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-~~NOTOC~~
+<html>
+<h2>Publications</h2>
-===== Publications =====
+<div class="level2">&nbsp;</div>
-==== 2016 ====
+<h3>2018</h3>
-[[http://bioinformatics.oxfordjournals.org/content/early/2016/02/11/bioinformatics.btw074.short?rss=1|Gene expression inference with deep learning]]\\
+<div class="level3">
-Chen Y, Li Y, Narayan R, Subramanian A, and Xie X\\
+<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 />
-Bioinformatics, 2016
+Zhu W, Vang YS, Huang Y, Xie X</p>
-==== 2015 ====
+<p>Sequential Embedding Induced Nonparametric Text Clustering<br />
+Duan T, Lou Q, Xie X</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/1802.00931" rel="nofollow" title="https://arxiv.org/abs/1802.00931">Deep Learning Framework for Multi-class Breast Cancer Histology Image Classification</a><br />
-Zhu W, et al.\\
+Vang S, Chen Z, Xie X<br />
-AAAI Conference on Artificial Intelligence
+th International Conference on Image Analysis and Recognition, 2018</p>
-Hobbes3: Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings\\
+<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 />
-Kim J, Chen L, and Xie X\\
+IEEE Winter Conf. on Applications of Computer Vision 2018</p>
-nd IEEE International Conference on Data Engineering - ICDE 2016
-[[http://biorxiv.org/content/early/2015/12/20/032821|DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences]]\\
+<p><a class="urlextern" href="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 />
-Quang D and Xie X
+IEEE Winter Conf. on Applications of Computer Vision 2018</p>
-[[http://www.ncbi.nlm.nih.gov/pubmed/25338716|DANN: a deep learning approach for annotating the pathogenicity of genetic variants]]\\
+<p>Adversarial Deep Structured Nets for Mass Segmentation from Mammograms<br />
-Quang D, Chen Y and Xie X\\
+W Zhu, X Xiang, T Tran, GD Hager, X Xie<br />
-Bioinformatics, 31(5):761-3, 2015
+IEEE International Symposium on Biomedical Imaging</p>
-[[http://www.biomedcentral.com/1471-2164/16/S2/S1|MixClone: a mixture model for inferring tumor subclonal populations]]\\
+<p>Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural Networks<br />
-Li Y and Xie X\\
+H Tang, D Kim, X Xie<br />
-BMC Genomics, 2015
+IEEE International Symposium on Biomedical Imaging</p>
-Identifying unanticipated genes and mechanisms in serious mental illness: GWAS based imaging genetics strategies\\
+<p>Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.<br />
-Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X\\
+Zhu Y, Wang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.<br />
-Neuroimaging genetics : principles and practices, 2015
+Mol Cell. 2018 Jan 4;69(1):62-74.e4.</p>
+</div>
-==== 2014 ====
+<h3>2017</h3>
-[[http://link.springer.com/article/10.1007/s10032-014-0229-4|Handwritten Hangul recognition using deep convolutional neural networks]]\\
+<div class="level3">
-Kim I 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 />
-International Journal on Document Analysis and Recognition, 2014\\
+W Zhu, C Liu, W Fan, X Xie<br />
-[[http://www.ics.uci.edu/~xhx/publications/HHR.pdf| preprint]]
+arXiv preprint arXiv:1709.05538</p>
-[[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.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 />
-Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K\\
+D Quang, X Xie<br />
-Development, 2014
+bioRxiv, 151274</p>
-[[http://bioinformatics.oxfordjournals.org/content/early/2014/04/21/bioinformatics.btu174|Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity]]\\
+<p><a class="urlextern" href="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 />
-Li Y and Xie X\\
+Wentao Zhu, Qi Lou, Yeeleng Scott Vang, Xiaohui Xie<br />
-Bioinformatics, 2014
+arXiv:1612.05968<br />
+<a class="urlextern" href="http://www.miccai2017.org/" rel="nofollow" title="http://www.miccai2017.org/">MICCAI, 2017</a></p>
-[[http://bioinformatics.oxfordjournals.org/content/early/2014/02/14/bioinformatics.btu093.abstract|EXTREME: An Online EM Algorithm for Motif Discovery]]\\
+<p>Understanding sequence conservation with deep learning<br />
-Quang D and Xie X\\
+Li Y, Quang D, and Xie X<br />
-Bioinformatics, 2014
+ACM BCB, 2017</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/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, Li C and Xie X\\
+Vang YS and Xie X<br />
-BMC Bioinformatics, 2014, 15(1):42
+Bioinformatics, 2017</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><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 />
-Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X\\
+Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW<br />
-PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317
+Dev Cell. 27;40(6):595-607.e4, 2017</p>
+</div>
-[[http://www.biomedcentral.com/1752-0509/8/3/abstract|Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns]] \\
+<h3>2016</h3>
-Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q\\
-BMC Systems Biology 2014, 8:3
-[[http://emboj.embopress.org/content/early/2014/03/04/embj.201386537|Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal]]\\
+<div class="level3">
-Lackford 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\\
+<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 />
-EMBO J. 2014 Mar 4.
