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publications [2018/02/06 11:40]
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">​ 
-Sequential Embedding Induced Nonparametric Text Clustering\\ +<​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 /> 
-Duan TLou Q, Xie X\\+Zhu W, Vang YSHuang Y, Xie X</p>
  
-[https://​arxiv.org/​abs/​1802.00931 | Deep Learning Framework for Multi-class Breast Cancer Histology Image Classification]\\ +<​p>​Sequential Embedding Induced Nonparametric Text Clustering<​br ​/> 
-Vang SChen Z, Xie X\\+Duan TLou Q, Xie X</p>
  
-Structed Triplets ​Learning ​with Pos-tag Guided Attention ​for Visual Question Answering\\ +<​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 /> 
-IEEE Winter Conf. on Applications of Computer Vision ​2018+Vang S, Chen Z, Xie X<br /> 
 +15th International Conference ​on Image Analysis and Recognition, ​2018</p>
  
-DeepLungDeep 3D Dual Path Nets for Automated Pulmonary Nodule Detection and Classification\\ +<​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 /> 
-IEEE Winter Conf. on Applications of Computer Vision 2018+IEEE Winter Conf. on Applications of Computer Vision 2018</p>
  
-Adversarial ​Deep Structured ​Nets for Mass Segmentation from Mammograms\\ +<​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 /> 
-W Zhu, X Xiang, T Tran, GD Hager, X Xie\\ +IEEE Winter Conf. on Applications of Computer Vision 2018</​p>​
-IEEE International Symposium ​on Biomedical Imaging+
  
-Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural Networks\\ +<​p>​Adversarial ​Deep Structured Nets for Mass Segmentation from Mammograms<​br /> 
-H TangD Kim, X Xie\\ +W ZhuX Xiang, T Tran, GD Hager, X Xie<br /> 
-IEEE International Symposium on Biomedical Imaging+IEEE International Symposium on Biomedical Imaging</p>
  
-Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.\\ +<​p>​Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural Networks<​br /> 
-Zhu YWang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.\\ +H Tang, D Kim, X Xie<br /> 
-Mol Cell. 2018 Jan 4;​69(1):​62-74.e4.+IEEE International Symposium on Biomedical Imaging</​p>​
  
-==== 2017 ====+<​p>​Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.<​br /> 
 +Zhu Y, Wang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.<br /> 
 +Mol Cell. 2018 Jan 4;​69(1):​62-74.e4.</​p>​ 
 +</​div>​
  
-[[https://​arxiv.org/​abs/​1709.05538 | DeepLung: 3D Deep Convolutional Nets for Automated Pulmonary Nodule Detection and Classification]]\\ +<​h3>​2017<​/h3>
-W Zhu, C Liu, W Fan, X Xie\\ +
-arXiv preprint arXiv:​1709.05538+
  
 +<div class="​level3">​
 +<​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 />
 +W Zhu, C Liu, W Fan, X Xie<br />
 +arXiv preprint arXiv:​1709.05538</​p>​
  
-[[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]]\\ +<​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\\ +D Quang, X Xie<br /> 
-bioRxiv, 151274+bioRxiv, 151274</p>
  
 +<​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 />
 +Wentao Zhu, Qi Lou, Yeeleng Scott Vang, Xiaohui Xie<br />
 +arXiv:​1612.05968<​br />
 +<a class="​urlextern"​ href="​http://​www.miccai2017.org/"​ rel="​nofollow"​ title="​http://​www.miccai2017.org/">​MICCAI,​ 2017</​a></​p>​
  
-[[https://​arxiv.org/​abs/​1612.05968|Deep Multi-instance Networks with Sparse Label Assignment for Whole Mammogram Classification]]\\ +<​p>​Understanding sequence conservation with deep learning<​br ​/> 
-Wentao ZhuQi LouYeeleng Scott Vang, Xiaohui ​Xie \\ +Li YQuang Dand Xie X<br /> 
-arXiv:​1612.05968\\ +ACM BCB, 2017</p>
-[[http://​www.miccai2017.org/​| MICCAI, 2017]]+
  
-Understanding sequence conservation with deep learning\\ +<​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 /> 
-Li Y, Quang D, and Xie X\\ +Vang YS and Xie X<br /> 
-ACM BCB, 2017+Bioinformatics, 2017</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/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 /> 
-Vang YS and Xie X\\ +Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW<br /> 
-Bioinformatics, 2017+Dev Cell. 27;​40(6):​595-607.e4, 2017</​p>​ 
 +</​div>​
  
-[[https://​www.ncbi.nlm.nih.gov/​pubmed/​28325473|Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program]]\\ +<​h3>​2016<​/h3>
-Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW\\ +
-Dev Cell. 27;​40(6):​595-607.e4,​ 2017+
  
