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+ | <h2>Publications</h2> | ||
+ | <div class="level2"> </div> | ||
- | ===== Publications ===== | + | <h3>2018</h3> |
- | ==== 2017 ==== | + | <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> | ||
- | Adversarial Deep Structured Nets for Mass Segmentation from Mammograms\\ | + | <p>Sequential Embedding Induced Nonparametric Text Clustering<br /> |
- | W Zhu, X Xiang, T Tran, GD Hager, X Xie\\ | + | Duan T, Lou Q, Xie X</p> |
- | IEEE International Symposium on Biomedical Imaging | + | |
- | Automated Pulmonary Nodule Detection Using 3D Deep Convolutional Neural Networks\\ | + | <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 /> |
- | H Tang, D Kim, X Xie\\ | + | Vang S, Chen Z, Xie X<br /> |
- | IEEE International Symposium on Biomedical Imaging | + | 15th International Conference on Image Analysis and Recognition, 2018</p> |
- | Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.\\ | + | <p><a class="urlextern" href="https://arxiv.org/abs/1801.07853" rel="nofollow" title="https://arxiv.org/abs/1801.07853">Structed Triplets Learning with Pos-tag Guided Attention for Visual Question Answering</a><br /> |
- | Zhu Y, Wang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.\\ | + | IEEE Winter Conf. on Applications of Computer Vision 2018</p> |
- | Mol Cell. 2018 Jan 4;69(1):62-74.e4. | + | |
+ | <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> | ||
- | [[https://arxiv.org/abs/1709.05538 | DeepLung: 3D Deep Convolutional Nets for Automated Pulmonary Nodule Detection and Classification]]\\ | + | <p>Adversarial Deep Structured Nets for Mass Segmentation from Mammograms<br /> |
- | W Zhu, C Liu, W Fan, X Xie\\ | + | W Zhu, X Xiang, T Tran, GD Hager, X Xie<br /> |
- | arXiv preprint arXiv:1709.05538 | + | 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> | ||
- | [[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>Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.<br /> |
- | D Quang, X Xie\\ | + | Zhu Y, Wang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y.<br /> |
- | bioRxiv, 151274 | + | Mol Cell. 2018 Jan 4;69(1):62-74.e4.</p> |
+ | </div> | ||
+ | <h3>2017</h3> | ||
- | [[https://arxiv.org/abs/1612.05968|Deep Multi-instance Networks with Sparse Label Assignment for Whole Mammogram Classification]]\\ | + | <div class="level3"> |
- | Wentao Zhu, Qi Lou, Yeeleng Scott Vang, Xiaohui Xie \\ | + | <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 /> |
- | arXiv:1612.05968\\ | + | W Zhu, C Liu, W Fan, X Xie<br /> |
- | [[http://www.miccai2017.org/| MICCAI, 2017]] | + | arXiv preprint arXiv:1709.05538</p> |
- | Understanding sequence conservation with deep learning\\ | + | <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 /> |
- | Li Y, Quang D, and Xie X\\ | + | D Quang, X Xie<br /> |
- | ACM BCB, 2017 | + | bioRxiv, 151274</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://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 /> |
- | Vang YS and Xie X\\ | + | Wentao Zhu, Qi Lou, Yeeleng Scott Vang, Xiaohui Xie<br /> |
- | Bioinformatics, 2017 | + | arXiv:1612.05968<br /> |
+ | <a class="urlextern" href="http://www.miccai2017.org/" rel="nofollow" title="http://www.miccai2017.org/">MICCAI, 2017</a></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>Understanding sequence conservation with deep learning<br /> |
- | Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW\\ | + | Li Y, Quang D, and Xie X<br /> |
- | Dev Cell. 27;40(6):595-607.e4, 2017 | + | ACM BCB, 2017</p> |
- | ==== 2016 ==== | + | <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> | ||
- | [[https://arxiv.org/abs/1612.05970|Adversarial Deep Structural Networks for Mammographic Mass Segmentation]]\\ | + | <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 /> |
- | Wentao Zhu, Xiaohui Xie\\ | + | Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW<br /> |
- | arXiv:1612.05970 | + | Dev Cell. 27;40(6):595-607.e4, 2017</p> |
+ | </div> | ||
- | [[https://www.ncbi.nlm.nih.gov/pubmed/27418388|Developmentally regulated long non-coding RNAs in Xenopus tropicalis]]\\ | + | <h3>2016</h3> |
- | Forouzmand et al. \\ | + | |
- | Developmental Biology, (16)30120-8 2016 | + | |
- | [[http://bioinformatics.oxfordjournals.org/content/early/2016/02/11/bioinformatics.btw074.short?rss=1|Gene expression inference with deep learning]]\\ | + | <div class="level3"> |
- | Chen Y, Li Y, Narayan R, Subramanian A, 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 /> |
- | Bioinformatics, 2016 | + | Wentao Zhu, Xiaohui Xie<br /> |
+ | arXiv:1612.05970</p> | ||
- | DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences\\ | + | <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 /> |
- | Quang D and Xie X\\ | + | Forouzmand et al.<br /> |
- | Nucleic Acids Research, 2016 | + | Developmental Biology, (16)30120-8 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://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 /> |
- | Weng L, Li Y, Xie X, and Shi Y\\ | + | Chen Y, Li Y, Narayan R, Subramanian A, and Xie X<br /> |
- | RNA, 2016 | + | Bioinformatics, 2016</p> |
