Xiaohui Xie - Publications

Affiliations: 
Harvard University, Cambridge, MA, United States 
Area:
genomics, bioinformatics, computational neuroscience

115 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Li X, Wu Z, Du X, Wu Y, Xie X, Shi L. Interventions for Preventing Cardiotoxicity in Breast Cancer Patients Receiving Trastuzumab: A Systemic Review and Bayesian Network Meta-Analysis. Frontiers in Pharmacology. 12: 718086. PMID 34483926 DOI: 10.3389/fphar.2021.718086  1
2021 Yang X, Wu G, Yang F, He L, Xie X, Li L, Yang L, Ma Y, Zhang Q, Chen J, Zou S, Han Q, Wang Y, Liu S, Li J, et al. Elevated LINC00909 Promotes Tumor Progression of Ovarian Cancer via Regulating the miR-23b-3p/MRC2 Axis. Oxidative Medicine and Cellular Longevity. 2021: 5574130. PMID 34336102 DOI: 10.1155/2021/5574130  1
2021 Cao Y, Fu L, Wu J, Peng Q, Nie Q, Zhang J, Xie X. SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration. Bioinformatics (Oxford, England). 37: i317-i326. PMID 34252968 DOI: 10.1093/bioinformatics/btab303  1
2021 Chen X, Sun S, Bai N, Tang H, Liu Q, Yao S, Han K, Zhang C, Lu Z, Huang Q, Zhao G, Xu Y, Chen T, Xie X, Liu Y. A deep learning-based auto-segmentation system for organs-at-risk on whole-body computed tomography images for radiation therapy. Radiotherapy and Oncology : Journal of the European Society For Therapeutic Radiology and Oncology. PMID 33961914 DOI: 10.1016/j.radonc.2021.04.019  1
2021 Loveless TB, Grotts JH, Schechter MW, Forouzmand E, Carlson CK, Agahi BS, Liang G, Ficht M, Liu B, Xie X, Liu CC. Lineage tracing and analog recording in mammalian cells by single-site DNA writing. Nature Chemical Biology. PMID 33753928 DOI: 10.1038/s41589-021-00769-8  1
2021 Zheng Z, Jiang X, Chen J, He D, Xie X, Lu Y. Continuous versus intermittent use of furosemide in patients with heart failure and moderate chronic renal dysfunction. Esc Heart Failure. PMID 33689236 DOI: 10.1002/ehf2.13286  1
2020 Ren J, Song K, Deng C, Ahlgren NA, Fuhrman JA, Li Y, Xie X, Poplin R, Sun F. Identifying viruses from metagenomic data using deep learning. Quantitative Biology (Beijing, China). 8: 64-77. PMID 34084563 DOI: 10.1007/s40484-019-0187-4  1
2020 Fu L, Zhang L, Dollinger E, Peng Q, Nie Q, Xie X. Predicting transcription factor binding in single cells through deep learning. Science Advances. 6. PMID 33355120 DOI: 10.1126/sciadv.aba9031  1
2020 Chow DS, Glavis-Bloom J, Soun JE, Weinberg B, Loveless TB, Xie X, Mutasa S, Monuki E, Park JI, Bota D, Wu J, Thompson L, Boden-Albala B, Khan S, Amin AN, et al. Development and external validation of a prognostic tool for COVID-19 critical disease. Plos One. 15: e0242953. PMID 33296357 DOI: 10.1371/journal.pone.0242953  1
2020 Zhang T, He K, Bai T, Lv H, Xie X, Nie J, Xie W, Zhu C, Wang K, Tian Y. Altered neural activity in the reward-related circuit and executive control network associated with amelioration of anhedonia in major depressive disorder by electroconvulsive therapy. Progress in Neuro-Psychopharmacology & Biological Psychiatry. 110193. PMID 33285263 DOI: 10.1016/j.pnpbp.2020.110193  1
2020 Li X, Huang C, Xie X, Wu Z, Tian X, Wu Y, Du X, Shi L. The impact of smoking status on the progression-free survival of non-small cell lung cancer patients receiving molecularly target therapy or immunotherapy versus chemotherapy: A meta-analysis. Journal of Clinical Pharmacy and Therapeutics. PMID 33152129 DOI: 10.1111/jcpt.13309  1
2020 Wu Z, Chen S, Du X, Wu Y, Xie X. Hepatotoxicity with epidermal growth factor receptor tyrosine kinase inhibitors in non-small-cell lung cancer patients: A network meta-analysis. Journal of Clinical Pharmacy and Therapeutics. PMID 33031574 DOI: 10.1111/jcpt.13281  1
2020 Zhao C, Xie X, Ge D, Wu D, Xie Q, Xin H, Yang T. Cerebral infarction as the first symptom in acute promyelocytic leukemia: A case report and literature review. Zhong Nan Da Xue Xue Bao. Yi Xue Ban = Journal of Central South University. Medical Sciences. 45: 476-480. PMID 32879075 DOI: 10.11817/j.issn.1672-7347.2020.190008  1