+Wentao Zhu, Xiaohui Xie<br />
-==== 2013 ====
+arXiv:1612.05970</p>
-[[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082146|Low-Rank Regularization for Learning Gene Expression Programs]] \\
+<p><a class="urlextern" href="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 />
-Ye G, Tang M, Nie Q and Xie X\\
+Forouzmand et al.<br />
-//PLOS ONE//, 2013
+Developmental Biology, (16)30120-8 2016</p>
-[[http://www.hindawi.com/journals/cmmm/2013/873595/|A gradient boosting algorithm for survival analysis via direct optimization of concordance index]] \\
+<p><a class="urlextern" href="http://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 />
-Chen Y, Jia Z, Mercola D and Xie X\\
+Chen Y, Li Y, Narayan R, Subramanian A, and Xie X<br />
-//Comput Math Methods Med.//, 2013
+Bioinformatics, 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>DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences<br />
-Blitz I, Biesinger J, Xie X, and Cho K\\
+Quang D and Xie X<br />
-//Genesis//, 2013.
+Nucleic Acids Research, 2016</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 3â² processing]]\\
+<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 />
-Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y\\
+Weng L, Li Y, Xie X, and Shi Y<br />
-//RNA//, 2013
+RNA, 2016</p>
-[[http://arxiv.org/abs/1305.0855|Inference in Kingman's Coalescent with Particle Markov Chain Monte Carlo Method]] \\
+<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 />
-Chen Y and Xie X \\
+Zhu W, et al.<br />
-//arXiv//, 2013
+AAAI Conference on Artificial Intelligence, 2016</p>
+</div>
-[[http://www.biomedcentral.com/content/pdf/1471-2105-14-S5-S4.pdf|Discovering and Mapping Chromatin States Using a Tree Hidden Markov Model]] \\
+<h3>2015</h3>
-Biesinger J, Wang Y, and Xie X \\
-//BMC Bioinformatics// 2013, 14(S5):S4, 2013 \\
-[[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]] \\
+<div class="level3">
-Li Y and Xie X \\
+<p>Hobbes3: Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings<br />
-//BMC Bioinformatics// 2013, 14(Suppl 5):S11, 2013
+Kim J, Chen L, and Xie X<br />
+nd IEEE International Conference on Data Engineering - ICDE 2016</p>
-[[http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6544889|Efficient direct search on compressed genomic data]] \\
+<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 />
-Yang X, Wang B, Li C, Wang J, and Xie X \\
+Quang D and Xie X</p>
-//IEEE International Conference on Data Engineering (ICDE)//, 2013
-==== 2012 ====
-[[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/25338716" rel="nofollow" title="http://www.ncbi.nlm.nih.gov/pubmed/25338716">DANN: a deep learning approach for annotating the pathogenicity of genetic variants</a><br />
-Ye G and Xie X \\
+Quang D, Chen Y and Xie X<br />
-Machine Learning Journal, 87(3):303-355, 2012 \\
+Bioinformatics, 31(5):761-3, 2015</p>
-[[http://www.ics.uci.edu/~xhx/publications/SGL.pdf|Preprint]]
-[[http://www.ncbi.nlm.nih.gov/pubmed/23112178|Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation]] \\
+<p><a class="urlextern" href="http://www.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 />
-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
+BMC Genomics, 2015</p>
-[[http://www.ncbi.nlm.nih.gov/pubmed/22296850|Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR]] \\
+<p><a class="urlextern" href="http://www.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 />
-Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF \\
+Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X<br />
-BMC Genomics, 2012
+Neuroimaging genetics : principles and practices, 2015</p>
+</div>
-[[http://www.ncbi.nlm.nih.gov/pubmed/22199254|Hobbes: optimized gram-based methods for efficient read alignment]] \\
+<h3>2014</h3>
-Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X  \\
-Nucleic Acids Research, 40(6):e41,  2012 \\
-Software: [[http://hobbes.ics.uci.edu/|Hobbes]]
-==== 2011 ====
+<div class="level3">
+<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 />
+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://arxiv.org/pdf/1110.3076v1|Efficient latent variable graphical model selection via split Bregman method]] \\
+<p><a class="urlextern" href="http://www.ncbi.nlm.nih.gov/pubmed/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, Wang Y, Chen Y, and Xie X \\
+Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K<br />
-arXiv:1110.3076v1, 2011
