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publications [2018/05/16 13:16]
xhx [2018]
publications [2018/08/15 23:25] (current)
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 +<​html>​
 +<​h2>​Publications</​h2>​
  
 +<div class="​level2">&​nbsp;</​div>​
  
-===== Publications =====+<​h3>​2018</​h3>​
  
-==== 2018 ====+<div class="​level3">​ 
 +<​p><​a class="​urlextern"​ href="​https://​arxiv.org/​abs/​1805.05373"​ rel="​nofollow"​ title="​https://​arxiv.org/​abs/​1805.05373">​DeepEM:​ Deep 3D ConvNets With EM For Weakly Supervised Pulmonary Nodule Detection</​a><​br /> 
 +Zhu W, Vang YS, Huang Y, Xie X</p>
  
-[[https://​arxiv.org/​abs/​1805.05373 | DeepEM: Deep 3D ConvNets With EM For Weakly Supervised Pulmonary Nodule Detection]]\\ +<​p>​Sequential Embedding Induced Nonparametric Text Clustering<​br ​/> 
-Zhu WVang YS, Huang Y, Xie X\\+Duan TLou Q, Xie X</p>
  
 +<​p><​a class="​urlextern"​ href="​https://​arxiv.org/​abs/​1802.00931"​ rel="​nofollow"​ title="​https://​arxiv.org/​abs/​1802.00931">​Deep Learning Framework for Multi-class Breast Cancer Histology Image Classification</​a><​br />
 +Vang S, Chen Z, Xie X<br />
 +15th International Conference on Image Analysis and Recognition,​ 2018</​p>​
  
-Sequential Embedding Induced Nonparametric Text Clustering\\ +<​p><​a class="​urlextern"​ href="​https://​arxiv.org/​abs/​1801.07853"​ rel="​nofollow"​ title="​https://​arxiv.org/​abs/​1801.07853">​Structed Triplets Learning with Pos-tag Guided Attention for Visual Question Answering</​a><​br /> 
-Duan T, Lou Q, Xie X\\+IEEE Winter Conf. on Applications of Computer Vision 2018</​p>​
  
-[[https://​arxiv.org/​abs/​1802.00931 | Deep Learning Framework ​for Multi-class Breast Cancer Histology Image Classification]]\\ +<​p><​a class="​urlextern"​ href="https://​arxiv.org/​abs/​1801.09555" rel="​nofollow"​ title="​https://​arxiv.org/​abs/​1801.09555">​DeepLung: ​Deep 3D Dual Path Nets for Automated Pulmonary Nodule Detection and Classification</​a><​br /> 
-Vang S, Chen Z, Xie X\\ +IEEE Winter Conf. on Applications of Computer Vision ​2018</p>
-15th International Conference ​on Image Analysis and Recognition, ​2018+
  
-[[https://arxiv.org/​abs/​1801.07853 | Structed Triplets Learning with Pos-tag Guided Attention for Visual Question Answering]]\\ +<​p>​Adversarial Deep Structured Nets for Mass Segmentation from Mammograms<​br ​/
-IEEE Winter Conf. on Applications of Computer Vision 2018+W Zhu, X Xiang, T Tran, GD Hager, X Xie<​br ​/> 
 +IEEE International Symposium ​on Biomedical Imaging</​p>​
  
-[[https://​arxiv.org/​abs/​1801.09555 | DeepLung: Deep 3D Dual Path Nets for Automated Pulmonary Nodule Detection ​and Classification]]\\ +<p>Automated Pulmonary Nodule Detection ​Using 3D Deep Convolutional Neural Networks<​br /> 
-IEEE Winter Conf. on Applications of Computer Vision 2018+H Tang, D Kim, X Xie<br /> 
 +IEEE International Symposium ​on Biomedical Imaging</​p>​
  
-Adversarial Deep Structured Nets for Mass Segmentation from Mammograms\\ +<​p>​Molecular Mechanisms ​for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.<​br /> 
-Zhu, X XiangT TranGD HagerXie\\ +Zhu YWang X, Forouzmand EJeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.<br /> 
-IEEE International Symposium on Biomedical Imaging+Mol Cell. 2018 Jan 4;​69(1):​62-74.e4.</​p>​ 
 +</​div>​
  
-Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural Networks\\ +<​h3>​2017</​h3>​
-H Tang, D Kim, X Xie\\ +
-IEEE International Symposium on Biomedical Imaging+
  
-Molecular Mechanisms ​for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.\\ +<div class="​level3">​ 
-Zhu YWang XForouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.\\ +<​p><​a class="​urlextern"​ href="​https://​arxiv.org/​abs/​1709.05538"​ rel="​nofollow"​ title="​https://​arxiv.org/​abs/​1709.05538">​DeepLung:​ 3D Deep Convolutional Nets for Automated Pulmonary Nodule Detection and Classification</​a><​br /> 
-Mol Cell. 2018 Jan 4;69(1):62-74.e4.+Zhu, C LiuW FanXie<br /> 
 +arXiv preprint arXiv:1709.05538</​p>​
  
-==== 2017 ====+<​p><​a class="​urlextern"​ href="​https://​www.biorxiv.org/​content/​early/​2017/​06/​28/​151274"​ rel="​nofollow"​ title="​https://​www.biorxiv.org/​content/​early/​2017/​06/​28/​151274">​FactorNet:​ a deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data</​a><​br /> 
 +D Quang, X Xie<br /> 
 +bioRxiv, 151274</​p>​
  
-[[https://​arxiv.org/​abs/​1709.05538 | DeepLung3D Deep Convolutional Nets for Automated Pulmonary Nodule Detection and Classification]]\\ +<​p><​a class="​urlextern"​ href="https://​arxiv.org/​abs/​1612.05968" rel="​nofollow"​ title="​https://​arxiv.org/​abs/​1612.05968">​Deep Multi-instance Networks with Sparse Label Assignment ​for Whole Mammogram ​Classification</​a><​br /> 
-Zhu, C LiuW FanXie\\ +Wentao ​Zhu, Qi LouYeeleng Scott VangXiaohui ​Xie<br /> 
-arXiv preprint ​arXiv:1709.05538+arXiv:1612.05968<br /> 
 +<a class="​urlextern"​ href="​http://​www.miccai2017.org/"​ rel="​nofollow"​ title="​http://​www.miccai2017.org/">​MICCAI,​ 2017</​a></​p>​
  
 +<​p>​Understanding sequence conservation with deep learning<​br />
 +Li Y, Quang D, and Xie X<br />
 +ACM BCB, 2017</​p>​
  
-[[https://www.biorxiv.org/​content/​early/​2017/​06/28/151274 | FactorNeta deep learning framework for predicting cell type specific transcription factor ​binding ​from nucleotide-resolution sequential data]]\\ +<​p><​a class="​urlextern"​ href="​http://​biorxiv.org/​content/​early/​2017/​01/10/099358"​ rel="​nofollow"​ title="​http://​biorxiv.org/​content/​early/​2017/​01/​10/​099358">​HLA class I binding ​prediction via convolutional neural networks</​a><​br /> 
-D Quang, X Xie\\ +Vang YS and Xie X<br /> 
-bioRxiv151274+Bioinformatics2017</​p>​
  
 +<​p><​a class="​urlextern"​ href="​https://​www.ncbi.nlm.nih.gov/​pubmed/​28325473"​ rel="​nofollow"​ title="​https://​www.ncbi.nlm.nih.gov/​pubmed/​28325473">​Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program</​a><​br />
 +Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW<br />
 +Dev Cell. 27;​40(6):​595-607.e4,​ 2017</​p>​
 +</​div>​
  
-[[https://​arxiv.org/​abs/​1612.05968|Deep Multi-instance Networks with Sparse Label Assignment for Whole Mammogram Classification]]\\ +<​h3>​2016<​/h3>
-Wentao Zhu, Qi Lou, Yeeleng Scott Vang, Xiaohui Xie \\ +
-arXiv:​1612.05968\\ +
-[[http://​www.miccai2017.org/​| MICCAI, 2017]]+
  
-Understanding sequence conservation with deep learning\\ +<div class="​level3">​ 
-Li YQuang D, and Xie X\\ +<​p><​a class="​urlextern"​ href="​https://​arxiv.org/​abs/​1612.05970"​ rel="​nofollow"​ title="​https://​arxiv.org/​abs/​1612.05970">​Adversarial Deep Structural Networks for Mammographic Mass Segmentation</​a><​br /> 
-ACM BCB, 2017+Wentao ZhuXiaohui ​Xie<br /> 
 +arXiv:​1612.05970</​p>​
  
-[[http://biorxiv.org/content/early/2017/01/10/099358|HLA class I binding prediction via convolutional neural networks]]\\ +<​p><​a class="​urlextern"​ href="​https://www.ncbi.nlm.nih.gov/pubmed/27418388"​ rel="​nofollow"​ title="​https:​//www.ncbi.nlm.nih.gov/pubmed/27418388">​Developmentally regulated long non-coding RNAs in Xenopus tropicalis</​a><​br /> 
-Vang YS and Xie X\\ +Forouzmand et al.<br /> 
-Bioinformatics2017+Developmental Biology(16)30120-8 2016</​p>​
  
-[[https://www.ncbi.nlm.nih.gov/pubmed/28325473|Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm ​Gene Program]]\\ +<​p><​a class="​urlextern"​ href="​http://bioinformatics.oxfordjournals.org/​content/​early/​2016/​02/​11/​bioinformatics.btw074.short?​rss=1"​ rel="​nofollow"​ title="​http:​//bioinformatics.oxfordjournals.org/​content/​early/​2016/​02/​11/​bioinformatics.btw074.short?​rss=1">​Gene expression inference with deep learning</​a><​br /> 
-Charney RM, Forouzmand E, Cho JSCheung J, Paraiso KD, Yasuoka ​Y, Takahashi STaira M, Blitz IL, Xie X, Cho KW\\ +Chen YLi Y, Narayan RSubramanian Aand Xie X<br /> 
-Dev Cell. 27;​40(6):​595-607.e42017+Bioinformatics2016</​p>​
  
-==== 2016 ====+<​p>​DanQ:​ a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences<​br /> 
 +Quang D and Xie X<br /> 
 +Nucleic Acids Research, ​2016</p>
  
-[[https://arxiv.org/abs/1612.05970|Adversarial Deep Structural Networks ​for Mammographic Mass Segmentation]]\\ +<​p><​a class="​urlextern"​ href="​http://rnajournal.cshlp.org/content/early/​2016/​04/​19/​rna.055681.115.abstract"​ rel="​nofollow"​ title="​http://​rnajournal.cshlp.org/​content/​early/​2016/​04/​19/​rna.055681.115.abstract">​Poly(A) code analyses reveal key determinants ​for tissue-specific mRNA alternative polyadenylation</​a><​br /> 
-Wentao ZhuXiaohui ​Xie\\ +Weng L, Li Y, Xie X, and Shi Y<br /> 
-arXiv:​1612.05970+RNA, 2016</​p>​
  
