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publications [2018/01/10 13:44]
xhx [2017]
publications [2018/08/15 23:25] (current)
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 +<​html>​
 +<​h2>​Publications</​h2>​
  
 +<div class="​level2">&​nbsp;</​div>​
  
-===== Publications =====+<​h3>​2018</​h3>​
  
-==== 2017 ====+<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>
  
-Adversarial Deep Structured Nets for Mass Segmentation from Mammograms\\ +<​p>​Sequential Embedding Induced Nonparametric Text Clustering<​br /> 
-W Zhu, X Xiang, ​TranGD Hager, X Xie\\ +Duan T, Lou QXie X</p>
-IEEE International Symposium on Biomedical Imaging+
  
-Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural Networks\\ +<​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 /> 
-H TangD KimXie\\ +Vang SChen Z, Xie X<br /> 
-IEEE International ​Symposium ​on Biomedical Imaging+15th International ​Conference ​on Image Analysis and Recognition,​ 2018</​p>​
  
-Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.\\ +<​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 /> 
-Zhu Y, Wang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.\\ +IEEE Winter Confon Applications of Computer Vision ​2018</p>
-Mol Cell. 2018 Jan 4;​69(1):​62-74.e4.+
  
 +<​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 />
 +IEEE Winter Conf. on Applications of Computer Vision 2018</​p>​
  
-[[https://​arxiv.org/​abs/​1709.05538 | DeepLung: 3D Deep Convolutional ​Nets for Automated Pulmonary Nodule Detection and Classification]]\\ +<​p>​Adversarial ​Deep Structured ​Nets for Mass Segmentation from Mammograms<​br /> 
-W Zhu, C LiuW Fan, X Xie\\ +W Zhu, X XiangT Tran, GD Hager, X Xie<br /> 
-arXiv preprint arXiv:​1709.05538+IEEE International Symposium on Biomedical Imaging</​p>​
  
 +<​p>​Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural Networks<​br />
 +H Tang, D Kim, X Xie<br />
 +IEEE International Symposium on Biomedical Imaging</​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>​Molecular Mechanisms ​for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.<​br /> 
-D Quang, X Xie\\ +Zhu YWang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie XHertel KJ, Shi Y.<br /> 
-bioRxiv151274+Mol Cell. 2018 Jan 4;​69(1):​62-74.e4.</​p>​ 
 +</​div>​
  
 +<​h3>​2017</​h3>​
  
-[[https://​arxiv.org/​abs/​1612.05968|Deep Multi-instance Networks with Sparse Label Assignment ​for Whole Mammogram ​Classification]]\\ +<div class="​level3">​ 
-Wentao ​Zhu, Qi LouYeeleng Scott VangXiaohui ​Xie \\ +<​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 /> 
-arXiv:1612.05968\\ +Zhu, C LiuW FanXie<br /> 
-[[http://​www.miccai2017.org/​| MICCAI, 2017]]+arXiv preprint ​arXiv:1709.05538</p>
  
-Understanding sequence conservation with deep learning\\ +<​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 /> 
-Li Y, Quang D, and Xie X\\ +Quang, X Xie<br /> 
-ACM BCB2017+bioRxiv151274</​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://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 /> 
-Vang YS and Xie X\\ +Wentao Zhu, Qi Lou, Yeeleng Scott Vang, Xiaohui ​Xie<br /> 
-Bioinformatics, 2017+arXiv:​1612.05968<​br /> 
 +<a class="​urlextern"​ href="​http://​www.miccai2017.org/"​ rel="​nofollow"​ title="​http://​www.miccai2017.org/">​MICCAI, 2017</​a></​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>​Understanding sequence conservation with deep learning<​br ​/> 
-Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka ​Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW\\ +Li Y, Quang Dand Xie X<br /> 
-Dev Cell. 27;​40(6):​595-607.e4, 2017+ACM BCB, 2017</p>
  
-==== 2016 ====+<​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 /> 
 +Vang YS and Xie X<br /> 
 +Bioinformatics,​ 2017</​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/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 /> 
-Wentao ZhuXiaohui ​Xie\\ +Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW<br /> 
-arXiv:1612.05970+Dev Cell. 27;40(6):595-607.e4, 2017</​p>​ 
 +</​div>​
  
