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--- publications [2017/05/16 11:24]
xhx [2016]
+++ publications [2018/08/15 23:25] (current)
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+<html>
+<h2>Publications</h2>
+<div class="level2">&nbsp;</div>
-===== Publications =====
+<h3>2018</h3>
-==== 2017 ====
+<div class="level3">
-[[http://biorxiv.org/content/early/2017/01/10/099358 | HLA class I binding prediction via convolutional neural networks]]\\
+<p><a class="urlextern" href="https://arxiv.org/abs/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 />
-Vang YS and Xie X\\
+Zhu W, Vang YS, Huang Y, Xie X</p>
-Bioinformatics, 2017
-[[https://www.ncbi.nlm.nih.gov/pubmed/28325473 | Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program]]\\
+<p>Sequential Embedding Induced Nonparametric Text Clustering<br />
-Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW\\
+Duan T, Lou Q, Xie X</p>
-Dev Cell. 27;40(6):595-607.e4, 2017
-==== 2016 ====
-[[https://arxiv.org/abs/1612.05970|Adversarial Deep Structural Networks for Mammographic Mass Segmentation]]\\
+<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 />
-Wentao Zhu, Xiaohui Xie\\
+Vang S, Chen Z, Xie X<br />
-arXiv:1612.05970
+th International Conference on Image Analysis and Recognition, 2018</p>
-[[https://www.ncbi.nlm.nih.gov/pubmed/27418388|Developmentally regulated long non-coding RNAs in Xenopus tropicalis]]\\
+<p><a class="urlextern" href="https://arxiv.org/abs/1801.07853" rel="nofollow" title="https://arxiv.org/abs/1801.07853">Structed Triplets Learning with Pos-tag Guided Attention for Visual Question Answering</a><br />
-Forouzmand et al. \\
+IEEE Winter Conf. on Applications of Computer Vision 2018</p>
-Developmental Biology, (16)30120-8 2016
-[[http://bioinformatics.oxfordjournals.org/content/early/2016/02/11/bioinformatics.btw074.short?rss=1|Gene expression inference with deep learning]]\\
+<p><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 />
-Chen Y, Li Y, Narayan R, Subramanian A, and Xie X\\
+IEEE Winter Conf. on Applications of Computer Vision 2018</p>
-Bioinformatics, 2016
-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 />
-Nucleic Acids Research, 2016
+IEEE International Symposium on Biomedical Imaging</p>
-[[http://rnajournal.cshlp.org/content/early/2016/04/19/rna.055681.115.abstract|Poly(A) code analyses reveal key determinants for tissue-specific mRNA alternative polyadenylation]]\\
+<p>Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural Networks<br />
-Weng L, Li Y, Xie X, and Shi Y\\
+H Tang, D Kim, X Xie<br />
-RNA, 2016
+IEEE International Symposium on Biomedical Imaging</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>Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.<br />
-Zhu W, et al.\\
+Zhu Y, Wang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.<br />
-AAAI Conference on Artificial Intelligence, 2016
+Mol Cell. 2018 Jan 4;69(1):62-74.e4.</p>
+</div>
-==== 2015 ====
+<h3>2017</h3>
-Hobbes3: Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings\\
+<div class="level3">
-Kim J, Chen L, 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 />
-nd IEEE International Conference on Data Engineering - ICDE 2016
+W Zhu, C Liu, W Fan, X Xie<br />
+arXiv preprint arXiv:1709.05538</p>
-[[http://biorxiv.org/content/early/2015/12/20/032821|DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences]]\\
+<p><a class="urlextern" href="https://www.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 />
-Quang D and Xie X
+D Quang, X Xie<br />
+bioRxiv, 151274</p>
-[[http://www.ncbi.nlm.nih.gov/pubmed/25338716|DANN: a deep learning approach for annotating the pathogenicity of genetic variants]]\\
+<p><a class="urlextern" href="https://arxiv.org/abs/1612.05968" rel="nofollow" title="https://arxiv.org/abs/1612.05968">Deep Multi-instance Networks with Sparse Label Assignment for Whole Mammogram Classification</a><br />
-Quang D, Chen Y and Xie X\\
+Wentao Zhu, Qi Lou, Yeeleng Scott Vang, Xiaohui Xie<br />
-Bioinformatics, 31(5):761-3, 2015
+arXiv:1612.05968<br />
+<a class="urlextern" href="http://www.miccai2017.org/" rel="nofollow" title="http://www.miccai2017.org/">MICCAI, 2017</a></p>
-[[http://www.biomedcentral.com/1471-2164/16/S2/S1|MixClone: a mixture model for inferring tumor subclonal populations]]\\
