Guanghua Xiao

Guanghua Xiao

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Guanghua Xiao

Publications by authors named "Guanghua Xiao"

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99Publications

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TLR9 and beclin 1 crosstalk regulates muscle AMPK activation in exercise.

Nature 2020 Feb 12. Epub 2020 Feb 12.

Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.

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http://dx.doi.org/10.1038/s41586-020-1992-7DOI Listing
February 2020

Correction: LCE: an open web portal to explore gene expression and clinical associations in lung cancer.

Oncogene 2020 Jan;39(3):718-719

Quantitative Biomedical Research Center, Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA.

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http://dx.doi.org/10.1038/s41388-019-1000-6DOI Listing
January 2020

ConvPath: A software tool for lung adenocarcinoma digital pathological image analysis aided by a convolutional neural network.

EBioMedicine 2019 Dec 22;50:103-110. Epub 2019 Nov 22.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2019.10.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6921240PMC
December 2019

VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning.

PLoS Comput Biol 2020 Jan 13;16(1):e1007511. Epub 2020 Jan 13.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007511DOI Listing
January 2020

Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets.

Genes (Basel) 2020 01 3;11(1). Epub 2020 Jan 3.

Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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http://dx.doi.org/10.3390/genes11010054DOI Listing
January 2020

Mice With Increased Numbers of Polyploid Hepatocytes Maintain Regenerative Capacity but Develop Fewer Tumors Following Chronic Liver Injury.

Gastroenterology 2020 Jan 20. Epub 2020 Jan 20.

Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2020.01.026DOI Listing
January 2020

Type and case volume of health care facility influences survival and surgery selection in cases with early-stage non-small cell lung cancer.

Cancer 2019 Dec 10;125(23):4252-4259. Epub 2019 Sep 10.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas.

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https://onlinelibrary.wiley.com/doi/abs/10.1002/cncr.32377
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http://dx.doi.org/10.1002/cncr.32377DOI Listing
December 2019

Metabolic Diversity in Human Non-Small Cell Lung Cancer Cells.

Mol Cell 2019 12 26;76(5):838-851.e5. Epub 2019 Sep 26.

Children's Medical Center Research Institute at UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.08.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6898782PMC
December 2019

ConvPath: A software tool for lung adenocarcinoma digital pathological image analysis aided by a convolutional neural network.

EBioMedicine 2019 Dec 22;50:103-110. Epub 2019 Nov 22.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2019.10.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6921240PMC
December 2019

Integrating germline and somatic genetics to identify genes associated with lung cancer.

Genet Epidemiol 2019 Dec 10. Epub 2019 Dec 10.

Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota.

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http://dx.doi.org/10.1002/gepi.22275DOI Listing
December 2019

A Bayesian zero-inflated negative binomial regression model for the integrative analysis of microbiome data.

Biostatistics 2019 Dec 17. Epub 2019 Dec 17.

Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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http://dx.doi.org/10.1093/biostatistics/kxz050DOI Listing
December 2019

A Bayesian hidden Potts mixture model for analyzing lung cancer pathology images.

Biostatistics 2019 10;20(4):565-581

Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, USA.

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http://dx.doi.org/10.1093/biostatistics/kxy019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6797059PMC
October 2019

Artificial Intelligence in Lung Cancer Pathology Image Analysis.

Cancers (Basel) 2019 Oct 28;11(11). Epub 2019 Oct 28.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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http://dx.doi.org/10.3390/cancers11111673DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6895901PMC
October 2019

Pathology Image Analysis Using Segmentation Deep Learning Algorithms.

Am J Pathol 2019 Sep 11;189(9):1686-1698. Epub 2019 Jun 11.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas. Electronic address:

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http://dx.doi.org/10.1016/j.ajpath.2019.05.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6723214PMC
September 2019

Systematic Analysis of Gene Expression in Lung Adenocarcinoma and Squamous Cell Carcinoma with a Case Study of and .

Cancers (Basel) 2019 Jun 25;11(6). Epub 2019 Jun 25.

Quantitative Biomedical Research Center, Department of Population and Data Sciences, Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.

