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publications [2018/05/25 08:43]
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>​
  
-__false__+<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>
  
-__false__+<​p>​Sequential Embedding Induced Nonparametric Text Clustering<​br /> 
 +Duan T, Lou Q, Xie X</p>
  
-==== 2016 ====+<​p><​a class="​urlextern"​ href="​https://​arxiv.org/​abs/​1802.00931"​ rel="​nofollow"​ title="​https://​arxiv.org/​abs/​1802.00931">​Deep Learning Framework for Multi-class Breast Cancer Histology Image Classification</​a><​br /> 
 +Vang S, Chen Z, Xie X<br /> 
 +15th International Conference on Image Analysis and Recognition,​ 2018</​p>​
  
-[[https://​arxiv.org/​abs/​1612.05970|Adversarial Deep Structural Networks ​for Mammographic Mass Segmentation]]\\ +<​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 /> 
-Wentao Zhu, Xiaohui Xie\\ +IEEE Winter Confon Applications of Computer Vision 2018</​p>​
-arXiv:1612.05970+
  
-[[https://www.ncbi.nlm.nih.gov/pubmed/27418388|Developmentally regulated long non-coding RNAs in Xenopus tropicalis]]\\ +<​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 ​/> 
-Forouzmand et al\\ +IEEE Winter Confon Applications of Computer Vision 2018</​p>​
-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]]\\ +<​p>​Adversarial Deep Structured Nets for Mass Segmentation from Mammograms<​br ​/> 
-Chen YLi YNarayan RSubramanian Aand Xie X\\ +W ZhuX XiangT TranGD HagerXie<br /> 
-Bioinformatics,​ 2016+IEEE International Symposium on Biomedical Imaging</​p>​
  
-DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences\\ +<​p>​Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural Networks<​br /> 
-Quang and Xie X\\ +H Tang, Kim, Xie<br /> 
-Nucleic Acids Research, 2016+IEEE International Symposium on Biomedical Imaging</​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>​Molecular Mechanisms ​for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.<​br /> 
-Weng L, Li Y, Xie X, and Shi Y\\ +Zhu Y, Wang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.<br /> 
-RNA, 2016+Mol Cell. 2018 Jan 4;​69(1):​62-74.e4.</​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>​2017<​/h3>
-Zhu W, et al.\\ +
-AAAI Conference on Artificial Intelligence,​ 2016+
  
-==== 2015 ====+<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>​
  
-Hobbes3Dynamic Generation of Variable-Length Signatures ​for Efficient Approximate Subsequence Mappings\\ +<​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 /> 
-Kim JChen L, and Xie X\\ +D Quang, X Xie<br /> 
-32nd IEEE International Conference on Data Engineering - ICDE 2016+bioRxiv, 151274</​p>​
  
-[[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="​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 /> 
-Quang D and Xie X+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>​
  
-[[http://​www.ncbi.nlm.nih.gov/​pubmed/​25338716|DANN:​ a deep learning ​approach for annotating the pathogenicity of genetic variants]]\\ +<​p>​Understanding sequence conservation with deep learning<br /> 
-Quang D, Chen Y and Xie X\\ +Li Y, Quang D, and Xie X<br /> 
-Bioinformatics31(5):​761-3,​ 2015+ACM BCB2017</​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/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 and Xie X\\ +Vang YS and Xie X<br /> 
-BMC Genomics2015+Bioinformatics2017</​p>​
  
 +<​p><​a class="​urlextern"​ href="​https://​www.ncbi.nlm.nih.gov/​pubmed/​28325473"​ rel="​nofollow"​ title="​https://​www.ncbi.nlm.nih.gov/​pubmed/​28325473">​Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program</​a><​br />
 +Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW<br />
 +Dev Cell. 27;​40(6):​595-607.e4,​ 2017</​p>​
 +</​div>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​ImagingGenetics.pdf |Identifying unanticipated genes and mechanisms in serious mental illness]]\\ +<​h3>​2016<​/h3>
-Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X\\ +
-Neuroimaging genetics : principles and practices, 2015+
  
