LDAP: couldn't connect to LDAP server

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
publications [2018/08/15 23:06]
xhx
publications [2018/08/15 23:25] (current)
Line 1: Line 1:
-__false__+<​html>​ 
 +<​h2>​Publications</​h2>​ 
 + 
 +<div class="​level2">&​nbsp;</​div>​ 
 + 
 +<​h3>​2018</​h3>​ 
 + 
 +<div class="​level3">​ 
 +<​p><​a class="​urlextern"​ href="​https://​arxiv.org/​abs/​1805.05373"​ rel="​nofollow"​ title="​https://​arxiv.org/​abs/​1805.05373">​DeepEM:​ Deep 3D ConvNets With EM For Weakly Supervised Pulmonary Nodule Detection</​a><​br /> 
 +Zhu W, Vang YS, Huang Y, Xie X</​p>​ 
 + 
 +<​p>​Sequential Embedding Induced Nonparametric Text Clustering<​br /> 
 +Duan T, Lou Q, Xie X</​p>​ 
 + 
 +<​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 /> 
 +Vang S, Chen Z, Xie X<br /> 
 +15th International Conference on Image Analysis and Recognition,​ 2018</​p>​ 
 + 
 +<​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 /> 
 +IEEE Winter Conf. on Applications of Computer Vision 2018</​p>​ 
 + 
 +<​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>​ 
 + 
 +<​p>​Adversarial Deep Structured Nets for Mass Segmentation from Mammograms<​br /> 
 +W Zhu, X Xiang, T Tran, GD Hager, X Xie<br /> 
 +IEEE International Symposium on Biomedical Imaging</​p>​ 
 + 
 +<​p>​Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural Networks<​br /> 
 +H Tang, D Kim, X Xie<br /> 
 +IEEE International Symposium on Biomedical Imaging</​p>​ 
 + 
 +<​p>​Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.<​br /> 
 +Zhu Y, Wang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.<br /> 
 +Mol Cell. 2018 Jan 4;​69(1):​62-74.e4.</​p>​ 
 +</​div>​ 
 + 
 +<​h3>​2017</​h3>​ 
 + 
 +<div class="​level3">​ 
 +<​p><​a class="​urlextern"​ href="​https://​arxiv.org/​abs/​1709.05538"​ rel="​nofollow"​ title="​https://​arxiv.org/​abs/​1709.05538">​DeepLung:​ 3D Deep Convolutional Nets for Automated Pulmonary Nodule Detection and Classification</​a><​br /> 
 +W Zhu, C Liu, W Fan, X Xie<br /> 
 +arXiv preprint arXiv:​1709.05538</​p>​ 
 + 
 +<​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>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​https://​arxiv.org/​abs/​1612.05968"​ rel="​nofollow"​ title="​https://​arxiv.org/​abs/​1612.05968">​Deep Multi-instance Networks with Sparse Label Assignment for Whole Mammogram Classification</​a><​br /> 
 +Wentao Zhu, Qi Lou, Yeeleng Scott Vang, Xiaohui Xie<br /> 
 +arXiv:​1612.05968<​br /> 
 +<a class="​urlextern"​ href="​http://​www.miccai2017.org/"​ rel="​nofollow"​ title="​http://​www.miccai2017.org/">​MICCAI,​ 2017</​a></​p>​ 
 + 
 +<​p>​Understanding sequence conservation with deep learning<​br /> 
 +Li Y, Quang D, and Xie X<br /> 
 +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>​ 
 + 
 +<​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 /> 
 +Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW<br /> 
 +Dev Cell. 27;​40(6):​595-607.e4,​ 2017</​p>​ 
 +</​div>​ 
 + 
 +<​h3>​2016</​h3>​ 
 + 
 +<div class="​level3">​ 
 +<​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 /> 
 +Wentao Zhu, Xiaohui Xie<br /> 
 +arXiv:​1612.05970</​p>​ 
 + 
 +<​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 /> 
 +Forouzmand et al.<br /> 
 +Developmental Biology, (16)30120-8 2016</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​bioinformatics.oxfordjournals.org/​content/​early/​2016/​02/​11/​bioinformatics.btw074.short?​rss=1"​ rel="​nofollow"​ title="​http://​bioinformatics.oxfordjournals.org/​content/​early/​2016/​02/​11/​bioinformatics.btw074.short?​rss=1">​Gene expression inference with deep learning</​a><​br /> 
 +Chen Y, Li Y, Narayan R, Subramanian A, and Xie X<br /> 
 +Bioinformatics,​ 2016</​p>​ 
 + 
 +<​p>​DanQ:​ a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences<​br /> 
 +Quang D and Xie X<br /> 
 +Nucleic Acids Research, 2016</​p>​ 
 + 
 +<​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 /> 
 +Weng L, Li Y, Xie X, and Shi Y<br /> 
 +RNA, 2016</​p>​ 
 + 
 +<​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 /> 