+Development, 2014</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://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 />
-Daily K, Patel VR, Rigor P, Xie X, Baldi P. \\
+Li Y and Xie X<br />
-BMC Bioinformatics, 2011
+Bioinformatics, 2014</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://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 />
-Lindblad-Toh, Barber, Zuk, Lin, et al. \\
+Quang D and Xie X<br />
-Nature, 2011
+Bioinformatics, 2014</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/1471-2105/15/42" rel="nofollow" title="http://www.biomedcentral.com/1471-2105/15/42">Improving Read Mapping Using Additional Prefix Grams</a><br />
-Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X \\
+Kim J, Li C and Xie X<br />
-BMC Bioinformatics, 2011  \\
+BMC Bioinformatics, 2014, 15(1):42</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 a Novel Role in Autophagy ]] \\
+<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 />
-Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF \\
+Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X<br />
-//Cell Metabolism//, 13:367-75, 2011  \\
+PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317</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://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 />
-Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X \\
+Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q<br />
-//J Comput Biol.//, 2011 \\
+BMC Systems Biology 2014, 8:3</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://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, Chen Y, 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 />
-AI & STATS , 2011
+EMBO J. 2014 Mar 4.</p>
+</div>
-==== 2010 ====
+<h3>2013</h3>
-[[http://arxiv4.library.cornell.edu/abs/1012.0975|Split Bregman method for sparse inverse covariance estimation with matrix iteration acceleration]] \\
+<div class="level3">
-Ye G, Cai J, and Xie X \\
+<p><a class="urlextern" href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082146" rel="nofollow" title="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082146">Low-Rank Regularization for Learning Gene Expression Programs</a><br />
-arXiv:1012.0975v1, 2010
+Ye G, Tang M, Nie Q and Xie X<br />
+<em>PLOS ONE</em>, 2013</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.hindawi.com/journals/cmmm/2013/873595/" rel="nofollow" title="http://www.hindawi.com/journals/cmmm/2013/873595/">A gradient boosting algorithm for survival analysis via direct optimization of concordance index</a><br />
-Ye G-B and Xie X \\
+Chen Y, Jia Z, Mercola D and Xie X<br />
-Computational Statistics and Data Analysis, doi:10.1016/j.csda.2010.10.021, 2010  \\
+<em>Comput Math Methods Med.</em>, 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://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 />
-Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J \\
+Blitz I, Biesinger J, Xie X, and Cho K<br />
-//Bioinformatics//, 26(18):2321-2327, 2010  \\
+<em>Genesis</em>, 2013.</p>
-[[http://ipubmed.ics.uci.edu/|iPubMed Search]]
-[[http://arxiv.org/abs/1006.5060|Variable selection and dimension reduction via sparse gradients]] \\
+<p><a class="urlextern" href="http://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-B 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 />
-arXiv:1006.5060v2, 2010
+<em>RNA</em>, 2013</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://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 />
-Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X \\
+Chen Y and Xie X<br />
-//NeuroImage// 53:839-847, 2010
+<em>arXiv</em>, 2013</p>
-[[http://www.biomedcentral.com/1752-0509/4/99|Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent]] \\
+<p><a class="urlextern" href="http://www.biomedcentral.com/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 />
-Wang Y, Christley S, Mjolsness E, and Xie X \\
+Biesinger J, Wang Y, and Xie X<br />
-//BMC Systems Biology//, 4:99 doi:10.1186/1752-0509-4-99, 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.springerlink.com/content/428v02087m218878/fulltext.pdf|Site-frequency Spectrum of Linked Sites]] \\
+<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 />
-Xie X   \\
+Li Y and Xie X<br />
-//Bulletin of Mathematical Biology//, DOI: 10.1007/s11538-010-9534-3, 2010
+<em>BMC Bioinformatics</em> 2013, 14(Suppl 5):S11, 2013</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://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 />
-Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and Osborne TF \\
+Yang X, Wang B, Li C, Wang J, and Xie X<br />
-Nucleic Acids Research, doi:10.1093/nar/gkq397, 2010 \\
+<em>IEEE International Conference on Data Engineering (ICDE)</em>, 2013</p>
-[[http://cbcl.ics.uci.edu/public_data/FXR/|Online Supplementary Materials]]
+</div>
-[[http://www.biomedcentral.com/1471-2164/11/208/abstract|Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes]] \\
+<h3>2012</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://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 />
-//Nature// 464:367-373, 2010 \\
+Ye G and Xie X<br />
-[[http://www.broadinstitute.org/news/1439|The chromosomal secrets of a plant pathogen]] \\
+Machine Learning Journal, 87(3):303-355, 2012<br />
-[[http://www.genomeweb.com//node/936293?hq_e=el&hq_m=655129&hq_l=3&hq_v=dfec329446|Comparative genomics reveals horizontal gene transfer in pathogenic fungus]] \\
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/SGL.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/SGL.pdf">Preprint</a></p>
-[[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/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://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.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 />
-Christley S, Nie Q and Xie X \\
+Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF<br />
-//PLoS ONE// 4(8): e6799. doi:10.1371/journal.pone.0006799 (2009)
+BMC Genomics, 2012</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.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 />
-Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF \\
+Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X<br />
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0904246106 (2009)
+Nucleic Acids Research, 40(6):e41, 2012<br />
+Software: <a class="urlextern" href="http://hobbes.ics.uci.edu/" rel="nofollow" title="http://hobbes.ics.uci.edu/">Hobbes</a></p>
+</div>
-[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/12/i54|Identifying novel constrained elements by exploiting biased substitution patterns]] \\
+<h3>2011</h3>
-Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X \\
-//Bioinformatics//25:i54-i62 (2009)  \\
-[[http://www.ics.uci.edu/~xhx/publications/siphy_suppinfo.pdf|Supplementary Methods]] \\
-[[http://www.broadinstitute.org/genome_bio/siphy/|SiPhy (SIte-specific PHYlogenetic analysis) Java software package]]
-[[http://www.pnas.org/content/early/2009/02/11/0813264106.abstract|Comparative genomics allows the discovery of cis-regulatory elements in mosquitoes]] \\
+<div class="level3">
-Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA  \\
+<p><a class="urlextern" href="http://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 />
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0813264106 (2009)
+Ye G, Wang Y, Chen Y, and Xie X<br />
+arXiv:1110.3076v1, 2011</p>
-[[http://genome.cshlp.org/content/19/4/567.long|Common polymorphic transcript variation in human disease]] \\
+<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 />
-Fraser H and Xie X  \\
+Daily K, Patel VR, Rigor P, Xie X, Baldi P.<br />
-//Genome Research// doi:10.1101/gr.083477.108 (2009) \\
+BMC Bioinformatics, 2011</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.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 />
-Xie X, Rigor P, and Baldi P  \\
+Lindblad-Toh, Barber, Zuk, Lin, et al.<br />
-//Bioinformatics// 25: 167-174 (2009) \\
+Nature, 2011</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><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 />
-Christley S, Lu Y, Li C, and Xie X  \\
+Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X<br />
-//Bioinformatics // 25: 274-275 (2009) \\
+BMC Bioinformatics, 2011<br />
-[[http://www.ics.uci.edu/~xhx/project/DNAzip|DNAzip: DNA sequence compression using a reference genome]] \\
+Software: <a class="urlextern" href="http://cbcl.ics.uci.edu/SSEA/" rel="nofollow" title="http://cbcl.ics.uci.edu/SSEA/">SNP Set Enrichment Analysis (SSEA)</a></p>
-[[http://www.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.cell.com/cell-metabolism/abstract/S1550-4131(11)00092-1" rel="nofollow" title="http://www.cell.com/cell-metabolism/abstract/S1550-4131(11)00092-1">Genome-wide Positioning of SREBP-2 in Hepatic Chromatin Predicts a Novel Role in Autophagy </a><br />
+Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF<br />