-[[https://​www.ncbi.nlm.nih.gov/​pubmed/​27418388|Developmentally regulated long non-coding RNAs in Xenopus tropicalis]]\\ +<​h3>​2016<​/h3>
-Forouzmand et al. \\ +
-Developmental Biology, (16)30120-8 2016+
  
-[[http://bioinformatics.oxfordjournals.org/content/early/2016/02/11/bioinformatics.btw074.short?​rss=1|Gene expression inference with deep learning]]\\ +<div class="​level3">​ 
-Chen Y, Li YNarayan R, Subramanian A, 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 /> 
-Bioinformatics,​ 2016+Wentao ZhuXiaohui ​Xie<br /> 
 +arXiv:​1612.05970</​p>​
  
-DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences\\ +<​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 /> 
-Quang D and Xie X\\ +Forouzmand et al.<br /> 
-Nucleic Acids Research, 2016+Developmental Biology(16)30120-8 ​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://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 /> 
-Weng L, Li Y, Xie X, and Shi Y\\ +Chen Y, Li Y, Narayan R, Subramanian A, and Xie X<br /> 
-RNA, 2016+Bioinformatics, 2016</p>
  
-[[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>​DanQa hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences<​br ​/
-Zhu W, et al.\\ +Quang D and Xie X<​br ​/> 
-AAAI Conference on Artificial Intelligence, 2016+Nucleic Acids Research, 2016</p>
  
-==== 2015 ====+<​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 /> 
 +Weng L, Li Y, Xie X, and Shi Y<br /> 
 +RNA, 2016</​p>​
  
-Hobbes3Dynamic Generation of Variable-Length Signatures ​for Efficient Approximate Subsequence Mappings\\ +<​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 /> 
-Kim JChen L, and Xie X\\ +Zhu Wet al.<br /> 
-32nd IEEE International ​Conference on Data Engineering - ICDE 2016+AAAI Conference on Artificial Intelligence, ​2016</​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>2015</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 and Xie X\\ +<​p>​Hobbes3Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings<​br ​/> 
-Bioinformatics,​ 31(5):761-3, 2015+Kim J, Chen L, and Xie X<br /> 
 +32nd IEEE International Conference on Data Engineering ​ICDE 2016</​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://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 /> 
-Li Y and Xie X\\ +Quang D and Xie X</p>
-BMC Genomics, 2015+
  
 +<​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, Chen Y and Xie X<br />
 +Bioinformatics,​ 31(5):​761-3,​ 2015</​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://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 /> 
-Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X\\ +Li Y and Xie X<br /> 
-Neuroimaging genetics : principles and practices, 2015+BMC Genomics, 2015</p>
  
-==== 2014 ====+<​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 /> 
 +Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X<br /> 
 +Neuroimaging genetics : principles and practices, 2015</​p>​ 
 +</​div>​
  
-[[http://​link.springer.com/​article/​10.1007/​s10032-014-0229-4|Handwritten Hangul recognition using deep convolutional neural networks]]\\ +<h3>2014</h3>
-Kim I and Xie X\\ +
-International Journal on Document Analysis and Recognition, ​2014\\ +
-[[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\\ +<div class="​level3">​ 
-Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K\\ +<​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 ​/> 
-Development, 2014+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>​
  
-[[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.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 /> 
-Bioinformatics, 2014+Development, 2014</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://​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 /> 
-Quang D and Xie X\\ +Li Y and Xie X<br /> 
-Bioinformatics,​ 2014+Bioinformatics,​ 2014</p>
  
