Xiaohui Xie

Xiaohui Xie

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Xiaohui Xie

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Asparagine Synthetase and Filamin A Have Different Roles in Ovarian Cancer.

Authors:
Liang Zeng Qiong Wang Congmin Gu Li Yuan Xiaohui Xie Lijuan He Kai Chen Pingping Tan Lei Xue Sanqian Huang Kun Shi

Front Oncol 2019 18;9:1072. Epub 2019 Oct 18.

Department of Gynecology and Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.

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http://dx.doi.org/10.3389/fonc.2019.01072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6813569PMC
October 2019

Inhalation of sodium hydrosulfide (NaHS) alleviates NO-induced pulmonary function and hematological impairment in rats.

Authors:
Zili Zhang Jian Wang Guihua Xu Mingjing Ding Fei Liu Liang Yuan Tao Wang Jingyi Xu Xiaohui Xie Bingxian Deng Dejun Sun Wenju Lu

Life Sci 2019 Sep 11;232:116650. Epub 2019 Jul 11.

State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, PR China; Department of Laboratory Medicine, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, PR China. Electronic address:

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http://dx.doi.org/10.1016/j.lfs.2019.116650DOI Listing
September 2019

FactorNet: A deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data.

Authors:
Daniel Quang Xiaohui Xie

Methods 2019 Aug 26;166:40-47. Epub 2019 Mar 26.

University of California, Department of Computer Science, Irvine, CA 92697, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2019.03.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6708499PMC
August 2019

Magnetic Graphene Field-Effect Transistor Biosensor for Single-Strand DNA Detection.

Authors:
Jinjin Sun Xiaohui Xie Ke Xie Shicai Xu Shouzhen Jiang Junfeng Ren Yuefeng Zhao Huaqiang Xu Jingjing Wang Weiwei Yue

Nanoscale Res Lett 2019 Jul 24;14(1):248. Epub 2019 Jul 24.

Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, Jinan, 250358, People's Republic of China.

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http://dx.doi.org/10.1186/s11671-019-3048-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6656833PMC
July 2019

Immobilizing argatroban and mPEG-NH on a polyethersulfone membrane surface to prepare an effective nonthrombogenic biointerface.

Authors:
Yanling Dai Siyuan Dai Xiaohui Xie Jianping Ning

J Biomater Sci Polym Ed 2019 06 4;30(8):608-628. Epub 2019 Apr 4.

a Department of Nephrology , Xiangya Hospital of Central South University , Changsha , Hunan , China.

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http://dx.doi.org/10.1080/09205063.2019.1595891DOI Listing
June 2019

Recent advances in nanofabrication techniques for SERS substrates and their applications in food safety analysis.

Authors:
Xiaohui Xie Hongbin Pu Da-Wen Sun

Crit Rev Food Sci Nutr 2018 24;58(16):2800-2813. Epub 2017 Aug 24.

a School of Food Science and Engineering , South China University of Technology , Guangzhou , China.

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http://dx.doi.org/10.1080/10408398.2017.1341866DOI Listing
May 2019

Interdigitating dendritic cell sarcoma of the spleen with hepatic failure after chemotherapy: A case report.

Authors:
Chengchen Zhao Xiaohui Xie Dong Zheng Gai Dengshu Wu Hongya Xin Tianlun Yang

Medicine (Baltimore) 2019 May;98(19):e15535

Cardiovascular Division.

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http://dx.doi.org/10.1097/MD.0000000000015535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6531197PMC
May 2019

Double strand DNA functionalized Au@Ag Nps for ultrasensitive detection of 17β-estradiol using surface-enhanced raman spectroscopy.

Authors:
Hongbin Pu Xiaohui Xie Da-Wen Sun Qingyi Wei Yingfen Jiang

Talanta 2019 Apr 13;195:419-425. Epub 2018 Oct 13.

School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, Guangzhou Higher Education Mega Center, Guangzhou 510006, China.

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https://linkinghub.elsevier.com/retrieve/pii/S00399140183105
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http://dx.doi.org/10.1016/j.talanta.2018.10.021DOI Listing
April 2019

Parallel clustering of single cell transcriptomic data with split-merge sampling on Dirichlet process mixtures.

Authors:
Tiehang Duan José P Pinto Xiaohui Xie

Bioinformatics 2019 03;35(6):953-961

Department of Computer Science, University of California, Irvine, CA, USA.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/bty702DOI Listing
March 2019

AnatomyNet: Deep learning for fast and fully automated whole-volume segmentation of head and neck anatomy.

Authors:
Wentao Zhu Yufang Huang Liang Zeng Xuming Chen Yong Liu Zhen Qian Nan Du Wei Fan Xiaohui Xie

Med Phys 2019 Feb 17;46(2):576-589. Epub 2018 Dec 17.

Department of Computer Science, University of California, Irvine, CA, USA.

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http://dx.doi.org/10.1002/mp.13300DOI Listing
February 2019

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.

Authors:
Liqun Wang Ruirui Zhou Xiaohui Xie

J Asthma 2019 01 8;56(1):69-78. Epub 2018 Feb 8.

a Department of Pharmacy Administration and Clinical Pharmacy, School of Pharmaceutical Sciences , Peking University , Beijing , China.

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http://dx.doi.org/10.1080/02770903.2018.1424192DOI Listing
January 2019

The effect of Nipped-B-like (Nipbl) haploinsufficiency on genome-wide cohesin binding and target gene expression: modeling Cornelia de Lange syndrome.

Authors:
Daniel A Newkirk Yen-Yun Chen Richard Chien Weihua Zeng Jacob Biesinger Ebony Flowers Shimako Kawauchi Rosaysela Santos Anne L Calof Arthur D Lander Xiaohui Xie Kyoko Yokomori

Clin Epigenetics 2017 25;9:89. Epub 2017 Aug 25.

Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697 USA.

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http://dx.doi.org/10.1186/s13148-017-0391-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574093PMC
May 2018

Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.

