Yuji Zhang

Yuji Zhang

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Publications by authors named "Yuji Zhang"

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Alcohol consumption and serum metabolite concentrations in young women.

Cancer Causes Control 2020 Feb 11;31(2):113-126. Epub 2019 Dec 11.

Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.

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http://dx.doi.org/10.1007/s10552-019-01256-1DOI Listing
February 2020

Exploring the effect of library preparation on RNA sequencing experiments.

Genomics 2019 12 6;111(6):1752-1759. Epub 2018 Dec 6.

Division of Biostatistics and Bioinformatics, University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, United States; Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ygeno.2018.11.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6551333PMC
December 2019

Intratumor genetic heterogeneity in squamous cell carcinoma of the oral cavity.

Head Neck 2019 08 14;41(8):2514-2524. Epub 2019 Mar 14.

Department of Medicine, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland.

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http://dx.doi.org/10.1002/hed.25719DOI Listing
August 2019

RIP sequencing in mantle cell lymphoma identifies functional long non-coding RNAs associated with translation machinery.

Blood Cancer J 2019 07 26;9(8):55. Epub 2019 Jul 26.

Division of Hematology, Mayo Clinic, Rochester, MN, 55905, USA.

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http://dx.doi.org/10.1038/s41408-019-0216-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6659685PMC
July 2019

Decomposing the effect of drug benefit program on antihypertensive medication adherence among the elderly in urban China.

Patient Prefer Adherence 2019 11;13:1111-1123. Epub 2019 Jul 11.

Department of Public Health, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, People's Republic of China.

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http://dx.doi.org/10.2147/PPA.S201707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6628968PMC
July 2019

A statistical analysis of vaccine-adverse event data.

BMC Med Inform Decis Mak 2019 05 28;19(1):101. Epub 2019 May 28.

Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, 21201, MD, USA.

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http://dx.doi.org/10.1186/s12911-019-0818-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6540382PMC
May 2019

Integrative Genome-Wide Analysis of Long Noncoding RNAs in Diverse Immune Cell Types of Melanoma Patients.

Cancer Res 2018 08 12;78(15):4411-4423. Epub 2018 Jun 12.

Division of Biostatistics and Bioinformatics, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland.

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http://dx.doi.org/10.1158/0008-5472.CAN-18-0529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6072578PMC
August 2018

Adverse event detection by integrating twitter data and VAERS.

J Biomed Semantics 2018 06 20;9(1):19. Epub 2018 Jun 20.

Department of Epidemiology & Public Health, University of Maryland School of Medicine, Baltimore, MD, USA.

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http://dx.doi.org/10.1186/s13326-018-0184-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6011255PMC
June 2018

Systematic identification of latent disease-gene associations from PubMed articles.

PLoS One 2018 26;13(1):e0191568. Epub 2018 Jan 26.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0191568PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786305PMC
February 2018

Gender differences in fibrosis remodeling in patients with long-standing persistent atrial fibrillation.

Oncotarget 2017 Aug 17;8(32):53714-53729. Epub 2017 Mar 17.

Department of Cardiovascular Surgery, Shenyang Northern Hospital, Shenyang, China.

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http://dx.doi.org/10.18632/oncotarget.16342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5581144PMC
August 2017

A Multiyear Model of Influenza Vaccination in the United States.

Int J Environ Res Public Health 2017 07 28;14(8). Epub 2017 Jul 28.

Lexington High School, Lexington, MA 02421, USA.

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http://dx.doi.org/10.3390/ijerph14080849DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5580553PMC
July 2017

[Application of three-stitch preventive transverse colostomy in anterior resection of low rectal cancer].

Zhonghua Wei Chang Wai Ke Za Zhi 2017 Apr;20(4):439-442

Department of Gastrointestinal Surgery, Tumor Hospital of Zhengzhou University, Zhengzhou 450008, China.

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April 2017

Systematic identification and characterization of cardiac long intergenic noncoding RNAs in zebrafish.

Sci Rep 2017 04 28;7(1):1250. Epub 2017 Apr 28.

Department of Epidemiology & Public Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.

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http://dx.doi.org/10.1038/s41598-017-00823-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5430783PMC
April 2017

Relation of Mitochondrial DNA Copy Number in Peripheral Blood to Postoperative Atrial Fibrillation After Isolated Off-Pump Coronary Artery Bypass Grafting.

Am J Cardiol 2017 Feb 1;119(3):473-477. Epub 2016 Nov 1.

Department of Cardiovascular Surgery, General Hospital of Shenyang Military Area Command, Shenyang, Liaoning, China. Electronic address:

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http://dx.doi.org/10.1016/j.amjcard.2016.10.017DOI Listing
February 2017

Pathophysiological mechanisms underlying phenotypic differences in pulmonary radioresponse.

Sci Rep 2016 Nov 15;6(1):36579. Epub 2016 Nov 15.

Division of Translational Radiation Sciences, Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, 21201, MD, USA.

