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+<html>
+<h2>Publications</h2>
+<div class="level2">&nbsp;</div>
-__false__
+<h3>2018</h3>
-==== 2016 ====
+<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<br />
+MICCAI, 2018</p>
-[[https://arxiv.org/abs/1612.05970|Adversarial Deep Structural Networks for Mammographic Mass Segmentation]]\\
-Wentao Zhu, Xiaohui Xie\\
-arXiv:1612.05970
-[[https://www.ncbi.nlm.nih.gov/pubmed/27418388|Developmentally regulated long non-coding RNAs in Xenopus tropicalis]]\\
+<p>Sequential Embedding Induced Nonparametric Text Clustering<br />
-Forouzmand et al. \\
+Duan T, Lou Q, Xie X</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><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 />
-Chen Y, Li Y, Narayan R, Subramanian A, and Xie X\\
+Vang S, Chen Z, Xie X<br />
-Bioinformatics, 2016
+th International Conference on Image Analysis and Recognition, 2018</p>
-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/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 />
-Quang D and Xie X\\
+IEEE Winter Conf. on Applications of Computer Vision 2018</p>
-Nucleic Acids Research, 2016
-[[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://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 />
-Weng L, Li Y, Xie X, and Shi Y\\
+IEEE Winter Conf. on Applications of Computer Vision 2018</p>
-RNA, 2016
-[[https://www.researchgate.net/profile/Wentao_Zhu4/publication/283748673_Co-occurrence_Feature_Learning_for_Skeleton_based_Action_Recognition_using_Regularized_Deep_LSTM_Networks/links/567a2bc808ae7fea2e98bf6b.pdf|Co-occurrence Feature Learning for Skeleton based Action Recognition using Regularized Deep LSTM Networks]]\\
+<p>Adversarial Deep Structured Nets for Mass Segmentation from Mammograms<br />
-Zhu W, et al.\\
+W Zhu, X Xiang, T Tran, GD Hager, X Xie<br />
-AAAI Conference on Artificial Intelligence, 2016
+IEEE International Symposium on Biomedical Imaging</p>
-==== 2015 ====
+<p>Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural Networks<br />
+H Tang, D Kim, X Xie<br />
+IEEE International Symposium on Biomedical Imaging</p>
-Hobbes3: Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings\\
+<p>Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.<br />
-Kim J, Chen L, and Xie X\\
+Zhu Y, Wang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.<br />
-nd IEEE International Conference on Data Engineering - ICDE 2016
+Mol Cell. 2018 Jan 4;69(1):62-74.e4.</p>
+</div>
-[[http://biorxiv.org/content/early/2015/12/20/032821|DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences]]\\
+<h3>2017</h3>
-Quang D and Xie X
-[[http://www.ncbi.nlm.nih.gov/pubmed/25338716|DANN: a deep learning approach for annotating the pathogenicity of genetic variants]]\\
+<div class="level3">
-Quang D, Chen Y and Xie X\\
+<p><a class="urlextern" href="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 />
-Bioinformatics, 31(5):761-3, 2015
+W Zhu, C Liu, W Fan, X Xie<br />
+arXiv preprint arXiv:1709.05538</p>
-[[http://www.biomedcentral.com/1471-2164/16/S2/S1|MixClone: a mixture model for inferring tumor subclonal populations]]\\
+<p><a class="urlextern" href="https://www.biorxiv.org/content/early/2017/06/28/151274" rel="nofollow" title="https://www.biorxiv.org/content/early/2017/06/28/151274">FactorNet: a deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data</a><br />
-Li Y and Xie X\\
+D Quang, X Xie<br />
-BMC Genomics, 2015
+bioRxiv, 151274</p>
+<p><a class="urlextern" href="https://arxiv.org/abs/1612.05968" rel="nofollow" title="https://arxiv.org/abs/1612.05968">Deep Multi-instance Networks with Sparse Label Assignment for Whole Mammogram Classification</a><br />
+Wentao Zhu, Qi Lou, Yeeleng Scott Vang, Xiaohui Xie<br />
+arXiv:1612.05968<br />
+<a class="urlextern" href="http://www.miccai2017.org/" rel="nofollow" title="http://www.miccai2017.org/">MICCAI, 2017</a></p>