+<em>Cell Metabolism</em>, 13:367-75, 2011<br />
+<a class="urlextern" href="http://www.sciencedaily.com/releases/2011/04/110405122330.htm" rel="nofollow" title="http://www.sciencedaily.com/releases/2011/04/110405122330.htm">Science Daily coverage</a></p>
-[[http://www.ics.uci.edu/~xhx/publications/wu_motif_2008.pdf|Discovering regulatory motifs in the Plasmodium genome using comparative genomics ]] \\
+<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 />
-Wu J, Sieglaff DH, Gervin J, and Xie X  \\
+Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X<br />
-//Bioinformatics // 24:1843-9 (2008) \\
+<em>J Comput Biol.</em>, 2011<br />
-[[http://www.ics.uci.edu/~xhx/project/mdos/|MDOS software]]: A method for Motif Discovery using Orthologous Sequences (alignment independent). \\
+Software: <a class="urlextern" href="http://sourceforge.net/projects/arem" rel="nofollow" title="http://sourceforge.net/projects/arem">AREM</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://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 />
-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, Chen Y, and Xie X<br />
-//PLoS Genetics//4(10):e1000242 (2008)
+AI &amp; STATS , 2011</p>
-==== 2007 ====
+</div>
-[[http://www.pnas.org/content/104/49/19428|Distinguishing protein-coding and noncoding genes in the human genome ]] \\
+<h3>2010</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://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 />
-//Nature//449:913-918 (2007)
+Ye G, Cai J, and Xie X<br />
+arXiv:1012.0975v1, 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.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 />
-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. \\
+Ye G-B and Xie X<br />
-//Nature// 448:553-60 (2007)
+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/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/btq414" rel="nofollow" title="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq414">Interactive and fuzzy search: a dynamic way to explore MEDLINE </a><br />
-Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES. \\
+Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J<br />
-//Proc Natl Acad Sci USA//104:7145-7150 (2007)  \\
+<em>Bioinformatics</em>, 26(18):2321-2327, 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://ipubmed.ics.uci.edu/" rel="nofollow" title="http://ipubmed.ics.uci.edu/">iPubMed Search</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://arxiv.org/abs/1006.5060" rel="nofollow" title="http://arxiv.org/abs/1006.5060">Variable selection and dimension reduction via sparse gradients</a><br />
-Mikkelsen TS, Wakefield MJ, et al.  \\
+Ye G-B and Xie X<br />
-//Nature// 447:167-177 (2007)
+arXiv:1006.5060v2, 2010</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://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 />
-Xie X, Kamal M, 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//103:11659-11664 (2006)  \\
+<em>NeuroImage</em> 53:839-847, 2010</p>
-[[http://www.broad.mit.edu/seq/pubs/xie_pnas2006/|Supplementary website]] [[http://www.pnas.org/cgi/content/full/0604768103/DC1|Supporting Information]] [[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=1881|News story]]
-==== 2006 or before ====
+<p><a class="urlextern" href="http://www.biomedcentral.com/1752-0509/4/99" rel="nofollow" title="http://www.biomedcentral.com/1752-0509/4/99">Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent</a><br />
+Wang Y, Christley S, Mjolsness E, and Xie X<br />
+<em>BMC Systems Biology</em>, 4:99 doi:10.1186/1752-0509-4-99, 2010</p>
-[[http://www.ics.uci.edu/~xhx/publications/mer121.PNAS2006.pdf|A large family of ancient repeat elements in the human genome is under strong selection]] \\
+<p><a class="urlextern" href="http://www.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 />
-Kamal M, Xie X, and Lander ES.  \\
+Xie X<br />
-//Proc Natl Acad Sci USA//103:2740-2745 (2006)  \\
+<em>Bulletin of Mathematical Biology</em>, DOI: 10.1007/s11538-010-9534-3, 2010</p>
-[[http://www.broad.mit.edu/seq/pubs/xie_pnas2006/html/clusteredAMCNE/AMCNE1.similarAMCNE.html|Supplementary website]] [[http://www.pnas.org/cgi/content/full/0511238103/DC1|Supporting Information]] \\
-[[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=381|News story]]
-[[http://download.cell.com/pdfs/0092-8674/PIIS0092867406003801.pdf|A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells]] \\
