing Hung Wong (2011)
    The Analysis of ChIP-Seq Data.
    Methods in Enzymology, Volume 497, 51-73. doi:10.1016/B978-0-12-385075-1.00003-2. [online]
  • Baiyu Zhou and Wing Hung Wong (2011)
    A Bootstrap-based Non-parametric ANOVA Method with Applications to Factorial Microarray Data.
    Statistica Sinica, 21:495-514. [preprint]
  • Yuqiong Pan, Zhengqing Ouyang, Wing Hung Wong, Julie C. Baker (2011)
    A New FACS Approach Isolates hESC Derived Endoderm Using Transcription Factors.
    PLoS ONE 6(3): e17536. doi:10.1371/journal.pone.0017536. [online]
2010
  • Martin A. Tanner and Wing H. Wong (2010)
    From EM to Data Augmentation: The Emergence of MCMC Bayesian Computation in the 1980s.
    Statistical Science 2010, Vol. 25, No. 4, 506–516. doi: 10.1214/10-STS341 [arxiv]
  • Hong Yang, Xi Chen and Wing Hung Wong (2010)
    Completely phased genome sequencing through chromosome sorting.
    Proc. Natl. Acad. Sci. USA, January 4, 2011, vol. 108 no. 1, 12-17; published online before print December 15, 2010, doi: 10.1073/pnas.1016725108. [online]
  • Sun Y, Fan XY, Cao DM, Tang W, He K, Zhu JY, He JX, Bai MY, Zhu S, Oh E, Patil S, Kim TW, Ji H, Wong WH, Rhee SY, Wang ZY (2010)
    Integration of brassinosteroid signal transduction with the transcription network for plant growth regulation in Arabidopsis.
    Dev Cell, (19):765-77. doi:10.1016/j.devcel.2010.10.010. [online]
  • Banerjee P, Choi B, Shahine LK, Jun SH, O'Leary K, Lathi RB, Westphal LM, Wong WH, Yao MW (2010)
    Deep phenotyping to predict live birth outcomes in in vitro fertilization.
    Proc Natl Acad Sci U S A. 2010 Aug 3;107(31):13570-5. Epub 2010 Jul 19. doi: 10.1073/pnas.1002296107. [online]
  • Narges Bani Asadi, Christopher Fletcher, Greg Gibeling, Eric N. Glass, Karen Sachs, Daniel Burke, Zoey Zhou, John Wawrzynek, Wing H. Wong, Garry P. Nolan (2010)
    ParaLearn: A Massively Parallel, Scalable System for Learning Interaction Networks on FPGAs.
    Best Student Paper Award, Proceedings of 24th International Conference on SuperComputing, Tsukuba, Japan, 2010. [online] [preprint]
  • Talk on RNA-seq Analysis, presented by Wing H. Wong
    at the Joint Statistical Meetings on August 3, 2010 in Vancouver, Canada. [slides]
  • Hui Jiang, Fan Wang, Nigel P. Dyer and Wing Hung Wong (2010)
    CisGenome Browser: A flexible tool for genomic data visualization.
    Bioinformatics (2010) 26 (14):1781-1782. doi:10.1093/bioinformatics/btq286. [online] [software]
  • Jun Li, Hui Jiang and Wing Hung Wong (2010)
    Modeling non-uniformity in short-read rates in RNA-Seq data.
    Genome Biology 2010, 11:R50; doi:10.1186/gb-2010-11-5-r50. [online]
  • Baiyu Zhou, Weihong Xu, David Herndon, Ronald Tompkins, Ronald Davis, Wenzhong Xiaob, Wing Hung Wong, and Inflammation and Host Response to Injury Program (2010)
    Analysis of factorial time-course microarrays with application to a clinical study of burn injury.
    Proc. Natl. Acad. Sci. USA, 2010 107 (22) 9923-9928. doi: 10.1073/pnas.1002757107. [online]
  • Eunice Y. Lee, Hongkai Ji, Zhengqing Ouyang, Baiyu Zhou, Wenxiu Ma, Steven A. Vokes, Andrew P. McMahon, Wing H. Wong, and Matthew P. Scott (2010)
    Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis.
    Proc. Natl. Acad. Sci. USA, 2010 107 (21) 9736-9741; doi:10.1073/pnas.1004602107. [online]
  • Li Ma, Themistocles L. Assimes, Narges B. Asadi, Carlos Iribarren, Thomas Quertermous, Wing H. Wong (2010)
    An “almost exhaustive" search-based sequential permutation method for detecting epistasis in disease association studies.