-[[http://www.ics.uci.edu/~xhx/publications/ImagingGenetics.pdf |Identifying unanticipated genes and mechanisms in serious mental illness]]\\
+<p>Understanding sequence conservation with deep learning<br />
-Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X\\
+Li Y, Quang D, and Xie X<br />
-Neuroimaging genetics : principles and practices, 2015
+ACM BCB, 2017</p>
-==== 2014 ====
+<p><a class="urlextern" href="http://biorxiv.org/content/early/2017/01/10/099358" rel="nofollow" title="http://biorxiv.org/content/early/2017/01/10/099358">HLA class I binding prediction via convolutional neural networks</a><br />
+Vang YS and Xie X<br />
+Bioinformatics, 2017</p>
-[[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/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 />
-Kim I 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 />
-International Journal on Document Analysis and Recognition, 2014\\
+Dev Cell. 27;40(6):595-607.e4, 2017</p>
-[[http://www.ics.uci.edu/~xhx/publications/HHR.pdf| preprint]]
+</div>
-[[http://www.ncbi.nlm.nih.gov/pubmed/25359723|Genome-wide view of TGFbeta/Foxh1 regulation of the early mesendoderm]] program\\
+<h3>2016</h3>
-Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K\\
-Development, 2014
-[[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]]\\
+<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 />
-Bioinformatics, 2014
+Wentao Zhu, Xiaohui Xie<br />
+arXiv:1612.05970</p>
-[[http://bioinformatics.oxfordjournals.org/content/early/2014/02/14/bioinformatics.btu093.abstract|EXTREME: An Online EM Algorithm for Motif Discovery]]\\
+<p><a class="urlextern" href="https://www.ncbi.nlm.nih.gov/pubmed/27418388" rel="nofollow" title="https://www.ncbi.nlm.nih.gov/pubmed/27418388">Developmentally regulated long non-coding RNAs in Xenopus tropicalis</a><br />
-Quang D and Xie X\\
+Forouzmand et al.<br />
-Bioinformatics, 2014
+Developmental Biology, (16)30120-8 2016</p>
-[[http://www.biomedcentral.com/1471-2105/15/42|Improving Read Mapping Using Additional Prefix Grams]]\\
+<p><a class="urlextern" href="http://bioinformatics.oxfordjournals.org/content/early/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 />
-Kim J, Li C and Xie X\\
+Chen Y, Li Y, Narayan R, Subramanian A, and Xie X<br />
-BMC Bioinformatics, 2014, 15(1):42
+Bioinformatics, 2016</p>
-[[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]]\\
+<p>DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences<br />
-Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X\\
+Quang D and Xie X<br />
-PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317
+Nucleic Acids Research, 2016</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://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 />
-Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q\\
+Weng L, Li Y, Xie X, and Shi Y<br />
-BMC Systems Biology 2014, 8:3
+RNA, 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="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 />
-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\\
+Zhu W, et al.<br />
-EMBO J. 2014 Mar 4.
+AAAI Conference on Artificial Intelligence, 2016</p>
-==== 2013 ====
+</div>
-[[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082146|Low-Rank Regularization for Learning Gene Expression Programs]] \\
+<h3>2015</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>Hobbes3: Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings<br />
-//Comput Math Methods Med.//, 2013
+Kim J, Chen L, and Xie X<br />
+nd IEEE International Conference on Data Engineering - ICDE 2016</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://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 />
-Blitz I, Biesinger J, Xie X, and Cho K\\
+Quang D and Xie X</p>
-//Genesis//, 2013.
