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publications [2017/10/12 22:11]
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>
  
-[[https://​arxiv.org/​abs/​1612.05968|Deep Multi-instance Networks with Sparse Label Assignment for Whole Mammogram Classification]]\\ +<​p>​Sequential Embedding Induced Nonparametric Text Clustering<​br ​/> 
-Wentao ZhuQi Lou, Yeeleng Scott Vang, Xiaohui ​Xie \\ +Duan T, Lou Q, Xie X</p>
-arXiv:​1612.05968\\ +
-[[http://​www.miccai2017.org/​| MICCAI, 2017]]+
  
-Understanding sequence conservation with deep learning\\ +<​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 /> 
-Li YQuang Dand Xie X\\ +Vang SChen Z, Xie X<br /> 
-ACM BCB2017+15th International Conference on Image Analysis and Recognition2018</​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/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 /> 
-Vang YS and Xie X\\ +IEEE Winter Conf. on Applications of Computer Vision 2018</​p>​
-Bioinformatics,​ 2017+
  
-[[https://www.ncbi.nlm.nih.gov/pubmed/28325473|Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program]]\\ +<​p><​a class="​urlextern"​ href="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 ​/> 
-Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW\\ +IEEE Winter Confon Applications of Computer Vision 2018</​p>​
-Dev Cell27;​40(6):​595-607.e4,​ 2017+
  
-==== 2016 ====+<​p>​Adversarial Deep Structured Nets for Mass Segmentation from Mammograms<​br /> 
 +W Zhu, X Xiang, T Tran, GD Hager, X Xie<br /> 
 +IEEE International Symposium on Biomedical Imaging</​p>​
  
-[[https://​arxiv.org/​abs/​1612.05970|Adversarial ​Deep Structural ​Networks ​for Mammographic Mass Segmentation]]\\ +<​p>​Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural ​Networks<br /> 
-Wentao ZhuXiaohui ​Xie\\ +H TangD Kim, X Xie<br /> 
-arXiv:​1612.05970+IEEE International Symposium on Biomedical Imaging</​p>​
  
-[[https://​www.ncbi.nlm.nih.gov/pubmed/​27418388|Developmentally regulated long non-coding RNAs in Xenopus tropicalis]]\\ +<​p>​Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.<​br ​/> 
-Forouzmand ​et al\\ +Zhu Y, Wang X, Forouzmand ​E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.<br /> 
-Developmental Biology, ​(16)30120-8 2016+Mol Cell. 2018 Jan 4;69(1):62-74.e4.</​p>​ 
 +</​div>​
  
-[[http://​bioinformatics.oxfordjournals.org/​content/​early/​2016/​02/​11/​bioinformatics.btw074.short?​rss=1|Gene expression inference with deep learning]]\\ +<​h3>​2017<​/h3>
-Chen Y, Li Y, Narayan R, Subramanian A, and Xie X\\ +
-Bioinformatics,​ 2016+
  
-DanQ: hybrid convolutional and recurrent deep neural network ​for quantifying the function of DNA sequences\\ +<div class="​level3">​ 
-Quang D and Xie X\\ +<​p><​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 /> 
-Nucleic Acids Research2016+W ZhuC Liu, W Fan, X Xie<br /> 
 +arXiv preprint arXiv:​1709.05538</​p>​
  
-[[http://rnajournal.cshlp.org/​content/​early/​2016/04/19/rna.055681.115.abstract|Poly(A) code analyses reveal key determinants ​for tissue-specific ​mRNA alternative polyadenylation]]\\ +<​p><​a class="​urlextern"​ href="​https://www.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 /> 
-Weng LLi Y, Xie X, and Shi Y\\ +D Quang, X Xie<br /> 
-RNA2016+bioRxiv151274</​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><​a class="​urlextern"​ href="https://arxiv.org/abs/1612.05968"​ rel="​nofollow"​ title="​https:​//arxiv.org/abs/1612.05968">​Deep Multi-instance ​Networks ​with Sparse Label Assignment for Whole Mammogram Classification</​a><​br /> 
-Zhu Wet al.\\ +Wentao ​Zhu, Qi Lou, Yeeleng Scott Vang, Xiaohui Xie<br /> 
-AAAI Conference on Artificial Intelligence2016+arXiv:1612.05968<br /> 
 +<a class="​urlextern"​ href="​http://​www.miccai2017.org/"​ rel="​nofollow"​ title="​http://​www.miccai2017.org/">​MICCAI2017</​a></​p>​
  
-==== 2015 ====+<​p>​Understanding sequence conservation with deep learning<​br /> 
 +Li Y, Quang D, and Xie X<br /> 
 +ACM BCB, 2017</​p>​
  