-==== 2014 ====+<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>​
  
-[[http://link.springer.com/​article/​10.1007/s10032-014-0229-4|Handwritten Hangul recognition using deep convolutional neural networks]]\\ +<​p><​a class="​urlextern"​ href="​https://www.ncbi.nlm.nih.gov/pubmed/​27418388"​ rel="​nofollow"​ title="​https://www.ncbi.nlm.nih.gov/pubmed/27418388">​Developmentally regulated long non-coding RNAs in Xenopus tropicalis<​/a><br /> 
-Kim I and Xie X\\ +Forouzmand et al.<br /> 
-International Journal on Document Analysis and Recognition,​ 2014\\ +Developmental Biology, (16)30120-8 2016</​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/​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 /> 
-Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger JXie X, and Cho K\\ +Chen Y, Li Y, Narayan RSubramanian A, and Xie X<br /> 
-Development2014+Bioinformatics2016</​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>​DanQa hybrid convolutional ​and recurrent deep neural network for quantifying the function ​of DNA sequences<​br /> 
-Li Y and Xie X\\ +Quang D and Xie X<br /> 
-Bioinformatics2014+Nucleic Acids Research2016</​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://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 /> 
-Bioinformatics2014+RNA2016</​p>​
  
-[[http://www.biomedcentral.com/1471-2105/15/42|Improving Read Mapping Using Additional Prefix Grams]]\\ +<​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 JLi C and Xie X\\ +Zhu Wet al.<br /> 
-BMC Bioinformatics2014, 15(1):42+AAAI Conference on Artificial Intelligence2016</​p>​ 
 +</​div>​
  
-[[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]]\\ +<​h3>​2015<​/h3>
-Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X\\ +
-PLOS ONE, 2014, DOI: 10.1371/​journal.pone.0092317+
  
-[[http://​www.biomedcentral.com/​1752-0509/8/​3/​abstract|Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns]] \\ +<div class="​level3">​ 
-Zheng ZChristley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q\\ +<​p>​Hobbes3Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings<​br ​/> 
-BMC Systems Biology 2014, 8:3+Kim JChen Land Xie X<br /> 
 +32nd IEEE International Conference on Data Engineering - ICDE 2016</​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://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 /> 
-Lackford B, Yao C, Charles GM, Weng L, Zheng X, Choi EA, Xie X, Wan J, Xing Y, Freudenberg JM, Yang P, Jothi R, Hu G, Shi Y\\ +Quang D and Xie X</p>
-EMBO J. 2014 Mar 4. +
-==== 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://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 /> 
-Ye GTang M, Nie Q and Xie X\\ +Quang DChen Y and Xie X<​br ​/
-//PLOS ONE//, 2013+Bioinformatics31(5):​761-3,​ 2015</​p>​
  
-[[http://www.hindawi.com/journals/cmmm/2013/873595/|A gradient boosting algorithm ​for survival analysis via direct optimization of concordance index]] \\ +<​p><​a class="​urlextern"​ href="http://www.biomedcentral.com/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 /> 
-Chen Y, Jia Z, Mercola D and Xie X\\ +Li Y and Xie X<​br ​/
-//Comput Math Methods Med.//, 2013+BMC Genomics2015</​p>​
  
-[[http://onlinelibrary.wiley.com/doi/10.1002/dvg.22719/abstract|Biallelic genome modification ​in F0 Xenopus tropicalis embryos using the CRISPR/Cas system]]\\ +<​p><​a class="​urlextern"​ href="http://www.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 ​/> 
-Blitz IBiesinger J, Xie Xand Cho K\\ +Potkin SGvan Erp TGMLing S, Macciardi F, and Xie X<br /> 
-//Genesis//, 2013.+Neuroimaging genetics : principles ​and practices, 2015</​p>​ 
 +</div>
  
-[[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]]\\ +<​h3>​2014<​/h3>
-Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y\\ +
-//RNA//, 2013+
  
-[[http://arxiv.org/abs/1305.0855|Inference in Kingman'​s Coalescent with Particle Markov Chain Monte Carlo Method]] \\ +<div class="​level3">​ 
-Chen Y and Xie X \\ +<​p><​a class="​urlextern"​ href="http://link.springer.com/article/10.1007/​s10032-014-0229-4"​ rel="​nofollow"​ title="​http://​link.springer.com/​article/​10.1007/​s10032-014-0229-4">​Handwritten Hangul recognition using deep convolutional neural networks</​a><​br /> 
-//arXiv//, 2013+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://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.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 /> 
-Biesinger J, Wang Y, and Xie X \\ +Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K<br /> 
-//BMC Bioinformatics//​ 201314(S5):S4, 2013 \\ +Development2014</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://bioinformatics.oxfordjournals.org/content/early/2014/04/​21/​bioinformatics.btu174"​ rel="​nofollow"​ title="​http://​bioinformatics.oxfordjournals.org/​content/​early/​2014/​04/​21/​bioinformatics.btu174">​Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity</​a><​br /> 
-Li Y and Xie X \\ +Li Y and Xie X<​br ​/
-//BMC Bioinformatics// 201314(Suppl 5):S11, 2013+Bioinformatics, ​2014</​p>​
  