-[[http://www.biomedcentral.com/1471-2105/15/42|Improving Read Mapping Using Additional Prefix Grams]]\\ +<​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 /> 
-Kim J, Li C and Xie X\\ +Quang D and Xie X<br /> 
-BMC Bioinformatics,​ 2014, 15(1):42+Bioinformatics,​ 2014</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.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 /> 
-Watanabe K, Biesinger ​J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X\\ +Kim J, Li C and Xie X<br /> 
-PLOS ONE, 2014, DOI10.1371/journal.pone.0092317+BMC Bioinformatics, 2014, 15(1):42</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://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 /> 
-Zheng ZChristley SChiu WT, Blitz IL, Xie X, Cho KW, Nie Q\\ +Watanabe KBiesinger JSalmans ML, Roberts BS, Arthur ​WT, Cleary M, Andersen B, Xie X, and Dai X<br /> 
-BMC Systems Biology ​2014, 8:3+PLOS ONE, 2014, DOI10.1371/​journal.pone.0092317</​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://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 /> 
-Lackford BYao CCharles GMWeng L, Zheng X, Choi EA, Xie X, Wan JXing Y, Freudenberg JM, Yang P, Jothi R, Hu G, Shi Y\\ +Zheng ZChristley SChiu WTBlitz IL, Xie X, Cho KWNie Q<br /> 
-EMBO J. 2014 Mar 4. +BMC Systems Biology ​2014, 8:​3</​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://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 /> 
-Ye GTang MNie Q and Xie X\\ +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<br /> 
-//PLOS ONE//, 2013+EMBO J. 2014 Mar 4.</p> 
 +</div>
  
-[[http://​www.hindawi.com/​journals/​cmmm/​2013/873595/|A gradient boosting algorithm for survival analysis via direct optimization of concordance index]] \\ +<h3>2013</h3>
-Chen Y, Jia Z, Mercola D and Xie X\\ +
-//Comput Math Methods Med.//, 2013+
  
-[[http://onlinelibrary.wiley.com/doi/10.1002/dvg.22719/abstract|Biallelic genome modification in F0 Xenopus tropicalis embryos using the CRISPR/Cas system]]\\ +<div class="​level3">​ 
-Blitz IBiesinger J, Xie X, and Cho K\\ +<​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 /> 
-//Genesis//, 2013.+Ye GTang MNie Q and Xie X<br /> 
 +<​em>​PLOS ONE</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://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 /> 
-Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y\\ +Chen Y, Jia ZMercola D and Xie X<​br ​/
-//RNA//, 2013+<​em>​Comput Math Methods Med.</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://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 Y and Xie X \\ +Blitz I, Biesinger J, Xie X, and Cho K<br /> 
-//arXiv//, 2013+<​em>​Genesis<​/em>, 2013.</p>
  
-[[http://www.biomedcentral.com/content/pdf/1471-2105-14-S5-S4.pdf|Discovering and Mapping Chromatin States Using a Tree Hidden Markov Model]] \\ +<​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 /> 
-Biesinger J, Wang Y, and Xie X \\ +Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y<br /> 
-//BMC Bioinformatics// 2013, 14(S5):S4, 2013 \\ +<​em>​RNA</​em>,​ 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://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 /> 
-Li Y and Xie X \\ +Chen Y and Xie X<​br ​/
-//BMC Bioinformatics//​ 2013, 14(Suppl 5):S11, 2013+<​em>​arXiv<​/em>, 2013</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.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 /> 
-Yang X, Wang B, Li C, Wang J, and Xie X \\ +Biesinger J, Wang Y, and Xie X<​br ​/
-//IEEE International Conference on Data Engineering ​(ICDE)//, 2013 +<​em>​BMC Bioinformatics<​/em> 2013, 14(S5):S4, 2013<br /> 
-==== 2012 ====+<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.springerlink.com/content/4l2m27p3867xj584/|Learning sparse gradients ​for variable selection and dimension reduction]] \\ +<​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 /> 
-Ye G and Xie X \\ +Li Y and Xie X<br /> 
-Machine Learning Journal87(3):303-3552012 \\ +<​em>​BMC Bioinformatics</​em>​ 201314(Suppl 5):S112013</p>
-[[http://​www.ics.uci.edu/​~xhx/​publications/​SGL.pdf|Preprint]]+
  
-[[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://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 C, Biesinger ​J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y \\ +Yang X, Wang B, Li C, Wang J, and Xie X<br /> 
-PNAS, 109(46):18773-82012+<​em>​IEEE International Conference on Data Engineering ​(ICDE)</em>2013</​p>​ 
 +</​div>​
  