-Hobbes3Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings\\ +<​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 /> 
-Kim J, Chen L, and Xie X\\ +Vang YS and Xie X<br /> 
-32nd IEEE International Conference on Data Engineering - ICDE 2016+Bioinformatics,​ 2017</​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://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 /> 
-Quang D and Xie X+Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW<br /> 
 +Dev Cell. 27;​40(6):​595-607.e4,​ 2017</​p>​ 
 +</​div>​
  
-[[http://​www.ncbi.nlm.nih.gov/​pubmed/​25338716|DANN:​ a deep learning approach for annotating the pathogenicity of genetic variants]]\\ +<​h3>​2016<​/h3>
-Quang D, Chen Y and Xie X\\ +
-Bioinformatics,​ 31(5):​761-3,​ 2015+
  
-[[http://www.biomedcentral.com/1471-2164/16/S2/S1|MixClone:​ a mixture model for inferring tumor subclonal populations]]\\ +<div class="​level3">​ 
-Li Y 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 /> 
-BMC Genomics, 2015+Wentao Zhu, Xiaohui ​Xie<br /> 
 +arXiv:​1612.05970</​p>​
  
 +<​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 />
 +Forouzmand et al.<br />
 +Developmental Biology, (16)30120-8 2016</​p>​
  
-[[http://www.ics.uci.edu/~xhx/publications/ImagingGenetics.pdf |Identifying unanticipated genes and mechanisms in serious mental illness]]\\ +<​p><​a class="​urlextern"​ href="http://bioinformatics.oxfordjournals.org/​content/​early/​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 /> 
-Potkin SGvan Erp TGMLing SMacciardi F, and Xie X\\ +Chen YLi YNarayan RSubramanian A, and Xie X<br /> 
-Neuroimaging genetics : principles and practices2015+Bioinformatics2016</​p>​
  
-==== 2014 ====+<​p>​DanQ:​ a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences<​br /> 
 +Quang D and Xie X<br /> 
 +Nucleic Acids Research, 2016</​p>​
  
-[[http://link.springer.com/article/10.1007/s10032-014-0229-4|Handwritten Hangul recognition using deep convolutional neural networks]]\\ +<​p><​a class="​urlextern"​ href="http://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 /> 
-Kim I and Xie X\\ +Weng L, Li Y, Xie X, and Shi Y<br /> 
-International Journal on Document Analysis and Recognition,​ 2014\\ +RNA, 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="​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 /> 
-Chiu WTLe R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K\\ +Zhu Wet al.<br /> 
-Development2014+AAAI Conference on Artificial Intelligence2016</​p>​ 
 +</​div>​
  
-[[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]]\\ +<​h3>​2015<​/h3>
-Li Y and Xie X\\ +
-Bioinformatics,​ 2014+
  
-[[http://​bioinformatics.oxfordjournals.org/​content/​early/​2014/​02/​14/​bioinformatics.btu093.abstract|EXTREME:​ An Online EM Algorithm for Motif Discovery]]\\ +<div class="​level3">​ 
-Quang D and Xie X\\ +<​p>​Hobbes3Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings<​br ​/> 
-Bioinformatics,​ 2014+Kim J, Chen L, and Xie X<br /> 
 +32nd IEEE International Conference on Data Engineering - ICDE 2016</​p>​
  
-[[http://www.biomedcentral.com/1471-2105/15/42|Improving Read Mapping Using Additional Prefix Grams]]\\ +<​p><​a class="​urlextern"​ href="http://biorxiv.org/​content/​early/​2015/​12/​20/​032821"​ rel="​nofollow"​ title="​http://​biorxiv.org/content/early/2015/​12/​20/​032821">​DanQ:​ a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences</​a><​br /> 
-Kim J, Li C and Xie X\\ +Quang D and Xie X</p>
-BMC Bioinformatics,​ 2014, 15(1):42+
  
-[[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.ncbi.nlm.nih.gov/pubmed/25338716"​ rel="​nofollow"​ title="​http://www.ncbi.nlm.nih.gov/pubmed/​25338716">​DANN: ​deep learning approach for annotating the pathogenicity of genetic variants</​a><​br /> 
-Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X\\ +Quang DChen Y and Xie X<br /> 
-PLOS ONE, 2014DOI10.1371/journal.pone.0092317+Bioinformatics31(5):761-3, 2015</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.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 /> 
-Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q\\ +Li Y and Xie X<br /> 
-BMC Systems Biology 20148:3+BMC Genomics2015</​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.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 /> 
-Lackford BYao CCharles GMWeng L, Zheng X, Choi EA, Xie X, Wan J, Xing Y, Freudenberg JM, Yang P, Jothi R, Hu G, Shi Y\\ +Potkin SGvan Erp TGMLing SMacciardi Fand Xie X<br /> 
-EMBO J. 2014 Mar 4. +Neuroimaging genetics : principles and practices2015</​p>​ 
-==== 2013 ====+</​div>​
  
