Melissa Haendel

Melissa Haendel

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Melissa Haendel

Publications by authors named "Melissa Haendel"

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New models for human disease from the International Mouse Phenotyping Consortium.

Mamm Genome 2019 Jun 24;30(5-6):143-150. Epub 2019 May 24.

William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK.

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http://dx.doi.org/10.1007/s00335-019-09804-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6606664PMC
June 2019

Ten quick tips for biocuration.

PLoS Comput Biol 2019 May 2;15(5):e1006906. Epub 2019 May 2.

Linus Pauling Institute, Oregon State University, Corvallis, Oregon, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6497217PMC
May 2019

The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution.

Dev Cell 2019 Apr 28;49(1):10-29. Epub 2019 Mar 28.

Department of Biomedical Informatics, University of Cincinnati College of Medicine, and Cincinnati Children's Hospital Medical Center, Division of Biomedical Informatics, Cincinnati, OH 45229, USA.

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http://dx.doi.org/10.1016/j.devcel.2019.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6616346PMC
April 2019

An analysis and metric of reusable data licensing practices for biomedical resources.

PLoS One 2019 27;14(3):e0213090. Epub 2019 Mar 27.

Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0213090PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6436688PMC
March 2019

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.

Nucleic Acids Res 2019 Jan;47(D1):D1018-D1027

Monarch Initiative, monarchinitiative.org.

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https://academic.oup.com/nar/advance-article/doi/10.1093/nar
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http://dx.doi.org/10.1093/nar/gky1105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324074PMC
January 2019

Classification, Ontology, and Precision Medicine.

N Engl J Med 2018 10;379(15):1452-1462

From the Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, and the Linus Pauling Institute and the Center for Genome Research and Biocomputing, Oregon State University, Corvallis (M.A.H.); Johns Hopkins University Schools of Medicine, Public Health, and Nursing, Baltimore (C.G.C.); and the Jackson Laboratory for Genomic Medicine and the Institute for Systems Genomics, University of Connecticut - both in Farmington (P.N.R.).

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http://www.nejm.org/doi/10.1056/NEJMra1615014
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http://dx.doi.org/10.1056/NEJMra1615014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6503847PMC
October 2018

Matchmaker Exchange.

Curr Protoc Hum Genet 2017 10 18;95:9.31.1-9.31.15. Epub 2017 Oct 18.

The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.

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http://dx.doi.org/10.1002/cphg.50DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6016856PMC
October 2017

Reproducible and reusable research: are journal data sharing policies meeting the mark?

PeerJ 2017 25;5:e3208. Epub 2017 Apr 25.

OHSU Library, Oregon Health & Science University, Portland, OR, United States.

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http://dx.doi.org/10.7717/peerj.3208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5407277PMC
April 2017

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease.

Am J Hum Genet 2016 09 25;99(3):595-606. Epub 2016 Aug 25.

Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse, 14195 Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2016.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5011059PMC
September 2016

Laying a Community-Based Foundation for Data-Driven Semantic Standards in Environmental Health Sciences.

Environ Health Perspect 2016 08 12;124(8):1136-40. Epub 2016 Feb 12.

Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA.

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http://dx.doi.org/10.1289/ehp.1510438DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4977056PMC
August 2016

Reproducibility and conflicts in immune epitope data.

Immunology 2016 Mar 5;147(3):349-54. Epub 2016 Feb 5.

Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA.

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http://dx.doi.org/10.1111/imm.12566DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4754615PMC
March 2016

The Resource Identification Initiative: A Cultural Shift in Publishing.

J Comp Neurol 2016 Jan;524(1):8-22

Oregon Health & Science University (OHSU) Library, Department of Medical Informatics & Clinical Epidemiology, Portland, Oregon, USA.

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http://dx.doi.org/10.1002/cne.23913DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684178PMC
January 2016

The Resource Identification Initiative: a cultural shift in publishing.

Brain Behav 2016 01 8;6(1):e00417. Epub 2015 Dec 8.

Department of Medical Informatics & Clinical Epidemiology OHSU Library Oregon Health and Science University 3181 SW Sam Jackson Park Road Portland, Oregon 97239 USA.

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http://dx.doi.org/10.1002/brb3.417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834942PMC
January 2016

Disease insights through cross-species phenotype comparisons.

Mamm Genome 2015 Oct 20;26(9-10):548-55. Epub 2015 Jun 20.

Skarnes Faculty Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1007/s00335-015-9577-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4602072PMC
October 2015

Capturing phenotypes for precision medicine.

Cold Spring Harb Mol Case Stud 2015 Oct;1(1):a000372

Oregon Health and Science University, Portland, Oregon 97239, USA.

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http://dx.doi.org/10.1101/mcs.a000372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4850887PMC
October 2015

Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network.

J Biomed Inform 2015 Aug 3;56:127-44. Epub 2015 Jun 3.

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.jbi.2015.05.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532611PMC
August 2015

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.