+<p>Understanding sequence conservation with deep learning<br />
-Li Y and Xie X\\
+Li Y, Quang D, and Xie X<br />
-BMC Genomics, 2015
+ACM BCB, 2017</p>
+<p><a class="urlextern" href="http://biorxiv.org/content/early/2017/01/10/099358" rel="nofollow" title="http://biorxiv.org/content/early/2017/01/10/099358">HLA class I binding prediction via convolutional neural networks</a><br />
+Vang YS and Xie X<br />
+Bioinformatics, 2017</p>
-[[http://www.ics.uci.edu/~xhx/publications/ImagingGenetics.pdf |Identifying unanticipated genes and mechanisms in serious mental illness]]\\
+<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 />
-Potkin SG, van Erp TGM, Ling S, Macciardi F, 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 />
-Neuroimaging genetics : principles and practices, 2015
+Dev Cell. 27;40(6):595-607.e4, 2017</p>
+</div>
-==== 2014 ====
+<h3>2016</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/1612.05970" rel="nofollow" title="https://arxiv.org/abs/1612.05970">Adversarial Deep Structural Networks for Mammographic Mass Segmentation</a><br />
-International Journal on Document Analysis and Recognition, 2014\\
+Wentao Zhu, Xiaohui Xie<br />
-[[http://www.ics.uci.edu/~xhx/publications/HHR.pdf| preprint]]
+arXiv:1612.05970</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.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 />
-Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K\\
+Forouzmand et al.<br />
-Development, 2014
+Developmental Biology, (16)30120-8 2016</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="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 />
-Li Y and Xie X\\
+Chen Y, Li Y, Narayan R, Subramanian A, and Xie X<br />
-Bioinformatics, 2014
+Bioinformatics, 2016</p>
-[[http://bioinformatics.oxfordjournals.org/content/early/2014/02/14/bioinformatics.btu093.abstract|EXTREME: An Online EM Algorithm for Motif Discovery]]\\
+<p>DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences<br />
-Quang D and Xie X\\
+Quang D and Xie X<br />
-Bioinformatics, 2014
+Nucleic Acids Research, 2016</p>
-[[http://www.biomedcentral.com/1471-2105/15/42|Improving Read Mapping Using Additional Prefix Grams]]\\
+<p><a class="urlextern" href="http://rnajournal.cshlp.org/content/early/2016/04/19/rna.055681.115.abstract" rel="nofollow" title="http://rnajournal.cshlp.org/content/early/2016/04/19/rna.055681.115.abstract">Poly(A) code analyses reveal key determinants for tissue-specific mRNA alternative polyadenylation</a><br />
-Kim J, Li C and Xie X\\
+Weng L, Li Y, Xie X, and Shi Y<br />
-BMC Bioinformatics, 2014, 15(1):42
+RNA, 2016</p>
-[[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092317|Integrative ChIP-seq/Microarray Analysis Identifies a CTNNB1 Target Signature Enriched in Intestinal Stem Cells and Colon Cancer]]\\
+<p><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 />
-Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X\\
+Zhu W, et al.<br />
-PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317
+AAAI Conference on Artificial Intelligence, 2016</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>2015</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>Hobbes3: Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings<br />
-EMBO J. 2014 Mar 4.
+Kim J, Chen L, and Xie X<br />
-==== 2013 ====
+nd IEEE International Conference on Data Engineering - ICDE 2016</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="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 />
-Ye G, Tang M, Nie Q and Xie X\\
+Quang D and Xie X</p>
-//PLOS ONE//, 2013
-[[http://www.hindawi.com/journals/cmmm/2013/873595/|A gradient boosting algorithm for survival analysis via direct optimization of concordance index]] \\
+<p><a class="urlextern" href="http://www.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 />
-Chen Y, Jia Z, Mercola D and Xie X\\
+Quang D, Chen Y and Xie X<br />
-//Comput Math Methods Med.//, 2013
+Bioinformatics, 31(5):761-3, 2015</p>
-[[http://onlinelibrary.wiley.com/doi/10.1002/dvg.22719/abstract|Biallelic genome modification in F0 Xenopus tropicalis embryos using the CRISPR/Cas system]]\\
+<p><a class="urlextern" href="http://www.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 />
-Blitz I, Biesinger J, Xie X, and Cho K\\
+Li Y and Xie X<br />
-//Genesis//, 2013.