 +Zhu W, et al.<br /> 
 +AAAI Conference on Artificial Intelligence,​ 2016</​p>​ 
 +</​div>​ 
 + 
 +<​h3>​2015</​h3>​ 
 + 
 +<div class="​level3">​ 
 +<​p>​Hobbes3:​ Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings<​br /> 
 +Kim J, Chen L, and Xie X<br /> 
 +32nd IEEE International Conference on Data Engineering - ICDE 2016</​p>​ 
 + 
 +<​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 /> 
 +Quang D and Xie X</​p>​ 
 + 
 +<​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 /> 
 +Quang D, Chen Y and Xie X<br /> 
 +Bioinformatics,​ 31(5):​761-3,​ 2015</​p>​ 
 + 
 +<​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 /> 
 +Li Y and Xie X<br /> 
 +BMC Genomics, 2015</​p>​ 
 + 
 +<​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 /> 
 +Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X<br /> 
 +Neuroimaging genetics : principles and practices, 2015</​p>​ 
 +</​div>​ 
 + 
 +<​h3>​2014</​h3>​ 
 + 
 +<div class="​level3">​ 
 +<​p><​a class="​urlextern"​ href="​http://​link.springer.com/​article/​10.1007/​s10032-014-0229-4"​ rel="​nofollow"​ title="​http://​link.springer.com/​article/​10.1007/​s10032-014-0229-4">​Handwritten Hangul recognition using deep convolutional neural networks</​a><​br /> 
 +Kim I and Xie X<br /> 
 +International Journal on Document Analysis and Recognition,​ 2014<br /> 
 +<a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​HHR.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​HHR.pdf">​preprint</​a></​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ncbi.nlm.nih.gov/​pubmed/​25359723"​ rel="​nofollow"​ title="​http://​www.ncbi.nlm.nih.gov/​pubmed/​25359723">​Genome-wide view of TGFbeta/​Foxh1 regulation of the early mesendoderm</​a>​ program<​br /> 
 +Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K<br /> 
 +Development,​ 2014</​p>​ 
 + 
 +<​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>​ 
 + 
 +<​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 /> 
 +Quang D and Xie X<br /> 
 +Bioinformatics,​ 2014</​p>​ 
 + 
 +<​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 /> 
 +Kim J, Li C and Xie X<br /> 
 +BMC Bioinformatics,​ 2014, 15(1):​42</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.plosone.org/​article/​info:​doi/​10.1371/​journal.pone.0092317"​ rel="​nofollow"​ title="​http://​www.plosone.org/​article/​info:​doi/​10.1371/​journal.pone.0092317">​Integrative ChIP-seq/​Microarray Analysis Identifies a CTNNB1 Target Signature Enriched in Intestinal Stem Cells and Colon Cancer</​a><​br /> 
 +Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X<br /> 
 +PLOS ONE, 2014, DOI: 10.1371/​journal.pone.0092317</​p>​ 
 + 
 +<​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 /> 
 +Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q<br /> 
 +BMC Systems Biology 2014, 8:​3</​p>​ 
 + 
 +<​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>​ 
 + 
 +<​h3>​2013</​h3>​ 
 + 
 +<div class="​level3">​ 
 +<​p><​a class="​urlextern"​ href="​http://​www.plosone.org/​article/​info:​doi/​10.1371/​journal.pone.0082146"​ rel="​nofollow"​ title="​http://​www.plosone.org/​article/​info:​doi/​10.1371/​journal.pone.0082146">​Low-Rank Regularization for Learning Gene Expression Programs</​a><​br /> 
 +Ye G, Tang M, Nie Q and Xie X<br /> 
 +<​em>​PLOS ONE</​em>,​ 2013</​p>​ 
 + 
 +<​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>​ 
 + 
 +<​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 /> 
 +Blitz I, Biesinger J, Xie X, and Cho K<br /> 
 +<​em>​Genesis</​em>,​ 2013.</​p>​ 
 + 
 +<​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 /> 
 +Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y<br /> 
 +<​em>​RNA</​em>,​ 2013</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​arxiv.org/​abs/​1305.0855"​ rel="​nofollow"​ title="​http://​arxiv.org/​abs/​1305.0855">​Inference in Kingman&#​39;​s Coalescent with Particle Markov Chain Monte Carlo Method</​a><​br /> 
 +Chen Y and Xie X<br /> 
 +<​em>​arXiv</​em>,​ 2013</​p>​ 
 + 
 +<​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 /> 
 +Biesinger J, Wang Y, and Xie X<br /> 