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http://dx.doi.org/10.3390/cancers11060886DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6627508PMC
June 2019

DIGREM: an integrated web-based platform for detecting effective multi-drug combinations.

Bioinformatics 2019 May;35(10):1792-1794

Department of Clinical Science, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty860DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6513155PMC
May 2019

Development and Validation of a Pathology Image Analysis-based Predictive Model for Lung Adenocarcinoma Prognosis - A Multi-cohort Study.

Sci Rep 2019 May 3;9(1):6886. Epub 2019 May 3.

Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA.

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http://dx.doi.org/10.1038/s41598-019-42845-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499884PMC
May 2019

LCE: an open web portal to explore gene expression and clinical associations in lung cancer.

Oncogene 2019 04 7;38(14):2551-2564. Epub 2018 Dec 7.

Quantitative Biomedical Research Center, Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA.

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http://dx.doi.org/10.1038/s41388-018-0588-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6477796PMC
April 2019

Development and Validation of a Nomogram Prognostic Model for Patients With Advanced Non-Small-Cell Lung Cancer.

Cancer Inform 2019 5;18:1176935119837547. Epub 2019 Apr 5.

Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.

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http://dx.doi.org/10.1177/1176935119837547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6452590PMC
April 2019

A comparative study of rank aggregation methods for partial and top ranked lists in genomic applications.

Brief Bioinform 2019 01;20(1):178-189

Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX.

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http://dx.doi.org/10.1093/bib/bbx101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357556PMC
January 2019

GeNeCK: a web server for gene network construction and visualization.

BMC Bioinformatics 2019 Jan 7;20(1):12. Epub 2019 Jan 7.

Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, 75390, TX, United States.

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http://dx.doi.org/10.1186/s12859-018-2560-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323745PMC
January 2019

Development and Validation of a Nomogram Prognostic Model for SCLC Patients.

J Thorac Oncol 2018 09 11;13(9):1338-1348. Epub 2018 Jun 11.

Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas. Electronic address:

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http://dx.doi.org/10.1016/j.jtho.2018.05.037DOI Listing
September 2018

Deep Integrative Analysis for Survival Prediction.

Pac Symp Biocomput 2018 ;23:343-352

Colleyville Heritage High School, Colleyville, TX, 76034, USA, ²Highland Park High School, Dallas, TX, 75205, USA, ³Department of Clinical Science, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.

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August 2018

Genetic and Epigenetic Features of Rapidly Progressing IDH-Mutant Astrocytomas.

J Neuropathol Exp Neurol 2018 07;77(7):542-548

Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas.

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http://dx.doi.org/10.1093/jnen/nly026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6005148PMC
July 2018

Usefulness of a Simple Algorithm to Identify Hypertensive Patients Who Benefit from Intensive Blood Pressure Lowering.

Am J Cardiol 2018 07 11;122(2):248-254. Epub 2018 Apr 11.

Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas. Electronic address:

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http://dx.doi.org/10.1016/j.amjcard.2018.03.361DOI Listing
July 2018

Comprehensive analysis of lung cancer pathology images to discover tumor shape and boundary features that predict survival outcome.

Sci Rep 2018 Jul 10;8(1):10393. Epub 2018 Jul 10.

Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA.

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http://dx.doi.org/10.1038/s41598-018-27707-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6039531PMC
July 2018

Main bronchus location is a predictor for metastasis and prognosis in lung adenocarcinoma: A large cohort analysis.

Lung Cancer 2018 06 19;120:22-26. Epub 2018 Mar 19.

Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA; Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, 75390, USA. Electronic address:

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http://dx.doi.org/10.1016/j.lungcan.2018.03.011DOI Listing
June 2018

A two-stage approach of gene network analysis for high-dimensional heterogeneous data.

Biostatistics 2018 04;19(2):216-232

Quantitative Biomedical Research Center, Department of Clinical Sciences, Department of Bioinformatics, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA.

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http://dx.doi.org/10.1093/biostatistics/kxx033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862270PMC
April 2018

Increased autophagy blocks HER2-mediated breast tumorigenesis.