-[[http://rnajournal.cshlp.org/content/early/2013/10/22/rna.042317.113.abstract|Overlapping and distinct functions of CstF64 and CstF64t in mammalian mRNA 3â² processing]]\\
+<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 />
-Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y\\
+Quang D, Chen Y and Xie X<br />
-//RNA//, 2013
+Bioinformatics, 31(5):761-3, 2015</p>
-[[http://arxiv.org/abs/1305.0855|Inference in Kingman's Coalescent with Particle Markov Chain Monte Carlo Method]] \\
+<p><a class="urlextern" href="http://www.biomedcentral.com/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 and Xie X \\
+Li Y and Xie X<br />
-//arXiv//, 2013
+BMC Genomics, 2015</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.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 />
-Biesinger J, Wang Y, and Xie X \\
+Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X<br />
-//BMC Bioinformatics// 2013, 14(S5):S4, 2013 \\
+Neuroimaging genetics : principles and practices, 2015</p>
-[[http://www.biomedcentral.com/content/supplementary/1471-2105-14-s5-s4-s1.pdf|Supplemental Information]]
+</div>
-[[http://www.biomedcentral.com/1471-2105/14/S5/S11|A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues]] \\
+<h3>2014</h3>
-Li Y and Xie X \\
-//BMC Bioinformatics// 2013, 14(Suppl 5):S11, 2013
-[[http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6544889|Efficient direct search on compressed genomic data]] \\
+<div class="level3">
-Yang X, Wang B, Li C, Wang J, 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 />
-//IEEE International Conference on Data Engineering (ICDE)//, 2013
+Kim I and Xie X<br />
-==== 2012 ====
+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.springerlink.com/content/4l2m27p3867xj584/|Learning sparse gradients for variable selection and dimension reduction]] \\
+<p><a class="urlextern" href="http://www.ncbi.nlm.nih.gov/pubmed/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 />
-Ye G and Xie X \\
+Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K<br />
-Machine Learning Journal, 87(3):303-355, 2012 \\
+Development, 2014</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://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, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y \\
+Li Y and Xie X<br />
-PNAS, 109(46):18773-8, 2012
+Bioinformatics, 2014</p>
-[[http://www.ncbi.nlm.nih.gov/pubmed/22296850|Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR]] \\
+<p><a class="urlextern" href="http://bioinformatics.oxfordjournals.org/content/early/2014/02/14/bioinformatics.btu093.abstract" rel="nofollow" title="http://bioinformatics.oxfordjournals.org/content/early/2014/02/14/bioinformatics.btu093.abstract">EXTREME: An Online EM Algorithm for Motif Discovery</a><br />
-Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF \\
+Quang D and Xie X<br />
-BMC Genomics, 2012
+Bioinformatics, 2014</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.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 />
-Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X  \\
+Kim J, Li C and Xie X<br />
-Nucleic Acids Research, 40(6):e41,  2012 \\
+BMC Bioinformatics, 2014, 15(1):42</p>
-Software: [[http://hobbes.ics.uci.edu/|Hobbes]]
-==== 2011 ====
+<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 />
+Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X<br />
+PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317</p>
-[[http://arxiv.org/pdf/1110.3076v1|Efficient latent variable graphical model selection via split Bregman method]] \\
+<p><a class="urlextern" href="http://www.biomedcentral.com/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 />
-Ye G, Wang Y, Chen Y, and Xie X \\
+Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q<br />
-arXiv:1110.3076v1, 2011
+BMC Systems Biology 2014, 8:3</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://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 />
-Daily K, Patel VR, Rigor P, Xie X, Baldi P. \\
+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 />
-BMC Bioinformatics, 2011
+EMBO J. 2014 Mar 4.</p>
+</div>
-[[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10530.html|A high-resolution map of human evolutionary constraint using 29 mammals]] \\
+<h3>2013</h3>
-Lindblad-Toh, Barber, Zuk, Lin, et al. \\
-Nature, 2011
-[[http://www.biomedcentral.com/1471-2105/12/99|SNP-based pathway enrichment analysis for genome-wide association studies]] \\
+<div class="level3">
-Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X \\
+<p><a class="urlextern" href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082146" rel="nofollow" title="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082146">Low-Rank Regularization for Learning Gene Expression Programs</a><br />