-[[https://​www.ncbi.nlm.nih.gov/pubmed/27418388|Developmentally regulated long non-coding RNAs in Xenopus tropicalis]]\\ +<​p><​a class="​urlextern"​ href="https://​www.researchgate.net/​profile/​Wentao_Zhu4/​publication/​283748673_Co-occurrence_Feature_Learning_for_Skeleton_based_Action_Recognition_using_Regularized_Deep_LSTM_Networks/​links/​567a2bc808ae7fea2e98bf6b.pdf" rel="​nofollow"​ title="​https://​www.researchgate.net/profile/Wentao_Zhu4/​publication/​283748673_Co-occurrence_Feature_Learning_for_Skeleton_based_Action_Recognition_using_Regularized_Deep_LSTM_Networks/​links/​567a2bc808ae7fea2e98bf6b.pdf">​Co-occurrence Feature Learning for Skeleton based Action Recognition using Regularized Deep LSTM Networks</​a><​br /> 
-Forouzmand ​et al. \\ +Zhu W, et al.<br /> 
-Developmental Biology(16)30120-8 ​2016+AAAI Conference on Artificial Intelligence, 2016</​p>​ 
 +</​div>​
  
-[[http://​bioinformatics.oxfordjournals.org/​content/​early/​2016/​02/​11/​bioinformatics.btw074.short?​rss=1|Gene expression inference with deep learning]]\\ +<​h3>​2015<​/h3>
-Chen Y, Li Y, Narayan R, Subramanian A, and Xie X\\ +
-Bioinformatics,​ 2016+
  
-DanQa hybrid convolutional and recurrent deep neural network for quantifying the function ​of DNA sequences\\ +<div class="​level3">​ 
-Quang D and Xie X\\ +<​p>​Hobbes3Dynamic Generation ​of Variable-Length Signatures for Efficient Approximate Subsequence Mappings<​br /> 
-Nucleic Acids Research, ​2016+Kim J, Chen L, and Xie X<br /> 
 +32nd IEEE International Conference on Data Engineering - ICDE 2016</p>
  
-[[http://rnajournal.cshlp.org/​content/​early/​2016/04/19/rna.055681.115.abstract|Poly(A) code analyses reveal key determinants ​for tissue-specific mRNA alternative polyadenylation]]\\ +<​p><​a class="​urlextern"​ href="http://biorxiv.org/​content/​early/​2015/12/20/032821"​ rel="​nofollow"​ title="​http://​biorxiv.org/​content/​early/​2015/​12/​20/​032821">​DanQ:​ a hybrid convolutional and recurrent deep neural network ​for quantifying the function of DNA sequences</​a><​br /> 
-Weng L, Li Y, Xie X, and Shi Y\\ +Quang D and Xie X</p>
-RNA, 2016+
  
-[[https://www.researchgate.net/profile/Wentao_Zhu4/publication/283748673_Co-occurrence_Feature_Learning_for_Skeleton_based_Action_Recognition_using_Regularized_Deep_LSTM_Networks/links/567a2bc808ae7fea2e98bf6b.pdf|Co-occurrence Feature Learning ​for Skeleton based Action Recognition using Regularized Deep LSTM Networks]]\\ +<​p><​a class="​urlextern"​ href="​http://www.ncbi.nlm.nih.gov/pubmed/25338716"​ rel="​nofollow"​ title="​http:​//www.ncbi.nlm.nih.gov/pubmed/25338716">​DANN:​ a deep learning approach ​for annotating the pathogenicity of genetic variants</​a><​br /> 
-Zhu Wet al.\\ +Quang DChen Y and Xie X<br /> 
-AAAI Conference on Artificial Intelligence2016+Bioinformatics31(5):​761-3,​ 2015</​p>​
  
-==== 2015 ====+<​p><​a class="​urlextern"​ href="​http://​www.biomedcentral.com/​1471-2164/​16/​S2/​S1"​ rel="​nofollow"​ title="​http://​www.biomedcentral.com/​1471-2164/​16/​S2/​S1">​MixClone:​ a mixture model for inferring tumor subclonal populations</​a><​br /> 
 +Li Y and Xie X<br /> 
 +BMC Genomics, ​2015</p>
  
-Hobbes3Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings\\ +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​ImagingGenetics.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​ImagingGenetics.pdf">​Identifying unanticipated genes and mechanisms in serious mental illness</​a><​br /> 
-Kim JChen L, and Xie X\\ +Potkin SGvan Erp TGM, Ling S, Macciardi F, and Xie X<br /> 
-32nd IEEE International Conference on Data Engineering - ICDE 2016+Neuroimaging genetics : principles and practices, 2015</​p>​ 
 +</​div>​
  
-[[http://​biorxiv.org/​content/​early/​2015/​12/​20/​032821|DanQ:​ a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences]]\\ +<​h3>​2014<​/h3>
-Quang D and Xie X+
  
-[[http://www.ncbi.nlm.nih.gov/pubmed/25338716|DANN:​ a deep learning approach for annotating the pathogenicity of genetic variants]]\\ +<div class="​level3">​ 
-Quang D, Chen Y and Xie X\\ +<​p><​a class="​urlextern"​ href="http://link.springer.com/​article/​10.1007/​s10032-014-0229-4"​ rel="​nofollow"​ title="​http://​link.springer.com/article/10.1007/​s10032-014-0229-4">​Handwritten Hangul recognition using deep convolutional neural networks</​a><​br /> 
-Bioinformatics31(5):761-3, 2015+Kim I and Xie X<br /> 
 +International Journal on Document Analysis and Recognition2014<br /> 
 +<a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​HHR.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​HHR.pdf">​preprint</​a></​p>​
  
-[[http://www.biomedcentral.com/1471-2164/16/S2/S1|MixClone: ​mixture model for inferring tumor subclonal populations]]\\ +<​p><​a class="​urlextern"​ href="http://www.ncbi.nlm.nih.gov/pubmed/25359723"​ rel="​nofollow"​ title="​http:​//www.ncbi.nlm.nih.gov/​pubmed/​25359723">​Genome-wide view of TGFbeta/​Foxh1 regulation of the early mesendoderm</​a> program<​br /> 
-Li Y and Xie X\\ +Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K<br /> 
-BMC Genomics2015+Development2014</​p>​
  
 +<​p><​a class="​urlextern"​ href="​http://​bioinformatics.oxfordjournals.org/​content/​early/​2014/​04/​21/​bioinformatics.btu174"​ rel="​nofollow"​ title="​http://​bioinformatics.oxfordjournals.org/​content/​early/​2014/​04/​21/​bioinformatics.btu174">​Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity</​a><​br />
 +Li Y and Xie X<br />
 +Bioinformatics,​ 2014</​p>​
  
-[[http://www.ics.uci.edu/~xhx/publications/ImagingGenetics.pdf |Identifying unanticipated genes and mechanisms in serious mental illness]]\\ +<​p><​a class="​urlextern"​ href="http://bioinformatics.oxfordjournals.org/​content/​early/​2014/​02/​14/​bioinformatics.btu093.abstract"​ rel="​nofollow"​ title="​http:​//bioinformatics.oxfordjournals.org/​content/​early/​2014/​02/​14/bioinformatics.btu093.abstract">​EXTREME:​ An Online EM Algorithm for Motif Discovery</​a><​br /> 
-Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X\\ +Quang D and Xie X<br /> 
-Neuroimaging genetics : principles and practices2015+Bioinformatics2014</​p>​
  
-==== 2014 ====+<​p><​a class="​urlextern"​ href="​http://​www.biomedcentral.com/​1471-2105/​15/​42"​ rel="​nofollow"​ title="​http://​www.biomedcentral.com/​1471-2105/​15/​42">​Improving Read Mapping Using Additional Prefix Grams</​a><​br /> 
 +Kim J, Li C and Xie X<br /> 
 +BMC Bioinformatics, ​2014, 15(1):​42</​p>​
  
-[[http://link.springer.com/​article/​10.1007/s10032-014-0229-4|Handwritten Hangul recognition using deep convolutional neural networks]]\\ +<​p><​a class="​urlextern"​ href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092317"​ rel="​nofollow"​ title="​http://www.plosone.org/​article/​info:​doi/​10.1371/journal.pone.0092317">​Integrative ChIP-seq/Microarray Analysis Identifies a CTNNB1 Target Signature Enriched in Intestinal Stem Cells and Colon Cancer</a><br /> 
-Kim I and Xie X\\ +Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X<br /> 
-International Journal on Document Analysis and Recognition,​ 2014\\ +PLOS ONE, 2014, DOI: 10.1371/​journal.pone.0092317</​p>​
-[[http://www.ics.uci.edu/~xhx/publications/HHR.pdf| preprint]]+
  
-[[http://www.ncbi.nlm.nih.gov/pubmed/25359723|Genome-wide view of TGFbeta/Foxh1 regulation ​of the early mesendoderm]] program\\ +<​p><​a class="​urlextern"​ href="http://www.biomedcentral.com/​1752-0509/​8/​3/​abstract"​ rel="​nofollow"​ title="​http://​www.biomedcentral.com/1752-0509/8/​3/​abstract">​Inference ​of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns</​a><​br /> 
-Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K\\ +Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KWNie Q<br /> 
-Development, 2014+BMC Systems Biology ​2014, 8:​3</​p>​
  
-[[http://bioinformatics.oxfordjournals.org/​content/​early/​2014/​04/​21/bioinformatics.btu174|Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity]]\\ +<​p><​a class="​urlextern"​ href="http://emboj.embopress.org/​content/​early/​2014/03/04/embj.201386537"​ rel="​nofollow"​ title="​http:​//emboj.embopress.org/​content/​early/​2014/​03/​04/​embj.201386537">​Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal</​a><​br /> 
-Li Y and Xie X\\ +Lackford B, Yao C, Charles GM, Weng L, Zheng X, Choi EA, Xie X, Wan J, Xing Y, Freudenberg JM, Yang P, Jothi R, Hu G, Shi Y<br /> 
-Bioinformatics, 2014+EMBO J. 2014 Mar 4.</​p>​ 
 +</​div>​
  
-[[http://​bioinformatics.oxfordjournals.org/​content/​early/​2014/​02/​14/​bioinformatics.btu093.abstract|EXTREME:​ An Online EM Algorithm for Motif Discovery]]\\ +<​h3>​2013<​/h3>
-Quang D and Xie X\\ +
-Bioinformatics,​ 2014+
  
-[[http://www.biomedcentral.com/1471-2105/15/42|Improving Read Mapping Using Additional Prefix Grams]]\\ +<div class="​level3">​ 
-Kim JLi C and Xie X\\ +<​p><​a class="​urlextern"​ href="http://www.plosone.org/article/​info:​doi/​10.1371/​journal.pone.0082146"​ rel="​nofollow"​ title="​http://​www.plosone.org/​article/​info:​doi/​10.1371/​journal.pone.0082146">​Low-Rank Regularization for Learning Gene Expression Programs<​/a><​br ​/> 
-BMC Bioinformatics2014, 15(1):42+Ye GTang M, Nie Q and Xie X<br /> 
 +<​em>​PLOS ONE</​em>​2013</​p>​
  
