Works by Lewis, Suzanna

Results: 46

Finding Our Way through Phenotypes.

Published in:

2015

By:

Deans, Andrew R.;
Lewis, Suzanna E.;
Huala, Eva;
Anzaldo, Salvatore S.;
Ashburner, Michael;
Balhoff, James P.;
Blackburn, David C.;
Blake, Judith A.;
Burleigh, J. Gordon;
Chanet, Bruno;
Cooper, Laurel D.;
Courtot, Mélanie;
Csösz, Sándor;
Cui, Hong;
Dahdul, Wasila;
Das, Sandip;
Dececchi, T. Alexander;
Dettai, Agnes;
Diogo, Rui;
Druzinsky, Robert E.

Publication type:

Opinion

Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation.

Published in:

PLoS Biology, 2009, v. 7, n. 11, p. 1, doi. 10.1371/journal.pbio.1000247

By:

Washington, Nicole L.;
Haendel, Melissa A.;
Mungall, Christopher J.;
Ashburner, Michael;
Westerfield, Monte;
Lewis, Suzanna E.

Publication type:

Article

The environment ontology: contextualising biological and biomedical entities.

Published in:

Journal of Biomedical Semantics, 2013, v. 4, n. 1, p. 2, doi. 10.1186/2041-1480-4-43

By:

Buttigieg, Pier Luigi;
Morrison, Norman;
Smith, Barry;
Mungall, Christopher J.;
Lewis, Suzanna E.

Publication type:

Article

Wrestling with SUMO and bio-ontologies.

Published in:

2006

By:

Musen, Mark A.;
Lewis, Suzanna;
Smith, Barry

Publication type:

Letter

modMine: flexible access to modENCODE data.

Published in:

Nucleic Acids Research, 2012, p. D1082, doi. 10.1093/nar/gkr921

By:

Contrino, Sergio;
Smith, Richard N.;
Butano, Daniela;
Carr, Adrian;
Hu, Fengyuan;
Lyne, Rachel;
Rutherford, Kim;
Kalderimis, Alex;
Sullivan, Julie;
Carbon, Seth;
Kephart, Ellen T.;
Lloyd, Paul;
Stinson, E. O.;
Washington, Nicole L.;
Perry, Marc D.;
Ruzanov, Peter;
Zha, Zheng;
Lewis, Suzanna E.;
Stein, Lincoln D.;
Micklem, Gos

Publication type:

Article

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium.

Published in:

Nucleic Acids Research, 2010, v. 38, p. D204, doi. 10.1093/nar/gkp1019

By:

Huaiyu Mi;
Qing Dong;
Muruganujan, Anushya;
Gaudet, Pascale;
Lewis, Suzanna;
Thomas, Paul D.

Publication type:

Article

Reactome knowledgebase of human biological pathways and processes.

Published in:

Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D619, doi. 10.1093/nar/gkn863

By:

Matthews, Lisa;
Gopinath, Gopal;
Gillespie, Marc;
Caudy, Michael;
Croft, David;
de Bono, Bernard;
Garapati, Phani;
Hemish, Jill;
Hermjakob, Henning;
Jassal, Bijay;
Kanapin, Alex;
Lewis, Suzanna;
Mahajan, Shahana;
May, Bruce;
Schmidt, Esther;
Vastrik, Imre;
Wu, Guanming;
Birney, Ewan;
Stein, Lincoln;
D’Eustachio, Peter

Publication type:

Article

Gene Ontology: tool for the unification of biology.

Published in:

Nature Genetics, 2000, v. 25, n. 1, p. 25, doi. 10.1038/75556

By:

Ashburner, Michael;
Ball, Catherine A.;
Blake, Judith A.;
Botstein, David;
Butler, Heather;
Cherry, J. Michael;
Davis, Allan P.;
Dolinski, Kara;
Dwight, Selina S.;
Eppig, Janan T.;
Harris, Midori A.;
Hill, David P.;
Issel-Tarver, Laurie;
Kasarskis, Andrew;
Lewis, Suzanna;
Matese, John C.;
Richardson, Joel E.;
Ringwald, Martin;
Rubin, Gerald M.

Publication type:

Article

OBO-Edit an ontology editor for biologists.