+<p><a class="urlextern" href="http://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 />
-Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al.  \\
+Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and Osborne TF<br />
-//Cell// 125:315-26 (2006)
+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://genomebiology.com/2006/7/9/R85|Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression ]] \\
+<p><a class="urlextern" href="http://www.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 J and Xie X \\
+Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X<br />
-//Genome Biology//7(9):R85 (2006) (Highly accessed)  \\
+<em>BMC Genomics</em> 11:208, 2010<br />
-[[http://www.broad.mit.edu/personal/xhx/projects/NRSE|Supplementary website]]
+<a class="urlextern" href="http://www.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html" rel="nofollow" title="http://www.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html">Supplementary Information</a><br />
+<a class="urlextern" href="http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html" rel="nofollow" title="http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html">Fusarium Comparative Database</a></p>
-[[http://www.nature.com/ng/journal/v38/n5/pdf/ng1776.pdf|Systematic identification of human mitochondrial disease genes through integrative genomics ]] \\
+<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 />
-Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK. \\
+Ma L-J, et al.<br />
-//Nature Genetics//, 38:576-82 (2006)
+<em>Nature</em> 464:367-373, 2010<br />
+<a class="urlextern" href="http://www.broadinstitute.org/news/1439" rel="nofollow" title="http://www.broadinstitute.org/news/1439">The chromosomal secrets of a plant pathogen</a><br />
+<a class="urlextern" href="http://www.genomeweb.com//node/936293?hq_e=el&amp;hq_m=655129&amp;hq_l=3&amp;hq_v=dfec329446" rel="nofollow" title="http://www.genomeweb.com//node/936293?hq_e=el&amp;hq_m=655129&amp;hq_l=3&amp;hq_v=dfec329446">Comparative genomics reveals horizontal gene transfer in pathogenic fungus</a><br />
+<a class="urlextern" href="http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html" rel="nofollow" title="http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html">Fusarium Comparative Database</a></p>
+</div>
-[[http://www.ics.uci.edu/~xhx/publications/xie05_motif_paper.pdf|Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals ]] \\
+<h3>2009</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 C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R.  \\
+<p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/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 />
-//Genome Resesarch//, 16:1056-72 (2006)
+Christley S, Nie Q and Xie X<br />
+<em>PLoS ONE</em> 4(8): e6799. doi:10.1371/journal.pone.0006799 (2009)</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.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 />
-Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M.  \\
+Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF<br />
-//Cell// 125:187-99 (2006)
+<em>Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0904246106 (2009)</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://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 />
-Werfel J, Xie X and Seung HS.  \\
+Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X<br />
-//Neural Computation//, 2005;17:2699-718
+<em>Bioinformatics</em>25:i54-i62 (2009)<br />
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/siphy_suppinfo.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/siphy_suppinfo.pdf">Supplementary Methods</a><br />
+<a class="urlextern" href="http://www.broadinstitute.org/genome_bio/siphy/" rel="nofollow" title="http://www.broadinstitute.org/genome_bio/siphy/">SiPhy (SIte-specific PHYlogenetic analysis) Java software package</a></p>
-[[http://www.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.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 />
-Lindblad-Toh K, Wade CM, et al.  \\
+Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA<br />
-//Nature// 438:803-19 2005
+<em>Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0813264106 (2009)</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://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 />
-Giallourakis C, Henson C, Reich M, Xie X, and Mootha VK.  \\
+Fraser H and Xie X<br />
-//Annu. Rev. Genomics Hum. Genet.// 2005:22:381-406.