+BMC Genomics, 2015</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://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, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y\\
+Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X<br />
-//RNA//, 2013
+Neuroimaging genetics : principles and practices, 2015</p>
+</div>
-[[http://arxiv.org/abs/1305.0855|Inference in Kingman's Coalescent with Particle Markov Chain Monte Carlo Method]] \\
+<h3>2014</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><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 />
-//BMC Bioinformatics// 2013, 14(S5):S4, 2013 \\
+Kim I and Xie X<br />
-[[http://www.biomedcentral.com/content/supplementary/1471-2105-14-s5-s4-s1.pdf|Supplemental Information]]
+International Journal on Document Analysis and Recognition, 2014<br />
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/HHR.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/HHR.pdf">preprint</a></p>
-[[http://www.biomedcentral.com/1471-2105/14/S5/S11|A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues]] \\
+<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 />
-Li Y and Xie X \\
+Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K<br />
-//BMC Bioinformatics// 2013, 14(Suppl 5):S11, 2013
+Development, 2014</p>
-[[http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6544889|Efficient direct search on compressed genomic data]] \\
+<p><a class="urlextern" href="http://bioinformatics.oxfordjournals.org/content/early/2014/04/21/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 />
-Yang X, Wang B, Li C, Wang J, and Xie X \\
+Li Y and Xie X<br />
-//IEEE International Conference on Data Engineering (ICDE)//, 2013
+Bioinformatics, 2014</p>
-==== 2012 ====
-[[http://www.springerlink.com/content/4l2m27p3867xj584/|Learning sparse gradients for variable selection and dimension reduction]] \\
+<p><a class="urlextern" href="http://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 />
-Ye G and Xie X \\
+Quang D and Xie X<br />
-Machine Learning Journal, 87(3):303-355, 2012 \\
+Bioinformatics, 2014</p>
-[[http://www.ics.uci.edu/~xhx/publications/SGL.pdf|Preprint]]
-[[http://www.ncbi.nlm.nih.gov/pubmed/23112178|Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation]] \\
+<p><a class="urlextern" href="http://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 />
-Yao C, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y \\
+Kim J, Li C and Xie X<br />
-PNAS, 109(46):18773-8, 2012
+BMC Bioinformatics, 2014, 15(1):42</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.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 />
-Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF \\
+Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X<br />
-BMC Genomics, 2012
+PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317</p>
-[[http://www.ncbi.nlm.nih.gov/pubmed/22199254|Hobbes: optimized gram-based methods for efficient read alignment]] \\
+<p><a class="urlextern" href="http://www.biomedcentral.com/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 />
-Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X  \\
+Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q<br />
-Nucleic Acids Research, 40(6):e41,  2012 \\
+BMC Systems Biology 2014, 8:3</p>
-Software: [[http://hobbes.ics.uci.edu/|Hobbes]]
-==== 2011 ====
+<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 />
+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 />
+EMBO J. 2014 Mar 4.</p>
+</div>
-[[http://arxiv.org/pdf/1110.3076v1|Efficient latent variable graphical model selection via split Bregman method]] \\
+<h3>2013</h3>
-Ye G, Wang Y, Chen Y, and Xie X \\
-arXiv:1110.3076v1, 2011
-[[http://www.ncbi.nlm.nih.gov/pubmed/22208852|MotifMap: integrative genome-wide maps of regulatory motif sites for model species. ]] \\
+<div class="level3">
-Daily K, Patel VR, Rigor P, Xie X, Baldi P. \\
+<p><a class="urlextern" href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082146" rel="nofollow" title="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082146">Low-Rank Regularization for Learning Gene Expression Programs</a><br />
-BMC Bioinformatics, 2011
+Ye G, Tang M, Nie Q and Xie X<br />
+<em>PLOS ONE</em>, 2013</p>
-[[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10530.html|A high-resolution map of human evolutionary constraint using 29 mammals]] \\
+<p><a class="urlextern" href="http://www.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 />
-Lindblad-Toh, Barber, Zuk, Lin, et al. \\
+Chen Y, Jia Z, Mercola D and Xie X<br />
-Nature, 2011
+<em>Comput Math Methods Med.</em>, 2013</p>
-[[http://www.biomedcentral.com/1471-2105/12/99|SNP-based pathway enrichment analysis for genome-wide association studies]] \\
+<p><a class="urlextern" href="http://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 />
-Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X \\
+Blitz I, Biesinger J, Xie X, and Cho K<br />