Published in:

Bioinformatics, 2007, v. 23, n. 16, p. 2198

By:

John Day-Richter;
Midori A. Harris;
Melissa Haendel;
The Gene Ontology OBO-Edit Working Group;
Suzanna Lewis

Publication type:

Article

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

Published in:

Genome Biology & Evolution, 2015, v. 7, n. 7, p. 1988, doi. 10.1093/gbe/evv121

By:

Boeckmann, Brigitte;
Marcet-Houben, Marina;
Rees, Jonathan A.;
Forslund, Kristoffer;
Huerta-Cepas, Jaime;
Muffato, Matthieu;
Yilmaz, Pelin;
Xenarios, Ioannis;
Bork, Peer;
Lewis, Suzanna E.;
Gabaldón, Toni

Publication type:

Article

Graft-vs-host Disease and Toxic Epidermal Necrolysis Following Hematopoietic Stem Cell Transplantation.

Published in:

2022

By:

Vera, Nora;
Lewis, Suzanna;
Seminario-Vidal, Lucia

Publication type:

Case Study

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

Published in:

Briefings in Bioinformatics, 2011, v. 12, n. 5, p. 449, doi. 10.1093/bib/bbr042

By:

Gaudet, Pascale;
Livstone, Michael S.;
Lewis, Suzanna E.;
Thomas, Paul D.

Publication type:

Article

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

Published in:

Science Translational Medicine, 2014, v. 6, n. 252, p. 1, doi. 10.1126/scitranslmed.3009262

By:

Zemojtel, Tomasz;
Köhler, Sebastian;
Mackenroth, Luisa;
Jäger, Marten;
Hecht, Jochen;
Krawitz, Peter;
Graul-Neumann, Luitgard;
Doelken, Sandra;
Ehmke, Nadja;
Spielmann, Malte;
Øien, Nancy Christine;
Schweiger, Michal R.;
Krüger, Ulrike;
Frommer, Götz;
Fischer, Björn;
Kornak, Uwe;
Flöttmann, Ricarda;
Ardeshirdavani, Amin;
Moreau, Yves;
Lewis, Suzanna E.

Publication type:

Article

Large-Scale Trends in the Evolution<br /> of Gene Structures within 11 Animal Genomes.

Published in:

PLoS Computational Biology, 2006, v. 2, n. 3, p. e15, doi. 10.1371/journal.pcbi.0020015

By:

Yandell, Mark;
Mungall, Chris J.;
Smith, Chris;
Prochnik, Simon;
Kaminker, Joshua;
Hartzell, George;
Lewis, Suzanna;
Rubin, Gerald M.

Publication type:

Article

MSAViewer: interactive JavaScript visualization of multiple sequence alignments.

Published in:

Bioinformatics, 2016, v. 32, n. 22, p. 3501, doi. 10.1093/bioinformatics/btw474

By:

Yachdav, Guy;
Wilzbach, Sebastian;
Rauscher, Benedikt;
Sheridan, Robert;
Sillitoe, Ian;
Procter, James;
Lewis, Suzanna E.;
Rost, Burkhard;
Goldberg, Tatyana

Publication type:

Article

Apollo: a community resource for genome annotation editing.

Published in:

Bioinformatics, 2009, v. 25, n. 14, p. 1836, doi. 10.1093/bioinformatics/btp314

By:

Lee Ed;
Harris Nomi;
Gibson Mark;
Chetty Raymond;
Lewis Suzanna

Publication type:

Article

AmiGO: online access to ontology and annotation data.

Published in:

Bioinformatics, 2009, v. 25, n. 2, p. 288

By:

Seth Carbon;
Amelia Ireland;
Christopher J. Mungall;
ShengQiang Shu;
Brad Marshall;
Suzanna Lewis;
the AmiGO Hub;
the Web Presence Working Group

Publication type:

Article

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

Published in:

Frontiers in Neuroinformatics, 2013, v. 7, p. 1, doi. 10.3389/fninf.2013.00007

By:

Maynard, Sarah M.;
Mungall, Christopher J.;
Lewis, Suzanna E.;
Imam, Fahim T.;
Martone, Maryann E.

