• Yingxin Lin, Tung-Yu Wu, Xi Chen, Sheng Wan, Brian Chao, Jingxue Xin, Jean Yang, Wing Hung Wong, and Y.X. Rachel Wang
  Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE Genome Research (2023): gr-277960. [online]

• Shuo Li, Xiaohui Ni, Qiao Liu, Wenyuan Li, Mary L. Stackpole, Yonggang Zhou, Arjan Gower, Kostyantyn Krysan, Preeti Ahuja, David S. Lu, Steven S. Raman, William Hsu, Denise R. Aberle, Clara E. Magyar, Samuel W. French, Steven-Huy B. Han, Edward B. Garon, Vatche G. Agopian, Wing Hung Wong, Steven M. Dubinett, and Xianghong Jasmine Zhou
  Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring Proc Natl Acad Sci U S A, July 3, 2023; 120 (28) e2305236120 [online]

• Zheng Wei, Kui Hua, Lei Wei, Shining Ma, Rui Jiang, Xuegong Zhang, Yanda Li, Wing H. Wong, and Xiaowo Wang
  NeuronMotif: Deciphering cis-regulatory codes by layer-wise demixing of deep neural networks Proc Natl Acad Sci U S A, April 6, 2023; 120 (15): e2216698120 [online]

• Linxi Liu, Danga Li, Wing Hung Wong
  Convergence rates of a class of multivariate density estimation methods based on adaptive partitioning Journal of Machine Learning Research, 24 (2023) 1-64 [online]

• Qiao Liu, Zhongren Chen, Wing Hung Wong
  CausalEGM: a general causal inference framework by encoding generative modeling arXiv:2212.05925 [preprint]

• Xianghong Zhou, Mary Stackpole, Weihua Zeng, Shuo Li, Chun-Chi Liu, Yonggang Zhou, Shanshan He, Angela Yeh, Ziye Wang, Fengzhu Sun, Qingjiao Li, Zuyang Yuan, Asli Yildirim, Pin-Jung Chen, Paul Winograd, Benjamin Tran, Yi-Te Lee, Paul Li, Zorawar Noor, Megumi Yokomizo, Preeti Ahuja, Yazhen Zhu, Hsian-Rong Tseng, James Tomlinson, Edward Garon, Samuel French, Clara Magyar, Sarah Dry, Clara Lajonchere, Daniel Geschwind, Gina Choi, Sammy Saab, Frank Alber, Wing Wong, Steven Dubinett, Denise Aberle, Vatche Agopian, Steven-Huy Han, Xiaohui Ni, and Wenyuan Li
  Cost-effective Methylome Sequencing of Cell-free DNA for Accurately Detecting and Locating Cancer Nature communications 13.1 (2022): 5566 [online]

• Xueqiu Lin, Yanxia Liu, Shuai Liu, Xiang Zhu, Lingling Wu, Yanyu Zhu, Dehua Zhao, Xiaoshu Xu, Augustine Chemparathy, Haifeng Wang, Yaqiang Cao, Muneaki Nakamura, Jasprina N. Noordermeer, Marie La Russa, Wing Hung Wong, Keji Zhao, and Lei S. Qi
  Nested epistasis enhancer networks for robust genome regulation Science, 377(6610), 1077-1085 [online]

• Wanwen Zeng, Qiao Liu, Qijin Yin, Rui Jiang and Wing Hung Wong
  HiChIPdb: a comprehensive database of HiChIP regulatory interactions Nucleic Acids Research, (2022) [online]

• Xi Xi, Haochen Li, Shengquan Chen, Tingting Lv, Tianxing Ma, Rui Jiang, Ping Zhang, Wing Hung Wong and Xuegong Zhang
  Unfolding the genotype-to-phenotype black box of cardiovascular diseases through cross-scale modeling Iscience 25.8 (2022): 104790 [online]

• Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, and Rui Jiang
  DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility Genomics, Proteomics & Bioinformatics 20.3 (2022): 496-507 [online]

• Zhana Duren, Fengge Chang, Fnu Naqing, Jingxue Xin, Qiao Liu and Wing Hung Wong
  Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG Genome Biol 23, 114 (2022) [online]

• Hangjin Jiang, Xuhui Huang, Han Li, Wing Hung Wong, Xiaodan Fan
  Revealing Free Energy Landscape from MD Data via Conditional Angle Partition Tree IEEE/ACM Transactions on Computational Biology and Bioinformatics 20.2 (2022): 1384-1394 [online]

