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--- publications [2016/06/01 10:09]
yil8 [2016]
+++ publications [2018/08/15 23:25] (current)
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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>
-DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences\\
+<p>Sequential Embedding Induced Nonparametric Text Clustering<br />
-Quang D and Xie X\\
+Duan T, Lou Q, Xie X</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/1802.00931" rel="nofollow" title="https://arxiv.org/abs/1802.00931">Deep Learning Framework for Multi-class Breast Cancer Histology Image Classification</a><br />
-Weng L, Li Y, Xie X, and Shi Y\\
+Vang S, Chen Z, Xie X<br />
-RNA, 2016
+th International Conference on Image Analysis and Recognition, 2018</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/1801.07853" rel="nofollow" title="https://arxiv.org/abs/1801.07853">Structed Triplets Learning with Pos-tag Guided Attention for Visual Question Answering</a><br />
-Zhu W, et al.\\
+IEEE Winter Conf. on Applications of Computer Vision 2018</p>
-AAAI Conference on Artificial Intelligence, 2016
-==== 2015 ====
-Hobbes3: Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings\\
+<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 />
-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>Adversarial Deep Structured Nets for Mass Segmentation from Mammograms<br />
-Quang D and Xie X
+W Zhu, X Xiang, T Tran, GD Hager, X Xie<br />
+IEEE International Symposium on Biomedical Imaging</p>
-[[http://www.ncbi.nlm.nih.gov/pubmed/25338716|DANN: a deep learning approach for annotating the pathogenicity of genetic variants]]\\
+<p>Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural Networks<br />
-Quang D, Chen Y and Xie X\\
+H Tang, D Kim, 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>Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.<br />
-Li Y and Xie X\\
+Zhu Y, Wang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.<br />
-BMC Genomics, 2015
+Mol Cell. 2018 Jan 4;69(1):62-74.e4.</p>
+</div>
-Identifying unanticipated genes and mechanisms in serious mental illness: GWAS based imaging genetics strategies\\
+<h3>2017</h3>
-Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X\\
-Neuroimaging genetics : principles and practices, 2015
-==== 2014 ====
+<div class="level3">
+<p><a class="urlextern" href="https://arxiv.org/abs/1709.05538" rel="nofollow" title="https://arxiv.org/abs/1709.05538">DeepLung: 3D Deep Convolutional Nets for Automated Pulmonary Nodule Detection and Classification</a><br />
+W Zhu, C Liu, W Fan, X Xie<br />
+arXiv preprint arXiv:1709.05538</p>
-[[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.biorxiv.org/content/early/2017/06/28/151274" rel="nofollow" title="https://www.biorxiv.org/content/early/2017/06/28/151274">FactorNet: a deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data</a><br />
-Kim I and Xie X\\
+D Quang, X Xie<br />
-International Journal on Document Analysis and Recognition, 2014\\
+bioRxiv, 151274</p>
-[[http://www.ics.uci.edu/~xhx/publications/HHR.pdf| preprint]]
-[[http://www.ncbi.nlm.nih.gov/pubmed/25359723|Genome-wide view of TGFbeta/Foxh1 regulation of the early mesendoderm]] program\\
+<p><a class="urlextern" href="https://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 />
-Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K\\
+Wentao Zhu, Qi Lou, Yeeleng Scott Vang, Xiaohui Xie<br />
-Development, 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/2014/04/21/bioinformatics.btu174|Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity]]\\
+<p>Understanding sequence conservation with deep learning<br />
-Li Y and Xie X\\
+Li Y, Quang D, and Xie X<br />
-Bioinformatics, 2014
+ACM BCB, 2017</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="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 />
-Quang D and Xie X\\
+Vang YS and Xie X<br />
-Bioinformatics, 2014
+Bioinformatics, 2017</p>
-[[http://www.biomedcentral.com/1471-2105/15/42|Improving Read Mapping Using Additional Prefix Grams]]\\
+<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 J, Li C 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 />
-BMC Bioinformatics, 2014, 15(1):42
+Dev Cell. 27;40(6):595-607.e4, 2017</p>
+</div>
-[[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092317|Integrative ChIP-seq/Microarray Analysis Identifies a CTNNB1 Target Signature Enriched in Intestinal Stem Cells and Colon Cancer]]\\
+<h3>2016</h3>
-Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X\\
-PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317
-[[http://www.biomedcentral.com/1752-0509/8/3/abstract|Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns]] \\
+<div class="level3">
-Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q\\
+<p><a class="urlextern" href="https://arxiv.org/abs/1612.05970" rel="nofollow" title="https://arxiv.org/abs/1612.05970">Adversarial Deep Structural Networks for Mammographic Mass Segmentation</a><br />
-BMC Systems Biology 2014, 8:3
+Wentao Zhu, Xiaohui Xie<br />
+arXiv:1612.05970</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.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 />
-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\\
+Forouzmand et al.<br />
-EMBO J. 2014 Mar 4.