- | [[https://www.researchgate.net/profile/Wentao_Zhu4/publication/283748673_Co-occurrence_Feature_Learning_for_Skeleton_based_Action_Recognition_using_Regularized_Deep_LSTM_Networks/links/567a2bc808ae7fea2e98bf6b.pdf|Co-occurrence Feature Learning for Skeleton based Action Recognition using Regularized Deep LSTM Networks]]\\ | + | <p>DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences<br /> |
- | Zhu W, et al.\\ | + | Quang D and Xie X<br /> |
- | AAAI Conference on Artificial Intelligence, 2016 | + | Nucleic Acids Research, 2016</p> |
- | ==== 2015 ==== | + | <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> | ||
- | Hobbes3: Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings\\ | + | <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 /> |
- | Kim J, Chen L, and Xie X\\ | + | Zhu W, et al.<br /> |
- | 32nd IEEE International Conference on Data Engineering - ICDE 2016 | + | AAAI Conference on Artificial Intelligence, 2016</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>2015</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>Hobbes3: Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings<br /> |
- | Bioinformatics, 31(5):761-3, 2015 | + | Kim J, Chen L, and Xie X<br /> |
+ | 32nd IEEE International Conference on Data Engineering - ICDE 2016</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://biorxiv.org/content/early/2015/12/20/032821" rel="nofollow" title="http://biorxiv.org/content/early/2015/12/20/032821">DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences</a><br /> |
- | Li Y and Xie X\\ | + | Quang D and Xie X</p> |
- | BMC Genomics, 2015 | + | |
+ | <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> | ||
- | [[http://www.ics.uci.edu/~xhx/publications/ImagingGenetics.pdf |Identifying unanticipated genes and mechanisms in serious mental illness]]\\ | + | <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 /> |
- | Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X\\ | + | Li Y and Xie X<br /> |
- | Neuroimaging genetics : principles and practices, 2015 | + | BMC Genomics, 2015</p> |
- | ==== 2014 ==== | + | <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> | ||
- | [[http://link.springer.com/article/10.1007/s10032-014-0229-4|Handwritten Hangul recognition using deep convolutional neural networks]]\\ | + | <h3>2014</h3> |
- | Kim I and Xie X\\ | + | |
- | International Journal on Document Analysis and Recognition, 2014\\ | + | |
- | [[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\\ | + | <div class="level3"> |
- | Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K\\ | + | <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 /> |
- | Development, 2014 | + | 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://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://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 /> |
- | Bioinformatics, 2014 | + | Development, 2014</p> |
- | [[http://bioinformatics.oxfordjournals.org/content/early/2014/02/14/bioinformatics.btu093.abstract|EXTREME: An Online EM Algorithm for Motif Discovery]]\\ | + | <p><a class="urlextern" href="http://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 /> |
- | Quang D and Xie X\\ | + | Li Y and Xie X<br /> |
- | Bioinformatics, 2014 | + | Bioinformatics, 2014</p> |
- | [[http://www.biomedcentral.com/1471-2105/15/42|Improving Read Mapping Using Additional Prefix Grams]]\\ | + | <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 /> |
- | Kim J, Li C and Xie X\\ | + | Quang D and Xie X<br /> |
- | BMC Bioinformatics, 2014, 15(1):42 | + | Bioinformatics, 2014</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.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 /> |
- | Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X\\ | + | Kim J, Li C and Xie X<br /> |
- | PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317 | + | BMC Bioinformatics, 2014, 15(1):42</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://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 /> |
- | Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q\\ | + | Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X<br /> |
- | BMC Systems Biology 2014, 8:3 | + | PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317</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://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 /> |
- | 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\\ | + | Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q<br /> |
- | EMBO J. 2014 Mar 4. | + | BMC Systems Biology 2014, 8:3</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://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 /> |
- | Ye G, Tang M, Nie Q 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 /> |
- | //PLOS ONE//, 2013 | + | EMBO J. 2014 Mar 4.</p> |
+ | </div> | ||
- | [[http://www.hindawi.com/journals/cmmm/2013/873595/|A gradient boosting algorithm for survival analysis via direct optimization of concordance index]] \\ | + | <h3>2013</h3> |
- | Chen Y, Jia Z, Mercola D and Xie X\\ | + | |
- | //Comput Math Methods Med.//, 2013 | + | |
- | [[http://onlinelibrary.wiley.com/doi/10.1002/dvg.22719/abstract|Biallelic genome modification in F0 Xenopus tropicalis embryos using the CRISPR/Cas system]]\\ | + | <div class="level3"> |
