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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
-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 ====
+<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 />
+IEEE Winter Conf. on Applications of Computer Vision 2018</p>
-Hobbes3: Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings\\
+<p>Adversarial Deep Structured Nets for Mass Segmentation from Mammograms<br />
-Kim J, Chen L, and Xie X\\
+W Zhu, X Xiang, T Tran, GD Hager, X Xie<br />
-nd IEEE International Conference on Data Engineering - ICDE 2016
+IEEE International Symposium on Biomedical Imaging</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>Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural Networks<br />
-Quang D and Xie X
+H Tang, D Kim, 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>Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.<br />
-Quang D, Chen 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 />
-Bioinformatics, 31(5):761-3, 2015
+Mol Cell. 2018 Jan 4;69(1):62-74.e4.</p>
+</div>
-[[http://www.biomedcentral.com/1471-2164/16/S2/S1|MixClone: a mixture model for inferring tumor subclonal populations]]\\
+<h3>2017</h3>
-Li Y and Xie X\\
-BMC Genomics, 2015
-Identifying unanticipated genes and mechanisms in serious mental illness: GWAS based imaging genetics strategies\\
+<div class="level3">
-Potkin SG, van Erp TGM, Ling S, Macciardi F, 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 />
-Neuroimaging genetics : principles and practices, 2015
+W Zhu, C Liu, W Fan, X Xie<br />
+arXiv preprint arXiv:1709.05538</p>
-==== 2014 ====
+<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 />
+D Quang, X Xie<br />
+bioRxiv, 151274</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://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 />
-Kim I and Xie X\\
+Wentao Zhu, Qi Lou, Yeeleng Scott Vang, Xiaohui Xie<br />
-International Journal on Document Analysis and Recognition, 2014\\
+arXiv:1612.05968<br />
-[[http://www.ics.uci.edu/~xhx/publications/HHR.pdf| preprint]]
+<a class="urlextern" href="http://www.miccai2017.org/" rel="nofollow" title="http://www.miccai2017.org/">MICCAI, 2017</a></p>
-[[http://www.ncbi.nlm.nih.gov/pubmed/25359723|Genome-wide view of TGFbeta/Foxh1 regulation of the early mesendoderm]] program\\
+<p>Understanding sequence conservation with deep learning<br />
-Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K\\
+Li Y, Quang D, and Xie X<br />
-Development, 2014
+ACM BCB, 2017</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://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 />
-Li Y and Xie X\\
+Vang YS and Xie X<br />
-Bioinformatics, 2014
+Bioinformatics, 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="https://www.ncbi.nlm.nih.gov/pubmed/28325473" rel="nofollow" title="https://www.ncbi.nlm.nih.gov/pubmed/28325473">Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program</a><br />
-Quang D and Xie X\\
+Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW<br />
-Bioinformatics, 2014
+Dev Cell. 27;40(6):595-607.e4, 2017</p>
+</div>
-[[http://www.biomedcentral.com/1471-2105/15/42|Improving Read Mapping Using Additional Prefix Grams]]\\
+<h3>2016</h3>
-Kim J, Li C and Xie X\\
-BMC Bioinformatics, 2014, 15(1):42
-[[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]]\\
+<div class="level3">
-Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai 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 />
-PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317
+Wentao Zhu, Xiaohui Xie<br />
+arXiv:1612.05970</p>
-[[http://www.biomedcentral.com/1752-0509/8/3/abstract|Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns]] \\
+<p><a class="urlextern" href="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 />
-Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q\\
+Forouzmand et al.<br />
-BMC Systems Biology 2014, 8:3
+Developmental Biology, (16)30120-8 2016</p>
-[[http://emboj.embopress.org/content/early/2014/03/04/embj.201386537|Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal]]\\
+<p><a class="urlextern" href="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 />
-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\\
+Chen Y, Li Y, Narayan R, Subramanian A, and Xie X<br />
-EMBO J. 2014 Mar 4.