-[[http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&​arnumber=6544889|Efficient direct search on compressed genomic data]] \\ +<​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 /> 
-Yang X, Wang B, Li C, Wang J, and Xie X \\ +Quang D and Xie X<​br ​/> 
-//IEEE International Conference on Data Engineering (ICDE)//, 2013 +Bioinformatics,​ 2014</​p>​
-==== 2012 ====+
  
-[[http://www.springerlink.com/content/4l2m27p3867xj584/|Learning sparse gradients for variable selection and dimension reduction]] \\ +<​p><​a class="​urlextern"​ href="http://www.biomedcentral.com/1471-2105/15/42" rel="​nofollow"​ title="​http://www.biomedcentral.com/1471-2105/15/42">​Improving Read Mapping Using Additional Prefix Grams</​a><​br /> 
-Ye G and Xie X \\ +Kim J, Li C and Xie X<br /> 
-Machine Learning Journal, 87(3):​303-355,​ 2012 \\ +BMC Bioinformatics,​ 2014, 15(1):​42</​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://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 /> 
-Yao C, Biesinger J,Wan J,Weng LBusch AXing Y, Xie X, and Shi Y \\ +Watanabe K, Biesinger J, Salmans MLRoberts BSArthur WTCleary M, Andersen B, Xie X, and Dai X<br /> 
-PNAS109(46):​18773-82012+PLOS ONE2014DOI: 10.1371/​journal.pone.0092317</​p>​
  
-[[http://www.ncbi.nlm.nih.gov/pubmed/22296850|Genome-wide analysis ​of hepatic LRH-1 reveals a promoter binding preference ​and suggests ​role in regulating genes of lipid metabolism in concert with FXR]] \\ +<​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 Chong HBiesinger JSeo YK, Xie X, Osborne TF \\ +Zheng ZChristley SChiu WT, Blitz IL, Xie X, Cho KW, Nie Q<br /> 
-BMC Genomics2012+BMC Systems Biology 20148:​3</​p>​
  
-[[http://www.ncbi.nlm.nih.gov/pubmed/22199254|Hobbes:​ optimized gram-based methods for efficient read alignment]] \\ +<​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 /> 
-Ahmadi ABehm A, Honnalli N, Li C, Weng L, and Xie X  \\ +Lackford BYao C, Charles GM, Weng L, Zheng X, Choi EA, Xie X, Wan JXing Y, Freudenberg JM, Yang P, Jothi R, Hu G, Shi Y<​br ​/
-Nucleic Acids Research40(6):e41 2012 \\ +EMBO J2014 Mar 4.</​p>​ 
-Software: [[http://hobbes.ics.uci.edu/|Hobbes]]+</div>
  
-==== 2011 ====+<​h3>​2013</​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://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 /> 
-arXiv:​1110.3076v12011+Ye G, Tang MNie Q and Xie X<br /> 
 +<​em>​PLOS ONE</​em>​2013</​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.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 /> 
-Daily KPatel VR, Rigor P, Xie X, Baldi P. \\ +Chen YJia ZMercola D and Xie X<br /> 
-BMC Bioinformatics2011+<​em>​Comput Math Methods Med.</​em>​2013</​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://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 /> 
-Lindblad-TohBarberZukLin, et al. \\ +Blitz IBiesinger JXie Xand Cho K<br /> 
-Nature2011+<​em>​Genesis</​em>​2013.</​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://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 /> 
-Weng L, Macciardi FSubramanian AGuffanti GPotkin SGYu Z, and Xie X \\ +Yao C, Choi E, Weng L, Xie XWan JXing YMoresco JJTu PG, Yates JR, and Shi Y<br /> 
-BMC Bioinformatics,​ 2011  \\ +<​em>​RNA<​/em>, 2013</p>
-Software: [[http://cbcl.ics.uci.edu/​SSEA/​|SNP Set Enrichment Analysis (SSEA)]]+
  