Proc Natl Acad Sci U S A 2018 04 2;115(16):4176-4181. Epub 2018 Apr 2.

Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390;

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http://dx.doi.org/10.1073/pnas.1717800115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5910832PMC
April 2018

Microvessel prediction in H&E Stained Pathology Images using fully convolutional neural networks.

BMC Bioinformatics 2018 02 27;19(1):64. Epub 2018 Feb 27.

Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, 5325 Harry Hines Blvd, Dallas, TX, 75390, USA.

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http://dx.doi.org/10.1186/s12859-018-2055-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828328PMC
February 2018

Finding RNA-Protein Interaction Sites Using HMMs.

Methods Mol Biol 2017 ;1552:177-184

Department of Mathematics, University of Texas at Arlington, Arlington, TX, 76019, USA.

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http://dx.doi.org/10.1007/978-1-4939-6753-7_13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568642PMC
January 2018

Learning gene regulatory networks from next generation sequencing data.

Biometrics 2017 12 10;73(4):1221-1230. Epub 2017 Mar 10.

Department of Biostatistics, University of Florida, Gainesville, Florida, U.S.A.

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http://dx.doi.org/10.1111/biom.12682DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258556PMC
December 2017

Genomic regression analysis of coordinated expression.

Nat Commun 2017 12 19;8(1):2187. Epub 2017 Dec 19.

Quantitative Biomedical Research Center at UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA.

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http://www.nature.com/articles/s41467-017-02181-0
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http://dx.doi.org/10.1038/s41467-017-02181-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736603PMC
December 2017

Integrative gene set enrichment analysis utilizing isoform-specific expression.

Genet Epidemiol 2017 09 4;41(6):498-510. Epub 2017 Jun 4.

Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.

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http://dx.doi.org/10.1002/gepi.22052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5598160PMC
September 2017

Evaluation of the 7 and 8 editions of the AJCC/UICC TNM staging systems for lung cancer in a large North American cohort.

Oncotarget 2017 Sep 24;8(40):66784-66795. Epub 2017 May 24.

Department of Clinical Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA.

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http://www.oncotarget.com/fulltext/18158
Publisher Site
http://dx.doi.org/10.18632/oncotarget.18158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5620136PMC
September 2017

A permutation-based non-parametric analysis of CRISPR screen data.

BMC Genomics 2017 07 19;18(1):545. Epub 2017 Jul 19.

Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.

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http://dx.doi.org/10.1186/s12864-017-3938-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5518132PMC
July 2017

Lung Cancer Pathological Image Analysis Using a Hidden Potts Model.

Cancer Inform 2017 5;16:1176935117711910. Epub 2017 Jun 5.

Department of Biostatistics, University of Florida, Gainesville, FL, USA.

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http://dx.doi.org/10.1177/1176935117711910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5462552PMC
June 2017

Automatic extraction of cell nuclei from H&E-stained histopathological images.

J Med Imaging (Bellingham) 2017 Apr 21;4(2):027502. Epub 2017 Jun 21.

University of Texas Southwestern Medical Center, Quantitative Biomedical Research Center, Department of Clinical Science, Dallas, Texas, United States.

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http://dx.doi.org/10.1117/1.JMI.4.2.027502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478972PMC
April 2017

Comparison of Ambulatory Blood Pressure Patterns in Patients With Intradialytic Hypertension and Hemodialysis Controls.

Kidney Blood Press Res 2016 22;41(3):240-9. Epub 2016 Apr 22.

Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.

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http://dx.doi.org/10.1159/000443427DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4919278PMC
March 2017

Comprehensive Computational Pathological Image Analysis Predicts Lung Cancer Prognosis.

J Thorac Oncol 2017 03 4;12(3):501-509. Epub 2016 Nov 4.

Department of Bioinformatics, University of Texas Southwestern Medical Center at Dallas, Texas; Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center at Dallas, Texas. Electronic address:

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http://dx.doi.org/10.1016/j.jtho.2016.10.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5462113PMC
March 2017

Extracellular Volume Overload and Increased Vasoconstriction in Patients With Recurrent Intradialytic Hypertension.