- | Blitz I, Biesinger J, Xie X, and Cho K\\ | + | <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 /> |
- | //Genesis//, 2013. | + | Ye G, Tang M, Nie Q and Xie X<br /> |
+ | <em>PLOS ONE</em>, 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://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 /> |
- | Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y\\ | + | Chen Y, Jia Z, Mercola D and Xie X<br /> |
- | //RNA//, 2013 | + | <em>Comput Math Methods Med.</em>, 2013</p> |
- | [[http://arxiv.org/abs/1305.0855|Inference in Kingman's Coalescent with Particle Markov Chain Monte Carlo Method]] \\ | + | <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 /> |
- | Chen Y and Xie X \\ | + | Blitz I, Biesinger J, Xie X, and Cho K<br /> |
- | //arXiv//, 2013 | + | <em>Genesis</em>, 2013.</p> |
- | [[http://www.biomedcentral.com/content/pdf/1471-2105-14-S5-S4.pdf|Discovering and Mapping Chromatin States Using a Tree Hidden Markov Model]] \\ | + | <p><a class="urlextern" href="http://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 /> |
- | Biesinger J, Wang Y, and Xie X \\ | + | Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y<br /> |
- | //BMC Bioinformatics// 2013, 14(S5):S4, 2013 \\ | + | <em>RNA</em>, 2013</p> |
- | [[http://www.biomedcentral.com/content/supplementary/1471-2105-14-s5-s4-s1.pdf|Supplemental Information]] | + | |
- | [[http://www.biomedcentral.com/1471-2105/14/S5/S11|A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues]] \\ | + | <p><a class="urlextern" href="http://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 /> |
- | Li Y and Xie X \\ | + | Chen Y and Xie X<br /> |
- | //BMC Bioinformatics// 2013, 14(Suppl 5):S11, 2013 | + | <em>arXiv</em>, 2013</p> |
- | [[http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6544889|Efficient direct search on compressed genomic data]] \\ | + | <p><a class="urlextern" href="http://www.biomedcentral.com/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 /> |
- | Yang X, Wang B, Li C, Wang J, and Xie X \\ | + | Biesinger J, Wang Y, and Xie X<br /> |
- | //IEEE International Conference on Data Engineering (ICDE)//, 2013 | + | <em>BMC Bioinformatics</em> 2013, 14(S5):S4, 2013<br /> |
- | ==== 2012 ==== | + | <a class="urlextern" href="http://www.biomedcentral.com/content/supplementary/1471-2105-14-s5-s4-s1.pdf" rel="nofollow" title="http://www.biomedcentral.com/content/supplementary/1471-2105-14-s5-s4-s1.pdf">Supplemental Information</a></p> |
- | [[http://www.springerlink.com/content/4l2m27p3867xj584/|Learning sparse gradients for variable selection and dimension reduction]] \\ | + | <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 /> |
- | Ye G and Xie X \\ | + | Li Y and Xie X<br /> |
- | Machine Learning Journal, 87(3):303-355, 2012 \\ | + | <em>BMC Bioinformatics</em> 2013, 14(Suppl 5):S11, 2013</p> |
- | [[http://www.ics.uci.edu/~xhx/publications/SGL.pdf|Preprint]] | + | |
- | [[http://www.ncbi.nlm.nih.gov/pubmed/23112178|Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation]] \\ | + | <p><a class="urlextern" href="http://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, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y \\ | + | Yang X, Wang B, Li C, Wang J, and Xie X<br /> |
- | PNAS, 109(46):18773-8, 2012 | + | <em>IEEE International Conference on Data Engineering (ICDE)</em>, 2013</p> |
+ | </div> | ||
- | [[http://www.ncbi.nlm.nih.gov/pubmed/22296850|Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR]] \\ | + | <h3>2012</h3> |
- | Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF \\ | + | |
- | BMC Genomics, 2012 | + | |
- | [[http://www.ncbi.nlm.nih.gov/pubmed/22199254|Hobbes: optimized gram-based methods for efficient read alignment]] \\ | + | <div class="level3"> |
- | Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X \\ | + | <p><a class="urlextern" href="http://www.springerlink.com/content/4l2m27p3867xj584/" rel="nofollow" title="http://www.springerlink.com/content/4l2m27p3867xj584/">Learning sparse gradients for variable selection and dimension reduction</a><br /> |
- | Nucleic Acids Research, 40(6):e41, 2012 \\ | + | Ye G and Xie X<br /> |
- | Software: [[http://hobbes.ics.uci.edu/|Hobbes]] | + | 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> | ||
- | ==== 2011 ==== | + | <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> | ||
- | [[http://arxiv.org/pdf/1110.3076v1|Efficient latent variable graphical model selection via split Bregman method]] \\ | + | <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 /> |
- | Ye G, Wang Y, Chen Y, and Xie X \\ | + | Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF<br /> |
- | arXiv:1110.3076v1, 2011 | + | BMC Genomics, 2012</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.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 /> |
- | Daily K, Patel VR, Rigor P, Xie X, Baldi P. \\ | + | Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X<br /> |
- | BMC Bioinformatics, 2011 | + | Nucleic Acids Research, 40(6):e41, 2012<br /> |
+ | Software: <a class="urlextern" href="http://hobbes.ics.uci.edu/" rel="nofollow" title="http://hobbes.ics.uci.edu/">Hobbes</a></p> | ||
+ | </div> | ||