-[[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://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 /> 
-Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF \\ +Chen and Xie X<br /> 
-//Cell Metabolism//​13:367-75, 2011  \\ +<​em>​arXiv<​/em>2013</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.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 /> 
-Newkirk D, BiesingerJ, Chon A, Yokomori K, and Xie X \\ +Biesinger J, Wang Y, and Xie X<br /> 
-//J Comput Biol.//, 2011 \\ +<​em>​BMC Bioinformatics<​/em> 2013, 14(S5):S4, 2013<​br ​/
-Software: [[http://sourceforge.net/projects/arem|AREM]]+<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://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/1471-2105/14/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, Chen Yand Xie X \\ +Li Y and Xie X<br /> 
-AI & STATS 2011+<​em>​BMC Bioinformatics</​em>​ 201314(Suppl 5):S11, 2013</​p>​
  
-==== 2010 ====+<​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 /> 
 +Yang X, Wang B, Li C, Wang J, and Xie X<br /> 
 +<​em>​IEEE International Conference on Data Engineering (ICDE)</​em>,​ 2013</​p>​ 
 +</​div>​
  
-[[http://​arxiv4.library.cornell.edu/​abs/​1012.0975|Split Bregman method for sparse inverse covariance estimation with matrix iteration acceleration]] \\ +<​h3>​2012<​/h3>
-Ye G, Cai J, and Xie X \\ +
-arXiv:​1012.0975v1,​ 2010+
  
-[[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]] \\ +<div class="​level3">​ 
-Ye G-B 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 /> 
-Computational Statistics and Data Analysisdoi:10.1016/j.csda.2010.10.021,​ 2010  \\ +Ye G and Xie X<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]] \\ +Machine Learning Journal87(3):303-355, 2012<​br ​/> 
-Daily K, Rigor P, Christley S, Xie X and Baldi P  \\ +<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>
-//BMC Bioinformatics//,​11:​514,​ 2010+
  
-[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq414|Interactive and fuzzy search: ​dynamic way to explore MEDLINE ]] \\ +<​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 /> 
-Wang J, Cetindil IJi SLi C, Xie X, Li G and Feng J \\ +Yao C, Biesinger ​J,Wan J,Weng LBusch A, Xing Y, Xie X, and Shi Y<​br ​/
-//​Bioinformatics/​/, 26(18):2321-23272010  \\ +PNAS109(46):18773-82012</p>
-[[http://​ipubmed.ics.uci.edu/|iPubMed Search]]+
  
-[[http://arxiv.org/abs/1006.5060|Variable selection and dimension reduction via sparse gradients]] \\ +<​p><​a class="​urlextern"​ href="http://www.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 G-and Xie X \\ +Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF<br /> 
-arXiv:​1006.5060v22010+BMC Genomics2012</​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.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 /> 
-Potkin SG, Macciardi F, Guffanti GWang Q, Turner JA, Lakatos ​A, Miles MFLander AVawter MP, Xie X \\ +Ahmadi ABehm A, Honnalli NLi CWeng Land Xie X<br /> 
-//NeuroImage// 53:839-847, 2010+Nucleic Acids Research, 40(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.biomedcentral.com/​1752-0509/​4/​99|Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent]] \\ +<​h3>​2011<​/h3>
-Wang Y, Christley S, Mjolsness E, and Xie X \\ +
-//BMC Systems Biology//, 4:99 doi:​10.1186/​1752-0509-4-99,​ 2010+
  
-[[http://www.springerlink.com/content/428v02087m218878/fulltext.pdf|Site-frequency Spectrum of Linked Sites]] \\ +<div class="​level3">​ 
-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 ​/
-//Bulletin of Mathematical Biology//, DOI10.1007/​s11538-010-9534-32010+Ye GWang Y, Chen Y, and Xie X<br /> 
 +arXiv:1110.3076v12011</​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://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 /> 
-Chong HInfante ASeo Y, Jeon T, Ahang Y, Edwards ​P, Xie X, and Osborne TF \\ +Daily KPatel VRRigor P, Xie X, Baldi P.<​br ​/
-Nucleic Acids Research, doi:10.1093/nar/gkq3972010 \\ +BMC Bioinformatics2011</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.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 ​/
-Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X  \\ +Lindblad-Toh,​ Barber, Zuk, Lin, et al.<​br ​/
-//BMC Genomics// 11:208, 2010 \\ +Nature, 2011</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.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 ​/
-Ma L-J, et al \\ +Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X<​br ​/
-//Nature// 464:367-373, 2010 \\ +BMC Bioinformatics,​ 2011<​br ​/> 
-[[http://www.broadinstitute.org/news/1439|The chromosomal secrets of a plant pathogen]] \\ +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.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://​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://​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.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 /> 
-Christley SNie Q and Xie X \\ +Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X<br /> 
-//PLoS ONE// 4(8): e6799doi:10.1371/journal.pone.0006799 (2009)+<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.pnas.org/content/early/2009/08/03/0904246106.abstract|Genome-wide analysis of SREBP-1 binding ​in mouse liver chromatin reveals ​preference for promoter proximal binding to a new motif]] \\ +<​p><​a class="​urlextern"​ href="http://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 /> 
-Seo YKChong HK, Infante AM, Im S, Xie X, and Osborne TF \\ +Ye GChen Yand Xie X<br /> 
-//Proc Natl Acad Sci USA// doi:​10.1073/​pnas.0904246106 (2009)+AI &amp; STATS 2011</​p>​ 
 +</div>
  
