Xiaohui Xie

Xiaohui Xie

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Xiaohui Xie

Publications by authors named "Xiaohui Xie"

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87Publications

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

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.

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.

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.

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.

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.

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

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

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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

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

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

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

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.

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

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

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.

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.

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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http://dx.doi.org/10.1038/nature10530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357PMC
October 2011

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

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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http://dx.doi.org/10.1016/j.cmet.2011.03.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3086264PMC
April 2011

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

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

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

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http://dx.doi.org/10.1186/1471-2105-12-99DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102637PMC
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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http://dx.doi.org/10.1007/s11538-010-9534-3DOI Listing
March 2011

Identifying gene regulatory networks in schizophrenia.

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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http://dx.doi.org/10.1016/j.neuroimage.2010.06.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055795PMC
November 2010

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

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.

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://dx.doi.org/10.1186/1471-2105-11-514DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2964686PMC
October 2010

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

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

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

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btq414DOI Listing
September 2010

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

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://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
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http://dx.doi.org/10.1186/1752-0509-4-99DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2914651PMC
July 2010

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

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.

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://journals.plos.org/plosone/article?id=10.1371/journal.pone.0006799PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2729382PMC
August 2009

Identifying novel constrained elements by exploiting biased substitution patterns.

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.

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.

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.

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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http://dx.doi.org/10.1093/bioinformatics/btn582DOI Listing
January 2009

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

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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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btn605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732295PMC
January 2009

Discovering regulatory motifs in the Plasmodium genome using comparative genomics.

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.

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.pnas.org/cgi/doi/10.1073/pnas.0709013104
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http://dx.doi.org/10.1073/pnas.0709013104DOI Listing
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

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

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.

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.

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.

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.

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

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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February 2006

Disease gene discovery through integrative genomics.

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

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

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December 2005

Learning curves for stochastic gradient descent in linear feedforward networks.

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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December 2005

Learning in neural networks by reinforcement of irregular spiking.

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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April 2004

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

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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February 2003

Selectively grouping neurons in recurrent networks of lateral inhibition.

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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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.

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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October 2002

Nonlinear dynamics of direction-selective recurrent neural media.

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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May 2002