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+ | <h2>Publications</h2> | ||
+ | <div class="level2"> </div> | ||
- | ===== Publications ===== | + | <h3>2018</h3> |
- | ==== 2018 ==== | + | <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> | ||
- | [[https://arxiv.org/abs/1805.05373 | DeepEM: Deep 3D ConvNets With EM For Weakly Supervised Pulmonary Nodule Detection]]\\ | + | <p>Sequential Embedding Induced Nonparametric Text Clustering<br /> |
- | Zhu W, Vang YS, Huang Y, Xie X\\ | + | 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> | ||
- | Sequential Embedding Induced Nonparametric Text Clustering\\ | + | <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 /> |
- | Duan T, Lou Q, Xie X\\ | + | IEEE Winter Conf. on Applications of Computer Vision 2018</p> |
- | [[https://arxiv.org/abs/1802.00931 | Deep Learning Framework for Multi-class Breast Cancer Histology Image Classification]]\\ | + | <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 /> |
- | Vang S, Chen Z, Xie X\\ | + | IEEE Winter Conf. on Applications of Computer Vision 2018</p> |
- | 15th International Conference on Image Analysis and Recognition, 2018 | + | |
- | [[https://arxiv.org/abs/1801.07853 | Structed Triplets Learning with Pos-tag Guided Attention for Visual Question Answering]]\\ | + | <p>Adversarial Deep Structured Nets for Mass Segmentation from Mammograms<br /> |
- | IEEE Winter Conf. on Applications of Computer Vision 2018 | + | W Zhu, X Xiang, T Tran, GD Hager, X Xie<br /> |
+ | IEEE International Symposium on Biomedical Imaging</p> | ||
- | [[https://arxiv.org/abs/1801.09555 | DeepLung: Deep 3D Dual Path Nets for Automated Pulmonary Nodule Detection and Classification]]\\ | + | <p>Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural Networks<br /> |
- | IEEE Winter Conf. on Applications of Computer Vision 2018 | + | H Tang, D Kim, X Xie<br /> |
+ | IEEE International Symposium on Biomedical Imaging</p> | ||
- | Adversarial Deep Structured Nets for Mass Segmentation from Mammograms\\ | + | <p>Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.<br /> |
- | W Zhu, X Xiang, T Tran, GD Hager, X Xie\\ | + | Zhu Y, Wang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.<br /> |
- | IEEE International Symposium on Biomedical Imaging | + | Mol Cell. 2018 Jan 4;69(1):62-74.e4.</p> |
+ | </div> | ||
- | Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural Networks\\ | + | <h3>2017</h3> |
- | H Tang, D Kim, X Xie\\ | + | |
- | IEEE International Symposium on Biomedical Imaging | + | |
- | Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.\\ | + | <div class="level3"> |
- | Zhu Y, Wang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.\\ | + | <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 /> |
- | Mol Cell. 2018 Jan 4;69(1):62-74.e4. | + | W Zhu, C Liu, W Fan, X Xie<br /> |
+ | arXiv preprint arXiv:1709.05538</p> | ||
- | ==== 2017 ==== | + | <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> | ||
- | [[https://arxiv.org/abs/1709.05538 | DeepLung: 3D Deep Convolutional Nets for Automated Pulmonary Nodule Detection and Classification]]\\ | + | <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 /> |
- | W Zhu, C Liu, W Fan, X Xie\\ | + | Wentao Zhu, Qi Lou, Yeeleng Scott Vang, Xiaohui Xie<br /> |
- | arXiv preprint arXiv:1709.05538 | + | 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> | ||
- | [[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]]\\ | + | <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 /> |
- | D Quang, X Xie\\ | + | Vang YS and Xie X<br /> |
- | bioRxiv, 151274 | + | 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> | ||
- | [[https://arxiv.org/abs/1612.05968|Deep Multi-instance Networks with Sparse Label Assignment for Whole Mammogram Classification]]\\ | + | <h3>2016</h3> |
- | Wentao Zhu, Qi Lou, Yeeleng Scott Vang, Xiaohui Xie \\ | + | |
- | arXiv:1612.05968\\ | + | |
- | [[http://www.miccai2017.org/| MICCAI, 2017]] | + | |
- | Understanding sequence conservation with deep learning\\ | + | <div class="level3"> |
- | Li Y, Quang D, and Xie X\\ | + | <p><a class="urlextern" href="https://arxiv.org/abs/1612.05970" rel="nofollow" title="https://arxiv.org/abs/1612.05970">Adversarial Deep Structural Networks for Mammographic Mass Segmentation</a><br /> |
- | ACM BCB, 2017 | + | Wentao Zhu, Xiaohui Xie<br /> |
+ | arXiv:1612.05970</p> | ||
- | [[http://biorxiv.org/content/early/2017/01/10/099358|HLA class I binding prediction via convolutional neural networks]]\\ | + | <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 /> |
- | Vang YS and Xie X\\ | + | Forouzmand et al.<br /> |
- | Bioinformatics, 2017 | + | Developmental Biology, (16)30120-8 2016</p> |
- | [[https://www.ncbi.nlm.nih.gov/pubmed/28325473|Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program]]\\ | + | <p><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 /> |
- | Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW\\ | + | Chen Y, Li Y, Narayan R, Subramanian A, and Xie X<br /> |
- | Dev Cell. 27;40(6):595-607.e4, 2017 | + | Bioinformatics, 2016</p> |
- | ==== 2016 ==== | + | <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> | ||
- | [[https://arxiv.org/abs/1612.05970|Adversarial Deep Structural Networks for Mammographic Mass Segmentation]]\\ | + | <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 /> |
- | Wentao Zhu, Xiaohui Xie\\ | + | Weng L, Li Y, Xie X, and Shi Y<br /> |