Kidney Blood Press Res 2016 11;41(6):802-814. Epub 2016 Nov 11.

University of Texas Southwestern Medical Center, Department of Internal Medicine, Division of Nephrology, Dallas, TX, USA.

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http://dx.doi.org/10.1159/000450565DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5183549PMC
March 2017

Enhanced construction of gene regulatory networks using hub gene information.

BMC Bioinformatics 2017 Mar 23;18(1):186. Epub 2017 Mar 23.

Department of Clinical Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA.

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http://dx.doi.org/10.1186/s12859-017-1576-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5364645PMC
March 2017

Integrative Analysis of Gene Networks and Their Application to Lung Adenocarcinoma Studies.

Cancer Inform 2017 23;16:1176935117690778. Epub 2017 Feb 23.

Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.

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http://dx.doi.org/10.1177/1176935117690778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5392014PMC
February 2017

SHOX2 is a Potent Independent Biomarker to Predict Survival of WHO Grade II-III Diffuse Gliomas.

EBioMedicine 2016 Nov 28;13:80-89. Epub 2016 Oct 28.

The Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; The Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2016.10.040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5264450PMC
November 2016

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Nat Commun 2016 10 10;7:13205. Epub 2016 Oct 10.

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http://dx.doi.org/10.1038/ncomms13205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062501PMC
October 2016

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Nat Commun 2016 08 23;7:12460. Epub 2016 Aug 23.

Sage Bionetworks, Seattle, Washington 98115, USA.

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http://dx.doi.org/10.1038/ncomms12460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996969PMC
August 2016

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.

Authors:
Genevera I Allen Nicola Amoroso Catalina Anghel Venkat Balagurusamy Christopher J Bare Derek Beaton Roberto Bellotti David A Bennett Kevin L Boehme Paul C Boutros Laura Caberlotto Cristian Caloian Frederick Campbell Elias Chaibub Neto Yu-Chuan Chang Beibei Chen Chien-Yu Chen Ting-Ying Chien Tim Clark Sudeshna Das Christos Davatzikos Jieyao Deng Donna Dillenberger Richard J B Dobson Qilin Dong Jimit Doshi Denise Duma Rosangela Errico Guray Erus Evan Everett David W Fardo Stephen H Friend Holger Fröhlich Jessica Gan Peter St George-Hyslop Satrajit S Ghosh Enrico Glaab Robert C Green Yuanfang Guan Ming-Yi Hong Chao Huang Jinseub Hwang Joseph Ibrahim Paolo Inglese Anandhi Iyappan Qijia Jiang Yuriko Katsumata John S K Kauwe Arno Klein Dehan Kong Roland Krause Emilie Lalonde Mario Lauria Eunjee Lee Xihui Lin Zhandong Liu Julie Livingstone Benjamin A Logsdon Simon Lovestone Tsung-Wei Ma Ashutosh Malhotra Lara M Mangravite Taylor J Maxwell Emily Merrill John Nagorski Aishwarya Namasivayam Manjari Narayan Mufassra Naz Stephen J Newhouse Thea C Norman Ramil N Nurtdinov Yen-Jen Oyang Yudi Pawitan Shengwen Peng Mette A Peters Stephen R Piccolo Paurush Praveen Corrado Priami Veronica Y Sabelnykova Philipp Senger Xia Shen Andrew Simmons Aristeidis Sotiras Gustavo Stolovitzky Sabina Tangaro Andrea Tateo Yi-An Tung Nicholas J Tustison Erdem Varol George Vradenburg Michael W Weiner Guanghua Xiao Lei Xie Yang Xie Jia Xu Hojin Yang Xiaowei Zhan Yunyun Zhou Fan Zhu Hongtu Zhu Shanfeng Zhu

Alzheimers Dement 2016 06 11;12(6):645-53. Epub 2016 Apr 11.

School of Computer Science, Fudan University, Shanghai, Shanghai, China; Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, Shanghai, China; Centre for Computational Systems Biology, Fudan University, Shanghai, China.

