Scott Newman

Scott Newman

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Scott Newman

Scott Newman

Publications by authors named "Scott Newman"

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RNAIndel: discovering somatic coding indels from tumor RNA-Seq data.

Bioinformatics 2019 Oct 8. Epub 2019 Oct 8.

Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz753DOI Listing
October 2019

VCF2CNA: A tool for efficiently detecting copy-number alterations in VCF genotype data and tumor purity.

Sci Rep 2019 Jul 17;9(1):10357. Epub 2019 Jul 17.

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.

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http://dx.doi.org/10.1038/s41598-019-45938-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6637131PMC
July 2019

Investigating Home Range, Movement Pattern, and Habitat Selection of Bar-headed Geese during Breeding Season at Qinghai Lake, China.

Animals (Basel) 2018 Oct 18;8(10). Epub 2018 Oct 18.

e-Science Technology and Application Laboratory, Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China.

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http://dx.doi.org/10.3390/ani8100182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6209964PMC
October 2018

Clear cell sarcoma of kidney involving a horseshoe kidney and harboring EGFR internal tandem duplication.

Pediatr Blood Cancer 2017 Nov 25;64(11). Epub 2017 Apr 25.

Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.

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http://dx.doi.org/10.1002/pbc.26602DOI Listing
November 2017

CD86 regulates myeloma cell survival.

Blood Adv 2017 Nov 16;1(25):2307-2319. Epub 2017 Nov 16.

Department of Hematology and Oncology, Winship Cancer Institute, Emory University, Atlanta, GA.

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http://dx.doi.org/10.1182/bloodadvances.2017011601DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5729629PMC
November 2017

CD36-positive B-lymphoblasts Predict Poor Outcome in Children With B-lymphoblastic Leukemia.

Pediatr Dev Pathol 2017 Jun 8;20(3):224-231. Epub 2017 Feb 8.

6 Department of Pathology, Children's Healthcare of Atlanta - Egleston, Emory University, Atlanta, Georgia, USA.

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http://dx.doi.org/10.1177/1093526616688753DOI Listing
June 2017

Prevalence and diversity of H9N2 avian influenza in chickens of Northern Vietnam, 2014.

Infect Genet Evol 2016 10 20;44:530-540. Epub 2016 Jun 20.

Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam; Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5036934PMC
http://dx.doi.org/10.1016/j.meegid.2016.06.038DOI Listing
October 2016

Investigating poultry trade patterns to guide avian influenza surveillance and control: a case study in Vietnam.

Sci Rep 2016 07 12;6:29463. Epub 2016 Jul 12.

Emergency Center for the Control of Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Hanoi, Vietnam.

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http://dx.doi.org/10.1038/srep29463DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4942603PMC
July 2016

Assessment of genetic variation for pathogen-specific mastitis resistance in Valle del Belice dairy sheep.

BMC Vet Res 2016 Jul 28;12(1):158. Epub 2016 Jul 28.

Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Viale delle Scienze, Palermo, 90128, Italy.

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http://bmcvetres.biomedcentral.com/articles/10.1186/s12917-0
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http://dx.doi.org/10.1186/s12917-016-0781-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4964260PMC
July 2016

Spatial Modeling of Wild Bird Risk Factors for Highly Pathogenic A(H5N1) Avian Influenza Virus Transmission.

Avian Dis 2016 05;60(1 Suppl):329-36

Department of Geography and Environmental Systems, University of Maryland Baltimore County, Baltimore, MD 21250.

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http://dx.doi.org/10.1637/11125-050615-RegDOI Listing
May 2016

Gene integrated set profile analysis: a context-based approach for inferring biological endpoints.

Nucleic Acids Res 2016 Apr 29;44(7):e69. Epub 2016 Jan 29.

Winship Cancer Institute, Emory University, Atlanta, GA 30333, USA Department of Hematology and Medical Oncology, School of Medicine, Emory University, Atlanta, GA 30322, USA.