- | arXiv:1612.05970 | + | RNA, 2016</p> |
- | [[https://www.ncbi.nlm.nih.gov/pubmed/27418388|Developmentally regulated long non-coding RNAs in Xenopus tropicalis]]\\ | + | <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 /> |
- | Forouzmand et al. \\ | + | Zhu W, et al.<br /> |
- | Developmental Biology, (16)30120-8 2016 | + | AAAI Conference on Artificial Intelligence, 2016</p> |
+ | </div> | ||
- | [[http://bioinformatics.oxfordjournals.org/content/early/2016/02/11/bioinformatics.btw074.short?rss=1|Gene expression inference with deep learning]]\\ | + | <h3>2015</h3> |
- | Chen Y, Li Y, Narayan R, Subramanian A, and Xie X\\ | + | |
- | Bioinformatics, 2016 | + | |
- | DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences\\ | + | <div class="level3"> |
- | Quang D and Xie X\\ | + | <p>Hobbes3: Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings<br /> |
- | Nucleic Acids Research, 2016 | + | Kim J, Chen L, and Xie X<br /> |
+ | 32nd IEEE International Conference on Data Engineering - ICDE 2016</p> | ||
- | [[http://rnajournal.cshlp.org/content/early/2016/04/19/rna.055681.115.abstract|Poly(A) code analyses reveal key determinants for tissue-specific mRNA alternative polyadenylation]]\\ | + | <p><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 /> |
- | Weng L, Li Y, Xie X, and Shi Y\\ | + | Quang D and Xie X</p> |
- | RNA, 2016 | + | |
- | [[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="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 /> |
- | Zhu W, et al.\\ | + | Quang D, Chen Y and Xie X<br /> |
- | AAAI Conference on Artificial Intelligence, 2016 | + | Bioinformatics, 31(5):761-3, 2015</p> |
- | ==== 2015 ==== | + | <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> | ||
- | Hobbes3: Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings\\ | + | <p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/ImagingGenetics.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/ImagingGenetics.pdf">Identifying unanticipated genes and mechanisms in serious mental illness</a><br /> |
- | Kim J, Chen L, and Xie X\\ | + | Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X<br /> |
- | 32nd IEEE International Conference on Data Engineering - ICDE 2016 | + | Neuroimaging genetics : principles and practices, 2015</p> |
+ | </div> | ||
- | [[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]]\\ | + | <h3>2014</h3> |
- | Quang D and Xie X | + | |
- | [[http://www.ncbi.nlm.nih.gov/pubmed/25338716|DANN: a deep learning approach for annotating the pathogenicity of genetic variants]]\\ | + | <div class="level3"> |
- | Quang D, Chen Y and Xie X\\ | + | <p><a class="urlextern" href="http://link.springer.com/article/10.1007/s10032-014-0229-4" rel="nofollow" title="http://link.springer.com/article/10.1007/s10032-014-0229-4">Handwritten Hangul recognition using deep convolutional neural networks</a><br /> |
- | Bioinformatics, 31(5):761-3, 2015 | + | 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.biomedcentral.com/1471-2164/16/S2/S1|MixClone: a mixture model for inferring tumor subclonal populations]]\\ | + | <p><a class="urlextern" href="http://www.ncbi.nlm.nih.gov/pubmed/25359723" rel="nofollow" title="http://www.ncbi.nlm.nih.gov/pubmed/25359723">Genome-wide view of TGFbeta/Foxh1 regulation of the early mesendoderm</a> program<br /> |
- | Li Y and Xie X\\ | + | Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K<br /> |
- | BMC Genomics, 2015 | + | 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> | ||
- | [[http://www.ics.uci.edu/~xhx/publications/ImagingGenetics.pdf |Identifying unanticipated genes and mechanisms in serious mental illness]]\\ | + | <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 /> |
- | Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X\\ | + | Quang D and Xie X<br /> |
- | Neuroimaging genetics : principles and practices, 2015 | + | Bioinformatics, 2014</p> |
- | ==== 2014 ==== | + | <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> | ||
- | [[http://link.springer.com/article/10.1007/s10032-014-0229-4|Handwritten Hangul recognition using deep convolutional neural networks]]\\ | + | <p><a class="urlextern" href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092317" rel="nofollow" title="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092317">Integrative ChIP-seq/Microarray Analysis Identifies a CTNNB1 Target Signature Enriched in Intestinal Stem Cells and Colon Cancer</a><br /> |
- | Kim I and Xie X\\ | + | Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X<br /> |
- | International Journal on Document Analysis and Recognition, 2014\\ | + | PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317</p> |
- | [[http://www.ics.uci.edu/~xhx/publications/HHR.pdf| preprint]] | + | |
- | [[http://www.ncbi.nlm.nih.gov/pubmed/25359723|Genome-wide view of TGFbeta/Foxh1 regulation of the early mesendoderm]] program\\ | + | <p><a class="urlextern" href="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 /> |
- | Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K\\ | + | Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q<br /> |
- | Development, 2014 | + | BMC Systems Biology 2014, 8:3</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://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 /> |
- | Li Y and Xie X\\ | + | Lackford B, Yao C, Charles GM, Weng L, Zheng X, Choi EA, Xie X, Wan J, Xing Y, Freudenberg JM, Yang P, Jothi R, Hu G, Shi Y<br /> |