+Bioinformatics, 2016</p>
-==== 2013 ====
-[[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082146|Low-Rank Regularization for Learning Gene Expression Programs]] \\
+<p>DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences<br />
-Ye G, Tang M, Nie Q and Xie X\\
+Quang D and Xie X<br />
-//PLOS ONE//, 2013
+Nucleic Acids Research, 2016</p>
-[[http://www.hindawi.com/journals/cmmm/2013/873595/|A gradient boosting algorithm for survival analysis via direct optimization of concordance index]] \\
+<p><a class="urlextern" href="http://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 />
-Chen Y, Jia Z, Mercola D and Xie X\\
+Weng L, Li Y, Xie X, and Shi Y<br />
-//Comput Math Methods Med.//, 2013
+RNA, 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="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 />
-Blitz I, Biesinger J, Xie X, and Cho K\\
+Zhu W, et al.<br />
-//Genesis//, 2013.
+AAAI Conference on Artificial Intelligence, 2016</p>
+</div>
-[[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]]\\
+<h3>2015</h3>
-Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y\\
-//RNA//, 2013
-[[http://arxiv.org/abs/1305.0855|Inference in Kingman's Coalescent with Particle Markov Chain Monte Carlo Method]] \\
+<div class="level3">
-Chen Y and Xie X \\
+<p>Hobbes3: Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings<br />
-//arXiv//, 2013
+Kim J, Chen L, and Xie X<br />
+nd IEEE International Conference on Data Engineering - ICDE 2016</p>
-[[http://www.biomedcentral.com/content/pdf/1471-2105-14-S5-S4.pdf|Discovering and Mapping Chromatin States Using a Tree Hidden Markov Model]] \\
+<p><a class="urlextern" href="http://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 />
-Biesinger J, Wang Y, and Xie X \\
+Quang D and Xie X</p>
-//BMC Bioinformatics// 2013, 14(S5):S4, 2013 \\
-[[http://www.biomedcentral.com/content/supplementary/1471-2105-14-s5-s4-s1.pdf|Supplemental Information]]
-[[http://www.biomedcentral.com/1471-2105/14/S5/S11|A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues]] \\
+<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 />
-Li Y and Xie X \\
+Quang D, Chen Y and Xie X<br />
-//BMC Bioinformatics// 2013, 14(Suppl 5):S11, 2013
+Bioinformatics, 31(5):761-3, 2015</p>
-[[http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6544889|Efficient direct search on compressed genomic data]] \\
+<p><a class="urlextern" href="http://www.biomedcentral.com/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 />
-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
+BMC Genomics, 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.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 />
-Ye G and Xie X \\
+Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X<br />
-Machine Learning Journal, 87(3):303-355, 2012 \\
+Neuroimaging genetics : principles and practices, 2015</p>
-[[http://www.ics.uci.edu/~xhx/publications/SGL.pdf|Preprint]]
+</div>
-[[http://www.ncbi.nlm.nih.gov/pubmed/23112178|Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation]] \\
+<h3>2014</h3>
-Yao C, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y \\
-PNAS, 109(46):18773-8, 2012
-[[http://www.ncbi.nlm.nih.gov/pubmed/22296850|Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR]] \\
+<div class="level3">
-Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF \\
+<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 Genomics, 2012
+Kim I and Xie X<br />
+International Journal on Document Analysis and Recognition, 2014<br />
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/HHR.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/HHR.pdf">preprint</a></p>
-[[http://www.ncbi.nlm.nih.gov/pubmed/22199254|Hobbes: optimized gram-based methods for efficient read alignment]] \\
+<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 />
-Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X  \\
+Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K<br />
-Nucleic Acids Research, 40(6):e41,  2012 \\
+Development, 2014</p>
-Software: [[http://hobbes.ics.uci.edu/|Hobbes]]
-==== 2011 ====
+<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 />
+Li Y and Xie X<br />
+Bioinformatics, 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/2014/02/14/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, Wang Y, Chen Y, and Xie X \\
+Quang D 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://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 />
-Daily K, Patel VR, Rigor P, Xie X, Baldi P. \\
+Kim J, Li C and Xie X<br />
-BMC Bioinformatics, 2011