-==== 2016 ====+<div class="​level3">​ 
 +<​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 /> 
 +Wentao Zhu, Xiaohui Xie<br /> 
 +arXiv:​1612.05970</​p>​
  
-[[https://arxiv.org/abs/1612.05970|Adversarial Deep Structural Networks for Mammographic Mass Segmentation]]\\ +<​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 /> 
-Wentao Zhu, Xiaohui Xie\\ +Forouzmand et al.<br /> 
-arXiv:1612.05970+Developmental Biology, (16)30120-8 2016</​p>​
  
-[[https://www.ncbi.nlm.nih.gov/pubmed/27418388|Developmentally regulated long non-coding RNAs in Xenopus tropicalis]]\\ +<​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 /> 
-Forouzmand et al\\ +Chen Y, Li Y, Narayan R, Subramanian A, and Xie X<br /> 
-Developmental Biology(16)30120-8 ​2016+Bioinformatics, 2016</p>
  
-[[http://​bioinformatics.oxfordjournals.org/​content/​early/​2016/​02/​11/​bioinformatics.btw074.short?​rss=1|Gene expression inference with deep learning]]\\ +<​p>​DanQa hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences<​br ​/> 
-Chen Y, Li Y, Narayan R, Subramanian A, and Xie X\\ +Quang D and Xie X<br /> 
-Bioinformatics, 2016+Nucleic Acids Research, 2016</p>
  
-DanQ: hybrid convolutional and recurrent deep neural network ​for quantifying the function of DNA sequences\\ +<​p><​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 /> 
-Quang D and Xie X\\ +Weng L, Li Y, Xie X, and Shi Y<br /> 
-Nucleic Acids Research, 2016+RNA, 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="​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 /> 
-Weng LLi Y, Xie X, and Shi Y\\ +Zhu Wet al.<br /> 
-RNA, 2016+AAAI Conference on Artificial Intelligence, 2016</​p>​ 
 +</​div>​
  
-[[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]]\\ +<​h3>​2015<​/h3>
-Zhu W, et al.\\ +
-AAAI Conference on Artificial Intelligence,​ 2016+
  
-==== 2015 ====+<div class="​level3">​ 
 +<​p>​Hobbes3:​ Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings<​br /> 
 +Kim J, Chen L, and Xie X<br /> 
 +32nd IEEE International Conference on Data Engineering - ICDE 2016</​p>​
  
-Hobbes3Dynamic Generation of Variable-Length Signatures ​for Efficient Approximate Subsequence Mappings\\ +<​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 /> 
-Kim J, Chen L, and Xie X\\ +Quang D and Xie X</p>
-32nd IEEE International Conference on Data Engineering - ICDE 2016+
  
-[[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]]\\ +<​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 /> 
-Quang D and Xie X+Quang D, Chen Y and Xie X<br /> 
 +Bioinformatics,​ 31(5):​761-3,​ 2015</​p>​
  
-[[http://www.ncbi.nlm.nih.gov/pubmed/25338716|DANN: a deep learning approach ​for annotating the pathogenicity of genetic variants]]\\ +<​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 /> 
-Quang D, Chen Y and Xie X\\ +Li Y and Xie X<br /> 
-Bioinformatics,​ 31(5):761-3, 2015+BMC Genomics, 2015</p>
  
-[[http://www.biomedcentral.com/1471-2164/16/S2/​S1|MixClone: a mixture model for inferring tumor subclonal populations]]\\ +<​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 /> 
-Li Y and Xie X\\ +Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X<br /> 
-BMC Genomics, 2015+Neuroimaging genetics : principles and practices, 2015</​p>​ 
 +</​div>​
  
 +<​h3>​2014</​h3>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​ImagingGenetics.pdf |Identifying unanticipated genes and mechanisms in serious mental illness]]\\ +<div class="​level3">​ 
-Potkin SG, van Erp TGM, Ling S, Macciardi F, 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 /> 
-Neuroimaging genetics ​principles and practices, 2015+Kim I and Xie X<br /> 
 +International Journal on Document Analysis and Recognition,​ 2014<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>​
  
-==== 2014 ====+<​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 /> 
 +Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K<br /> 
 +Development, ​2014</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://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 /> 
-Kim I and Xie X\\ +Li Y and Xie X<br /> 
-International Journal on Document Analysis and Recognition, ​2014\\ +Bioinformatics,​ 2014</​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://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 /> 
-Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K\\ +Quang D and Xie X<br /> 
-Development, 2014+Bioinformatics, 2014</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://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 /> 
-Li and Xie X\\ +Kim J, Li and Xie X<br /> 
-Bioinformatics,​ 2014+BMC Bioinformatics,​ 2014, 15(1):​42</​p>​
  