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http://dx.doi.org/10.1038/srep36579DOI Listing
November 2016

Pathophysiological mechanisms underlying phenotypic differences in pulmonary radioresponse.

Sci Rep 2016 11 15;6:36579. Epub 2016 Nov 15.

Division of Translational Radiation Sciences, Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.

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http://dx.doi.org/10.1038/srep36579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5109047PMC
November 2016

microRNA expression profiling and functional annotation analysis of their targets modulated by oxidative stress during embryonic heart development in diabetic mice.

Reprod Toxicol 2016 10 11;65:365-374. Epub 2016 Sep 11.

Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, United States; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine Baltimore, MD 21201, United States. Electronic address:

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http://dx.doi.org/10.1016/j.reprotox.2016.09.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5288404PMC
October 2016

Data on the gene expression of cardiomyocyte exposed to hypothermia.

Data Brief 2016 Sep 11;8:45-8. Epub 2016 May 11.

Department of Cardiovascular Surgery, General Hospital of Shenyang Military Area Command, No. 83, Wenhua Road, Shenhe District, Shenyang City, Liaoning 110016, China.

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http://dx.doi.org/10.1016/j.dib.2016.04.061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4885011PMC
September 2016

The transcriptome responses of cardiomyocyte exposed to hypothermia.

Cryobiology 2016 06 31;72(3):244-50. Epub 2016 Mar 31.

Department of Cardiovascular Surgery, General Hospital of Shenyang Military Area Command, No.83, Wenhua Road, Shenhe District, Shenyang City 110016, Liaoning, China. Electronic address:

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http://dx.doi.org/10.1016/j.cryobiol.2016.03.011DOI Listing
June 2016

Gene expression patterns in CD4+ peripheral blood cells in healthy subjects and stage IV melanoma patients.

Cancer Immunol Immunother 2015 Nov 6;64(11):1437-47. Epub 2015 Aug 6.

Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066565PMC
http://dx.doi.org/10.1007/s00262-015-1745-xDOI Listing
November 2015

Next generation informatics for big data in precision medicine era.

BioData Min 2015 3;8:34. Epub 2015 Nov 3.

Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA.

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http://biodatamining.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13040-015-0064-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632361PMC
November 2015

Identification of sex-associated network patterns in Vaccine-Adverse Event Association Network in VAERS.

J Biomed Semantics 2015 19;6:33. Epub 2015 Aug 19.

School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas USA.

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http://dx.doi.org/10.1186/s13326-015-0032-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4541751PMC
August 2015

Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge.

Authors:
Yuji Zhang

BioData Min 2015 28;8:26. Epub 2015 Aug 28.

Division of Biostatistics and Bioinformatics, University of Maryland Greenebaum Cancer Center, Baltimore, USA ; Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, USA.

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http://dx.doi.org/10.1186/s13040-015-0057-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4552361PMC
August 2015

Cardiac transcriptome and dilated cardiomyopathy genes in zebrafish.

Circ Cardiovasc Genet 2015 Apr 11;8(2):261-9. Epub 2015 Jan 11.

From the Department of Biochemistry and Molecular Biology (Y.-H.S., Y.D., X.X.), Information Technology (C.A.R.), Department of Molecular Pharmacology and Experimental Therapeutics (H.L.), Department of Pediatric and Adolescent Medicine (T.M.O.), and Division of Cardiovascular Diseases (T.M.O., X.X.), Mayo Clinic, Rochester, MN; Division of Biostatistics and Bioinformatics, University of Maryland Greenebaum Cancer Center, Baltimore (Y.Z.); and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (Y.Z.).

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http://dx.doi.org/10.1161/CIRCGENETICS.114.000702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406804PMC
April 2015

Correction to "Network Analysis of Cancer-focused Association Network Reveals Distinct Network Association Patterns".

Authors:
Yuji Zhang Cui Tao

Cancer Inform 2014 20;13(Suppl 3):89. Epub 2014 Nov 20.

School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.4137/CIN.S21316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4240213PMC
March 2015

Linked vaccine adverse event data from VAERS for biomedical data analysis and longitudinal studies.

BioData Min 2014 31;7:36. Epub 2014 Dec 31.

Division of Biostatistics and Bioinformatics, University of Maryland Greenebaum Cancer Center, Baltimore, MD USA ; Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD USA.

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http://dx.doi.org/10.1186/s13040-014-0036-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333877PMC
February 2015

MACE: model based analysis of ChIP-exo.

Nucleic Acids Res 2014 Nov 23;42(20):e156. Epub 2014 Sep 23.

Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA

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http://dx.doi.org/10.1093/nar/gku846DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227761PMC
November 2014

Network Analysis of Cancer-focused Association Network Reveals Distinct Network Association Patterns.

Authors:
Yuji Zhang Cui Tao

Cancer Inform 2014 16;13(Suppl 3):45-51. Epub 2014 Oct 16.

School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.4137/CIN.S14033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214591PMC
November 2014

Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network.

J Biomed Semantics 2014 6;5:33. Epub 2014 Aug 6.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.