 +<​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>​ 
 + 
 +<​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>​ 
 + 
 +<​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 /> 
 +Yang X, Wang B, Li C, Wang J, and Xie X<br /> 
 +<​em>​IEEE International Conference on Data Engineering (ICDE)</​em>,​ 2013</​p>​ 
 +</​div>​ 
 + 
 +<​h3>​2012</​h3>​ 
 + 
 +<div class="​level3">​ 
 +<​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 /> 
 +Ye G and Xie X<br /> 
 +Machine Learning Journal, 87(3):​303-355,​ 2012<br /> 
 +<a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​SGL.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​SGL.pdf">​Preprint</​a></​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ncbi.nlm.nih.gov/​pubmed/​23112178"​ rel="​nofollow"​ title="​http://​www.ncbi.nlm.nih.gov/​pubmed/​23112178">​Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation</​a><​br /> 
 +Yao C, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y<br /> 
 +PNAS, 109(46):​18773-8,​ 2012</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ncbi.nlm.nih.gov/​pubmed/​22296850"​ rel="​nofollow"​ title="​http://​www.ncbi.nlm.nih.gov/​pubmed/​22296850">​Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR</​a><​br /> 
 +Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF<br /> 
 +BMC Genomics, 2012</​p>​ 
 + 
 +<​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>​ 
 + 
 +<​h3>​2011</​h3>​ 
 + 
 +<div class="​level3">​ 
 +<​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 /> 
 +Ye G, Wang Y, Chen Y, and Xie X<br /> 
 +arXiv:​1110.3076v1,​ 2011</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ncbi.nlm.nih.gov/​pubmed/​22208852"​ rel="​nofollow"​ title="​http://​www.ncbi.nlm.nih.gov/​pubmed/​22208852">​MotifMap:​ integrative genome-wide maps of regulatory motif sites for model species. </​a><​br /> 
 +Daily K, Patel VR, Rigor P, Xie X, Baldi P.<br /> 
 +BMC Bioinformatics,​ 2011</​p>​ 
 + 
 +<​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 /> 
 +Lindblad-Toh,​ Barber, Zuk, Lin, et al.<br /> 
 +Nature, 2011</​p>​ 
 + 
 +<​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>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.cell.com/​cell-metabolism/​abstract/​S1550-4131(11)00092-1"​ rel="​nofollow"​ title="​http://​www.cell.com/​cell-metabolism/​abstract/​S1550-4131(11)00092-1">​Genome-wide Positioning of SREBP-2 in Hepatic Chromatin Predicts a Novel Role in Autophagy </​a><​br /> 
 +Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF<br /> 
 +<​em>​Cell Metabolism</​em>,​ 13:367-75, 2011<br /> 
 +<a class="​urlextern"​ href="​http://​www.sciencedaily.com/​releases/​2011/​04/​110405122330.htm"​ rel="​nofollow"​ title="​http://​www.sciencedaily.com/​releases/​2011/​04/​110405122330.htm">​Science Daily coverage</​a></​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​arem_recomb.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​arem_recomb.pdf">​AREM:​ aligning short reads from ChIP-sequencing by expectation maximization</​a><​br /> 
 +Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X<br /> 
 +<em>J Comput Biol.</​em>,​ 2011<br /> 
 +Software: <a class="​urlextern"​ href="​http://​sourceforge.net/​projects/​arem"​ rel="​nofollow"​ title="​http://​sourceforge.net/​projects/​arem">​AREM</​a></​p>​ 
 + 
 +<​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>​ 
 + 
 +<​h3>​2010</​h3>​ 
 + 
 +<div class="​level3">​ 
 +<​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 /> 
 +Ye G, Cai J, and Xie X<br /> 
 +arXiv:​1012.0975v1,​ 2010</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.sciencedirect.com/​science?​_ob=ArticleURL&​amp;​_udi=B6V8V-51BBKR7-1&​amp;​_user=10&​amp;​_coverDate=10/​27/​2010&​amp;​_rdoc=1&​amp;​_fmt=high&​amp;​_orig=search&​amp;​_origin=search&​amp;​_sort=d&​amp;​_docanchor=&​amp;​view=c&​amp;​_acct=C000050221&​amp;​_version=1&​amp;​_urlVersion=0&​amp;​_userid=10&​amp;​md5=6ff4ea0404367278249b06c9a59f84fd&​amp;​searchtype=a"​ rel="​nofollow"​ title="​http://​www.sciencedirect.com/​science?​_ob=ArticleURL&​amp;​_udi=B6V8V-51BBKR7-1&​amp;​_user=10&​amp;​_coverDate=10/​27/​2010&​amp;​_rdoc=1&​amp;​_fmt=high&​amp;​_orig=search&​amp;​_origin=search&​amp;​_sort=d&​amp;​_docanchor=&​amp;​view=c&​amp;​_acct=C000050221&​amp;​_version=1&​amp;​_urlVersion=0&​amp;​_userid=10&​amp;​md5=6ff4ea0404367278249b06c9a59f84fd&​amp;​searchtype=a">​Split Bregman method for large scale fused Lasso</​a><​br /> 