    Genetic Epidemiology, Volume 34, Issue 5, pages 434–443, July 2010. doi: 10.1002/gepi.20496.
  • Wing Hung Wong and Li Ma (2010)
    Optional Polya Tree and Bayesian Inference.
    Annals of Statistics, 38: 1433-1459. [online]
  • Kin F. Au, Hui Jiang, Lan Ling, Yi Xing, Wing H. Wong (2010)
    Detection of splice junctions from paired-end RNA-seq data by SpliceMap.
    Nucleic Acids Res. 2010 38 (14): 4570-4578. doi:10.1093/nar/gkq211. [online]
  • Jun Cai, Dan Xie, Zhewen Fan, Hiram Chipperfield, John Marden, Wing H. Wong, Sheng Zhong (2010)
    Modeling Co-Expression across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem Cells.
    PLoS Comput Biol, 6(3): e1000707; doi:10.1371/journal.pcbi.1000707. [online]
2009
  • Zhengqing Ouyang, Qing Zhou and Wing Hung Wong (2009)
    ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells.
    Proc. Natl. Acad. Sci. USA, 106:21521-21526; doi:10.1073/pnas.0904863106. [online]
  • David Hiller, Hui Jiang, Weihong Xu and Wing Hung Wong (2009)
    Identifiability of isoform deconvolution from junction arrays and RNA-Seq.
    Bioinformatics, doi:10.1093/bioinformatics/btp544. [online] [preprint]
  • Qing Zhou and Wing Hung Wong (2009)
    Energy landscape of a spin-glass model: Exploration and characterization.
    Physical Review E, Volume 79, Issue 5; doi: 10.1103/PhysRevE.79.051117. [online]
  • Lan Lin, Song Liu, Heather Brockway, Junhee Seok, Peng Jiang, Wing Hung Wong and Yi Xing (2009)
    Using high-density exon arrays to profile gene expression in closely related species.
    Nucleic Acids Research, doi:10.1093/nar/gkp420. [online]
  • Hui Jiang and Wing Hung Wong (2009)
    Statistical Inferences for Isoform Expression in RNA-Seq.
    Bioinformatics 2009; doi:10.1093/bioinformatics/btp113. [online] [preprint]
  • Yuichi Nishi, Hongkai Ji, Wing H Wong, Andrew P. McMahon and Steven A. Vokes (2009)
    Modeling the spatio-temporal network that drives patterning in the vertebrate central nervous system.
    BBA - Gene Regulatory Mechanisms. 1789: 299-305. [online]
2008
  • Karen Kapur, Hui Jiang, Yi Xing and Wing Hung Wong (2008)
    Cross-hybridization modeling on Affymetrix exon arrays.
    Bioinformatics 2008, 24(24):2887-2893; doi:10.1093/bioinformatics/btn571 [online]
  • Qing Zhou and Wing Hung Wong (2008)
    Reconstructing the energy landscape of a distribution from Monte Carlo samples.
    The Annals of Applied Statistics 2008, Vol. 2, No. 4, 1307?331. doi: 10.1214/08-AOAS196. [online]
  • Hongwu Zheng, Haoqiang Ying, Haiyan Yan, Alec C Kimmelman, David J Hiller, An-Jou Chen, Samuel R Perry, Giovanni Tonon, Gerald C Chu, Zhihu Ding, Jayne M Stommel, Katherine L Dunn, Ruprecht Wiedemeyer, Mingjian J You, Cameron Brennan, Alan Y Wang, Keith L Ligon, Wing H Wong, Lynda Chin, Ronald A Depinho (2008)
    p53 and Pten control neural and glioma stem/progenitor cell renewal and differentiation.
    Nature. Vol. 455, No. 7216., pp. 1129-1133. doi: 10.1038/nature07443. [online]
  • Narges Bani Asadi, Teresa Meng and Wing Hung Wong (2008)
    Reconfigurable Computing for Learning Bayesian Networks.
    International Symposium on Field Programmable Gate Arrays.
    Proceedings of the 16th international ACM/SIGDA symposium on Field programmable gate arrays
    . Monterey, California, USA, Pages 203-211. [online]
  • Hongkai Ji, Hui Jiang, Wenxiu Ma, David S Johnson, Richard M Myers, Wing H Wong (2008)
    An integrated software system for analyzing ChIP-chip and ChIP-seq data.
    Nature Biotechnology. 26, 1293-1300, doi:10.1038/nbt.1505.