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http://dx.doi.org/10.1186/2041-1480-5-33DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137727PMC
August 2014

Detection of 1α,25-dihydroxyvitamin D-regulated miRNAs in zebrafish by whole transcriptome sequencing.

Zebrafish 2014 Jun 20;11(3):207-18. Epub 2014 Mar 20.

1 Nephrology and Hypertension Research, Department of Internal Medicine, Mayo Clinic , Rochester, Minnesota.

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http://dx.doi.org/10.1089/zeb.2013.0899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4050706PMC
June 2014

Module-based breast cancer classification.

Int J Data Min Bioinform 2013 ;7(3):284-302

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736598PMC
http://dx.doi.org/10.1504/ijdmb.2013.053309DOI Listing
March 2014

Calculating sample size estimates for RNA sequencing data.

J Comput Biol 2013 Dec 20;20(12):970-8. Epub 2013 Aug 20.

1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic , Rochester, Minnesota.

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http://dx.doi.org/10.1089/cmb.2012.0283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842884PMC
December 2013

APOBEC3B upregulation and genomic mutation patterns in serous ovarian carcinoma.

Cancer Res 2013 Dec 23;73(24):7222-31. Epub 2013 Oct 23.

Authors' Affiliations: Biochemistry, Molecular Biology and Biophysics Department; Masonic Cancer Center, University of Minnesota, Minneapolis; Division of Biomedical Statistics and Informatics, Department of Health Sciences Research; Medical Genome Facility and Department of Laboratory Medicine and Pathology; Department of Laboratory Medicine and Pathology; Division of Medical Oncology, Department of Oncology; Division of Epidemiology, Department of Health Sciences Research; Division of Oncology Research, Department of Oncology; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic; Women's Cancer Program, Mayo Clinic Cancer Center, Rochester, Minnesota; Department of Cancer Biology, University of Kansas, Kansas City, Kansas; Department of Obstetrics & Gynecology, University of Washington School of Medicine, Seattle, Washington; and Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, Cambridge, United Kingdom.

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http://dx.doi.org/10.1158/0008-5472.CAN-13-1753DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3867573PMC
December 2013

Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology.

J Biomed Semantics 2013 Nov 11;4(1):33. Epub 2013 Nov 11.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1186/2041-1480-4-33DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177205PMC
November 2013

Viral metagenomics analysis of planktonic viruses in East Lake, Wuhan, China.

Virol Sin 2013 Oct 30;28(5):280-90. Epub 2013 Sep 30.

Center for Emerging Infectious Diseases, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.

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http://dx.doi.org/10.1007/s12250-013-3365-yDOI Listing
October 2013

Study of the dynamics of Microcystis aeruginosa and its cyanophage in East Lake using quantitative PCR.

Virol Sin 2013 Oct 29;28(5):309-11. Epub 2013 Sep 29.

Virus Resource and Bioinformatics Center, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.

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http://dx.doi.org/10.1007/s12250-013-3368-8DOI Listing
October 2013

Serological evidence of ebolavirus infection in bats, China.

Virol J 2012 Oct 13;9:236. Epub 2012 Oct 13.

State Key Laboratory of Virology, Wuhan Institute of Virology-Chinese Academy of Sciences, Wuhan, Hubei 430071, P R China.

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http://dx.doi.org/10.1186/1743-422X-9-236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3492202PMC
October 2012

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.

Bioinformatics 2012 Aug 10;28(16):2180-1. Epub 2012 Jun 10.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413387PMC
August 2012

Identification of aberrant pathways and network activities from high-throughput data.

Brief Bioinform 2012 Jul 27;13(4):406-19. Epub 2012 Jan 27.

Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA.

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http://dx.doi.org/10.1093/bib/bbs001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3404398PMC
July 2012

Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration.

PLoS One 2010 Apr 21;5(4):e10268. Epub 2010 Apr 21.

Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0010268PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2858157PMC
April 2010

Reverse engineering module networks by PSO-RNN hybrid modeling.

BMC Genomics 2009 Jul 7;10 Suppl 1:S15. Epub 2009 Jul 7.

Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.

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http://dx.doi.org/10.1186/1471-2164-10-S1-S15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709258PMC
July 2009

Network motif-based identification of breast cancer susceptibility genes.

Conf Proc IEEE Eng Med Biol Soc 2008 ;2008:5696-9

Department of Electrical and Computer Engineering, Advanced Research Institute, Virginia Polytechnic Institute and State University, 4300 Wilson Blvd, Arlington, 22203, USA.

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http://dx.doi.org/10.1109/IEMBS.2008.4650507DOI Listing
May 2009

Inferring network interactions using recurrent neural networks and swarm intelligence.

Conf Proc IEEE Eng Med Biol Soc 2006 ;1:4241-4

Dept. of Biostat., Bioinf., & Biomath., Georgetown Univ., Washington, DC 20057, USA.

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http://dx.doi.org/10.1109/IEMBS.2006.259812DOI Listing
March 2008