| Year |
Citation |
Score |
| 2019 |
Quang D, Xie X. FactorNet: a deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data. Methods (San Diego, Calif.). PMID 30922998 DOI: 10.1016/j.ymeth.2019.03.020 |
0.362 |
|
| 2017 |
Newkirk DA, Chen YY, Chien R, Zeng W, Biesinger J, Flowers E, Kawauchi S, Santos R, Calof AL, Lander AD, Xie X, Yokomori K. The effect of Nipped-B-like (Nipbl) haploinsufficiency on genome-wide cohesin binding and target gene expression: modeling Cornelia de Lange syndrome. Clinical Epigenetics. 9: 89. PMID 28855971 DOI: 10.1186/S13148-017-0391-X |
0.315 |
|
| 2017 |
Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW. Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program. Developmental Cell. PMID 28325473 DOI: 10.1016/J.Devcel.2017.02.017 |
0.324 |
|
| 2016 |
Forouzmand E, Owens ND, Blitz IL, Paraiso KD, Khokha MK, Gilchrist MJ, Xie X, Cho KW. Developmentally regulated long non-coding RNAs in Xenopus tropicalis. Developmental Biology. PMID 27418388 DOI: 10.1016/j.ydbio.2016.06.016 |
0.315 |
|
| 2016 |
Quang D, Xie X. DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences. Nucleic Acids Research. PMID 27084946 DOI: 10.1093/nar/gkw226 |
0.333 |
|
| 2016 |
Chen Y, Li Y, Narayan R, Subramanian A, Xie X. Gene expression inference with deep learning. Bioinformatics (Oxford, England). PMID 26873929 DOI: 10.1093/Bioinformatics/Btw074 |
0.324 |
|
| 2015 |
Li Y, Xie X. MixClone: a mixture model for inferring tumor subclonal populations. Bmc Genomics. 16: S1. PMID 25707430 DOI: 10.1186/1471-2164-16-S2-S1 |
0.322 |
|
| 2015 |
Quang D, Chen Y, Xie X. DANN: a deep learning approach for annotating the pathogenicity of genetic variants. Bioinformatics (Oxford, England). 31: 761-3. PMID 25338716 DOI: 10.1093/bioinformatics/btu703 |
0.31 |
|
| 2015 |
Kim I, Xie X. Handwritten Hangul recognition using deep convolutional neural networks International Journal On Document Analysis and Recognition. 18: 1-13. DOI: 10.1007/S10032-014-0229-4 |
0.301 |
|
| 2014 |
Chiu WT, Charney Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, Cho KW. Genome-wide view of TGFβ/Foxh1 regulation of the early mesendoderm program. Development (Cambridge, England). 141: 4537-47. PMID 25359723 DOI: 10.1242/dev.107227 |
0.315 |
|
| 2014 |
Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, Dai X. Integrative ChIP-seq/microarray analysis identifies a CTNNB1 target signature enriched in intestinal stem cells and colon cancer. Plos One. 9: e92317. PMID 24651522 DOI: 10.1371/Journal.Pone.0092317 |
0.307 |
|
| 2014 |
Quang D, Xie X. EXTREME: an online EM algorithm for motif discovery. Bioinformatics (Oxford, England). 30: 1667-73. PMID 24532725 DOI: 10.1093/bioinformatics/btu093 |
0.33 |
|
| 2014 |
Kim J, Li C, Xie X. Improving read mapping using additional prefix grams. Bmc Bioinformatics. 15: 42. PMID 24499321 DOI: 10.1186/1471-2105-15-42 |
0.302 |
|
| 2014 |
Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q. Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns. Bmc Systems Biology. 8: 3. PMID 24397936 DOI: 10.1186/1752-0509-8-3 |
0.326 |
|
| 2013 |
Ye G, Tang M, Cai JF, Nie Q, Xie X. Low-rank regularization for learning gene expression programs. Plos One. 8: e82146. PMID 24358148 DOI: 10.1371/Journal.Pone.0082146 |
0.331 |
|
| 2013 |
Blitz IL, Biesinger J, Xie X, Cho KW. Biallelic genome modification in F(0) Xenopus tropicalis embryos using the CRISPR/Cas system. Genesis (New York, N.Y. : 2000). 51: 827-34. PMID 24123579 DOI: 10.1002/dvg.22719 |
