Publications by authors named "Carl J Schmidt"

81Publications

Abusive Pediatric Thoracolumbar Fracture Due to Forced Hyperextension: Case Report, Biomechanical Considerations, and Review of the Literature.

J Forensic Sci 2020 Aug 17. Epub 2020 Aug 17.

Wayne County Medical Examiner's Office, Michigan Medicine, 1300 Warren Avenue, Detroit, Michigan, 48207.

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http://dx.doi.org/10.1111/1556-4029.14521DOI Listing
August 2020

fRNAkenseq: a fully powered-by-CyVerse cloud integrated RNA-sequencing analysis tool.

PeerJ 2020 14;8:e8592. Epub 2020 May 14.

Department of Animal and Food Sciences, University of Delaware, Newark, DE, USA.

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http://dx.doi.org/10.7717/peerj.8592DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7231498PMC
May 2020

Evaluating Bioinformatic Pipeline Performance for Forensic Microbiome Analysis.

J Forensic Sci 2020 Mar 28;65(2):513-525. Epub 2019 Oct 28.

Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824.

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http://dx.doi.org/10.1111/1556-4029.14213DOI Listing
March 2020

Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data.

PLoS One 2019 23;14(9):e0216838. Epub 2019 Sep 23.

Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216838PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6756534PMC
March 2020

Total RNA Analysis of Bacterial Community Structural and Functional Shifts Throughout Vertebrate Decomposition.

J Forensic Sci 2019 Nov 6;64(6):1707-1719. Epub 2019 Jun 6.

Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762.

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http://dx.doi.org/10.1111/1556-4029.14083DOI Listing
November 2019

Detection of critical antibiotic resistance genes through routine microbiome surveillance.

PLoS One 2019 14;14(3):e0213280. Epub 2019 Mar 14.

Department of Biological Sciences, Mississippi State University, Starkville, MS, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0213280PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417727PMC
December 2019

Gene expression profiling of the early pathogenesis of wooden breast disease in commercial broiler chickens using RNA-sequencing.

PLoS One 2018 5;13(12):e0207346. Epub 2018 Dec 5.

Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0207346PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6281187PMC
May 2019

Identifying mechanisms of regulation to model carbon flux during heat stress and generate testable hypotheses.

PLoS One 2018 26;13(10):e0205824. Epub 2018 Oct 26.

Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0205824PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6203350PMC
April 2019

Accidental Carbon Monoxide Poisoning While Driving: A Case Report With Review of the Literature.

Am J Forensic Med Pathol 2018 Sep;39(3):270-272

Department of Pathology, University of Michigan, Ann Arbor, MI.

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http://Insights.ovid.com/crossref?an=00000433-900000000-9921
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http://dx.doi.org/10.1097/PAF.0000000000000400DOI Listing
September 2018

TransAtlasDB: an integrated database connecting expression data, metadata and variants.

Database (Oxford) 2018 01;2018

Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA.

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http://dx.doi.org/10.1093/database/bay014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5824778PMC
January 2018

A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition.

Sci Rep 2018 04 10;8(1):5724. Epub 2018 Apr 10.

Michigan State University, Department of Entomology, East Lansing, MI, 48824, USA.

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http://dx.doi.org/10.1038/s41598-018-23989-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5893548PMC
April 2018

Commentary on: Schuman MJ, Hutchins KD. Severe retinal hemorrhages with retinoschisis in infants are not pathognomonic for abusive head trauma. J Forensic Sci 2017;62(3):807-11.

J Forensic Sci 2017 11;62(6):1677-1678

Department of Pathology, University of Michigan and Wayne County Medical Examiner, Detroit, MI, 49007.

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http://dx.doi.org/10.1111/1556-4029.13628DOI Listing
November 2017

Chicken hepatic response to chronic heat stress using integrated transcriptome and metabolome analysis.

PLoS One 2017 31;12(7):e0181900. Epub 2017 Jul 31.