- | Bioinformatics, 2014 | + | EMBO J. 2014 Mar 4.</p> |
+ | </div> | ||
- | [[http://bioinformatics.oxfordjournals.org/content/early/2014/02/14/bioinformatics.btu093.abstract|EXTREME: An Online EM Algorithm for Motif Discovery]]\\ | + | <h3>2013</h3> |
- | Quang D and Xie X\\ | + | |
- | Bioinformatics, 2014 | + | |
- | [[http://www.biomedcentral.com/1471-2105/15/42|Improving Read Mapping Using Additional Prefix Grams]]\\ | + | <div class="level3"> |
- | Kim J, Li C 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 /> |
- | BMC Bioinformatics, 2014, 15(1):42 | + | Ye G, Tang M, Nie Q and Xie X<br /> |
+ | <em>PLOS ONE</em>, 2013</p> | ||
- | [[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092317|Integrative ChIP-seq/Microarray Analysis Identifies a CTNNB1 Target Signature Enriched in Intestinal Stem Cells and Colon Cancer]]\\ | + | <p><a class="urlextern" href="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 /> |
- | Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X\\ | + | Chen Y, Jia Z, Mercola D and Xie X<br /> |
- | PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317 | + | <em>Comput Math Methods Med.</em>, 2013</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="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 /> |
- | Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q\\ | + | Blitz I, Biesinger J, Xie X, and Cho K<br /> |
- | BMC Systems Biology 2014, 8:3 | + | <em>Genesis</em>, 2013.</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://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 3â² processing</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\\ | + | Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y<br /> |
- | EMBO J. 2014 Mar 4. | + | <em>RNA</em>, 2013</p> |
- | ==== 2013 ==== | + | |
- | [[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082146|Low-Rank Regularization for Learning Gene Expression Programs]] \\ | + | <p><a class="urlextern" href="http://arxiv.org/abs/1305.0855" rel="nofollow" title="http://arxiv.org/abs/1305.0855">Inference in Kingman's Coalescent with Particle Markov Chain Monte Carlo Method</a><br /> |
- | Ye G, Tang M, Nie Q and Xie X\\ | + | Chen Y and Xie X<br /> |
- | //PLOS ONE//, 2013 | + | <em>arXiv</em>, 2013</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://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 /> |
- | Chen Y, Jia Z, Mercola D and Xie X\\ | + | Biesinger J, Wang Y, and Xie X<br /> |
- | //Comput Math Methods Med.//, 2013 | + | <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://onlinelibrary.wiley.com/doi/10.1002/dvg.22719/abstract|Biallelic genome modification in F0 Xenopus tropicalis embryos using the CRISPR/Cas system]]\\ | + | <p><a class="urlextern" href="http://www.biomedcentral.com/1471-2105/14/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 /> |
- | Blitz I, Biesinger J, Xie X, and Cho K\\ | + | Li Y and Xie X<br /> |
- | //Genesis//, 2013. | + | <em>BMC Bioinformatics</em> 2013, 14(Suppl 5):S11, 2013</p> |
- | [[http://rnajournal.cshlp.org/content/early/2013/10/22/rna.042317.113.abstract|Overlapping and distinct functions of CstF64 and CstF64t in mammalian mRNA 3â² processing]]\\ | + | <p><a class="urlextern" href="http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6544889" rel="nofollow" title="http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6544889">Efficient direct search on compressed genomic data</a><br /> |
- | Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y\\ | + | Yang X, Wang B, Li C, Wang J, and Xie X<br /> |
- | //RNA//, 2013 | + | <em>IEEE International Conference on Data Engineering (ICDE)</em>, 2013</p> |
+ | </div> | ||
- | [[http://arxiv.org/abs/1305.0855|Inference in Kingman's Coalescent with Particle Markov Chain Monte Carlo Method]] \\ | + | <h3>2012</h3> |
- | Chen Y and Xie X \\ | + | |
- | //arXiv//, 2013 | + | |
- | [[http://www.biomedcentral.com/content/pdf/1471-2105-14-S5-S4.pdf|Discovering and Mapping Chromatin States Using a Tree Hidden Markov Model]] \\ | + | <div class="level3"> |
- | Biesinger J, Wang Y, and Xie X \\ | + | <p><a class="urlextern" href="http://www.springerlink.com/content/4l2m27p3867xj584/" rel="nofollow" title="http://www.springerlink.com/content/4l2m27p3867xj584/">Learning sparse gradients for variable selection and dimension reduction</a><br /> |
- | //BMC Bioinformatics// 2013, 14(S5):S4, 2013 \\ | + | Ye G and Xie X<br /> |
- | [[http://www.biomedcentral.com/content/supplementary/1471-2105-14-s5-s4-s1.pdf|Supplemental Information]] | + | 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/1471-2105/14/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/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 /> |
- | Li Y and Xie X \\ | + | Yao C, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y<br /> |
- | //BMC Bioinformatics// 2013, 14(Suppl 5):S11, 2013 | + | PNAS, 109(46):18773-8, 2012</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.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 /> |
- | Yang X, Wang B, Li C, Wang J, and Xie X \\ | + | Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF<br /> |
- | //IEEE International Conference on Data Engineering (ICDE)//, 2013 | + | BMC Genomics, 2012</p> |
- | ==== 2012 ==== | + | |