Authors:
Yong Zhu Xiuye Wang Elmira Forouzmand Joshua Jeong Feng Qiao Gregory A Sowd Alan N Engelman Xiaohui Xie Klemens J Hertel Yongsheng Shi

Mol Cell 2018 01 21;69(1):62-74.e4. Epub 2017 Dec 21.

Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765173089
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http://dx.doi.org/10.1016/j.molcel.2017.11.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5756121PMC
January 2018

Formyl peptide receptor 2 expression predicts poor prognosis and promotes invasion and metastasis in epithelial ovarian cancer.

Authors:
Xiaohui Xie Mengyuan Yang Yiling Ding Ling Yu Jianlin Chen

Oncol Rep 2017 Dec 13;38(6):3297-3308. Epub 2017 Oct 13.

Department of Obstetrics and Gynecology, Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China.

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http://dx.doi.org/10.3892/or.2017.6034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5783575PMC
December 2017

HLA class I binding prediction via convolutional neural networks.

Authors:
Yeeleng S Vang Xiaohui Xie

Bioinformatics 2017 Sep;33(17):2658-2665

Department of Computer Science, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx264DOI Listing
September 2017

Microbial infection, inflammation and epithelial ovarian cancer.

Authors:
Xiaohui Xie Mengyuan Yang Yiling Ding Jianlin Chen

Oncol Lett 2017 Aug 15;14(2):1911-1919. Epub 2017 Jun 15.

Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410001, P.R. China.

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http://dx.doi.org/10.3892/ol.2017.6388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529868PMC
August 2017

Developmentally regulated long non-coding RNAs in Xenopus tropicalis.

Authors:
Elmira Forouzmand Nick D L Owens Ira L Blitz Kitt D Paraiso Mustafa K Khokha Michael J Gilchrist Xiaohui Xie Ken W Y Cho

Dev Biol 2017 06 12;426(2):401-408. Epub 2016 Jul 12.

Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ydbio.2016.06.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5233649PMC
June 2017

Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program.

Authors:
Rebekah M Charney Elmira Forouzmand Jin Sun Cho Jessica Cheung Kitt D Paraiso Yuuri Yasuoka Shuji Takahashi Masanori Taira Ira L Blitz Xiaohui Xie Ken W Y Cho

Dev Cell 2017 03 17;40(6):595-607.e4. Epub 2017 Mar 17.

Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2017.02.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5434453PMC
March 2017

Gene expression inference with deep learning.

Authors:
Yifei Chen Yi Li Rajiv Narayan Aravind Subramanian Xiaohui Xie

Bioinformatics 2016 06 11;32(12):1832-9. Epub 2016 Feb 11.

Department of Computer Science, University of California, Irvine, CA 92697, USA Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908320PMC
June 2016

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.

Authors:
Daniel Quang Xiaohui Xie

Nucleic Acids Res 2016 06 15;44(11):e107. Epub 2016 Apr 15.

Department of Computer Science University of California, Irvine, CA 92697, USA Center for Complex Biological Systems University of California, Irvine, CA 92697, USA

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http://dx.doi.org/10.1093/nar/gkw226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914104PMC
June 2016

Poly(A) code analyses reveal key determinants for tissue-specific mRNA alternative polyadenylation.

Authors:
Lingjie Weng Yi Li Xiaohui Xie Yongsheng Shi

RNA 2016 06 19;22(6):813-21. Epub 2016 Apr 19.

Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, California 92697, USA.

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http://dx.doi.org/10.1261/rna.055681.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878608PMC
June 2016

SALL4 is a marker of poor prognosis in serous ovarian carcinoma promoting invasion and metastasis.

Authors:
Mengyuan Yang Xiaohui Xie Yiling Ding

Oncol Rep 2016 Mar 5;35(3):1796-806. Epub 2016 Jan 5.

Department of Obstetrics and Gynecology, Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China.

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http://dx.doi.org/10.3892/or.2016.4545DOI Listing
March 2016

MixClone: a mixture model for inferring tumor subclonal populations.

Authors:
Yi Li Xiaohui Xie

BMC Genomics 2015 21;16 Suppl 2:S1. Epub 2015 Jan 21.

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http://dx.doi.org/10.1186/1471-2164-16-S2-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331709PMC
December 2015

DANN: a deep learning approach for annotating the pathogenicity of genetic variants.

Authors:
Daniel Quang Yifei Chen Xiaohui Xie

Bioinformatics 2015 Mar 22;31(5):761-3. Epub 2014 Oct 22.

Department of Computer Science and Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA Department of Computer Science and Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btu703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4341060PMC
March 2015

Integrative ChIP-seq/microarray analysis identifies a CTNNB1 target signature enriched in intestinal stem cells and colon cancer.

Authors:
Kazuhide Watanabe Jacob Biesinger Michael L Salmans Brian S Roberts William T Arthur Michele Cleary Bogi Andersen Xiaohui Xie Xing Dai

PLoS One 2014 20;9(3):e92317. Epub 2014 Mar 20.

Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America; Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092317PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3961325PMC
December 2014

Genome-wide view of TGFβ/Foxh1 regulation of the early mesendoderm program.

Authors:
William T Chiu Rebekah Charney Le Ira L Blitz Margaret B Fish Yi Li Jacob Biesinger Xiaohui Xie Ken W Y Cho

Development 2014 Dec 30;141(23):4537-47. Epub 2014 Oct 30.

Department of Developmental and Cell Biology, University of California, Irvine, CA 92697-2300, USA

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http://dx.doi.org/10.1242/dev.107227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302925PMC
December 2014

Low-rank regularization for learning gene expression programs.

Authors:
Guibo Ye Mengfan Tang Jian-Feng Cai Qing Nie Xiaohui Xie

PLoS One 2013 17;8(12):e82146. Epub 2013 Dec 17.

Department of Computer Science, University of California Irvine, Irvine, California, United States of America ; Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082146PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866120PMC
September 2014

A gradient boosting algorithm for survival analysis via direct optimization of concordance index.

Authors:
Yifei Chen Zhenyu Jia Dan Mercola Xiaohui Xie

Comput Math Methods Med 2013 20;2013:873595. Epub 2013 Nov 20.