-[[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092317|Integrative ChIP-seq/Microarray Analysis Identifies ​CTNNB1 Target Signature Enriched in Intestinal Stem Cells and Colon Cancer]]\\ +<​p><​a class="​urlextern"​ href="http://www.hindawi.com/journals/cmmm/​2013/​873595/"​ rel="​nofollow"​ title="​http://www.hindawi.com/​journals/​cmmm/​2013/​873595/">​A gradient boosting algorithm for survival analysis via direct optimization of concordance index</a><br /> 
-Watanabe KBiesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X\\ +Chen YJia ZMercola D and Xie X<br /> 
-PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317+<​em>​Comput Math Methods Med.</em>, 2013</​p>​
  
-[[http://www.biomedcentral.com/1752-0509/8/3/abstract|Inference of the Xenopus tropicalis ​embryonic regulatory network and spatial gene expression patterns]] \\ +<​p><​a class="​urlextern"​ href="http://onlinelibrary.wiley.com/doi/10.1002/dvg.22719/abstract" rel="​nofollow"​ title="​http://​onlinelibrary.wiley.com/​doi/​10.1002/​dvg.22719/​abstract">​Biallelic genome modification in F0 Xenopus tropicalis ​embryos using the CRISPR/Cas system</​a><​br /> 
-Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q\\ +Blitz I, Biesinger J, Xie X, and Cho K<br /> 
-BMC Systems Biology 20148:3+<​em>​Genesis</​em>​2013.</​p>​
  
-[[http://emboj.embopress.org/​content/​early/​2014/03/04/embj.201386537|Fip1 regulates ​mRNA alternative polyadenylation to promote stem cell self-renewal]]\\ +<​p><​a class="​urlextern"​ href="http://rnajournal.cshlp.org/​content/​early/​2013/10/22/rna.042317.113.abstract"​ rel="​nofollow"​ title="​http://​rnajournal.cshlp.org/​content/​early/​2013/​10/​22/​rna.042317.113.abstract">​Overlapping and distinct functions of CstF64 and CstF64t in mammalian ​mRNA 3&​acirc;​€&​sup2;​ processing</​a><​br /> 
-Lackford B, Yao C, Charles GM, Weng L, Zheng X, Choi EA, Xie X, Wan J, Xing Y, Freudenberg JMYang PJothi R, Hu G, Shi Y\\ +Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJTu PGYates JRand Shi Y<br /> 
-EMBO J. 2014 Mar 4. +<​em>​RNA</​em>, ​2013</p>
-==== 2013 ====+
  
-[[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082146|Low-Rank Regularization for Learning Gene Expression Programs]] \\ +<​p><​a class="​urlextern"​ href="http://arxiv.org/abs/1305.0855"​ rel="​nofollow"​ title="​http://arxiv.org/abs/1305.0855">​Inference in Kingman&#​39;​s Coalescent with Particle Markov Chain Monte Carlo Method</​a><​br /> 
-Ye G, Tang M, Nie Q and Xie X\\ +Chen Y and Xie X<br /> 
-//PLOS ONE//, 2013+<​em>​arXiv<​/em>, 2013</p>
  
-[[http://www.hindawi.com/journals/cmmm/2013/873595/|A gradient boosting algorithm for survival analysis via direct optimization of concordance index]] \\ +<​p><​a class="​urlextern"​ href="http://www.biomedcentral.com/content/pdf/1471-2105-14-S5-S4.pdf"​ rel="​nofollow"​ title="​http:​//www.biomedcentral.com/​content/​pdf/​1471-2105-14-S5-S4.pdf">​Discovering and Mapping Chromatin States Using a Tree Hidden Markov Model</​a><​br /> 
-Chen Y, Jia Z, Mercola D and Xie X\\ +Biesinger J, Wang Y, and Xie X<br /> 
-//Comput Math Methods Med.//, 2013+<​em>​BMC Bioinformatics<​/em> 2013, 14(S5):S4, 2013<​br ​/
 +<a class="​urlextern"​ href="​http://​www.biomedcentral.com/content/supplementary/​1471-2105-14-s5-s4-s1.pdf"​ rel="​nofollow"​ title="​http://​www.biomedcentral.com/​content/​supplementary/​1471-2105-14-s5-s4-s1.pdf">​Supplemental Information</​a></​p>​
  
-[[http://onlinelibrary.wiley.com/doi/10.1002/dvg.22719/abstract|Biallelic genome modification ​in F0 Xenopus tropicalis embryos using the CRISPR/Cas system]]\\ +<​p><​a class="​urlextern"​ href="http://www.biomedcentral.com/1471-2105/​14/​S5/​S11"​ rel="​nofollow"​ title="​http:​//www.biomedcentral.com/​1471-2105/​14/​S5/S11">​A mixture model for expression deconvolution from RNA-seq ​in heterogeneous tissues</a><br /> 
-Blitz I, Biesinger J, Xie X, and Cho K\\ +Li Y and Xie X<br /> 
-//Genesis//, 2013.+<​em>​BMC Bioinformatics<​/em> 2013, 14(Suppl 5):S11, 2013</p>
  
-[[http://rnajournal.cshlp.org/content/early/2013/10/22/rna.042317.113.abstract|Overlapping and distinct functions of CstF64 and CstF64t in mammalian mRNA 3′ processing]]\\ +<​p><​a class="​urlextern"​ href="http://ieeexplore.ieee.org/stamp/stamp.jsp?​tp=&​amp;​arnumber=6544889"​ rel="​nofollow"​ title="​http:​//ieeexplore.ieee.org/stamp/stamp.jsp?​tp=&​amp;​arnumber=6544889">​Efficient direct search on compressed genomic data</​a><​br /> 
-Yao CChoi EWeng LXie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y\\ +Yang XWang BLi CWang J, and Xie X<​br ​/
-//RNA//, 2013+<​em>​IEEE International Conference on Data Engineering (ICDE)</em>, 2013</​p>​ 
 +</​div>​
  
-[[http://​arxiv.org/​abs/​1305.0855|Inference in Kingman'​s Coalescent with Particle Markov Chain Monte Carlo Method]] \\ +<​h3>​2012<​/h3>
-Chen Y and Xie X \\ +
-//arXiv//, 2013+
  
-[[http://www.biomedcentral.com/​content/​pdf/1471-2105-14-S5-S4.pdf|Discovering ​and Mapping Chromatin States Using Tree Hidden Markov Model]] \\ +<div class="​level3">​ 
-Biesinger J, Wang Y, and Xie X \\ +<​p><​a class="​urlextern"​ href="http://www.springerlink.com/​content/​4l2m27p3867xj584/" rel="​nofollow"​ title="​http://​www.springerlink.com/​content/​4l2m27p3867xj584/">​Learning sparse gradients for variable selection ​and dimension reduction</​a><br /> 
-//BMC Bioinformatics//​ 201314(S5):S42013 \\ +Ye G and Xie X<​br ​/
-[[http://www.biomedcentral.com/content/supplementary/1471-2105-14-s5-s4-s1.pdf|Supplemental Information]]+Machine Learning Journal87(3):303-3552012<br /> 
 +<a class="​urlextern"​ href="http://www.ics.uci.edu/~xhx/publications/SGL.pdf" rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​SGL.pdf">​Preprint</​a></​p>​
  
-[[http://www.biomedcentral.com/1471-2105/14/S5/S11|A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues]] \\ +<​p><​a class="​urlextern"​ href="http://www.ncbi.nlm.nih.gov/pubmed/23112178"​ rel="​nofollow"​ title="​http:​//www.ncbi.nlm.nih.gov/​pubmed/​23112178">​Transcriptome-wide analyses of CstF64-RNA interactions ​in global regulation of mRNA alternative polyadenylation</​a><​br /> 
-Li and Xie X \\ +Yao C, Biesinger J,Wan J,Weng L, Busch A, Xing YXie X, and Shi Y<​br ​/
-//BMC Bioinformatics// 201314(Suppl 5):S112013+PNAS109(46):18773-82012</​p>​
  
-[[http://ieeexplore.ieee.org/stamp/stamp.jsp?​tp=&​arnumber=6544889|Efficient direct search on compressed genomic data]] \\ +<​p><​a class="​urlextern"​ href="http://www.ncbi.nlm.nih.gov/pubmed/22296850"​ rel="​nofollow"​ title="​http://​www.ncbi.nlm.nih.gov/​pubmed/​22296850">​Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR</​a><​br /> 
-Yang XWang B, Li C, Wang J, and Xie X \\ +Kim Chong HBiesinger ​J, Seo YK, Xie X, Osborne TF<​br ​/> 
-//IEEE International Conference on Data Engineering (ICDE)//, 2013 +BMC Genomics, ​2012</p>
-==== 2012 ====+
  
-[[http://www.springerlink.com/content/4l2m27p3867xj584/|Learning sparse gradients ​for variable selection and dimension reduction]] \\ +<​p><​a class="​urlextern"​ href="http://www.ncbi.nlm.nih.gov/pubmed/22199254"​ rel="​nofollow"​ title="​http:​//​www.ncbi.nlm.nih.gov/​pubmed/​22199254">​Hobbes:​ optimized gram-based methods ​for efficient read alignment</​a><​br /> 
-Ye G and Xie X \\ +Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X<br /> 
-Machine Learning Journal87(3):303-355, 2012 \\ +Nucleic Acids Research40(6):e41, 2012<br /> 
-[[http://www.ics.uci.edu/​~xhx/publications/SGL.pdf|Preprint]]+Software: <a class="​urlextern"​ href="http://hobbes.ics.uci.edu/​" rel="​nofollow"​ title="​http:​//hobbes.ics.uci.edu/">​Hobbes</​a></​p>​ 
 +</​div>​
  
-[[http://​www.ncbi.nlm.nih.gov/​pubmed/​23112178|Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation]] \\ +<​h3>​2011<​/h3>
-Yao C, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y \\ +
-PNAS, 109(46):​18773-8,​ 2012+
  
-[[http://www.ncbi.nlm.nih.gov/pubmed/22296850|Genome-wide analysis of hepatic LRH-1 reveals ​promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR]] \\ +<div class="​level3">​ 
-Kim Chong HBiesinger JSeo YK, Xie X, Osborne TF \\ +<​p><​a class="​urlextern"​ href="http://arxiv.org/​pdf/​1110.3076v1"​ rel="​nofollow"​ title="​http://​arxiv.org/pdf/​1110.3076v1">​Efficient latent variable graphical model selection via split Bregman method</a><br /> 
-BMC Genomics2012+Ye GWang YChen Yand Xie X<br /> 
 +arXiv:​1110.3076v12011</​p>​
  