-[[http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​12/​i54|Identifying novel constrained elements by exploiting biased substitution patterns]] \\ +<​h3>​2010<​/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 DHDunn WA, Xie X, Megy K, Marinotti O, and James AA  \\ +<​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 /> 
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0813264106 (2009)+Ye GCai Jand Xie X<​br ​/
 +arXiv:1012.0975v1, 2010</p>
  
-[[http://genome.cshlp.org/content/19/4/567.long|Common polymorphic transcript variation in human disease]] \\ +<​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 /> 
-Fraser H and Xie X  \\ +Ye G-B and Xie X<​br ​/
-//Genome Research// doi:10.1101/gr.083477.108 (2009) \\ +Computational Statistics and Data Analysis, ​doi:10.1016/j.csda.2010.10.021,​ 2010<br /> 
-[[http://www.ics.uci.edu/~xhx/publications/PTV_GR2009.pdf|PDF]]+<a class="​urlextern"​ href="http://arxiv.org/​abs/​1006.5086" rel="​nofollow"​ title="​http://​arxiv.org/abs/1006.5086">​arXiv version</a> <a class="​urlextern"​ href="​http://​www.biomedcentral.com/​1471-2105/​11/​514"​ rel="​nofollow"​ title="​http://​www.biomedcentral.com/​1471-2105/​11/​514">​Data Structures and Compression Algorithms for High-Throughput Sequencing Technologies</​a><​br /> 
 +Daily K, Rigor P, Christley S, Xie X and Baldi P<br /> 
 +<​em>​BMC Bioinformatics</​em>,​11:​514,​ 2010</​p>​
  
-[[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/​btq414"​ rel="​nofollow"​ title="​http:​//bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​btq414">​Interactive and fuzzy search: a dynamic way to explore MEDLINE </​a><​br /> 
-Xie X, Rigor P, and Baldi P  \\ +Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J<br /> 
-//Bioinformatics/​/ 25: 167-174 ​(2009\\ +<em>Bioinformatics</em>, 26(18):2321-2327, 2010<br /> 
-[[http://www.ics.uci.edu/​~xhx/​publications/​MotifMap_Supp_Info.pdf|Supplementary Methods]] \\ +<a class="​urlextern"​ href="http://ipubmed.ics.uci.edu/​" rel="​nofollow"​ title="​http://ipubmed.ics.uci.edu/​">​iPubMed Search</​a></​p>​
-[[http://motifmap.ics.uci.edu/​|MotifMap Server]]+
  
-[[http://bioinformatics.oxfordjournals.org/cgi/content/​abstract/​25/​2/​274|Human genomes as email attachments ]] \\ +<​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 ​/> 
-Christley S, Lu Y, Li C, and Xie X  \\ +Ye G-B and Xie X<​br ​/> 
-//​Bioinformatics // 25: 274-275 (2009) \\ +arXiv:1006.5060v2, 2010</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://​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<br /> 
 +<​em>​NeuroImage</​em>​ 53:839-847, 2010</​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://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 /> 
-Wu J, Sieglaff DH, Gervin J, and Xie X  \\ +Wang Y, Christley S, Mjolsness E, and Xie X<​br ​/
-//​Bioinformatics // 24:1843-9 (2008) \\ +<​em>​BMC Systems Biology</em>, 4:99 doi:10.1186/1752-0509-4-99,​ 2010</p>
-[[http://www.ics.uci.edu/~xhx/project/mdos/|MDOS software]]: A method ​for Motif Discovery ​using Orthologous Sequences (alignment independent). \\ +
-[[http://www.ics.uci.edu/~xhx/publications/​wu_motif_2008_suppinfo.pdf|Supplementary Information on the MDOS algorithm]]+
  