2020 Xie X, Zu M, Zhang L, Bai T, Wei L, Huang W, Ji GJ, Qiu B, Hu P, Tian Y, Wang K. A common variant of the NOTCH4 gene modulates functional connectivity of the occipital cortex and its relationship with schizotypal traits. Bmc Psychiatry. 20: 363. PMID 32646407 DOI: 10.1186/s12888-020-02773-z  1
2020 Xie X, Dai S, Dai Y, Ning J. Influence of dietary fiber on chronic kidney disease: Base on the gut-kidney axis theory. Zhong Nan Da Xue Xue Bao. Yi Xue Ban = Journal of Central South University. Medical Sciences. 45: 193-197. PMID 32386047 DOI: 10.11817/j.issn.1672-7347.2020.180758  1
2020 Zhang Z, Wang J, Zheng Z, Chen X, Xu G, Chen S, Liu F, Chen L, Ding M, Yuan L, Li Y, Qian J, Xie X, Deng B, Lu W. A protective polymorphism in MMP16, improved blood-gas levels, and chronic obstructive pulmonary diseases: Family and two population-based studies. Human Mutation. PMID 32196811 DOI: 10.1002/humu.24013  1
2020 Xie X, Fu Q, Bao Z, Zhang Y, Zhou D. Clinical value of different anti-D immunoglobulin strategies for preventing Rh hemolytic disease of the fetus and newborn: A network meta-analysis. Plos One. 15: e0230073. PMID 32163467 DOI: 10.1371/journal.pone.0230073  1
2020 Yu F, Zhang S, Chen B, Zhou Y, Ma C, Yang S, Tang Y, Huang D, Xie X, Xiao Q, Wang L. Evaluation of the Diagnostic Accuracy of the CareStart™ Glucose-6-Phosphate Dehydrogenase Deficiency Rapid Diagnostic Test among Chinese Newborns. Journal of Tropical Pediatrics. PMID 32040187 DOI: 10.1093/tropej/fmaa003  1
2020 Bai T, Zhang L, Xie X, Xiao G, Huang W, Li D, Zu M, Wei L, Zuo X, Gong-Jun JI, Hu P, Zhu C, Qiu B, Tian Y, Wang K. Common variant of CNTNAP2 gene modulate the social performances and functional connectivity of posterior right temporoparietal junction. Social Cognitive and Affective Neuroscience. PMID 31993662 DOI: 10.1093/scan/nsaa008  1
2019 Zeng L, Wang Q, Gu C, Yuan L, Xie X, He L, Chen K, Tan P, Xue L, Huang S, Shi K. Asparagine Synthetase and Filamin A Have Different Roles in Ovarian Cancer. Frontiers in Oncology. 9: 1072. PMID 31681605 DOI: 10.3389/fonc.2019.01072  1
2019 Sun J, Xie X, Xie K, Xu S, Jiang S, Ren J, Zhao Y, Xu H, Wang J, Yue W. Magnetic Graphene Field-Effect Transistor Biosensor for Single-Strand DNA Detection. Nanoscale Research Letters. 14: 248. PMID 31342195 DOI: 10.1186/s11671-019-3048-1  1
2019 Zhang Z, Wang J, Xu G, Ding M, Liu F, Yuan L, Wang T, Xu J, Xie X, Deng B, Sun D, Lu W. Inhalation of sodium hydrosulfide (NaHS) alleviates NO-induced pulmonary function and hematological impairment in rats. Life Sciences. 116650. PMID 31302196 DOI: 10.1016/j.lfs.2019.116650  1
2019 Zhao C, Xie X, Gai DZ, Wu D, Xin H, Yang T. Interdigitating dendritic cell sarcoma of the spleen with hepatic failure after chemotherapy: A case report. Medicine. 98: e15535. PMID 31083204 DOI: 10.1097/MD.0000000000015535  1
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  1
2019 Dai Y, Dai S, Xie X, Ning J. Immobilizing argatroban and mPEG-NH on a polyethersulfone membrane surface to prepare an effective nonthrombogenic biointerface. Journal of Biomaterials Science. Polymer Edition. 1-18. PMID 30907698 DOI: 10.1080/09205063.2019.1595891  1
2019 Pu H, Xie X, Sun DW, Wei Q, Jiang Y. Double strand DNA functionalized Au@Ag Nps for ultrasensitive detection of 17β-estradiol using surface-enhanced raman spectroscopy. Talanta. 195: 419-425. PMID 30625564 DOI: 10.1016/j.talanta.2018.10.021  1
2019 Tang H, Chen X, Liu Y, Lu Z, You J, Yang M, Yao S, Zhao G, Xu Y, Chen T, Liu Y, Xie X. Clinically applicable deep learning framework for organs at risk delineation in CT images Nature Machine Intelligence. 1: 480-491. DOI: 10.1038/S42256-019-0099-Z  1