• Yingxin Lin, Tung-Yu Wu, Sheng Wan, Jean Y.H. Yang, Wing H. Wong and Y. X. Rachel Wang
  scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning Nature Biotechnology. 2022 Jan 20:1-8 [online]

• Shining Ma, Xi Chen, Xiang Zhu, Philip S. Tsao and Wing Hung Wong
  Leveraging cell type-specific regulatory networks to interpret genetic variants in abdominal aortic aneurysm Proc Natl Acad Sci U S A, 2022 Jan 4; 119(1): e2115601119 [online]

• . Juan A. Ferrer-Bonsoms, Xabier Morales, Pegah T. Afshar, Wing H. Wong and Angel Rubio
  On the identifiability of the isoform deconvolution problem: application to select the proper fragment length in an RNAseq library Bioinformatics, Volume 38, Issue 6, 15 March 2022, Pages 1491–1496 [online]

• Wing Hung Wong
  An equation for the identification of average causal effect in nonlinear models Statistica Sinica. DOI 10.5705/ss.202021.0191 [online]

• Yunzhang Zhu, Xiaotong Shen, Hui Jiang, and Wing Hung Wong
  Collaborative Multilabel Classification Journal of the American Statistical Association (2021): 1-12 [online]

• Duren Zhana, Wenhui Sophia Lu, Joseph G. Arthur, Preyas Shah, Jingxue Xin, Francesca Meschi, Miranda Lin Li, Corey M. Nemec, Yifeng Yin, and Wing Hung Wong
  Sc-compReg enables the comparison of gene regulatory networks between conditions using single-cell data Nature Communications 12, 4763 (2021) [online]

• David G. Gennert, Rachel C. Lynn, Jeff M. Granja, Evan W. Weber, Maxwell R. Mumbach, Yang Zhao, Zhana Duren, Elena Sotillo, William J. Greenleaf, Wing H. Wong, Ansuman T. Satpathy, Crystal L. Mackall, and Howard Y. Chang
  Dynamic chromatin regulatory landscape of human CAR T cell exhaustion Proc Natl Acad Sci USA July 27, 2021 118 (30) e2104758118 [online]

• Shuo Li, Zorawar S. Noor, Weihua Zeng, Mary L. Stackpole, Xiaohui Ni, Yonggang Zhou, Zuyang Yuan, Wing Hung Wong, Vatche G. Agopian, Steven M. Dubinett, Frank Alber, Wenyuan Li, Edward B. Garon, and Xianghong Jasmine Zhou
  Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis Nature Communications 12, 4172 (2021) [online]

• Xiang Zhu, Duren Zhana, Wing Hung Wong
  Modeling regulatory network topology improves genome wide analysis of complex human traits Nature communications 12, 2851 (2021) [online]

• Qiao Liu, Jiaze Xu, Rui Jiang, Wing Hung Wong
  Density estimation using deep generative neural networks Proceedings of the National Academy of Sciences Apr 2021, 118 (15) e2101344118 [online]

• Qiao Liu, Shengquan Chen, Rui Jiang, Wing Hung Wong
  Simultaneous deep generative modelling and clustering of single-cell genomic data Nature Machine Intelligence, 2021, Published: May 10, 2021 [online]

• Zhanying Feng, Zhana Duren, Ziyi Xiong, Sijia Wang, Fan Liu, Wing Hung Wong, Yong Wang
  Reconstructing human regulatory network of cranial neural crest cell and annotating variants in developmental context Communications Biology (2021) 4:442 [online]

• Sheng Wan , Tung-Yu Wu, Heng-Wei Hsu , Wing Hung Wong , and Chen-Yi Lee
  Feature Consistency Training with JPEG Compressed Images IEEE Transactions on Circuits and Systems for Video Technology, Vol. 30, No. 12, December 2020, pages 4769-4780 [online]

• Wenran Li, Zhana Duren, Rui Jiang, and Wing Hung Wong
  A method for scoring the cell type-specific impacts of noncoding variants in personal genomes PNAS September 1, 2020 117 (35) 21364-21372; first published August 17, 2020 [online]

• Ben Dai, Xiaotong Shen, and Wing Wong
  Coupled generation Journal of the American Statistical Association, 2020 [online]