    [online]
    [software] [PubMed Central]
  • Steven A. Vokes, Hongkai Ji, Wing H. Wong, and Andrew P. McMahon (2008)
    A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb.
    Genes Dev. 2008 22: 2651-2663. [Preprint]
  • Byron Ellis and Wing Hung Wong (2008)
    Learning Causal Bayesian Network Structures From Experimental Data.
    Journal of the American Statistical Association. Volume 103, Number 482, June 2008, pp. 778-789(12). [Preprint] [Data] [Software]
  • Hui Jiang and Wing Hung Wong (2008)
    SeqMap : mapping massive amount of oligonucleotides to the genome.
    Bioinformatics, , 24(20):2395-2396. doi: 10.1093/bioinformatics/btn429. [online]
    [software]
  • Jun SH, Choi B, Shahine L, Westphal LM, Behr B, Reijo Pera RA, Wong WH, Yao MWM (2008)
    Defining Human Embryo Phenotypes by Cohort-Specific Prognostic Factors.
    PLoS ONE 3(7): e2562. doi:10.1371/journal.pone.0002562. [online]
  • Eric Chiao, Menashe Elazar, Yi Xing, Anming Xiong, Muriel Kmet, Maria T. Millan, Jeffrey S. Glenn, Wing H. Wong, Julie Baker (2008)
    Isolation and Transcriptional Profiling of Purified Hepatic Cells Derived from Human Embryonic Stem Cells.
    Stem Cells. 2008 Jun 5; doi:10.1634/stemcells.2007- 0964. [online]
  • Yi Xing, Peter Stoilov, Karen Kapur, Areum Han, Hui Jiang, Shihao Shen, Douglas L. Black, Wing Hung Wong (2008)
    MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays.
    RNA. 14: 1470-1479, doi:10.1261/rna.1070208. [online] [dataset] [software]
2007
  • Gopi Goswami, Jun S. Liu, Wing H. Wong (2007)
    Evolutionary Monte Carlo Methods for Clustering.
    Journal of Computational & Graphical Statistics, Vol. 16, No. 4, pp.855-876. [preprint]
  • Qing Zhou, Hiram Chipperfield, Douglas A Melton, Wing Hung Wong (2007)
    A gene regulatory network in mouse embryonic stem cells.
    Proc. Natl. Acad. Sci. USA, 104:16438-16443. doi_10.1073_pnas.0701014104. [online]
  • Qing Zhou and Wing Hung Wong (2007)
    Coupling hidden Markov models for the discovery of cis-regulatory modules in multiple species.
    Annals of Applied Statistics, 1:36-65. DOI:10.1214/07-AOAS103. [preprint]
    [software]
  • Steven A. Vokes, Hongkai Ji, Scott McCuine, Toyoaki Tenzen, Shane Giles, Sheng Zhong, William J. R. Longabaugh, Eric H. Davidson, Wing H. Wong and Andrew P. McMahon (2007)
    Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning.
    Development, 134, 1977-1989. doi: 10.1242/dev.001966. [online]
    [in the news]
  • Karen Kapur, Yi Xing, Zhengqing Ouyang and Wing Hung Wong (2007)
    Exon array assessment of gene expression.
    Genome Biology, 2007, 8:R82. doi:10.1186/gb-2007-8-5-r82. [online]
  • Yi Xing, Zhengqing Ouyang, Karen Kapur, Matthew P. Scott, Wing Hung Wong (2007)
    Assessing the Conservation of Mammalian Gene Expression Using High-density Exon Arrays.
    Molecular Biology and Evolution, 2007 24(6):1283-1285; doi:10.1093/molbev/msm061. [online]
    [Supplementary Data]
  • Ji-Hye Paik, Ramya Kollipara, Gerald Chu, Hongkai Ji, Yonghong Xiao, Zhihu Ding, Lili Miao, Zuzana Tothova, James W. Horner, Daniel R. Carrasco, Shan Jiang,  D. Gary Gilliland, Lynda Chin, Wing H. Wong, Diego H. Castrillon, and Ronald A. DePinho (2007)
    FoxOs Are Lineage-Restricted Redundant Tumor Suppressors and Regulate Endothelial Cell Homeostasis.
    Cell, Vol 128, 309?23. DOI 10.1016/j.cell.2006.12.029 . [online]
2006
  • Xuegong Zhang, Xin Lu, Qian Shi, Xiu-qin Xu, Hon-chiu E Leung, Lyndsay N Harris, James D Iglehart, Alexander Miron, Jun S Liu, and Wing H Wong (2006)
    Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data.