- | [[http://www.springerlink.com/content/4l2m27p3867xj584/|Learning sparse gradients for variable selection and dimension reduction]] \\ | + | <p><a class="urlextern" href="http://www.ncbi.nlm.nih.gov/pubmed/22199254" rel="nofollow" title="http://www.ncbi.nlm.nih.gov/pubmed/22199254">Hobbes: optimized gram-based methods for efficient read alignment</a><br /> |
- | Ye G and Xie X \\ | + | Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X<br /> |
- | Machine Learning Journal, 87(3):303-355, 2012 \\ | + | Nucleic Acids Research, 40(6):e41, 2012<br /> |
- | [[http://www.ics.uci.edu/~xhx/publications/SGL.pdf|Preprint]] | + | Software: <a class="urlextern" href="http://hobbes.ics.uci.edu/" rel="nofollow" title="http://hobbes.ics.uci.edu/">Hobbes</a></p> |
+ | </div> | ||
- | [[http://www.ncbi.nlm.nih.gov/pubmed/23112178|Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation]] \\ | + | <h3>2011</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://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 /> |
- | BMC Genomics, 2012 | + | Ye G, Wang Y, Chen Y, and Xie X<br /> |
+ | arXiv:1110.3076v1, 2011</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/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 /> |
- | Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X \\ | + | Daily K, Patel VR, Rigor P, Xie X, Baldi P.<br /> |
- | Nucleic Acids Research, 40(6):e41, 2012 \\ | + | BMC Bioinformatics, 2011</p> |
- | Software: [[http://hobbes.ics.uci.edu/|Hobbes]] | + | |
- | ==== 2011 ==== | + | <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> | ||
- | [[http://arxiv.org/pdf/1110.3076v1|Efficient latent variable graphical model selection via split Bregman method]] \\ | + | <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 /> |
- | Ye G, Wang Y, Chen Y, and Xie X \\ | + | Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X<br /> |
- | arXiv:1110.3076v1, 2011 | + | BMC Bioinformatics, 2011<br /> |
+ | Software: <a class="urlextern" href="http://cbcl.ics.uci.edu/SSEA/" rel="nofollow" title="http://cbcl.ics.uci.edu/SSEA/">SNP Set Enrichment Analysis (SSEA)</a></p> | ||
- | [[http://www.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.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 /> |
- | Daily K, Patel VR, Rigor P, Xie X, Baldi P. \\ | + | Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF<br /> |
- | BMC Bioinformatics, 2011 | + | <em>Cell Metabolism</em>, 13:367-75, 2011<br /> |
+ | <a class="urlextern" href="http://www.sciencedaily.com/releases/2011/04/110405122330.htm" rel="nofollow" title="http://www.sciencedaily.com/releases/2011/04/110405122330.htm">Science Daily coverage</a></p> | ||
- | [[http://www.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.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 /> |
- | Lindblad-Toh, Barber, Zuk, Lin, et al. \\ | + | Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X<br /> |
- | Nature, 2011 | + | <em>J Comput Biol.</em>, 2011<br /> |
+ | Software: <a class="urlextern" href="http://sourceforge.net/projects/arem" rel="nofollow" title="http://sourceforge.net/projects/arem">AREM</a></p> | ||
- | [[http://www.biomedcentral.com/1471-2105/12/99|SNP-based pathway enrichment analysis for genome-wide association studies]] \\ | + | <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 /> |
- | Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X \\ | + | Ye G, Chen Y, and Xie X<br /> |
- | BMC Bioinformatics, 2011 \\ | + | AI & STATS , 2011</p> |
- | Software: [[http://cbcl.ics.uci.edu/SSEA/|SNP Set Enrichment Analysis (SSEA)]] | + | </div> |
- | [[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 ]] \\ | + | <h3>2010</h3> |
- | Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF \\ | + | |
- | //Cell Metabolism//, 13:367-75, 2011 \\ | + | |
- | [[http://www.sciencedaily.com/releases/2011/04/110405122330.htm|Science Daily coverage]] | + | |
- | [[http://www.ics.uci.edu/~xhx/publications/arem_recomb.pdf|AREM: aligning short reads from ChIP-sequencing by expectation maximization]] \\ | + | <div class="level3"> |
- | Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X \\ | + | <p><a class="urlextern" href="http://arxiv4.library.cornell.edu/abs/1012.0975" rel="nofollow" title="http://arxiv4.library.cornell.edu/abs/1012.0975">Split Bregman method for sparse inverse covariance estimation with matrix iteration acceleration</a><br /> |
- | //J Comput Biol.//, 2011 \\ | + | Ye G, Cai J, and Xie X<br /> |
- | Software: [[http://sourceforge.net/projects/arem|AREM]] | + | arXiv:1012.0975v1, 2010</p> |
- | [[http://jmlr.csail.mit.edu/proceedings/papers/v15/ye11a/ye11a.pdf|Efficient variable selection in support vector machines via the alternating direction method of multipliers ]] \\ | + | <p><a class="urlextern" href="http://www.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" rel="nofollow" title="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</a><br /> |
- | Ye G, Chen Y, and Xie X \\ | + | Ye G-B and Xie X<br /> |
- | AI & STATS , 2011 | + | 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> | ||
- | ==== 2010 ==== | + | <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> | ||
- | [[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://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, Cai J, and Xie X \\ | + | Ye G-B and Xie X<br /> |
- | arXiv:1012.0975v1, 2010 | + | arXiv:1006.5060v2, 2010</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://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" rel="nofollow" title="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</a><br /> |