- | [[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10530.html|A high-resolution map of human evolutionary constraint using 29 mammals]] \\ | + | <h3>2011</h3> |
- | Lindblad-Toh, Barber, Zuk, Lin, et al. \\ | + | |
- | Nature, 2011 | + | |
- | [[http://www.biomedcentral.com/1471-2105/12/99|SNP-based pathway enrichment analysis for genome-wide association studies]] \\ | + | <div class="level3"> |
- | Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X \\ | + | <p><a class="urlextern" href="http://arxiv.org/pdf/1110.3076v1" rel="nofollow" title="http://arxiv.org/pdf/1110.3076v1">Efficient latent variable graphical model selection via split Bregman method</a><br /> |
- | BMC Bioinformatics, 2011 \\ | + | Ye G, Wang Y, Chen Y, and Xie X<br /> |
- | Software: [[http://cbcl.ics.uci.edu/SSEA/|SNP Set Enrichment Analysis (SSEA)]] | + | arXiv:1110.3076v1, 2011</p> |
- | [[http://www.cell.com/cell-metabolism/abstract/S1550-4131(11)00092-1|Genome-wide Positioning of SREBP-2 in Hepatic Chromatin Predicts a Novel Role in Autophagy ]] \\ | + | <p><a class="urlextern" href="http://www.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 /> |
- | Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF \\ | + | Daily K, Patel VR, Rigor P, Xie X, Baldi P.<br /> |
- | //Cell Metabolism//, 13:367-75, 2011 \\ | + | BMC Bioinformatics, 2011</p> |
- | [[http://www.sciencedaily.com/releases/2011/04/110405122330.htm|Science Daily coverage]] | + | |
- | [[http://www.ics.uci.edu/~xhx/publications/arem_recomb.pdf|AREM: aligning short reads from ChIP-sequencing by expectation maximization]] \\ | + | <p><a class="urlextern" href="http://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 /> |
- | Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X \\ | + | Lindblad-Toh, Barber, Zuk, Lin, et al.<br /> |
- | //J Comput Biol.//, 2011 \\ | + | Nature, 2011</p> |
- | Software: [[http://sourceforge.net/projects/arem|AREM]] | + | |
- | [[http://jmlr.csail.mit.edu/proceedings/papers/v15/ye11a/ye11a.pdf|Efficient variable selection in support vector machines via the alternating direction method of multipliers ]] \\ | + | <p><a class="urlextern" href="http://www.biomedcentral.com/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, Chen Y, and Xie X \\ | + | Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and Xie X<br /> |
- | AI & STATS , 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> | ||
- | ==== 2010 ==== | + | <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> | ||
- | [[http://arxiv4.library.cornell.edu/abs/1012.0975|Split Bregman method for sparse inverse covariance estimation with matrix iteration acceleration]] \\ | + | <p><a class="urlextern" href="http://www.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 /> |
- | Ye G, Cai J, and Xie X \\ | + | Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X<br /> |
- | arXiv:1012.0975v1, 2010 | + | <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.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://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-B and Xie X \\ | + | Ye G, Chen Y, and Xie X<br /> |
- | Computational Statistics and Data Analysis, doi:10.1016/j.csda.2010.10.021, 2010 \\ | + | AI & STATS , 2011</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]] \\ | + | </div> |
- | 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 ]] \\ | + | <h3>2010</h3> |
- | Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J \\ | + | |
- | //Bioinformatics//, 26(18):2321-2327, 2010 \\ | + | |
- | [[http://ipubmed.ics.uci.edu/|iPubMed Search]] | + | |
- | [[http://arxiv.org/abs/1006.5060|Variable selection and dimension reduction via sparse gradients]] \\ | + | <div class="level3"> |
- | Ye G-B 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 /> |
- | arXiv:1006.5060v2, 2010 | + | Ye G, Cai J, and Xie X<br /> |
+ | arXiv:1012.0975v1, 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://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 /> |
- | Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X \\ | + | Ye G-B and Xie X<br /> |
- | //NeuroImage// 53:839-847, 2010 | + | Computational Statistics and Data Analysis, doi:10.1016/j.csda.2010.10.021, 2010<br /> |
+ | <a class="urlextern" href="http://arxiv.org/abs/1006.5086" rel="nofollow" title="http://arxiv.org/abs/1006.5086">arXiv version</a> <a class="urlextern" href="http://www.biomedcentral.com/1471-2105/11/514" rel="nofollow" title="http://www.biomedcentral.com/1471-2105/11/514">Data Structures and Compression Algorithms for High-Throughput Sequencing Technologies</a><br /> | ||
+ | Daily K, Rigor P, Christley S, Xie X and Baldi P<br /> | ||
+ | <em>BMC Bioinformatics</em>,11:514, 2010</p> | ||
- | [[http://www.biomedcentral.com/1752-0509/4/99|Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent]] \\ | + | <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 Y, Christley S, Mjolsness E, and Xie X \\ | + | Wang J, Cetindil I, Ji S, Li C, Xie X, Li G and Feng J<br /> |
- | //BMC Systems Biology//, 4:99 doi:10.1186/1752-0509-4-99, 2010 | + | <em>Bioinformatics</em>, 26(18):2321-2327, 2010<br /> |
+ | <a class="urlextern" href="http://ipubmed.ics.uci.edu/" rel="nofollow" title="http://ipubmed.ics.uci.edu/">iPubMed Search</a></p> | ||