+BMC Bioinformatics, 2014, 15(1):42</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.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 />
-Lindblad-Toh, Barber, Zuk, Lin, et al. \\
+Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X<br />
-Nature, 2011
+PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317</p>
-[[http://www.biomedcentral.com/1471-2105/12/99|SNP-based pathway enrichment analysis for genome-wide association studies]] \\
+<p><a class="urlextern" href="http://www.biomedcentral.com/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 />
-Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X \\
+Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q<br />
-BMC Bioinformatics, 2011  \\
+BMC Systems Biology 2014, 8:3</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://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 />
-Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF \\
+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 />
-//Cell Metabolism//, 13:367-75, 2011  \\
+EMBO J. 2014 Mar 4.</p>
-[[http://www.sciencedaily.com/releases/2011/04/110405122330.htm|Science Daily coverage]]
+</div>
-[[http://www.ics.uci.edu/~xhx/publications/arem_recomb.pdf|AREM: aligning short reads from ChIP-sequencing by expectation maximization]] \\
+<h3>2013</h3>
-Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X \\
-//J Comput Biol.//, 2011 \\
-Software: [[http://sourceforge.net/projects/arem|AREM]]
-[[http://jmlr.csail.mit.edu/proceedings/papers/v15/ye11a/ye11a.pdf|Efficient variable selection in support vector machines via the alternating direction method of multipliers ]] \\
+<div class="level3">
-Ye G, Chen Y, and Xie X \\
+<p><a class="urlextern" href="http://www.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 />
-AI & STATS , 2011
+Ye G, Tang M, Nie Q and Xie X<br />
+<em>PLOS ONE</em>, 2013</p>
-==== 2010 ====
+<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 />
+Chen Y, Jia Z, Mercola D and Xie X<br />
+<em>Comput Math Methods Med.</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://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, Cai J, and Xie X \\
+Blitz I, Biesinger J, Xie X, and Cho K<br />
-arXiv:1012.0975v1, 2010
+<em>Genesis</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://rnajournal.cshlp.org/content/early/2013/10/22/rna.042317.113.abstract" rel="nofollow" title="http://rnajournal.cshlp.org/content/early/2013/10/22/rna.042317.113.abstract">Overlapping and distinct functions of CstF64 and CstF64t in mammalian mRNA 3&acirc;&sup2; processing</a><br />
-Ye G-B and Xie X \\
+Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y<br />
-Computational Statistics and Data Analysis, doi:10.1016/j.csda.2010.10.021, 2010  \\
+<em>RNA</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://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 />
-Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J \\
+Chen Y and Xie X<br />
-//Bioinformatics//, 26(18):2321-2327, 2010  \\
+<em>arXiv</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://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-B and Xie X \\
+Biesinger J, Wang Y, and Xie X<br />
-arXiv:1006.5060v2, 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://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/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 />
-Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X \\
+Li Y and Xie X<br />
-//NeuroImage// 53:839-847, 2010
+<em>BMC Bioinformatics</em> 2013, 14(Suppl 5):S11, 2013</p>
-[[http://www.biomedcentral.com/1752-0509/4/99|Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent]] \\
+<p><a class="urlextern" href="http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&amp;arnumber=6544889" rel="nofollow" title="http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&amp;arnumber=6544889">Efficient direct search on compressed genomic data</a><br />
-Wang Y, Christley S, Mjolsness E, and Xie X \\
+Yang X, Wang B, Li C, Wang J, and Xie X<br />
-//BMC Systems Biology//, 4:99 doi:10.1186/1752-0509-4-99, 2010
+<em>IEEE International Conference on Data Engineering (ICDE)</em>, 2013</p>
+</div>
-[[http://www.springerlink.com/content/428v02087m218878/fulltext.pdf|Site-frequency Spectrum of Linked Sites]] \\
+<h3>2012</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://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 />
-Nucleic Acids Research, doi:10.1093/nar/gkq397, 2010 \\
+Ye G and Xie X<br />
-[[http://cbcl.ics.uci.edu/public_data/FXR/|Online Supplementary Materials]]
+Machine Learning Journal, 87(3):303-355, 2012<br />