 +Ye G-B and Xie X<br /> 
 +Computational Statistics and Data Analysis, doi:​10.1016/​j.csda.2010.10.021,​ 2010<br /> 
 +<a class="​urlextern"​ href="​http://​arxiv.org/​abs/​1006.5086"​ rel="​nofollow"​ title="​http://​arxiv.org/​abs/​1006.5086">​arXiv version</​a>​ <a class="​urlextern"​ href="​http://​www.biomedcentral.com/​1471-2105/​11/​514"​ rel="​nofollow"​ title="​http://​www.biomedcentral.com/​1471-2105/​11/​514">​Data Structures and Compression Algorithms for High-Throughput Sequencing Technologies</​a><​br /> 
 +Daily K, Rigor P, Christley S, Xie X and Baldi P<br /> 
 +<​em>​BMC Bioinformatics</​em>,​11:​514,​ 2010</​p>​ 
 + 
 +<​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 /> 
 +Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J<br /> 
 +<​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>​ 
 + 
 +<​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>​ 
 + 
 +<​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 /> 
 +Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X<br /> 
 +<​em>​NeuroImage</​em>​ 53:839-847, 2010</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.biomedcentral.com/​1752-0509/​4/​99"​ rel="​nofollow"​ title="​http://​www.biomedcentral.com/​1752-0509/​4/​99">​Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent</​a><​br /> 
 +Wang Y, Christley S, Mjolsness E, and Xie X<br /> 
 +<​em>​BMC Systems Biology</​em>,​ 4:99 doi:​10.1186/​1752-0509-4-99,​ 2010</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.springerlink.com/​content/​428v02087m218878/​fulltext.pdf"​ rel="​nofollow"​ title="​http://​www.springerlink.com/​content/​428v02087m218878/​fulltext.pdf">​Site-frequency Spectrum of Linked Sites</​a><​br /> 
 +Xie X<br /> 
 +<​em>​Bulletin of Mathematical Biology</​em>,​ DOI: 10.1007/​s11538-010-9534-3,​ 2010</​p>​ 
 + 
 +<​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>​ 
 + 
 +<​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 /> 
 +Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X<br /> 
 +<​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>​ 
 + 
 +<​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 /> 
 +Ma L-J, et al.<br /> 
 +<​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>​ 
 + 
 +<​h3>​2009</​h3>​ 
 + 
 +<div class="​level3">​ 
 +<​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 /> 
 +Christley S, Nie Q and Xie X<br /> 
 +<​em>​PLoS ONE</​em>​ 4(8): e6799. doi:​10.1371/​journal.pone.0006799 (2009)</​p>​ 
 + 
 +<​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>​ 
 + 
 +<​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 /> 
 +Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X<br /> 
 +<​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>​ 
 + 
 +<​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 /> 
 +Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA<br /> 
 +<​em>​Proc Natl Acad Sci USA</​em>​ doi:​10.1073/​pnas.0813264106 (2009)</​p>​ 
 + 
 +<​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 /> 
 +Fraser H and Xie X<br /> 
 +<​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>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​2/​167"​ rel="​nofollow"​ title="​http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​25/​2/​167">​MotifMap:​ a human genome-wide map of candidate regulatory motif sites </​a><​br /> 
 +Xie X, Rigor P, and Baldi P<br /> 
 +<​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>​ 
 + 
 +<​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 /> 
 +Christley S, Lu Y, Li C, and Xie X<br /> 
 +<​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-watsonâ��s-genome-e-mail-uc-irvine-team-develops-method-compress-genomic-data"​ rel="​nofollow"​ title="​http://​www.genomeweb.com/​informatics/​jim-watsonâ��s-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>​ 