Department of Computer Science, University of California Irvine, Irvine, CA 92697, USA ; Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1155/2013/873595DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3853154PMC
August 2014

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity.

Authors:
Yi Li Xiaohui Xie

Bioinformatics 2014 Aug 2;30(15):2121-9. Epub 2014 Apr 2.

Department of Computer Science, Institute for Genomics and Bioinformatics and Center for Machine Learning and Intelligent Systems, University of California, Irvine, CA 92697, USADepartment of Computer Science, Institute for Genomics and Bioinformatics and Center for Machine Learning and Intelligent Systems, University of California, Irvine, CA 92697, USADepartment of Computer Science, Institute for Genomics and Bioinformatics and Center for Machine Learning and Intelligent Systems, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103592PMC
August 2014

EXTREME: an online EM algorithm for motif discovery.

Authors:
Daniel Quang Xiaohui Xie

Bioinformatics 2014 Jun 14;30(12):1667-73. Epub 2014 Feb 14.

Department of Computer Science, University of California, Irvine, CA 92697, USA and Center for Complex Biological Systems, University of California, Irvine, CA 92697, USADepartment of Computer Science, University of California, Irvine, CA 92697, USA and Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058924PMC
June 2014

Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal.

Authors:
Brad Lackford Chengguo Yao Georgette M Charles Lingjie Weng Xiaofeng Zheng Eun-A Choi Xiaohui Xie Ji Wan Yi Xing Johannes M Freudenberg Pengyi Yang Raja Jothi Guang Hu Yongsheng Shi

EMBO J 2014 Apr 4;33(8):878-89. Epub 2014 Mar 4.

Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.

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http://dx.doi.org/10.1002/embj.201386537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194112PMC
April 2014

Improving read mapping using additional prefix grams.

Authors:
Jongik Kim Chen Li Xiaohui Xie

BMC Bioinformatics 2014 Feb 5;15:42. Epub 2014 Feb 5.

Department of Computer Science, University of California, Irvine, USA.

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http://dx.doi.org/10.1186/1471-2105-15-42DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927682PMC
February 2014

Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns.

Authors:
Zhenzhen Zheng Scott Christley William T Chiu Ira L Blitz Xiaohui Xie Ken W Y Cho Qing Nie

BMC Syst Biol 2014 Jan 8;8. Epub 2014 Jan 8.

Department of Mathematics, University of California, Irvine, CA 92697, USA.

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http://escholarship.org/uc/item/7gn8h1fv.pdf
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http://www.biomedcentral.com/1752-0509/8/3
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http://dx.doi.org/10.1186/1752-0509-8-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3896677PMC
January 2014

Discovering and mapping chromatin states using a tree hidden Markov model.

Authors:
Jacob Biesinger Yuanfeng Wang Xiaohui Xie

BMC Bioinformatics 2013 10;14 Suppl 5:S4. Epub 2013 Apr 10.

Department of Computer Science, University of California-Irvine, CA, USA.

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http://dx.doi.org/10.1186/1471-2105-14-S5-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3622631PMC
December 2013

A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues.

Authors:
Yi Li Xiaohui Xie

BMC Bioinformatics 2013 10;14 Suppl 5:S11. Epub 2013 Apr 10.

Department of Computer Science, University of California-Irvine, CA, USA.

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http://dx.doi.org/10.1186/1471-2105-14-S5-S11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3622628PMC
December 2013

Biallelic genome modification in F(0) Xenopus tropicalis embryos using the CRISPR/Cas system.

Authors:
Ira L Blitz Jacob Biesinger Xiaohui Xie Ken W Y Cho

Genesis 2013 Dec 21;51(12):827-34. Epub 2013 Nov 21.

Department of Developmental and Cell Biology, University of California, Irvine, California.

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http://dx.doi.org/10.1002/dvg.22719DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4039559PMC
December 2013

Overlapping and distinct functions of CstF64 and CstF64τ in mammalian mRNA 3' processing.

Authors:
Chengguo Yao Eun-A Choi Lingjie Weng Xiaohui Xie Ji Wan Yi Xing James J Moresco Patricia G Tu John R Yates Yongsheng Shi

RNA 2013 Dec 22;19(12):1781-90. Epub 2013 Oct 22.

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http://dx.doi.org/10.1261/rna.042317.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3884657PMC
December 2013

Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation.

Authors:
Chengguo Yao Jacob Biesinger Ji Wan Lingjie Weng Yi Xing Xiaohui Xie Yongsheng Shi

Proc Natl Acad Sci U S A 2012 Nov 29;109(46):18773-8. Epub 2012 Oct 29.

Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1073/pnas.1211101109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3503179PMC
November 2012

Effect of replacing soybean meal with cottonseed meal on growth, hematology, antioxidant enzymes activity and expression for juvenile grass carp, Ctenopharyngodon idellus.

Authors:
Qingmei Zheng Xiaobo Wen Chunyan Han Haobo Li Xiaohui Xie

Fish Physiol Biochem 2012 Aug;38(4):1059-69

College of Animal Sciences, South China Agricultural University, Guangzhou 510642, China.

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http://dx.doi.org/10.1007/s10695-011-9590-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389240PMC
August 2012

[Modeling and analysis of volume conduction based on field-circuit coupling].

Authors:
Zhide Tang Hailong Liu Xiaohui Xie Xiufa Chen Deming Hou

Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 2012 Aug;29(4):609-14

State Key Laboratory of Power Transmission Equipment & System Security and New Technology, Chongqing University, Chongqing 400044, China.

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August 2012

Hobbes: optimized gram-based methods for efficient read alignment.

Authors:
Athena Ahmadi Alexander Behm Nagesh Honnalli Chen Li Lingjie Weng Xiaohui Xie

Nucleic Acids Res 2012 Mar 22;40(6):e41. Epub 2011 Dec 22.

Department of Computer Science, University of California, Irvine, CA 92697, USA.