-[[http://​www.plosone.org/​article/​info:​doi/​10.1371/​journal.pone.0082146|Low-Rank Regularization for Learning Gene Expression Programs]] \\ +<​h3>​2014<​/h3>
-Ye G, Tang M, Nie Q and Xie X\\ +
-//PLOS ONE//, 2013+
  
-[[http://www.hindawi.com/journals/cmmm/2013/873595/|A gradient boosting algorithm for survival analysis via direct optimization of concordance index]] \\ +<div class="​level3">​ 
-Chen Y, Jia Z, Mercola D 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 /> 
-//Comput Math Methods Med.//, 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://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.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 /> 
-Blitz I, Biesinger J, Xie X, and Cho K\\ +Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K<​br ​/
-//Genesis//, 2013.+Development2014</​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://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 /> 
-Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y\\ +Li Y and Xie X<​br ​/
-//RNA//, 2013+Bioinformatics2014</​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://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 /> 
-Chen Y and Xie X \\ +Quang D and Xie X<​br ​/
-//arXiv//, 2013+Bioinformatics2014</​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://​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 /> 
-Biesinger ​J, Wang Y, and Xie X \\ +Kim J, Li C and Xie X<br /> 
-//BMC Bioinformatics// 201314(S5):S4, 2013 \\ +BMC Bioinformatics, ​2014, 15(1):42</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://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 /> 
-Li Y and Xie X \\ +Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X<​br ​/
-//BMC Bioinformatics// 201314(Suppl 5):S112013+PLOS ONE2014DOI: 10.1371/​journal.pone.0092317</​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/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 /> 
-Yang XWang BLi CWang Jand Xie X \\ +Zheng ZChristley SChiu WTBlitz IL, Xie X, Cho KW, Nie Q<​br ​/> 
-//IEEE International Conference on Data Engineering (ICDE)//, 2013 +BMC Systems Biology 2014, 8:​3</​p>​
-==== 2012 ====+
  
-[[http://www.springerlink.com/content/4l2m27p3867xj584/|Learning sparse gradients for variable selection and dimension reduction]] \\ +<​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 G and Xie X \\ +Lackford B, Yao C, Charles GM, Weng L, Zheng X, Choi EA, Xie X, Wan J, Xing Y, Freudenberg JM, Yang P, Jothi R, Hu G, Shi Y<​br ​/
-Machine Learning Journal, 87(3):​303-355,​ 2012 \\ +EMBO J2014 Mar 4.</​p>​ 
-[[http://www.ics.uci.edu/~xhx/publications/SGL.pdf|Preprint]]+</​div>​
  
-[[http://​www.ncbi.nlm.nih.gov/​pubmed/​23112178|Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation]] \\ +<​h3>​2013<​/h3>
-Yao C, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y \\ +
-PNAS, 109(46):​18773-8,​ 2012+
  
-[[http://www.ncbi.nlm.nih.gov/pubmed/22296850|Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests ​role in regulating genes of lipid metabolism in concert with FXR]] \\ +<div class="​level3">​ 
-Kim Chong HBiesinger J, Seo YK, Xie X, Osborne TF \\ +<​p><​a class="​urlextern"​ href="http://www.plosone.org/​article/​info:​doi/​10.1371/​journal.pone.0082146"​ rel="​nofollow"​ title="​http:​//www.plosone.org/​article/​info:​doi/​10.1371/​journal.pone.0082146">​Low-Rank Regularization for Learning Gene Expression Programs</​a><br /> 
-BMC Genomics2012+Ye GTang MNie Q and Xie X<br /> 
 +<​em>​PLOS ONE</​em>​2013</​p>​
  
-[[http://www.ncbi.nlm.nih.gov/pubmed/22199254|Hobbes:​ optimized gram-based methods ​for efficient read alignment]] \\ +<​p><​a class="​urlextern"​ href="http://www.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 /> 
-Ahmadi ABehm A, Honnalli N, Li C, Weng L, and Xie X  \\ +Chen YJia ZMercola D and Xie X<​br ​/
-Nucleic Acids Research, 40(6):​e41, ​ 2012 \\ +<​em>​Comput Math Methods Med.</​em>,​ 2013</p>
-Software: [[http://hobbes.ics.uci.edu/|Hobbes]]+
  
-==== 2011 ====+<​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 /> 
 +Blitz I, Biesinger J, Xie X, and Cho K<br /> 
 +<​em>​Genesis</​em>,​ 2013.</​p>​
  