 + 
 +<​h3>​2008</​h3>​ 
 + 
 +<div class="​level3">​ 
 +<​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 /> 
 +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>​ 
 + 
 +<​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 /> 
 +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 /> 
 +<​em>​PLoS </​em><​em>​Genetics</​em>​4(10):​e1000242 (2008)</​p>​ 
 +</​div>​ 
 + 
 +<​h3>​2007</​h3>​ 
 + 
 +<div class="​level3">​ 
 +<​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 /> 
 +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>​ 
 + 
 +<​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 /> 
 +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 /> 
 +<​em>​Nature</​em>​449:​913-918 (2007)</​p>​ 
 + 
 +<​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 /> 
 +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 /> 
 +<​em>​Nature</​em>​ 448:553-60 (2007)</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​insulators_pnas06.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​insulators_pnas06.pdf">​Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites </​a><​br /> 
 +Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES.<br /> 
 +<​em>​Proc Natl Acad Sci </​em><​em>​USA</​em>​104:​7145-7150 (2007)<​br /> 
 +<a class="​urlextern"​ href="​http://​www.broad.mit.edu/​personal/​xhx/​projects/​CNEMOTIF/"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​personal/​xhx/​projects/​CNEMOTIF/">​Supplementary website</​a>​ <a class="​urlextern"​ href="​http://​www.pnas.org/​cgi/​content/​full/​0701811104/​DC1"​ rel="​nofollow"​ title="​http://​www.pnas.org/​cgi/​content/​full/​0701811104/​DC1">​Supporting Information</​a>​ <a class="​urlextern"​ href="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=3042"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=3042">​News story</​a></​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.nature.com/​nature/​journal/​v447/​n7141/​pdf/​nature05805.pdf"​ rel="​nofollow"​ title="​http://​www.nature.com/​nature/​journal/​v447/​n7141/​pdf/​nature05805.pdf">​Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences </​a><​br /> 
 +Mikkelsen TS, Wakefield MJ, et al.<br /> 
 +<​em>​Nature</​em>​ 447:167-177 (2007)</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​Xie_AMCNE.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​Xie_AMCNE.pdf">​A family of conserved noncoding elements derived from an ancient transposable element</​a><​br /> 
 +Xie X, Kamal M, and Lander ES.<br /> 
 +<​em>​Proc Natl Acad Sci </​em><​em>​USA</​em>​103:​11659-11664 (2006)<​br /> 
 +<a class="​urlextern"​ href="​http://​www.broad.mit.edu/​seq/​pubs/​xie_pnas2006/"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​seq/​pubs/​xie_pnas2006/">​Supplementary website</​a>​ <a class="​urlextern"​ href="​http://​www.pnas.org/​cgi/​content/​full/​0604768103/​DC1"​ rel="​nofollow"​ title="​http://​www.pnas.org/​cgi/​content/​full/​0604768103/​DC1">​Supporting Information</​a>​ <a class="​urlextern"​ href="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=1881"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=1881">​News story</​a></​p>​ 
 +</​div>​ 
 + 
 +<​h3>​2006 or before</​h3>​ 
 + 
 +<div class="​level3">​ 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​mer121.PNAS2006.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​mer121.PNAS2006.pdf">​A large family of ancient repeat elements in the human genome is under strong selection</​a><​br /> 
 +Kamal M, Xie X, and Lander ES.<br /> 
 +<​em>​Proc Natl Acad Sci </​em><​em>​USA</​em>​103:​2740-2745 (2006)<​br /> 
 +<a class="​urlextern"​ href="​http://​www.broad.mit.edu/​seq/​pubs/​xie_pnas2006/​html/​clusteredAMCNE/​AMCNE1.similarAMCNE.html"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​seq/​pubs/​xie_pnas2006/​html/​clusteredAMCNE/​AMCNE1.similarAMCNE.html">​Supplementary website</​a>​ <a class="​urlextern"​ href="​http://​www.pnas.org/​cgi/​content/​full/​0511238103/​DC1"​ rel="​nofollow"​ title="​http://​www.pnas.org/​cgi/​content/​full/​0511238103/​DC1">​Supporting Information</​a><​br /> 