    BMC Bioinformatics, 2006; 7: 197. Published online 2006 April 10. doi: 10.1186/1471-2105-7-197. [online]
  • Yi Xing, Karen Kapur, Wing Hung Wong (2006)
    Probe Selection and Expression Index Computation of Affymetrix Exon Arrays.
    PLos ONE, 1(1): e88. doi:10.1371/journal.pone.0000088. [online] [pdf]
  • Hongkai Ji, Steven A. Vokes, Wing Hung Wong (2006)
    A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors.
    Nucleic Acids Research, doi:10.1093/nar/gkl803. [online]
  • Hongkai Ji and Wing Hung Wong (2006)
    Computational Biology: Toward Deciphering Gene Regulatory Information in Mammalian Genomes.
    Biometrics, 62:645-663. [preprint] [online]
  • Ovidiu Lipan and Wing H. Wong (2006)
    Is the future biology Shakespearean or Newtonian?
    Mol. BioSyst., 2006, 2, 411?16. [html] [pdf]
  • S.C. Kou, Jason Oh and Wing Hung Wong (2006)
    A study of density of states and ground states in hydrophobic-hydrophilic protein folding models by equi-energy sampling.
    The Journal of Chemical Physics, 124, 244903. DOI: 10.1063/1.2208607. [pdf]
  • Beroukhim R, Lin M, Park Y, Hao K, Zhao X, Garraway LA, Fox E, Hochberg EP, Mellinghoff IK, Hofer MD, Descazeaud A, Rubin M, Meyerson M, Wong WH, Sellers WR, Li C (2006)
    Inferring loss-of-heterozygosity from tumor-only samples using high-density oligonucleotide SNP arrays.
    PLoS Comput Biol, 2(5): e41, DOI: 10.1371/journal.pcbi.0020041.eor. [pdf]
  • Sam Kou, Qing Zhou and Wing Hung Wong (2006)
    Rejoinder to the discussions of "Equi-energy sampler with applications in statistical inference and statistical mechanics".
    Annals of Statistics, 34: 1646-1652.
  • Sam Kou, Qing Zhou and Wing Hung Wong (2006)
    Equi-energy sampler with applications in statistical inference and statistical mechanics.
    Annals of Statistics, 34: 1581-1619. [preprint]
  • Ryung S Kim, Hongkai Ji and Wing H Wong (2006)
    An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse..
    BMC Bioinformatics 2006, 7:44. doi:10.1186/1741-2105-7-44. [pdf]
  • Wing Hung Wong (2006)
    Estimation of the loss of an estimate.
    In Frontiers of Statistics (Editors: Jianqing Fan, Hira L. Koul), pages
    491-506. Imperial College Press, London. [pdf]

2005

  • Sijin Liu, Xiaotong Shen, and Wing Hung Wong (2005)
    Computational Developments of ø-learning.  
    In Proceedings of the Fifth SIAM International Conference on Data Mining, pages 1-11. Volume edited by Hillol Kargupta, Chandrika Kamath, Jaideep Srivastava, Arnold Goodman. Published by Society for Industrial and Applied Mathematics, Philadelphia. [download]
  • Xiaoman Li, Sheng Zhong and Wing H. Wong (2005)
    Reliable prediction of transcription factor binding sites by phylogenetic verification.
    PNAS, volume 102: 16945-16950. DOI/10.1073/PNAS.0504201102. [pdf]
  • Hongkai Ji and Wing Hung Wong (2005)
    TileMap: create chromosomal map of tiling array hybridizations.
    Bioinformatics, 21: 3629-3636 [pdf]
  • David S. Johnson, Qing Zhou, Kasumi Yagi, Nori Satoh, Wing Wong, and Arend Sidow (2005)
    De novo discovery of a tissue-specific gene regulatory module in a chordate.
    Genome Research, Advanced Online: September 16, 2005, 10.1101/gr.4062605 [pdf]
  • Xiaoman Li and Wing Hung Wong (2005)
    Sampling motifs on phylogenetic trees.
    Proc. Natl. Acad. Sci. USA, vol. 102, no. 27, 9481-9486. [pdf] [software]
  • Pengyu Hong, Sheng Zhong, Wing H. Wong (2005)
    UBIC2 - Towards Ubiquitous Bio-Information Computing: Data Protocols, Middleware, and Web Services for Heterogeneous Biological Information Integration and Retrieval.
    International Journal of Software Engineering and Knowledge Engineering.