-BMC Bioinformatics, 2011  \\
+Ye G, Tang M, Nie Q and Xie X<br />
-Software: [[http://cbcl.ics.uci.edu/SSEA/|SNP Set Enrichment Analysis (SSEA)]]
+<em>PLOS ONE</em>, 2013</p>
-[[http://www.cell.com/cell-metabolism/abstract/S1550-4131(11)00092-1|Genome-wide Positioning of SREBP-2 in Hepatic Chromatin Predicts a Novel Role in Autophagy ]] \\
+<p><a class="urlextern" href="http://www.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 />
-Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF \\
+Chen Y, Jia Z, Mercola D and Xie X<br />
-//Cell Metabolism//, 13:367-75, 2011  \\
+<em>Comput Math Methods Med.</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|AREM: aligning short reads from ChIP-sequencing by expectation maximization]] \\
+<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 />
-Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X \\
+Blitz I, Biesinger J, Xie X, and Cho K<br />
-//J Comput Biol.//, 2011 \\
+<em>Genesis</em>, 2013.</p>
-Software: [[http://sourceforge.net/projects/arem|AREM]]
-[[http://jmlr.csail.mit.edu/proceedings/papers/v15/ye11a/ye11a.pdf|Efficient variable selection in support vector machines via the alternating direction method of multipliers ]] \\
+<p><a class="urlextern" href="http://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 G, Chen Y, and Xie X \\
+Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y<br />
-AI & STATS , 2011
+<em>RNA</em>, 2013</p>
-==== 2010 ====
+<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 />
+Chen Y and Xie X<br />
+<em>arXiv</em>, 2013</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.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 />
-Ye G, Cai J, and Xie X \\
+Biesinger J, Wang Y, and Xie X<br />
-arXiv:1012.0975v1, 2010
+<em>BMC Bioinformatics</em> 2013, 14(S5):S4, 2013<br />
+<a class="urlextern" href="http://www.biomedcentral.com/content/supplementary/1471-2105-14-s5-s4-s1.pdf" rel="nofollow" title="http://www.biomedcentral.com/content/supplementary/1471-2105-14-s5-s4-s1.pdf">Supplemental Information</a></p>
-[[http://www.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.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-B and Xie X \\
+Li Y and Xie X<br />
-Computational Statistics and Data Analysis, doi:10.1016/j.csda.2010.10.021, 2010  \\
+<em>BMC Bioinformatics</em> 2013, 14(Suppl 5):S11, 2013</p>
-[[http://arxiv.org/abs/1006.5086|arXiv version]] [[http://www.biomedcentral.com/1471-2105/11/514|Data Structures and Compression Algorithms for High-Throughput Sequencing Technologies]] \\
-Daily K, Rigor P, Christley S, Xie X and Baldi P  \\
-//BMC Bioinformatics//,11:514, 2010
-[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq414|Interactive and fuzzy search: a dynamic way to explore MEDLINE ]] \\
+<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 />
-Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J \\
+Yang X, Wang B, Li C, Wang J, and Xie X<br />
-//Bioinformatics//, 26(18):2321-2327, 2010  \\
+<em>IEEE International Conference on Data Engineering (ICDE)</em>, 2013</p>
-[[http://ipubmed.ics.uci.edu/|iPubMed Search]]
+</div>
-[[http://arxiv.org/abs/1006.5060|Variable selection and dimension reduction via sparse gradients]] \\
+<h3>2012</h3>
-Ye G-B and Xie X \\
-arXiv:1006.5060v2, 2010
-[[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]] \\
+<div class="level3">
-Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, 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 />
-//NeuroImage// 53:839-847, 2010
+Ye G and Xie X<br />
+Machine Learning Journal, 87(3):303-355, 2012<br />
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/SGL.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/SGL.pdf">Preprint</a></p>
-[[http://www.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.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 Y, Christley S, Mjolsness E, and Xie X \\
+Yao C, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y<br />
-//BMC Systems Biology//, 4:99 doi:10.1186/1752-0509-4-99, 2010
+PNAS, 109(46):18773-8, 2012</p>
-[[http://www.springerlink.com/content/428v02087m218878/fulltext.pdf|Site-frequency Spectrum of Linked Sites]] \\
+<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 />
-Xie X   \\
+Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF<br />
-//Bulletin of Mathematical Biology//, DOI: 10.1007/s11538-010-9534-3, 2010
+BMC Genomics, 2012</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/22199254" rel="nofollow" title="http://www.ncbi.nlm.nih.gov/pubmed/22199254">Hobbes: optimized gram-based methods for efficient read alignment</a><br />
-Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and Osborne TF \\
+Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X<br />
-Nucleic Acids Research, doi:10.1093/nar/gkq397, 2010 \\
+Nucleic Acids Research, 40(6):e41, 2012<br />
-[[http://cbcl.ics.uci.edu/public_data/FXR/|Online Supplementary Materials]]
+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/1471-2164/11/208/abstract|Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes]] \\
+<h3>2011</h3>
-Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X  \\
-//BMC Genomics// 11:208, 2010 \\
-[[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]] \\
+<div class="level3">
-Ma L-J, et al.  \\
+<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 />
-//Nature// 464:367-373, 2010 \\
+Ye G, Wang Y, Chen Y, and Xie X<br />
-[[http://www.broadinstitute.org/news/1439|The chromosomal secrets of a plant pathogen]] \\
+arXiv:1110.3076v1, 2011</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.ncbi.nlm.nih.gov/pubmed/22208852" rel="nofollow" title="http://www.ncbi.nlm.nih.gov/pubmed/22208852">MotifMap: integrative genome-wide maps of regulatory motif sites for model species. </a><br />
+Daily K, Patel VR, Rigor P, Xie X, Baldi P.<br />
+BMC Bioinformatics, 2011</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.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 />
-Christley S, Nie Q and Xie X \\
+Lindblad-Toh, Barber, Zuk, Lin, et al.<br />
-//PLoS ONE// 4(8): e6799. doi:10.1371/journal.pone.0006799 (2009)
+Nature, 2011</p>
-[[http://www.pnas.org/content/early/2009/08/03/0904246106.abstract|Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif]] \\
+<p><a class="urlextern" href="http://www.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 />
-Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF \\
+Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X<br />
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0904246106 (2009)
+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://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/12/i54|Identifying novel constrained elements by exploiting biased substitution patterns]] \\
+<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 />
-Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X \\
+Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF<br />
-//Bioinformatics//25:i54-i62 (2009)  \\
+<em>Cell Metabolism</em>, 13:367-75, 2011<br />
-[[http://www.ics.uci.edu/~xhx/publications/siphy_suppinfo.pdf|Supplementary Methods]] \\
+<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.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://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 />
-Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA  \\
+Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X<br />
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0813264106 (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://genome.cshlp.org/content/19/4/567.long|Common polymorphic transcript variation in human disease]] \\
+<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 />
-Fraser H and Xie X  \\
+Ye G, Chen Y, and Xie X<br />
-//Genome Research// doi:10.1101/gr.083477.108 (2009) \\
+AI &amp; STATS , 2011</p>
-[[http://www.ics.uci.edu/~xhx/publications/PTV_GR2009.pdf|PDF]]
+</div>
-[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/167|MotifMap: a human genome-wide map of candidate regulatory motif sites ]] \\
+<h3>2010</h3>
-Xie X, Rigor P, and Baldi P  \\
-//Bioinformatics// 25: 167-174 (2009) \\
-[[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 ]] \\
+<div class="level3">
-Christley S, Lu Y, Li C, 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 />
-//Bioinformatics // 25: 274-275 (2009) \\
+Ye G, Cai J, and Xie X<br />
-[[http://www.ics.uci.edu/~xhx/project/DNAzip|DNAzip: DNA sequence compression using a reference genome]] \\
+arXiv:1012.0975v1, 2010</p>
-[[http://www.ics.uci.edu/~xhx/publications/DNAzip.pdf|PDF]] \\
-[[http://www.genomeweb.com/informatics/jim-watsonâï¿½ï¿½s-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://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6V8V-51BBKR7-1&amp;_user=10&amp;_coverDate=10/27/2010&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000050221&amp;_version=1&amp;_urlVersion=0&amp;_userid=10&amp;md5=6ff4ea0404367278249b06c9a59f84fd&amp;searchtype=a" rel="nofollow" title="http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6V8V-51BBKR7-1&amp;_user=10&amp;_coverDate=10/27/2010&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000050221&amp;_version=1&amp;_urlVersion=0&amp;_userid=10&amp;md5=6ff4ea0404367278249b06c9a59f84fd&amp;searchtype=a">Split Bregman method for large scale fused Lasso</a><br />