-[[http://​www.ncbi.nlm.nih.gov/​pubmed/​22199254|Hobbesoptimized gram-based methods ​for efficient read alignment]] \\ +<​p><​a class="​urlextern"​ href="http://​www.ncbi.nlm.nih.gov/​pubmed/​22208852"​ rel="​nofollow"​ title="​http://​www.ncbi.nlm.nih.gov/​pubmed/​22208852">​MotifMapintegrative genome-wide maps of regulatory motif sites for model species. </​a><​br /> 
-Ahmadi ABehm AHonnalli NLi C, Weng L, and Xie X  \\ +Daily KPatel VRRigor P, Xie X, Baldi P.<br /> 
-Nucleic Acids Research40(6):​e41, ​ 2012 \\ +BMC Bioinformatics,​ 2011</p>
-Software: [[http://​hobbes.ics.uci.edu/|Hobbes]]+
  
-==== 2011 ====+<​p><​a class="​urlextern"​ href="​http://​www.nature.com/​nature/​journal/​vaop/​ncurrent/​full/​nature10530.html"​ rel="​nofollow"​ title="​http://​www.nature.com/​nature/​journal/​vaop/​ncurrent/​full/​nature10530.html">​A high-resolution map of human evolutionary constraint using 29 mammals</​a><​br /> 
 +Lindblad-Toh,​ Barber, Zuk, Lin, et al.<br /> 
 +Nature, ​2011</p>
  
-[[http://arxiv.org/pdf/1110.3076v1|Efficient latent variable graphical model selection via split Bregman method]] \\ +<​p><​a class="​urlextern"​ href="http://www.biomedcentral.com/1471-2105/12/99" rel="​nofollow"​ title="​http://​www.biomedcentral.com/​1471-2105/​12/​99">​SNP-based pathway enrichment analysis for genome-wide association studies</​a><​br /> 
-Ye G, Wang YChen Y, and Xie X \\ +Weng L, Macciardi F, Subramanian A, Guffanti ​G, Potkin SGYu Z, and Xie X<br /> 
-arXiv:​1110.3076v1, 2011+BMC Bioinformatics, 2011<br /> 
 +Software: <a class="​urlextern"​ href="​http://​cbcl.ics.uci.edu/​SSEA/"​ rel="​nofollow"​ title="​http://​cbcl.ics.uci.edu/​SSEA/">​SNP Set Enrichment Analysis (SSEA)</​a></​p>​
  
-[[http://www.ncbi.nlm.nih.gov/pubmed/22208852|MotifMap:​ integrative genome-wide maps of regulatory motif sites for model species. ]] \\ +<​p><​a class="​urlextern"​ href="http://www.cell.com/​cell-metabolism/​abstract/​S1550-4131(11)00092-1"​ rel="​nofollow"​ title="​http://​www.cell.com/cell-metabolism/abstract/​S1550-4131(11)00092-1">​Genome-wide Positioning ​of SREBP-2 in Hepatic Chromatin Predicts a Novel Role in Autophagy </​a><​br /> 
-Daily KPatel VRRigor P, Xie X, Baldi P. \\ +Seo YJeon T Chong H, Beisinger J, Xie X, and Osborne TF<br /> 
-BMC Bioinformatics, 2011+<​em>​Cell Metabolism</​em>,​ 13:367-75, 2011<br /> 
 +<a class="​urlextern"​ href="​http://​www.sciencedaily.com/​releases/​2011/​04/​110405122330.htm"​ rel="​nofollow"​ title="​http://​www.sciencedaily.com/​releases/​2011/​04/​110405122330.htm">​Science Daily coverage</​a></​p>​
  
-[[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10530.html|A high-resolution map of human evolutionary constraint using 29 mammals]] \\ +<​p><​a class="​urlextern"​ href="http://www.ics.uci.edu/~xhx/publications/arem_recomb.pdf"​ rel="​nofollow"​ title="​http:​//www.ics.uci.edu/~xhx/​publications/​arem_recomb.pdf">​AREM:​ aligning short reads from ChIP-sequencing by expectation maximization</​a><​br /> 
-Lindblad-TohBarberZukLinet al. \\ +Newkirk DBiesingerJChon AYokomori K, and Xie X<br /> 
-Nature, 2011+<em>J Comput Biol.</​em>​, 2011<br /> 
 +Software: <a class="​urlextern"​ href="​http://​sourceforge.net/​projects/​arem"​ rel="​nofollow"​ title="​http://​sourceforge.net/​projects/​arem">​AREM</​a></​p>​
  
-[[http://www.biomedcentral.com/1471-2105/12/99|SNP-based pathway enrichment analysis for genome-wide association studies]] \\ +<​p><​a class="​urlextern"​ href="http://jmlr.csail.mit.edu/proceedings/​papers/​v15/​ye11a/​ye11a.pdf"​ rel="​nofollow"​ title="​http://​jmlr.csail.mit.edu/​proceedings/​papers/​v15/​ye11a/​ye11a.pdf">​Efficient variable selection in support vector machines via the alternating direction method of multipliers </a><​br ​/> 
-Weng L, Macciardi F, Subramanian A, Guffanti ​G, Potkin SG, Yu Z, and Xie X \\ +Ye G, Chen Y, and Xie X<br /> 
-BMC Bioinformatics, 2011  \\ +AI &amp; STATS , 2011</p> 
-Software: [[http://cbcl.ics.uci.edu/​SSEA/​|SNP Set Enrichment Analysis (SSEA)]]+</div>
  
-[[http://​www.cell.com/​cell-metabolism/​abstract/​S1550-4131(11)00092-1|Genome-wide Positioning of SREBP-2 in Hepatic Chromatin Predicts a Novel Role in Autophagy ]] \\ +<​h3>​2010<​/h3>
-Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF \\ +
-//Cell Metabolism//,​ 13:367-75, 2011  \\ +
-[[http://​www.sciencedaily.com/​releases/​2011/​04/​110405122330.htm|Science Daily coverage]]+
  
-[[http://www.ics.uci.edu/~xhx/publications/arem_recomb.pdf|AREM: aligning short reads from ChIP-sequencing by expectation maximization]] \\ +<div class="​level3">​ 
-Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X \\ +<​p><​a class="​urlextern"​ href="http://arxiv4.library.cornell.edu/abs/1012.0975"​ rel="​nofollow"​ title="​http:​//​arxiv4.library.cornell.edu/​abs/​1012.0975">​Split Bregman method for sparse inverse covariance estimation with matrix iteration acceleration</​a><​br /> 
-//J Comput Biol.//, 2011 \\ +Ye GCai J, and Xie X<​br ​/> 
-Software[[http://​sourceforge.net/​projects/arem|AREM]]+arXiv:1012.0975v1, 2010</p>
  
-[[http://jmlr.csail.mit.edu/proceedings/papers/v15/ye11a/ye11a.pdf|Efficient variable selection in support vector machines via the alternating direction ​method ​of multipliers ]] \\ +<​p><​a class="​urlextern"​ href="http://www.sciencedirect.com/science?​_ob=ArticleURL&​amp;​_udi=B6V8V-51BBKR7-1&​amp;​_user=10&​amp;​_coverDate=10/27/2010&​amp;​_rdoc=1&​amp;​_fmt=high&​amp;​_orig=search&​amp;​_origin=search&​amp;​_sort=d&​amp;​_docanchor=&​amp;​view=c&​amp;​_acct=C000050221&​amp;​_version=1&​amp;​_urlVersion=0&​amp;​_userid=10&​amp;​md5=6ff4ea0404367278249b06c9a59f84fd&​amp;​searchtype=a"​ rel="​nofollow"​ title="​http:​//www.sciencedirect.com/​science?​_ob=ArticleURL&​amp;​_udi=B6V8V-51BBKR7-1&​amp;​_user=10&​amp;​_coverDate=10/​27/​2010&​amp;​_rdoc=1&​amp;​_fmt=high&​amp;​_orig=search&​amp;​_origin=search&​amp;​_sort=d&​amp;​_docanchor=&​amp;​view=c&​amp;​_acct=C000050221&​amp;​_version=1&​amp;​_urlVersion=0&​amp;​_userid=10&​amp;​md5=6ff4ea0404367278249b06c9a59f84fd&​amp;​searchtype=a">​Split Bregman ​method ​for large scale fused Lasso</​a><​br /> 
-Ye G, Chen Y, and Xie X \\ +Ye G-B and Xie X<br /> 
-AI & STATS 2011+Computational Statistics and Data Analysisdoi:​10.1016/​j.csda.2010.10.0212010<br /> 
 +<a class="​urlextern"​ href="​http://​arxiv.org/​abs/​1006.5086"​ rel="​nofollow"​ title="​http://​arxiv.org/​abs/​1006.5086">​arXiv version</​a>​ <a class="​urlextern"​ href="​http://​www.biomedcentral.com/​1471-2105/​11/​514"​ rel="​nofollow"​ title="​http://​www.biomedcentral.com/​1471-2105/​11/​514">​Data Structures ​and Compression Algorithms for High-Throughput Sequencing Technologies</​a><​br /> 
 +Daily K, Rigor P, Christley S, Xie X and Baldi P<br /> 
 +<​em>​BMC Bioinformatics</​em>​,11:514, 2010</​p>​
  
-==== 2010 ====+<​p><​a class="​urlextern"​ href="​http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​btq414"​ rel="​nofollow"​ title="​http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​btq414">​Interactive and fuzzy search: a dynamic way to explore MEDLINE </​a><​br /> 
 +Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J<br /> 
 +<​em>​Bioinformatics</​em>,​ 26(18):​2321-2327, ​2010<br /> 
 +<a class="​urlextern"​ href="​http://​ipubmed.ics.uci.edu/"​ rel="​nofollow"​ title="​http://​ipubmed.ics.uci.edu/">​iPubMed Search</​a></​p>​
  
-[[http://arxiv4.library.cornell.edu/abs/1012.0975|Split Bregman method for sparse ​inverse covariance estimation with matrix iteration acceleration]] \\ +<​p><​a class="​urlextern"​ href="http://arxiv.org/​abs/​1006.5060" rel="​nofollow"​ title="​http://​arxiv.org/abs/1006.5060">​Variable selection and dimension reduction via sparse ​gradients</​a><​br /> 
-Ye G, Cai J, and Xie X \\ +Ye G-B and Xie X<br /> 
-arXiv:1012.0975v1, 2010+arXiv:1006.5060v2, 2010</p>
  