0.309 |
|
| 2013 |
Biesinger J, Wang Y, Xie X. Discovering and mapping chromatin states using a tree hidden Markov model. Bmc Bioinformatics. 14: S4. PMID 23734743 DOI: 10.7490/F1000Research.1093084.1 |
0.328 |
|
| 2012 |
Chong HK, Biesinger J, Seo YK, Xie X, Osborne TF. 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. Bmc Genomics. 13: 51. PMID 22296850 DOI: 10.1186/1471-2164-13-51 |
0.308 |
|
| 2012 |
Ahmadi A, Behm A, Honnalli N, Li C, Weng L, Xie X. Hobbes: optimized gram-based methods for efficient read alignment. Nucleic Acids Research. 40: e41. PMID 22199254 DOI: 10.1093/nar/gkr1246 |
0.305 |
|
| 2011 |
Daily K, Patel VR, Rigor P, Xie X, Baldi P. MotifMap: integrative genome-wide maps of regulatory motif sites for model species. Bmc Bioinformatics. 12: 495. PMID 22208852 DOI: 10.1186/1471-2105-12-495 |
0.358 |
|
| 2011 |
Newkirk D, Biesinger J, Chon A, Yokomori K, Xie X. AREM: aligning short reads from ChIP-sequencing by expectation maximization. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1495-505. PMID 22035330 DOI: 10.1089/Cmb.2011.0185 |
0.354 |
|
| 2011 |
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, ... ... Xie X, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/Nature10530 |
0.339 |
|
| 2011 |
Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, Xie X. SNP-based pathway enrichment analysis for genome-wide association studies. Bmc Bioinformatics. 12: 99. PMID 21496265 DOI: 10.1186/1471-2105-12-99 |
0.301 |
|
| 2011 |
Seo YK, Jeon TI, Chong HK, Biesinger J, Xie X, Osborne TF. Genome-wide localization of SREBP-2 in hepatic chromatin predicts a role in autophagy. Cell Metabolism. 13: 367-75. PMID 21459322 DOI: 10.1016/J.Cmet.2011.03.005 |
0.314 |
|
| 2010 |
Potkin SG, Macciardi F, Guffanti G, Fallon JH, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X. Identifying gene regulatory networks in schizophrenia. Neuroimage. 53: 839-47. PMID 20600988 DOI: 10.1016/J.Neuroimage.2010.06.036 |
0.338 |
|
| 2010 |
Chong HK, Infante AM, Seo YK, Jeon TI, Zhang Y, Edwards PA, Xie X, Osborne TF. Genome-wide interrogation of hepatic FXR reveals an asymmetric IR-1 motif and synergy with LRH-1. Nucleic Acids Research. 38: 6007-17. PMID 20483916 DOI: 10.1093/Nar/Gkq397 |
0.339 |
|
| 2010 |
Kumar L, Breakspear A, Kistler C, Ma LJ, Xie X. Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes. Bmc Genomics. 11: 208. PMID 20346147 DOI: 10.1186/1471-2164-11-208 |
0.337 |
|
| 2009 |
Christley S, Nie Q, Xie X. Incorporating existing network information into gene network inference. Plos One. 4: e6799. PMID 19710931 DOI: 10.1371/Journal.Pone.0006799 |
0.344 |
|
| 2009 |
Seo YK, Chong HK, Infante AM, Im SS, Xie X, Osborne TF. Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif. Proceedings of the National Academy of Sciences of the United States of America. 106: 13765-9. PMID 19666523 DOI: 10.1073/Pnas.0904246106 |
0.331 |
|
| 2009 |
Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics (Oxford, England). 25: i54-62. PMID 19478016 DOI: 10.1093/Bioinformatics/Btp190 |
0.344 |
|
| 2009 |
Xie X, Rigor P, Baldi P. MotifMap: a human genome-wide map of candidate regulatory motif sites. Bioinformatics (Oxford, England). 25: 167-74. PMID 19017655 DOI: 10.1093/Bioinformatics/Btn605 |
0.343 |
|
| 2009 |
Christley S, Lu Y, Li C, Xie X. Human genomes as email attachments. Bioinformatics (Oxford, England). 25: 274-5. PMID 18996942 DOI: 10.1093/Bioinformatics/Btn582 |
0.311 |
|
| 2008 |