-[[http://arxiv.org/pdf/1110.3076v1|Efficient latent variable graphical model selection via split Bregman method]] \\ +<​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 /> 
-Ye GWang YChen Yand Xie X \\ +Yao CChoi EWeng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y<br /> 
-arXiv:​1110.3076v12011+<​em>​RNA</​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://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 /> 
-Daily K, Patel VR, Rigor P, Xie X, Baldi P. \\ +Chen Y and Xie X<br /> 
-BMC Bioinformatics2011+<​em>​arXiv</​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://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 /> 
-Lindblad-TohBarberZukLinet al. \\ +Biesinger JWang Yand Xie X<br /> 
-Nature, 2011+<​em>​BMC Bioinformatics</​em>​ 201314(S5):S42013<br /> 
 +<a class="​urlextern"​ href="​http://​www.biomedcentral.com/​content/​supplementary/​1471-2105-14-s5-s4-s1.pdf"​ rel="​nofollow"​ title="​http://​www.biomedcentral.com/​content/​supplementary/​1471-2105-14-s5-s4-s1.pdf">​Supplemental Information</​a></​p>​
  
-[[http://​www.biomedcentral.com/​1471-2105/​12/99|SNP-based pathway enrichment analysis ​for genome-wide association studies]] \\ +<​p><​a class="​urlextern"​ href="http://​www.biomedcentral.com/​1471-2105/​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 /> 
-Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X \\ +Li Y and Xie X<br /> 
-BMC Bioinformatics, 2011  \\ +<em>BMC Bioinformatics</em> 2013, 14(Suppl 5):S11, 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://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 /> 
-Seo YJeon T Chong HBeisinger ​J, Xie X, and Osborne TF \\ +Yang XWang BLi CWang J, and Xie X<br /> 
-//Cell Metabolism//,​ 13:367-75, 2011  \\ +<​em>​IEEE International Conference on Data Engineering (ICDE)</em>, 2013</p> 
-[[http://​www.sciencedaily.com/​releases/​2011/​04/​110405122330.htm|Science Daily coverage]]+</div>
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​arem_recomb.pdf|AREM:​ aligning short reads from ChIP-sequencing by expectation maximization]] \\ +<​h3>​2012<​/h3>
-Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X \\ +
-//J Comput Biol.//, 2011 \\ +
-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 ]] \\ +<div class="​level3">​ 
-Ye G, Chen Y, and Xie X \\ +<​p><​a class="​urlextern"​ href="http://www.springerlink.com/content/4l2m27p3867xj584/" rel="​nofollow"​ title="​http:​//www.springerlink.com/​content/​4l2m27p3867xj584/">​Learning sparse gradients for variable selection ​and dimension reduction</​a><​br /> 
-AI & STATS 2011+Ye G and Xie X<br /> 
 +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>​
  
-==== 2010 ====+<​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://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.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 GCai J, and Xie X \\ +Kim Chong HBiesinger ​J, Seo YK, Xie X, Osborne TF<br /> 
-arXiv:​1012.0975v12010+BMC Genomics2012</​p>​
  
-[[http://www.sciencedirect.com/science?_ob=ArticleURL&​_udi=B6V8V-51BBKR7-1&​_user=10&​_coverDate=10/27/2010&​_rdoc=1&​_fmt=high&​_orig=search&​_origin=search&​_sort=d&​_docanchor=&​view=c&​_acct=C000050221&​_version=1&​_urlVersion=0&​_userid=10&​md5=6ff4ea0404367278249b06c9a59f84fd&​searchtype=a|Split Bregman method for large scale fused Lasso]] \\ +<​p><​a class="​urlextern"​ href="http://www.ncbi.nlm.nih.gov/pubmed/​22199254"​ rel="​nofollow"​ title="​http://​www.ncbi.nlm.nih.gov/​pubmed/​22199254">​Hobbes:​ optimized gram-based methods for efficient read alignment<​/a><​br ​/> 
-Ye G-B and Xie X \\ +Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X<br /> 
-Computational Statistics and Data Analysisdoi:10.1016/j.csda.2010.10.021,​ 2010  \\ +Nucleic Acids Research40(6):e41, 2012<​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]] \\ +Software: <a class="​urlextern"​ href="http://hobbes.ics.uci.edu/"​ rel="​nofollow"​ title="​http://hobbes.ics.uci.edu/">​Hobbes<​/a></p> 
-Daily K, Rigor P, Christley S, Xie X and Baldi P  \\ +</div>
-//BMC Bioinformatics//,​11:​514,​ 2010+
  
-[[http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​btq414|Interactive and fuzzy search: a dynamic way to explore MEDLINE ]] \\ +<​h3>​2011<​/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://​arxiv.org/​pdf/1110.3076v1"​ rel="​nofollow"​ title="​http://​arxiv.org/​pdf/​1110.3076v1">​Efficient latent variable graphical model selection via split Bregman method</​a><​br /> 
-arXiv:1006.5060v22010+Ye G, Wang Y, Chen Y, and Xie X<br /> 
 +arXiv:1110.3076v12011</​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/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 /> 
-Potkin SGMacciardi FGuffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X \\ +Daily KPatel VRRigor P, Xie X, Baldi P.<br /> 
-//​NeuroImage//​ 53:839-847, 2010+BMC Bioinformatics,​ 2011</p>
  