+Developmental Biology, (16)30120-8 2016</p>
-==== 2013 ====
-[[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082146|Low-Rank Regularization for Learning Gene Expression Programs]] \\
+<p><a class="urlextern" href="http://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 />
-Ye G, Tang M, Nie Q and Xie X\\
+Chen Y, Li Y, Narayan R, Subramanian A, and Xie X<br />
-//PLOS ONE//, 2013
+Bioinformatics, 2016</p>
-[[http://www.hindawi.com/journals/cmmm/2013/873595/|A gradient boosting algorithm for survival analysis via direct optimization of concordance index]] \\
+<p>DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences<br />
-Chen Y, Jia Z, Mercola D and Xie X\\
+Quang D and Xie X<br />
-//Comput Math Methods Med.//, 2013
+Nucleic Acids Research, 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://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 />
-Blitz I, Biesinger J, Xie X, and Cho K\\
+Weng L, Li Y, Xie X, and Shi Y<br />
-//Genesis//, 2013.
+RNA, 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="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 />
-Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y\\
+Zhu W, et al.<br />
-//RNA//, 2013
+AAAI Conference on Artificial Intelligence, 2016</p>
+</div>
-[[http://arxiv.org/abs/1305.0855|Inference in Kingman's Coalescent with Particle Markov Chain Monte Carlo Method]] \\
+<h3>2015</h3>
-Chen Y and Xie X \\
-//arXiv//, 2013
-[[http://www.biomedcentral.com/content/pdf/1471-2105-14-S5-S4.pdf|Discovering and Mapping Chromatin States Using a Tree Hidden Markov Model]] \\
+<div class="level3">
-Biesinger J, Wang Y, and Xie X \\
+<p>Hobbes3: Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings<br />
-//BMC Bioinformatics// 2013, 14(S5):S4, 2013 \\
+Kim J, Chen L, and Xie X<br />
-[[http://www.biomedcentral.com/content/supplementary/1471-2105-14-s5-s4-s1.pdf|Supplemental Information]]
+nd IEEE International Conference on Data Engineering - ICDE 2016</p>
-[[http://www.biomedcentral.com/1471-2105/14/S5/S11|A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues]] \\
+<p><a class="urlextern" href="http://biorxiv.org/content/early/2015/12/20/032821" rel="nofollow" title="http://biorxiv.org/content/early/2015/12/20/032821">DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences</a><br />
-Li Y and Xie X \\
+Quang D and Xie X</p>
-//BMC Bioinformatics// 2013, 14(Suppl 5):S11, 2013
-[[http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6544889|Efficient direct search on compressed genomic data]] \\
+<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 />
-Yang X, Wang B, Li C, Wang J, and Xie X \\
+Quang D, Chen Y and Xie X<br />
-//IEEE International Conference on Data Engineering (ICDE)//, 2013
+Bioinformatics, 31(5):761-3, 2015</p>
-==== 2012 ====
-[[http://www.springerlink.com/content/4l2m27p3867xj584/|Learning sparse gradients for variable selection and dimension reduction]] \\
+<p><a class="urlextern" href="http://www.biomedcentral.com/1471-2164/16/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 />
-Ye G and Xie X \\
+Li Y and Xie X<br />
-Machine Learning Journal, 87(3):303-355, 2012 \\
+BMC Genomics, 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.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 />
-Yao C, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y \\
+Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X<br />
-PNAS, 109(46):18773-8, 2012
+Neuroimaging genetics : principles and practices, 2015</p>
+</div>
-[[http://www.ncbi.nlm.nih.gov/pubmed/22296850|Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR]] \\
+<h3>2014</h3>
-Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF \\
-BMC Genomics, 2012
-[[http://www.ncbi.nlm.nih.gov/pubmed/22199254|Hobbes: optimized gram-based methods for efficient read alignment]] \\
+<div class="level3">
-Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X  \\
+<p><a class="urlextern" href="http://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 />
-Nucleic Acids Research, 40(6):e41,  2012 \\
+Kim I and Xie X<br />
-Software: [[http://hobbes.ics.uci.edu/|Hobbes]]
+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>
-==== 2011 ====
+<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 />
+Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K<br />
+Development, 2014</p>
-[[http://arxiv.org/pdf/1110.3076v1|Efficient latent variable graphical model selection via split Bregman method]] \\
+<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 />
-Ye G, Wang Y, Chen Y, and Xie X \\
+Li Y and Xie X<br />
-arXiv:1110.3076v1, 2011
+Bioinformatics, 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/2014/02/14/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 />
-Daily K, Patel VR, Rigor P, Xie X, Baldi P. \\
+Quang D 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://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 />