+<em>Genome Research</em> doi:10.1101/gr.083477.108 (2009)<br />
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/PTV_GR2009.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/PTV_GR2009.pdf">PDF</a></p>
-[[http://www.ics.uci.edu/~xhx/publications/PhysRevE_69_041909.pdf|Learning in neural networks by reinforcement of irregular spiking. ]] \\
+<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 and Seung HS.  \\
+Xie X, Rigor P, and Baldi P<br />
-//Phys Rev E//, 2004;69:041909
+<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/mootha_pgc1a.pdf|Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle]] \\
+<p><a class="urlextern" href="http://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 />
-Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al.  \\
+Christley S, Lu Y, Li C, and Xie X<br />
-//Proc Natl Acad Sci USA//, 2004;101:6570-5
+<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/PhysRevE_66_041902.pdf|The double-ring network modeling of the head-direction system]] \\
+<h3>2008</h3>
-Xie X, Hahnloser RH, and Seung HS.  \\
-//Physical Review E//, 2002;66:041902
-[[http://www.ics.uci.edu/~xhx/publications/PhysRevE_65_051904.pdf|Nonlinear dynamics of direction-selective recurrent neural media]] \\
+<div class="level3">
-Xie X and Giese MA.  \\
+<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 />
-//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]] \\
+Wu J, Sieglaff DH, Gervin J, and Xie X<br />
-Giese MA and Xie X  \\
+<em>Bioinformatics </em> 24:1843-9 (2008)<br />
-//Neurocomputing// 2002;44:417-422
+<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/lwta.pdf|Learning winner-take-all competition between groups of neurons in lateral inhibitory networks ]] \\
+<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 />
-Xie X, Hahnloser HR, and Seung HS.  \\
+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 />
-//Advances in Neural Information Processing Systems//2001;13:350-356
+<em>PLoS </em><em>Genetics</em>4(10):e1000242 (2008)</p>
+</div>
-[[http://www.ics.uci.edu/~xhx/publications/nc_vel_tuning.pdf|Generating velocity tuning by asymmetric recurrent connections]] \\
+<h3>2007</h3>
-Xie X and Giese MA.  \\
-//Advances in Neural Information Processing Systems//2002;13:325-332
-[[http://www.ics.uci.edu/~xhx/publications/gwta_nc.pdf|Selectively Grouping Neurons in Recurrent Networks of Lateral Inhibition]] \\
+<div class="level3">
-Xie X, Hahnloser RH, and Seung HS.  \\
+<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 />
-//Neural Computation//, 2002;14:2627-2646
+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/chl_nc.pdf|Equivalence of backpropagation and contrastive Hebbian learning in a layered network]] \\
+<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 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 />
-//Neural Computation//, 2003;16:441-454
+<em>Nature</em>449:913-918 (2007)</p>
-[[http://www.ics.uci.edu/~xhx/publications/network_pop.pdf|Threshold behavior of maximum likelihood method in population decoding]] \\
+<p><a class="urlextern" href="http://www.nature.com/nature/journal/v448/n7153/abs/nature06008.html" rel="nofollow" title="http://www.nature.com/nature/journal/v448/n7153/abs/nature06008.html">Geome-wide maps of chromatin state in pluripotent and lineage-committed cells </a><br />
-Xie X \\
+Mikkelsen TS, 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 />
-//Network: Comput. Neural Syst.// 2002;13:447-456
+<em>Nature</em> 448:553-60 (2007)</p>
+<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, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES.<br />
+<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>
+<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 />
+Mikkelsen TS, Wakefield MJ, et al.<br />
+<em>Nature</em> 447:167-177 (2007)</p>
+<p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/Xie_AMCNE.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/Xie_AMCNE.pdf">A family of conserved noncoding elements derived from an ancient transposable element</a><br />
+Xie X, Kamal M, and Lander ES.<br />
+<em>Proc Natl Acad Sci </em><em>USA</em>103:11659-11664 (2006)<br />
+<a class="urlextern" href="http://www.broad.mit.edu/seq/pubs/xie_pnas2006/" rel="nofollow" title="http://www.broad.mit.edu/seq/pubs/xie_pnas2006/">Supplementary website</a> <a class="urlextern" href="http://www.pnas.org/cgi/content/full/0604768103/DC1" rel="nofollow" title="http://www.pnas.org/cgi/content/full/0604768103/DC1">Supporting Information</a> <a class="urlextern" href="http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=1881" rel="nofollow" title="http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=1881">News story</a></p>
+</div>
+<h3>2006 or before</h3>
+<div class="level3">
+<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 />
+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>
-[[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