-[[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]] \\ +<​h3>​2012<​/h3>
-Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF \\ +
-BMC Genomics, 2012+
  
-[[http://www.ncbi.nlm.nih.gov/pubmed/22199254|Hobbes:​ optimized gram-based methods ​for efficient read alignment]] \\ +<div class="​level3">​ 
-Ahmadi A, Behm A, Honnalli N, Li C, Weng L, 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 /> 
-Nucleic Acids Research40(6):e41 2012 \\ +Ye G and Xie X<br /> 
-Software[[http://hobbes.ics.uci.edu/​|Hobbes]]+Machine Learning Journal87(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>​
  
-==== 2011 ====+<​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<br /> 
 +PNAS, 109(46):​18773-8,​ 2012</​p>​
  
-[[http://arxiv.org/pdf/1110.3076v1|Efficient latent variable graphical model selection via split Bregman method]] \\ +<​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 /> 
-Ye GWang YChen Yand Xie X \\ +Kim Chong HBiesinger JSeo YK, Xie X, Osborne TF<br /> 
-arXiv:​1110.3076v12011+BMC Genomics2012</​p>​
  
-[[http://​www.ncbi.nlm.nih.gov/​pubmed/​22208852|MotifMapintegrative genome-wide maps of regulatory motif sites for model species. ]] \\ +<​p><​a class="​urlextern"​ href="http://​www.ncbi.nlm.nih.gov/​pubmed/​22199254"​ rel="​nofollow"​ title="​http://​www.ncbi.nlm.nih.gov/​pubmed/​22199254">​Hobbesoptimized gram-based methods ​for efficient read alignment</​a><​br /> 
-Daily KPatel VRRigor P, Xie X, Baldi P\\ +Ahmadi ABehm AHonnalli NLi C, Weng L, and Xie X<br /> 
-BMC Bioinformatics,​ 2011+Nucleic Acids Research40(6):e41, 2012<br /> 
 +Software: <a class="​urlextern"​ href="​http://​hobbes.ics.uci.edu/"​ rel="​nofollow"​ title="​http://​hobbes.ics.uci.edu/">​Hobbes</​a></​p>​ 
 +</​div>​
  
-[[http://​www.nature.com/​nature/​journal/​vaop/​ncurrent/​full/​nature10530.html|A high-resolution map of human evolutionary constraint using 29 mammals]] \\ +<​h3>​2011<​/h3>
-Lindblad-Toh,​ Barber, Zuk, Lin, et al. \\ +
-Nature, 2011+
  
-[[http://www.biomedcentral.com/1471-2105/12/99|SNP-based pathway enrichment analysis for genome-wide association studies]] \\ +<div class="​level3">​ 
-Weng L, Macciardi F, Subramanian A, Guffanti ​G, Potkin SGYu Z, 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 /> 
-BMC Bioinformatics,​ 2011  \\ +Ye G, Wang YChen Y, and Xie X<br /> 
-Software[[http://​cbcl.ics.uci.edu/​SSEA/|SNP Set Enrichment Analysis (SSEA)]]+arXiv:1110.3076v1, 2011</p>
  
-[[http://www.cell.com/cell-metabolism/abstract/S1550-4131(11)00092-1|Genome-wide Positioning ​of SREBP-2 in Hepatic Chromatin Predicts ​Novel Role in Autophagy ]] \\ +<​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 /> 
-Seo YJeon T Chong H, Beisinger J, Xie X, and Osborne TF \\ +Daily KPatel VRRigor P, Xie X, Baldi P.<br /> 
-//Cell Metabolism//,​ 13:367-75, 2011  \\ +BMC Bioinformatics, 2011</p>
-[[http://​www.sciencedaily.com/​releases/​2011/​04/​110405122330.htm|Science Daily coverage]]+
  