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https://academic.oup.com/nar/article/40/6/e41/2409442
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http://dx.doi.org/10.1093/nar/gkr1246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315303PMC
March 2012

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.

Authors:
Hansook Kim Chong Jacob Biesinger Young-Kyo Seo Xiaohui Xie Timothy F Osborne

BMC Genomics 2012 Feb 1;13:51. Epub 2012 Feb 1.

Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-13-51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3295688PMC
February 2012

MotifMap: integrative genome-wide maps of regulatory motif sites for model species.

Authors:
Kenneth Daily Vishal R Patel Paul Rigor Xiaohui Xie Pierre Baldi

BMC Bioinformatics 2011 Dec 30;12:495. Epub 2011 Dec 30.

Department of Computer Science, University of California Irvine, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1186/1471-2105-12-495DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293935PMC
December 2011

AREM: aligning short reads from ChIP-sequencing by expectation maximization.

Authors:
Daniel Newkirk Jacob Biesinger Alvin Chon Kyoko Yokomori Xiaohui Xie

J Comput Biol 2011 Nov 28;18(11):1495-505. Epub 2011 Oct 28.

Department of Biological Chemistry, University of California, Irvine, California 92697, USA.

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http://dx.doi.org/10.1089/cmb.2011.0185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216101PMC
November 2011

A high-resolution map of human evolutionary constraint using 29 mammals.

Authors:
Kerstin Lindblad-Toh Manuel Garber Or Zuk Michael F Lin Brian J Parker Stefan Washietl Pouya Kheradpour Jason Ernst Gregory Jordan Evan Mauceli Lucas D Ward Craig B Lowe Alisha K Holloway Michele Clamp Sante Gnerre Jessica Alföldi Kathryn Beal Jean Chang Hiram Clawson James Cuff Federica Di Palma Stephen Fitzgerald Paul Flicek Mitchell Guttman Melissa J Hubisz David B Jaffe Irwin Jungreis W James Kent Dennis Kostka Marcia Lara Andre L Martins Tim Massingham Ida Moltke Brian J Raney Matthew D Rasmussen Jim Robinson Alexander Stark Albert J Vilella Jiayu Wen Xiaohui Xie Michael C Zody Jen Baldwin Toby Bloom Chee Whye Chin Dave Heiman Robert Nicol Chad Nusbaum Sarah Young Jane Wilkinson Kim C Worley Christie L Kovar Donna M Muzny Richard A Gibbs Andrew Cree Huyen H Dihn Gerald Fowler Shalili Jhangiani Vandita Joshi Sandra Lee Lora R Lewis Lynne V Nazareth Geoffrey Okwuonu Jireh Santibanez Wesley C Warren Elaine R Mardis George M Weinstock Richard K Wilson Kim Delehaunty David Dooling Catrina Fronik Lucinda Fulton Bob Fulton Tina Graves Patrick Minx Erica Sodergren Ewan Birney Elliott H Margulies Javier Herrero Eric D Green David Haussler Adam Siepel Nick Goldman Katherine S Pollard Jakob S Pedersen Eric S Lander Manolis Kellis

Nature 2011 Oct 12;478(7370):476-82. Epub 2011 Oct 12.

Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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October 2011

Genome-wide localization of SREBP-2 in hepatic chromatin predicts a role in autophagy.

Authors:
Young-Kyo Seo Tae-Il Jeon Hansook Kim Chong Jacob Biesinger Xiaohui Xie Timothy F Osborne

Cell Metab 2011 Apr;13(4):367-375

Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA; Metabolic Signaling and Disease Program, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA. Electronic address:

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April 2011

SNP-based pathway enrichment analysis for genome-wide association studies.

Authors:
Lingjie Weng Fabio Macciardi Aravind Subramanian Guia Guffanti Steven G Potkin Zhaoxia Yu Xiaohui Xie

BMC Bioinformatics 2011 Apr 15;12:99. Epub 2011 Apr 15.

Department of Computer Science, University of California, Irvine, USA.

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April 2011

The site-frequency spectrum of linked sites.

Authors:
Xiaohui Xie

Bull Math Biol 2011 Mar 27;73(3):459-94. Epub 2010 Mar 27.

Department of Computer Science, Center for Complex Biological Systems, Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA.

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March 2011

Identifying gene regulatory networks in schizophrenia.

Authors:
Steven G Potkin Fabio Macciardi Guia Guffanti James H Fallon Qi Wang Jessica A Turner Anita Lakatos Michael F Miles Arthur Lander Marquis P Vawter Xiaohui Xie

Neuroimage 2010 Nov 22;53(3):839-47. Epub 2010 Jun 22.

Department of Psychiatry & Human Behavior, 5251 California Avenue, Suite 240, University of California, Irvine, CA 92617, USA.

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November 2010

Genome-wide interrogation of hepatic FXR reveals an asymmetric IR-1 motif and synergy with LRH-1.

Authors:
Hansook Kim Chong Aniello M Infante Young-Kyo Seo Tae-Il Jeon Yanqiao Zhang Peter A Edwards Xiaohui Xie Timothy F Osborne

Nucleic Acids Res 2010 Oct 18;38(18):6007-17. Epub 2010 May 18.

Department of Molecular Biology and Biochemistry, Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1093/nar/gkq397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952856PMC
October 2010

Data structures and compression algorithms for high-throughput sequencing technologies.

Authors:
Kenny Daily Paul Rigor Scott Christley Xiaohui Xie Pierre Baldi

BMC Bioinformatics 2010 Oct 14;11:514. Epub 2010 Oct 14.

Department of Computer Science, University of California Irvine, Irvine, CA 92697 USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2964686PMC
October 2010

Interactive and fuzzy search: a dynamic way to explore MEDLINE.

Authors:
Jiannan Wang Inci Cetindil Shengyue Ji Chen Li Xiaohui Xie Guoliang Li Jianhua Feng

Bioinformatics 2010 Sep 12;26(18):2321-7. Epub 2010 Jul 12.

Department of Computer Science, Tsinghua University, Beijing, China.

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September 2010

Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent.