Publication type:

Article

Use of animal models for exome prioritization of rare disease genes

Published in:

Orphanet Journal of Rare Diseases, 2014, v. 9, n. 1, p. 1, doi. 10.1186/1750-1172-9-S1-O19

By:

Smedley, Damian;
Kohler, Sebastian;
Bone, William;
Oellrich, Anika;
Jacobsen, Jules;
Genetics Project, Sanger Mouse;
Kai Wang;
Mungall, Chris;
Washington, Nicole;
Bauer, Sebastian;
Seelow, Dominic;
Krawitz, Peter;
Boerkel, Cornelius;
Gilissen, Christian;
Haendel, Melissa;
Lewis, Suzanna E;
Robinson, Peter N

Publication type:

Article

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

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0097-6

By:

Buttigieg, Pier Luigi;
Pafilis, Evangelos;
Lewis, Suzanna E.;
Schildhauer, Mark P.;
Walls, Ramona L.;
Mungall, Christopher J.

Publication type:

Article

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.

Published in:

Journal of Biomedical Semantics, 2014, v. 5, n. 1, p. 1, doi. 10.1186/2041-1480-5-21

By:

Haendel, Melissa A.;
Balhoff, James P.;
Bastian, Frederic B.;
Blackburn, David C.;
Blake, Judith A.;
Bradford, Yvonne;
Comte, Aurelie;
Dahdul, Wasila M.;
Dececchi, Thomas A.;
Druzinsky, Robert E.;
Hayamizu, Terry F.;
Ibrahim, Nizar;
Lewis, Suzanna E.;
Mabee, Paula M.;
Niknejad, Anne;
Robinson-Rechavi, Marc;
Sereno, Paul C.;
Mungall, Christopher J.

Publication type:

Article

Survey-based naming conventions for use in OBO Foundry ontology development.

Published in:

BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-125

By:

Schober, Daniel;
Smith, Barry;
Lewis, Suzanna E.;
Kusnierczyk, Waclaw;
Lomax, Jane;
Mungall, Chris;
Taylor, Chris F.;
Rocca-Serra, Philippe;
Sansone, Susanna-Assunta

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2012, v. 8, n. 2, p. 1, doi. 10.1371/journal.pcbi.1002386

By:

Thomas, Paul D.;
Wood, Valerie;
Mungall, Christopher J.;
Lewis, Suzanna E.;
Blake, Judith A.

Publication type:

Article

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.

Published in:

Nucleic Acids Research, 2017, v. 45, n. D1, p. D712, doi. 10.1093/nar/gkw1128

By:

Mungall, Christopher J.;
McMurry, Julie A.;
Köhler3, Sebastian;
Balhoff, James P.;
Borromeo, Charles;
Brush, Matthew;
Carbon, Seth;
Conlin, Tom;
Dunn, Nathan;
Engelstad, Mark;
Foster, Erin;
Gourdine, J. P.;
Jacobsen, Julius O. B.;
Keith, Dan;
Laraway, Bryan;
Lewis, Suzanna E.;
NguyenXuan, Jeremy;
Shefchek, Kent;
Vasilevsky, Nicole;
Zhou Yuan

Publication type:

Article

JBrowse: a dynamic web platform for genome visualization and analysis.

Published in:

Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-0924-1

By:

Buels, Robert;
Yao, Eric;
Diesh, Colin M.;
Hayes, Richard D.;
Munoz-Torres, Monica;
Helt, Gregg;
Goodstein, David M.;
Elsik, Christine G.;
Lewis, Suzanna E.;
Stein, Lincoln;
Holmes, Ian H.

Publication type:

Article

Deletions of chromosomal regulatory boundaries are associated with congenital disease.

Published in:

Genome Biology, 2014, v. 15, n. 7, p. 423, doi. 10.1186/s13059-014-0423-1

By:

Ibn-Salem, Jonas;
Köhler, Sebastian;
Love, Michael I.;
Ho-Ryun Chung;
Ni Huang;
Hurles, Matthew E.;
Haendel, Melissa;
Washington, Nicole L.;
Smedley, Damian;
Mungall, Christopher J.;
Lewis, Suzanna E.;
Ott, Claus-Eric;
Bauer, Sebastian;
Schofield, Paul N.;
Mundlos, Stefan;
Spielmann, Malte;
Robinson, Peter N.