2018 Zhu W, Huang Y, Zeng L, Chen X, Liu Y, Qian Z, Du N, Fan W, Xie X. AnatomyNet: Deep Learning for Fast and Fully Automated Whole-volume Segmentation of Head and Neck Anatomy. Medical Physics. PMID 30480818 DOI: 10.1002/Mp.13300  1
2018 Dai S, Dai Y, Peng J, Xie X, Ning J. Simplified colonic dialysis with hemodialysis solutions delays the progression of chronic kidney disease. Qjm : Monthly Journal of the Association of Physicians. PMID 30407603 DOI: 10.1093/qjmed/hcy260  1
2018 Duan T, Pinto JP, Xie X. Parallel Clustering of Single Cell Transcriptomic Data with Split-Merge Sampling on Dirichlet Process Mixtures. Bioinformatics (Oxford, England). PMID 30165477 DOI: 10.1093/Bioinformatics/Bty702  0.01
2018 Wu H, Shen X, Huang L, Zeng Y, Gao Y, Shao L, Lu B, Zhong Y, Miao B, Xu Y, Wang Y, Li Y, Xiong L, Lu S, Xie XS, et al. Genotyping single-sperm cells by universal MARSALA enables the acquisition of linkage information for combined pre-implantation genetic diagnosis and genome screening. Journal of Assisted Reproduction and Genetics. PMID 29790070 DOI: 10.1007/S10815-018-1158-9  1
2018 Wang L, Zhou R, Xie X. Tiotropium added to low- to medium-dose inhaled corticosteroids (ICS) versus low- to medium-dose ICS alone for adults with mild to moderate uncontrolled persistent asthma: A systematic review and meta-analysis. The Journal of Asthma : Official Journal of the Association For the Care of Asthma. 1-10. PMID 29420077 DOI: 10.1080/02770903.2018.1424192  0.04
2018 Zhu Y, Wang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi Y. Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation. Molecular Cell. 69: 62-74.e4. PMID 29276085 DOI: 10.1016/J.Molcel.2017.11.031  1
2017 Xie X, Yang M, Ding Y, Yu L, Chen J. Formyl peptide receptor 2 expression predicts poor prognosis and promotes invasion and metastasis in epithelial ovarian cancer. Oncology Reports. PMID 29039544 DOI: 10.3892/or.2017.6034  1
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  1
2017 Xie X, Yang M, Ding Y, Chen J. Microbial infection, inflammation and epithelial ovarian cancer. Oncology Letters. 14: 1911-1919. PMID 28789426 DOI: 10.3892/ol.2017.6388  1
2017 Xie X, Pu H, Sun DW. Recent Advances in Nanofabrication Techniques for SERS Substrates and Their Applications in Food Safety Analysis. Critical Reviews in Food Science and Nutrition. 0. PMID 28665689 DOI: 10.1080/10408398.2017.1341866  1
2017 Vang YS, Xie X. HLA class I binding prediction via convolutional neural networks. Bioinformatics (Oxford, England). PMID 28444127 DOI: 10.1093/bioinformatics/btx264  0.01
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  1
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  1
2016 Weng L, Li Y, Xie X, Shi Y. Poly(A) code analyses reveal key determinants for tissue-specific mRNA alternative polyadenylation. Rna (New York, N.Y.). PMID 27095026 DOI: 10.1261/rna.055681.115  1
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  1
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  1
2016 Yang M, Xie X, Ding Y. SALL4 is a marker of poor prognosis in serous ovarian carcinoma promoting invasion and metastasis. Oncology Reports. PMID 26750614 DOI: 10.3892/or.2016.4545  1
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  1
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  1
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  0.01
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  1
2014 Li Y, Xie X. Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. Bioinformatics (Oxford, England). 30: 2121-9. PMID 24695406 DOI: 10.1093/bioinformatics/btu174  1
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  1
2014 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. Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal. The Embo Journal. 33: 878-89. PMID 24596251 DOI: 10.1002/Embj.201386537  1
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  1
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  1
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  1