    Special Issue: Software Engineering and Bioinformatics. 15(3) 475-485. [abstract] [pdf as tech report] [software]
  • Russell K. Dorer, Sheng Zhong, John A. Tallarico, Wing H. Wong, Timothy J. Mitchison, and Andrew W. Murray. (2005)
    A Small Molecule Inhibitor of Mps1 Blocks the Spindle Checkpoint Response to a Lack of Tension on Mitotic Chromosome.
    Current Biology, 15(11): 1070-1076 [abstract] [pdf]
  • Jan-Hermen Dannenberg, Gregory David, Sheng Zhong, Jaco van der Torre, Wing H. Wong, Ronald A. DePinho (2005)
    mSin3A co-repressor regulates diverse transcriptional networks governing normal and neoplastic growth and survival.
    Genes & Development, 19: 1581-1595. [abstract] [pdf]
  • Pengyu Hong, X. Shirley Liu, Qing Zhou, Xin Lu, Jun S. Liu and Wing H. Wong (2005).
    A boosting approach for motif modeling using ChIP-chip data.
    Bioinformatics, 21(11): 2636-2643 [abstract] [pdf]
  • Nabeel Bardessy, Minjung Kim, Jin Xu, Ryung-Suk Kim, Qiong Shen, Marcus W. Bosenberg, Wing Hung Wong and Lynda Chin (2005)
    Role of Epidermal Growth Factor Receptor Signaling in RAS-driven melanoma.
    Molecular and Cellular Biology, 25: 4176-4188 [abstract] [pdf]
  • Ovidiu Lipan and Wing Hung Wong (2005)
    The use of oscillatory signals in the study of genetic networks.
    Proc. Natl. Acad. Sci. USA, 102: 7063-7068. doi/10.1073/PNAS.0403790102 [abstract] [pdf]
  • George C. Tseng and Wing H. Wong. (2005)
    Tight Clustering: A Resampling-based Approach for Identifying Stable and Tight Patterns in Data.
    Biometrics 61(1):10-16(7). [Tech Report] [Software]
  • Pengyu Hong and Wing H Wong (2005)
    GeneNotes - A novel information management software for biologists.
    BMC Bioinformatics 6:20 doi:10.1186/1471-2105-6-20 [pdf]
  • Igor Leykin, Ke Hao, Junsheng Cheng, Nicole Meyer, Martin R Pollak, Richard JH Smith, Wing Hung Wong, Carsten Rosenow, Cheng Li
    Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data

    BMC Genetics 2005, 6:7 [abstract] [pdf]
  • Xianghong Jasmine Zhou, Ming-Chih J Kao, Haiyan Huang, Angela Wong, Juan Nunez-Iglesias, Michael Primig, Oscar M Aparicio, Caleb E Finch, Todd E Morgan, Wing Hung Wong (2005)
    Functional Annotation and Network Reconstruction through Cross-platform Integration of Microarray Data.
    Nature Biotechnology. Nature Biotechnology 23, 238 - 243. [pdf]

2004

  • Ke Hao, Cheng Li, Carsten Rosenow, Wing Hung Wong (2004)
    Estimation of Genotype Error Rate Using Samples with Pedigree Information -- An application on GeneChip Mapping 10K array.
    Genomics. 84(4):623-630. [pdf]
  • Zhong S, Storch F, Lipan O, Kao MJ, Weitz C, Wong WH (2004)
    GoSurfer: a graphical interactive tool for comparative analysis of large gene sets in Gene Ontology space.
    Applied Bioinformatics 3(4): 1-5. [Software]
  • Ke Hao, Cheng Li, Carsten Rosenow, Wing H. Wong (2004)
    Detect and Adjust for Population Stratification in Population-Based Association Study using Genomic Control Markers -- An application of Affymetrix Genechip Human Mapping 10K array.
    European Journal of Human Genetics. 12:1001-1006. [pdf]
  • Qing Zhou and Wing Hung Wong (2004)
    CisModule: De Novo discovery of cis-regulatory modules by hierarchical mixture modeling.
    Proc. Natl. Acad. Sci. 101(33): 12114-12119 [pdf]
  • Ming Lin, Lee-Jen Wei, William R. Sellers, Marshall Lieberfarb, Wing Hung Wong, and Cheng Li (2004).
    dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data.
    Bioinformatics 20: 1233-1240 [Abstract]
  • Cai L, Huang H, Blackshaw S, Liu JS, Cepko C, Wong WH (2004).
    Clusteri
    ng analysis of SAGE data using a Poisson approach.
