Suzanna E Lewis

Suzanna E Lewis

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Suzanna E Lewis

Suzanna E Lewis

Publications by authors named "Suzanna E Lewis"

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Apollo: Democratizing genome annotation.

PLoS Comput Biol 2019 02 6;15(2):e1006790. Epub 2019 Feb 6.

Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380598PMC
February 2019

The Vision and Challenges of the Gene Ontology.

Authors:
Suzanna E Lewis

Methods Mol Biol 2017 ;1446:291-302

Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.

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http://link.springer.com/10.1007/978-1-4939-3743-1_21
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http://dx.doi.org/10.1007/978-1-4939-3743-1_21DOI Listing
December 2017

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes.

Database (Oxford) 2016 26;2016. Epub 2016 Dec 26.

Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA and.

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http://dx.doi.org/10.1093/database/baw155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199145PMC
November 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

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.

J Biomed Semantics 2016 Sep 23;7(1):57. Epub 2016 Sep 23.

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

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http://dx.doi.org/10.1186/s13326-016-0097-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5035502PMC
September 2016

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.

Database (Oxford) 2015 9;2015:bav043. Epub 2015 May 9.

Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland, Department of Medicine and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA, School of Information, University of South Florida, Tampa, FL, 33647, USA, Genomics Division, Lawrence Berkeley National Lab, 1 Cyclotron Rd., Berkeley, 94720 CA USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland, ETH Zurich, Department of Computer Science, Universitätstr. 19, 8092 Zürich, Switzerland, SIB Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zürich, Switzerland and University College London, Gower St, London WC1E 6BT, UK Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland, Department of Medicine and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA, School of Information, University of South Florida, Tampa, FL, 33647, USA, Genomics Division, Lawrence Berkeley Nat

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http://dx.doi.org/10.1093/database/bav043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425939PMC
December 2015

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

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

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Genome Biol Evol 2015 Jul 1;7(7):1988-99. Epub 2015 Jul 1.

Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain Universitat Pompeu Fabra, Barcelona, Spain Institució Catalana de Recerca I Estudis Avançats, Barcelona, Spain.

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http://dx.doi.org/10.1093/gbe/evv121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524488PMC
July 2015

Standardized description of scientific evidence using the Evidence Ontology (ECO).

Database (Oxford) 2014 22;2014. Epub 2014 Jul 22.

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Saccharomyces Genome Database, Department of Genetics, Stanford University, Stanford, CA 94305, USA, Computational Biology and Bioinformatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK, Department of Epidemiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA and Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USAInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Saccharomyces Genome Database, Department of Genetics, Stanford University, Stanford, CA 94305, USA, Computational Biology and Bioinformatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK, Department of Epidemiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA and Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.

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http://dx.doi.org/10.1093/database/bau075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105709PMC
February 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

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

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 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

The environment ontology: contextualising biological and biomedical entities.

J Biomed Semantics 2013 Dec 11;4(1):43. Epub 2013 Dec 11.

HGF-MPG Research Group on Deep-Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven 27570, Germany.

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http://dx.doi.org/10.1186/2041-1480-4-43DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3904460PMC
December 2013

A knowledge based approach to matching human neurodegenerative disease and animal models.

Front Neuroinform 2013 14;7. Epub 2013 May 14.

Department of Neurosciences, Center for Research in Biological Systems, University of California San Diego, San Diego, CA, USA.

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http://dx.doi.org/10.3389/fninf.2013.00007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3653101PMC
May 2013

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.

PLoS Comput Biol 2012 16;8(2):e1002386. Epub 2012 Feb 16.

Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280971PMC
June 2012

MouseFinder: Candidate disease genes from mouse phenotype data.

Hum Mutat 2012 May 16;33(5):858-66. Epub 2012 Mar 16.

Vertebrate Genomics Team, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://doi.wiley.com/10.1002/humu.22051
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http://dx.doi.org/10.1002/humu.22051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3327758PMC
May 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

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.

Brief Bioinform 2011 Sep 27;12(5):449-62. Epub 2011 Aug 27.

Swiss Institute for Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland.

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http://dx.doi.org/10.1093/bib/bbr042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178059PMC
September 2011

Sequence ontology annotation guide.

Comp Funct Genomics 2004 ;5(8):642-7

Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, California 94729-3200, USA.

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http://dx.doi.org/10.1002/cfg.446DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447471PMC
June 2010

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

Modelling data across labs, genomes, space and time.

Nat Cell Biol 2006 Nov;8(11):1190-4

Division of Gene Regulation and Expression, Wellcome Trust Biocentre, Faculty of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.

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http://dx.doi.org/10.1038/ncb1496DOI Listing
November 2006

The Sequence Ontology: a tool for the unification of genome annotations.

Genome Biol 2005 29;6(5):R44. Epub 2005 Apr 29.

Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729-3200, USA.

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http://dx.doi.org/10.1186/gb-2005-6-5-r44DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1175956PMC
May 2006

Gene Ontology: looking backwards and forwards.

Authors:
Suzanna E Lewis

Genome Biol 2005 15;6(1):103. Epub 2004 Dec 15.

Department of Molecular and Cell Biology, University of California, 539 Life Sciences Addition, Berkeley, CA 94720-3200, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2004-6-1-103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC549054PMC
October 2005

Systematic determination of patterns of gene expression during Drosophila embryogenesis.

Genome Biol 2002 23;3(12):RESEARCH0088. Epub 2002 Dec 23.

Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, 539 Life Sciences Addition, Berkeley, CA 94720-3200, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC151190PMC
http://dx.doi.org/10.1186/gb-2002-3-12-research0088DOI Listing
June 2003