-Lindblad-Toh, Barber, Zuk, Lin, et al. \\
+Kim J, Li C and Xie X<br />
-Nature, 2011
+BMC Bioinformatics, 2014, 15(1):42</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.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 />
-Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X \\
+Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X<br />
-BMC Bioinformatics, 2011  \\
+PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317</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.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 />
-Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF \\
+Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q<br />
-//Cell Metabolism//, 13:367-75, 2011  \\
+BMC Systems Biology 2014, 8:3</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://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 />
-Newkirk D, Biesinger, J, Chon A, Yokomori K, 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 />
-//J Comput Biol.//, 2011 \\
+EMBO J. 2014 Mar 4.</p>
-Software: [[http://sourceforge.net/projects/arem|AREM]]
+</div>
-[[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 ]] \\
+<h3>2013</h3>
-Ye G, Chen Y, and Xie X \\
-AI & STATS , 2011
-==== 2010 ====
+<div class="level3">
+<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 />
+Ye G, Tang M, Nie Q and Xie X<br />
+<em>PLOS ONE</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.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, Cai J, and Xie X \\
+Chen Y, Jia Z, Mercola D and Xie X<br />
-arXiv:1012.0975v1, 2010
+<em>Comput Math Methods Med.</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://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 />
-Ye G-B and Xie X \\
+Blitz I, Biesinger J, Xie X, and Cho K<br />
-Computational Statistics and Data Analysis, doi:10.1016/j.csda.2010.10.021, 2010  \\
+<em>Genesis</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://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 />
-Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J \\
+Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y<br />
-//Bioinformatics//, 26(18):2321-2327, 2010  \\
+<em>RNA</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://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 />
-Ye G-B and Xie X \\
+Chen Y and Xie X<br />
-arXiv:1006.5060v2, 2010
+<em>arXiv</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://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 />
-Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X \\
+Biesinger J, Wang Y, and Xie X<br />
-//NeuroImage// 53:839-847, 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.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/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 />
-Wang Y, Christley S, Mjolsness E, and Xie X \\
+Li Y and Xie X<br />
-//BMC Systems Biology//, 4:99 doi:10.1186/1752-0509-4-99, 2010
+<em>BMC Bioinformatics</em> 2013, 14(Suppl 5):S11, 2013</p>
-[[http://www.springerlink.com/content/428v02087m218878/fulltext.pdf|Site-frequency Spectrum of Linked Sites]] \\
+<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 />
-Xie X   \\
+Yang X, Wang B, Li C, Wang J, and Xie X<br />
-//Bulletin of Mathematical Biology//, DOI: 10.1007/s11538-010-9534-3, 2010
+<em>IEEE International Conference on Data Engineering (ICDE)</em>, 2013</p>
+</div>
-[[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]] \\
+<h3>2012</h3>
-Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and Osborne TF \\
-Nucleic Acids Research, doi:10.1093/nar/gkq397, 2010 \\
-[[http://cbcl.ics.uci.edu/public_data/FXR/|Online Supplementary Materials]]
-[[http://www.biomedcentral.com/1471-2164/11/208/abstract|Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes]] \\
+<div class="level3">
-Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X  \\
+<p><a class="urlextern" href="http://www.springerlink.com/content/4l2m27p3867xj584/" rel="nofollow" title="http://www.springerlink.com/content/4l2m27p3867xj584/">Learning sparse gradients for variable selection and dimension reduction</a><br />
-//BMC Genomics// 11:208, 2010 \\
+Ye G and Xie X<br />
-[[http://www.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html|Supplementary Information]] \\
+Machine Learning Journal, 87(3):303-355, 2012<br />
-[[http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html|Fusarium Comparative Database]]
+<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.nature.com/nature/journal/v464/n7287/abs/nature08850.html|Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium oxysporum]] \\
+<p><a class="urlextern" href="http://www.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 />
-Ma L-J, et al.  \\
+Yao C, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y<br />
-//Nature// 464:367-373, 2010 \\
+PNAS, 109(46):18773-8, 2012</p>
-[[http://www.broadinstitute.org/news/1439|The chromosomal secrets of a plant pathogen]] \\