+Ye G-B and Xie X<br />
+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://www.ics.uci.edu/~xhx/publications/wu_motif_2008.pdf|Discovering regulatory motifs in the Plasmodium genome using comparative genomics ]] \\
+<p><a class="urlextern" href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq414" rel="nofollow" title="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq414">Interactive and fuzzy search: a dynamic way to explore MEDLINE </a><br />
-Wu J, Sieglaff DH, Gervin J, and Xie X  \\
+Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J<br />
-//Bioinformatics // 24:1843-9 (2008) \\
+<em>Bioinformatics</em>, 26(18):2321-2327, 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://ipubmed.ics.uci.edu/" rel="nofollow" title="http://ipubmed.ics.uci.edu/">iPubMed Search</a></p>
-[[http://www.ics.uci.edu/~xhx/publications/wu_motif_2008_suppinfo.pdf|Supplementary Information on the MDOS algorithm]]
-[[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2567431&blobtype=pdf|Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains ]] \\
+<p><a class="urlextern" href="http://arxiv.org/abs/1006.5060" rel="nofollow" title="http://arxiv.org/abs/1006.5060">Variable selection and dimension reduction via sparse gradients</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  \\
+Ye G-B and Xie X<br />
-//PLoS Genetics//4(10):e1000242 (2008)
+arXiv:1006.5060v2, 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://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 />
-Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, and Lander ES. \\
+Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X<br />
-//Proc Natl Acad Sci USA//104(49):19428-33 (2007)
+<em>NeuroImage</em> 53:839-847, 2010</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/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 />
-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  \\
+Wang Y, Christley S, Mjolsness E, and Xie X<br />
-//Nature//449:913-918 (2007)
+<em>BMC Systems Biology</em>, 4:99 doi:10.1186/1752-0509-4-99, 2010</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.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 />
-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'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. \\
+Xie X<br />
-//Nature// 448:553-60 (2007)
+<em>Bulletin of Mathematical Biology</em>, DOI: 10.1007/s11538-010-9534-3, 2010</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://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 />
-Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES. \\
+Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and Osborne TF<br />
-//Proc Natl Acad Sci USA//104:7145-7150 (2007)  \\
+Nucleic Acids Research, doi:10.1093/nar/gkq397, 2010<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://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/v447/n7141/pdf/nature05805.pdf|Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences ]] \\
+<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 />
-Mikkelsen TS, Wakefield MJ, et al.  \\
+Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X<br />
-//Nature// 447:167-177 (2007)
+<em>BMC Genomics</em> 11:208, 2010<br />
+<a class="urlextern" href="http://www.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html" rel="nofollow" title="http://www.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html">Supplementary Information</a><br />
+<a class="urlextern" href="http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html" rel="nofollow" title="http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html">Fusarium Comparative Database</a></p>
-[[http://www.ics.uci.edu/~xhx/publications/Xie_AMCNE.pdf|A family of conserved noncoding elements derived from an ancient transposable element]] \\
+<p><a class="urlextern" href="http://www.nature.com/nature/journal/v464/n7287/abs/nature08850.html" rel="nofollow" title="http://www.nature.com/nature/journal/v464/n7287/abs/nature08850.html">Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium oxysporum</a><br />
-Xie X, Kamal M, and Lander ES. \\
+Ma L-J, et al.<br />
-//Proc Natl Acad Sci USA//103:11659-11664 (2006)  \\
+<em>Nature</em> 464:367-373, 2010<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.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>
-==== 2006 or before ====
+<h3>2009</h3>
-[[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]] \\
+<div class="level3">
-Kamal M, Xie X, and Lander ES.  \\
+<p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf">Incorporating existing network information into gene network inference</a><br />