 +<a class="​urlextern"​ href="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=381"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=381">​News story</​a></​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​download.cell.com/​pdfs/​0092-8674/​PIIS0092867406003801.pdf"​ rel="​nofollow"​ title="​http://​download.cell.com/​pdfs/​0092-8674/​PIIS0092867406003801.pdf">​A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells</​a><​br /> 
 +Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al.<br /> 
 +<​em>​Cell</​em>​ 125:315-26 (2006)</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​genomebiology.com/​2006/​7/​9/​R85"​ rel="​nofollow"​ title="​http://​genomebiology.com/​2006/​7/​9/​R85">​Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression </​a><​br /> 
 +Wu J and Xie X<br /> 
 +<​em>​Genome </​em><​em>​Biology</​em>​7(9):​R85 (2006) (Highly accessed)<​br /> 
 +<a class="​urlextern"​ href="​http://​www.broad.mit.edu/​personal/​xhx/​projects/​NRSE"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​personal/​xhx/​projects/​NRSE">​Supplementary website</​a></​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.nature.com/​ng/​journal/​v38/​n5/​pdf/​ng1776.pdf"​ rel="​nofollow"​ title="​http://​www.nature.com/​ng/​journal/​v38/​n5/​pdf/​ng1776.pdf">​Systematic identification of human mitochondrial disease genes through integrative genomics </​a><​br /> 
 +Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK.<br /> 
 +<​em>​Nature Genetics</​em>,​ 38:576-82 (2006)</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​xie05_motif_paper.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​xie05_motif_paper.pdf">​Systematic discovery of regulatory motifs in human promoters and 3&#39; UTRs by comparison of several mammals </​a><​br /> 
 +Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M.<br /> 
 +<​em>​Nature</​em>​2005;​ 434:​338-45<​br /> 
 +<a class="​urlextern"​ href="​http://​www.broad.mit.edu/​seq/​HumanMotifs/"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​seq/​HumanMotifs/">​Supplementary Website</​a>​ <a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​nature03441-s1.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​nature03441-s1.pdf">​Supplementary Information</​a>​ <a class="​urlextern"​ href="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=134"​ rel="​nofollow"​ title="​http://​www.broad.mit.edu/​cgi-bin/​news/​display_news.cgi?​id=134">​News story</​a></​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.genome.org/​cgi/​reprint/​gr.5285206v1"​ rel="​nofollow"​ title="​http://​www.genome.org/​cgi/​reprint/​gr.5285206v1">​A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands</​a><​br /> 
 +Giallourakis C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R.<br /> 
 +<​em>​Genome Resesarch</​em>,​ 16:1056-72 (2006)</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​download.cell.com/​pdfs/​0092-8674/​PIIS0092867406003692.pdf"​ rel="​nofollow"​ title="​http://​download.cell.com/​pdfs/​0092-8674/​PIIS0092867406003692.pdf">​A Mammalian Organelle Map by Protein Correlation Profiling</​a><​br /> 
 +Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M.<br /> 
 +<​em>​Cell</​em>​ 125:187-99 (2006)</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​WerfelXieSeung2005.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​WerfelXieSeung2005.pdf">​Learning curves for stochastic gradient descent in linear feedforward networks. </​a><​br /> 
 +Werfel J, Xie X and Seung HS.<br /> 
 +<​em>​Neural Computation</​em>,​ 2005;​17:​2699-718</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.nature.com/​nature/​journal/​v438/​n7069/​pdf/​nature04338.pdf"​ rel="​nofollow"​ title="​http://​www.nature.com/​nature/​journal/​v438/​n7069/​pdf/​nature04338.pdf">​Genome sequence, comparative analysis and haplotype structure of the domestic dog </​a><​br /> 
 +Lindblad-Toh K, Wade CM, et al.<br /> 