- | [[http://www.springerlink.com/content/428v02087m218878/fulltext.pdf|Site-frequency Spectrum of Linked Sites]] \\ | + | <p><a class="urlextern" href="http://arxiv.org/abs/1006.5060" rel="nofollow" title="http://arxiv.org/abs/1006.5060">Variable selection and dimension reduction via sparse gradients</a><br /> |
- | Xie X \\ | + | Ye G-B and Xie X<br /> |
- | //Bulletin of Mathematical Biology//, DOI: 10.1007/s11538-010-9534-3, 2010 | + | arXiv:1006.5060v2, 2010</p> |
- | [[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]] \\ | + | <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 /> |
- | Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and Osborne TF \\ | + | Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X<br /> |
- | Nucleic Acids Research, doi:10.1093/nar/gkq397, 2010 \\ | + | <em>NeuroImage</em> 53:839-847, 2010</p> |
- | [[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]] \\ | + | <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 /> |
- | Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X \\ | + | Wang Y, Christley S, Mjolsness E, and Xie X<br /> |
- | //BMC Genomics// 11:208, 2010 \\ | + | <em>BMC Systems Biology</em>, 4:99 doi:10.1186/1752-0509-4-99, 2010</p> |
- | [[http://www.broadinstitute.org/annotation/genome/fusarium_group/SupplementalMaterials.html|Supplementary Information]] \\ | + | |
- | [[http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html|Fusarium Comparative Database]] | + | |
- | [[http://www.nature.com/nature/journal/v464/n7287/abs/nature08850.html|Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium oxysporum]] \\ | + | <p><a class="urlextern" href="http://www.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 /> |
- | Ma L-J, et al. \\ | + | Xie X<br /> |
- | //Nature// 464:367-373, 2010 \\ | + | <em>Bulletin of Mathematical Biology</em>, DOI: 10.1007/s11538-010-9534-3, 2010</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://nar.oxfordjournals.org/cgi/content/abstract/gkq397" rel="nofollow" title="http://nar.oxfordjournals.org/cgi/content/abstract/gkq397">Genome-Wide Interrogation of Hepatic FXR Reveals an Asymmetric IR-1 Motif and Synergy with LRH-1</a><br /> |
+ | Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and Osborne TF<br /> | ||
+ | Nucleic Acids Research, doi:10.1093/nar/gkq397, 2010<br /> | ||
+ | <a class="urlextern" href="http://cbcl.ics.uci.edu/public_data/FXR/" rel="nofollow" title="http://cbcl.ics.uci.edu/public_data/FXR/">Online Supplementary Materials</a></p> | ||
- | [[http://www.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf|Incorporating existing network information into gene network inference]] \\ | + | <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 /> |
- | Christley S, Nie Q and Xie X \\ | + | Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X<br /> |
- | //PLoS ONE// 4(8): e6799. doi:10.1371/journal.pone.0006799 (2009) | + | <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.pnas.org/content/early/2009/08/03/0904246106.abstract|Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif]] \\ | + | <p><a class="urlextern" href="http://www.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 /> |
- | Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF \\ | + | Ma L-J, et al.<br /> |
- | //Proc Natl Acad Sci USA// doi:10.1073/pnas.0904246106 (2009) | + | <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://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/12/i54|Identifying novel constrained elements by exploiting biased substitution patterns]] \\ | + | <h3>2009</h3> |
- | Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X \\ | + | |
- | //Bioinformatics//25:i54-i62 (2009) \\ | + | |
- | [[http://www.ics.uci.edu/~xhx/publications/siphy_suppinfo.pdf|Supplementary Methods]] \\ | + | |
- | [[http://www.broadinstitute.org/genome_bio/siphy/|SiPhy (SIte-specific PHYlogenetic analysis) Java software package]] | + | |
- | [[http://www.pnas.org/content/early/2009/02/11/0813264106.abstract|Comparative genomics allows the discovery of cis-regulatory elements in mosquitoes]] \\ | + | <div class="level3"> |
- | Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA \\ | + | <p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/journal.pone.0006799.pdf">Incorporating existing network information into gene network inference</a><br /> |
- | //Proc Natl Acad Sci USA// doi:10.1073/pnas.0813264106 (2009) | + | Christley S, Nie Q and Xie X<br /> |
+ | <em>PLoS ONE</em> 4(8): e6799. doi:10.1371/journal.pone.0006799 (2009)</p> | ||
- | [[http://genome.cshlp.org/content/19/4/567.long|Common polymorphic transcript variation in human disease]] \\ | + | <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 /> |
- | Fraser H and Xie X \\ | + | Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF<br /> |
- | //Genome Research// doi:10.1101/gr.083477.108 (2009) \\ | + | <em>Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0904246106 (2009)</p> |
- | [[http://www.ics.uci.edu/~xhx/publications/PTV_GR2009.pdf|PDF]] | + | |
- | [[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/167|MotifMap: a human genome-wide map of candidate regulatory motif sites ]] \\ | + | <p><a class="urlextern" href="http://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 /> |
