Andrew Jaffe

Andrew Jaffe

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Andrew Jaffe

Publications by authors named "Andrew Jaffe"

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Transverse Velocities with the Moving Lens Effect.

Phys Rev Lett 2019 Aug;123(6):061301

Canadian Institute for Theoretical Astrophysics, University of Toronto, 60 Saint George Street, Toronto, Ontario M5S 3H8, Canada.

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http://dx.doi.org/10.1103/PhysRevLett.123.061301DOI Listing
August 2019

Prefrontal Coexpression of Schizophrenia Risk Genes Is Associated With Treatment Response in Patients.

Biol Psychiatry 2019 Jul 3;86(1):45-55. Epub 2019 Apr 3.

Group of Psychiatric Neuroscience, Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy; Azienda Ospedaliero-Universitaria Consorziale Policlinico, Bari, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.biopsych.2019.03.981DOI Listing
July 2019

Regional Heterogeneity in Gene Expression, Regulation, and Coherence in the Frontal Cortex and Hippocampus across Development and Schizophrenia.

Neuron 2019 Jul 4;103(2):203-216.e8. Epub 2019 Jun 4.

Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA; Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2019.05.013DOI Listing
July 2019

Addressing confounding artifacts in reconstruction of gene co-expression networks.

Genome Biol 2019 05 16;20(1):94. Epub 2019 May 16.

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.

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http://dx.doi.org/10.1186/s13059-019-1700-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6521369PMC
May 2019

Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer's disease.

Acta Neuropathol 2019 Apr 2;137(4):557-569. Epub 2019 Feb 2.

Lieber Institute for Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe St, Suite 300, Baltimore, MD, 21205, USA.

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http://dx.doi.org/10.1007/s00401-019-01966-5DOI Listing
April 2019

Cytokine, Chemokine, and Cytokine Receptor Changes Are Associated With Metabolic Improvements After Bariatric Surgery.

J Clin Endocrinol Metab 2019 Mar;104(3):947-956

Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland.

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http://dx.doi.org/10.1210/jc.2018-02245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364507PMC
March 2019

A Bayesian framework for multiple trait colocalization from summary association statistics.

Bioinformatics 2018 08;34(15):2538-2545

Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061859PMC
August 2018

Improving the value of public RNA-seq expression data by phenotype prediction.

Nucleic Acids Res 2018 05;46(9):e54

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, USA.

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http://dx.doi.org/10.1093/nar/gky102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5961118PMC
May 2018

recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor.

F1000Res 2017 24;6:1558. Epub 2017 Aug 24.

Lieber Institute for Brain Development, Baltimore, MD, 21205, USA.

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http://dx.doi.org/10.12688/f1000research.12223.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5621122PMC
August 2017

qSVA framework for RNA quality correction in differential expression analysis.

Proc Natl Acad Sci U S A 2017 07 20;114(27):7130-7135. Epub 2017 Jun 20.

Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205.

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http://dx.doi.org/10.1073/pnas.1617384114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502589PMC
July 2017

qSVA framework for RNA quality correction in differential expression analysis.

Proc Natl Acad Sci U S A 2017 07 20;114(27):7130-7135. Epub 2017 Jun 20.

Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205.

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http://dx.doi.org/10.1073/pnas.1617384114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502589PMC
July 2017

Reproducible RNA-seq analysis using recount2.

Nat Biotechnol 2017 04;35(4):319-321

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1038/nbt.3838DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742427PMC
April 2017

Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses.

Nat Methods 2017 02;14(3):216-217

CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.1038/nmeth.4187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6659733PMC
February 2017

Flexible expressed region analysis for RNA-seq with derfinder.

Nucleic Acids Res 2017 01 29;45(2):e9. Epub 2016 Sep 29.

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA

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http://dx.doi.org/10.1093/nar/gkw852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5314792PMC
January 2017

Assessment of genetic risk for distribution of total interstitial white matter neurons in dorsolateral prefrontal cortex: role in schizophrenia.

Schizophr Res 2016 10 27;176(2-3):141-143. Epub 2016 May 27.

Clinical Brain Disorders Branch, Genes Cognition and Psychosis, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, United States; Lieber Institute for Brain Development, Rangos Building, Johns Hopkins Medical Campus, Baltimore, MD 21205, United States.