• Jingxue Xin, Hui Zhang, Yaoxi He, Zhana Duren, Caijuan Bai, Lang Chen, Xin Luo, Dong-Sheng Yan, Chaoyu Zhang, Xiang Zhu, Qiuyue Yuan, Zhanying Feng, Chaoying Cui, Xuebin Qi, Ouzhuluobu, Wing Hung Wong, Yong Wang & Bing Su
  Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation Nature Communications 11, 4928 (2020) [online]

• Zhana Duren, Xi Chen, Jingxue Xin, Yong Wang, and Wing Hung Wong
  Time course regulatory analysis based on paired expression and chromatin accessibility data Genome Res. 2020. 30: 622-634. Published in Advance March 18, 2020 [online]

• Xianglong Zhang, David Hong, Shining Ma, Thomas Ward, Marcus Ho, Reenal Pattni, Zhana Duren, Atanas Stankov, Sharon Bade Shrestha, Joachim Hallmayer, Wing Hung Wong, Allan L Reiss, Alexander E Urban
  Integrated functional genomic analyses of Klinefelter and Turner syndromes reveal global network effects of altered X chromosome dosage Proceedings of the National Academy of Sciences (2020), Published: March 3, 2020 117 (9) 4864-4873; first published February 18, 2020 [online]

• Zhixiang Lin, Mahdi Zamanighomi, Timothy Daley, Shining Ma, and Wing Hung Wong
  Model-based approach to the joint analysis of single-cell data on chromatin accessibility and gene expression Statist. Sci., Volume 35, Number 1 (2020), 2-13 [online]

• Wanwen Zeng, Xi Chen, Zhana Duren, Yong Wang, Rui Jiang, Wing Hung Wong
  DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data Nature Communications volume 10, Article number: 4613 (2019) [online]

• Leying Guan, Xi Chen and Wing Hung Wong
  Detecting Strong Signals in Gene Perturbation Experiments: An Adaptive Approach With Power Guarantee and FDR Control Journal of the American Statistical Association (2019), Published: 14 August 2019 [online]

• Wenran Li, Wing Hung Wong and Rui Jiang
  DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning Nucleic Acids Research (2019), Published: 14 March 2019 [online]

• Lingjie Li, Yong Wang, Jessica L.Torkelson, Gautam Shankar, Jillian M.Pattison, Hanson H.Zhen, Fengqin Fang, Zhana Duren, JingxueXin, Sadhana Gaddam, Sandra P.Melo, Samantha N.Piekos, Jiang Li, Eric J.Liaw, Lang Chen, Rui Li, Marius Wernig, Wing H. Wong, Howard Y. Chang, Anthony E. Oro
  TFAP2C- and p63-Dependent Networks Sequentially Rearrange Chromatin Landscapes to Drive Human Epidermal Lineage Commitment Cell Stem Cell (2019), Published: 24 January 2019 [online]

• Qigang Li, Keyan Zhao, Carlos D. Bustamante, Xin Ma, Wing H. Wong
  Xrare: a machine learning method jointly modeling phenotypes and genetic evidence for rare disease diagnosis Genetics in Medicine (2019), Published: 24 January 2019 [online] Software [download]

• Bo Zhou, Joseph G. Arthur, Steve S. Ho, Reenal Pattni, Yiling Huang, Wing H. Wong & Alexander E. Urban
  Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools Scientific Data volume 5, Article number: 180261 (2018) [online]

• Bo-Cheng Lai, Tung-Yu Wu, Tsou-Han Chiu, Kun-Chun Li, Chia-Ying Lee, Wei-Chen Chien, Wing Hung Wong
  Towards high performance data analytic on heterogeneous many-core systems: A study on Bayesian sequential partitioning J. Parallel Distrib. Comput.(2018) [online]

• Timothy P. Daley, Zhixiang Lin, Xueqiu Lin, Yanxia Liu, Wing H. Wong and Lei S. Qi
  CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens Genome Biology (2018) 19:159 [online]

• Bai Jiang, Tung-Yu Wu, Yifan Jin and Wing H. Wong
  Convergence of contrastive divergence algorithm in exponential family Annals of Statistics, Volume 46, Number 6A (2018), 3067-3098 arXiv:1603.05729 [online]