2014 Ye G, Tang M, Cai JF, Nie Q, Xie X. Correction: Low-rank regularization for learning gene expression programs (PLoS ONE) Plos One. 9. DOI: 10.1371/Annotation/Ab5352A4-6B6F-44E6-8Ab5-6644794Bc247  1
2014 Potkin SG, Macciardi F, Erp Tv, Keator D, Guffanti G, Xie X. 6:00 Pm The Role Of Imaging Genetics In Unanticipated Schizophrenia Risk Gene Discovery: Tnik And Microrna-137 Schizophrenia Research. 153. DOI: 10.1016/S0920-9964(14)70199-9  1
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  1
2013 Chen Y, Jia Z, Mercola D, Xie X. A gradient boosting algorithm for survival analysis via direct optimization of concordance index. Computational and Mathematical Methods in Medicine. 2013: 873595. PMID 24348746 DOI: 10.1155/2013/873595  1
2013 Yao C, Choi EA, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, Shi Y. Overlapping and distinct functions of CstF64 and CstF64Ï„ in mammalian mRNA 3' processing. Rna (New York, N.Y.). 19: 1781-90. PMID 24149845 DOI: 10.1261/Rna.042317.113  1
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  1
2013 Li Y, Xie X. A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues. Bmc Bioinformatics. 14: S11. PMID 23735186 DOI: 10.1186/1471-2105-14-S5-S11  1
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  1
2012 Yao C, Biesinger J, Wan J, Weng L, Xing Y, Xie X, Shi Y. Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation. Proceedings of the National Academy of Sciences of the United States of America. 109: 18773-8. PMID 23112178 DOI: 10.1073/Pnas.1211101109  1
2012 Tang Z, Liu H, Xie X, Chen X, Hou D. [Modeling and analysis of volume conduction based on field-circuit coupling]. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi = Journal of Biomedical Engineering = Shengwu Yixue Gongchengxue Zazhi. 29: 609-14. PMID 23016401  1
2012 Zheng Q, Wen X, Han C, Li H, Xie X. Effect of replacing soybean meal with cottonseed meal on growth, hematology, antioxidant enzymes activity and expression for juvenile grass carp, Ctenopharyngodon idellus. Fish Physiology and Biochemistry. 38: 1059-69. PMID 22297837 DOI: 10.1007/s10695-011-9590-0  0.01
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  1
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  1
2012 Ye G, Xie X. Learning sparse gradients for variable selection and dimension reduction Machine Learning. 87: 303-355. DOI: 10.1007/S10994-012-5284-9  1
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  1
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  1
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  1
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  1
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  1
2011 Xie X. The site-frequency spectrum of linked sites. Bulletin of Mathematical Biology. 73: 459-94. PMID 20349153 DOI: 10.1007/s11538-010-9534-3  1
2011 Ye G, Xie X. Split Bregman method for large scale fused Lasso Computational Statistics & Data Analysis. 55: 1552-1569. DOI: 10.1016/J.Csda.2010.10.021  1
2010 Daily K, Rigor P, Christley S, Xie X, Baldi P. Data structures and compression algorithms for high-throughput sequencing technologies. Bmc Bioinformatics. 11: 514. PMID 20946637 DOI: 10.1186/1471-2105-11-514  1
2010 Wang Y, Christley S, Mjolsness E, Xie X. Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent. Bmc Systems Biology. 4: 99. PMID 20663171 DOI: 10.1186/1752-0509-4-99  1
2010 Wang J, Cetindil I, Ji S, Li C, Xie X, Li G, Feng J. Interactive and fuzzy search: a dynamic way to explore MEDLINE. Bioinformatics (Oxford, England). 26: 2321-7. PMID 20624778 DOI: 10.1093/bioinformatics/btq414  1
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  1
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  1
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  0.01
2010 Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature. 464: 367-73. PMID 20237561 DOI: 10.1038/Nature08850  1