-[[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V8V-51BBKR7-1&_user=10&​_coverDate=10/27/2010&​_rdoc=1&​_fmt=high&​_orig=search&​_origin=search&_sort=d&_docanchor=&view=c&​_acct=C000050221&​_version=1&​_urlVersion=0&​_userid=10&​md5=6ff4ea0404367278249b06c9a59f84fd&​searchtype=a|Split Bregman method for large scale fused Lasso]] \\ +<​p><​a class="​urlextern"​ href="http://nl.sitestat.com/elsevier/​elsevier-com/​s?sciencedirect&amp;ns_type=clickout&amp;ns_url=http://www.sciencedirect.com/​science?​_ob=GatewayURL&amp;_origin=IRSSCONTENT&amp;_method=citationSearch&amp;_piikey=S1053811910008803&amp;_version=1&​amp;md5=09cea6babd4cf018d170933615df4755"​ rel="​nofollow"​ title="​http://nl.sitestat.com/elsevier/elsevier-com/​s?​sciencedirect&​amp;​ns_type=clickout&​amp;​ns_url=http://www.sciencedirect.com/science?​_ob=GatewayURL&​amp;​_origin=IRSSCONTENT&​amp;​_method=citationSearch&​amp;​_piikey=S1053811910008803&​amp;​_version=1&​amp;​md5=09cea6babd4cf018d170933615df4755">​Identifying gene regulatory networks in Schizophrenia<​/a><​br ​/> 
-Ye G-B and Xie X \\ +Potkin SGMacciardi FGuffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X<br /> 
-Computational Statistics and Data Analysis, doi:​10.1016/​j.csda.2010.10.021,​ 2010  \\ +<​em>​NeuroImage<​/em> 53:839-847, 2010</p>
-[[http://arxiv.org/abs/1006.5086|arXiv version]] [[http://www.biomedcentral.com/1471-2105/11/514|Data Structures and Compression Algorithms for High-Throughput Sequencing Technologies]] \\ +
-Daily KRigor PChristley S, Xie X and Baldi P  \\ +
-//BMC Bioinformatics//,​11:514, 2010+
  
-[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/​btq414|Interactive and fuzzy search: a dynamic way to explore MEDLINE ]] \\ +<​p><​a class="​urlextern"​ href="http://www.biomedcentral.com/1752-0509/4/99" rel="​nofollow"​ title="​http://​www.biomedcentral.com/​1752-0509/​4/​99">​Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent</​a><br /> 
-Wang JCetindil I, Ji S, Li C, Xie X, Li G and Feng J \\ +Wang YChristley ​S, Mjolsness Eand Xie X<br /> 
-//​Bioinformatics//​26(18):2321-2327, 2010  \\ +<​em>​BMC Systems Biology</em>4:99 doi:​10.1186/​1752-0509-4-99, 2010</p>
-[[http://​ipubmed.ics.uci.edu/|iPubMed Search]]+
  
-[[http://arxiv.org/abs/1006.5060|Variable selection and dimension reduction via sparse gradients]] \\ +<​p><​a class="​urlextern"​ href="http://www.springerlink.com/content/428v02087m218878/​fulltext.pdf" rel="​nofollow"​ title="​http://​www.springerlink.com/​content/​428v02087m218878/​fulltext.pdf">​Site-frequency Spectrum of Linked Sites</​a><​br /> 
-Ye G-B and Xie X \\ +Xie X<br /> 
-arXiv:1006.5060v2, 2010+<​em>​Bulletin of Mathematical Biology</​em>,​ DOI10.1007/​s11538-010-9534-3, 2010</p>
  
-[[http://nl.sitestat.com/elsevier/elsevier-com/s?​sciencedirect&​ns_type=clickout&​ns_url=http://www.sciencedirect.com/science?​_ob=GatewayURL&​_origin=IRSSCONTENT&​_method=citationSearch&​_piikey=S1053811910008803&​_version=1&​md5=09cea6babd4cf018d170933615df4755|Identifying gene regulatory networks in Schizophrenia]] \\ +<​p><​a class="​urlextern"​ href="http://nar.oxfordjournals.org/cgi/content/​abstract/gkq397"​ rel="​nofollow"​ title="http://nar.oxfordjournals.org/cgi/​content/​abstract/​gkq397">​Genome-Wide Interrogation of Hepatic FXR Reveals an Asymmetric IR-Motif and Synergy with LRH-1</​a><​br /> 
-Potkin SGMacciardi FGuffanti GWang QTurner JALakatos AMiles MFLander AVawter MPXie X \\ +Chong HInfante ASeo YJeon TAhang YEdwards PXie Xand Osborne TF<br /> 
-//NeuroImage// 53:839-847, 2010+Nucleic Acids Researchdoi:​10.1093/​nar/​gkq3972010<br /> 
 +<a class="​urlextern"​ href="​http:​//cbcl.ics.uci.edu/public_data/FXR/" rel="​nofollow"​ title="​http://​cbcl.ics.uci.edu/​public_data/​FXR/">​Online Supplementary Materials</​a></​p>​
  
-[[http://​www.biomedcentral.com/​1752-0509/4/99|Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent]] \\ +<​p><​a class="​urlextern"​ href="http://​www.biomedcentral.com/​1471-2164/11/208/​abstract"​ rel="​nofollow"​ title="​http://​www.biomedcentral.com/​1471-2164/​11/​208/​abstract">​Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes</​a><​br /> 
-Wang YChristley SMjolsness E, and Xie X \\ +Kumar LBreakspear AKistler HC, Ma L-J, and Xie X<br /> 
-//BMC Systems Biology//, 4:99 doi:10.1186/1752-0509-4-99,​ 2010+<​em>​BMC Genomics<​/em> 11:208, 2010<​br ​/
 +<a class="​urlextern"​ href="​http:​//www.broadinstitute.org/​annotation/​genome/​fusarium_group/​SupplementalMaterials.html"​ rel="​nofollow"​ title="​http://​www.broadinstitute.org/​annotation/​genome/​fusarium_group/​SupplementalMaterials.html">​Supplementary Information</​a><​br /> 
 +<a class="​urlextern"​ href="​http://​www.broadinstitute.org/annotation/​genome/​fusarium_group/​MultiHome.html"​ rel="​nofollow"​ title="​http://​www.broadinstitute.org/​annotation/​genome/​fusarium_group/​MultiHome.html">​Fusarium Comparative Database</​a></​p>​
  
-[[http://www.springerlink.com/content/428v02087m218878/fulltext.pdf|Site-frequency Spectrum of Linked Sites]] \\ +<​p><​a class="​urlextern"​ href="http://www.nature.com/nature/journal/v464/​n7287/​abs/​nature08850.html" rel="​nofollow"​ title="​http://​www.nature.com/​nature/​journal/​v464/​n7287/​abs/​nature08850.html">​Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium oxysporum</​a><​br /> 
-Xie X   \\ +Ma L-J, et al.<br /> 
-//Bulletin ​of Mathematical Biology//, DOI10.1007/s11538-010-9534-3, 2010+<​em>​Nature</​em>​ 464:​367-373,​ 2010<br /> 
 +<a class="​urlextern"​ href="​http://​www.broadinstitute.org/​news/​1439"​ rel="​nofollow"​ title="​http://​www.broadinstitute.org/news/1439">​The chromosomal secrets ​of a plant pathogen<​/a><​br ​/
 +<a class="​urlextern"​ href="​http://www.genomeweb.com//​node/​936293?​hq_e=el&​amp;​hq_m=655129&​amp;​hq_l=3&​amp;​hq_v=dfec329446"​ rel="​nofollow"​ title="​http://​www.genomeweb.com//​node/​936293?​hq_e=el&​amp;​hq_m=655129&​amp;​hq_l=3&​amp;​hq_v=dfec329446">​Comparative genomics reveals horizontal gene transfer in pathogenic fungus</​a><​br /> 
 +<a class="​urlextern"​ href="​http://​www.broadinstitute.org/​annotation/​genome/​fusarium_group/​MultiHome.html"​ rel="​nofollow"​ title="​http://​www.broadinstitute.org/​annotation/​genome/​fusarium_group/​MultiHome.html">​Fusarium Comparative Database</​a></​p>​ 
 +</​div>​
  
-[[http://​nar.oxfordjournals.org/​cgi/​content/​abstract/​gkq397|Genome-Wide Interrogation of Hepatic FXR Reveals an Asymmetric IR-1 Motif and Synergy with LRH-1]] \\ +<​h3>​2009<​/h3>
-Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and Osborne TF \\ +
-Nucleic Acids Research, doi:​10.1093/​nar/​gkq397,​ 2010 \\ +
-[[http://​cbcl.ics.uci.edu/​public_data/​FXR/​|Online Supplementary Materials]]+
  
-[[http://www.biomedcentral.com/1471-2164/11/208/​abstract|Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes]] \\ +<div class="​level3">​ 
-Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X  \\ +<​p><​a class="​urlextern"​ href="http://www.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf"​ rel="​nofollow"​ title="​http://www.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf">​Incorporating existing network information into gene network inference<​/a><br /> 
-//BMC Genomics// 11:208, 2010 \\ +Christley S, Nie Q and Xie X<​br ​/
-[[http://www.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html|Supplementary Information]] \\ +<​em>​PLoS ONE</em> 4(8): e6799doi:10.1371/journal.pone.0006799 (2009)</p>
-[[http://www.broadinstitute.org/annotation/genome/​fusarium_group/​MultiHome.html|Fusarium Comparative Database]]+
  
-[[http://www.nature.com/nature/journal/v464/n7287/abs/nature08850.html|Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium oxysporum]] \\ +<​p><​a class="​urlextern"​ href="http://www.pnas.org/content/early/2009/08/03/0904246106.abstract"​ rel="​nofollow"​ title="​http://www.pnas.org/content/early/2009/08/​03/​0904246106.abstract">​Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif</a><​br ​/
-Ma L-J, et al.  \\ +Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF<​br ​/> 
-//Nature// 464:​367-373,​ 2010 \\ +<​em>​Proc Natl Acad Sci USA</​em>​ doi:10.1073/pnas.0904246106 (2009)</p>
-[[http://www.broadinstitute.org/news/1439|The chromosomal secrets of a plant pathogen]] \\ +
-[[http://www.genomeweb.com//node/936293?​hq_e=el&​hq_m=655129&​hq_l=3&​hq_v=dfec329446|Comparative genomics reveals horizontal gene transfer in pathogenic fungus]] \\ +
-[[http://www.broadinstitute.org/annotation/​genome/​fusarium_group/​MultiHome.html|Fusarium Comparative Database]]+
  
-==== 2009 ====+<​p><​a class="​urlextern"​ href="​http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​12/​i54"​ rel="​nofollow"​ title="​http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​12/​i54">​Identifying novel constrained elements by exploiting biased substitution patterns</​a><​br /> 
 +Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X<br /> 
 +<​em>​Bioinformatics</​em>​25:​i54-i62 (2009)<br /> 
 +<a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​siphy_suppinfo.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​siphy_suppinfo.pdf">​Supplementary Methods</​a><​br /> 
 +<a class="​urlextern"​ href="​http://​www.broadinstitute.org/​genome_bio/​siphy/"​ rel="​nofollow"​ title="​http://​www.broadinstitute.org/​genome_bio/​siphy/">​SiPhy (SIte-specific PHYlogenetic analysis) Java software package</​a></​p>​
  
-[[http://www.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf|Incorporating existing network information into gene network inference]] \\ +<​p><​a class="​urlextern"​ href="http://www.pnas.org/content/early/2009/​02/​11/​0813264106.abstract"​ rel="​nofollow"​ title="​http://​www.pnas.org/​content/​early/​2009/​02/​11/​0813264106.abstract">​Comparative genomics allows the discovery of cis-regulatory elements in mosquitoes</​a><​br /> 
-Christley SNie Q and Xie X \\ +Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA<​br ​/
-//PLoS ONE// 4(8): e6799. ​doi:10.1371/journal.pone.0006799 ​(2009)+<​em>​Proc Natl Acad Sci USA</em> ​doi:10.1073/pnas.0813264106 ​(2009)</p>
  