    Genome Biology. 5:R51 [Software][website]
  • Seth Blackshaw, Sanjiv Harpavat, Jeff Trimarchi, Li Cai, Haiyan Huang, Winston P. Kuo, Griffin Weber, Kyungjoon Lee, Rebecca E. Fraioli, Seo-Hee Cho, Rachel Yung, Elizabeth Asch, Lucila Ohno-Machado, Wing H. Wong, Constance L. Cepko (2004).
    Genomic Analysis of Mouse Retinal Development.
    PloS Biology 2(9): e247 [website]
  • Zhong S, Tian L, Li C, Storch FK and Wong WH (2004).
    Comparative Analysis of Gene Sets in the Gene Ontology Space under the Multiple Hypothesis Testing Framework.
    Proc. IEEE Comp Systems Bioinformatics. 2004:425-435 [Software] [pdf] [Erratum]
  • Yan Cui, Mi Zhou, Wing Hung Wong (2004)
    Integrated Analysis of Microarray Data and Gene Function Information.
    OMICS 8: 106-117 [Software][pdf]
  • Zhong S, Storch FK, Lipan O, Kao MJ, Weitz C, Wong WH (2004).
    GoSurfer: A graphical interactive tool for comparative analysis of large gene sets in Gene Ontology space.
    Appl. Bioinformatics. Accepted. [Software]
  • RM Bachoo, RS Kim, KL Ligon, EA Maher, C Brennan, N Billings, S Chan, C Li, DH Rowitch, WH Wong and RA DePinho (2004)
    Molecular Diversity of Astrocytes: A Global Prospective on Their Physiology With Links to Common Neurological Disorders.
    Proc. Natl. Acad. Sci. 101(22):8384-8389. [pdf]
  • Huang H, Kao MC, Zhou X, Liu JS, Wong WH (2004).
    Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification.
    Journal of Comput Biol 11(1):1-14.
    [Abstract]
2003
  • O'Hagan RC, Brennan CW, Strahs A, Zhang X, Kannan K, Donovan M, Cauwels C, Sharpless NE, Wong WH, Chin L. (2003)
    Array Comparative Genome Hybridization for Tumor Classification and Gene Discovery in Mouse Models of Malignant Melanoma.
    Cancer Res. 63(17):5352-5356.
    [pdf]
  • FE Davies, AM Dring, C Li, AC Rawstron, MA Shammas, SM O'Connor, JA Fenton, T Hideshima, D Chauhan, IT Tai, E Robinson, D Auclair, K Rees, D Gonzalez, AJ Ashcroft, R Dasgupta, C Mitsiades, N Mitsiades, LB Chen, WH Wong, NC Munshi, GJ Morgan and KC Anderson (2003)
    Insights into the multistep transformation of MGUS to myeloma using microarray expression analysis.
    Blood. 102(13):4504-11. [Abstract][pdf]
  • Xiaotong Shen, George C. Tseng, Xuegong Zhang, Wing Hung Wong (2003)
    On Psi-learning.
    Journal of American Statistical Association. 98:724-734. [pdf]
  • Sheng Zhong, Cheng Li and Wing Hung Wong (2003)
    ChipInfo: Software for Extracting Gene Annotation and Gene Ontology Information for Microarray Analysis.
    Nucleic Acids Research. Vol. 31, 3483-3486. [Abstract][software][pdf]
  • Chauhan D, Li G, Auclair D, Hideshima T, Richardson P, Podar K, Mitsiades N, Mitsiades C, Li C, Kim RS, Munshi N, Chen LB, Wong W and Anderson KC (2003)
    Identification of genes regulated by 2-methoxyestradiol (2ME2) in multiple myeloma cells using oligonucleotide arrays.
    Blood. 101: 3606-3614 [Abstract][pdf]
  • Cheng Li, George C. Tseng and Wing Hung Wong (2003)
    Model-based analysis of oligonucleotide arrays and issues in cDNA microarray analysis. In Statistical analysis of gene expression microarray data. Edited by Terry Speed.
    CRC Press. 1-34. [Amazon; consists of 3 previous papers: 1, 2, 3]
  • Cheng Li and Wing Hung Wong (2003)
    DNA-Chip Analyzer (dChip). In The analysis of gene expression data: methods and software. Edited by G Parmigiani, ES Garrett, R Irizarry and SL Zeger.
    Springer, NY. 120-141. [website][Color figures][Amazon][software]
  • Zhou X, Krueger JG, Kao MJ, Lee E, Du F, Menter A, Wong WH, Bowcock AM (2003)
    Novel mechanisms of T-cell and dendritic cell activation revealed by profiling of psoriasis on the 63,100-element oligonucleotide array.