-[[http://www.genomeweb.com//node/936293?hq_e=el&hq_m=655129&hq_l=3&hq_v=dfec329446|Comparative genomics reveals horizontal gene transfer in pathogenic fungus]] \\
-[[http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html|Fusarium Comparative Database]]
-==== 2009 ====
+<p><a class="urlextern" href="http://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 />
+Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF<br />
+BMC Genomics, 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/22199254" rel="nofollow" title="http://www.ncbi.nlm.nih.gov/pubmed/22199254">Hobbes: optimized gram-based methods for efficient read alignment</a><br />
-Christley S, Nie Q and Xie X \\
+Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X<br />
-//PLoS ONE// 4(8): e6799. doi:10.1371/journal.pone.0006799 (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://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]] \\
+<h3>2011</h3>
-Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF \\
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0904246106 (2009)
-[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/12/i54|Identifying novel constrained elements by exploiting biased substitution patterns]] \\
+<div class="level3">
-Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X \\
+<p><a class="urlextern" href="http://arxiv.org/pdf/1110.3076v1" rel="nofollow" title="http://arxiv.org/pdf/1110.3076v1">Efficient latent variable graphical model selection via split Bregman method</a><br />
-//Bioinformatics//25:i54-i62 (2009)  \\
+Ye G, Wang Y, Chen Y, and Xie X<br />
-[[http://www.ics.uci.edu/~xhx/publications/siphy_suppinfo.pdf|Supplementary Methods]] \\
+arXiv:1110.3076v1, 2011</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.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 />
-Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA  \\
+Daily K, Patel VR, Rigor P, Xie X, Baldi P.<br />
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0813264106 (2009)
+BMC Bioinformatics, 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.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 />
-Fraser H and Xie X  \\
+Lindblad-Toh, Barber, Zuk, Lin, et al.<br />
-//Genome Research// doi:10.1101/gr.083477.108 (2009) \\
+Nature, 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.biomedcentral.com/1471-2105/12/99" rel="nofollow" title="http://www.biomedcentral.com/1471-2105/12/99">SNP-based pathway enrichment analysis for genome-wide association studies</a><br />
-Xie X, Rigor P, and Baldi P  \\
+Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X<br />
-//Bioinformatics// 25: 167-174 (2009) \\
+BMC Bioinformatics, 2011<br />
-[[http://www.ics.uci.edu/~xhx/publications/MotifMap_Supp_Info.pdf|Supplementary Methods]] \\
+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://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.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 />
-Christley S, Lu Y, Li C, and Xie X  \\
+Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF<br />
-//Bioinformatics // 25: 274-275 (2009) \\
+<em>Cell Metabolism</em>, 13:367-75, 2011<br />
-[[http://www.ics.uci.edu/~xhx/project/DNAzip|DNAzip: DNA sequence compression using a reference genome]] \\
+<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/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.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 />
+Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X<br />
+<em>J Comput Biol.</em>, 2011<br />
+Software: <a class="urlextern" href="http://sourceforge.net/projects/arem" rel="nofollow" title="http://sourceforge.net/projects/arem">AREM</a></p>
-[[http://www.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://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 />
-Wu J, Sieglaff DH, Gervin J, and Xie X  \\
+Ye G, Chen Y, and Xie X<br />
-//Bioinformatics // 24:1843-9 (2008) \\
+AI &amp; STATS , 2011</p>
-[[http://www.ics.uci.edu/~xhx/project/mdos/|MDOS software]]: A method for Motif Discovery using Orthologous Sequences (alignment independent). \\
+</div>
-[[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 ]] \\
+<h3>2010</h3>
-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  \\
-//PLoS Genetics//4(10):e1000242 (2008)
-==== 2007 ====
-[[http://www.pnas.org/content/104/49/19428|Distinguishing protein-coding and noncoding genes in the human genome ]] \\
+<div class="level3">
-Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, and Lander ES. \\
+<p><a class="urlextern" href="http://arxiv4.library.cornell.edu/abs/1012.0975" rel="nofollow" title="http://arxiv4.library.cornell.edu/abs/1012.0975">Split Bregman method for sparse inverse covariance estimation with matrix iteration acceleration</a><br />
-//Proc Natl Acad Sci USA//104(49):19428-33 (2007)
+Ye G, Cai J, and Xie X<br />