-BMC Bioinformatics, 2011  \\
+<em>Genesis</em>, 2013.</p>
-Software: [[http://cbcl.ics.uci.edu/SSEA/|SNP Set Enrichment Analysis (SSEA)]]
-[[http://www.cell.com/cell-metabolism/abstract/S1550-4131(11)00092-1|Genome-wide Positioning of SREBP-2 in Hepatic Chromatin Predicts a Novel Role in Autophagy ]] \\
+<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 />
-Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF \\
+Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y<br />
-//Cell Metabolism//, 13:367-75, 2011  \\
+<em>RNA</em>, 2013</p>
-[[http://www.sciencedaily.com/releases/2011/04/110405122330.htm|Science Daily coverage]]
-[[http://www.ics.uci.edu/~xhx/publications/arem_recomb.pdf|AREM: aligning short reads from ChIP-sequencing by expectation maximization]] \\
+<p><a class="urlextern" href="http://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 />
-Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X \\
+Chen Y and Xie X<br />
-//J Comput Biol.//, 2011 \\
+<em>arXiv</em>, 2013</p>
-Software: [[http://sourceforge.net/projects/arem|AREM]]
-[[http://jmlr.csail.mit.edu/proceedings/papers/v15/ye11a/ye11a.pdf|Efficient variable selection in support vector machines via the alternating direction method of multipliers ]] \\
+<p><a class="urlextern" href="http://www.biomedcentral.com/content/pdf/1471-2105-14-S5-S4.pdf" rel="nofollow" title="http://www.biomedcentral.com/content/pdf/1471-2105-14-S5-S4.pdf">Discovering and Mapping Chromatin States Using a Tree Hidden Markov Model</a><br />
-Ye G, Chen Y, and Xie X \\
+Biesinger J, Wang Y, and Xie X<br />
-AI & STATS , 2011
+<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>
-==== 2010 ====
+<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 />
+Li Y and Xie X<br />
+<em>BMC Bioinformatics</em> 2013, 14(Suppl 5):S11, 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://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 />
-Ye G, Cai J, and Xie X \\
+Yang X, Wang B, Li C, Wang J, and Xie X<br />
-arXiv:1012.0975v1, 2010
+<em>IEEE International Conference on Data Engineering (ICDE)</em>, 2013</p>
+</div>
-[[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]] \\
+<h3>2012</h3>
-Ye G-B and Xie X \\
-Computational Statistics and Data Analysis, doi:10.1016/j.csda.2010.10.021, 2010  \\
-[[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 ]] \\
+<div class="level3">
-Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J \\
+<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 />
-//Bioinformatics//, 26(18):2321-2327, 2010  \\
+Ye G and Xie X<br />
-[[http://ipubmed.ics.uci.edu/|iPubMed Search]]
+Machine Learning Journal, 87(3):303-355, 2012<br />
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/SGL.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/SGL.pdf">Preprint</a></p>
-[[http://arxiv.org/abs/1006.5060|Variable selection and dimension reduction via sparse gradients]] \\
+<p><a class="urlextern" href="http://www.ncbi.nlm.nih.gov/pubmed/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 />
-Ye G-B and Xie X \\
+Yao C, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y<br />
-arXiv:1006.5060v2, 2010
+PNAS, 109(46):18773-8, 2012</p>
-[[http://nl.sitestat.com/elsevier/elsevier-com/s?sciencedirect&ns_type=clickout&ns_url=http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=IRSSCONTENT&_method=citationSearch&_piikey=S1053811910008803&_version=1&md5=09cea6babd4cf018d170933615df4755|Identifying gene regulatory networks in Schizophrenia]] \\
+<p><a class="urlextern" href="http://www.ncbi.nlm.nih.gov/pubmed/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 />
-Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X \\
+Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF<br />
-//NeuroImage// 53:839-847, 2010
+BMC Genomics, 2012</p>
-[[http://www.biomedcentral.com/1752-0509/4/99|Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent]] \\
+<p><a class="urlextern" href="http://www.ncbi.nlm.nih.gov/pubmed/22199254" rel="nofollow" title="http://www.ncbi.nlm.nih.gov/pubmed/22199254">Hobbes: optimized gram-based methods for efficient read alignment</a><br />
-Wang Y, Christley S, Mjolsness E, and Xie X \\
+Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X<br />
-//BMC Systems Biology//, 4:99 doi:10.1186/1752-0509-4-99, 2010
+Nucleic Acids Research, 40(6):e41, 2012<br />
+Software: <a class="urlextern" href="http://hobbes.ics.uci.edu/" rel="nofollow" title="http://hobbes.ics.uci.edu/">Hobbes</a></p>
+</div>
-[[http://www.springerlink.com/content/428v02087m218878/fulltext.pdf|Site-frequency Spectrum of Linked Sites]] \\
+<h3>2011</h3>
-Xie X   \\
-//Bulletin of Mathematical Biology//, DOI: 10.1007/s11538-010-9534-3, 2010
-[[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]] \\
+<div class="level3">
-Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and Osborne TF \\
+<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 />
-Nucleic Acids Research, doi:10.1093/nar/gkq397, 2010 \\