Am J Hum Genet 2015 Jul 25;97(1):111-24. Epub 2015 Jun 25.

Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany; Berlin Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Institute of Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.05.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4572507PMC
July 2015

Finding our way through phenotypes.

PLoS Biol 2015 Jan 6;13(1):e1002033. Epub 2015 Jan 6.

Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1002033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285398PMC
January 2015

Clinical interpretation of CNVs with cross-species phenotype data.

J Med Genet 2014 Nov 3;51(11):766-772. Epub 2014 Oct 3.

Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin,Berlin, Germany.

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http://dx.doi.org/10.1136/jmedgenet-2014-102633DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4501634PMC
November 2014

Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome.

Sci Transl Med 2014 Sep;6(252):252ra123

Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany. Berlin-Brandenburg Center for Regenerative Therapies, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany. Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany.

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http://dx.doi.org/10.1126/scitranslmed.3009262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4512639PMC
September 2014

The influence of disease categories on gene candidate predictions from model organism phenotypes.

J Biomed Semantics 2014 3;5(Suppl 1 Proceedings of the Bio-Ontologies Spec Interest G):S4. Epub 2014 Jun 3.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA Hinxton, UK.

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http://dx.doi.org/10.1186/2041-1480-5-S1-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108905PMC
August 2014

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.

J Biomed Semantics 2014 11;5:34. Epub 2014 Aug 11.

Library and Department of Medical Informatics & Epidemiology, Oregon Health & Science University, Portland, OR, USA.

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http://dx.doi.org/10.1186/2041-1480-5-34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137724PMC
August 2014

Thematic series on biomedical ontologies in JBMS: challenges and new directions.

J Biomed Semantics 2014 6;5:15. Epub 2014 Mar 6.

Department of Computational Linguistics, University of Zürich, Binzmühlestrasse 14, 8050 Zürich, Switzerland ; European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1186/2041-1480-5-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4006457PMC
June 2014

A sea of standards for omics data: sink or swim?

J Am Med Inform Assoc 2014 Mar-Apr;21(2):200-3. Epub 2013 Sep 27.

Duke Translational Medicine Institute, Duke University, Durham, North Carolina, USA.

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https://academic.oup.com/jamia/article-lookup/doi/10.1136/am
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http://dx.doi.org/10.1136/amiajnl-2013-002066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932466PMC
May 2014

Improved exome prioritization of disease genes through cross-species phenotype comparison.

Genome Res 2014 Feb 25;24(2):340-8. Epub 2013 Oct 25.

Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany;

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http://dx.doi.org/10.1101/gr.160325.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912424PMC
February 2014

The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio.

J Biomed Semantics 2014 Feb 25;5(1):12. Epub 2014 Feb 25.

ZFIN, 5291 University of Oregon, Eugene, OR 97403-5291, USA.

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http://dx.doi.org/10.1186/2041-1480-5-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3944782PMC
February 2014

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.

Nucleic Acids Res 2014 Jan 11;42(Database issue):D966-74. Epub 2013 Nov 11.

Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Lawrence Berkeley National Laboratory, Mail Stop 84R0171, Berkeley, CA 94720, USA, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Department of Medical Genetics, Cambridge University Addenbrooke's Hospital, Cambridge CB2 2QQ, UK, Université Paul Sabatier, Faculté de Chirurgie Dentaire, CHU Toulouse, France, Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), Manchester, UK, Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, MAHSC, Manchester M13 9WL, UK, Institute of Genetic Medicine. Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK, Department of Computer Science, University of Toronto, Ontario, Canada, Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Clinical Genetics, Leeds Teaching Hospitals NHS Trust, Leeds LS2 9NS, UK, MRC Human Genetics Unit, MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, The Jackson Laboratory, Bar Harbor, ME 04609, USA, Center for Molecular and Vascular Biology, University of Leuven, Belgium, Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Kiel Campus, 24105 Kiel, Germany, NE Thames Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK, Drexel University College of Medicine, Philadelphia, PA 19102, USA, Department of Haematology, University of Cambridge and NHS Blood and Transplant Cambridge, CB2 0PT Cambridge, UK, Autism and Developmental Medicine Institute, Geisinger Health System

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http://dx.doi.org/10.1093/nar/gkt1026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965098PMC
January 2014

What is an anatomy ontology?

Anat Rec (Hoboken) 2013 Dec 11;296(12):1797-9. Epub 2013 Oct 11.

Department of Oral Biology, College of Dentistry, University of Illinois, Chicago.

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http://dx.doi.org/10.1002/ar.22805DOI Listing
December 2013

An ontology-based method for secondary use of electronic dental record data.

AMIA Jt Summits Transl Sci Proc 2013 18;2013:234-8. Epub 2013 Mar 18.

Center for Dental Informatics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3845770PMC
December 2013

From EHRs to Linked Data: representing and mining encounter data for clinical expertise evaluation.