Publication type:

Article

Web Apollo: a web-based genomic annotation editing platform.

Published in:

Genome Biology, 2013, v. 14, n. 8, p. R93, doi. 10.1186/gb-2013-14-8-r93

By:

Eduardo Lee;
Helt, Gregg A;
Reese, Justin T;
Munoz-Torres, Monica C;
Childers, Chris P;
Buels, Robert M;
Stein, Lincoln;
Holmes, Ian H;
Elsik, Christine G;
Lewis, Suzanna E

Publication type:

Article

Uberon, an integrative multi-species anatomy ontology.

Published in:

Genome Biology, 2012, v. 13, n. 1, p. 1, doi. 10.1186/gb-2012-13-1-r5

By:

Mungall, Christopher J.;
Torniai, Carlo;
Gkoutos, Georgios V.;
Lewis, Suzanna E.;
Haendel, Melissa A.

Publication type:

Article

Practical and effective diagnosis of animal anthrax in endemic low-resource settings.

Published in:

PLoS Neglected Tropical Diseases, 2020, v. 14, n. 9, p. 1, doi. 10.1371/journal.pntd.0008655

By:

Aminu, Olubunmi R.;
Lembo, Tiziana;
Zadoks, Ruth N.;
Biek, Roman;
Lewis, Suzanna;
Kiwelu, Ireen;
Mmbaga, Blandina T.;
Mshanga, Deogratius;
Shirima, Gabriel;
Denwood, Matt;
Forde, Taya L.

Publication type:

Article

Apollo: Democratizing genome annotation.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006790

By:

Dunn, Nathan A.;
Unni, Deepak R.;
Diesh, Colin;
Munoz-Torres, Monica;
Harris, Nomi L.;
Yao, Eric;
Rasche, Helena;
Holmes, Ian H.;
Elsik, Christine G.;
Lewis, Suzanna E.

Publication type:

Article

Real‐world drug survival and reasons for treatment discontinuation of biologics and apremilast in patients with psoriasis in an academic center.

Published in:

Dermatologic Therapy, 2021, v. 34, n. 2, p. 1, doi. 10.1111/dth.14826

By:

Zeb, Lawangeen;
Mhaskar, Rahul;
Lewis, Suzanna;
Patel, Nishit S.;
Sadhwani, Divya;
Patel, Nupur;
Ekhlassi, Erfon;
Lu, Yuanyuan;
Seminario‐Vidal, Lucia

Publication type:

Article

Modelling data across labs, genomes, space and time.

Published in:

Nature Cell Biology, 2006, v. 8, n. 11, p. 1190, doi. 10.1038/ncb1496

By:

Swedlow, Jason R.;
Lewis, Suzanna E.;
Goldberg, Ilya G.

Publication type:

Article

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.

Published in:

Database: The Journal of Biological Databases & Curation, 2021, v. 2021, p. 1, doi. 10.1093/database/baab069

By:

Jackson, Rebecca;
Matentzoglu, Nicolas;
Overton, James A;
Vita, Randi;
Balhoff, James P;
Buttigieg, Pier Luigi;
Carbon, Seth;
Courtot, Melanie;
Diehl, Alexander D;
Dooley, Damion M;
Duncan, William D;
Harris, Nomi L;
Haendel, Melissa A;
Lewis, Suzanna E;
Natale, Darren A;
Osumi-Sutherland, David;
Ruttenberg, Alan;
Schriml, Lynn M;
Smith, Barry;
Stoeckert Jr., Christian J

Publication type:

Article

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

Published in:

Database: The Journal of Biological Databases & Curation, 2016, v. 2016, p. 1, doi. 10.1093/database/baw155

By:

Feuermann, Marc;
Gaudet, Pascale;
Huaiyu Mi;
Lewis, Suzanna E.;
Thomas, Paul D.