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http://dx.doi.org/10.1016/j.schres.2016.04.007DOI Listing
October 2016

Genetic and epigenetic analysis of schizophrenia in blood-a no-brainer?

Genome Med 2016 Sep 21;8(1):96. Epub 2016 Sep 21.

Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.

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http://dx.doi.org/10.1186/s13073-016-0354-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5031351PMC
September 2016

regionReport: Interactive reports for region-level and feature-level genomic analyses.

F1000Res 2015 1;4:105. Epub 2015 May 1.

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, 21205, USA; Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, 21205, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4934510PMC
http://dx.doi.org/10.12688/f1000research.6379.2DOI Listing
July 2016

C1q/TNF-Related Protein-9 (CTRP9) Levels Are Associated With Obesity and Decrease Following Weight Loss Surgery.

J Clin Endocrinol Metab 2016 05 16;101(5):2211-7. Epub 2016 Mar 16.

Departments of Pediatrics (R.M.W.), Surgery (K.E.S., L.A.P., M.A.S., T.H.M.), and Physiology (X.Z., G.W.W.), and Center for Metabolism and Obesity Research (R.M.W., G.W.W.), The Johns Hopkins University School of Medicine, Baltimore, Maryland; Lieber Institute for Brain Development (A.E.J.), Johns Hopkins Medical Campus, Baltimore, Maryland; and Departments of Mental Health (A.E.J.) and Biostatistics (A.E.J.), Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.

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http://dx.doi.org/10.1210/jc.2016-1027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4870852PMC
May 2016

Psychiatric Risk Gene Transcription Factor 4 Regulates Intrinsic Excitability of Prefrontal Neurons via Repression of SCN10a and KCNQ1.

Neuron 2016 Apr 10;90(1):43-55. Epub 2016 Mar 10.

Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2016.02.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824652PMC
April 2016

Postmortem human brain genomics in neuropsychiatric disorders--how far can we go?

Authors:
Andrew E Jaffe

Curr Opin Neurobiol 2016 Feb 10;36:107-11. Epub 2015 Dec 10.

Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, United States; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, United States; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, United States. Electronic address:

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http://dx.doi.org/10.1016/j.conb.2015.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4857188PMC
February 2016

The PsychENCODE project.

Nat Neurosci 2015 Dec;18(12):1707-12

Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1038/nn.4156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675669PMC
December 2015

Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis.

BMC Bioinformatics 2015 Nov 6;16:372. Epub 2015 Nov 6.

Lieber Institute for Brain Development, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA.

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http://dx.doi.org/10.1186/s12859-015-0808-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636836PMC
November 2015

Polyester: simulating RNA-seq datasets with differential transcript expression.

Bioinformatics 2015 Sep 28;31(17):2778-84. Epub 2015 Apr 28.

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Center for Computational Biology and.

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http://biorxiv.org/content/biorxiv/early/2014/06/06/006015.f
Web Search
http://bioinformatics.oxfordjournals.org/content/early/2015/
Web Search
http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btv272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4635655PMC
September 2015

Investigation of the prenatal expression patterns of 108 schizophrenia-associated genetic loci.

Biol Psychiatry 2015 Jun 22;77(11):e43-51. Epub 2014 Oct 22.

Lieber Institute for Brain Development, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland; Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland. Electronic address:

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http://dx.doi.org/10.1016/j.biopsych.2014.10.008DOI Listing
June 2015

Ballgown bridges the gap between transcriptome assembly and expression analysis.

Nat Biotechnol 2015 Mar;33(3):243-6

1] Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA. [2] Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1038/nbt.3172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792117PMC
March 2015

Mouse-human experimental epigenetic analysis unmasks dietary targets and genetic liability for diabetic phenotypes.

Cell Metab 2015 Jan;21(1):138-49

Department of Medicine, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cmet.2014.12.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340475PMC
January 2015

Pattern identification in time-course gene expression data with the CoGAPS matrix factorization.

Methods Mol Biol 2014 ;1101:87-112

Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD, USA.

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http://dx.doi.org/10.1007/978-1-62703-721-1_6DOI Listing
June 2014

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.

Bioinformatics 2014 May 28;30(10):1363-9. Epub 2014 Jan 28.

Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, Department of Biostatistics, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, Lieber Institute of Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe Street, Baltimore, MD 21205, USA, Department of Computer Science, University of Maryland, College Park, MD 20742, USA, Department of Epidemiology, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe Street, Baltimore, MD 21205, USA and Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016708PMC
May 2014

Genome-wide and gene-specific epigenomic platforms for hepatocellular carcinoma biomarker development trials.

Gastroenterol Res Pract 2014 17;2014:597164. Epub 2014 Apr 17.

Department of Otolaryngology, Division of Head and Neck Cancer Research, School of Medicine, The Johns Hopkins University, Baltimore, MD 21231, USA ; Department of Obstetrics and Gynecology, University of Puerto Rico School of Medicine, San Juan, PR 00927, USA.

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http://dx.doi.org/10.1155/2014/597164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009191PMC
May 2014

TE-array--a high throughput tool to study transposon transcription.

BMC Genomics 2013 Dec 10;14:869. Epub 2013 Dec 10.

The Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building (MRB) Room 469, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1186/1471-2164-14-869DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878892PMC
December 2013

Gene set bagging for estimating the probability a statistically significant result will replicate.

BMC Bioinformatics 2013 Dec 12;14:360. Epub 2013 Dec 12.

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD 21205, USA.

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http://dx.doi.org/10.1186/1471-2105-14-360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890500PMC
December 2013

Use of postmortem human dura mater and scalp for deriving human fibroblast cultures.

PLoS One 2012 27;7(9):e45282. Epub 2012 Sep 27.

Section on Neuropathology, Clinical Brain Disorders Branch, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0045282PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3459947PMC
February 2013

MULTIPLE TESTING OF LOCAL MAXIMA FOR DETECTION OF PEAKS IN CHIP-SEQ DATA.

Ann Appl Stat 2013 ;7(1):471-494

Department of Biostatistics, Harvard School of Public Health and Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute, 450 Brookline Ave., CLS-11007, Boston, MA 02115, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233463PMC
January 2013

The sva package for removing batch effects and other unwanted variation in high-throughput experiments.

Bioinformatics 2012 Mar 17;28(6):882-3. Epub 2012 Jan 17.

Department of Biostatistics, JHU Bloomberg School of Public Health, Baltimore, MD, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3307112PMC
March 2012

Significance analysis and statistical dissection of variably methylated regions.

Biostatistics 2012 Jan 17;13(1):166-78. Epub 2011 Jun 17.

Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.

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https://academic.oup.com/biostatistics/article-lookup/doi/10
Publisher Site
http://dx.doi.org/10.1093/biostatistics/kxr013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276267PMC
January 2012

Identification of functional genetic variation in exome sequence analysis.

BMC Proc 2011 Nov 29;5 Suppl 9:S13. Epub 2011 Nov 29.

Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1186/1753-6561-5-S9-S13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287847PMC
November 2011

Genome-wide analysis of promoter methylation associated with gene expression profile in pancreatic adenocarcinoma.

Clin Cancer Res 2011 Jul 24;17(13):4341-54. Epub 2011 May 24.

Department of Pathology, Oncology, and Medicine, Bloomberg School of Public Health, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Johns Hopkins University, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1158/1078-0432.CCR-10-3431DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3131423PMC
July 2011

Imprints of spherical nontrivial topologies on the cosmic microwave background.

Phys Rev Lett 2007 Aug 24;99(8):081302. Epub 2007 Aug 24.

Blackett Laboratory, Imperial College London, Prince Consort Road, London, UK.

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http://dx.doi.org/10.1103/PhysRevLett.99.081302DOI Listing
August 2007

The use of the melolabial Burow's graft in the reconstruction of combination nasal sidewall-cheek defects.

Dermatol Surg 2004 Feb;30(2 Pt 1):205-7

Department of Dermatology, State University of New York Downstate Medical Center, Brooklyn, New York, USA.

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http://dx.doi.org/10.1111/j.1524-4725.2004.30064.xDOI Listing
February 2004

The Norelco Sport Fanatics Survey: examining behaviors of sport fans.

Psychol Rep 2003 Jun;92(3 Pt 1):930-6

Department of Psychology, Murray State University, KY 42071, USA.

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http://dx.doi.org/10.2466/pr0.2003.92.3.930DOI Listing
June 2003