-[[http://bioinformatics.oxfordjournals.org/content/early/2014/02/14/bioinformatics.btu093.abstract|EXTREMEAn Online EM Algorithm for Motif Discovery]]\\ +<​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 /> 
-Quang D and Xie X\\ +Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X<br /> 
-Bioinformatics, 2014+PLOS ONE, 2014, DOI: 10.1371/​journal.pone.0092317</​p>​
  
-[[http://​www.biomedcentral.com/​1471-2105/15/42|Improving Read Mapping Using Additional Prefix Grams]]\\ +<​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 /> 
-Kim JLi C and Xie X\\ +Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q<br /> 
-BMC Bioinformatics, ​2014, 15(1):42+BMC Systems Biology ​2014, 8:3</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://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 /> 
-Watanabe KBiesinger JSalmans MLRoberts BSArthur WTCleary M, Andersen B, Xie X, and Dai X\\ +Lackford BYao CCharles GMWeng LZheng XChoi EA, Xie X, Wan JXing YFreudenberg JM, Yang P, Jothi R, Hu G, Shi Y<​br ​/
-PLOS ONE2014DOI: 10.1371/journal.pone.0092317+EMBO J2014 Mar 4.</​p>​ 
 +</​div>​
  
-[[http://​www.biomedcentral.com/​1752-0509/​8/​3/​abstract|Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns]] \\ +<​h3>​2013<​/h3>
-Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q\\ +
-BMC Systems Biology 2014, 8:3+
  
-[[http://emboj.embopress.org/content/early/2014/03/04/embj.201386537|Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal]]\\ +<div class="​level3">​ 
-Lackford BYao 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\\ +<​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 /> 
-EMBO J. 2014 Mar 4. +Ye GTang MNie Q and Xie X<br /> 
-==== 2013 ====+<​em>​PLOS ONE</​em>, ​2013</p>
  
-[[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://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 /> 
-Ye GTang MNie Q and Xie X\\ +Chen YJia ZMercola D and Xie X<br /> 
-//PLOS ONE//, 2013+<​em>​Comput Math Methods Med.</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://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 ​/> 
-Chen YJia ZMercola D and Xie X\\ +Blitz IBiesinger J, Xie X, and Cho K<br /> 
-//Comput Math Methods Med.//, 2013+<​em>​Genesis<​/em>, 2013.</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://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 ​/> 
-Blitz IBiesinger J, Xie X, and Cho K\\ +Yao CChoi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y<br /> 
-//Genesis//, 2013.+<​em>​RNA<​/em>, 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://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 /> 
-Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y\\ +Chen Y and Xie X<br /> 
-//RNA//, 2013+<​em>​arXiv<​/em>, 2013</p>
  
-[[http://arxiv.org/abs/1305.0855|Inference in Kingman'​s Coalescent with Particle ​Markov ​Chain Monte Carlo Method]] \\ +<​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 and Xie X \\ +Biesinger J, Wang Yand Xie X<br /> 
-//arXiv//, 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://​www.biomedcentral.com/​content/pdf/1471-2105-14-S5-S4.pdf|Discovering and Mapping Chromatin States Using Tree Hidden Markov Model]] \\ +<​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 /> 
-Biesinger J, Wang Yand Xie X \\ +Li Y and Xie X<br /> 
-//BMC Bioinformatics/​2013, 14(S5):S4, 2013 \\ +<em>BMC Bioinformatics</em> ​2013, 14(Suppl 5):S11, 2013</p>
-[[http://​www.biomedcentral.com/​content/​supplementary/​1471-2105-14-s5-s4-s1.pdf|Supplemental Information]]+
  
-[[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://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 ​/> 
-Li and Xie X \\ +Yang X, Wang B, Li C, Wang J, and Xie X<​br ​/
-//BMC Bioinformatics//​ 2013, 14(Suppl 5):S11, 2013+<​em>​IEEE International Conference on Data Engineering ​(ICDE)</em>, 2013</​p>​ 
 +</​div>​
  
-[[http://​ieeexplore.ieee.org/​stamp/​stamp.jsp?​tp=&​arnumber=6544889|Efficient direct search on compressed genomic data]] \\ +<​h3>​2012<​/h3>
-Yang X, Wang B, Li C, Wang J, and Xie X \\ +
-//IEEE International Conference on Data Engineering (ICDE)//, 2013 +
-==== 2012 ====+
  