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/SGL.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/SGL.pdf">Preprint</a></p>
-[[http://www.biomedcentral.com/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/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 />
-Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X  \\
+Yao C, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y<br />
-//BMC Genomics// 11:208, 2010 \\
+PNAS, 109(46):18773-8, 2012</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.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 />
-Ma L-J, et al.  \\
+Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF<br />
-//Nature// 464:367-373, 2010 \\
+BMC Genomics, 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/22199254" rel="nofollow" title="http://www.ncbi.nlm.nih.gov/pubmed/22199254">Hobbes: optimized gram-based methods for efficient read alignment</a><br />
+Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X<br />
+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.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf|Incorporating existing network information into gene network inference]] \\
+<h3>2011</h3>
-Christley S, Nie Q and Xie X \\
-//PLoS ONE// 4(8): e6799. doi:10.1371/journal.pone.0006799 (2009)
-[[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]] \\
+<div class="level3">
-Seo YK, Chong HK, Infante AM, Im S, 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 />
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0904246106 (2009)
+Ye G, Wang Y, Chen Y, and Xie X<br />
+arXiv:1110.3076v1, 2011</p>
-[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/12/i54|Identifying novel constrained elements by exploiting biased substitution patterns]] \\
+<p><a class="urlextern" href="http://www.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 />
-Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X \\
+Daily K, Patel VR, Rigor P, Xie X, Baldi P.<br />
-//Bioinformatics//25:i54-i62 (2009)  \\
+BMC Bioinformatics, 2011</p>
-[[http://www.ics.uci.edu/~xhx/publications/siphy_suppinfo.pdf|Supplementary Methods]] \\
-[[http://www.broadinstitute.org/genome_bio/siphy/|SiPhy (SIte-specific PHYlogenetic analysis) Java software package]]
-[[http://www.pnas.org/content/early/2009/02/11/0813264106.abstract|Comparative genomics allows the discovery of cis-regulatory elements in mosquitoes]] \\
+<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 />
-Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA  \\
+Lindblad-Toh, Barber, Zuk, Lin, et al.<br />
-//Proc Natl Acad Sci USA// doi:10.1073/pnas.0813264106 (2009)
+Nature, 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.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 />
-Fraser H and Xie X  \\
+Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X<br />
-//Genome Research// doi:10.1101/gr.083477.108 (2009) \\
+BMC Bioinformatics, 2011<br />
-[[http://www.ics.uci.edu/~xhx/publications/PTV_GR2009.pdf|PDF]]
+Software: <a class="urlextern" href="http://cbcl.ics.uci.edu/SSEA/" rel="nofollow" title="http://cbcl.ics.uci.edu/SSEA/">SNP Set Enrichment Analysis (SSEA)</a></p>
-[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/167|MotifMap: a human genome-wide map of candidate regulatory motif sites ]] \\
+<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 />
-Xie X, Rigor P, and Baldi P  \\
+Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF<br />
-//Bioinformatics// 25: 167-174 (2009) \\
+<em>Cell Metabolism</em>, 13:367-75, 2011<br />
-[[http://www.ics.uci.edu/~xhx/publications/MotifMap_Supp_Info.pdf|Supplementary Methods]] \\
+<a class="urlextern" href="http://www.sciencedaily.com/releases/2011/04/110405122330.htm" rel="nofollow" title="http://www.sciencedaily.com/releases/2011/04/110405122330.htm">Science Daily coverage</a></p>
-[[http://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.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 />
-Christley S, Lu Y, Li C, and Xie X  \\
+Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X<br />
-//Bioinformatics // 25: 274-275 (2009) \\
+<em>J Comput Biol.</em>, 2011<br />
-[[http://www.ics.uci.edu/~xhx/project/DNAzip|DNAzip: DNA sequence compression using a reference genome]] \\
+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/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://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 />
+Ye G, Chen Y, and Xie X<br />
+AI &amp; STATS , 2011</p>
+</div>
-[[http://www.ics.uci.edu/~xhx/publications/wu_motif_2008.pdf|Discovering regulatory motifs in the Plasmodium genome using comparative genomics ]] \\