Authors:
Yuanfeng Wang Scott Christley Eric Mjolsness Xiaohui Xie

BMC Syst Biol 2010 Jul 21;4:99. Epub 2010 Jul 21.

Department of Physics and Astronomy, University of California, Irvine, 92617, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2914651PMC
July 2010

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium.

Authors:
Li-Jun Ma H Charlotte van der Does Katherine A Borkovich Jeffrey J Coleman Marie-Josée Daboussi Antonio Di Pietro Marie Dufresne Michael Freitag Manfred Grabherr Bernard Henrissat Petra M Houterman Seogchan Kang Won-Bo Shim Charles Woloshuk Xiaohui Xie Jin-Rong Xu John Antoniw Scott E Baker Burton H Bluhm Andrew Breakspear Daren W Brown Robert A E Butchko Sinead Chapman Richard Coulson Pedro M Coutinho Etienne G J Danchin Andrew Diener Liane R Gale Donald M Gardiner Stephen Goff Kim E Hammond-Kosack Karen Hilburn Aurélie Hua-Van Wilfried Jonkers Kemal Kazan Chinnappa D Kodira Michael Koehrsen Lokesh Kumar Yong-Hwan Lee Liande Li John M Manners Diego Miranda-Saavedra Mala Mukherjee Gyungsoon Park Jongsun Park Sook-Young Park Robert H Proctor Aviv Regev M Carmen Ruiz-Roldan Divya Sain Sharadha Sakthikumar Sean Sykes David C Schwartz B Gillian Turgeon Ilan Wapinski Olen Yoder Sarah Young Qiandong Zeng Shiguo Zhou James Galagan Christina A Cuomo H Corby Kistler Martijn Rep

Nature 2010 Mar;464(7287):367-73

The Broad Institute, Cambridge, Massachusetts 02141, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048781PMC
March 2010

Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes.

Authors:
Lokesh Kumar Andrew Breakspear Corby Kistler Li-Jun Ma Xiaohui Xie

BMC Genomics 2010 Mar 26;11:208. Epub 2010 Mar 26.

Broad Institute, Cambridge, MA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853525PMC
March 2010

Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif.

Authors:
Young-Kyo Seo Hansook Kim Chong Aniello M Infante Seung-Soon Im Xiaohui Xie Timothy F Osborne

Proc Natl Acad Sci U S A 2009 Aug 4;106(33):13765-9. Epub 2009 Aug 4.

Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1073/pnas.0904246106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728968PMC
August 2009

Incorporating existing network information into gene network inference.

Authors:
Scott Christley Qing Nie Xiaohui Xie

PLoS One 2009 Aug 27;4(8):e6799. Epub 2009 Aug 27.

Department of Mathematics, University of California Irvine, Irvine, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2729382PMC
August 2009

Identifying novel constrained elements by exploiting biased substitution patterns.

Authors:
Manuel Garber Mitchell Guttman Michele Clamp Michael C Zody Nir Friedman Xiaohui Xie

Bioinformatics 2009 Jun;25(12):i54-62

Department of Biology, Broad Institute of MIT and Harvard, 7 Cambridge Center, MIT, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687944PMC
June 2009

Common polymorphic transcript variation in human disease.

Authors:
Hunter B Fraser Xiaohui Xie

Genome Res 2009 Apr 2;19(4):567-75. Epub 2009 Feb 2.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1101/gr.083477.108DOI Listing
April 2009

Comparative genomics allows the discovery of cis-regulatory elements in mosquitoes.

Authors:
Douglas H Sieglaff W Augustine Dunn Xiaohui S Xie Karyn Megy Osvaldo Marinotti Anthony A James

Proc Natl Acad Sci U S A 2009 Mar 11;106(9):3053-8. Epub 2009 Feb 11.

Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1073/pnas.0813264106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2640218PMC
March 2009

Human genomes as email attachments.

Authors:
Scott Christley Yiming Lu Chen Li Xiaohui Xie

Bioinformatics 2009 Jan 7;25(2):274-5. Epub 2008 Nov 7.

Department of Computer Science, University of California Irvine, Irvine, CA 92697, USA.

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January 2009

MotifMap: a human genome-wide map of candidate regulatory motif sites.

Authors:
Xiaohui Xie Paul Rigor Pierre Baldi

Bioinformatics 2009 Jan 18;25(2):167-74. Epub 2008 Nov 18.

Department of Computer Sciences, University of California, Irvine, CA 92697, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732295PMC
January 2009

Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.

Authors:
Manching Ku Richard P Koche Esther Rheinbay Eric M Mendenhall Mitsuhiro Endoh Tarjei S Mikkelsen Aviva Presser Chad Nusbaum Xiaohui Xie Andrew S Chi Mazhar Adli Simon Kasif Leon M Ptaszek Chad A Cowan Eric S Lander Haruhiko Koseki Bradley E Bernstein

PLoS Genet 2008 Oct 31;4(10):e1000242. Epub 2008 Oct 31.

Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.

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http://dx.doi.org/10.1371/journal.pgen.1000242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567431PMC
October 2008

Discovering regulatory motifs in the Plasmodium genome using comparative genomics.

Authors:
Jie Wu Douglas H Sieglaff Joshua Gervin Xiaohui S Xie

Bioinformatics 2008 Sep 8;24(17):1843-9. Epub 2008 Jul 8.

Department of Computer Sciences, University of California, Irvine, CA 92697, CODA Genomics, Laguna Hills, CA 92656, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4168299PMC
September 2008

Distinguishing protein-coding and noncoding genes in the human genome.

Authors:
Michele Clamp Ben Fry Mike Kamal Xiaohui Xie James Cuff Michael F Lin Manolis Kellis Kerstin Lindblad-Toh Eric S Lander

Proc Natl Acad Sci U S A 2007 Dec 26;104(49):19428-33. Epub 2007 Nov 26.

Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2148306PMC
December 2007

Genome-wide detection and characterization of positive selection in human populations.