Department of Animal and Food Sciences, University of Delaware, Newark, DE, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0181900PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536301PMC
October 2017

Evidence and role of phlebitis and lipid infiltration in the onset and pathogenesis of Wooden Breast Disease in modern broiler chickens.

Avian Pathol 2017 Dec 3;46(6):623-643. Epub 2017 Jul 3.

a Department of Animal and Food Sciences , University of Delaware , Newark , DE , USA.

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http://dx.doi.org/10.1080/03079457.2017.1339346DOI Listing
December 2017

WebGIVI: a web-based gene enrichment analysis and visualization tool.

BMC Bioinformatics 2017 May 4;18(1):237. Epub 2017 May 4.

Department of Animal and Food Sciences, University of Delaware, Newark, DE, USA.

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http://dx.doi.org/10.1186/s12859-017-1664-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5418709PMC
May 2017

Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast- and slow-growing broilers under heat stress.

BMC Genomics 2017 04 13;18(1):295. Epub 2017 Apr 13.

Department of Animal Science, Iowa State University, 806 Stange Rd, 2255 Kildee Hall, Ames, IA, 50011, USA.

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http://dx.doi.org/10.1186/s12864-017-3675-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5390434PMC
April 2017

Frozen: Thawing and Its Effect on the Postmortem Microbiome in Two Pediatric Cases.

J Forensic Sci 2017 Sep 25;62(5):1399-1405. Epub 2017 Jan 25.

Department of Entomology; Department of Osteopathic Medical Specialties; and Ecology, Evolutionary Biology and Behavior, Michigan State University, 243 Natural Science Building, East Lansing, MI.

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http://dx.doi.org/10.1111/1556-4029.13419DOI Listing
September 2017

Liver transcriptome response to hyperthermic stress in three distinct chicken lines.

BMC Genomics 2016 11 22;17(1):955. Epub 2016 Nov 22.

Department of Animal Science, Iowa State University, Ames, IA, USA.

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http://dx.doi.org/10.1186/s12864-016-3291-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5118885PMC
November 2016

Transcriptomic changes throughout post-hatch development in Gallus gallus pituitary.

J Mol Endocrinol 2017 01 17;58(1):43-55. Epub 2016 Nov 17.

Animal and Food ScienceUniversity of Delaware, Newark, Delaware, USA.

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http://dx.doi.org/10.1530/JME-16-0186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5148799PMC
January 2017

Commode Cardia-Death by Valsalva Maneuver: A Case Series.

J Forensic Sci 2016 Nov 22;61(6):1541-1545. Epub 2016 Sep 22.

Department of Pathology, University of Michigan, 1301 Catherine Street, Ann Arbor, MI, 48109.

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http://dx.doi.org/10.1111/1556-4029.13196DOI Listing
November 2016

Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology.

Integr Comp Biol 2016 12 17;56(6):1183-1191. Epub 2016 Sep 17.

Romberg Tiburon Center for Environmental Studies and Department of Biology, San Francisco State University, Tiburon, CA 94920, USA.

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http://dx.doi.org/10.1093/icb/icw083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5146710PMC
December 2016

The Disappearance of Sudden Infant Death Syndrome.

Authors:
Carl J Schmidt

JAMA Pediatr 2016 10;170(10):1025-1026

Chief Medical Examiner, Wayne County, Detroit, Michigan.

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http://dx.doi.org/10.1001/jamapediatrics.2016.1811DOI Listing
October 2016

Distinct functional responses to stressors of bone marrow derived dendritic cells from diverse inbred chicken lines.

Dev Comp Immunol 2016 10 27;63:96-110. Epub 2016 May 27.

Department of Animal Science, Iowa State University, Ames, IA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.dci.2016.05.016DOI Listing
October 2016

miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases.

J Biomed Semantics 2016 04 29;7(1). Epub 2016 Apr 29.

Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA.

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http://dx.doi.org/10.1186/s13326-015-0044-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877743PMC
April 2016

Corrigendum to 'Herpesvirus of turkeys: Microarray analysis of host gene responses to infection' [Virology 318 (2004) 102-111].