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http://dx.doi.org/10.1093/nar/gkv1503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838358PMC
April 2016

Farewell to GBM-O: Genomic and transcriptomic profiling of glioblastoma with oligodendroglioma component reveals distinct molecular subgroups.

Acta Neuropathol Commun 2016 Jan 13;4. Epub 2016 Jan 13.

Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 1648 Pierce Dr NE, Atlanta, GA, 30307, USA.

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http://dx.doi.org/10.1186/s40478-015-0270-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4711079PMC
January 2016

Heregulin and HER3 are prognostic biomarkers in oropharyngeal squamous cell carcinoma.

Cancer 2015 Oct 20;121(20):3600-11. Epub 2015 Jul 20.

Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia.

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http://dx.doi.org/10.1002/cncr.29549DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4592409PMC
October 2015

Interactive analysis of large cancer copy number studies with Copy Number Explorer.

Authors:
Scott Newman

Bioinformatics 2015 Sep 7;31(17):2874-6. Epub 2015 May 7.

Biostatistics & Bioinformatics Shared Resource, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547619PMC
September 2015

A new method for discovering behavior patterns among animal movements.

Int J Geogr Inf Sci 2016;30(5):929-947. Epub 2015 Sep 29.

Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1080/13658816.2015.1091462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874732PMC
September 2015

Movement analysis of free-grazing domestic ducks in Poyang Lake, China: a disease connection.

Int J Geogr Inf Sci 2016;30(5):869-880. Epub 2015 Jul 13.

Emergency Center for Transboundary Animal Disease, Food and Agriculture Organization of the United Nations (FAO) - Vietnam, Hanoi, Vietnam.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5042146PMC
http://dx.doi.org/10.1080/13658816.2015.1065496DOI Listing
July 2015

Stable Isotopes Suggest Low Site Fidelity in Bar-headed Geese () in Mongolia: Implications for Disease Transmission.

Waterbirds 2015 Jun;38(2):123-132

Food and Agriculture Organization of the United Nations, Emergency Centre for Transboundary Animal Diseases, No. 3 Nguyen Gia Thieu Street, Hanoi, Viet Nam.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5042147PMC
http://dx.doi.org/10.1675/063.038.0201DOI Listing
June 2015

Genomics in aquaculture to better understand species biology and accelerate genetic progress.

Front Genet 2015 1;6:128. Epub 2015 Apr 1.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Midlothian, UK.

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http://dx.doi.org/10.3389/fgene.2015.00128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381651PMC
April 2015

Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints.

Am J Hum Genet 2015 Feb 29;96(2):208-20. Epub 2015 Jan 29.

Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2014.12.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4320257PMC
February 2015

Mapping migratory flyways in Asia using dynamic Brownian bridge movement models.

Mov Ecol 2015 2;3(1). Epub 2015 Feb 2.

U.S. Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station, Vallejo, CA 94592 USA ; National Audubon Society, Science Division, 220 Montgomery Street, San Francisco, CA 94104 USA.

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http://dx.doi.org/10.1186/s40462-015-0029-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4337761PMC
February 2015

Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic analysis.

PLoS Med 2015 Feb 24;12(2):e1001789. Epub 2015 Feb 24.

Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom; Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pmed.1001789DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4339382PMC
February 2015

Avian influenza H5N1 viral and bird migration networks in Asia.

Proc Natl Acad Sci U S A 2015 Jan 22;112(1):172-7. Epub 2014 Dec 22.

State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing 100875, People's Republic of China; Ministry of Education Key Laboratory for Earth System Modelling, Center for Earth System Science, and School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; Department of Geography, University of Utah, Salt Lake City, UT 84112

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http://dx.doi.org/10.1073/pnas.1405216112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4291667PMC
January 2015

Genetics and genomics of disease resistance in salmonid species.

Front Genet 2014 26;5:415. Epub 2014 Nov 26.

Genus plc, Hendersonville TN, USA.