Authors:
Pardis C Sabeti Patrick Varilly Ben Fry Jason Lohmueller Elizabeth Hostetter Chris Cotsapas Xiaohui Xie Elizabeth H Byrne Steven A McCarroll Rachelle Gaudet Stephen F Schaffner Eric S Lander Kelly A Frazer Dennis G Ballinger David R Cox David A Hinds Laura L Stuve Richard A Gibbs John W Belmont Andrew Boudreau Paul Hardenbol Suzanne M Leal Shiran Pasternak David A Wheeler Thomas D Willis Fuli Yu Huanming Yang Changqing Zeng Yang Gao Haoran Hu Weitao Hu Chaohua Li Wei Lin Siqi Liu Hao Pan Xiaoli Tang Jian Wang Wei Wang Jun Yu Bo Zhang Qingrun Zhang Hongbin Zhao Hui Zhao Jun Zhou Stacey B Gabriel Rachel Barry Brendan Blumenstiel Amy Camargo Matthew Defelice Maura Faggart Mary Goyette Supriya Gupta Jamie Moore Huy Nguyen Robert C Onofrio Melissa Parkin Jessica Roy Erich Stahl Ellen Winchester Liuda Ziaugra David Altshuler Yan Shen Zhijian Yao Wei Huang Xun Chu Yungang He Li Jin Yangfan Liu Yayun Shen Weiwei Sun Haifeng Wang Yi Wang Ying Wang Xiaoyan Xiong Liang Xu Mary M Y Waye Stephen K W Tsui Hong Xue J Tze-Fei Wong Luana M Galver Jian-Bing Fan Kevin Gunderson Sarah S Murray Arnold R Oliphant Mark S Chee Alexandre Montpetit Fanny Chagnon Vincent Ferretti Martin Leboeuf Jean-François Olivier Michael S Phillips Stéphanie Roumy Clémentine Sallée Andrei Verner Thomas J Hudson Pui-Yan Kwok Dongmei Cai Daniel C Koboldt Raymond D Miller Ludmila Pawlikowska Patricia Taillon-Miller Ming Xiao Lap-Chee Tsui William Mak You Qiang Song Paul K H Tam Yusuke Nakamura Takahisa Kawaguchi Takuya Kitamoto Takashi Morizono Atsushi Nagashima Yozo Ohnishi Akihiro Sekine Toshihiro Tanaka Tatsuhiko Tsunoda Panos Deloukas Christine P Bird Marcos Delgado Emmanouil T Dermitzakis Rhian Gwilliam Sarah Hunt Jonathan Morrison Don Powell Barbara E Stranger Pamela Whittaker David R Bentley Mark J Daly Paul I W de Bakker Jeff Barrett Yves R Chretien Julian Maller Steve McCarroll Nick Patterson Itsik Pe'er Alkes Price Shaun Purcell Daniel J Richter Pardis Sabeti Richa Saxena Stephen F Schaffner Pak C Sham Patrick Varilly David Altshuler Lincoln D Stein Lalitha Krishnan Albert Vernon Smith Marcela K Tello-Ruiz Gudmundur A Thorisson Aravinda Chakravarti Peter E Chen David J Cutler Carl S Kashuk Shin Lin Gonçalo R Abecasis Weihua Guan Yun Li Heather M Munro Zhaohui Steve Qin Daryl J Thomas Gilean McVean Adam Auton Leonardo Bottolo Niall Cardin Susana Eyheramendy Colin Freeman Jonathan Marchini Simon Myers Chris Spencer Matthew Stephens Peter Donnelly Lon R Cardon Geraldine Clarke David M Evans Andrew P Morris Bruce S Weir Tatsuhiko Tsunoda Todd A Johnson James C Mullikin Stephen T Sherry Michael Feolo Andrew Skol Houcan Zhang Changqing Zeng Hui Zhao Ichiro Matsuda Yoshimitsu Fukushima Darryl R Macer Eiko Suda Charles N Rotimi Clement A Adebamowo Ike Ajayi Toyin Aniagwu Patricia A Marshall Chibuzor Nkwodimmah Charmaine D M Royal Mark F Leppert Missy Dixon Andy Peiffer Renzong Qiu Alastair Kent Kazuto Kato Norio Niikawa Isaac F Adewole Bartha M Knoppers Morris W Foster Ellen Wright Clayton Jessica Watkin Richard A Gibbs John W Belmont Donna Muzny Lynne Nazareth Erica Sodergren George M Weinstock David A Wheeler Imtaz Yakub Stacey B Gabriel Robert C Onofrio Daniel J Richter Liuda Ziaugra Bruce W Birren Mark J Daly David Altshuler Richard K Wilson Lucinda L Fulton Jane Rogers John Burton Nigel P Carter Christopher M Clee Mark Griffiths Matthew C Jones Kirsten McLay Robert W Plumb Mark T Ross Sarah K Sims David L Willey Zhu Chen Hua Han Le Kang Martin Godbout John C Wallenburg Paul L'Archevêque Guy Bellemare Koji Saeki Hongguang Wang Daochang An Hongbo Fu Qing Li Zhen Wang Renwu Wang Arthur L Holden Lisa D Brooks Jean E McEwen Mark S Guyer Vivian Ota Wang Jane L Peterson Michael Shi Jack Spiegel Lawrence M Sung Lynn F Zacharia Francis S Collins Karen Kennedy Ruth Jamieson John Stewart

Nature 2007 Oct;449(7164):913-8

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA.

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October 2007

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.

Authors:
Tarjei S Mikkelsen Manching Ku David B Jaffe Biju Issac Erez Lieberman Georgia Giannoukos Pablo Alvarez William Brockman Tae-Kyung Kim Richard P Koche William Lee Eric Mendenhall Aisling O'Donovan Aviva Presser Carsten Russ Xiaohui Xie Alexander Meissner Marius Wernig Rudolf Jaenisch Chad Nusbaum Eric S Lander Bradley E Bernstein

Nature 2007 Aug 1;448(7153):553-60. Epub 2007 Jul 1.

Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.

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August 2007

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.