Virology 2015 Sep 12;486. Epub 2015 Sep 12.

Department of Animal and Food Sciences, University of Delaware, Newark, DE 19717-2150, USA. Electronic address:

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http://dx.doi.org/10.1016/j.virol.2015.09.001DOI Listing
September 2015

Third Report on Chicken Genes and Chromosomes 2015.

Authors:
Michael Schmid Jacqueline Smith David W Burt Bronwen L Aken Parker B Antin Alan L Archibald Chris Ashwell Perry J Blackshear Clarissa Boschiero C Titus Brown Shane C Burgess Hans H Cheng William Chow Derrick J Coble Amanda Cooksey Richard P M A Crooijmans Joana Damas Richard V N Davis Dirk-Jan de Koning Mary E Delany Thomas Derrien Takele T Desta Ian C Dunn Matthew Dunn Hans Ellegren Lél Eöry Ionas Erb Marta Farré Mario Fasold Damarius Fleming Paul Flicek Katie E Fowler Laure Frésard David P Froman Valerie Garceau Paul P Gardner Almas A Gheyas Darren K Griffin Martien A M Groenen Thomas Haaf Olivier Hanotte Alan Hart Julien Häsler S Blair Hedges Jana Hertel Kerstin Howe Allen Hubbard David A Hume Pete Kaiser Darek Kedra Stephen J Kemp Christophe Klopp Kalmia E Kniel Richard Kuo Sandrine Lagarrigue Susan J Lamont Denis M Larkin Raman A Lawal Sarah M Markland Fiona McCarthy Heather A McCormack Marla C McPherson Akira Motegi Stefan A Muljo Andrea Münsterberg Rishi Nag Indrajit Nanda Michael Neuberger Anne Nitsche Cedric Notredame Harry Noyes Rebecca O'Connor Elizabeth A O'Hare Andrew J Oler Sheila C Ommeh Helio Pais Michael Persia Frédérique Pitel Likit Preeyanon Pablo Prieto Barja Elizabeth M Pritchett Douglas D Rhoads Charmaine M Robinson Michael N Romanov Max Rothschild Pierre-François Roux Carl J Schmidt Alisa-Sophia Schneider Matthew G Schwartz Steve M Searle Michael A Skinner Craig A Smith Peter F Stadler Tammy E Steeves Claus Steinlein Liang Sun Minoru Takata Igor Ulitsky Qing Wang Ying Wang Wesley C Warren Jonathan M D Wood David Wragg Huaijun Zhou

Cytogenet Genome Res 2015 14;145(2):78-179. Epub 2015 Jul 14.

Department of Human Genetics, University of Würzburg, Würzburg, Germany.

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http://dx.doi.org/10.1159/000430927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120589PMC
October 2015

Identification of long noncoding RNAs dysregulated in the midbrain of human cocaine abusers.

J Neurochem 2015 Oct 1;135(1):50-9. Epub 2015 Sep 1.

Department of Pharmacology, Wayne State University School of Medicine, Detroit, Michigan, USA.

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http://dx.doi.org/10.1111/jnc.13255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4830632PMC
October 2015

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Science 2014 Dec 11;346(6215):1254449. Epub 2014 Dec 11.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.

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http://jarvislab.net/wp-content/uploads/2012/02/Green-et-al-
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http://www.sciencemag.org/cgi/doi/10.1126/science.1254449
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http://dx.doi.org/10.1126/science.1254449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873PMC
December 2014

Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats.

Mol Biol Evol 2014 Jun 1;31(6):1536-45. Epub 2014 Apr 1.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityInstitute for Genomics, Biocomputing and Biotechnology, Mississippi State University

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http://dx.doi.org/10.1093/molbev/msu112DOI Listing
June 2014

Authors' response.

J Forensic Sci 2013 Mar;58(2):562

Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI.