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  1
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  1
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  1
2009 Sieglaff DH, Dunn WA, Xie XS, Megy K, Marinotti O, James AA. Comparative genomics allows the discovery of cis-regulatory elements in mosquitoes. Proceedings of the National Academy of Sciences of the United States of America. 106: 3053-8. PMID 19211788 DOI: 10.1073/Pnas.0813264106  1
2009 Fraser HB, Xie X. Common polymorphic transcript variation in human disease. Genome Research. 19: 567-75. PMID 19189928 DOI: 10.1101/Gr.083477.108  1
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  1
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  1
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  1
2008 Wu J, Sieglaff DH, Gervin J, Xie XS. Discovering regulatory motifs in the Plasmodium genome using comparative genomics. Bioinformatics (Oxford, England). 24: 1843-9. PMID 18611947 DOI: 10.1093/bioinformatics/btn348  1
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  1
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  1
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  1
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  1
2006 Wu J, Xie X. Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression. Genome Biology. 7: R85. PMID 17002790 DOI: 10.1186/gb-2006-7-9-r85  1
2006 Xie X, Kamal M, Lander ES. A family of conserved noncoding elements derived from an ancient transposable element. Proceedings of the National Academy of Sciences of the United States of America. 103: 11659-64. PMID 16864796 DOI: 10.1073/pnas.0604768103  1
2006 Giallourakis C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R. A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands. Genome Research. 16: 1056-72. PMID 16825666 DOI: 10.1101/Gr.5285206  1
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  1
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  1
2006 Calvo S, Jain M, Xie X, Sheth SA, Chang B, Goldberger OA, Spinazzola A, Zeviani M, Carr SA, Mootha VK. Systematic identification of human mitochondrial disease genes through integrative genomics. Nature Genetics. 38: 576-82. PMID 16582907 DOI: 10.1016/J.Mito.2007.08.068  1
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  1
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  1
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  1
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  1
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  1
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  1
2004 Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J, Sihag S, Yang W, Altshuler D, Puigserver P, Patterson N, Willy PJ, Schulman IG, Heyman RA, Lander ES, Spiegelman BM. Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle. Proceedings of the National Academy of Sciences of the United States of America. 101: 6570-5. PMID 15100410 DOI: 10.1073/Pnas.0401401101  1
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  1
2002 Xie X. Threshold behaviour of the maximum likelihood method in population decoding. Network (Bristol, England). 13: 447-56. PMID 12463339 DOI: 10.1088/0954-898X/13/4/302  1
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  1
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  1
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  1
2002 Giese M, Xie X. Exact solution of the nonlinear dynamics of recurrent neural mechanisms for direction selectivity Neurocomputing. 44: 417-422. DOI: 10.1016/S0925-2312(02)00394-6  1
2000 Kitamoto T, Xie X, Wu CF, Salvaterra PM. Isolation and characterization of mutants for the vesicular acetylcholine transporter gene in Drosophila melanogaster. Journal of Neurobiology. 42: 161-71. PMID 10640324 DOI: 10.1002/(SICI)1097-4695(20000205)42:2<161::AID-NEU1>3.0.CO;2-P  1
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