-[[http://www.pnas.org/​content/​early/2009/08/03/0904246106.abstract|Genome-wide analysis of SREBP-1 binding ​in mouse liver chromatin reveals ​preference for promoter proximal binding to a new motif]] \\ +<​p><​a class="​urlextern"​ href="http://genome.cshlp.org/​content/​19/4/567.long"​ rel="​nofollow"​ title="​http:​//genome.cshlp.org/​content/​19/​4/​567.long">​Common polymorphic transcript variation ​in human disease</​a><br /> 
-Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF \\ +Fraser H and Xie X<br /> 
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0904246106 ​(2009)+<​em>​Genome Research<​/em> ​doi:10.1101/gr.083477.108 ​(2009)<br /> 
 +<a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​PTV_GR2009.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​PTV_GR2009.pdf">​PDF</​a></​p>​
  
-[[http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​12/i54|Identifying novel constrained elements by exploiting biased substitution patterns]] \\ +<​p><​a class="​urlextern"​ href="http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​2/167" rel="​nofollow"​ title="​http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​2/​167">​MotifMap:​ a human genome-wide map of candidate regulatory motif sites </​a><​br /> 
-Garber MGuttman1 M, Clamp M, Zody MG, Friedman N, and Xie X \\ +Xie XRigor P, and Baldi P<br /> 
-//Bioinformatics/​/25:i54-i62 (2009) ​ \\ +<em>Bioinformatics</em> ​25: 167-174 (2009)<br /> 
-[[http://​www.ics.uci.edu/​~xhx/​publications/​siphy_suppinfo.pdf|Supplementary Methods]] \\ +<a class="​urlextern"​ href="http://​www.ics.uci.edu/​~xhx/​publications/​MotifMap_Supp_Info.pdf" rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​MotifMap_Supp_Info.pdf">​Supplementary Methods</​a><​br /> 
-[[http://www.broadinstitute.org/genome_bio/siphy/|SiPhy (SIte-specific PHYlogenetic analysis) Java software package]]+<a class="​urlextern"​ href="http://motifmap.ics.uci.edu/" rel="​nofollow"​ title="​http:​//motifmap.ics.uci.edu/">​MotifMap Server</​a></​p>​
  
-[[http://www.pnas.org/​content/​early/2009/02/11/0813264106.abstract|Comparative genomics allows the discovery of cis-regulatory elements in mosquitoes]] \\ +<​p><​a class="​urlextern"​ href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/274" rel="​nofollow"​ title="​http:​//​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​2/​274">​Human genomes as email attachments </​a><​br /> 
-Sieglaff DHDunn WAXie X, Megy K, Marinotti O, and James AA  \\ +Christley SLu YLi C, and Xie X<br /> 
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0813264106 (2009)+<​em>​Bioinformatics </em> 25: 274-275 (2009)<​br ​/
 +<a class="​urlextern"​ href="​http:​//www.ics.uci.edu/​~xhx/​project/​DNAzip"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/~xhx/​project/​DNAzip">​DNAzip:​ DNA sequence compression using a reference genome</​a><​br /> 
 +<a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​DNAzip.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​DNAzip.pdf">​PDF</​a><​br /> 
 +<a class="​urlextern"​ href="​http://​www.genomeweb.com/​informatics/​jim-watsonâ��s-genome-e-mail-uc-irvine-team-develops-method-compress-genomic-data"​ rel="​nofollow"​ title="​http://​www.genomeweb.com/​informatics/​jim-watsonâ��s-genome-e-mail-uc-irvine-team-develops-method-compress-genomic-data">​News featured in genomeweb</​a><​br /> 
 +<a class="​urlextern"​ href="​http://​www.bio-itworld.com/​news/​2009/​01/​30/​Email-compression-genome.html"​ rel="​nofollow"​ title="​http://​www.bio-itworld.com/​news/​2009/​01/​30/​Email-compression-genome.html">​News featured in bio-itworld</​a><​br /> 
 +<a class="​urlextern"​ href="​http://​www.amia.org/​content/​2009-summit-translational-bioinformatics-closing-session"​ rel="​nofollow"​ title="​http://​www.amia.org/​content/​2009-summit-translational-bioinformatics-closing-session">​One of the 20 most important papers in Translational Bioinformatics in </​a><​a class="​urlextern"​ href="​http://​www.amia.org/​content/​2009-summit-translational-bioinformatics-closing-session"​ rel="​nofollow"​ title="​http://​www.amia.org/​content/​2009-summit-translational-bioinformatics-closing-session">​2009</​a>​as reviewed by Russ Altman of Stanford</​p>​ 
 +</​div>​
  
-[[http://​genome.cshlp.org/​content/​19/​4/​567.long|Common polymorphic transcript variation in human disease]] \\ +<​h3>​2008<​/h3>
-Fraser H and Xie X  \\ +
-//Genome Research// doi:​10.1101/​gr.083477.108 (2009) \\ +
-[[http://​www.ics.uci.edu/​~xhx/​publications/​PTV_GR2009.pdf|PDF]]+
  
-[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/167|MotifMap:​ a human genome-wide map of candidate ​regulatory ​motif sites ]] \\ +<div class="​level3">​ 
-Xie XRigor P, and Baldi P  \\ +<​p><​a class="​urlextern"​ href="http://www.ics.uci.edu/~xhx/publications/wu_motif_2008.pdf"​ rel="​nofollow"​ title="​http:​//www.ics.uci.edu/~xhx/​publications/​wu_motif_2008.pdf">​Discovering ​regulatory ​motifs in the Plasmodium genome using comparative genomics </​a><​br /> 
-//Bioinformatics// 25167-174 ​(2009\\ +Wu JSieglaff DH, Gervin J, and Xie X<br /> 
-[[http://​www.ics.uci.edu/​~xhx/​publications/​MotifMap_Supp_Info.pdf|Supplementary Methods]] \\ +<​em>​Bioinformatics </em> 24:1843-9 (2008)<​br ​/
-[[http://motifmap.ics.uci.edu/​|MotifMap Server]]+<a class="​urlextern"​ href="​http:​//www.ics.uci.edu/​~xhx/​project/​mdos/"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​project/​mdos/">​MDOS software</​a>:​ A method for Motif Discovery using Orthologous Sequences ​(alignment independent).<br /> 
 +<a class="​urlextern"​ href="http://​www.ics.uci.edu/​~xhx/​publications/​wu_motif_2008_suppinfo.pdf" rel="​nofollow"​ title="​http://www.ics.uci.edu/​~xhx/​publications/​wu_motif_2008_suppinfo.pdf">​Supplementary Information on the MDOS algorithm</​a></​p>​
  
-[[http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​2/​274|Human genomes as email attachments ]] \\ +<​p><​a class="​urlextern"​ href="http://www.pubmedcentral.nih.gov/picrender.fcgi?​artid=2567431&​amp;​blobtype=pdf"​ rel="​nofollow"​ title="​http://www.pubmedcentral.nih.gov/picrender.fcgi?​artid=2567431&​amp;​blobtype=pdf">​Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains </a><​br ​/
-Christley S, Lu Y, Li C, and Xie X  \\ +Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE<​br ​/> 
-//​Bioinformatics // 25: 274-275 (2009) \\ +<​em>​PLoS </em><​em>​Genetics<​/em>​4(10):​e1000242 (2008)</p> 
-[[http://www.ics.uci.edu/~xhx/​project/​DNAzip|DNAzip:​ DNA sequence compression using a reference genome]] \\ +</div>
-[[http://www.ics.uci.edu/~xhx/​publications/​DNAzip.pdf|PDF]] \\ +
-[[http://www.genomeweb.com/informatics/​jim-watsonâ��s-genome-e-mail-uc-irvine-team-develops-method-compress-genomic-data|News featured in genomeweb]] \\ +
-[[http://www.bio-itworld.com/news/​2009/​01/​30/​Email-compression-genome.html|News featured in bio-itworld]] \\ +
-[[http://​www.amia.org/​content/​2009-summit-translational-bioinformatics-closing-session|One of the 20 most important papers in Translational Bioinformatics in 2009]]as reviewed by Russ Altman of Stanford+
  
-==== 2008 ====+<​h3>​2007</​h3>​
  
-[[http://www.ics.uci.edu/~xhx/publications/wu_motif_2008.pdf|Discovering regulatory motifs ​in the Plasmodium ​genome ​using comparative genomics ]] \\ +<div class="​level3">​ 
-Wu JSieglaff DHGervin ​J, and Xie X  \\ +<​p><​a class="​urlextern"​ href="http://www.pnas.org/​content/​104/​49/​19428"​ rel="​nofollow"​ title="​http://​www.pnas.org/content/104/49/​19428">​Distinguishing protein-coding and noncoding genes in the human genome ​</​a><​br /> 
-//Bioinformatics // 24:​1843-9 ​(2008\\ +Clamp MFry BKamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, and Lander ES.<br /> 
-[[http://​www.ics.uci.edu/​~xhx/​project/​mdos/​|MDOS software]]: A method for Motif Discovery using Orthologous Sequences ​(alignment independent). \\ +<​em>​Proc Natl Acad Sci </em><​em>​USA<​/em>104(49):19428-33 ​(2007)</p>
-[[http://​www.ics.uci.edu/​~xhx/​publications/​wu_motif_2008_suppinfo.pdf|Supplementary Information on the MDOS algorithm]]+
  
-[[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2567431&​blobtype=pdf|Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes ​of bivalent domains ]] \\ +<​p><​a class="​urlextern"​ href="http://www.nature.com/nature/​journal/​v449/​n7164/​abs/​nature06250.html" rel="​nofollow"​ title="​http://​www.nature.com/​nature/​journal/​v449/​n7164/​abs/​nature06250.html">​Genome-wide detection ​and characterization ​of positive selection in human populations </​a><​br /> 
-Ku MKoche RPRheinbay EMendenhall EMEndoh MMikkelsen TS, Presser A, Nusbaum ​C, Xie X, Chi ASAdli MKasif SPtaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE  \\ +Sabeti PCVarilly PFry BLohmueller JHostetter ECotsapas ​C, Xie X, Byrne EHMcCarroll SAGaudet RSchaffner SF, Lander ES and International HapMap Consortium<​br /> 
-//PLoS Genetics//​4(10):e1000242 ​(2008) +<​em>​Nature<​/em>449:913-918 ​(2007)</p>
-==== 2007 ====+
  
-[[http://www.pnas.org/content/104/49/19428|Distinguishing protein-coding and noncoding genes in the human genome ]] \\ +<​p><​a class="​urlextern"​ href="http://www.nature.com/nature/journal/v448/n7153/​abs/​nature06008.html"​ rel="​nofollow"​ title="​http://​www.nature.com/​nature/​journal/​v448/​n7153/​abs/​nature06008.html">​Geome-wide maps of chromatin state in pluripotent and lineage-committed cells </​a><​br /> 
-Clamp M, Fry B, Kamal M, Xie X, Cuff JLin MF, Kellis ​M, Lindblad-Toh Kand Lander ES. \\ +Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O&#​39;​Donovan A, Presser A, Russ C, Xie X, Meissner AWernig ​M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE.<​br ​/
-//Proc Natl Acad Sci USA//​104(49):19428-33 (2007)+<​em>​Nature<​/em> 448:553-60 (2007)</p>
  