-[[http://www.ics.uci.edu/~xhx/publications/arem_recomb.pdf|AREMaligning short reads from ChIP-sequencing by expectation maximization]] \\ +<​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 /> 
-Newkirk DBiesingerJChon AYokomori K, and Xie X \\ +Lindblad-TohBarberZukLinet al.<​br ​/
-//J Comput Biol.//, 2011 \\ +Nature, 2011</p>
-Software: [[http://​sourceforge.net/​projects/arem|AREM]]+
  
-[[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.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, Chen Y, and Xie X \\ +Weng L, Macciardi F, Subramanian A, Guffanti ​G, Potkin SG, Yu Z, and Xie X<br /> 
-AI & STATS , 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>​
  
-==== 2010 ====+<​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<br /> 
 +<​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://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://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 /> 
-Ye GCai J, and Xie X \\ +Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X<br /> 
-arXiv:1012.0975v12010+<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.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://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-B and Xie X \\ +Ye GChen Yand Xie X<br /> 
-Computational Statistics and Data Analysis, doi:10.1016/j.csda.2010.10.021, 2010  \\ +AI &amp; STATS , 2011</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]] \\ +</div>
-Daily KRigor P, Christley 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 ]] \\ +<h3>2010</h3>
-Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J \\ +
-//​Bioinformatics//,​ 26(18):​2321-2327, ​2010  \\ +
-[[http://​ipubmed.ics.uci.edu/|iPubMed Search]]+
  
-[[http://arxiv.org/abs/1006.5060|Variable selection and dimension reduction via sparse ​gradients]] \\ +<div class="​level3">​ 
-Ye G-B 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:1006.5060v2, 2010+Ye G, Cai J, and Xie X<br /> 
 +arXiv:1012.0975v1, 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://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 /> 
-Potkin SG, Macciardi F, Guffanti ​G, Wang QTurner JALakatos AMiles MF, Lander A, Vawter MP, Xie X \\ +Ye G-B and Xie X<br /> 
-//​NeuroImage//​ 53:839-847, 2010+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 KRigor PChristley S, Xie X and Baldi P<br /> 
 +<​em>​BMC Bioinformatics<​/em>,11:514, 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://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 YChristley ​S, Mjolsness Eand Xie X \\ +Wang JCetindil I, Ji S, Li C, Xie X, Li G and Feng J<br /> 
-//BMC Systems Biology//, 4:99 doi:10.1186/1752-0509-4-99,​ 2010+<​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://www.springerlink.com/content/428v02087m218878/fulltext.pdf|Site-frequency Spectrum of Linked Sites]] \\ +<​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 /> 
-Xie X   \\ +Ye G-B and Xie X<​br ​/
-//Bulletin of Mathematical Biology//, DOI10.1007/​s11538-010-9534-3, 2010+arXiv:1006.5060v2, 2010</p>
  
-[[http://nar.oxfordjournals.org/cgi/content/abstract/gkq397|Genome-Wide Interrogation of Hepatic FXR Reveals an Asymmetric IR-Motif and Synergy with LRH-1]] \\ +<​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 /> 
-Chong HInfante ASeo YJeon TAhang YEdwards P, Xie X, and Osborne TF \\ +Potkin SGMacciardi FGuffanti GWang QTurner JALakatos A, Miles MF, Lander A, Vawter MP, Xie X<br /> 
-Nucleic Acids Research, doi:10.1093/nar/gkq397, 2010 \\ +<​em>​NeuroImage<​/em> 53:839-847, 2010</p>
-[[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]] \\ +<​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 /> 
-Kumar LBreakspear AKistler HC, Ma L-J, and Xie X  \\ +Wang YChristley SMjolsness E, and Xie X<br /> 
-//BMC Genomics// 11:2082010 \\ +<em>BMC Systems Biology</em>4:99 doi:10.1186/1752-0509-4-99,​ 2010</p>
-[[http://​www.broadinstitute.org/​annotation/​genome/​fusarium_group/​SupplementalMaterials.html|Supplementary Information]] \\ +
-[[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.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 ​/
-Ma L-J, et al.  \\ +Xie X<​br ​/> 
-//Nature// 464:​367-373,​ 2010 \\ +<​em>​Bulletin of Mathematical Biology</​em>,​ DOI10.1007/s11538-010-9534-3,​ 2010</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://​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<br /> 
 +Nucleic Acids Research, doi:​10.1093/​nar/​gkq397,​ 2010<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.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf|Incorporating existing network information into gene network inference]] \\ +<​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 /> 
-Christley SNie Q and Xie X \\ +Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X<br /> 
-//PLoS ONE// 4(8)e6799doi:10.1371/journal.pone.0006799 (2009)+<​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.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.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 /> 
-Seo YKChong HK, Infante AM, Im S, Xie Xand Osborne TF \\ +Ma L-Jet al.<br /> 
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0904246106 (2009)+<​em>​Nature</​em>​ 464:367-3732010<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://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​12/​i54|Identifying novel constrained elements by exploiting biased substitution patterns]] \\ +<h3>2009</h3>
-Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X \\ +
-//​Bioinformatics//​25:​i54-i62 (2009)  \\ +
-[[http://​www.ics.uci.edu/​~xhx/​publications/​siphy_suppinfo.pdf|Supplementary Methods]] \\ +
-[[http://​www.broadinstitute.org/​genome_bio/​siphy/|SiPhy (SIte-specific PHYlogenetic analysis) Java software package]]+
  