- | Ye G-B and Xie X \\ | + | Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X<br /> |
- | Computational Statistics and Data Analysis, doi:10.1016/j.csda.2010.10.021, 2010 \\ | + | <em>NeuroImage</em> 53:839-847, 2010</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://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 J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J \\ | + | Wang Y, Christley S, Mjolsness E, and Xie X<br /> |
- | //Bioinformatics//, 26(18):2321-2327, 2010 \\ | + | <em>BMC Systems Biology</em>, 4:99 doi:10.1186/1752-0509-4-99, 2010</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.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 /> |
- | Ye G-B and Xie X \\ | + | Xie X<br /> |
- | arXiv:1006.5060v2, 2010 | + | <em>Bulletin of Mathematical Biology</em>, DOI: 10.1007/s11538-010-9534-3, 2010</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://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 /> |
- | Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X \\ | + | Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and Osborne TF<br /> |
- | //NeuroImage// 53:839-847, 2010 | + | 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.biomedcentral.com/1752-0509/4/99|Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent]] \\ | + | <p><a class="urlextern" href="http://www.biomedcentral.com/1471-2164/11/208/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 /> |
- | Wang Y, Christley S, Mjolsness E, and Xie X \\ | + | Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X<br /> |
- | //BMC Systems Biology//, 4:99 doi:10.1186/1752-0509-4-99, 2010 | + | <em>BMC Genomics</em> 11:208, 2010<br /> |
+ | <a class="urlextern" href="http://www.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html" rel="nofollow" title="http://www.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html">Supplementary Information</a><br /> | ||
+ | <a class="urlextern" href="http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html" rel="nofollow" title="http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html">Fusarium Comparative Database</a></p> | ||
- | [[http://www.springerlink.com/content/428v02087m218878/fulltext.pdf|Site-frequency Spectrum of Linked Sites]] \\ | + | <p><a class="urlextern" href="http://www.nature.com/nature/journal/v464/n7287/abs/nature08850.html" rel="nofollow" title="http://www.nature.com/nature/journal/v464/n7287/abs/nature08850.html">Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium oxysporum</a><br /> |
- | Xie X \\ | + | Ma L-J, et al.<br /> |
- | //Bulletin of Mathematical Biology//, DOI: 10.1007/s11538-010-9534-3, 2010 | + | <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&hq_m=655129&hq_l=3&hq_v=dfec329446" rel="nofollow" title="http://www.genomeweb.com//node/936293?hq_e=el&hq_m=655129&hq_l=3&hq_v=dfec329446">Comparative genomics reveals horizontal gene transfer in pathogenic fungus</a><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://nar.oxfordjournals.org/cgi/content/abstract/gkq397|Genome-Wide Interrogation of Hepatic FXR Reveals an Asymmetric IR-1 Motif and Synergy with LRH-1]] \\ | + | <h3>2009</h3> |
- | Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and Osborne TF \\ | + | |
- | Nucleic Acids Research, doi:10.1093/nar/gkq397, 2010 \\ | + | |
- | [[http://cbcl.ics.uci.edu/public_data/FXR/|Online Supplementary Materials]] | + | |
- | [[http://www.biomedcentral.com/1471-2164/11/208/abstract|Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes]] \\ | + | <div class="level3"> |
- | Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X \\ | + | <p><a class="urlextern" href="http://www.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 /> |
- | //BMC Genomics// 11:208, 2010 \\ | + | Christley S, Nie Q and Xie X<br /> |
- | [[http://www.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html|Supplementary Information]] \\ | + | <em>PLoS ONE</em> 4(8): e6799. doi:10.1371/journal.pone.0006799 (2009)</p> |
- | [[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.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 /> |
- | Ma L-J, et al. \\ | + | Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF<br /> |
- | //Nature// 464:367-373, 2010 \\ | + | <em>Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0904246106 (2009)</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://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> | ||
- | [[http://www.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf|Incorporating existing network information into gene network inference]] \\ | + | <p><a class="urlextern" href="http://www.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 /> |
- | Christley S, Nie Q and Xie X \\ | + | Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA<br /> |
- | //PLoS ONE// 4(8): e6799. doi:10.1371/journal.pone.0006799 (2009) | + | <em>Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0813264106 (2009)</p> |
- | [[http://www.pnas.org/content/early/2009/08/03/0904246106.abstract|Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif]] \\ | + | <p><a class="urlextern" href="http://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 /> |
- | Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF \\ | + | Fraser H and Xie X<br /> |