+<h3>2010</h3>
-Wu J, Sieglaff DH, Gervin J, and Xie X  \\
-//Bioinformatics // 24:1843-9 (2008) \\
-[[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 ]] \\
+<div class="level3">
-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  \\
+<p><a class="urlextern" href="http://arxiv4.library.cornell.edu/abs/1012.0975" rel="nofollow" title="http://arxiv4.library.cornell.edu/abs/1012.0975">Split Bregman method for sparse inverse covariance estimation with matrix iteration acceleration</a><br />
-//PLoS Genetics//4(10):e1000242 (2008)
+Ye G, Cai J, and Xie X<br />
-==== 2007 ====
+arXiv:1012.0975v1, 2010</p>
-[[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.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 />
-Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, and Lander ES. \\
+Ye G-B and Xie X<br />
-//Proc Natl Acad Sci USA//104(49):19428-33 (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/v449/n7164/abs/nature06250.html|Genome-wide detection and characterization of positive selection in human populations ]] \\
+<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 />
-Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES and International HapMap Consortium  \\
+Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J<br />
-//Nature//449:913-918 (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.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://arxiv.org/abs/1006.5060" rel="nofollow" title="http://arxiv.org/abs/1006.5060">Variable selection and dimension reduction via sparse gradients</a><br />
-Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. \\
+Ye G-B and Xie X<br />
-//Nature// 448:553-60 (2007)
+arXiv:1006.5060v2, 2010</p>
-[[http://www.ics.uci.edu/~xhx/publications/insulators_pnas06.pdf|Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites ]] \\
+<p><a class="urlextern" href="http://nl.sitestat.com/elsevier/elsevier-com/s?sciencedirect&amp;ns_type=clickout&amp;ns_url=http://www.sciencedirect.com/science?_ob=GatewayURL&amp;_origin=IRSSCONTENT&amp;_method=citationSearch&amp;_piikey=S1053811910008803&amp;_version=1&amp;md5=09cea6babd4cf018d170933615df4755" rel="nofollow" title="http://nl.sitestat.com/elsevier/elsevier-com/s?sciencedirect&amp;ns_type=clickout&amp;ns_url=http://www.sciencedirect.com/science?_ob=GatewayURL&amp;_origin=IRSSCONTENT&amp;_method=citationSearch&amp;_piikey=S1053811910008803&amp;_version=1&amp;md5=09cea6babd4cf018d170933615df4755">Identifying gene regulatory networks in Schizophrenia</a><br />
-Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES. \\
+Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X<br />
-//Proc Natl Acad Sci USA//104:7145-7150 (2007)  \\
+<em>NeuroImage</em> 53:839-847, 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://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 />
-Mikkelsen TS, Wakefield MJ, et al.  \\
+Wang Y, Christley S, Mjolsness E, and Xie X<br />
-//Nature// 447:167-177 (2007)
+<em>BMC Systems Biology</em>, 4:99 doi:10.1186/1752-0509-4-99, 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.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, Kamal M, and Lander ES. \\
+Xie X<br />
-//Proc Natl Acad Sci USA//103:11659-11664 (2006)  \\
+<em>Bulletin of Mathematical Biology</em>, DOI: 10.1007/s11538-010-9534-3, 2010</p>
-[[http://www.broad.mit.edu/seq/pubs/xie_pnas2006/|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://nar.oxfordjournals.org/cgi/content/abstract/gkq397" rel="nofollow" title="http://nar.oxfordjournals.org/cgi/content/abstract/gkq397">Genome-Wide Interrogation of Hepatic FXR Reveals an Asymmetric IR-1 Motif and Synergy with LRH-1</a><br />
+Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and Osborne TF<br />
+Nucleic Acids Research, doi:10.1093/nar/gkq397, 2010<br />
+<a class="urlextern" href="http://cbcl.ics.uci.edu/public_data/FXR/" rel="nofollow" title="http://cbcl.ics.uci.edu/public_data/FXR/">Online Supplementary Materials</a></p>
-[[http://www.ics.uci.edu/~xhx/publications/mer121.PNAS2006.pdf|A large family of ancient repeat elements in the human genome is under strong selection]] \\
+<p><a class="urlextern" href="http://www.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 />
-Kamal M, Xie X, and Lander ES.  \\
+Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X<br />
-//Proc Natl Acad Sci USA//103:2740-2745 (2006)  \\
+<em>BMC Genomics</em> 11:208, 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://www.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html" rel="nofollow" title="http://www.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html">Supplementary Information</a><br />