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http://dx.doi.org/10.1111/1556-4029.12080DOI Listing
March 2013

Fentanyl-associated fatalities among illicit drug users in Wayne County, Michigan (July 2005-May 2006).

J Med Toxicol 2013 Mar;9(1):106-15

Centers for Disease Control and Prevention, National Center for Environmental Health, Division of Environmental Hazards and Health Effects, Health Studies Branch, Atlanta, GA, USA.

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http://link.springer.com/10.1007/s13181-012-0285-4
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http://dx.doi.org/10.1007/s13181-012-0285-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3576499PMC
March 2013

Developing a biocuration workflow for AgBase, a non-model organism database.

Database (Oxford) 2012 17;2012:bas038. Epub 2012 Nov 17.

Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, MS 39762, USA.

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http://dx.doi.org/10.1093/database/bas038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3500517PMC
April 2013

Ventral midbrain correlation between genetic variation and expression of the dopamine transporter gene in cocaine-abusing versus non-abusing subjects.

Addict Biol 2014 Jan 26;19(1):122-31. Epub 2011 Oct 26.

Department of Psychiatry, Harvard Medical School and Division of Alcohol and Drug Abuse, McLean Hospital, Belmont, MA, USA Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA Department of Statistics, Harvard University, Cambridge, MA, USA.

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http://doi.wiley.com/10.1111/j.1369-1600.2011.00391.x
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http://dx.doi.org/10.1111/j.1369-1600.2011.00391.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3270208PMC
January 2014

Microbial community analysis of perchlorate-reducing cultures growing on zero-valent iron.

J Hazard Mater 2011 Jan 25;185(2-3):669-76. Epub 2010 Sep 25.

Department of Civil Engineering, Auburn University, Auburn, AL 36849, United States.

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https://linkinghub.elsevier.com/retrieve/pii/S03043894100123
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http://dx.doi.org/10.1016/j.jhazmat.2010.09.070DOI Listing
January 2011

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

PLoS Biol 2010 Sep 7;8(9). Epub 2010 Sep 7.

Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1000475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935454PMC
September 2010

eGIFT: mining gene information from the literature.

BMC Bioinformatics 2010 Aug 9;11:418. Epub 2010 Aug 9.

Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-11-418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929241PMC
August 2010

The Chicken Gene Nomenclature Committee report.

BMC Genomics 2009 Jul 14;10 Suppl 2:S5. Epub 2009 Jul 14.

Department of Genomics and Genetics, Roslin Institute and Royal (Dick) School of Veterinary Studies, Midlothian, UK.

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http://dx.doi.org/10.1186/1471-2164-10-S2-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2966335PMC
July 2009

Gallus GBrowse: a unified genomic database for the chicken.

Nucleic Acids Res 2008 Jan 11;36(Database issue):D719-23. Epub 2007 Oct 11.

Department of Animal and Food Sciences, University of Delaware, Newark, DE 19706, USA.

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http://dx.doi.org/10.1093/nar/gkm783DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238981PMC
January 2008

Infant death scene investigation and the assessment of potential risk factors for asphyxia: a review of 209 sudden unexpected infant deaths.

J Forensic Sci 2007 Jul 6;52(4):924-9. Epub 2007 Jun 6.

New York City Office of Chief Medical Examiner, 520 First Ave., New York, NY 10016, USA.

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http://dx.doi.org/10.1111/j.1556-4029.2007.00477.xDOI Listing
July 2007

Fatal bromethalin poisoning.

J Forensic Sci 2006 Sep;51(5):1154-7

Office of the Chief Medical Examiner, 520 First Avenue, New York, NY 10016, USA.

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http://doi.wiley.com/10.1111/j.1556-4029.2006.00218.x
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http://dx.doi.org/10.1111/j.1556-4029.2006.00218.xDOI Listing
September 2006

Distinctive profiles of gene expression in the human nucleus accumbens associated with cocaine and heroin abuse.

Neuropsychopharmacology 2006 Oct 3;31(10):2304-12. Epub 2006 May 3.