- | Xie X, Rigor P, and Baldi P \\ | + | Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X<br /> |
- | //Bioinformatics// 25: 167-174 (2009) \\ | + | <em>Bioinformatics</em>25:i54-i62 (2009)<br /> |
- | [[http://www.ics.uci.edu/~xhx/publications/MotifMap_Supp_Info.pdf|Supplementary Methods]] \\ | + | <a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/siphy_suppinfo.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/siphy_suppinfo.pdf">Supplementary Methods</a><br /> |
- | [[http://motifmap.ics.uci.edu/|MotifMap Server]] | + | <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://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/2/274|Human genomes as email attachments ]] \\ | + | <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, Lu Y, Li C, and Xie X \\ | + | Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA<br /> |
- | //Bioinformatics // 25: 274-275 (2009) \\ | + | <em>Proc Natl Acad Sci USA</em> doi:10.1073/pnas.0813264106 (2009)</p> |
- | [[http://www.ics.uci.edu/~xhx/project/DNAzip|DNAzip: DNA sequence compression using a reference genome]] \\ | + | |
- | [[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 ==== | + | <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> | ||
- | [[http://www.ics.uci.edu/~xhx/publications/wu_motif_2008.pdf|Discovering regulatory motifs in the Plasmodium genome using comparative genomics ]] \\ | + | <p><a class="urlextern" href="http://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 /> |
- | Wu J, Sieglaff DH, Gervin J, and Xie X \\ | + | Xie X, Rigor P, and Baldi P<br /> |
- | //Bioinformatics // 24:1843-9 (2008) \\ | + | <em>Bioinformatics</em> 25: 167-174 (2009)<br /> |
- | [[http://www.ics.uci.edu/~xhx/project/mdos/|MDOS software]]: A method for Motif Discovery using Orthologous Sequences (alignment independent). \\ | + | <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.ics.uci.edu/~xhx/publications/wu_motif_2008_suppinfo.pdf|Supplementary Information on the MDOS algorithm]] | + | <a class="urlextern" href="http://motifmap.ics.uci.edu/" rel="nofollow" title="http://motifmap.ics.uci.edu/">MotifMap Server</a></p> |
- | [[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://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 /> |
- | 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 \\ | + | Christley S, Lu Y, Li C, and Xie X<br /> |
- | //PLoS Genetics//4(10):e1000242 (2008) | + | <em>Bioinformatics </em> 25: 274-275 (2009)<br /> |
- | ==== 2007 ==== | + | <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://www.pnas.org/content/104/49/19428|Distinguishing protein-coding and noncoding genes in the human genome ]] \\ | + | <h3>2008</h3> |
- | Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, and Lander ES. \\ | + | |
- | //Proc Natl Acad Sci USA//104(49):19428-33 (2007) | + | |
- | [[http://www.nature.com/nature/journal/v449/n7164/abs/nature06250.html|Genome-wide detection and characterization of positive selection in human populations ]] \\ | + | <div class="level3"> |
- | 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 \\ | + | <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 /> |
- | //Nature//449:913-918 (2007) | + | Wu J, Sieglaff DH, Gervin J, and Xie X<br /> |
+ | <em>Bioinformatics </em> 24:1843-9 (2008)<br /> | ||
+ | <a class="urlextern" href="http://www.ics.uci.edu/~xhx/project/mdos/" rel="nofollow" title="http://www.ics.uci.edu/~xhx/project/mdos/">MDOS software</a>: A method for Motif Discovery using Orthologous Sequences (alignment independent).<br /> | ||
+ | <a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/wu_motif_2008_suppinfo.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/wu_motif_2008_suppinfo.pdf">Supplementary Information on the MDOS algorithm</a></p> | ||
- | [[http://www.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.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 /> |
- | 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. \\ | + | 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 /> |
- | //Nature// 448:553-60 (2007) | + | <em>PLoS </em><em>Genetics</em>4(10):e1000242 (2008)</p> |
+ | </div> | ||
- | [[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 ]] \\ | + | <h3>2007</h3> |
- | Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES. \\ | + | |
- | //Proc Natl Acad Sci USA//104:7145-7150 (2007) \\ | + | |
- | [[http://www.broad.mit.edu/personal/xhx/projects/CNEMOTIF/|Supplementary website]] [[http://www.pnas.org/cgi/content/full/0701811104/DC1|Supporting Information]] [[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=3042|News story]] | + | |
- | [[http://www.nature.com/nature/journal/v447/n7141/pdf/nature05805.pdf|Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences ]] \\ | + | <div class="level3"> |
- | Mikkelsen TS, Wakefield MJ, et al. \\ | + | <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 /> |
- | //Nature// 447:167-177 (2007) | + | Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, and Lander ES.<br /> |
+ | <em>Proc Natl Acad Sci </em><em>USA</em>104(49):19428-33 (2007)</p> | ||