-[[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=381|News story]]
+<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://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.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 />
-Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al.  \\
+Ma L-J, et al.<br />
-//Cell// 125:315-26 (2006)
+<em>Nature</em> 464:367-373, 2010<br />
+<a class="urlextern" href="http://www.broadinstitute.org/news/1439" rel="nofollow" title="http://www.broadinstitute.org/news/1439">The chromosomal secrets of a plant pathogen</a><br />
+<a class="urlextern" href="http://www.genomeweb.com//node/936293?hq_e=el&amp;hq_m=655129&amp;hq_l=3&amp;hq_v=dfec329446" rel="nofollow" title="http://www.genomeweb.com//node/936293?hq_e=el&amp;hq_m=655129&amp;hq_l=3&amp;hq_v=dfec329446">Comparative genomics reveals horizontal gene transfer in pathogenic fungus</a><br />
+<a class="urlextern" href="http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html" rel="nofollow" title="http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html">Fusarium Comparative Database</a></p>
+</div>
-[[http://genomebiology.com/2006/7/9/R85|Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression ]] \\
+<h3>2009</h3>
-Wu J and Xie X \\
-//Genome Biology//7(9):R85 (2006) (Highly accessed)  \\
-[[http://www.broad.mit.edu/personal/xhx/projects/NRSE|Supplementary website]]
-[[http://www.nature.com/ng/journal/v38/n5/pdf/ng1776.pdf|Systematic identification of human mitochondrial disease genes through integrative genomics ]] \\
+<div class="level3">
-Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK. \\
+<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 Genetics//, 38:576-82 (2006)
+Christley S, Nie Q and Xie X<br />
+<em>PLoS ONE</em> 4(8): e6799. doi:10.1371/journal.pone.0006799 (2009)</p>
-[[http://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://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 />
-Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M.  \\
+Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF<br />
-//Nature//2005; 434:338-45  \\
+<em>Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0904246106 (2009)</p>
-[[http://www.broad.mit.edu/seq/HumanMotifs/|Supplementary Website]] [[http://www.ics.uci.edu/~xhx/publications/nature03441-s1.pdf|Supplementary Information]] [[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=134|News story]]
-[[http://www.genome.org/cgi/reprint/gr.5285206v1|A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands]] \\
+<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 />
-Giallourakis C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R.  \\
+Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X<br />
-//Genome Resesarch//, 16:1056-72 (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://download.cell.com/pdfs/0092-8674/PIIS0092867406003692.pdf|A Mammalian Organelle Map by Protein Correlation Profiling]] \\
+<p><a class="urlextern" href="http://www.pnas.org/content/early/2009/02/11/0813264106.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 />
-Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M.  \\
+Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA<br />
-//Cell// 125:187-99 (2006)
+<em>Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0813264106 (2009)</p>
-[[http://www.ics.uci.edu/~xhx/publications/WerfelXieSeung2005.pdf|Learning curves for stochastic gradient descent in linear feedforward networks. ]] \\
+<p><a class="urlextern" href="http://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 />
-Werfel J, Xie X and Seung HS.  \\
+Fraser H and Xie X<br />
-//Neural Computation//, 2005;17:2699-718
+<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.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://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 />
-Lindblad-Toh K, Wade CM, et al.  \\
+Xie X, Rigor P, and Baldi P<br />
-//Nature// 438:803-19 2005
+<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/annurev.genom.6.080604.pdf|Disease gene discovery through integrative genomics. ]] \\
+<p><a class="urlextern" href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/274" rel="nofollow" title="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/274">Human genomes as email attachments </a><br />
-Giallourakis C, Henson C, Reich M, Xie X, and Mootha VK.  \\
+Christley S, Lu Y, Li C, and Xie X<br />
-//Annu. Rev. Genomics Hum. Genet.// 2005:22:381-406.