-[[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2567431&​blobtype=pdf|Genomewide analysis ​of PRC1 and PRC2 occupancy identifies two classes of bivalent domains ]] \\ +<​p><​a class="​urlextern"​ href="http://www.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 /> 
-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  \\ +Xie X<br /> 
-//PLoS Genetics//​4(10):​e1000242 (2008) +<​em>​Bulletin of Mathematical Biology</em>, DOI: 10.1007/s11538-010-9534-3,​ 2010</p>
-==== 2007 ====+
  
-[[http://www.pnas.org/​content/​104/49/19428|Distinguishing protein-coding ​and noncoding genes in the human genome ]] \\ +<​p><​a class="​urlextern"​ href="http://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 /> 
-Clamp MFry BKamal MXie XCuff JLin MFKellis M, Lindblad-Toh K, and Lander ES\\ +Chong HInfante ASeo YJeon TAhang YEdwards PXie X, and Osborne TF<br /> 
-//Proc Natl Acad Sci USA//104(49):19428-33 (2007)+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.nature.com/nature/journal/v449/n7164/abs/nature06250.html|Genome-wide detection and characterization ​of positive selection ​in human populations ]] \\ +<​p><​a class="​urlextern"​ href="http://www.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 /> 
-Sabeti PCVarilly PFry BLohmueller ​J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES and International HapMap Consortium ​ \\ +Kumar LBreakspear AKistler HCMa L-J, and Xie X<br /> 
-//Nature//449:913-918 (2007)+<​em>​BMC Genomics</​em>​ 11:2082010<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.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/​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 /> 
-Mikkelsen TS, Ku M, Jaffe DB, Issac BLieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'​Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE\\ +Ma L-J, et al.<br /> 
-//Nature// 448:553-60 (2007)+<​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://​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>​2009<​/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 MJ, et al.  \\ +<​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 /> 
-//Nature// 447:167-177 ​(2007)+Christley SNie Q and Xie X<br /> 
 +<​em>​PLoS ONE</em> 4(8)e6799. doi:​10.1371/​journal.pone.0006799 ​(2009)</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.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 ​/
-Xie X, Kamal M, and Lander ES. \\ +Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF<​br ​/
-//Proc Natl Acad Sci USA//​103:​11659-11664 (2006) ​ \\ +<​em>​Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0904246106 (2009)</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://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​12/​i54"​ rel="​nofollow"​ title="​http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​12/​i54">​Identifying novel constrained elements by exploiting biased substitution patterns</​a><​br /> 
 +Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X<br /> 
 +<​em>​Bioinformatics</​em>​25:​i54-i62 (2009)<​br /> 
 +<a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​siphy_suppinfo.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​siphy_suppinfo.pdf">​Supplementary Methods</​a><​br /> 
 +<a class="​urlextern"​ href="​http://​www.broadinstitute.org/​genome_bio/​siphy/"​ rel="​nofollow"​ title="​http://​www.broadinstitute.org/​genome_bio/​siphy/">​SiPhy (SIte-specific PHYlogenetic analysis) Java software package</​a></​p>​
  
-[[http://www.ics.uci.edu/~xhx/publications/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.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 ​/
-Kamal M, Xie X, and Lander ES.  \\ +Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA<​br ​/
-//Proc Natl Acad Sci USA//​103:​2740-2745 (2006) ​ \\ +<​em>​Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0813264106 (2009)</p>
-[[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|A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells]] \\ +<​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 /> 
-Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al \\ +Fraser H and Xie X<br /> 
-//Cell// 125:315-26 (2006)+<​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://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://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 J and Xie X \\ +Xie X, Rigor P, and Baldi P<​br ​/
-//Genome Biology//7(9):R85 (2006(Highly accessed) ​ \\ +<​em>​Bioinformatics<​/em> 25167-174 ​(2009)<br /> 
-[[http://www.broad.mit.edu/personal/xhx/projects/NRSE|Supplementary ​website]]+<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 /> 
 +<a class="​urlextern"​ href="​http://​motifmap.ics.uci.edu/"​ rel="​nofollow"​ title="​http://​motifmap.ics.uci.edu/">​MotifMap Server</​a></​p>​
  