-[[http://​www.springerlink.com/​content/​4l2m27p3867xj584/​|Learning sparse gradients for variable selection and dimension reduction]] \\ +<div class="​level3">​ 
-Ye G 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 /> 
-Machine Learning Journal, 87(3):​303-355,​ 2012 \\ +Ye G and Xie X<br /> 
-[[http://​www.ics.uci.edu/​~xhx/​publications/​SGL.pdf|Preprint]]+Machine Learning Journal, 87(3):​303-355,​ 2012<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.ncbi.nlm.nih.gov/​pubmed/​23112178|Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation]] \\ +<​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 /> 
-Yao C, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y \\ +Yao C, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y<br /> 
-PNAS, 109(46):​18773-8,​ 2012+PNAS, 109(46):​18773-8,​ 2012</p>
  
-[[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]] \\ +<​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 /> 
-Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF \\ +Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF<br /> 
-BMC Genomics, 2012+BMC Genomics, 2012</p>
  
-[[http://​www.ncbi.nlm.nih.gov/​pubmed/​22199254|Hobbes: optimized gram-based methods for efficient read alignment]] \\ +<​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 /> 
-Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X  \\ +Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X<br /> 
-Nucleic Acids Research, 40(6):​e41, ​ 2012 \\ +Nucleic Acids Research, 40(6):e41, 2012<br /> 
-Software: ​[[http://​hobbes.ics.uci.edu/​|Hobbes]]+Software: ​<a class="​urlextern"​ href="http://​hobbes.ics.uci.edu/​" rel="​nofollow"​ title="​http://​hobbes.ics.uci.edu/">​Hobbes</​a></​p>​ 
 +</​div>​
  
-==== 2011 ====+<h3>2011</h3>
  
-[[http://​arxiv.org/​pdf/​1110.3076v1|Efficient latent variable graphical model selection via split Bregman method]] \\ +<div class="​level3">​ 
-Ye G, Wang Y, Chen Y, and Xie X \\ +<​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 /> 
-arXiv:​1110.3076v1,​ 2011+Ye G, Wang Y, Chen Y, and Xie X<br /> 
 +arXiv:​1110.3076v1,​ 2011</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.ncbi.nlm.nih.gov/​pubmed/​22208852" rel="​nofollow"​ title="​http://​www.ncbi.nlm.nih.gov/​pubmed/​22208852">​MotifMap: integrative genome-wide maps of regulatory motif sites for model species. ​</​a><​br /> 
-Daily K, Patel VR, Rigor P, Xie X, Baldi P. \\ +Daily K, Patel VR, Rigor P, Xie X, Baldi P.<br /> 
-BMC Bioinformatics,​ 2011+BMC Bioinformatics,​ 2011</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.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. \\ +Lindblad-Toh,​ Barber, Zuk, Lin, et al.<br /> 
-Nature, 2011+Nature, 2011</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://​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 /> 
-Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X \\ +Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X<br /> 
-BMC Bioinformatics,​ 2011  \\ +BMC Bioinformatics,​ 2011<br /> 
-Software: ​[[http://​cbcl.ics.uci.edu/​SSEA/​|SNP Set Enrichment Analysis (SSEA)]]+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.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 ​]] \\ +<​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 /> 
-Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF \\ +Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF<​br ​/
-//Cell Metabolism//, 13:367-75, 2011  \\ +<em>Cell Metabolism</em>, 13:367-75, 2011<br /> 
-[[http://​www.sciencedaily.com/​releases/​2011/​04/​110405122330.htm|Science Daily coverage]]+<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.ics.uci.edu/​~xhx/​publications/​arem_recomb.pdf|AREM: aligning short reads from ChIP-sequencing by expectation maximization]] \\ +<​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 /> 
-Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X \\ +Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X<br /> 
-//J Comput Biol.//, 2011 \\ +<em>J Comput Biol.</em>, 2011<br /> 
-Software: ​[[http://​sourceforge.net/​projects/​arem|AREM]]+Software: ​<a class="​urlextern"​ href="http://​sourceforge.net/​projects/​arem" rel="​nofollow"​ title="​http://​sourceforge.net/​projects/​arem">​AREM</​a></​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://​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 /> 
-Ye G, Chen Y, and Xie X \\ +Ye G, Chen Y, and Xie X<br /> 
-AI & STATS , 2011+AI &amp; STATS , 2011</​p>​ 
 +</​div>​
  
-==== 2010 ====+<h3>2010</h3>
  
-[[http://​arxiv4.library.cornell.edu/​abs/​1012.0975|Split Bregman method for sparse inverse covariance estimation with matrix iteration acceleration]] \\ +<div class="​level3">​ 
-Ye G, Cai J, 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 /> 
-arXiv:​1012.0975v1,​ 2010+Ye G, Cai J, and Xie X<br /> 
 +arXiv:​1012.0975v1,​ 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://​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-B and Xie X \\ +Ye G-B and Xie X<br /> 
-Computational Statistics and Data Analysis, doi:​10.1016/​j.csda.2010.10.021,​ 2010  \\ +Computational Statistics and Data Analysis, doi:​10.1016/​j.csda.2010.10.021,​ 2010<br /> 
-[[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]] \\ +<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  \\ +Daily K, Rigor P, Christley S, Xie X and Baldi P<br /> 
-//BMC Bioinformatics/​/,11:514, 2010+<em>BMC Bioinformatics</em>,11:514, 2010</p>
  