+<em>Bioinformatics </em> 25: 274-275 (2009)<br />
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/project/DNAzip" rel="nofollow" title="http://www.ics.uci.edu/~xhx/project/DNAzip">DNAzip: DNA sequence compression using a reference genome</a><br />
+<a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/DNAzip.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/DNAzip.pdf">PDF</a><br />
+<a class="urlextern" href="http://www.genomeweb.com/informatics/jim-watsonâï¿½ï¿½s-genome-e-mail-uc-irvine-team-develops-method-compress-genomic-data" rel="nofollow" title="http://www.genomeweb.com/informatics/jim-watsonâï¿½ï¿½s-genome-e-mail-uc-irvine-team-develops-method-compress-genomic-data">News featured in genomeweb</a><br />
+<a class="urlextern" href="http://www.bio-itworld.com/news/2009/01/30/Email-compression-genome.html" rel="nofollow" title="http://www.bio-itworld.com/news/2009/01/30/Email-compression-genome.html">News featured in bio-itworld</a><br />
+<a class="urlextern" href="http://www.amia.org/content/2009-summit-translational-bioinformatics-closing-session" rel="nofollow" title="http://www.amia.org/content/2009-summit-translational-bioinformatics-closing-session">One of the 20 most important papers in Translational Bioinformatics in </a><a class="urlextern" href="http://www.amia.org/content/2009-summit-translational-bioinformatics-closing-session" rel="nofollow" title="http://www.amia.org/content/2009-summit-translational-bioinformatics-closing-session">2009</a>as reviewed by Russ Altman of Stanford</p>
+</div>
-[[http://www.ics.uci.edu/~xhx/publications/PhysRevE_69_041909.pdf|Learning in neural networks by reinforcement of irregular spiking. ]] \\
+<h3>2008</h3>
-Xie X and Seung HS.  \\
-//Phys Rev E//, 2004;69:041909
-[[http://www.ics.uci.edu/~xhx/publications/mootha_pgc1a.pdf|Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle]] \\
+<div class="level3">
-Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al.  \\
+<p><a class="urlextern" href="http://www.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 />
-//Proc Natl Acad Sci USA//, 2004;101:6570-5
+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_66_041902.pdf|The double-ring network modeling of the head-direction system]] \\
+<p><a class="urlextern" href="http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2567431&amp;blobtype=pdf" rel="nofollow" title="http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2567431&amp;blobtype=pdf">Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains </a><br />
-Xie X, Hahnloser RH, 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 />
-//Physical Review E//, 2002;66:041902
+<em>PLoS </em><em>Genetics</em>4(10):e1000242 (2008)</p>
+</div>
-[[http://www.ics.uci.edu/~xhx/publications/PhysRevE_65_051904.pdf|Nonlinear dynamics of direction-selective recurrent neural media]] \\
+<h3>2007</h3>
-Xie X and Giese MA.  \\
-//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]] \\
-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 ]] \\
+<div class="level3">
-Xie X, Hahnloser HR, and Seung HS.  \\
+<p><a class="urlextern" href="http://www.pnas.org/content/104/49/19428" rel="nofollow" title="http://www.pnas.org/content/104/49/19428">Distinguishing protein-coding and noncoding genes in the human genome </a><br />
-//Advances in Neural Information Processing Systems//2001;13:350-356
+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/nc_vel_tuning.pdf|Generating velocity tuning by asymmetric recurrent connections]] \\
+<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 Giese MA.  \\
+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 />
-//Advances in Neural Information Processing Systems//2002;13:325-332
+<em>Nature</em>449:913-918 (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/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, Hahnloser RH, 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//, 2002;14:2627-2646
+<em>Nature</em> 448:553-60 (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.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 and Seung HS.  \\
+Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES.<br />
-//Neural Computation//, 2003;16:441-454
+<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/network_pop.pdf|Threshold behavior of maximum likelihood method in population decoding]] \\
+<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 \\
+Mikkelsen TS, Wakefield MJ, et al.<br />
-//Network: Comput. Neural Syst.// 2002;13:447-456
+<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