- | [[http://www.ics.uci.edu/~xhx/publications/Xie_AMCNE.pdf|A family of conserved noncoding elements derived from an ancient transposable element]] \\ | + | <p><a class="urlextern" href="http://www.nature.com/nature/journal/v449/n7164/abs/nature06250.html" rel="nofollow" title="http://www.nature.com/nature/journal/v449/n7164/abs/nature06250.html">Genome-wide detection and characterization of positive selection in human populations </a><br /> |
- | Xie X, Kamal M, and Lander ES. \\ | + | 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 /> |
- | //Proc Natl Acad Sci USA//103:11659-11664 (2006) \\ | + | <em>Nature</em>449:913-918 (2007)</p> |
- | [[http://www.broad.mit.edu/seq/pubs/xie_pnas2006/|Supplementary website]] [[http://www.pnas.org/cgi/content/full/0604768103/DC1|Supporting Information]] [[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=1881|News story]] | + | |
- | ==== 2006 or before ==== | + | <p><a class="urlextern" href="http://www.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'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> | ||
- | [[http://www.ics.uci.edu/~xhx/publications/mer121.PNAS2006.pdf|A large family of ancient repeat elements in the human genome is under strong selection]] \\ | + | <p><a class="urlextern" href="http://www.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 /> |
- | Kamal M, Xie X, and Lander ES. \\ | + | Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES.<br /> |
- | //Proc Natl Acad Sci USA//103:2740-2745 (2006) \\ | + | <em>Proc Natl Acad Sci </em><em>USA</em>104:7145-7150 (2007)<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/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.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/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 /> |
- | Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al. \\ | + | Mikkelsen TS, Wakefield MJ, et al.<br /> |
- | //Cell// 125:315-26 (2006) | + | <em>Nature</em> 447:167-177 (2007)</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/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 /> |
- | Wu J and Xie X \\ | + | Xie X, Kamal M, and Lander ES.<br /> |
- | //Genome Biology//7(9):R85 (2006) (Highly accessed) \\ | + | <em>Proc Natl Acad Sci </em><em>USA</em>103:11659-11664 (2006)<br /> |
- | [[http://www.broad.mit.edu/personal/xhx/projects/NRSE|Supplementary website]] | + | <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/ng/journal/v38/n5/pdf/ng1776.pdf|Systematic identification of human mitochondrial disease genes through integrative genomics ]] \\ | + | <h3>2006 or before</h3> |
- | Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK. \\ | + | |
- | //Nature Genetics//, 38:576-82 (2006) | + | |
- | [[http://www.ics.uci.edu/~xhx/publications/xie05_motif_paper.pdf|Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals ]] \\ | + | <div class="level3"> |
- | Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M. \\ | + | <p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/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 /> |
- | //Nature//2005; 434:338-45 \\ | + | Kamal M, Xie X, and Lander ES.<br /> |
- | [[http://www.broad.mit.edu/seq/HumanMotifs/|Supplementary Website]] [[http://www.ics.uci.edu/~xhx/publications/nature03441-s1.pdf|Supplementary Information]] [[http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=134|News story]] | + | <em>Proc Natl Acad Sci </em><em>USA</em>103:2740-2745 (2006)<br /> |
+ | <a class="urlextern" href="http://www.broad.mit.edu/seq/pubs/xie_pnas2006/html/clusteredAMCNE/AMCNE1.similarAMCNE.html" rel="nofollow" title="http://www.broad.mit.edu/seq/pubs/xie_pnas2006/html/clusteredAMCNE/AMCNE1.similarAMCNE.html">Supplementary website</a> <a class="urlextern" href="http://www.pnas.org/cgi/content/full/0511238103/DC1" rel="nofollow" title="http://www.pnas.org/cgi/content/full/0511238103/DC1">Supporting Information</a><br /> | ||
+ | <a class="urlextern" href="http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=381" rel="nofollow" title="http://www.broad.mit.edu/cgi-bin/news/display_news.cgi?id=381">News story</a></p> | ||
- | [[http://www.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://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 /> |
- | Giallourakis C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R. \\ | + | Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al.<br /> |
- | //Genome Resesarch//, 16:1056-72 (2006) | + | <em>Cell</em> 125:315-26 (2006)</p> |
- | [[http://download.cell.com/pdfs/0092-8674/PIIS0092867406003692.pdf|A Mammalian Organelle Map by Protein Correlation Profiling]] \\ | + | <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 /> |
- | Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M. \\ | + | Wu J and Xie X<br /> |
- | //Cell// 125:187-99 (2006) | + | <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> | ||
- | [[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.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 /> |
- | Werfel J, Xie X and Seung HS. \\ | + | Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK.<br /> |
- | //Neural Computation//, 2005;17:2699-718 | + | <em>Nature Genetics</em>, 38:576-82 (2006)</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/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 /> |