• Wenyuan Li, Qingjiao Li, Shuli Kang, Mary Same, Yonggang Zhou, Carol Sun, Chun-Chi Liu, Lea Matsuoka, Linda Sher, Wing Hung Wong, Frank Alber and Xianghong Jasmine Zhou
  CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data Nucleic Acids Research gky423, Published: 12 June 2018 [online]

• Mahdi Zamanighomi, Zhixiang Lin, Timothy Daley, Xi Chen, Zhana Duren, Alicia Schep, William J. Greenleaf, Wing Hung Wong
  Unsupervised clustering and epigenetic classification of single cells Nature Communications volumn 9, Article 2410 (2018) [online]

• Zhana Duren, Xi Chen, Mahdi Zamanighomi, Wanwen Zeng, Ansuman T. Satpathy, Howard Y. Chang, Yong Wang, and Wing Hung Wong
  Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations Proceedings of the National Academy of SciencesJul 2018, 201805681; DOI: 10.1073/pnas.1805681115 [online] Software [github]

• Christopher De Sa, Vincent Chen, Wing Wong
  Minibatch Gibbs Sampling on Large Graphical Models ICML (to appear) arXiv:1806.06086 [online]

• Bai Jiang, Tung-Yu Wu and Wing Hung Wong
  Approximate Bayesian Computation with Kullback-Leibler Divergence as Data Discrepancy AISTATS 2018 (accepted)

• Linxi Liu, Dangna Li, Wing H. Wong
  partition based Bayesian multivariate density estimation method
  Advances in Neural Information Processing Systems2017, 4739-4747

• Chang-Hung Tsai, Wan-Ju Yu, Wing Hung Wong, Chen-Yi Lee
  A 41.3/26.7 pJ per Neuron Weight RBM Processor Supporting On-Chip Learning/Inference for IoT Applications
  Solid-State Circuits52(10): 2601-2612 (2017)

• Sayed Sahraeian, Marghoob Mohiyuddin, Robert Sebra, Hagen Tilgner, Pegah Tootoonchi Afshar, Kin Fai Au, Narges Bani Asadi, Mark Gerstein, Wing Wong, Michael Snyder, Eric Schadt, and Hugo Lam
  Gaining comprehensive biological insights into transcriptome by performing a broad-spectrum RNA-Seq analysis
  Nat Communication 201707 5;8(1):59. Epub 2017 Jul 5.

• Ye Henry Li , Dangna Li , Nikolay Samusik, Xiaowei Wang, Leying Guan, Garry P. Nolan, Wing Hung Wong
  Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks Plos Computational Biology December 27, 2017. https://doi.org/10.1371/journal.pcbi.1005875 [online]

• Mengmeng Wu, Zhixiang Lin, Shining Ma, Ting Chen, Rui Jiang, Wing Hung Wong Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networks Journal of Molecular Cell Biology doi:10.1093/jmcb/mjx059 [online]

• Ava C. Carter, Howard Y. Chang, George Church, Ashley Dombkowski, Joseph R Ecker, Elad Gil, Paul G. Giresi, Hank Greely, William J. Greenleaf, Nir Hacohen, Chuan He, David Hill, Justin Ko, Issac Kohane, Anshul Kundaje, Megan Palmer, Michael P Snyder, Joyce Tung, Alexander E. Urban, Wing Wong (alphabetical ordered) Challenges and recommendations for epigenomics in precision health from technology developers and end-users
  Nature Biotechnology 35(12):1128-1132 [online]

• Xi Chen, Hong Yang, Wing Hung Wong(2017)
  Phased Genome Sequencing Through Chromosome Sorting
  Methods in Mol.Bio 1551:171-188 doi:10.1038/ng.3449 [online]

• Bai Jiang, Tung-Yu Wu, Charles Zheng, Wing H.Wong(2017)
  Learning Summary Statistics for Approximation Bayesian Computation vis Deep Neural Network
  Statistics Sinica doi:10.5705/ss.202015.0340 [online]

• Li, Dangna, Kun Yang, and Wing Hung Wong(2017)
  Density Estimation via Discrepancy Based Adaptive Sequential Partition
  NIPS2016_6217 pp1091--1099 [online]

• Zhana Duren, Xi Chen, Rui Jiang, Yong Wang, Wing Hung Wong(2017)
  Modeling gene regulation from paired expression and chromatin accessibility data
  Proceedings of the National Academy of Sciences doi:10.1073/pnas.1704553114 [online]