-[[http://www.biomedcentral.com/1752-0509/4/99|Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent]] \\ +<​p><​a class="​urlextern"​ href="http://www.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 /> 
-Wang Y, Christley S, Mjolsness E, and Xie X \\ +Lindblad-TohBarber, Zuk, Lin, et al.<br /> 
-//BMC Systems Biology//, 4:99 doi:10.1186/1752-0509-4-992010+Nature, 2011</​p>​
  
-[[http://www.springerlink.com/content/428v02087m218878/fulltext.pdf|Site-frequency Spectrum of Linked Sites]] \\ +<​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 /> 
-Xie X   \\ +Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X<br /> 
-//Bulletin of Mathematical Biology//, DOI10.1007/s11538-010-9534-3,​ 2010+BMC Bioinformatics,​ 2011<​br ​/
 +Software: <a class="​urlextern"​ href="​http:​//cbcl.ics.uci.edu/SSEA/" rel="​nofollow"​ title="​http://cbcl.ics.uci.edu/SSEA/">​SNP Set Enrichment Analysis (SSEA)</​a></​p>​
  
-[[http://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.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 /> 
-Chong H, Infante A, Seo Y, Jeon T, Ahang YEdwards P, Xie X, and Osborne TF \\ +Seo Y, Jeon T , Chong HBeisinger J, Xie X, and Osborne TF<br /> 
-Nucleic Acids Researchdoi:10.1093/​nar/​gkq3972010 \\ +<​em>​Cell Metabolism</​em>​13:367-752011<br /> 
-[[http://cbcl.ics.uci.edu/public_data/FXR/|Online Supplementary Materials]]+<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.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.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 /> 
-Kumar LBreakspear AKistler HC, Ma L-J, and Xie X  \\ +Newkirk DBiesinger, J, Chon A, Yokomori K, and Xie X<br /> 
-//BMC Genomics// 11:208, 2010 \\ +<em>J Comput Biol.</em>, 2011<​br ​/> 
-[[http://www.broadinstitute.org/annotation/genome/​fusarium_group/​SupplementalMaterials.html|Supplementary Information]] \\ +Software: <a class="​urlextern"​ href="http://sourceforge.net/projects/arem" rel="​nofollow"​ title="​http://sourceforge.net/projects/arem">​AREM<​/a></p>
-[[http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html|Fusarium Comparative Database]]+
  
-[[http://www.nature.com/nature/journal/v464/n7287/abs/​nature08850.html|Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium oxysporum]] \\ +<​p><​a class="​urlextern"​ href="http://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 ​/
-Ma L-J, et al.  \\ +Ye G, Chen Y, and Xie X<​br ​/
-//Nature// 464:​367-373,​ 2010 \\ +AI &amp; STATS , 2011</​p>​ 
-[[http://www.broadinstitute.org/news/1439|The chromosomal secrets of a plant pathogen]] \\ +</div>
-[[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 ====+<​h3>​2010</​h3>​
  
-[[http://www.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf|Incorporating existing network information into gene network inference]] \\ +<div class="​level3">​ 
-Christley SNie Q 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 /> 
-//PLoS ONE// 4(8): e6799. doi:10.1371/journal.pone.0006799 (2009)+Ye G, Cai J, and Xie X<​br ​/
 +arXiv:1012.0975v1, 2010</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 new motif]] \\ +<​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 /> 
-Seo YK, Chong HK, Infante AM, Im S, Xie Xand Osborne TF \\ +Ye G-B and Xie X<br /> 
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0904246106 (2009)+Computational Statistics ​and Data Analysis, doi:​10.1016/​j.csda.2010.10.021,​ 2010<br /> 
 +<a class="​urlextern"​ href="​http:​//arxiv.org/abs/1006.5086"​ rel="​nofollow"​ title="​http://arxiv.org/abs/1006.5086">​arXiv version</​a>​ <a class="​urlextern"​ href="​http://​www.biomedcentral.com/​1471-2105/​11/​514"​ rel="​nofollow"​ title="​http://​www.biomedcentral.com/​1471-2105/​11/​514">​Data Structures and Compression Algorithms for High-Throughput Sequencing Technologies</​a><​br /> 
 +Daily K, Rigor P, Christley S, Xie X and Baldi P<br /> 
 +<​em>​BMC Bioinformatics</​em>,​11:​514,​ 2010</​p>​
  