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http://dx.doi.org/10.1016/j.jalz.2016.02.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5474755PMC
June 2016

Statistical completion of a partially identified graph with applications for the estimation of gene regulatory networks.

Biostatistics 2015 Oct 1;16(4):670-85. Epub 2015 Apr 1.

Department of Clinical Sciences, University of Texas Southwestern Medical Center, TX 75390, USA

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http://dx.doi.org/10.1093/biostatistics/kxv013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570579PMC
October 2015

iScreen: Image-Based High-Content RNAi Screening Analysis Tools.

J Biomol Screen 2015 Sep 29;20(8):998-1002. Epub 2014 Dec 29.

Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA

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http://dx.doi.org/10.1177/1087057114564348DOI Listing
September 2015

Nonoptimal codon usage influences protein structure in intrinsically disordered regions.

Mol Microbiol 2015 Sep 25;97(5):974-87. Epub 2015 Jun 25.

Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA.

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http://dx.doi.org/10.1111/mmi.13079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636118PMC
September 2015

Ensemble-based network aggregation improves the accuracy of gene network reconstruction.

PLoS One 2014 12;9(11):e106319. Epub 2014 Nov 12.

Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0106319PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4229114PMC
July 2015

Design and bioinformatics analysis of genome-wide CLIP experiments.

Nucleic Acids Res 2015 Jun 9;43(11):5263-74. Epub 2015 May 9.

Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA

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http://dx.doi.org/10.1093/nar/gkv439DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477666PMC
June 2015

Decreased mRNA Expression in Human Breast Cancer is Associated with Estrogen Receptor-Negative Subtypes and Poor Prognosis.

EBioMedicine 2015 Mar;2(3):255-263

Center for Autophagy Research, University of Texas Southwestern Medical Center, Dallas, Texas 75390 ; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 ; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390 ; Howard Hughes Medical Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390.

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http://dx.doi.org/10.1016/j.ebiom.2015.01.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376376PMC
March 2015

Acute effect of glucose on cerebral blood flow, blood oxygenation, and oxidative metabolism.

Hum Brain Mapp 2015 Feb 16;36(2):707-16. Epub 2014 Oct 16.

Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas.

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February 2015

A community computational challenge to predict the activity of pairs of compounds.

Nat Biotechnol 2014 Dec 17;32(12):1213-22. Epub 2014 Nov 17.

1] Department of Systems Biology, Columbia University, New York, New York, USA. [2] Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA. [3] Department of Biomedical Informatics, Columbia University, New York, New York, USA. [4] Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA. [5] Institute for Cancer Genetics, Columbia University, New York, New York, USA. [6] Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA.

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http://dx.doi.org/10.1038/nbt.3052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4399794PMC
December 2014

A model-based approach to identify binding sites in CLIP-Seq data.

PLoS One 2014 8;9(4):e93248. Epub 2014 Apr 8.

Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0093248PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3979666PMC
November 2014

Molecular neuropsychology: creation of test-specific blood biomarker algorithms.

Dement Geriatr Cogn Disord 2014 3;37(1-2):45-57. Epub 2013 Jan 3.

Department of Internal Medicine, University of North Texas Health Science Center, Fort Worth, Tex., USA.

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http://dx.doi.org/10.1159/000345605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4400831PMC
October 2014

Molecular markers of carcinogenesis for risk stratification of individuals with colorectal polyps: a case-control study.

Cancer Prev Res (Phila) 2014 Oct 4;7(10):1023-34. Epub 2014 Aug 4.

Department of Internal Medicine, Medical University of South Carolina, Charleston, South Carolina.

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http://dx.doi.org/10.1158/1940-6207.CAPR-14-0140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5234486PMC
October 2014

Autophagy is required for G₁/G₀ quiescence in response to nitrogen starvation in Saccharomyces cerevisiae.

Autophagy 2014 Oct 12;10(10):1702-11. Epub 2014 Aug 12.

Center for Autophagy Research; University of Texas Southwestern Medical Center; Dallas, TX USA; Department of Internal Medicine; University of Texas Southwestern Medical Center; Dallas, TX USA; Department of Microbiology; University of Texas Southwestern Medical Center; Dallas, TX USA; Howard Hughes Medical Institute; University of Texas Southwestern Medical Center; Dallas, TX USA.