- | //Proc Natl Acad Sci USA// doi:10.1073/pnas.0904246106 (2009) | + | <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://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/12/i54|Identifying novel constrained elements by exploiting biased substitution patterns]] \\ | + | <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 /> |
- | Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X \\ | + | Xie X, Rigor P, and Baldi P<br /> |
- | //Bioinformatics//25:i54-i62 (2009) \\ | + | <em>Bioinformatics</em> 25: 167-174 (2009)<br /> |
- | [[http://www.ics.uci.edu/~xhx/publications/siphy_suppinfo.pdf|Supplementary Methods]] \\ | + | <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 /> |
- | [[http://www.broadinstitute.org/genome_bio/siphy/|SiPhy (SIte-specific PHYlogenetic analysis) Java software package]] | + | <a class="urlextern" href="http://motifmap.ics.uci.edu/" rel="nofollow" title="http://motifmap.ics.uci.edu/">MotifMap Server</a></p> |
- | [[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://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 /> |
- | Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA \\ | + | Christley S, Lu Y, Li C, and Xie X<br /> |
- | //Proc Natl Acad Sci USA// doi:10.1073/pnas.0813264106 (2009) | + | <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-watson�s-genome-e-mail-uc-irvine-team-develops-method-compress-genomic-data" rel="nofollow" title="http://www.genomeweb.com/informatics/jim-watson�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> | ||
- | [[http://genome.cshlp.org/content/19/4/567.long|Common polymorphic transcript variation in human disease]] \\ | + | <h3>2008</h3> |
- | Fraser H and Xie X \\ | + | |
- | //Genome Research// doi:10.1101/gr.083477.108 (2009) \\ | + | |
- | [[http://www.ics.uci.edu/~xhx/publications/PTV_GR2009.pdf|PDF]] | + | |
- | [[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/167|MotifMap: a human genome-wide map of candidate regulatory motif sites ]] \\ | + | <div class="level3"> |
- | Xie X, Rigor P, and Baldi P \\ | + | <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 /> |
- | //Bioinformatics// 25: 167-174 (2009) \\ | + | Wu J, Sieglaff DH, Gervin J, and Xie X<br /> |
- | [[http://www.ics.uci.edu/~xhx/publications/MotifMap_Supp_Info.pdf|Supplementary Methods]] \\ | + | <em>Bioinformatics </em> 24:1843-9 (2008)<br /> |
- | [[http://motifmap.ics.uci.edu/|MotifMap Server]] | + | <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://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/274|Human genomes as email attachments ]] \\ | + | <p><a class="urlextern" href="http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2567431&blobtype=pdf" rel="nofollow" title="http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2567431&blobtype=pdf">Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains </a><br /> |
- | Christley S, Lu Y, Li C, and Xie X \\ | + | 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 /> |
- | //Bioinformatics // 25: 274-275 (2009) \\ | + | <em>PLoS </em><em>Genetics</em>4(10):e1000242 (2008)</p> |
- | [[http://www.ics.uci.edu/~xhx/project/DNAzip|DNAzip: DNA sequence compression using a reference genome]] \\ | + | </div> |
- | [[http://www.ics.uci.edu/~xhx/publications/DNAzip.pdf|PDF]] \\ | + | |
- | [[http://www.genomeweb.com/informatics/jim-watson�s-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 ==== | + | <h3>2007</h3> |
- | [[http://www.ics.uci.edu/~xhx/publications/wu_motif_2008.pdf|Discovering regulatory motifs in the Plasmodium genome using comparative genomics ]] \\ | + | <div class="level3"> |
- | Wu J, Sieglaff DH, Gervin J, and Xie X \\ | + | <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 /> |
- | //Bioinformatics // 24:1843-9 (2008) \\ | + | Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, and Lander ES.<br /> |
- | [[http://www.ics.uci.edu/~xhx/project/mdos/|MDOS software]]: A method for Motif Discovery using Orthologous Sequences (alignment independent). \\ | + | <em>Proc Natl Acad Sci </em><em>USA</em>104(49):19428-33 (2007)</p> |
- | [[http://www.ics.uci.edu/~xhx/publications/wu_motif_2008_suppinfo.pdf|Supplementary Information on the MDOS algorithm]] | + | |
- | [[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2567431&blobtype=pdf|Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains ]] \\ | + | <p><a class="urlextern" href="http://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 /> |
- | 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 \\ | + | 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 /> |
- | //PLoS Genetics//4(10):e1000242 (2008) | + | <em>Nature</em>449:913-918 (2007)</p> |
- | ==== 2007 ==== | + | |
- | [[http://www.pnas.org/content/104/49/19428|Distinguishing protein-coding and noncoding genes in the human genome ]] \\ | + | <p><a class="urlextern" href="http://www.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 /> |
- | Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, and Lander ES. \\ | + | 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.<br /> |
- | //Proc Natl Acad Sci USA//104(49):19428-33 (2007) | + | <em>Nature</em> 448:553-60 (2007)</p> |
- | [[http://www.nature.com/nature/journal/v449/n7164/abs/nature06250.html|Genome-wide detection and characterization of positive selection in human populations ]] \\ | + | <p><a class="urlextern" href="http://www.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 /> |
- | 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 \\ | + | Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES.<br /> |