-[[http://www.nature.com/nature/journal/v449/n7164/abs/nature06250.html|Genome-wide detection and characterization ​of positive selection ​in human populations ]] \\ +<​p><​a class="​urlextern"​ href="http://www.ics.uci.edu/~xhx/publications/insulators_pnas06.pdf"​ rel="​nofollow"​ title="​http:​//www.ics.uci.edu/~xhx/​publications/​insulators_pnas06.pdf">​Systematic discovery ​of regulatory motifs ​in conserved regions of the human genomeincluding thousands of CTCF insulator sites </​a><​br /> 
-Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EHMcCarroll SAGaudet R, Schaffner SF, Lander ES and International HapMap Consortium ​ \\ +Xie X, Mikkelsen TSGnirke ALindblad-Toh KKellis M and Lander ES.<br /> 
-//Nature//449:913-918 (2007)+<​em>​Proc Natl Acad Sci </em><​em>​USA<​/em>104:7145-7150 (2007)<br /> 
 +<a class="​urlextern"​ href="​http://​www.broad.mit.edu/​personal/​xhx/​projects/​CNEMOTIF/"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​personal/​xhx/​projects/​CNEMOTIF/">​Supplementary website</​a>​ <a class="​urlextern"​ href="​http://​www.pnas.org/​cgi/​content/​full/​0701811104/​DC1"​ rel="​nofollow"​ title="​http://​www.pnas.org/​cgi/​content/​full/​0701811104/​DC1">​Supporting Information</​a>​ <a class="​urlextern"​ href="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=3042"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=3042">​News story</​a></​p>​
  
-[[http://​www.nature.com/​nature/​journal/​v448/n7153/abs/nature06008.html|Geome-wide maps of chromatin state in pluripotent and lineage-committed cells ]] \\ +<​p><​a class="​urlextern"​ href="http://​www.nature.com/​nature/​journal/​v447/n7141/pdf/nature05805.pdf" rel="​nofollow"​ title="​http://​www.nature.com/​nature/​journal/​v447/​n7141/​pdf/​nature05805.pdf">​Genome ​of the marsupial Monodelphis domestica reveals innovation ​in non-coding sequences </​a><​br /> 
-Mikkelsen TS, Ku MJaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'​Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE\\ +Mikkelsen TS, Wakefield MJet al.<br /> 
-//Nature// 448:553-60 (2007)+<em>Nature</em> 447:167-177 (2007)</p>
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​insulators_pnas06.pdf|Systematic discovery ​of regulatory motifs in conserved ​regions of the human genome, including thousands of CTCF insulator sites ]] \\ +<​p><​a class="​urlextern"​ href="http://​www.ics.uci.edu/​~xhx/​publications/​Xie_AMCNE.pdf" rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​Xie_AMCNE.pdf">​A family ​of conserved ​noncoding elements derived from an ancient transposable element</​a><​br /> 
-Xie X, Mikkelsen TS, Gnirke ALindblad-Toh K, Kellis M and Lander ES. \\ +Xie X, Kamal M, and Lander ES.<br /> 
-//Proc Natl Acad Sci USA//104:7145-7150 (2007 \\ +<em>Proc Natl Acad Sci </​em><​em>​USA</em>103:11659-11664 (2006)<br /> 
-[[http://​www.broad.mit.edu/​personal/xhx/projects/CNEMOTIF/|Supplementary website]] [[http://​www.pnas.org/​cgi/​content/​full/​0701811104/DC1|Supporting Information]] [[http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=3042|News story]]+<a class="​urlextern"​ href="http://​www.broad.mit.edu/​seq/pubs/xie_pnas2006/" rel="​nofollow"​ title="​http:​//​www.broad.mit.edu/​seq/​pubs/​xie_pnas2006/">​Supplementary website</a> <a class="​urlextern"​ href="http://​www.pnas.org/​cgi/​content/​full/​0604768103/DC1" rel="​nofollow"​ title="​http://​www.pnas.org/​cgi/​content/​full/​0604768103/​DC1">​Supporting Information</a> <a class="​urlextern"​ href="http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=1881" rel="​nofollow"​ title="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=1881">​News story</​a></​p>​ 
 +</​div>​
  
-[[http://​www.nature.com/​nature/​journal/​v447/​n7141/​pdf/​nature05805.pdf|Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences ]] \\ +<​h3>​2006 or before</h3>
-Mikkelsen TS, Wakefield MJ, et al.  \\ +
-//Nature// 447:167-177 (2007)+
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​Xie_AMCNE.pdf|A family of conserved noncoding elements derived from an ancient ​transposable element]] \\ +<div class="​level3">​ 
-Xie X, Kamal M, and Lander ES. \\ +<​p><​a class="​urlextern"​ href="http://​www.ics.uci.edu/​~xhx/​publications/​mer121.PNAS2006.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​mer121.PNAS2006.pdf">large family of ancient ​repeat elements in the human genome is under strong selection</​a><​br /> 
-//Proc Natl Acad Sci USA//103:11659-11664 (2006) ​ \\ +Kamal M, Xie X, and Lander ES.<​br ​/
-[[http://​www.broad.mit.edu/​seq/​pubs/​xie_pnas2006/​|Supplementary website]] [[http://​www.pnas.org/​cgi/​content/​full/​0604768103/DC1|Supporting Information]] [[http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=1881|News story]]+<em>Proc Natl Acad Sci </em><​em>​USA<​/em>103:2740-2745 (2006)<br /> 
 +<a class="​urlextern"​ href="http://​www.broad.mit.edu/​seq/​pubs/​xie_pnas2006/​html/​clusteredAMCNE/​AMCNE1.similarAMCNE.html"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​seq/​pubs/​xie_pnas2006/​html/​clusteredAMCNE/​AMCNE1.similarAMCNE.html">​Supplementary website</a> <a class="​urlextern"​ href="http://​www.pnas.org/​cgi/​content/​full/​0511238103/DC1" rel="​nofollow"​ title="​http://​www.pnas.org/​cgi/​content/​full/​0511238103/​DC1">​Supporting Information</​a><​br /> 
 +<a class="​urlextern"​ href="http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=381" rel="​nofollow"​ title="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=381">​News story</​a></​p>​
  
-==== 2006 or before ====+<​p><​a class="​urlextern"​ href="​http://​download.cell.com/​pdfs/​0092-8674/​PIIS0092867406003801.pdf"​ rel="​nofollow"​ title="​http://​download.cell.com/​pdfs/​0092-8674/​PIIS0092867406003801.pdf">​A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells</​a><​br /> 
 +Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al.<br /> 
 +<​em>​Cell</​em>​ 125:315-26 (2006)</p>
  
-[[http://www.ics.uci.edu/~xhx/publications/mer121.PNAS2006.pdf|A large family of ancient repeat elements ​in the human genome is under strong selection]] \\ +<​p><​a class="​urlextern"​ href="http://genomebiology.com/2006/7/9/R85" rel="​nofollow"​ title="​http://​genomebiology.com/​2006/​7/​9/​R85">​Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression </​a><​br /> 
-Kamal M, Xie X, and Lander ES.  \\ +Wu J and Xie X<br /> 
-//Proc Natl Acad Sci USA//103:2740-2745 ​(2006) ​ \\ +<​em>​Genome </em><​em>​Biology<​/em>7(9):R85 (2006) ​(Highly accessed)<​br /> 
-[[http://​www.broad.mit.edu/​seq/pubs/xie_pnas2006/html/​clusteredAMCNE/​AMCNE1.similarAMCNE.html|Supplementary website]] [[http://​www.pnas.org/​cgi/​content/​full/​0511238103/​DC1|Supporting Information]] \\ +<a class="​urlextern"​ href="http://​www.broad.mit.edu/​personal/xhx/projects/NRSE" rel="​nofollow"​ title="​http://​www.broad.mit.edu/​personal/xhx/projects/​NRSE">​Supplementary website</​a></​p>​
-[[http://​www.broad.mit.edu/​cgi-bin/news/display_news.cgi?​id=381|News story]]+
  
-[[http://download.cell.com/pdfs/0092-8674/PIIS0092867406003801.pdf|A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells]] \\ +<​p><​a class="​urlextern"​ href="http://www.nature.com/ng/journal/​v38/​n5/​pdf/ng1776.pdf" rel="​nofollow"​ title="​http://​www.nature.com/​ng/​journal/​v38/​n5/​pdf/​ng1776.pdf">​Systematic identification of human mitochondrial disease genes through integrative genomics </​a><​br /> 
-Bernstein BEMikkelsen TS, Xie X, Kamal et al \\ +Calvo SJain M, Xie X, Chang B, Spinazzola A, Zeviani ​M, Carr S, and Mootha VK.<br /> 
-//Cell// 125:315-26 (2006)+<​em>​Nature Genetics<​/em>, 38:576-82 (2006)</p>
  
-[[http://genomebiology.com/2006/7/9/R85|Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression ]] \\ +<​p><​a class="​urlextern"​ href="http://www.ics.uci.edu/~xhx/publications/xie05_motif_paper.pdf"​ rel="​nofollow"​ title="​http:​//​www.ics.uci.edu/​~xhx/​publications/​xie05_motif_paper.pdf">​Systematic discovery of regulatory motifs ​in human promoters ​and 3&#39; UTRs by comparison of several mammals </​a><​br /> 
-Wu J and Xie X \\ +Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M.<br /> 
-//Genome Biology//7(9):R85 (2006) (Highly accessed) ​ \\ +<​em>​Nature<​/em>2005; 434:​338-45<​br ​/
-[[http://​www.broad.mit.edu/​personal/xhx/projects/NRSE|Supplementary ​website]]+<a class="​urlextern"​ href="​http:​//www.broad.mit.edu/​seq/​HumanMotifs/"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​seq/HumanMotifs/">​Supplementary Website</​a>​ <a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/publications/nature03441-s1.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​nature03441-s1.pdf">​Supplementary ​Information</​a>​ <a class="​urlextern"​ href="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=134"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=134">​News story</​a></​p>​
  
-[[http://www.nature.com/ng/journal/v38/n5/pdf/ng1776.pdf|Systematic identification of human mitochondrial disease genes through integrative genomics ]] \\ +<​p><​a class="​urlextern"​ href="http://www.genome.org/cgi/reprint/gr.5285206v1"​ rel="​nofollow"​ title="​http://​www.genome.org/cgi/reprint/gr.5285206v1">​A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands</​a><​br /> 
-Calvo SJain M, Xie X, Chang BSpinazzola A, Zeviani ​M, Carr Sand Mootha VK\\ +Giallourakis CCao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca MDaly M, Rioux JXavier R.<br /> 
-//Nature Genetics//38:576-82 (2006)+<​em>​Genome Resesarch<​/em>16:1056-72 (2006)</p>
  