 +<​em>​Nature</​em>​ 438:803-19 2005</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​annurev.genom.6.080604.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​annurev.genom.6.080604.pdf">​Disease gene discovery through integrative genomics. </​a><​br /> 
 +Giallourakis C, Henson C, Reich M, Xie X, and Mootha VK.<br /> 
 +<​em>​Annu. Rev. Genomics Hum. Genet.</​em>​ 2005:​22:​381-406.</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​PhysRevE_69_041909.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​PhysRevE_69_041909.pdf">​Learning in neural networks by reinforcement of irregular spiking. </​a><​br /> 
 +Xie X and Seung HS.<br /> 
 +<​em>​Phys Rev E</​em>,​ 2004;​69:​041909</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​mootha_pgc1a.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​mootha_pgc1a.pdf">​Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle</​a><​br /> 
 +Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al.<br /> 
 +<​em>​Proc Natl Acad Sci USA</​em>,​ 2004;​101:​6570-5</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​PhysRevE_66_041902.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​PhysRevE_66_041902.pdf">​The double-ring network modeling of the head-direction system</​a><​br /> 
 +Xie X, Hahnloser RH, and Seung HS.<br /> 
 +<​em>​Physical Review E</​em>,​ 2002;​66:​041902</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​PhysRevE_65_051904.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​PhysRevE_65_051904.pdf">​Nonlinear dynamics of direction-selective recurrent neural media</​a><​br /> 
 +Xie X and Giese MA.<br /> 
 +<​em>​Physical Review E</​em>,​ 2002;​65:​051904 <a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​neurocomp_giese.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​neurocomp_giese.pdf">​Exact solution of the nonlinear dynamics of recurrent neural mechanisms for direction selectivity</​a><​br /> 
 +Giese MA and Xie X<br /> 
 +<​em>​Neurocomputing</​em>​ 2002;​44:​417-422</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​lwta.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​lwta.pdf">​Learning winner-take-all competition between groups of neurons in lateral inhibitory networks </​a><​br /> 
 +Xie X, Hahnloser HR, and Seung HS.<br /> 
 +<​em>​Advances in Neural Information Processing </​em><​em>​Systems</​em>​2001;​13:​350-356</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​nc_vel_tuning.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​nc_vel_tuning.pdf">​Generating velocity tuning by asymmetric recurrent connections</​a><​br /> 
 +Xie X and Giese MA.<br /> 
 +<​em>​Advances in Neural Information Processing </​em><​em>​Systems</​em>​2002;​13:​325-332</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​gwta_nc.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​gwta_nc.pdf">​Selectively Grouping Neurons in Recurrent Networks of Lateral Inhibition</​a><​br /> 
 +Xie X, Hahnloser RH, and Seung HS.<br /> 
 +<​em>​Neural Computation</​em>,​ 2002;​14:​2627-2646</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​chl_nc.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​chl_nc.pdf">​Equivalence of backpropagation and contrastive Hebbian learning in a layered network</​a><​br /> 
 +Xie X and Seung HS.<br /> 
 +<​em>​Neural Computation</​em>,​ 2003;​16:​441-454</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​network_pop.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​network_pop.pdf">​Threshold behavior of maximum likelihood method in population decoding</​a><​br /> 
 +Xie X<br /> 
 +<​em>​Network:​ Comput. Neural Syst.</​em>​ 2002;​13:​447-456</​p>​ 
 + 
 +<​p><​a class="​urlextern"​ href="​http://​www.ics.uci.edu/​~xhx/​publications/​stdp00.pdf"​ rel="​nofollow"​ title="​http://​www.ics.uci.edu/​~xhx/​publications/​stdp00.pdf">​Spike-based learning rules and stabilization of persistent neural activity</​a><​br /> 
 +Xie X and Seung HS<br /> 
 +<​em>​Advances in Neural Information Processing Systems</​em>,​ 2000;​12:​199-205</​p>​ 
 +</​div>​ 
  
You are here: startpublications