    Physiological Genomics 13, 69-78
    [pdf][Abstract]
2002
  • Stephen M. Stigler, Wing Hung Wong and Daming Xu (Editors) (2002)
    R.R. Bahadur's Lectures on the Theory of Esti
    mation.
    [Cover, Preface, Table of Contents] [Read this book]
  • Zhou X, Kao MJ and Wong WH (2002)
    Transitive Functional Annotation By Shortest Path Analysis of Gene Expression Data.
    Proc Natl Acad Sci USA 99, 12783-12788
    [pdf][Abstract][Web supplement][Commentary in PNAS]
  • Storch K, Lipan O, Leykin I, Viswanathan N, Davis FC, Wong WH and Weitz CJ. (2002)
    Extensive and divergent circadian gene expression in liver and heart
    Nature. 417, 78-83. [pdf][Abstract][In news][in news 2]
  • Block-Alper L, Webster P, Zhou X, Supekov?L, Wong WH, Schultz PG and Meyer DI (2002)
    IN02, A Positive Regulator of Lipid Biosynthesis, Is Essential for the Formation of Inducible Membranes in Yeast.
    Mol. Biol. Cell 13: 40-51. [Abstract] [pdf]
  • Cui Y, Wong WH, Bornberg-Bauer E. and Chan HS. (2002)
    Recombinatoric Exploration of Novel Folded Structures: A Heteropolymer-Based Model of Protein Evolutionary Landscapes.
    Proc. Natl. Acad. Sci. USA. 99, 809-814.
    [Abstract][pdf]
2001
  • Eric E. Schadt, Cheng Li, Byron Ellis and Wing H. Wong (2001)
    Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data.
    Journal of Cellular Biochemistry. Supplement 37, 120-125 [Abstract][In news][pdf]
  • Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark EJ, Lander ES, Wong W, Johnson BE, Golub TR, Sugarbaker DJ and Meyerson M (2001)
    Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses.
    Proc. Natl. Acad. Sci. USA, Vol. 98, 13790-13795 [Abstract][supplement][pdf]
  • Cheng Li and Wing Hung Wong (2001b)
    Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application.
    Genome Biology 2(8): research0032.1-0032.11 [Abstract][pdf]
  • George C. Tseng, Min-Kyu Oh, Lars Rohlin, James C. Liao and Wing Hung Wong (2001)
    Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variation and assessment of gene effects.
    Nucleic Acids Research, Vol 29, No. 12. 2549-2557 [Abstract][Supplement][software][pdf]
  • Liang, F. and Wong, W.H. (2001)
    Evolutionary Monte Carlo for Protein Folding simulations.
    Journal of Chemical Physics, 115, 3374-3380 [pdf]
  • Hakak Y, Walker JR, Li C, Wong WH, Davis KL, Buxbaum JD, Haroutunian V and Fienberg AA (2001)
    Genome-wide expression analysis reveals dysregulation of myelination-related genes in chronic schizophrenia.
    Proc. Natl. Acad. Sci. Vol. 98, 4746-4751. [Abstract][In news][pdf]
  • Cheng Li and Wing Hung Wong (2001a)
    Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection.
    Proc. Natl. Acad. Sci. Vol. 98, 31-36. [Abstract][Video presentation][pdf]
  • Jun S. Liu, Faming Liang and Wing Hung Wong (2001)
    A theory for Dynamic Weighting in Monte Carlo Computation.
    J. Amer. Statist. Assoc. Vol. 96, No.454, 561-573 [pdf]
  • Faming Liang and Wing Hung Wong (2001)
    Real Parameters Evolutionary Monte Carlo with Applications to Bayesian Mixture Models.
    J. Amer. Statist. Assoc. Vol. 96, No.454, 653-666 [pdf]
  • Liang, F., Truong, Y.K. and Wong, W.H. (2001)
    Automatic Bayesian model averaging for linear regression and applications in Bayesian curve fitting.
    Statistica Sinica, 11, 1005-1029.
    [Abstract][pdf]
2000
  • Eric E. Schadt, Cheng Li, Cheng Su, Wing H. Wong (2000)
    Analyzing high-density oligonucleotide gene expression array data.
    Journal of Cellular Biochemistry. 80, 192-202.
    [Abstract][pdf]
  • Cui Y. and Wong, W.H (2000)
    Multiple sequence information provides protection against mis-specified potential energy function.