+Ye G, Wang Y, Chen Y, and Xie X<br />
-[[http://cbcl.ics.uci.edu/public_data/FXR/|Online Supplementary Materials]]
+arXiv:1110.3076v1, 2011</p>
-[[http://www.biomedcentral.com/1471-2164/11/208/abstract|Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes]] \\
+<p><a class="urlextern" href="http://www.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 />
-Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X  \\
+Daily K, Patel VR, Rigor P, Xie X, Baldi P.<br />
-//BMC Genomics// 11:208, 2010 \\
+BMC Bioinformatics, 2011</p>
-[[http://www.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html|Supplementary Information]] \\
-[[http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html|Fusarium Comparative Database]]
-[[http://www.nature.com/nature/journal/v464/n7287/abs/nature08850.html|Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium oxysporum]] \\
+<p><a class="urlextern" href="http://www.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 />
-Ma L-J, et al.  \\
+Lindblad-Toh, Barber, Zuk, Lin, et al.<br />
-//Nature// 464:367-373, 2010 \\
+Nature, 2011</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.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 />
+Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X<br />
+BMC Bioinformatics, 2011<br />
+Software: <a class="urlextern" href="http://cbcl.ics.uci.edu/SSEA/" rel="nofollow" title="http://cbcl.ics.uci.edu/SSEA/">SNP Set Enrichment Analysis (SSEA)</a></p>
-[[http://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.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, Nie Q and Xie X \\
+Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF<br />
-//PLoS ONE// 4(8): e6799. doi:10.1371/journal.pone.0006799 (2009)
+<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.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.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 />
-Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF \\
+Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X<br />
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0904246106 (2009)
+<em>J Comput Biol.</em>, 2011<br />
+Software: <a class="urlextern" href="http://sourceforge.net/projects/arem" rel="nofollow" title="http://sourceforge.net/projects/arem">AREM</a></p>
-[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/12/i54|Identifying novel constrained elements by exploiting biased substitution patterns]] \\
+<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 />
-Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X \\
+Ye G, Chen Y, and Xie X<br />
-//Bioinformatics//25:i54-i62 (2009)  \\
+AI &amp; STATS , 2011</p>
-[[http://www.ics.uci.edu/~xhx/publications/siphy_suppinfo.pdf|Supplementary Methods]] \\
+</div>
-[[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]] \\
+<h3>2010</h3>
-Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA  \\
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0813264106 (2009)
-[[http://genome.cshlp.org/content/19/4/567.long|Common polymorphic transcript variation in human disease]] \\
+<div class="level3">
-Fraser H and Xie X  \\
+<p><a class="urlextern" href="http://arxiv4.library.cornell.edu/abs/1012.0975" rel="nofollow" title="http://arxiv4.library.cornell.edu/abs/1012.0975">Split Bregman method for sparse inverse covariance estimation with matrix iteration acceleration</a><br />
-//Genome Research// doi:10.1101/gr.083477.108 (2009) \\
+Ye G, Cai J, and Xie X<br />
-[[http://www.ics.uci.edu/~xhx/publications/PTV_GR2009.pdf|PDF]]
+arXiv:1012.0975v1, 2010</p>
-[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/167|MotifMap: a human genome-wide map of candidate regulatory motif sites ]] \\
+<p><a class="urlextern" href="http://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 />
-Xie X, Rigor P, and Baldi P  \\
+Ye G-B and Xie X<br />
-//Bioinformatics// 25: 167-174 (2009) \\
+Computational Statistics and Data Analysis, doi:10.1016/j.csda.2010.10.021, 2010<br />
-[[http://www.ics.uci.edu/~xhx/publications/MotifMap_Supp_Info.pdf|Supplementary Methods]] \\
+<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 />
-[[http://motifmap.ics.uci.edu/|MotifMap Server]]
+Daily K, Rigor P, Christley S, Xie X and Baldi P<br />
+<em>BMC Bioinformatics</em>,11:514, 2010</p>
-[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/274|Human genomes as email attachments ]] \\
+<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 />
-Christley S, Lu Y, Li C, and Xie X  \\
+Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J<br />
-//Bioinformatics // 25: 274-275 (2009) \\
+<em>Bioinformatics</em>, 26(18):2321-2327, 2010<br />
-[[http://www.ics.uci.edu/~xhx/project/DNAzip|DNAzip: DNA sequence compression using a reference genome]] \\
+<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/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://arxiv.org/abs/1006.5060" rel="nofollow" title="http://arxiv.org/abs/1006.5060">Variable selection and dimension reduction via sparse gradients</a><br />