+arXiv:1012.0975v1, 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.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 />
-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  \\
+Ye G-B and Xie X<br />
-//Nature//449:913-918 (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.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://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 />
-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. \\
+Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J<br />
-//Nature// 448:553-60 (2007)
+<em>Bioinformatics</em>, 26(18):2321-2327, 2010<br />
+<a class="urlextern" href="http://ipubmed.ics.uci.edu/" rel="nofollow" title="http://ipubmed.ics.uci.edu/">iPubMed Search</a></p>
-[[http://www.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://arxiv.org/abs/1006.5060" rel="nofollow" title="http://arxiv.org/abs/1006.5060">Variable selection and dimension reduction via sparse gradients</a><br />
-Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES. \\
+Ye G-B and Xie X<br />
-//Proc Natl Acad Sci USA//104:7145-7150 (2007)  \\
+arXiv:1006.5060v2, 2010</p>
-[[http://www.broad.mit.edu/personal/xhx/projects/CNEMOTIF/|Supplementary website]] [[http://www.pnas.org/cgi/content/full/0701811104/DC1|Supporting Information]] [[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=3042|News story]]
-[[http://www.nature.com/nature/journal/v447/n7141/pdf/nature05805.pdf|Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences ]] \\
+<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 />
-Mikkelsen TS, Wakefield MJ, et al.  \\
+Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X<br />
-//Nature// 447:167-177 (2007)
+<em>NeuroImage</em> 53:839-847, 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://www.biomedcentral.com/1752-0509/4/99" rel="nofollow" title="http://www.biomedcentral.com/1752-0509/4/99">Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent</a><br />
-Xie X, Kamal M, and Lander ES. \\
+Wang Y, Christley S, Mjolsness E, and Xie X<br />
-//Proc Natl Acad Sci USA//103:11659-11664 (2006)  \\
+<em>BMC Systems Biology</em>, 4:99 doi:10.1186/1752-0509-4-99, 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.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 />
+Xie X<br />
+<em>Bulletin of Mathematical Biology</em>, DOI: 10.1007/s11538-010-9534-3, 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://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 />
-Kamal M, Xie X, 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//103:2740-2745 (2006)  \\
+Nucleic Acids Research, doi:10.1093/nar/gkq397, 2010<br />
-[[http://www.broad.mit.edu/seq/pubs/xie_pnas2006/html/clusteredAMCNE/AMCNE1.similarAMCNE.html|Supplementary website]] [[http://www.pnas.org/cgi/content/full/0511238103/DC1|Supporting Information]] \\
+<a class="urlextern" href="http://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.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.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 />
-Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al.  \\
+Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X<br />
-//Cell// 125:315-26 (2006)
+<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://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.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 />
-Wu J and Xie X \\
+Ma L-J, et al.<br />
-//Genome Biology//7(9):R85 (2006) (Highly accessed)  \\
+<em>Nature</em> 464:367-373, 2010<br />
-[[http://www.broad.mit.edu/personal/xhx/projects/NRSE|Supplementary website]]
+<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.nature.com/ng/journal/v38/n5/pdf/ng1776.pdf|Systematic identification of human mitochondrial disease genes through integrative genomics ]] \\
+<h3>2009</h3>
-Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK. \\
-//Nature Genetics//, 38:576-82 (2006)
-[[http://www.ics.uci.edu/~xhx/publications/xie05_motif_paper.pdf|Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals ]] \\
+<div class="level3">
-Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M.  \\
+<p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf">Incorporating existing network information into gene network inference</a><br />
-//Nature//2005; 434:338-45  \\
+Christley S, Nie Q and Xie X<br />
-[[http://www.broad.mit.edu/seq/HumanMotifs/|Supplementary Website]] [[http://www.ics.uci.edu/~xhx/publications/nature03441-s1.pdf|Supplementary Information]] [[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=134|News story]]
+<em>PLoS ONE</em> 4(8): e6799. doi:10.1371/journal.pone.0006799 (2009)</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://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 />
-Giallourakis C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R.  \\
+Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF<br />
-//Genome Resesarch//, 16:1056-72 (2006)