-[[http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​btq414|Interactive and fuzzy search: a dynamic way to explore MEDLINE ​]] \\ +<​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 \\ +Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J<​br ​/
-//​Bioinformatics/​/, 26(18):​2321-2327,​ 2010  \\ +<em>Bioinformatics</em>, 26(18):​2321-2327,​ 2010<br /> 
-[[http://​ipubmed.ics.uci.edu/​|iPubMed Search]]+<a class="​urlextern"​ href="http://​ipubmed.ics.uci.edu/​" rel="​nofollow"​ title="​http://​ipubmed.ics.uci.edu/">​iPubMed Search</​a></​p>​
  
-[[http://​arxiv.org/​abs/​1006.5060|Variable selection and dimension reduction via sparse gradients]] \\ +<​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-B and Xie X \\ +Ye G-B and Xie X<br /> 
-arXiv:​1006.5060v2,​ 2010+arXiv:​1006.5060v2,​ 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://​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 /> 
-Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X \\ +Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X<br /> 
-//NeuroImage/53:839-847, 2010+<em>NeuroImage</em> ​53:839-847, 2010</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/​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 Y, Christley S, Mjolsness E, and Xie X \\ +Wang Y, Christley S, Mjolsness E, and Xie X<​br ​/
-//BMC Systems Biology//, 4:99 doi:​10.1186/​1752-0509-4-99,​ 2010+<em>BMC Systems Biology</em>, 4:99 doi:​10.1186/​1752-0509-4-99,​ 2010</p>
  
-[[http://​www.springerlink.com/​content/​428v02087m218878/​fulltext.pdf|Site-frequency Spectrum of Linked Sites]] \\ +<​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 /> 
-Xie X   \\ +Xie X<br /> 
-//Bulletin of Mathematical Biology//, DOI: 10.1007/​s11538-010-9534-3,​ 2010+<em>Bulletin of Mathematical Biology</em>, DOI: 10.1007/​s11538-010-9534-3,​ 2010</p>
  
-[[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]] \\ +<​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-1 Motif and Synergy with LRH-1</​a><​br /> 
-Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and Osborne TF \\ +Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and Osborne TF<br /> 
-Nucleic Acids Research, doi:​10.1093/​nar/​gkq397,​ 2010 \\ +Nucleic Acids Research, doi:​10.1093/​nar/​gkq397,​ 2010<br /> 
-[[http://​cbcl.ics.uci.edu/​public_data/​FXR/​|Online Supplementary Materials]]+<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/​1471-2164/​11/​208/​abstract|Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes]] \\ +<​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 /> 
-Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X  \\ +Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X<​br ​/
-//BMC Genomics/11:208, 2010 \\ +<em>BMC Genomics</em> ​11:208, 2010<br /> 
-[[http://​www.broadinstitute.org/​annotation/​genome/​fusarium_group/​SupplementalMaterials.html|Supplementary Information]] \\ +<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 /> 
-[[http://​www.broadinstitute.org/​annotation/​genome/​fusarium_group/​MultiHome.html|Fusarium Comparative Database]]+<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.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.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 /> 
-Ma L-J, et al.  \\ +Ma L-J, et al.<br /> 
-//Nature/464:​367-373,​ 2010 \\ +<em>Nature</em> ​464:​367-373,​ 2010<br /> 
-[[http://​www.broadinstitute.org/​news/​1439|The chromosomal secrets of a plant pathogen]] \\ +<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 /> 
-[[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]] \\ +<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 /> 
-[[http://​www.broadinstitute.org/​annotation/​genome/​fusarium_group/​MultiHome.html|Fusarium Comparative Database]]+<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>​
  
-==== 2009 ====+<h3>2009</h3>
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​journal.pone.0006799.pdf|Incorporating existing network information into gene network inference]] \\ +<div class="​level3">​ 
-Christley S, Nie Q 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 /> 
-//PLoS ONE/4(8): e6799. doi:​10.1371/​journal.pone.0006799 (2009)+Christley S, Nie Q and Xie X<​br ​/
 +<em>PLoS ONE</em> ​4(8): e6799. doi:​10.1371/​journal.pone.0006799 (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 a preference for promoter proximal binding to a new motif]] \\ +<​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 /> 
-Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF \\ +Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF<br /> 
-//Proc Natl Acad Sci USA/doi:​10.1073/​pnas.0904246106 (2009)+<em>Proc Natl Acad Sci USA</em> ​doi:​10.1073/​pnas.0904246106 (2009)</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/​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 \\ +Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X<br /> 
-//Bioinformatics/​/25:i54-i62 (2009) ​ \\ +<em>Bioinformatics</em>25:i54-i62 (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/​siphy_suppinfo.pdf" rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​siphy_suppinfo.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://​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.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://​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 /> 
-Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA  \\ +Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA<​br ​/
-//Proc Natl Acad Sci USA/doi:​10.1073/​pnas.0813264106 (2009)+<em>Proc Natl Acad Sci USA</em> ​doi:​10.1073/​pnas.0813264106 (2009)</p>
  