AMIA Jt Summits Transl Sci Proc 2013 18;2013:165. Epub 2013 Mar 18.

OHSU Library and Department of Medical Informatics, Oregon Health & Science University, Portland, OR.

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December 2013

Ontology based molecular signatures for immune cell types via gene expression analysis.

BMC Bioinformatics 2013 Aug 30;14:263. Epub 2013 Aug 30.

Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, 100 High Street, Buffalo, NY 14203, USA.

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http://dx.doi.org/10.1186/1471-2105-14-263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844401PMC
August 2013

Lost and found in behavioral informatics.

Int Rev Neurobiol 2012 ;103:1-18

Oregon Health & Science University, Portland, Oregon, USA.

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http://dx.doi.org/10.1016/B978-0-12-388408-4.00001-0DOI Listing
May 2013

The field of bioinformatics. Preface.

Int Rev Neurobiol 2012 ;103:xi-xii

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http://dx.doi.org/10.1016/B978-0-12-388408-4.09986-XDOI Listing
May 2013

Dealing with data: a case study on information and data management literacy.

PLoS Biol 2012 29;10(5):e1001339. Epub 2012 May 29.

Library, Oregon Health & Science University, Portland, Oregon, USA.

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http://dx.doi.org/10.1371/journal.pbio.1001339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3362643PMC
August 2012

Research resources: curating the new eagle-i discovery system.

Database (Oxford) 2012 20;2012:bar067. Epub 2012 Mar 20.

Oregon Health & Science University, Library, LIB, 3181 S.W. Sam Jackson Park Rd., Portland, OR 97239-3098, USA.

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http://dx.doi.org/10.1093/database/bar067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308157PMC
June 2012

Uberon, an integrative multi-species anatomy ontology.

Genome Biol 2012 Jan 31;13(1):R5. Epub 2012 Jan 31.

Genomics Division, Lawrence Berkeley National Laboratory, 1 Cycltotron Road MS 64-121, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/gb-2012-13-1-r5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334586PMC
January 2012

Integrating phenotype ontologies across multiple species.

Genome Biol 2010 Jan 8;11(1):R2. Epub 2010 Jan 8.

Genome Dynamics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/gb-2010-11-1-r2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847714PMC
January 2010

Linking human diseases to animal models using ontology-based phenotype annotation.

PLoS Biol 2009 Nov 24;7(11):e1000247. Epub 2009 Nov 24.

Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

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http://dx.doi.org/10.1371/journal.pbio.1000247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774506PMC
November 2009

An F-domain introduced by alternative splicing regulates activity of the zebrafish thyroid hormone receptor alpha.

Gen Comp Endocrinol 2008 Jan 27;155(1):176-89. Epub 2007 Apr 27.

Institute of Molecular Biology, University of Oregon, Eugene, OR 97403-1229, USA.

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http://dx.doi.org/10.1016/j.ygcen.2007.04.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758257PMC
January 2008

Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish.

J Exp Zool B Mol Dev Evol 2007 Sep;308(5):655-68

Department of Biology, University of South Dakota, Vermillion, South Dakota 57069, USA.

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http://dx.doi.org/10.1002/jez.b.21181DOI Listing
September 2007

OBO-Edit--an ontology editor for biologists.

Bioinformatics 2007 Aug 1;23(16):2198-200. Epub 2007 Jun 1.

Berkeley Bioinformatics and Ontology Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm112DOI Listing
August 2007

Phenotype ontologies: the bridge between genomics and evolution.

Trends Ecol Evol 2007 Jul 9;22(7):345-50. Epub 2007 Apr 9.

Department of Biology, University of South Dakota, Vermillion, SD 57069, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S016953470700104
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http://dx.doi.org/10.1016/j.tree.2007.03.013DOI Listing
July 2007

Leukaemia inhibitory factor (LIF) is functionally linked to axotrophin and both LIF and axotrophin are linked to regulatory immune tolerance.

FEBS Lett 2005 Jan;579(3):609-14

Department of Surgery, University of Cambridge, Box 202, Level E9, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, UK.

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http://dx.doi.org/10.1016/j.febslet.2004.12.027DOI Listing
January 2005

Developmental toxicity of the dithiocarbamate pesticide sodium metam in zebrafish.

Toxicol Sci 2004 Oct 16;81(2):390-400. Epub 2004 Jun 16.

Linus Pauling Institute, Marine/Freshwater Biomedical Sciences Center, 571 Weniger Hall, Oregon State University, Corvallis, Oregon 97331, USA.

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https://academic.oup.com/toxsci/article-lookup/doi/10.1093/t
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http://dx.doi.org/10.1093/toxsci/kfh202DOI Listing
October 2004

Slow degeneration of zebrafish Rohon-Beard neurons during programmed cell death.

Dev Dyn 2004 Jan;229(1):30-41

Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA.

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http://dx.doi.org/10.1002/dvdy.10488DOI Listing
January 2004