-[[http://www.pnas.org/content/early/2009/02/11/0813264106.abstract|Comparative genomics allows the discovery of cis-regulatory elements in mosquitoes]] \\ +<div class="​level3">​ 
-Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA  \\ +<​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 /> 
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0813264106 ​(2009)+Christley SNie Q and Xie X<br /> 
 +<​em>​PLoS ONE</em> 4(8): e6799. ​doi:10.1371/journal.pone.0006799 ​(2009)</p>
  
-[[http://genome.cshlp.org/​content/​19/4/567.long|Common polymorphic transcript variation ​in human disease]] \\ +<​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 /> 
-Fraser H and Xie X  \\ +Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF<​br ​/
-//Genome Research// doi:10.1101/gr.083477.108 ​(2009) ​\\ +<​em>​Proc Natl Acad Sci USA</em> ​doi:10.1073/pnas.0904246106 ​(2009)</p>
-[[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 ]] \\ +<​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 /> 
-Xie XRigor P, and Baldi P  \\ +Garber M, Guttman1 M, Clamp M, Zody MGFriedman N, and Xie X<​br ​/
-//​Bioinformatics/​25: 167-174 (2009) ​\\ +<em>Bioinformatics</em>25:i54-i62 (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/​siphy_suppinfo.pdf" rel="​nofollow"​ title="​http://www.ics.uci.edu/​~xhx/​publications/​siphy_suppinfo.pdf">​Supplementary Methods</​a><​br /> 
-[[http://motifmap.ics.uci.edu/​|MotifMap Server]]+<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://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/274|Human genomes as email attachments ]] \\ +<​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 S, Lu Y, Li C, and Xie X  \\ +Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA<​br ​/
-//​Bioinformatics // 25: 274-275 (2009) \\ +<​em>​Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0813264106 (2009)</p>
-[[http://www.ics.uci.edu/~xhx/project/DNAzip|DNAzip:​ DNA sequence compression using a reference genome]] \\ +
-[[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 ====+<​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<br /> 
 +<​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://www.ics.uci.edu/~xhx/publications/wu_motif_2008.pdf|Discovering regulatory motifs in the Plasmodium ​genome ​using comparative genomics ]] \\ +<​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 /> 
-Wu JSieglaff DH, Gervin J, and Xie X  \\ +Xie XRigor P, and Baldi P<br /> 
-//Bioinformatics // 24:1843-(2008\\ +<em>Bioinformatics</em> 25167-174 (2009)<br /> 
-[[http://​www.ics.uci.edu/​~xhx/​project/mdos/|MDOS software]]: A method for Motif Discovery using Orthologous Sequences (alignment independent)\\ +<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.ics.uci.edu/​~xhx/​publications/​wu_motif_2008_suppinfo.pdf|Supplementary ​Information on the MDOS algorithm]]+<a class="​urlextern"​ href="​http://​motifmap.ics.uci.edu/"​ rel="​nofollow"​ title="​http://​motifmap.ics.uci.edu/">​MotifMap Server</​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://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 /> 
-Ku M, Koche RP, Rheinbay EMendenhall EMEndoh 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  \\ +Christley SLu YLi C, and Xie X<br /> 
-//PLoS Genetics//4(10):e1000242 (2008) +<​em>​Bioinformatics </em> 25: 274-275 (2009)<​br ​/
-==== 2007 ====+<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://​www.pnas.org/​content/​104/​49/​19428|Distinguishing protein-coding and noncoding genes in the human genome ]] \\ +<​h3>​2008<​/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 PFry BLohmueller ​J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES and International HapMap Consortium ​ \\ +<​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 /> 
-//Nature//449:913-918 ​(2007)+Wu JSieglaff DHGervin ​J, and Xie X<br /> 
 +<​em>​Bioinformatics </em> 24:1843-9 (2008)<​br ​/
 +<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.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.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 /> 
-Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall ​EO'​Donovan A, Presser A, Russ C, Xie X, Meissner AWernig ​M, Jaenisch RNusbaum C, Lander ES, Bernstein BE. \\ +Ku M, Koche RP, Rheinbay E, Mendenhall ​EMEndoh M, Mikkelsen TS, Presser A, Nusbaum ​C, Xie X, Chi ASAdli M, Kasif SPtaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE<br /> 
-//Nature// 448:553-60 ​(2007)+<​em>​PLoS </em><​em>​Genetics<​/em>4(10):e1000242 ​(2008)</​p>​ 
 +</​div>​
  