Authors:
Tarjei S Mikkelsen Matthew J Wakefield Bronwen Aken Chris T Amemiya Jean L Chang Shannon Duke Manuel Garber Andrew J Gentles Leo Goodstadt Andreas Heger Jerzy Jurka Michael Kamal Evan Mauceli Stephen M J Searle Ted Sharpe Michelle L Baker Mark A Batzer Panayiotis V Benos Katherine Belov Michele Clamp April Cook James Cuff Radhika Das Lance Davidow Janine E Deakin Melissa J Fazzari Jacob L Glass Manfred Grabherr John M Greally Wanjun Gu Timothy A Hore Gavin A Huttley Michael Kleber Randy L Jirtle Edda Koina Jeannie T Lee Shaun Mahony Marco A Marra Robert D Miller Robert D Nicholls Mayumi Oda Anthony T Papenfuss Zuly E Parra David D Pollock David A Ray Jacqueline E Schein Terence P Speed Katherine Thompson John L VandeBerg Claire M Wade Jerilyn A Walker Paul D Waters Caleb Webber Jennifer R Weidman Xiaohui Xie Michael C Zody Jennifer A Marshall Graves Chris P Ponting Matthew Breen Paul B Samollow Eric S Lander Kerstin Lindblad-Toh

Nature 2007 May;447(7141):167-77

Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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May 2007

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites.

Authors:
Xiaohui Xie Tarjei S Mikkelsen Andreas Gnirke Kerstin Lindblad-Toh Manolis Kellis Eric S Lander

Proc Natl Acad Sci U S A 2007 Apr 18;104(17):7145-50. Epub 2007 Apr 18.

Broad Institute of MIT and Harvard, Massachusetts Institute of Technology and Harvard Medical School, Cambridge, MA 02142, USA.

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April 2007

Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression.

Authors:
Jie Wu Xiaohui Xie

Genome Biol 2006 ;7(9):R85

Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA.

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January 2007

A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands.

Authors:
Cosmas Giallourakis Zhifang Cao Todd Green Heather Wachtel Xiaohui Xie Marco Lopez-Illasaca Mark Daly John Rioux Ramnik Xavier

Genome Res 2006 Aug 6;16(8):1056-72. Epub 2006 Jul 6.

Massachusetts General Hospital, Center for Computational and Integrative Biology, Harvard University Medical School, Boston, Massachusetts 02114, USA.

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August 2006

A family of conserved noncoding elements derived from an ancient transposable element.

Authors:
Xiaohui Xie Michael Kamal Eric S Lander

Proc Natl Acad Sci U S A 2006 Aug 24;103(31):11659-64. Epub 2006 Jul 24.

Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.

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August 2006

Systematic identification of human mitochondrial disease genes through integrative genomics.

Authors:
Sarah Calvo Mohit Jain Xiaohui Xie Sunil A Sheth Betty Chang Olga A Goldberger Antonella Spinazzola Massimo Zeviani Steven A Carr Vamsi K Mootha

Nat Genet 2006 May 2;38(5):576-82. Epub 2006 Apr 2.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.

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May 2006

A mammalian organelle map by protein correlation profiling.

Authors:
Leonard J Foster Carmen L de Hoog Yanling Zhang Yong Zhang Xiaohui Xie Vamsi K Mootha Matthias Mann

Cell 2006 Apr;125(1):187-99

Center for Experimental BioInformatics (CEBI), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.

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April 2006

A bivalent chromatin structure marks key developmental genes in embryonic stem cells.

Authors:
Bradley E Bernstein Tarjei S Mikkelsen Xiaohui Xie Michael Kamal Dana J Huebert James Cuff Ben Fry Alex Meissner Marius Wernig Kathrin Plath Rudolf Jaenisch Alexandre Wagschal Robert Feil Stuart L Schreiber Eric S Lander

Cell 2006 Apr;125(2):315-26

Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA.

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April 2006

A large family of ancient repeat elements in the human genome is under strong selection.

Authors:
Michael Kamal Xiaohui Xie Eric S Lander

Proc Natl Acad Sci U S A 2006 Feb 13;103(8):2740-5. Epub 2006 Feb 13.

Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1073/pnas.0511238103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1413850PMC
February 2006

Disease gene discovery through integrative genomics.

Authors:
Cosmas Giallourakis Charlotte Henson Michael Reich Xiaohui Xie Vamsi K Mootha

Annu Rev Genomics Hum Genet 2005 ;6:381-406

Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1146/annurev.genom.6.080604.162234DOI Listing
December 2005

Learning curves for stochastic gradient descent in linear feedforward networks.

Authors:
Justin Werfel Xiaohui Xie H Sebastian Seung

Neural Comput 2005 Dec;17(12):2699-718

Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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December 2005

Genome sequence, comparative analysis and haplotype structure of the domestic dog.