-[[http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/12/i54|Identifying novel constrained elements by exploiting biased substitution patterns]] \\ +<​p><​a class="​urlextern"​ href="http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​btq414"​ rel="​nofollow"​ title="​http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​btq414">​Interactive and fuzzy search: a dynamic way to explore MEDLINE </a><​br ​/> 
-Garber MGuttman1 MClamp MZody MGFriedman N, and Xie X \\ +Wang JCetindil IJi SLi CXie XLi G and Feng J<​br ​/
-//​Bioinformatics/​/​25:​i54-i62 ​(2009 \\ +<em>Bioinformatics</em>, 26(18):2321-2327, 2010<br /> 
-[[http://www.ics.uci.edu/​~xhx/​publications/​siphy_suppinfo.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://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]] \\ +<​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 /> 
-Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA  \\ +Ye G-B and Xie X<br /> 
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0813264106 (2009)+arXiv:1006.5060v2, 2010</p>
  
-[[http://genome.cshlp.org/content/19/4/567.long|Common polymorphic transcript variation in human disease]] \\ +<​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 ​/
-Fraser H and Xie X  \\ +Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X<br /> 
-//Genome Research// doi:10.1101/gr.083477.108 (2009) \\ +<​em>​NeuroImage</​em>​ 53:839-847, 2010</​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://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 /> 
-Xie X, Rigor P, and Baldi P  \\ +Wang Y, Christley S, Mjolsness E, and Xie X<​br ​/
-//Bioinformatics//​ 25: 167-174 (2009) \\ +<​em>​BMC Systems Biology</em>, 4:99 doi:10.1186/​1752-0509-4-99,​ 2010</p>
-[[http://www.ics.uci.edu/~xhx/publications/MotifMap_Supp_Info.pdf|Supplementary Methods]] \\ +
-[[http://motifmap.ics.uci.edu/|MotifMap Server]]+
  
-[[http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​2/​274|Human genomes as email attachments ]] \\ +<​p><​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 ​/
-Christley S, Lu Y, Li C, and Xie X  \\ +Xie X<​br ​/
-//​Bioinformatics // 25: 274-275 (2009) \\ +<​em>​Bulletin of Mathematical Biology</em>, DOI10.1007/s11538-010-9534-3, 2010</​p>​
-[[http://​www.ics.uci.edu/​~xhx/​project/​DNAzip|DNAzip:​ DNA sequence compression using 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://​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/wu_motif_2008.pdf|Discovering ​regulatory motifs in the Plasmodium genome using comparative genomics ]] \\ +<​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 /> 
-Wu JSieglaff DHGervin ​J, and Xie X  \\ +Kumar LBreakspear AKistler HC, Ma L-J, and Xie X<​br ​/
-//Bioinformatics ​// 24:1843-9 (2008) \\ +<​em>​BMC Genomics<​/em> 11:208, 2010<​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.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html"​ rel="​nofollow"​ title="​http://www.broadinstitute.org/​annotation/​genome/​fusarium_group/​SupplementalMaterials.html">​Supplementary Information</​a><​br /> 
-[[http://www.ics.uci.edu/~xhx/publications/wu_motif_2008_suppinfo.pdf|Supplementary Information on the MDOS algorithm]]+<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.pubmedcentral.nih.gov/picrender.fcgi?artid=2567431&​blobtype=pdf|Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains ]] \\ +<​p><​a class="​urlextern"​ href="http://www.nature.com/nature/​journal/​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 /> 
-Ku MKoche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser ANusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE  \\ +Ma L-Jet al.<br /> 
-//PLoS Genetics//4(10):e1000242 (2008) +<​em>​Nature</​em>​ 464:367-3732010<br /> 
-==== 2007 ====+<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.pnas.org/​content/​104/​49/​19428|Distinguishing protein-coding and noncoding genes in the human genome ]] \\ +<​h3>​2009<​/h3>
-Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, and Lander ES. \\ +
-//Proc Natl Acad Sci USA//​104(49):​19428-33 (2007)+
  
-[[http://www.nature.com/nature/journal/v449/n7164/abs/nature06250.html|Genome-wide detection and characterization of positive selection in human populations ]] \\ +<div class="​level3">​ 
-Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne 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/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//​449:913-918 ​(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.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.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 /> 
-Mikkelsen TSKu MJaffe DBIssac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'​Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. \\ +Seo YKChong HKInfante AMIm S, Xie X, and Osborne TF<br /> 
-//Nature// 448:553-60 ​(2007)+<​em>​Proc Natl Acad Sci USA</em> doi:10.1073/​pnas.0904246106 ​(2009)</p>
  