-[[http://www.nature.com/ng/journal/v38/n5/pdf/ng1776.pdf|Systematic identification of human mitochondrial disease genes through integrative genomics ]] \\ +<​p><​a class="​urlextern"​ href="http://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 /> 
-Calvo S, Jain MXie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK\\ +Christley ​S, Lu YLi C, and Xie X<br /> 
-//Nature Genetics//, 38:576-82 (2006)+<​em>​Bioinformatics </em> 25: 274-275 (2009)<​br /> 
 +<a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​project/​DNAzip"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​project/​DNAzip">​DNAzip:​ DNA sequence compression using a reference genome</​a><​br /> 
 +<a class="​urlextern"​ href="​http:​//www.ics.uci.edu/~xhx/publications/​DNAzip.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​DNAzip.pdf">​PDF</​a><​br /> 
 +<a class="​urlextern"​ href="​http://​www.genomeweb.com/​informatics/​jim-watsonâ��s-genome-e-mail-uc-irvine-team-develops-method-compress-genomic-data"​ rel="​nofollow"​ title="​http://​www.genomeweb.com/​informatics/​jim-watsonâ��s-genome-e-mail-uc-irvine-team-develops-method-compress-genomic-data">​News featured in genomeweb</​a><​br /> 
 +<a class="​urlextern"​ href="​http://​www.bio-itworld.com/​news/​2009/​01/​30/​Email-compression-genome.html"​ rel="​nofollow"​ title="​http://​www.bio-itworld.com/​news/​2009/​01/​30/​Email-compression-genome.html">​News featured in bio-itworld</​a><​br /> 
 +<a class="​urlextern"​ href="​http://​www.amia.org/​content/​2009-summit-translational-bioinformatics-closing-session"​ rel="​nofollow"​ title="​http://​www.amia.org/​content/​2009-summit-translational-bioinformatics-closing-session">​One of the 20 most important papers in Translational Bioinformatics in </​a><​a class="​urlextern"​ href="​http://​www.amia.org/​content/​2009-summit-translational-bioinformatics-closing-session"​ rel="​nofollow"​ title="​http://​www.amia.org/​content/​2009-summit-translational-bioinformatics-closing-session">​2009</​a>​as reviewed by Russ Altman of Stanford</​p>​ 
 +</​div>​
  
-[[http://​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 ]] \\ +<​h3>​2008<​/h3>
-Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M.  \\ +
-//​Nature//​2005;​ 434:​338-45 ​ \\ +
-[[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]] \\ +<div class="​level3">​ 
-Giallourakis CCao ZGreen T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R.  \\ +<​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 /> 
-//Genome Resesarch//, 16:1056-72 ​(2006)+Wu JSieglaff DHGervin Jand 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://download.cell.com/pdfs/0092-8674/PIIS0092867406003692.pdf|A Mammalian Organelle Map by Protein Correlation Profiling]] \\ +<​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 /> 
-Foster LJde Hoog CLZhang YZhang Y, Xie X, Mootha VKand Mann M.  \\ +Ku MKoche RPRheinbay EMendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi ASAdli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE<br /> 
-//Cell// 125:187-99 ​(2006)+<​em>​PLoS </em><​em>​Genetics<​/em>4(10):e1000242 ​(2008)</​p>​ 
 +</​div>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​WerfelXieSeung2005.pdf|Learning curves for stochastic gradient descent in linear feedforward networks. ]] \\ +<​h3>​2007<​/h3>
-Werfel J, Xie X and Seung HS.  \\ +
-//Neural Computation//,​ 2005;​17:​2699-718+
  