Authors:
Kerstin Lindblad-Toh Claire M Wade Tarjei S Mikkelsen Elinor K Karlsson David B Jaffe Michael Kamal Michele Clamp Jean L Chang Edward J Kulbokas Michael C Zody Evan Mauceli Xiaohui Xie Matthew Breen Robert K Wayne Elaine A Ostrander Chris P Ponting Francis Galibert Douglas R Smith Pieter J DeJong Ewen Kirkness Pablo Alvarez Tara Biagi William Brockman Jonathan Butler Chee-Wye Chin April Cook James Cuff Mark J Daly David DeCaprio Sante Gnerre Manfred Grabherr Manolis Kellis Michael Kleber Carolyne Bardeleben Leo Goodstadt Andreas Heger Christophe Hitte Lisa Kim Klaus-Peter Koepfli Heidi G Parker John P Pollinger Stephen M J Searle Nathan B Sutter Rachael Thomas Caleb Webber Jennifer Baldwin Adal Abebe Amr Abouelleil Lynne Aftuck Mostafa Ait-Zahra Tyler Aldredge Nicole Allen Peter An Scott Anderson Claudel Antoine Harindra Arachchi Ali Aslam Laura Ayotte Pasang Bachantsang Andrew Barry Tashi Bayul Mostafa Benamara Aaron Berlin Daniel Bessette Berta Blitshteyn Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Adam Brown Patrick Cahill Nadia Calixte Jody Camarata Yama Cheshatsang Jeffrey Chu Mieke Citroen Alville Collymore Patrick Cooke Tenzin Dawoe Riza Daza Karin Decktor Stuart DeGray Norbu Dhargay Kimberly Dooley Kathleen Dooley Passang Dorje Kunsang Dorjee Lester Dorris Noah Duffey Alan Dupes Osebhajajeme Egbiremolen Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Patricia Ferreira Sheila Fisher Mike FitzGerald Karen Foley Chelsea Foley Alicia Franke Dennis Friedrich Diane Gage Manuel Garber Gary Gearin Georgia Giannoukos Tina Goode Audra Goyette Joseph Graham Edward Grandbois Kunsang Gyaltsen Nabil Hafez Daniel Hagopian Birhane Hagos Jennifer Hall Claire Healy Ryan Hegarty Tracey Honan Andrea Horn Nathan Houde Leanne Hughes Leigh Hunnicutt M Husby Benjamin Jester Charlien Jones Asha Kamat Ben Kanga Cristyn Kells Dmitry Khazanovich Alix Chinh Kieu Peter Kisner Mayank Kumar Krista Lance Thomas Landers Marcia Lara William Lee Jean-Pierre Leger Niall Lennon Lisa Leuper Sarah LeVine Jinlei Liu Xiaohong Liu Yeshi Lokyitsang Tashi Lokyitsang Annie Lui Jan Macdonald John Major Richard Marabella Kebede Maru Charles Matthews Susan McDonough Teena Mehta James Meldrim Alexandre Melnikov Louis Meneus Atanas Mihalev Tanya Mihova Karen Miller Rachel Mittelman Valentine Mlenga Leonidas Mulrain Glen Munson Adam Navidi Jerome Naylor Tuyen Nguyen Nga Nguyen Cindy Nguyen Thu Nguyen Robert Nicol Nyima Norbu Choe Norbu Nathaniel Novod Tenchoe Nyima Peter Olandt Barry O'Neill Keith O'Neill Sahal Osman Lucien Oyono Christopher Patti Danielle Perrin Pema Phunkhang Fritz Pierre Margaret Priest Anthony Rachupka Sujaa Raghuraman Rayale Rameau Verneda Ray Christina Raymond Filip Rege Cecil Rise Julie Rogers Peter Rogov Julie Sahalie Sampath Settipalli Theodore Sharpe Terrance Shea Mechele Sheehan Ngawang Sherpa Jianying Shi Diana Shih Jessie Sloan Cherylyn Smith Todd Sparrow John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Sabrina Stone Sean Sykes Pierre Tchuinga Pema Tenzing Senait Tesfaye Dawa Thoulutsang Yama Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Vijay Venkataraman Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Shuli Yang Xiaoping Yang Geneva Young Qing Yu Joanne Zainoun Lisa Zembek Andrew Zimmer Eric S Lander

Nature 2005 Dec;438(7069):803-19

Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA.

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http://www.nature.com/articles/nature04338
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http://dx.doi.org/10.1038/nature04338DOI Listing
December 2005

Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals.

Authors:
Xiaohui Xie Jun Lu E J Kulbokas Todd R Golub Vamsi Mootha Kerstin Lindblad-Toh Eric S Lander Manolis Kellis

Nature 2005 Mar 27;434(7031):338-45. Epub 2005 Feb 27.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.

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http://dx.doi.org/10.1038/nature03441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923337PMC
March 2005

Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle.

Authors:
Vamsi K Mootha Christoph Handschin Dan Arlow Xiaohui Xie Julie St Pierre Smita Sihag Wenli Yang David Altshuler Pere Puigserver Nick Patterson Patricia J Willy Ira G Schulman Richard A Heyman Eric S Lander Bruce M Spiegelman

Proc Natl Acad Sci U S A 2004 Apr 20;101(17):6570-5. Epub 2004 Apr 20.

The Eli and Edythe L. Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139-1561, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0401401101
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http://dx.doi.org/10.1073/pnas.0401401101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC404086PMC
April 2004

Learning in neural networks by reinforcement of irregular spiking.

Authors:
Xiaohui Xie H Sebastian Seung

Phys Rev E Stat Nonlin Soft Matter Phys 2004 Apr 30;69(4 Pt 1):041909. Epub 2004 Apr 30.

Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1103/PhysRevE.69.041909DOI Listing
April 2004

Equivalence of backpropagation and contrastive Hebbian learning in a layered network.

Authors:
Xiaohui Xie H Sebastian Seung

Neural Comput 2003 Feb;15(2):441-54

Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1162/089976603762552988DOI Listing
February 2003

Selectively grouping neurons in recurrent networks of lateral inhibition.

Authors:
Xiaohui Xie Richard H R Hahnloser H Sebastian Seung

Neural Comput 2002 Nov;14(11):2627-46

Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1162/089976602760408008DOI Listing
November 2002

Threshold behaviour of the maximum likelihood method in population decoding.

Authors:
Xiaohui Xie

Network 2002 Nov;13(4):447-56

Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.

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November 2002

Double-ring network model of the head-direction system.

Authors:
Xiaohui Xie Richard H R Hahnloser H Sebastian Seung

Phys Rev E Stat Nonlin Soft Matter Phys 2002 Oct 9;66(4 Pt 1):041902. Epub 2002 Oct 9.

Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, E25-210, 45 Carleton Street, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1103/PhysRevE.66.041902DOI Listing
October 2002

Nonlinear dynamics of direction-selective recurrent neural media.

Authors:
Xiaohui Xie Martin A Giese

Phys Rev E Stat Nonlin Soft Matter Phys 2002 May 3;65(5 Pt 1):051904. Epub 2002 May 3.

Department of Brain and Cognitive Sciences and Center for Biological and Computational Learning, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1103/PhysRevE.65.051904DOI Listing
May 2002