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http://www.tandfonline.com/doi/abs/10.4161/auto.32122
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198356PMC
October 2014

Transcriptional interference by antisense RNA is required for circadian clock function.

Nature 2014 Oct 17;514(7524):650-3. Epub 2014 Aug 17.

Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.

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http://dx.doi.org/10.1038/nature13671DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214883PMC
October 2014

The role of homeostatic regulation between tumor suppressor DAB2IP and oncogenic Skp2 in prostate cancer growth.

Oncotarget 2014 Aug;5(15):6425-36

Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Graduate Institute of Cancer Biology, China Medical University, Taichung, Taiwan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4171641PMC
http://dx.doi.org/10.18632/oncotarget.2228DOI Listing
August 2014

Computational detection and suppression of sequence-specific off-target phenotypes from whole genome RNAi screens.

Nucleic Acids Res 2014 Jul 27;42(13):8214-22. Epub 2014 Jun 27.

Quantitative Biomedical Research Center, Dallas, TX, USA Department of Clinical Sciences, Dallas, TX, USA

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http://dx.doi.org/10.1093/nar/gku306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117740PMC
July 2014

Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP.

Biometrics 2014 Jun 24;70(2):430-40. Epub 2014 Feb 24.

Division of Biostatistics, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, 75290, USA.

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http://dx.doi.org/10.1111/biom.12147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4061157PMC
June 2014

Detection of candidate tumor driver genes using a fully integrated Bayesian approach.

Stat Med 2014 May 18;33(10):1784-800. Epub 2013 Dec 18.

Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, U.S.A.

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http://dx.doi.org/10.1002/sim.6066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981913PMC
May 2014

Adaptive prediction model in prospective molecular signature-based clinical studies.

Clin Cancer Res 2014 Feb 9;20(3):531-9. Epub 2013 Dec 9.

Authors' Affiliations: Quantitative Biomedical Research Center, Department of Clinical Sciences; Departments of Internal Medicine and Pharmacology; Simmons Cancer Center; Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, Dallas, Texas; and Department of Biostatistics, School of Public Health, Yale University, New Haven, Connecticut.

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http://dx.doi.org/10.1158/1078-0432.CCR-13-2127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3946561PMC
February 2014

Review of biological network data and its applications.

Genomics Inform 2013 Dec 31;11(4):200-10. Epub 2013 Dec 31.

Department of Clinical Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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http://dx.doi.org/10.5808/GI.2013.11.4.200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897847PMC
December 2013

Biomarkers of Alzheimer's disease among Mexican Americans.

J Alzheimers Dis 2013 ;34(4):841-9

Department of Internal Medicine, University of North Texas Health Sciences Center, Fort Worth, TX 76107, USA.

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http://dx.doi.org/10.3233/JAD-122074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608404PMC
September 2013

Alterations in resting functional connectivity due to recent motor task.

Neuroimage 2013 Sep 11;78:316-24. Epub 2013 Apr 11.

Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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http://dx.doi.org/10.1016/j.neuroimage.2013.04.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672369PMC
September 2013

SbacHTS: spatial background noise correction for high-throughput RNAi screening.

Bioinformatics 2013 Sep 28;29(17):2218-20. Epub 2013 Jun 28.

Quantitative Biomedical Research Center, Department of Clinical Science, Harold C. Simmons Comprehensive Cancer Center and Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740628PMC
September 2013

The mechanism of DAB2IP in chemoresistance of prostate cancer cells.

Clin Cancer Res 2013 Sep 9;19(17):4740-9. Epub 2013 Jul 9.

Department of Urology, The First Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, China.

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http://dx.doi.org/10.1158/1078-0432.CCR-13-0954DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4806645PMC
September 2013

EGFR-mediated Beclin 1 phosphorylation in autophagy suppression, tumor progression, and tumor chemoresistance.