-[[http://​genome.cshlp.org/​content/​19/​4/​567.long|Common polymorphic transcript variation in human disease]] \\ +<​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 /> 
-Fraser H and Xie X  \\ +Fraser H and Xie X<​br ​/
-//Genome Research/doi:​10.1101/​gr.083477.108 (2009) ​\\ +<em>Genome Research</em> ​doi:​10.1101/​gr.083477.108 (2009)<br /> 
-[[http://​www.ics.uci.edu/​~xhx/​publications/​PTV_GR2009.pdf|PDF]]+<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/​2/​167|MotifMap: a human genome-wide map of candidate regulatory motif sites ]] \\ +<​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 /> 
-Xie X, Rigor P, and Baldi P  \\ +Xie X, Rigor P, and Baldi P<br /> 
-//Bioinformatics/​25: 167-174 (2009) ​\\ +<em>Bioinformatics</em> ​25: 167-174 (2009)<br /> 
-[[http://​www.ics.uci.edu/​~xhx/​publications/​MotifMap_Supp_Info.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://​motifmap.ics.uci.edu/​|MotifMap Server]]+<a class="​urlextern"​ href="http://​motifmap.ics.uci.edu/​" rel="​nofollow"​ title="​http://​motifmap.ics.uci.edu/">​MotifMap Server</​a></​p>​
  
-[[http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​2/​274|Human genomes as email attachments ​]] \\ +<​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 /> 
-Christley S, Lu Y, Li C, and Xie X  \\ +Christley S, Lu Y, Li C, and Xie X<​br ​/
-//​Bioinformatics /25: 274-275 (2009) ​\\ +<em>Bioinformatics ​</em> ​25: 274-275 (2009)<br /> 
-[[http://​www.ics.uci.edu/​~xhx/​project/​DNAzip|DNAzip: DNA sequence compression using a reference genome]] \\ +<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 /> 
-[[http://​www.ics.uci.edu/​~xhx/​publications/​DNAzip.pdf|PDF]] \\ +<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 /> 
-[[http://​www.genomeweb.com/​informatics/​jim-watsonâ��s-genome-e-mail-uc-irvine-team-develops-method-compress-genomic-data|News featured in genomeweb]] \\ +<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 /> 
-[[http://​www.bio-itworld.com/​news/​2009/​01/​30/​Email-compression-genome.html|News featured in bio-itworld]] \\ +<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 /> 
-[[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+<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>​
  
-==== 2008 ====+<h3>2008</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 J, Sieglaff DH, Gervin J, and Xie X  \\ +<​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 /24:1843-9 (2008) ​\\ +Wu J, Sieglaff DH, Gervin J, and Xie X<​br ​/
-[[http://​www.ics.uci.edu/​~xhx/​project/​mdos/​|MDOS software]]: A method for Motif Discovery using Orthologous Sequences (alignment independent). ​\\ +<em>Bioinformatics ​</em> ​24:1843-9 (2008)<br /> 
-[[http://​www.ics.uci.edu/​~xhx/​publications/​wu_motif_2008_suppinfo.pdf|Supplementary Information on the MDOS algorithm]]+<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://​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.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 /> 
-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  \\ +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 /> 
-//PLoS Genetics//4(10):​e1000242 (2008) +<​em>​PLoS </em><​em>​Genetics</em>4(10):​e1000242 (2008)</p> 
-==== 2007 ====+</​div>​
  
-[[http://​www.pnas.org/​content/​104/​49/​19428|Distinguishing protein-coding and noncoding genes in the human genome ]] \\ +<​h3>​2007<​/h3>
-Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, and Lander ES. \\ +
-//Proc Natl Acad Sci USA//​104(49):​19428-33 (2007)+
  