- | Lindblad-Toh K, Wade CM, et al. \\ | + | Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M.<br /> |
- | //Nature// 438:803-19 2005 | + | <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> | ||
- | [[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.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, Henson C, Reich M, Xie X, and Mootha VK. \\ | + | Giallourakis C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R.<br /> |
- | //Annu. Rev. Genomics Hum. Genet.// 2005:22:381-406. | + | <em>Genome Resesarch</em>, 16:1056-72 (2006)</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://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 and Seung HS. \\ | + | Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M.<br /> |
- | //Phys Rev E//, 2004;69:041909 | + | <em>Cell</em> 125:187-99 (2006)</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/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 /> |
- | Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al. \\ | + | Werfel J, Xie X and Seung HS.<br /> |
- | //Proc Natl Acad Sci USA//, 2004;101:6570-5 | + | <em>Neural Computation</em>, 2005;17:2699-718</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.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 /> |
- | Xie X, Hahnloser RH, and Seung HS. \\ | + | Lindblad-Toh K, Wade CM, et al.<br /> |
- | //Physical Review E//, 2002;66:041902 | + | <em>Nature</em> 438:803-19 2005</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/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 /> |
- | Xie X and Giese MA. \\ | + | Giallourakis C, Henson C, Reich M, Xie X, and Mootha VK.<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>Annu. Rev. Genomics Hum. Genet.</em> 2005:22:381-406.</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/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, Hahnloser HR, and Seung HS. \\ | + | Xie X and Seung HS.<br /> |
- | //Advances in Neural Information Processing Systems//2001;13:350-356 | + | <em>Phys Rev E</em>, 2004;69:041909</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/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 /> |
- | Xie X and Giese MA. \\ | + | Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al.<br /> |
- | //Advances in Neural Information Processing Systems//2002;13:325-332 | + | <em>Proc Natl Acad Sci USA</em>, 2004;101:6570-5</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/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. \\ | + | Xie X, Hahnloser RH, and Seung HS.<br /> |
- | //Neural Computation//, 2002;14:2627-2646 | + | <em>Physical Review E</em>, 2002;66:041902</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/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 Seung HS. \\ | + | Xie X and Giese MA.<br /> |
- | //Neural Computation//, 2003;16:441-454 | + | <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/network_pop.pdf|Threshold behavior of maximum likelihood method in population decoding]] \\ | + | <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 \\ | + | Xie X, Hahnloser HR, and Seung HS.<br /> |
- | //Network: Comput. Neural Syst.// 2002;13:447-456 | + | <em>Advances in Neural Information Processing </em><em>Systems</em>2001;13:350-356</p> |
+ | |||
+ | <p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/nc_vel_tuning.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/nc_vel_tuning.pdf">Generating velocity tuning by asymmetric recurrent connections</a><br /> | ||
+ | Xie X and Giese MA.<br /> | ||
+ | <em>Advances in Neural Information Processing </em><em>Systems</em>2002;13:325-332</p> | ||
+ | |||
+ | <p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/gwta_nc.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/gwta_nc.pdf">Selectively Grouping Neurons in Recurrent Networks of Lateral Inhibition</a><br /> | ||
+ | Xie X, Hahnloser RH, and Seung HS.<br /> | ||
+ | <em>Neural Computation</em>, 2002;14:2627-2646</p> | ||
+ | |||
+ | <p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/chl_nc.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/chl_nc.pdf">Equivalence of backpropagation and contrastive Hebbian learning in a layered network</a><br /> | ||
+ | Xie X and Seung HS.<br /> | ||
+ | <em>Neural Computation</em>, 2003;16:441-454</p> | ||
+ | |||
+ | <p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/network_pop.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/network_pop.pdf">Threshold behavior of maximum likelihood method in population decoding</a><br /> | ||
+ | Xie X<br /> | ||
+ | <em>Network: Comput. Neural Syst.</em> 2002;13:447-456</p> | ||
+ | |||
+ | <p><a class="urlextern" href="http://www.ics.uci.edu/~xhx/publications/stdp00.pdf" rel="nofollow" title="http://www.ics.uci.edu/~xhx/publications/stdp00.pdf">Spike-based learning rules and stabilization of persistent neural activity</a><br /> | ||
+ | Xie X and Seung HS<br /> | ||
+ | <em>Advances in Neural Information Processing Systems</em>, 2000;12:199-205</p> | ||
+ | </div> | ||
- | [[http://www.ics.uci.edu/~xhx/publications/stdp00.pdf|Spike-based learning rules and stabilization of persistent neural activity]] \\ | ||
- | Xie X and Seung HS \\ | ||
- | //Advances in Neural Information Processing Systems//, 2000;12:199-205 | ||