+Ye G-B and Xie X<br />
+arXiv:1006.5060v2, 2010</p>
-[[http://www.ics.uci.edu/~xhx/publications/wu_motif_2008.pdf|Discovering regulatory motifs in the Plasmodium genome using comparative genomics ]] \\
+<p><a class="urlextern" href="http://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 />
-Wu J, Sieglaff DH, Gervin J, and Xie X  \\
+Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X<br />
-//Bioinformatics // 24:1843-9 (2008) \\
+<em>NeuroImage</em> 53:839-847, 2010</p>
-[[http://www.ics.uci.edu/~xhx/project/mdos/|MDOS software]]: A method for Motif Discovery using Orthologous Sequences (alignment independent). \\
-[[http://www.ics.uci.edu/~xhx/publications/wu_motif_2008_suppinfo.pdf|Supplementary Information on the MDOS algorithm]]
-[[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2567431&blobtype=pdf|Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains ]] \\
+<p><a class="urlextern" href="http://www.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 />
-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  \\
+Wang Y, Christley S, Mjolsness E, and Xie X<br />
-//PLoS Genetics//4(10):e1000242 (2008)
+<em>BMC Systems Biology</em>, 4:99 doi:10.1186/1752-0509-4-99, 2010</p>
-==== 2007 ====
-[[http://www.pnas.org/content/104/49/19428|Distinguishing protein-coding and noncoding genes in the human genome ]] \\
+<p><a class="urlextern" href="http://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 />
-Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, and Lander ES. \\
+Xie X<br />
-//Proc Natl Acad Sci USA//104(49):19428-33 (2007)
+<em>Bulletin of Mathematical Biology</em>, DOI: 10.1007/s11538-010-9534-3, 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://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 />
-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  \\
+Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and Osborne TF<br />
-//Nature//449:913-918 (2007)
+Nucleic Acids Research, doi:10.1093/nar/gkq397, 2010<br />
+<a class="urlextern" href="http://cbcl.ics.uci.edu/public_data/FXR/" rel="nofollow" title="http://cbcl.ics.uci.edu/public_data/FXR/">Online Supplementary Materials</a></p>
-[[http://www.nature.com/nature/journal/v448/n7153/abs/nature06008.html|Geome-wide maps of chromatin state in pluripotent and lineage-committed 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 />
-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. \\
+Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X<br />
-//Nature// 448:553-60 (2007)
+<em>BMC Genomics</em> 11:208, 2010<br />
+<a class="urlextern" href="http://www.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html" rel="nofollow" title="http://www.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html">Supplementary Information</a><br />
+<a class="urlextern" href="http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html" rel="nofollow" title="http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html">Fusarium Comparative Database</a></p>
-[[http://www.ics.uci.edu/~xhx/publications/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://www.nature.com/nature/journal/v464/n7287/abs/nature08850.html" rel="nofollow" title="http://www.nature.com/nature/journal/v464/n7287/abs/nature08850.html">Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium oxysporum</a><br />
-Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES. \\
+Ma L-J, et al.<br />
-//Proc Natl Acad Sci USA//104:7145-7150 (2007)  \\
+<em>Nature</em> 464:367-373, 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://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/nature/journal/v447/n7141/pdf/nature05805.pdf|Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences ]] \\
+<h3>2009</h3>
-Mikkelsen TS, Wakefield MJ, et al.  \\
-//Nature// 447:167-177 (2007)
-[[http://www.ics.uci.edu/~xhx/publications/Xie_AMCNE.pdf|A family of conserved noncoding elements derived from an ancient transposable element]] \\
+<div class="level3">
-Xie X, Kamal M, and Lander ES. \\
+<p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf">Incorporating existing network information into gene network inference</a><br />
-//Proc Natl Acad Sci USA//103:11659-11664 (2006)  \\
+Christley S, Nie Q and Xie X<br />
-[[http://www.broad.mit.edu/seq/pubs/xie_pnas2006/|Supplementary website]] [[http://www.pnas.org/cgi/content/full/0604768103/DC1|Supporting Information]] [[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=1881|News story]]
+<em>PLoS ONE</em> 4(8): e6799. doi:10.1371/journal.pone.0006799 (2009)</p>
-==== 2006 or before ====
+<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 />
+Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF<br />
+<em>Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0904246106 (2009)</p>
-[[http://www.ics.uci.edu/~xhx/publications/mer121.PNAS2006.pdf|A large family of ancient repeat elements in the human genome is under strong selection]] \\