-[[http://www.nature.com/nature/journal/v449/n7164/abs/nature06250.html|Genome-wide detection ​and characterization of positive selection ​in human populations ]] \\ +<div class="​level3">​ 
-Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EHMcCarroll SAGaudet RSchaffner SF, Lander ES and International HapMap Consortium ​ \\ +<​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 /> 
-//Nature//449:913-918 (2007)+Clamp M, Fry B, Kamal M, Xie X, Cuff JLin MFKellis MLindblad-Toh Kand Lander ES.<​br ​/
 +<​em>​Proc Natl Acad Sci </em><​em>​USA<​/em>​104(49):19428-33 (2007)</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/​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 /> 
-Mikkelsen TSKu MJaffe DB, Issac B, Lieberman EGiannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall ​E, O'​Donovan A, Presser A, Russ C, Xie X, Meissner AWernig MJaenisch ​R, Nusbaum C, Lander ES, Bernstein BE. \\ +Sabeti PCVarilly PFry B, Lohmueller JHostetter ​E, Cotsapas ​C, Xie X, Byrne EHMcCarroll SAGaudet ​R, Schaffner SF, Lander ES and International HapMap Consortium<​br /> 
-//Nature// 448:553-60 (2007)+<em>Nature</em>449:913-918 (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.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 ​/
-Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and 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 A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE.<​br ​/
-//Proc Natl Acad Sci USA//​104:​7145-7150 (2007) ​ \\ +<​em>​Nature<​/em> 448:553-60 (2007)</p>
-[[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]]+
  
-[[http://www.nature.com/nature/journal/v447/n7141/pdf/nature05805.pdf|Genome ​of the marsupial Monodelphis domestica reveals innovation ​in non-coding sequences ]] \\ +<​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 genome, including thousands of CTCF insulator sites </​a><​br /> 
-Mikkelsen TS, Wakefield MJet al \\ +Xie X, Mikkelsen TS, Gnirke ALindblad-Toh K, Kellis M and Lander ES.<br /> 
-//Nature// 447:167-177 (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.ics.uci.edu/~xhx/publications/Xie_AMCNE.pdf|A family of conserved noncoding elements derived from an ancient transposable element]] \\ +<​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 ​/
-Xie X, Kamal M, and Lander ES. \\ +Mikkelsen TS, Wakefield MJ, et al.<​br ​/
-//Proc Natl Acad Sci USA//​103:​11659-11664 (2006) ​ \\ +<​em>​Nature<​/em> 447:167-177 (2007)</p>
-[[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]]+
  
-==== 2006 or before ​====+<​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, Kamal M, and Lander ES.<br /> 
 +<​em>​Proc Natl Acad Sci </​em><​em>​USA</​em>​103:​11659-11664 (2006)<br /> 
 +<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.ics.uci.edu/​~xhx/​publications/​mer121.PNAS2006.pdf|A large family of ancient repeat elements in the human genome is under strong selection]] \\ +<h3>2006 or before</h3>
-Kamal M, Xie X, and Lander ES.  \\ +
-//Proc Natl Acad Sci USA//​103:​2740-2745 (2006)  \\ +
-[[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]] \\ +
-[[http://​www.broad.mit.edu/​cgi-bin/​news/display_news.cgi?​id=381|News story]]+
  
-[[http://download.cell.com/pdfs/0092-8674/PIIS0092867406003801.pdf|Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells]] \\ +<div class="​level3">​ 
-Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al \\ +<​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 /> 
-//Cell// 125:315-26 (2006)+Kamal M, Xie X, and Lander ES.<br /> 
 +<​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>​
  
-[[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://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 /> 
-Wu J and Xie X \\ +Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al.<br /> 
-//Genome Biology//​7(9):R85 (2006) ​(Highly accessed) ​ \\ +<​em>​Cell<​/em> 125:315-26 ​(2006)</p>
-[[http://​www.broad.mit.edu/​personal/​xhx/​projects/NRSE|Supplementary website]]+
  