-//Proc Natl Acad Sci USA//103:2740-2745 (2006)  \\
+Christley S, Nie Q and Xie X<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]] \\
+<em>PLoS ONE</em> 4(8): e6799. doi:10.1371/journal.pone.0006799 (2009)</p>
-[[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=381|News story]]
-[[http://download.cell.com/pdfs/0092-8674/PIIS0092867406003801.pdf|A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells]] \\
+<p><a class="urlextern" href="http://www.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 />
-Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al.  \\
+Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF<br />
-//Cell// 125:315-26 (2006)
+<em>Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0904246106 (2009)</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/25/12/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 />
-Wu J and Xie X \\
+Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X<br />
-//Genome Biology//7(9):R85 (2006) (Highly accessed)  \\
+<em>Bioinformatics</em>25:i54-i62 (2009)<br />
-[[http://www.broad.mit.edu/personal/xhx/projects/NRSE|Supplementary website]]
+<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/ng/journal/v38/n5/pdf/ng1776.pdf|Systematic identification of human mitochondrial disease genes through integrative genomics ]] \\
+<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 />
-Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK. \\
+Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA<br />
-//Nature Genetics//, 38:576-82 (2006)
+<em>Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0813264106 (2009)</p>
-[[http://www.ics.uci.edu/~xhx/publications/xie05_motif_paper.pdf|Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals ]] \\
+<p><a class="urlextern" href="http://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, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M.  \\
+Fraser H and Xie X<br />
-//Nature//2005; 434:338-45  \\
+<em>Genome Research</em> doi:10.1101/gr.083477.108 (2009)<br />
-[[http://www.broad.mit.edu/seq/HumanMotifs/|Supplementary Website]] [[http://www.ics.uci.edu/~xhx/publications/nature03441-s1.pdf|Supplementary Information]] [[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=134|News story]]
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/PTV_GR2009.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/PTV_GR2009.pdf">PDF</a></p>
-[[http://www.genome.org/cgi/reprint/gr.5285206v1|A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands]] \\
+<p><a class="urlextern" href="http://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 />
-Giallourakis C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R.  \\
+Xie X, Rigor P, and Baldi P<br />
-//Genome Resesarch//, 16:1056-72 (2006)
+<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://download.cell.com/pdfs/0092-8674/PIIS0092867406003692.pdf|A Mammalian Organelle Map by Protein Correlation Profiling]] \\
+<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 />
-Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M.  \\
+Christley S, Lu Y, Li C, and Xie X<br />
-//Cell// 125:187-99 (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-watsonâï¿½ï¿½s-genome-e-mail-uc-irvine-team-develops-method-compress-genomic-data" rel="nofollow" title="http://www.genomeweb.com/informatics/jim-watsonâï¿½ï¿½s-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/WerfelXieSeung2005.pdf|Learning curves for stochastic gradient descent in linear feedforward networks. ]] \\
+<h3>2008</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.ics.uci.edu/~xhx/publications/wu_motif_2008.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/wu_motif_2008.pdf">Discovering regulatory motifs in the Plasmodium genome using comparative genomics </a><br />
-//Nature// 438:803-19 2005
+Wu J, Sieglaff DH, Gervin J, and Xie X<br />
+<em>Bioinformatics </em> 24:1843-9 (2008)<br />
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/project/mdos/" rel="nofollow" title="http://www.ics.uci.edu/~xhx/project/mdos/">MDOS software</a>: A method for Motif Discovery using Orthologous Sequences (alignment independent).<br />
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/wu_motif_2008_suppinfo.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/wu_motif_2008_suppinfo.pdf">Supplementary Information on the MDOS algorithm</a></p>
-[[http://www.ics.uci.edu/~xhx/publications/annurev.genom.6.080604.pdf|Disease gene discovery 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 />
-Giallourakis C, Henson C, Reich M, Xie X, and Mootha VK.  \\
+Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE<br />
-//Annu. Rev. Genomics Hum. Genet.// 2005:22:381-406.