    Physical Review Letters, Vol. 85, No.24, 5242-5245 [Abstract][pdf]
  • Irizarry K, Kustanovich V, Li C, Brown N, Nelson S, Wong W and Lee CJ (2000)
    Genome-wide analysis of single-nucleotide polymorphisms in human expressed sequences.
    Nature Genetics. Vol. 26, 233-236 [Abstract][database][pdf]
  • Wing Hung Wong (2000)
    Computational Molecular Biology.
    J. Amer. Statist. Assoc. Vol. 95, No.449, 322-326 [pdf]
  • Yan Cui, Run Sheng Chen and Wing Hung Wong (2000)
    The Co-evolution of cell senescence and diploid sexual reproduction in unicellular organisms.
    Proc. Natl. Acad. Sci. Vol. 97, 3330-3335. [Abstract][pdf]
  • Wang N, Chen RS and Wong WH (2000)
    Conservation of ribosomal protein gene ordering in 16 complete genomes.
    Science in China (C), Vol.43, No.2, 120-128. [pdf]
  • Jianqing Fan, Hui-Nien Hung and Wing Hung Wong (2000)
    Geometric Understanding of Likelihood Ratio Statistics.
    J. Amer. Stat. Assoc., 95,836-841. [pdf]
  • Faming Liang and Wing Hung Wong (2000)
    Evolutionary Monte Carlo: Applications to Cp model sampling and changepoint problem.
    Statistica Sinica, Vol. 10, 317-342 [Abstract][pdf]
  • Jun S. Liu, Faming Liang and Wing Hung Wong (2000)
    The Use of Multiple-Try Method and Local Optimization in Metropolis Sampling.
    J. Amer. Statist. Assoc. Vol. 95, No.449, 121-134
    [pdf]
1999
  • Xiaotong Shen, Jian Shi and Wing Hung Wong (1999)
    Random sieve likelihood and general regression models.
    J. Amer. Statist. Assoc., 94, 835-846
    [pdf]
  • Hui-Nien Hung, Wing Hung Wong (1999)
    Averaging of Profiling of Likelihoods, and the Nuisance Parameter Problem.
    [pdf]
  • Faming Liang and Wing Hung Wong (1999)
    Dynamic Weighting in Simulations of Spin Systems
    Physics Letters A, 252 (5) pp. 257-262 [pdf]
  • Jason Cong, Tianming Kong, Dongming Xu, Faming Liang, Jus S. Liu and Wing Hung Wong (1999)
    Relaxed Simulated Tempering for VLSI Floorplan Designs.
    Proc. Asia and South Pacific Design Automation Conference'99, Hong Kong, China. 13-16. [pdf]
  • Wu X, Wen J and Wong WH (1999)
    Conditional entropy coding of VQ indexes for image compression.
    IEEE Transactions on Image Processing, 8:1005-1013.
    [Abstract]
1998
  • Yan Cui, Run Sheng Chen and Wing Hung Wong (1998)
    Protein folding simulation with genetic algorithm and supersecondary structure constraints.
    Proteins: Structure, Function, and Genetics, Vol. 31, No. 3, 247-257.
    [Abstract][pdf]
  • Cui Y, Chen RS and Wong WH (1998)
    Molecular Dynamics Simulation of Chaperone-mediated Protein Folding.
    Journal of Protein Chemistry, Vol. 17, No.4, 377-380, [Abstract]
  • Wing Hung Wong, Yan Cui and Run Sheng Chen (1998)
    Torsional relaxation for biopolymers.
    Journal of Computational Biology, Vol.5, No.4, 655-665 [Abstract]
  • Jason Cong, Tianming Kong, Dongming Xu, Faming Liang, Jus S. Liu and Wing Hung Wong (1998)
    Dynamic Weighting Monte Carlo for Constrained Floorplan Designs in Mixed Signal Application.
    Proc. Asia and South Pacific Design Automation Conf., Japan. [pdf]
  • Liu JS, Chen R and Wong WH (1998)
    Rejection control and sequential importance sampling.
    J Amer Statist Assoc., 93:1022-1031. [Abstract]
  • Kao CM, Pan X, Chen CT and Wong WH (1998)
    Image reconstruction with a Bayesian approach.
    Medical Physics, 25:600-613.
    [Abstract]

Research supported by National Institutes of Health and National Science Foundation.

     
 
  Wong Lab, Bio-X program, Stanford University |  James Clark Center, 318 Campus Drive, Stanford, CA 94305-4065