+<p><a class="urlextern" href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/12/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 />
-Kamal M, Xie X, and Lander ES.  \\
+Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X<br />
-//Proc Natl Acad Sci USA//103:2740-2745 (2006)  \\
+<em>Bioinformatics</em>25:i54-i62 (2009)<br />
-[[http://www.broad.mit.edu/seq/pubs/xie_pnas2006/html/clusteredAMCNE/AMCNE1.similarAMCNE.html|Supplementary website]] [[http://www.pnas.org/cgi/content/full/0511238103/DC1|Supporting Information]] \\
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/siphy_suppinfo.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/siphy_suppinfo.pdf">Supplementary Methods</a><br />
-[[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=381|News story]]
+<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://download.cell.com/pdfs/0092-8674/PIIS0092867406003801.pdf|A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells]] \\
+<p><a class="urlextern" href="http://www.pnas.org/content/early/2009/02/11/0813264106.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 />
-Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al.  \\
+Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA<br />
-//Cell// 125:315-26 (2006)
+<em>Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0813264106 (2009)</p>
-[[http://genomebiology.com/2006/7/9/R85|Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression ]] \\
+<p><a class="urlextern" href="http://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 />
-Wu J and Xie X \\
+Fraser H and Xie X<br />
-//Genome Biology//7(9):R85 (2006) (Highly accessed)  \\
+<em>Genome Research</em> doi:10.1101/gr.083477.108 (2009)<br />
-[[http://www.broad.mit.edu/personal/xhx/projects/NRSE|Supplementary website]]
+<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.nature.com/ng/journal/v38/n5/pdf/ng1776.pdf|Systematic identification of human mitochondrial disease genes through integrative genomics ]] \\
+<p><a class="urlextern" href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/167" 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 />
-Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK. \\
+Xie X, Rigor P, and Baldi P<br />
-//Nature Genetics//, 38:576-82 (2006)
+<em>Bioinformatics</em> 25: 167-174 (2009)<br />
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/MotifMap_Supp_Info.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/MotifMap_Supp_Info.pdf">Supplementary Methods</a><br />
+<a class="urlextern" href="http://motifmap.ics.uci.edu/" rel="nofollow" title="http://motifmap.ics.uci.edu/">MotifMap Server</a></p>
-[[http://www.ics.uci.edu/~xhx/publications/xie05_motif_paper.pdf|Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals ]] \\
+<p><a class="urlextern" href="http://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, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M.  \\
+Christley S, Lu Y, Li C, and Xie X<br />
-//Nature//2005; 434:338-45  \\
+<em>Bioinformatics </em> 25: 274-275 (2009)<br />
-[[http://www.broad.mit.edu/seq/HumanMotifs/|Supplementary Website]] [[http://www.ics.uci.edu/~xhx/publications/nature03441-s1.pdf|Supplementary Information]] [[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=134|News story]]
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/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.genome.org/cgi/reprint/gr.5285206v1|A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands]] \\
+<h3>2008</h3>
-Giallourakis C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R.  \\
-//Genome Resesarch//, 16:1056-72 (2006)
-[[http://download.cell.com/pdfs/0092-8674/PIIS0092867406003692.pdf|A Mammalian Organelle Map by Protein Correlation Profiling]] \\
+<div class="level3">
-Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M.  \\
+<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 />
-//Cell// 125:187-99 (2006)
+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/WerfelXieSeung2005.pdf|Learning curves for stochastic gradient descent in linear feedforward 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 />
-Werfel J, Xie X 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 />
-//Neural Computation//, 2005;17:2699-718
+<em>PLoS </em><em>Genetics</em>4(10):e1000242 (2008)</p>
+</div>
-[[http://www.nature.com/nature/journal/v438/n7069/pdf/nature04338.pdf|Genome sequence, comparative analysis and haplotype structure of the domestic dog ]] \\
+<h3>2007</h3>
-Lindblad-Toh K, Wade CM, et al.  \\
-//Nature// 438:803-19 2005
-[[http://www.ics.uci.edu/~xhx/publications/annurev.genom.6.080604.pdf|Disease gene discovery through integrative genomics. ]] \\
+<div class="level3">
-Giallourakis C, Henson C, Reich M, Xie X, and Mootha VK.  \\
+<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 />
-//Annu. Rev. Genomics Hum. Genet.// 2005:22:381-406.
+Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, and Lander ES.<br />
+<em>Proc Natl Acad Sci </em><em>USA</em>104(49):19428-33 (2007)</p>
-[[http://www.ics.uci.edu/~xhx/publications/PhysRevE_69_041909.pdf|Learning in neural networks by reinforcement of irregular spiking. ]] \\
+<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 />
-//Phys Rev E//, 2004;69:041909
+<em>Nature</em>449:913-918 (2007)</p>
-[[http://www.ics.uci.edu/~xhx/publications/mootha_pgc1a.pdf|Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle]] \\
+<p><a class="urlextern" href="http://www.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 />
-Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al.  \\
+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 />
-//Proc Natl Acad Sci USA//, 2004;101:6570-5
+<em>Nature</em> 448:553-60 (2007)</p>
-[[http://www.ics.uci.edu/~xhx/publications/PhysRevE_66_041902.pdf|The double-ring network modeling of the head-direction system]] \\
+<p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/insulators_pnas06.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/insulators_pnas06.pdf">Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites </a><br />
-Xie X, Hahnloser RH, and Seung HS.  \\
+Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES.<br />
-//Physical Review E//, 2002;66:041902
+<em>Proc Natl Acad Sci </em><em>USA</em>104:7145-7150 (2007)<br />
+<a class="urlextern" href="http://www.broad.mit.edu/personal/xhx/projects/CNEMOTIF/" rel="nofollow" title="http://www.broad.mit.edu/personal/xhx/projects/CNEMOTIF/">Supplementary website</a> <a class="urlextern" href="http://www.pnas.org/cgi/content/full/0701811104/DC1" rel="nofollow" title="http://www.pnas.org/cgi/content/full/0701811104/DC1">Supporting Information</a> <a class="urlextern" href="http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=3042" rel="nofollow" title="http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=3042">News story</a></p>
-[[http://www.ics.uci.edu/~xhx/publications/PhysRevE_65_051904.pdf|Nonlinear dynamics of direction-selective recurrent neural media]] \\
+<p><a class="urlextern" href="http://www.nature.com/nature/journal/v447/n7141/pdf/nature05805.pdf" rel="nofollow" title="http://www.nature.com/nature/journal/v447/n7141/pdf/nature05805.pdf">Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences </a><br />
-Xie X and Giese MA.  \\
+Mikkelsen TS, Wakefield MJ, et al.<br />
-//Physical Review E//, 2002;65:051904  [[http://www.ics.uci.edu/~xhx/publications/neurocomp_giese.pdf|Exact solution of the nonlinear dynamics of recurrent neural mechanisms for direction selectivity]] \\
+<em>Nature</em> 447:167-177 (2007)</p>
-Giese MA and Xie X  \\
-//Neurocomputing// 2002;44:417-422
-[[http://www.ics.uci.edu/~xhx/publications/lwta.pdf|Learning winner-take-all competition between groups of neurons in lateral inhibitory networks ]] \\
+<p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/Xie_AMCNE.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/Xie_AMCNE.pdf">A family of conserved noncoding elements derived from an ancient transposable element</a><br />
-Xie X, Hahnloser HR, and Seung HS.  \\
+Xie X, Kamal M, and Lander ES.<br />
-//Advances in Neural Information Processing Systems//2001;13:350-356
+<em>Proc Natl Acad Sci </em><em>USA</em>103:11659-11664 (2006)<br />
+<a class="urlextern" href="http://www.broad.mit.edu/seq/pubs/xie_pnas2006/" rel="nofollow" title="http://www.broad.mit.edu/seq/pubs/xie_pnas2006/">Supplementary website</a> <a class="urlextern" href="http://www.pnas.org/cgi/content/full/0604768103/DC1" rel="nofollow" title="http://www.pnas.org/cgi/content/full/0604768103/DC1">Supporting Information</a> <a class="urlextern" href="http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=1881" rel="nofollow" title="http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=1881">News story</a></p>
+</div>
-[[http://www.ics.uci.edu/~xhx/publications/nc_vel_tuning.pdf|Generating velocity tuning by asymmetric recurrent connections]] \\
+<h3>2006 or before</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.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 />
-//Neural Computation//, 2002;14:2627-2646
+Kamal M, Xie X, and Lander ES.<br />
+<em>Proc Natl Acad Sci </em><em>USA</em>103:2740-2745 (2006)<br />
+<a class="urlextern" href="http://www.broad.mit.edu/seq/pubs/xie_pnas2006/html/clusteredAMCNE/AMCNE1.similarAMCNE.html" rel="nofollow" title="http://www.broad.mit.edu/seq/pubs/xie_pnas2006/html/clusteredAMCNE/AMCNE1.similarAMCNE.html">Supplementary website</a> <a class="urlextern" href="http://www.pnas.org/cgi/content/full/0511238103/DC1" rel="nofollow" title="http://www.pnas.org/cgi/content/full/0511238103/DC1">Supporting Information</a><br />
+<a class="urlextern" href="http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=381" rel="nofollow" title="http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=381">News story</a></p>
-[[http://www.ics.uci.edu/~xhx/publications/chl_nc.pdf|Equivalence of backpropagation and contrastive Hebbian learning in a layered network]] \\
+<p><a class="urlextern" href="http://download.cell.com/pdfs/0092-8674/PIIS0092867406003801.pdf" rel="nofollow" title="http://download.cell.com/pdfs/0092-8674/PIIS0092867406003801.pdf">A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells</a><br />
-Xie X and Seung HS.  \\
+Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al.<br />
-//Neural Computation//, 2003;16:441-454
+<em>Cell</em> 125:315-26 (2006)</p>
-[[http://www.ics.uci.edu/~xhx/publications/network_pop.pdf|Threshold behavior of maximum likelihood method in population decoding]] \\
+<p><a class="urlextern" href="http://genomebiology.com/2006/7/9/R85" rel="nofollow" title="http://genomebiology.com/2006/7/9/R85">Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression </a><br />
-Xie X \\
+Wu J and Xie X<br />
-//Network: Comput. Neural Syst.// 2002;13:447-456
+<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