-[[http://www.ics.uci.edu/~xhx/publications/insulators_pnas06.pdf|Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites ]] \\ +<​p><​a class="​urlextern"​ href="http://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 XMikkelsen TSGnirke ALindblad-Toh KKellis M and Lander ES. \\ +Garber MGuttman1 MClamp MZody MG, Friedman N, and Xie X<​br ​/
-//Proc Natl Acad Sci USA//104:7145-7150 (2007 \\ +<​em>​Bioinformatics<​/em>25:i54-i62 (2009)<br /> 
-[[http://www.broad.mit.edu/personal/xhx/projects/​CNEMOTIF/|Supplementary website]] [[http://www.pnas.org/cgi/content/full/0701811104/DC1|Supporting Information]] [[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?​id=3042|News story]]+<a class="​urlextern"​ href="http://www.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.nature.com/nature/journal/v447/n7141/pdf/nature05805.pdf|Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences ]] \\ +<​p><​a class="​urlextern"​ href="http://www.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 /> 
-Mikkelsen TSWakefield MJet al.  \\ +Sieglaff DHDunn WAXie X, Megy K, Marinotti O, and James AA<br /> 
-//Nature// 447:167-177 ​(2007)+<​em>​Proc Natl Acad Sci USA</em> doi:10.1073/​pnas.0813264106 ​(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://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 /> 
-Xie X, Kamal M, and Lander ES. \\ +Fraser H and Xie X<​br ​/
-//Proc Natl Acad Sci USA//103:11659-11664 ​(2006 \\ +<​em>​Genome Research<​/em> doi:10.1101/​gr.083477.108 ​(2009)<br /> 
-[[http://www.broad.mit.edu/seq/pubs/xie_pnas2006/​|Supplementary website]] [[http://​www.pnas.org/​cgi/​content/​full/​0604768103/​DC1|Supporting Information]] [[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?​id=1881|News story]]+<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>​
  
-==== 2006 or before ​====+<​p><​a class="​urlextern"​ href="​http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​2/​167"​ rel="​nofollow"​ title="​http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​2/​167">​MotifMap:​ a human genome-wide map of candidate regulatory motif sites </​a><​br /> 
 +Xie X, Rigor P, and Baldi P<br /> 
 +<​em>​Bioinformatics</​em>​ 25: 167-174 (2009)<​br /> 
 +<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.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://​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 /> 
-Kamal M, Xie X, and Lander ES \\ +Christley S, Lu Y, Li C, and Xie X<br /> 
-//Proc Natl Acad Sci USA//103:2740-2745 (2006) ​ \\ +<​em>​Bioinformatics </em> 25: 274-275 (2009)<​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.ics.uci.edu/​~xhx/​project/DNAzip"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​project/​DNAzip">​DNAzip:​ DNA sequence compression using a reference ​genome</​a><​br /> 
-[[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?​id=381|News story]]+<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://​download.cell.com/​pdfs/​0092-8674/​PIIS0092867406003801.pdf|A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells]] \\ +<​h3>​2008<​/h3>
-Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al.  \\ +
-//Cell// 125:315-26 (2006)+
  
-[[http://genomebiology.com/2006/7/9/R85|Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression ]] \\ +<div class="​level3">​ 
-Wu J and Xie X \\ +<​p><​a class="​urlextern"​ href="http://www.ics.uci.edu/~xhx/publications/wu_motif_2008.pdf"​ rel="​nofollow"​ title="​http:​//​www.ics.uci.edu/​~xhx/​publications/​wu_motif_2008.pdf">​Discovering regulatory motifs ​in the Plasmodium genome using comparative genomics </​a><​br /> 
-//Genome Biology//7(9):R85 (2006(Highly accessed) ​ \\ +Wu J, Sieglaff DH, Gervin J, and Xie X<br /> 
-[[http://www.broad.mit.edu/personal/xhx/projects/NRSE|Supplementary ​website]]+<​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/ng/journal/v38/n5/pdf/ng1776.pdf|Systematic identification ​of human mitochondrial disease genes through integrative genomics ]] \\ +<​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 /> 
-Calvo SJain M, Xie X, Chang BSpinazzola A, Zeviani ​M, Carr S, and Mootha VK. \\ +Ku M, Koche RP, Rheinbay E, Mendenhall EMEndoh 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 /> 
-//​Nature ​Genetics//, 38:576-82 ​(2006)+<​em>​PLoS </em><​em>​Genetics</em>4(10):e1000242 ​(2008)</​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>​2007<​/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 MDaly M, Rioux JXavier R \\ +<​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 /> 
-//Genome Resesarch//,​ 16:1056-72 (2006)+Clamp MFry BKamal M, Xie X, Cuff JLin MF, Kellis ​M, Lindblad-Toh Kand Lander ES.<br /> 
 +<​em>​Proc Natl Acad Sci </em><​em>​USA<​/em>​104(49):19428-33 (2007)</p>
  