-[[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 ]] \\ +<h3>2007</h3>
-Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES. \\ +
-//Proc Natl Acad Sci USA//​104:​7145-7150 (2007)  \\ +
-[[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 ]] \\ +<div class="​level3">​ 
-Mikkelsen TSWakefield MJet al \\ +<​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// 447:167-177 (2007)+Clamp MFry BKamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, and Lander ES.<br /> 
 +<​em>​Proc Natl Acad Sci </em><​em>​USA<​/em>​104(49):19428-33 (2007)</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/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 ​/
-Xie X, Kamal M, and Lander ES. \\ +Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES and International HapMap Consortium<​br ​/
-//Proc Natl Acad Sci USA//​103:​11659-11664 (2006) ​ \\ +<​em>​Nature<​/em>449:913-918 (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.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 /> 
 +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 /> 
 +<​em>​Nature</​em>​ 448:553-60 (2007)</​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://​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 /> 
-Kamal M, Xie X, and Lander ES.  \\ +Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES.<​br ​/
-//Proc Natl Acad Sci USA//103:2740-2745 (2006 \\ +<em>Proc Natl Acad Sci </​em><​em>​USA</em>104:7145-7150 (2007)<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/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.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/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 /> 
-Bernstein BE, Mikkelsen TS, Xie XKamal M et al.  \\ +Mikkelsen TS, Wakefield MJ, et al.<br /> 
-//Cell// 125:315-26 (2006)+<​em>​Nature<​/em> 447:167-177 (2007)</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/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 /> 
-Wu J and Xie X \\ +Xie X, Kamal M, and Lander ES.<​br ​/
-//Genome Biology//7(9):R85 (2006) ​(Highly accessed) ​ \\ +<​em>​Proc Natl Acad Sci </em><​em>​USA<​/em>103:11659-11664 ​(2006)<br /> 
-[[http://​www.broad.mit.edu/​personal/xhx/projects/NRSE|Supplementary website]]+<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/​ng/​journal/​v38/​n5/​pdf/​ng1776.pdf|Systematic identification of human mitochondrial disease genes through integrative genomics ]] \\ +<​h3>​2006 or before</h3>
-Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK. \\ +
-//Nature Genetics//, 38:576-82 (2006)+
  
-[[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 ]] \\ +<div class="​level3">​ 
-Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M \\ +<​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">​A large family ​of ancient repeat elements ​in the human genome is under strong selection</​a><​br /> 
-//Nature//​2005;​ 434:338-45  \\ +Kamal M, Xie X, and Lander ES.<br /> 
-[[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]]+<​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://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://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 /> 
-Giallourakis CCao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca ​M, Daly M, Rioux J, Xavier R \\ +Bernstein BEMikkelsen TS, Xie X, Kamal et al.<br /> 
-//Genome Resesarch//,​ 16:1056-72 (2006)+<​em>​Cell<​/em> 125:315-26 (2006)</p>
  