-[[http://www.ics.uci.edu/~xhx/publications/xie05_motif_paper.pdf|Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals ]] \\ +<​p><​a class="​urlextern"​ href="http://download.cell.com/​pdfs/​0092-8674/​PIIS0092867406003692.pdf" rel="​nofollow"​ title="​http:​//download.cell.com/​pdfs/​0092-8674/PIIS0092867406003692.pdf">A Mammalian Organelle Map by Protein Correlation Profiling</​a><​br /> 
-Xie XLu JKulbokas EJGolub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis ​M.  \\ +Foster LJde Hoog CLZhang YZhang Y, Xie X, Mootha VK, and Mann M.<​br ​/> 
-//​Nature//​2005;​ 434:​338-45 ​ \\ +<​em>​Cell<​/em> 125:187-99 (2006)</p>
-[[http://​www.broad.mit.edu/​seq/​HumanMotifs/​|Supplementary Website]] [[http://​www.ics.uci.edu/​~xhx/​publications/​nature03441-s1.pdf|Supplementary Information]] [[http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=134|News story]]+
  
-[[http://www.genome.org/cgi/reprint/gr.5285206v1|A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands]] \\ +<​p><​a class="​urlextern"​ href="http://www.ics.uci.edu/~xhx/publications/WerfelXieSeung2005.pdf" rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​WerfelXieSeung2005.pdf">​Learning curves for stochastic gradient descent in linear feedforward networks. </​a><​br /> 
-Giallourakis C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R \\ +Werfel J, Xie X and Seung HS.<br /> 
-//Genome Resesarch//16:1056-72 (2006)+<​em>​Neural Computation<​/em>2005;17:2699-718</​p>​
  
-[[http://download.cell.com/pdfs/0092-8674/PIIS0092867406003692.pdf|A Mammalian Organelle Map by Protein Correlation Profiling]] \\ +<​p><​a class="​urlextern"​ href="http://www.nature.com/nature/journal/​v438/​n7069/​pdf/nature04338.pdf" rel="​nofollow"​ title="​http://​www.nature.com/​nature/​journal/​v438/​n7069/​pdf/​nature04338.pdf">​Genome sequence, comparative analysis and haplotype structure of the domestic dog </​a><​br /> 
-Foster LJ, de Hoog CLZhang YZhang Y, Xie X, Mootha VK, and Mann M \\ +Lindblad-Toh KWade CMet al.<br /> 
-//Cell// 125:187-99 (2006)+<​em>​Nature<​/em> 438:803-19 2005</​p>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​WerfelXieSeung2005.pdf|Learning curves for stochastic gradient descent in linear feedforward networks]] \\ +<​p><​a class="​urlextern"​ href="http://​www.ics.uci.edu/​~xhx/​publications/​annurev.genom.6.080604.pdf" rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​annurev.genom.6.080604.pdf">​Disease gene discovery through integrative genomics. </​a><​br /> 
-Werfel J, Xie X and Seung HS \\ +Giallourakis C, Henson C, Reich M, Xie Xand Mootha VK.<br /> 
-//Neural Computation//, ​2005;17:2699-718+<​em>​Annu. Rev. Genomics Hum. Genet.</em> ​2005:22:381-406.</​p>​
  
-[[http://www.nature.com/nature/journal/v438/n7069/pdf/nature04338.pdf|Genome sequence, comparative analysis and haplotype structure ​of the domestic dog ]] \\ +<​p><​a class="​urlextern"​ href="http://www.ics.uci.edu/~xhx/publications/PhysRevE_69_041909.pdf"​ rel="​nofollow"​ title="​http:​//www.ics.uci.edu/​~xhx/​publications/PhysRevE_69_041909.pdf">​Learning in neural networks by reinforcement ​of irregular spiking</a><​br ​/
-Lindblad-Toh K, Wade CM, et al \\ +Xie X and Seung HS.<​br ​/
-//Nature// 438:803-19 2005+<​em>​Phys Rev E</em>, 2004;69:041909</​p>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​annurev.genom.6.080604.pdf|Disease ​gene discovery through integrative genomics. ]] \\ +<​p><​a class="​urlextern"​ href="http://​www.ics.uci.edu/​~xhx/​publications/​mootha_pgc1a.pdf" rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​mootha_pgc1a.pdf">​Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation ​gene expression that is altered in diabetic muscle</​a><​br /> 
-Giallourakis CHenson ​C, Reich M, Xie X, and Mootha VK \\ +Mootha VKHandschin ​C, Arlow D, Xie X, St Pierre J et al.<br /> 
-//Annu. Rev. Genomics Hum. Genet.// 2005:22:381-406.+<​em>​Proc Natl Acad Sci USA</em>, 2004;101:6570-5</p>
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​PhysRevE_69_041909.pdf|Learning in neural networks by reinforcement of irregular spiking]] \\ +<​p><​a class="​urlextern"​ href="http://​www.ics.uci.edu/​~xhx/​publications/​PhysRevE_66_041902.pdf" rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​PhysRevE_66_041902.pdf">​The double-ring network modeling of the head-direction system</​a><​br /> 
-Xie X and Seung HS.  \\ +Xie X, Hahnloser RH, and Seung HS.<​br ​/
-//Phys Rev E//2004;69:041909+<​em>​Physical Review ​E</em>2002;66:041902</​p>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​mootha_pgc1a.pdf|Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle]] \\ +<​p><​a class="​urlextern"​ href="http://​www.ics.uci.edu/​~xhx/​publications/​PhysRevE_65_051904.pdf" rel="​nofollow"​ title="​http:​//​www.ics.uci.edu/​~xhx/​publications/​PhysRevE_65_051904.pdf">​Nonlinear dynamics of direction-selective recurrent neural media</​a><​br /> 
-Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al \\ +Xie X and Giese MA.<br /> 
-//Proc Natl Acad Sci USA//, 2004;101:6570-5+<​em>​Physical Review E</em>, 2002;​65:​051904 <a class="​urlextern"​ href="​http:​//www.ics.uci.edu/~xhx/​publications/​neurocomp_giese.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​neurocomp_giese.pdf">​Exact solution of the nonlinear dynamics of recurrent neural mechanisms for direction selectivity</​a><​br /> 
 +Giese MA and Xie X<br /> 
 +<​em>​Neurocomputing</​em>​ 2002;44:417-422</​p>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​PhysRevE_66_041902.pdf|The double-ring network modeling of the head-direction system]] \\ +<​p><​a class="​urlextern"​ href="http://​www.ics.uci.edu/​~xhx/​publications/​lwta.pdf" rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​lwta.pdf">​Learning winner-take-all competition between groups of neurons in lateral inhibitory networks </​a><​br /> 
-Xie X, Hahnloser ​RH, and Seung HS.  \\ +Xie X, Hahnloser ​HR, and Seung HS.<br /> 
-//Physical Review E//, 2002;66:041902+<​em>​Advances in Neural Information Processing </em><​em>​Systems<​/em>2001;13:350-356</​p>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​PhysRevE_65_051904.pdf|Nonlinear dynamics of direction-selective recurrent neural media]] \\ +<​p><​a class="​urlextern"​ href="http://​www.ics.uci.edu/​~xhx/​publications/​nc_vel_tuning.pdf" rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​nc_vel_tuning.pdf">​Generating velocity tuning by asymmetric ​recurrent ​connections</​a><​br /> 
-Xie X and Giese MA.  \\ +Xie X and Giese MA.<br /> 
-//Physical Review E//, 2002;​65:​051904 ​ [[http://​www.ics.uci.edu/​~xhx/​publications/​neurocomp_giese.pdf|Exact solution of the nonlinear dynamics of recurrent ​neural mechanisms for direction selectivity]] \\ +<​em>​Advances in Neural Information Processing </em><​em>​Systems<​/em>2002;13:325-332</​p>​
-Giese MA and Xie X  \\ +
-//Neurocomputing// ​2002;44:417-422+
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​lwta.pdf|Learning winner-take-all competition between groups of neurons ​in lateral inhibitory networks ]] \\ +<​p><​a class="​urlextern"​ href="http://​www.ics.uci.edu/​~xhx/​publications/​gwta_nc.pdf" rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​gwta_nc.pdf">​Selectively Grouping Neurons ​in Recurrent Networks of Lateral Inhibition</​a><​br /> 
-Xie X, Hahnloser ​HR, and Seung HS.  \\ +Xie X, Hahnloser ​RH, and Seung HS.<​br ​/
-//Advances in Neural ​Information Processing Systems//2001;13:350-356+<em>Neural ​Computation<​/em>, 2002;14:2627-2646</​p>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​nc_vel_tuning.pdf|Generating velocity tuning by asymmetric recurrent connections]] \\ +<​p><​a class="​urlextern"​ href="http://​www.ics.uci.edu/​~xhx/​publications/​chl_nc.pdf" rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​chl_nc.pdf">​Equivalence of backpropagation and contrastive Hebbian learning in a layered network</​a><​br /> 
-Xie X and Giese MA \\ +Xie X and Seung HS.<​br ​/
-//Advances in Neural ​Information Processing Systems//2002;13:325-332+<em>Neural ​Computation<​/em>, 2003;16:441-454</​p>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​gwta_nc.pdf|Selectively Grouping Neurons in Recurrent Networks ​of Lateral Inhibition]] \\ +<​p><​a class="​urlextern"​ href="http://​www.ics.uci.edu/​~xhx/​publications/​network_pop.pdf" rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​network_pop.pdf">​Threshold behavior ​of maximum likelihood method in population decoding</​a><​br /> 
-Xie X, Hahnloser RH, and Seung HS.  \\ +Xie X<​br ​/
-//​Neural ​Computation/​/2002;14:2627-2646+<​em>​Network:​ Comput. ​Neural ​Syst.</em> ​2002;13:447-456</​p>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​chl_nc.pdf|Equivalence of backpropagation and contrastive Hebbian ​learning ​in layered network]] \\ +<​p><​a class="​urlextern"​ href="http://​www.ics.uci.edu/​~xhx/​publications/​stdp00.pdf" rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​stdp00.pdf">​Spike-based ​learning ​rules and stabilization of persistent neural activity</​a><br /> 
-Xie X and Seung HS.  \\ +Xie X and Seung HS<​br ​/
-//​Neural ​Computation/​/, 2003;16:441-454+<​em>​Advances in Neural ​Information Processing Systems</em>2000;12:199-205</​p>​ 
 +</​div>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​network_pop.pdf|Threshold behavior of maximum likelihood method in population decoding]] \\ 
-Xie X \\ 
-//Network: Comput. Neural Syst.// 2002;​13:​447-456 
- 
-[[http://​www.ics.uci.edu/​~xhx/​publications/​stdp00.pdf|Spike-based learning rules and stabilization of persistent neural activity]] \\ 
-Xie X and Seung HS \\ 
-//Advances in Neural Information Processing Systems//, 2000;​12:​199-205 
  
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