Department of Psychiatry & Behavioral Neurosciences, Wayne State University School of Medicine, Detroit, MI 48201, USA.

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http://www.nature.com/doifinder/10.1038/sj.npp.1301089
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http://dx.doi.org/10.1038/sj.npp.1301089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2239258PMC
October 2006

Distinctive profiles of gene expression in the human nucleus accumbens associated with cocaine and heroin abuse.

Neuropsychopharmacology 2006 Oct 3;31(10):2304-12. Epub 2006 May 3.

Department of Psychiatry & Behavioral Neurosciences, Wayne State University School of Medicine, Detroit, MI 48201, USA.

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http://www.nature.com/doifinder/10.1038/sj.npp.1301089
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http://dx.doi.org/10.1038/sj.npp.1301089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2239258PMC
October 2006

Blunt force injury of the abdomen complicating previously undiagnosed peliosis hepatis in a 2-year-old female.

J Forensic Sci 2005 Jul;50(4):910-2

Wayne County Medical Examiner Office, 1300 East Warren Avenue, Detroit, MI 48207, USA.

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July 2005

Transcription factors specifying dopamine phenotype are decreased in cocaine users.

Neuroreport 2004 Mar;15(3):401-4

Department of Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine, 540 E. Canfield, Rm. 2309 Scott Hall, Detroit, MI 48201, USA.

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http://dx.doi.org/10.1097/00001756-200403010-00003DOI Listing
March 2004

Gene expression profile of the nucleus accumbens of human cocaine abusers: evidence for dysregulation of myelin.

J Neurochem 2004 Mar;88(5):1211-9

Departments of Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine, Detroit, Michigan 48201, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2215309PMC
http://dx.doi.org/10.1046/j.1471-4159.2003.02247.xDOI Listing
March 2004

Herpesvirus of turkeys: microarray analysis of host gene responses to infection.

Virology 2004 Jan;318(1):102-11

Department of Animal and Food Sciences, University of Delaware, Newark, DE 19717-2150, USA.

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http://dx.doi.org/10.1016/j.virol.2003.09.025DOI Listing
January 2004

GoFigure: automated Gene Ontology annotation.

Bioinformatics 2003 Dec;19(18):2484-5

Department of Computer and Information Sciences, University of Delaware, Newark, DE 19717, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg338DOI Listing
December 2003

Characterization of vnr-13, the first alphaherpesvirus gene of the bcl-2 family.

Virology 2003 Nov;316(2):256-66

IBCP, UMR 5086 CNRS-Université Claude Bernard 7, Passage du Vercors, F69367 Lyon Cedex 07, France.

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http://dx.doi.org/10.1016/j.virol.2003.08.014DOI Listing
November 2003

Decreased expression of the transcription factor NURR1 in dopamine neurons of cocaine abusers.

Proc Natl Acad Sci U S A 2002 Apr 16;99(9):6382-5. Epub 2002 Apr 16.

Department of Psychiatry and Behavioral Neurosciences, Pharmacology, and Pathology, Wayne State University School of Medicine, 2309 Scott Hall, 540 East Canfield Avenue, Detroit, MI 48201, USA.

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http://dx.doi.org/10.1073/pnas.092654299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC122957PMC
April 2002

Marek's disease virus VP22: subcellular localization and characterization of carboxyl terminal deletion Mutations.

Virology 2002 Jan;292(2):235-40

Department of Animal and Food Sciences, University of Delaware, Newark, Delaware 19717, USA.

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http://dx.doi.org/10.1006/viro.2001.1223DOI Listing
January 2002

The genome of herpesvirus of turkeys: comparative analysis with Marek's disease viruses.

J Gen Virol 2001 May;82(Pt 5):1123-1135

Department of Animal and Food Sciences, University of Delaware, Newark, DE 19717, USA1.

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http://dx.doi.org/10.1099/0022-1317-82-5-1123DOI Listing
May 2001