-[[http://download.cell.com/pdfs/0092-8674/PIIS0092867406003692.pdf|A Mammalian Organelle Map by Protein Correlation Profiling]] \\ +<​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 ​/
-Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M.  \\ +Wu J and Xie X<​br ​/
-//Cell// 125:187-99 ​(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/WerfelXieSeung2005.pdf|Learning curves for stochastic gradient descent in linear feedforward networks]] \\ +<​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 /> 
-Werfel J, Xie X and Seung HS \\ +Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK.<br /> 
-//Neural Computation//​2005;17:2699-718+<​em>​Nature Genetics<​/em>38:576-82 (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/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 /> 
-Lindblad-Toh K, Wade CMet al \\ +Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ESKellis M.<br /> 
-//Nature// 438:803-19 2005+<​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://www.ics.uci.edu/~xhx/publications/annurev.genom.6.080604.pdf|Disease gene discovery 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 /> 
-Giallourakis C, Henson CReich M, Xie X, and Mootha VK \\ +Giallourakis C, Cao ZGreen T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R.<br /> 
-//Annu. Rev. Genomics Hum. Genet.// 2005:22:381-406.+<​em>​Genome Resesarch<​/em>, 16:1056-72 (2006)</​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://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 X and Seung HS \\ +Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M.<br /> 
-//Phys Rev E//, 2004;69:041909+<​em>​Cell<​/em> 125:187-99 (2006)</​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/​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 /> 
-Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al \\ +Werfel J, Xie X and Seung HS.<br /> 
-//Proc Natl Acad Sci USA//2004;101:6570-5+<​em>​Neural Computation<​/em>2005;17:2699-718</​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.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 /> 
-Xie XHahnloser RHand Seung HS \\ +Lindblad-Toh KWade CMet al.<br /> 
-//Physical Review E//, 2002;66:041902+<​em>​Nature<​/em> 438:803-19 2005</​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/​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 Giese MA \\ +Giallourakis C, Henson C, Reich M, Xie X, and Mootha VK.<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>​Annu. Rev. Genomics Hum. Genet.</em> 2005:22:381-406.</​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_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 /> 
-Xie X, Hahnloser HR, and Seung HS.  \\ +Xie X and Seung HS.<br /> 
-//Advances in Neural Information Processing Systems//​2001;13:350-356+<​em>​Phys Rev E</em>, 2004;69:041909</​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/​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 and Giese MA \\ +Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al.<br /> 
-//Advances ​in Neural Information Processing Systems//2002;13:325-332+<​em>​Proc Natl Acad Sci USA</​em>,​ 2004;101:6570-5</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/​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, Hahnloser RH, and Seung HS.  \\ +Xie X, Hahnloser RH, and Seung HS.<br /> 
-//Neural Computation//​, 2002;14:2627-2646+<​em>​Physical Review E</em>, 2002;66:041902</​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/​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 and Seung HS \\ +Xie X and Giese MA.<br /> 
-//Neural Computation//, 2003;16:441-454+<​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/​network_pop.pdf|Threshold behavior of maximum likelihood method in population decoding]] \\ +<​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 \\ +Xie X, Hahnloser HR, and Seung HS.<br /> 
-//Network: Comput. Neural Syst./2002;​13:​447-456+<​em>​Advances in Neural Information Processing </​em><​em>​Systems</​em>​2001;​13:​350-356</​p>​ 
 + 
 +<​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.<br /> 
 +<​em>​Advances in Neural Information Processing </​em><​em>​Systems</​em>​2002;​13:​325-332</​p>​ 
 + 
 +<​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 RH, and Seung HS.<br /> 
 +<​em>​Neural Computation</​em>,​ 2002;​14:​2627-2646</​p>​ 
 + 
 +<​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 Seung HS.<br /> 
 +<​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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