- | //Nature//449:913-918 (2007) | + | <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.nature.com/nature/journal/v448/n7153/abs/nature06008.html|Geome-wide maps of chromatin state in pluripotent and lineage-committed cells ]] \\ | + | <p><a class="urlextern" href="http://www.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, 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. \\ | + | Mikkelsen TS, Wakefield MJ, et al.<br /> |
- | //Nature// 448:553-60 (2007) | + | <em>Nature</em> 447:167-177 (2007)</p> |
- | [[http://www.ics.uci.edu/~xhx/publications/insulators_pnas06.pdf|Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites ]] \\ | + | <p><a class="urlextern" href="http://www.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, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES. \\ | + | Xie X, Kamal M, and Lander ES.<br /> |
- | //Proc Natl Acad Sci USA//104:7145-7150 (2007) \\ | + | <em>Proc Natl Acad Sci </em><em>USA</em>103:11659-11664 (2006)<br /> |
- | [[http://www.broad.mit.edu/personal/xhx/projects/CNEMOTIF/|Supplementary website]] [[http://www.pnas.org/cgi/content/full/0701811104/DC1|Supporting Information]] [[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=3042|News story]] | + | <a class="urlextern" href="http://www.broad.mit.edu/seq/pubs/xie_pnas2006/" rel="nofollow" title="http://www.broad.mit.edu/seq/pubs/xie_pnas2006/">Supplementary website</a> <a class="urlextern" href="http://www.pnas.org/cgi/content/full/0604768103/DC1" rel="nofollow" title="http://www.pnas.org/cgi/content/full/0604768103/DC1">Supporting Information</a> <a class="urlextern" href="http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=1881" rel="nofollow" title="http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=1881">News story</a></p> |
+ | </div> | ||
- | [[http://www.nature.com/nature/journal/v447/n7141/pdf/nature05805.pdf|Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences ]] \\ | + | <h3>2006 or before</h3> |
- | Mikkelsen TS, Wakefield MJ, et al. \\ | + | |
- | //Nature// 447:167-177 (2007) | + | |
- | [[http://www.ics.uci.edu/~xhx/publications/Xie_AMCNE.pdf|A family of conserved noncoding elements derived from an ancient transposable element]] \\ | + | <div class="level3"> |
- | Xie X, Kamal M, and Lander ES. \\ | + | <p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/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 /> |
- | //Proc Natl Acad Sci USA//103:11659-11664 (2006) \\ | + | Kamal M, Xie X, and Lander ES.<br /> |
- | [[http://www.broad.mit.edu/seq/pubs/xie_pnas2006/|Supplementary website]] [[http://www.pnas.org/cgi/content/full/0604768103/DC1|Supporting Information]] [[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=1881|News story]] | + | <em>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> | ||
- | ==== 2006 or before ==== | + | <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> | ||
- | [[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://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 /> |
- | Kamal M, Xie X, and Lander ES. \\ | + | Wu J and Xie X<br /> |
- | //Proc Natl Acad Sci USA//103:2740-2745 (2006) \\ | + | <em>Genome </em><em>Biology</em>7(9):R85 (2006) (Highly accessed)<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.broad.mit.edu/personal/xhx/projects/NRSE" rel="nofollow" title="http://www.broad.mit.edu/personal/xhx/projects/NRSE">Supplementary website</a></p> |
- | [[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=381|News story]] | + | |
- | [[http://download.cell.com/pdfs/0092-8674/PIIS0092867406003801.pdf|A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells]] \\ | + | <p><a class="urlextern" href="http://www.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 /> |
- | Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al. \\ | + | Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK.<br /> |
- | //Cell// 125:315-26 (2006) | + | <em>Nature Genetics</em>, 38:576-82 (2006)</p> |
- | [[http://genomebiology.com/2006/7/9/R85|Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression ]] \\ | + | <p><a class="urlextern" href="http://www.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' UTRs by comparison of several mammals </a><br /> |
- | Wu J and Xie X \\ | + | Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M.<br /> |
- | //Genome Biology//7(9):R85 (2006) (Highly accessed) \\ | + | <em>Nature</em>2005; 434:338-45<br /> |
- | [[http://www.broad.mit.edu/personal/xhx/projects/NRSE|Supplementary website]] | + | <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> |
- | [[http://www.nature.com/ng/journal/v38/n5/pdf/ng1776.pdf|Systematic identification of human mitochondrial disease genes through integrative genomics ]] \\ | + | <p><a class="urlextern" href="http://www.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 /> |
- | Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK. \\ | + | Giallourakis C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R.<br /> |
- | //Nature Genetics//, 38:576-82 (2006) | + | <em>Genome Resesarch</em>, 16:1056-72 (2006)</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://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 /> |
- | Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M. \\ | + | Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M.<br /> |
- | //Nature//2005; 434:338-45 \\ | + | <em>Cell</em> 125:187-99 (2006)</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://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 /> |