+<em>PLoS </em><em>Genetics</em>4(10):e1000242 (2008)</p>
+</div>
-[[http://www.ics.uci.edu/~xhx/publications/PhysRevE_69_041909.pdf|Learning in neural networks by reinforcement of irregular spiking. ]] \\
+<h3>2007</h3>
-Xie X and Seung HS.  \\
-//Phys Rev E//, 2004;69:041909
-[[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]] \\
+<div class="level3">
-Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J 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 />
-//Proc Natl Acad Sci USA//, 2004;101:6570-5
+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/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/v449/n7164/abs/nature06250.html" rel="nofollow" title="http://www.nature.com/nature/journal/v449/n7164/abs/nature06250.html">Genome-wide detection and characterization of positive selection in human populations </a><br />
-Xie X, Hahnloser RH, and Seung HS.  \\
+Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES and International HapMap Consortium<br />
-//Physical Review E//, 2002;66:041902
+<em>Nature</em>449:913-918 (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.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 Giese MA.  \\
+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 />
-//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>Nature</em> 448:553-60 (2007)</p>
-Giese MA and Xie X  \\
-//Neurocomputing// 2002;44:417-422
-[[http://www.ics.uci.edu/~xhx/publications/lwta.pdf|Learning winner-take-all competition between groups of neurons in lateral inhibitory networks ]] \\
+<p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/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 />
-Xie X, Hahnloser HR, and Seung HS.  \\
+Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES.<br />
-//Advances in Neural Information Processing Systems//2001;13:350-356
+<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/nc_vel_tuning.pdf|Generating velocity tuning by asymmetric recurrent connections]] \\
+<p><a class="urlextern" href="http://www.nature.com/nature/journal/v447/n7141/pdf/nature05805.pdf" rel="nofollow" title="http://www.nature.com/nature/journal/v447/n7141/pdf/nature05805.pdf">Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences </a><br />
-Xie X and Giese MA.  \\
+Mikkelsen TS, Wakefield MJ, et al.<br />
-//Advances in Neural Information Processing Systems//2002;13:325-332
+<em>Nature</em> 447:167-177 (2007)</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/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, Hahnloser RH, and Seung HS.  \\
+Xie X, Kamal M, and Lander ES.<br />
-//Neural Computation//, 2002;14:2627-2646
+<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/chl_nc.pdf|Equivalence of backpropagation and contrastive Hebbian learning in a layered network]] \\
+<h3>2006 or before</h3>
-Xie X and Seung HS.  \\
-//Neural Computation//, 2003;16:441-454
-[[http://www.ics.uci.edu/~xhx/publications/network_pop.pdf|Threshold behavior of maximum likelihood method in population decoding]] \\
+<div class="level3">
-Xie X \\
+<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 />
-//Network: Comput. Neural Syst.// 2002;13:447-456
+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>
+<p><a class="urlextern" href="http://download.cell.com/pdfs/0092-8674/PIIS0092867406003801.pdf" rel="nofollow" title="http://download.cell.com/pdfs/0092-8674/PIIS0092867406003801.pdf">A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells</a><br />
+Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al.<br />
+<em>Cell</em> 125:315-26 (2006)</p>
+<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 />
+Wu J and Xie X<br />
+<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>
+<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 />
+Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK.<br />
+<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>
+</html>
-[[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