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, et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. Plos Genetics. 4: e1000242. PMID 18974828 DOI: 10.1371/Journal.Pgen.1000242 |
0.309 |
|
| 2007 |
Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, Lander ES. Distinguishing protein-coding and noncoding genes in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 104: 19428-33. PMID 18040051 DOI: 10.1073/Pnas.0709013104 |
0.322 |
|
| 2007 |
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, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 448: 553-60. PMID 17603471 DOI: 10.1038/Nature06008 |
0.343 |
|
| 2007 |
Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, ... ... Xie X, et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 447: 167-77. PMID 17495919 DOI: 10.1038/Nature05805 |
0.342 |
|
| 2007 |
Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M, Lander ES. Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proceedings of the National Academy of Sciences of the United States of America. 104: 7145-50. PMID 17442748 DOI: 10.1073/Pnas.0701811104 |
0.386 |
|
| 2006 |
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 125: 315-26. PMID 16630819 DOI: 10.1016/J.Cell.2006.02.041 |
0.322 |
|
| 2006 |
Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, Mann M. A mammalian organelle map by protein correlation profiling. Cell. 125: 187-99. PMID 16615899 DOI: 10.1016/J.Cell.2006.03.022 |
0.321 |
|
| 2006 |
Kamal M, Xie X, Lander ES. A large family of ancient repeat elements in the human genome is under strong selection. Proceedings of the National Academy of Sciences of the United States of America. 103: 2740-5. PMID 16477033 DOI: 10.1073/pnas.0511238103 |
0.322 |
|
| 2005 |
Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 438: 803-19. PMID 16341006 DOI: 10.1038/Nature04338 |
0.338 |
|
| 2005 |
Werfel J, Xie X, Seung HS. Learning curves for stochastic gradient descent in linear feedforward networks. Neural Computation. 17: 2699-718. PMID 16212768 DOI: 10.1162/089976605774320539 |
0.481 |
|
| 2005 |
Giallourakis C, Henson C, Reich M, Xie X, Mootha VK. Disease gene discovery through integrative genomics. Annual Review of Genomics and Human Genetics. 6: 381-406. PMID 16124867 DOI: 10.1146/Annurev.Genom.6.080604.162234 |
0.363 |
|
| 2005 |
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature. 434: 338-45. PMID 15735639 DOI: 10.1038/Nature03441 |
0.322 |
|
| 2004 |
Xie X, Seung HS. Learning in neural networks by reinforcement of irregular spiking. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 69: 041909. PMID 15169045 DOI: 10.1103/Physreve.69.041909 |
0.549 |
|
| 2003 |
Xie X, Seung HS. Equivalence of backpropagation and contrastive Hebbian learning in a layered network. Neural Computation. 15: 441-54. PMID 12590814 DOI: 10.1162/089976603762552988 |
0.553 |
|
| 2002 |
Xie X, Hahnloser RH, Seung HS. Double-ring network model of the head-direction system. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 66: 041902. PMID 12443230 DOI: 10.1103/PhysRevE.66.041902 |
0.663 |
|
| 2002 |
Xie X, Hahnloser RH, Seung HS. Selectively grouping neurons in recurrent networks of lateral inhibition. Neural Computation. 14: 2627-46. PMID 12433293 DOI: 10.1162/089976602760408008 |
0.666 |
|
| 2002 |
Xie X, Giese MA. Nonlinear dynamics of direction-selective recurrent neural media. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 65: 051904. PMID 12059590 DOI: 10.1103/Physreve.65.051904 |
0.327 |
|
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