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http://dx.doi.org/10.3389/fgene.2014.00415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245001PMC
December 2014

The relative timing of mutations in a breast cancer genome.

PLoS One 2013 10;8(6):e64991. Epub 2013 Jun 10.

Hutchison/MRC Research Centre and Department of Pathology, University of Cambridge, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064991PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677865PMC
February 2014

Large inverted duplications in the human genome form via a fold-back mechanism.

PLoS Genet 2014 Jan 30;10(1):e1004139. Epub 2014 Jan 30.

Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907307PMC
January 2014

Intravascular extension of a glomus jugulare.

Otol Neurotol 2013 Dec;34(9):e125-7

*Department of Otolaryngology, Tripler Army Medical Center; †Department of Radiology, and ‡Department of Pathology, Kaiser Permanent, Honolulu, Hawaii; and §Department of Otolaryngology, Maui, Hawaii, U.S.A.

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http://dx.doi.org/10.1097/MAO.0b013e318292fb53DOI Listing
December 2013

Movements of wild ruddy shelducks in the Central Asian Flyway and their spatial relationship to outbreaks of highly pathogenic avian influenza H5N1.

Viruses 2013 Sep 9;5(9):2129-52. Epub 2013 Sep 9.

San Francisco Bay Estuary Field Station, Western Ecological Research Center, U.S. Geological Survey, 505 Azuar Drive, Vallejo, CA 94592, USA.

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http://dx.doi.org/10.3390/v5092129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3798894PMC
September 2013

Serological evidence of West Nile virus infection in wild migratory and resident water birds in Eastern and Northern India.

Comp Immunol Microbiol Infect Dis 2012 Dec 25;35(6):591-8. Epub 2012 Aug 25.

High Security Animal Disease Laboratory, Indian Veterinary Research Institute, Anand Nagar, Bhopal, Madhya Pradesh 462 021, India.

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http://dx.doi.org/10.1016/j.cimid.2012.08.002DOI Listing
December 2012

Fourier-Bessel analysis of localized states and photonic bandgaps in 12-fold photonic quasi-crystals.

J Opt Soc Am A Opt Image Sci Vis 2012 Nov;29(11):2344-9

Department of Electronics, Carleton University, 1125 Colonel By Drive, Ontario K1S 5B6, Canada.

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https://www.osapublishing.org/abstract.cfm?URI=josaa-29-11-2
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http://dx.doi.org/10.1364/JOSAA.29.002344DOI Listing
November 2012

The role of tandem duplicator phenotype in tumour evolution in high-grade serous ovarian cancer.

J Pathol 2012 Apr 9;226(5):703-12. Epub 2012 Feb 9.

Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.

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http://dx.doi.org/10.1002/path.3980DOI Listing
April 2012

Modal analysis and device considerations of thin high index dielectric overlay slab waveguides.

Appl Opt 2012 Mar;51(9):1266-75

Department of Electronics, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada, K1S 5B6.

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http://dx.doi.org/10.1364/AO.51.001266DOI Listing
March 2012

Estimation of rearrangement phylogeny for cancer genomes.

Genome Res 2012 Feb 12;22(2):346-61. Epub 2011 Oct 12.

Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.

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http://dx.doi.org/10.1101/gr.118414.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266042PMC
February 2012

Single-molecule analysis of genome rearrangements in cancer.

Nucleic Acids Res 2011 Jul 27;39(13):e85. Epub 2011 Apr 27.

Hutchison/MRC Research Centre and Department of Pathology, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, UK.

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http://dx.doi.org/10.1093/nar/gkr227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141271PMC
July 2011

Aberrant chromosome morphology in human cells defective for Holliday junction resolution.

Nature 2011 Mar 13;471(7340):642-6. Epub 2011 Mar 13.

London Research Institute, Cancer Research UK, Clare Hall Laboratories, South Mimms, Hertfordshire EN6 3LD, UK.