+<em>Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0904246106 (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://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 />
-Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M.  \\
+Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X<br />
-//Cell// 125:187-99 (2006)
+<em>Bioinformatics</em>25:i54-i62 (2009)<br />
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/siphy_suppinfo.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/siphy_suppinfo.pdf">Supplementary Methods</a><br />
+<a class="urlextern" href="http://www.broadinstitute.org/genome_bio/siphy/" rel="nofollow" title="http://www.broadinstitute.org/genome_bio/siphy/">SiPhy (SIte-specific PHYlogenetic analysis) Java software package</a></p>
-[[http://www.ics.uci.edu/~xhx/publications/WerfelXieSeung2005.pdf|Learning curves for stochastic gradient descent in linear feedforward networks. ]] \\
+<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 />
-Werfel J, Xie X and Seung HS.  \\
+Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA<br />
-//Neural Computation//, 2005;17:2699-718
+<em>Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0813264106 (2009)</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://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 />
-Lindblad-Toh K, Wade CM, et al.  \\
+Fraser H and Xie X<br />
-//Nature// 438:803-19 2005
+<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/annurev.genom.6.080604.pdf|Disease gene discovery through integrative genomics. ]] \\
+<p><a class="urlextern" href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/167" rel="nofollow" title="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/167">MotifMap: a human genome-wide map of candidate regulatory motif sites </a><br />
-Giallourakis C, Henson C, Reich M, Xie X, and Mootha VK.  \\
+Xie X, Rigor P, and Baldi P<br />
-//Annu. Rev. Genomics Hum. Genet.// 2005:22:381-406.
+<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/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/25/2/274" rel="nofollow" title="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/274">Human genomes as email attachments </a><br />
-Xie X and Seung HS.  \\
+Christley S, Lu Y, Li C, and Xie X<br />
-//Phys Rev E//, 2004;69:041909
+<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/mootha_pgc1a.pdf|Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle]] \\
+<h3>2008</h3>
-Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al.  \\
-//Proc Natl Acad Sci USA//, 2004;101:6570-5
-[[http://www.ics.uci.edu/~xhx/publications/PhysRevE_66_041902.pdf|The double-ring network modeling of the head-direction system]] \\
+<div class="level3">
-Xie X, Hahnloser RH, and Seung HS.  \\
+<p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/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;66:041902
+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/PhysRevE_65_051904.pdf|Nonlinear dynamics of direction-selective recurrent neural media]] \\
+<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 and Giese MA.  \\
+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 />
-//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>PLoS </em><em>Genetics</em>4(10):e1000242 (2008)</p>
-Giese MA and Xie X  \\
+</div>
-//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 ]] \\
+<h3>2007</h3>
-Xie X, Hahnloser HR, and Seung HS.  \\
-//Advances in Neural Information Processing Systems//2001;13:350-356
-[[http://www.ics.uci.edu/~xhx/publications/nc_vel_tuning.pdf|Generating velocity tuning by asymmetric recurrent connections]] \\
+<div class="level3">
-Xie X and Giese MA.  \\
+<p><a class="urlextern" href="http://www.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 />
-//Advances in Neural Information Processing Systems//2002;13:325-332
+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/gwta_nc.pdf|Selectively Grouping Neurons in Recurrent Networks of Lateral Inhibition]] \\
+<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 />
-//Neural Computation//, 2002;14:2627-2646
+<em>Nature</em>449:913-918 (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/v448/n7153/abs/nature06008.html" rel="nofollow" title="http://www.nature.com/nature/journal/v448/n7153/abs/nature06008.html">Geome-wide maps of chromatin state in pluripotent and lineage-committed cells </a><br />
-Xie X and Seung HS.  \\
+Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O&#39;Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE.<br />
-//Neural Computation//, 2003;16:441-454
+<em>Nature</em> 448:553-60 (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.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 \\
+Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES.<br />
-//Network: Comput. Neural Syst.// 2002;13:447-456
+<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