Cell 2013 Sep;154(6):1269-84

Center for Autophagy Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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http://dx.doi.org/10.1016/j.cell.2013.08.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3917713PMC
September 2013

Beclin 2 functions in autophagy, degradation of G protein-coupled receptors, and metabolism.

Cell 2013 Aug 15;154(5):1085-1099. Epub 2013 Aug 15.

Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for Autophagy Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2013.07.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231430PMC
August 2013

Epigenetic change detection and pattern recognition via Bayesian hierarchical hidden Markov models.

Stat Med 2013 Jun 25;32(13):2292-307. Epub 2012 Oct 25.

Department of Statistical Science, Southern Methodist University, Dallas, TX 75275, USA.

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http://doi.wiley.com/10.1002/sim.5658
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009397PMC
June 2013

A powerful Bayesian meta-analysis method to integrate multiple gene set enrichment studies.

Bioinformatics 2013 Apr 15;29(7):862-9. Epub 2013 Feb 15.

Quantitative Biomedical Research Center, Department of Clinical Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605602PMC
April 2013

A 12-gene set predicts survival benefits from adjuvant chemotherapy in non-small cell lung cancer patients.

Clin Cancer Res 2013 Mar 28;19(6):1577-86. Epub 2013 Jan 28.

Quantitative Biomedical Research Center, Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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http://dx.doi.org/10.1158/1078-0432.CCR-12-2321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619002PMC
March 2013

Detection of epigenetic changes using ANOVA with spatially varying coefficients.

Stat Appl Genet Mol Biol 2013 Mar 13;12(2):189-205. Epub 2013 Mar 13.

Division of Biostatistics, Department of Clinical Sciences, The University of Texas Southwestern Medical Center at Dallas, TX 75390, USA.

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https://www.degruyter.com/view/j/sagmb.2013.12.issue-2/sagmb
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http://dx.doi.org/10.1515/sagmb-2012-0057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866591PMC
March 2013

Akt-mediated regulation of autophagy and tumorigenesis through Beclin 1 phosphorylation.

Science 2012 Nov 25;338(6109):956-9. Epub 2012 Oct 25.

Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1225967
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3507442PMC
November 2012

Effect of hypoxia and hyperoxia on cerebral blood flow, blood oxygenation, and oxidative metabolism.

J Cereb Blood Flow Metab 2012 Oct 27;32(10):1909-18. Epub 2012 Jun 27.

Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.

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http://dx.doi.org/10.1038/jcbfm.2012.93DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463882PMC
October 2012

Probe mapping across multiple microarray platforms.

Brief Bioinform 2012 Sep 23;13(5):547-54. Epub 2011 Dec 23.

UT Southwestern Medical Center, Dallas, TX 75390, USA.

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http://dx.doi.org/10.1093/bib/bbr076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431719PMC
September 2012

Slug, a unique androgen-regulated transcription factor, coordinates androgen receptor to facilitate castration resistance in prostate cancer.

Mol Endocrinol 2012 Sep 28;26(9):1496-507. Epub 2012 Jun 28.

Department of Urology, The First Affiliated Hospital, Medical School of Xi’an Jiaotong University, Xi’an 710061, China.

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http://dx.doi.org/10.1210/me.2011-1360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5416972PMC
September 2012

A blood-based screening tool for Alzheimer's disease that spans serum and plasma: findings from TARC and ADNI.

PLoS One 2011 7;6(12):e28092. Epub 2011 Dec 7.

Department of Neurology, F. Marie Hall Institute for Rural and Community Health, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028092PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3233542PMC
July 2012

Comparing statistical methods for constructing large scale gene networks.

PLoS One 2012 17;7(1):e29348. Epub 2012 Jan 17.

University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0029348PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3260142PMC
June 2012

Serum granulocyte colony-stimulating factor and Alzheimer's disease.

Dement Geriatr Cogn Dis Extra 2012 Jan 29;2(1):353-60. Epub 2012 Aug 29.

Institute of Aging and Alzheimer's Disease Research, University of North Texas Health Science Center, Fort Worth, Tex. ; Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Tex.

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http://dx.doi.org/10.1159/000341780DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457029PMC
January 2012