-[[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://genomebiology.com/2006/7/9/R85" rel="​nofollow"​ title="​http:​//genomebiology.com/​2006/​7/​9/​R85">​Comparative sequence analysis reveals an intricate network among RESTCREB and miRNA in mediating neuronal gene expression </a><​br ​/
-Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK. \\ +Wu J and Xie X<​br ​/
-//Nature Genetics//, 38:576-82 ​(2006)+<​em>​Genome </em><​em>​Biology</​em>​7(9):R85 (2006) ​(Highly accessed)<​br /> 
 +<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.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://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 ​/
-Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M.  \\ +Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK.<​br ​/
-//Nature//2005; 434:​338-45 ​ \\ +<​em>​Nature Genetics</​em>,​ 38:576-82 (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/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 /> 
-Giallourakis CCao ZGreen TWachtel HXie XLopez-Illasaca MDaly MRioux J, Xavier R \\ +Xie XLu JKulbokas EJGolub TRMootha VKLindblad-Toh KLander ESKellis M.<br /> 
-//Genome Resesarch//, 16:1056-72 (2006)+<​em>​Nature<​/em>2005; 434:​338-45<​br ​/
 +<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://download.cell.com/pdfs/0092-8674/PIIS0092867406003692.pdf|Mammalian Organelle Map by Protein Correlation Profiling]] \\ +<​p><​a class="​urlextern"​ href="http://www.genome.org/cgi/reprint/​gr.5285206v1"​ rel="​nofollow"​ title="​http://​www.genome.org/​cgi/​reprint/gr.5285206v1">​molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands</​a><​br /> 
-Foster LJde Hoog CLZhang YZhang Y, Xie X, Mootha VKand Mann M.  \\ +Giallourakis CCao ZGreen TWachtel H, Xie X, Lopez-Illasaca MDaly M, Rioux J, Xavier R.<br /> 
-//Cell// 125:187-99 (2006)+<​em>​Genome Resesarch<​/em>, 16:1056-72 (2006)</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://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 /> 
-Werfel J, Xie X and Seung HS \\ +Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M.<br /> 
-//Neural Computation//,​ 2005;17:2699-718+<​em>​Cell<​/em> 125:187-99 (2006)</​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/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 /> 
-Lindblad-Toh K, Wade CMet al \\ +Werfel JXie X and Seung HS.<br /> 
-//Nature// 438:803-19 2005+<​em>​Neural Computation<​/em>, 2005;17:2699-718</​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.nature.com/nature/journal/v438/​n7069/​pdf/​nature04338.pdf" rel="​nofollow"​ title="​http://​www.nature.com/​nature/​journal/​v438/​n7069/​pdf/​nature04338.pdf">​Genome sequencecomparative analysis ​and haplotype structure of the domestic dog </a><​br ​/
-Giallourakis C, Henson C, Reich M, Xie X, and Mootha VK.  \\ +Lindblad-Toh K, Wade CM, et al.<​br ​/
-//Annu. Rev. Genomics Hum. Genet.// 2005:22:381-406.+<​em>​Nature<​/em> 438:803-19 2005</​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/​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 /> 
-Xie X and Seung HS \\ +Giallourakis C, Henson C, Reich M, Xie Xand Mootha VK.<​br ​/
-//Phys Rev E//, 2004;69:041909+<​em>​Annu. ​Rev. Genomics Hum. Genet.</em> 2005:22:​381-406.</​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_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 /> 
-Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al \\ +Xie X and Seung HS.<br /> 
-//Proc Natl Acad Sci USA//, 2004;101:6570-5+<​em>​Phys Rev E</em>, 2004;69:041909</​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/​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 /> 
-Xie X, Hahnloser RH, and Seung HS \\ +Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al.<br /> 
-//Physical Review E//2002;66:041902+<​em>​Proc Natl Acad Sci USA</em>2004;101:6570-5</​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/​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 Giese MA.  \\ +Xie X, Hahnloser RH, and Seung HS.<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>​Physical Review E</em>, ​2002;66:041902</​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/​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 /> 
-Xie X, Hahnloser HR, and Seung HS \\ +Xie X and Giese MA.<br /> 
-//Advances in Neural Information Processing Systems//2001;13:350-356+<​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/​nc_vel_tuning.pdf|Generating velocity tuning by asymmetric recurrent connections]] \\ +<​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 and Giese MA \\ +Xie X, Hahnloser HR, and Seung HS.<​br ​/
-//Advances in Neural Information Processing Systems//2002;13:325-332+<em>Advances in Neural Information Processing ​</​em><​em>​Systems</em>2001;13:350-356</​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/​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, Hahnloser RH, and Seung HS \\ +Xie X and Giese MA.<​br ​/
-//​Neural ​Computation//2002;14:2627-2646+<​em>​Advances in Neural ​Information Processing </em><​em>​Systems<​/em>2002;13:325-332</​p>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​chl_nc.pdf|Equivalence of backpropagation and contrastive Hebbian learning ​in a layered network]] \\ +<​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 and Seung HS.  \\ +Xie X, Hahnloser RH, and Seung HS.<​br ​/
-//Neural Computation/​/2003;16:441-454+<em>Neural Computation</em>2002;14:2627-2646</​p>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​network_pop.pdf|Threshold behavior of maximum likelihood method in population decoding]] \\ +<​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 \\ +Xie X and Seung HS.<br /> 
-//Network: Comput. Neural Syst./2002;​13:​447-456+<​em>​Neural Computation</​em>,​ 2003;​16:​441-454</​p>​ 
 + 
 +<​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<​br ​/
 +<em>Network: Comput. Neural Syst.</em> ​2002;​13:​447-456</​p>​ 
 + 
 +<​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<br /> 
 +<​em>​Advances in Neural Information Processing Systems</​em>,​ 2000;​12:​199-205</​p>​ 
 +</​div>​
  
-[[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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