- | Giallourakis C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R. \\ | + | Werfel J, Xie X and Seung HS.<br /> |
- | //Genome Resesarch//, 16:1056-72 (2006) | + | <em>Neural Computation</em>, 2005;17:2699-718</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.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 /> |
- | Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M. \\ | + | Lindblad-Toh K, Wade CM, et al.<br /> |
- | //Cell// 125:187-99 (2006) | + | <em>Nature</em> 438:803-19 2005</p> |
- | [[http://www.ics.uci.edu/~xhx/publications/WerfelXieSeung2005.pdf|Learning curves for stochastic gradient descent in linear feedforward networks. ]] \\ | + | <p><a class="urlextern" href="http://www.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 /> |
- | Werfel J, Xie X and Seung HS. \\ | + | Giallourakis C, Henson C, Reich M, Xie X, and Mootha VK.<br /> |
- | //Neural Computation//, 2005;17:2699-718 | + | <em>Annu. Rev. Genomics Hum. Genet.</em> 2005:22:381-406.</p> |
- | [[http://www.nature.com/nature/journal/v438/n7069/pdf/nature04338.pdf|Genome sequence, comparative analysis and haplotype structure of the domestic dog ]] \\ | + | <p><a class="urlextern" href="http://www.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 /> |
- | Lindblad-Toh K, Wade CM, et al. \\ | + | Xie X and Seung HS.<br /> |
- | //Nature// 438:803-19 2005 | + | <em>Phys Rev E</em>, 2004;69:041909</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://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 /> |
- | Giallourakis C, Henson C, Reich M, Xie X, and Mootha VK. \\ | + | Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al.<br /> |
- | //Annu. Rev. Genomics Hum. Genet.// 2005:22:381-406. | + | <em>Proc Natl Acad Sci USA</em>, 2004;101:6570-5</p> |
- | [[http://www.ics.uci.edu/~xhx/publications/PhysRevE_69_041909.pdf|Learning in neural networks by reinforcement of irregular spiking. ]] \\ | + | <p><a class="urlextern" href="http://www.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 and Seung HS. \\ | + | Xie X, Hahnloser RH, and Seung HS.<br /> |
- | //Phys Rev E//, 2004;69:041909 | + | <em>Physical Review E</em>, 2002;66:041902</p> |
- | [[http://www.ics.uci.edu/~xhx/publications/mootha_pgc1a.pdf|Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle]] \\ | + | <p><a class="urlextern" href="http://www.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 /> |
- | Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al. \\ | + | Xie X and Giese MA.<br /> |
- | //Proc Natl Acad Sci USA//, 2004;101:6570-5 | + | <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> | ||
- | [[http://www.ics.uci.edu/~xhx/publications/PhysRevE_66_041902.pdf|The double-ring network modeling of the head-direction system]] \\ | + | <p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/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 RH, and Seung HS. \\ | + | Xie X, Hahnloser HR, and Seung HS.<br /> |
- | //Physical Review E//, 2002;66:041902 | + | <em>Advances in Neural Information Processing </em><em>Systems</em>2001;13:350-356</p> |
- | [[http://www.ics.uci.edu/~xhx/publications/PhysRevE_65_051904.pdf|Nonlinear dynamics of direction-selective recurrent neural media]] \\ | + | <p><a class="urlextern" href="http://www.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. \\ | + | Xie X and Giese MA.<br /> |
- | //Physical Review E//, 2002;65:051904 [[http://www.ics.uci.edu/~xhx/publications/neurocomp_giese.pdf|Exact solution of the nonlinear dynamics of recurrent neural mechanisms for direction selectivity]] \\ | + | <em>Advances in Neural Information Processing </em><em>Systems</em>2002;13:325-332</p> |
- | Giese MA and Xie X \\ | + | |
- | //Neurocomputing// 2002;44:417-422 | + | |
- | [[http://www.ics.uci.edu/~xhx/publications/lwta.pdf|Learning winner-take-all competition between groups of neurons in lateral inhibitory networks ]] \\ | + | <p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/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 HR, and Seung HS. \\ | + | Xie X, Hahnloser RH, and Seung HS.<br /> |
- | //Advances in Neural Information Processing Systems//2001;13:350-356 | + | <em>Neural Computation</em>, 2002;14:2627-2646</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.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 Giese MA. \\ | + | Xie X and Seung HS.<br /> |
- | //Advances in Neural Information Processing Systems//2002;13:325-332 | + | <em>Neural Computation</em>, 2003;16:441-454</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.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, Hahnloser RH, and Seung HS. \\ | + | Xie X<br /> |
- | //Neural Computation//, 2002;14:2627-2646 | + | <em>Network: Comput. Neural Syst.</em> 2002;13:447-456</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/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. \\ | + | Xie X and Seung HS<br /> |
- | //Neural Computation//, 2003;16:441-454 | + | <em>Advances in Neural Information Processing Systems</em>, 2000;12:199-205</p> |
+ | </div> | ||
- | [[http://www.ics.uci.edu/~xhx/publications/network_pop.pdf|Threshold behavior of maximum likelihood method in population decoding]] \\ | ||
- | Xie X \\ | ||
- | //Network: Comput. Neural Syst.// 2002;13:447-456 | ||
- | |||
- | [[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 | ||