-[[http://download.cell.com/pdfs/0092-8674/PIIS0092867406003692.pdf|A Mammalian Organelle Map by Protein Correlation Profiling]] \\ +<​p><​a class="​urlextern"​ href="http://www.nature.com/nature/journal/​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 /> 
-Foster LJde Hoog CLZhang YZhang Y, Xie X, Mootha VK, and Mann M.  \\ +Sabeti PCVarilly PFry BLohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EHMcCarroll SA, Gaudet R, Schaffner SF, Lander ES and International HapMap Consortium<​br /> 
-//Cell// 125:187-99 (2006)+<​em>​Nature<​/em>449:913-918 (2007)</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/​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 /> 
-Werfel J, Xie X and Seung HS \\ +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 /> 
-//Neural Computation//,​ 2005;17:2699-718+<​em>​Nature<​/em> 448:553-60 (2007)</​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/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 /> 
-Lindblad-Toh K, Wade CM, et al \\ +Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES.<br /> 
-//Nature// 438:803-19 2005+<​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/annurev.genom.6.080604.pdf|Disease gene discovery through integrative genomics]] \\ +<​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 /> 
-Giallourakis CHenson CReich M, Xie X, and Mootha VK \\ +Mikkelsen TSWakefield MJet al.<​br ​/
-//Annu. Rev. Genomics Hum. Genet.// 2005:22:381-406.+<​em>​Nature<​/em> 447:167-177 (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.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 Seung HS \\ +Xie X, Kamal M, and Lander ES.<br /> 
-//Phys Rev E//, 2004;69:041909+<​em>​Proc Natl Acad Sci </em><​em>​USA<​/em>​103:​11659-11664 (2006)<​br ​/
 +<a class="​urlextern"​ href="​http:​//​www.broad.mit.edu/​seq/​pubs/​xie_pnas2006/"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​seq/​pubs/​xie_pnas2006/">​Supplementary website</​a>​ <a class="​urlextern"​ href="​http://​www.pnas.org/​cgi/​content/​full/​0604768103/​DC1"​ rel="​nofollow"​ title="​http://​www.pnas.org/​cgi/​content/​full/​0604768103/​DC1">​Supporting Information</​a>​ <a class="​urlextern"​ href="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=1881"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=1881">​News story</​a></​p>​ 
 +</​div>​
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​mootha_pgc1a.pdf|Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle]] \\ +<​h3>​2006 or before</h3>
-Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al.  \\ +
-//Proc Natl Acad Sci USA//, 2004;​101:​6570-5+
  
-[[http://​www.ics.uci.edu/​~xhx/​publications/​PhysRevE_66_041902.pdf|The double-ring network modeling ​of the head-direction system]] \\ +<div class="​level3">​ 
-Xie X, Hahnloser RH, and Seung HS \\ +<​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 /> 
-//Physical Review E//, 2002;66:041902+Kamal M, Xie X, and Lander ES.<br /> 
 +<​em>​Proc Natl Acad Sci </em><​em>​USA<​/em>​103:​2740-2745 (2006)<​br ​/
 +<a class="​urlextern"​ href="​http:​//​www.broad.mit.edu/​seq/​pubs/​xie_pnas2006/​html/​clusteredAMCNE/​AMCNE1.similarAMCNE.html"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​seq/​pubs/​xie_pnas2006/​html/​clusteredAMCNE/​AMCNE1.similarAMCNE.html">​Supplementary website</​a>​ <a class="​urlextern"​ href="​http://​www.pnas.org/​cgi/​content/​full/​0511238103/​DC1"​ rel="​nofollow"​ title="​http://​www.pnas.org/​cgi/​content/​full/​0511238103/​DC1">​Supporting Information</​a><​br /> 
 +<a class="​urlextern"​ href="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=381"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=381">​News story</​a></​p>​
  
-[[http://www.ics.uci.edu/~xhx/publications/PhysRevE_65_051904.pdf|Nonlinear dynamics of direction-selective recurrent neural media]] \\ +<​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 and Giese MA.  \\ +Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al.<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>​Cell<​/em> 125:315-26 (2006)</​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://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, Hahnloser HR, and Seung HS.  \\ +Wu J and Xie X<br /> 
-//Advances in Neural Information Processing Systems//2001;13:350-356+<​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/nc_vel_tuning.pdf|Generating velocity tuning by asymmetric recurrent connections]] \\ +<​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 and Giese MA \\ +Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK.<br /> 
-//Advances in Neural Information Processing Systems//​2002;​13:325-332+<​em>​Nature Genetics<​/em>, 38:576-82 (2006)</​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/​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, Hahnloser RHand Seung HS \\ +Xie X, Lu JKulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M.<br /> 
-//Neural Computation//, 2002;14:2627-2646+<​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/chl_nc.pdf|Equivalence of backpropagation ​and contrastive Hebbian learning in layered network]] \\ +<​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 /> 
-Xie X and Seung HS \\ +Giallourakis C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R.<br /> 
-//Neural Computation//​2003;16:441-454+<​em>​Genome Resesarch<​/em>, 16:1056-72 (2006)</​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://​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 \\ +Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M.<br /> 
-//Network: Comput. Neural Syst./2002;​13:​447-456+<​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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