-[[http://www.nature.com/nature/journal/v438/n7069/pdf/nature04338.pdf|Genome sequence, comparative analysis ​and haplotype structure of the domestic dog ]] \\ +<div class="​level3">​ 
-Lindblad-Toh K, Wade CM, et 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// 438:803-19 2005+Clamp M, Fry B, Kamal 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/annurev.genom.6.080604.pdf|Disease gene discovery through integrative genomics]] \\ +<​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 /> 
-Giallourakis CHenson CReich M, Xie X, and Mootha VK.  \\ +Sabeti PCVarilly PFry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES and International HapMap Consortium<​br /> 
-//Annu. Rev. Genomics Hum. Genet.// 2005:22:381-406.+<​em>​Nature<​/em>449:913-918 (2007)</​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.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 and Seung HS \\ +Mikkelsen TSKu 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 /> 
-//Phys Rev E//, 2004;69:041909+<​em>​Nature</​em>​ 448:553-60 (2007)</​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/​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 /> 
-Mootha VKHandschin CArlow DXie XSt Pierre J et al \\ +Xie XMikkelsen TSGnirke ALindblad-Toh KKellis M and Lander ES.<br /> 
-//Proc Natl Acad Sci USA//, 2004;101:6570-5+<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/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/​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 XHahnloser RHand Seung HS \\ +Mikkelsen TSWakefield MJet al.<br /> 
-//Physical Review E//, 2002;66:041902+<​em>​Nature<​/em> 447:167-177 (2007)</​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/​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 and Giese MA.  \\ +Xie X, Kamal M, and Lander ES.<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>​Proc Natl Acad Sci </em><​em>​USA<​/em>​103:​11659-11664 (2006)<​br ​/
-Giese MA and Xie X  \\ +<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>​ 
-//Neurocomputing// 2002;44:417-422+</​div>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​lwta.pdf|Learning winner-take-all competition between groups of neurons in lateral inhibitory networks ]] \\ +<​h3>​2006 or before</h3>
-Xie X, Hahnloser HR, and Seung HS.  \\ +
-//Advances in Neural Information Processing Systems//​2001;​13:​350-356+
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​nc_vel_tuning.pdf|Generating velocity tuning by asymmetric recurrent connections]] \\ +<div class="​level3">​ 
-Xie X and Giese MA \\ +<​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 /> 
-//Advances in Neural ​Information ​Processing Systems//2002;13:325-332+Kamal M, Xie Xand 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://www.ics.uci.edu/~xhx/publications/gwta_nc.pdf|Selectively Grouping Neurons ​in Recurrent Networks of Lateral Inhibition]] \\ +<​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 /> 
-Xie X, Hahnloser RH, and Seung HS \\ +Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al.<br /> 
-//Neural Computation//,​ 2002;14:2627-2646+<​em>​Cell<​/em> 125:315-26 (2006)</​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://genomebiology.com/2006/7/9/R85" rel="​nofollow"​ title="​http://​genomebiology.com/​2006/​7/​9/​R85">​Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression </a><br /> 
-Xie X and Seung HS.  \\ +Wu J and Xie X<br /> 
-//Neural Computation//, 2003;16:441-454+<​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/​network_pop.pdf|Threshold behavior of maximum likelihood method in population decoding]] \\ +<​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 \\ +Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK.<br /> 
-//Network: Comput. Neural Syst./2002;​13:​447-456+<​em>​Nature Genetics</​em>,​ 38:576-82 (2006)</​p>​ 
 + 
 +<​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 /> 
 +Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M.<br /> 
 +<​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>​ 
 + 
 +<​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, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R.<br /> 
 +<​em>​Genome Resesarch</​em>,​ 16:1056-72 (2006)</​p>​ 
 + 
 +<​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 /> 
 +Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M.<br /> 
 +<​em>​Cell</​em>​ 125:187-99 (2006)</​p>​ 
 + 
 +<​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 /> 
 +Werfel J, Xie X and Seung HS.<br /> 
 +<​em>​Neural Computation</​em>,​ 2005;​17:​2699-718</​p>​ 
 + 
 +<​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 /> 
 +Lindblad-Toh K, Wade CM, et al.<br /> 
 +<​em>​Nature</​em>​ 438:803-19 2005</​p>​ 
 + 
 +<​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 /> 
 +Giallourakis C, Henson C, Reich M, Xie X, and Mootha VK.<br /> 
 +<​em>​Annu. Rev. Genomics Hum. Genet.</​em>​ 2005:​22:​381-406.</​p>​ 
 + 
 +<​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 and Seung HS.<br /> 
 +<​em>​Phys Rev E</​em>,​ 2004;​69:​041909</​p>​ 
 + 
 +<​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 /> 
 +Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al.<br /> 
 +<​em>​Proc Natl Acad Sci USA</​em>,​ 2004;​101:​6570-5</​p>​ 
 + 
 +<​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.<br /> 
 +<​em>​Physical Review E</​em>,​ 2002;​66:​041902</​p>​ 
 + 
 +<​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 Giese MA.<br /> 
 +<​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>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​lwta.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​lwta.pdf">​Learning winner-take-all competition between groups of neurons in lateral inhibitory networks </​a><​br /> 
 +Xie X, Hahnloser HR, and Seung HS.<br /> 
 +<​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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