• Pegah Tootoonchi Afshar, Wing Hung Wong(2017)
  COSINE: non-seeding method for mapping long noisy sequences
  Nucleic Acids Res gkx511 [online]

• Mahdi Zamanighomi, Zhixiang Lin, Yong Wang, Rui Jiang, Wing Hung Wong(2017)
  Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility, and gene expression data
  Nucleic Acids Res(2017)45(10):5666-56770.1093/nar/gkx358 [online]

• Jens Durruthy-Durruthy, Vittorio Sebastiano, Mark Wossidlo, Diana Cepeda, Jun Cui, Edward J Grow, Jonathan Davila, Moritz Mall, Wing H Wong, Joanna Wysocka, Kin Fai Au and Renee A Reijo Pera (2016)
  The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming.
  Nature Genetics 48, 44-5 (2016) doi:10.1038/ng.3449 [online]

• Zhixiang Lin, Can Yang, Ying Zhu, John Duchi, Yao Fu, Yong Wang, Bai Jiang, Mahdi Zamanighomi, Xuming Xu, Mingfeng Li, Nenad Sestan, Hongyu Zhao, Wing Hung Wong(2016)
  Simultaneous dimension reduction and adjustment for confounding variation
  Proceedings of the National Academy of Sciences, December 2016:113(51),14662-14667, doi:10.1073/pnas.1617317113 [online]

• Sarah E. B. Taylor, Ye Henry Li, Wing H. Wong and Nidhi Bhutani (2015)
  Genome-wide mapping of DNA hydroxymethylation in osteoarthritic chondrocytes.
  Arthritis & Rheumatology 67: 2129-2140. doi: 10.1002/art.39179
• Chang-Hung Tsai, Yu-Ting Chih, Wing Hung Wong, and Chen-Yi Lee (2015)
  A Hardware-Efficient Sigmoid Function with Adjustable Precision for Neural Network System.
  IEEE Transactions on circuits and systems-- II: Express Briefs , vol. 62, 1073-1077 [online]
• John C Mu, Pegah Tootoonchi Afshar, Marghoob Mohiyuddin, Xi Chen, Jian Li, Narges Bani Asadi, Mark B Gerstein, Wing H Wong, Hugo YK Lam (2015)
  Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods.
  Scientific reports 2015, 5: 14493. doi:10.1038/srep14493. [online]
• Li Tai Fang, Pegah Tootoonchi Afshar, Aparna Chhibber, Marghoob Mohiyuddin, Yu Fan, John C. Mu, Greg Gibeling, Sharon Barr, Narges Bani Asadi, Mark B. Gerstein, Daniel C. Koboldt, Wenyi Wang, Wing H. Wong and Hugo YK Lam (2015)
  An ensemble approach to accurately detect somatic mutations using SomaticSeq.
  Genome Biology 2015, 16:197. doi:10.1186/s13059-015-0758-2. [online]
• Jason L. Weirather, Pegah Tootoonchi Afshar, Tyson A. Clark, Elizabeth Tseng, Linda S. Powers, Jason G. Underwood, Joseph Zabner, Jonas Korlach, Wing Hung Wong, and Kin Fai Au (2015)
  Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing.
  Nucleic Acids Res. first published online June 3, 2015. doi:10.1093/nar/gkv562. [online]
• Marghoob Mohiyuddin, John C. Mu, Jian Li, Narges Bani Asadi, Mark B. Gerstein, Alexej Abyzov, Wing H. Wong, Hugo Y.K. Lam (2015)
  MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.
  Bioinformatics 2015, doi: 10.1093/bioinformatics/btv204 [online]
• Hui Jiang, John C. Mu, Kun Yang, Chao Du, Luo Lu, Wing Hung Wong (2015)
  Computational Aspects of Optional Polya Tree.
  Journal of Computational and Graphical Statistics, doi: 10.1080/10618600.2014.1002927 [online]

• John C. Mu, Marghoob Mohiyuddin, Jian Li, Narges Bani Asadi, Mark B. Gerstein, Alexej Abyzov, Wing H. Wong, Hugo Y.K. Lam (2014)
  VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.
  Bioinformatics 2014, doi: 10.1093/bioinformatics/btu828 [online]
• 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]

• 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]

• 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, Jos�-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]

• Li Ma and Wing Hung Wong (2011)
  Coupling optional P�lya 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]

• 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]

• 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]

• 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]

  Top

• 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]

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• 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]

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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]

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2004