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http://dx.doi.org/10.1038/nature09790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3560329PMC
March 2011

Amplification of the driving oncogene, KRAS or BRAF, underpins acquired resistance to MEK1/2 inhibitors in colorectal cancer cells.

Sci Signal 2011 Mar 29;4(166):ra17. Epub 2011 Mar 29.

Laboratory of Molecular Signalling, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.

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http://dx.doi.org/10.1126/scisignal.2001752DOI Listing
March 2011

The support of meat value chains by genetic technologies.

Meat Sci 2010 Sep 29;86(1):129-37. Epub 2010 Apr 29.

PIC North America and Genus plc, Hendersonville, TN 37075, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S03091740100016
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http://dx.doi.org/10.1016/j.meatsci.2010.04.034DOI Listing
September 2010

Comparing national and global data collection systems for reporting, outbreaks of H5N1 HPAI.

Prev Vet Med 2010 Jul;95(3-4):175-85

USDA-APHIS-VS-Centers for Epidemiology and Animal Health, 2150 Centre Avenue, Bldg. B, Mail Stop 2W4, Fort Collins, CO 80526, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S01675877100009
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http://dx.doi.org/10.1016/j.prevetmed.2010.03.012DOI Listing
July 2010

High-throughput analysis of chromosome translocations and other genome rearrangements in epithelial cancers.

Genome Med 2010 Mar 17;2(3):19. Epub 2010 Mar 17.

Hutchison-MRC Research Centre and Department of Pathology, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, UK.

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http://dx.doi.org/10.1186/gm140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873797PMC
March 2010

Migration of whooper swans and outbreaks of highly pathogenic avian influenza H5N1 virus in eastern Asia.

PLoS One 2009 May 28;4(5):e5729. Epub 2009 May 28.

EMPRES Wildlife Unit, Infectious Disease Group, Emergency Centre for Transboundary Animal Diseases, Animal Production and Health Division, Food & Agriculture Organization of the United Nations, Rome, Italy.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0005729PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684635PMC
May 2009

Health assessment of Black-crowned Night-herons (Nycticorax nycticorax) of the New York Harbor estuary.

Comp Biochem Physiol B Biochem Mol Biol 2007 Dec 14;148(4):363-74. Epub 2007 Jul 14.

Wildlife Trust, 460 West 34th Street, 17th Floor, New York, NY 10001, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S109649590700223
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http://dx.doi.org/10.1016/j.cbpb.2007.07.003DOI Listing
December 2007

Experimental verification of the application of lateral buildup ratio on the 4-MeV electron beam.

J Appl Clin Med Phys 2006 15;7(1):35-41. Epub 2006 Feb 15.

Medical Physics Department, 1 Grand River Regional Cancer Center, Grand River Hospital, P.O. Box 9056, 835 King Street West, Kitchener, Ontario, Canada.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5722474PMC
http://dx.doi.org/10.1120/jacmp.v7i1.2153DOI Listing
April 2006

The nature of emerging zoonotic diseases: ecology, prediction, and prevention.

MLO Med Lab Obs 2005 Jul;37(7):10-1, 14-6, 18-9; quiz 20-1

Cloumbia University, Department of Ecology, Evolution and Environmental Biology, USA.

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July 2005

Metastasizing atypical fibroxanthoma (cutaneous malignant histiocytoma): report of five cases.

Dermatol Surg 2005 Feb;31(2):221-5; discussion 225

Department of Dermatology, Division of Otolaryngology, University of Rochester Medical Center, Rochester, New York 14642, USA.

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http://dx.doi.org/10.1111/j.1524-4725.2005.31046DOI Listing
February 2005

Crosslinking of proteins to mtDNA.

Methods Mol Biol 2002 ;197:377-89

Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.

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http://dx.doi.org/10.1385/1-59259-284-8:377DOI Listing
November 2002

Privacy in personal medical information: a diagnosis.

Authors:
Scott Newman

Univ Fla Law Rev 1981 ;33(3):394-424

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April 1986