Publication type:

Article

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

Published in:

Database: The Journal of Biological Databases & Curation, 2015, v. 2015, p. 1, doi. 10.1093/database/bav043

By:

Bastian, Frederic B.;
Chibucos, Marcus C.;
Gaudet, Pascale;
Giglio, Michelle;
Holliday, Gemma L.;
Hong Huang;
Lewis, Suzanna E.;
Niknejad, Anne;
Orchard, Sandra;
Poux, Sylvain;
Skunca, Nives;
Robinson-Rechavi, Marc

Publication type:

Article

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

Published in:

Database: The Journal of Biological Databases & Curation, 2014, v. 2014, p. 1, doi. 10.1093/database/bau075

By:

Chibucos, Marcus C.;
Mungall, Christopher J.;
Balakrishnan, Rama;
Christie, Karen R.;
Huntley, Rachael P.;
White, Owen;
Blake, Judith A.;
Lewis, Suzanna E.;
Giglio, Michelle

Publication type:

Article

PhenoDigm: analyzing curated annotations to associate animal models with human diseases.

Published in:

Database: The Journal of Biological Databases & Curation, 2013, v. 2013, p. 1, doi. 10.1093/database/bat025

By:

Smedley, Damian;
Oellrich, Anika;
Köhler, Sebastian;
Ruef, Barbara;
Genetics Project, Sanger Mouse;
Westerfield, Monte;
Robinson, Peter;
Lewis, Suzanna;
Mungall, Christopher

Publication type:

Article

The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details.

Published in:

Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 23, p. 1

By:

Washington, Nicole L.;
Stinson, E. O.;
Perry, Marc D.;
Ruzanov, Peter;
Contrino, Sergio;
Smith, Richard;
Zha, Zheng;
Lyne, Rachel;
Carr, Adrian;
Lloyd, Paul;
Kephart, Ellen;
McKay, Sheldon J.;
Micklem, Gos;
Stein, Lincoln D.;
Lewis, Suzanna E.

Publication type:

Article

The RNA Ontology Consortium: An open invitation to the RNA community.

Published in:

Journal of Nuclear Medicine Technology, 2006, v. 34, n. 1, p. 1

By:

Leontis, Neocles B.;
Altman, Russ B.;
Berman, Helen M.;
Brenner, Steven E.;
Brown, James W.;
Engelke, David R.;
Harvey, Stephen C.;
Holbrook, Stephen R.;
Jossinet, Fabrice;
Lewis, Suzanna E.;
Major, François;
Mathews, David H.;
Richardson, Jane S.;
Williamson, James R.;
Westhof, Eric

Publication type:

Article

Navigating the Phenotype Frontier: The Monarch Initiative.

Published in:

Genetics, 2016, v. 203, n. 4, p. 1491, doi. 10.1534/genetics.116.188870

By:

McMurry, Julie A.;
Köhler, Sebastian;
Washington, Nicole L.;
Balhoff, James P.;
Borromeo, Charles;
Brush, Matthew;
Carbon, Seth;
Conlin, Tom;
Dunn, Nathan;
Engelstad, Mark;
Foster, Erin;
Gourdine, Jean-Philippe;
Jacobsen, Julius O. B.;
Keith, Daniel;
Laraway, Bryan;
Nguyen Xuan, Jeremy;
Shefchek, Kent;
Vasilevsky, Nicole A.;
Zhou Yuan;
Lewis, Suzanna E.

Publication type:

Article

Anatomy of BioJS, an open source community for the life sciences.

Published in:

2015

By:

YACHDAV, GUY;
GOLDBERG, TATYANA;
WILZBACH, SEBASTIAN;
DAO, DAVID;
SHIH, IRIS;
CHOUDHARY, SAKET;
CROUCH, STEVE;
FRANZ, MAX;
GARCÍA, ALEXANDER;
GARCIA, LEYLA J.;
GRÜNING, BJÖRN A.;
INUPAKUTIKA, DEVASENA;
SILLITOE, IAN;
THANKI, ANIL S.;
VIEIRA, BRUNO;
VILLAVECES, JOSÉ M.;
SCHNEIDER, MARIA V.;
LEWIS, SUZANNA;
PETTIFER, STEVE;
ROST, BURKHARD

Publication type:

Product Review

Coxsackie Eruption Arising in Areas of Epidermolytic Ichthyosis.

Published in:

Pediatric Dermatology, 2015, v. 32, n. 3, p. e132, doi. 10.1111/pde.12562

By:

Lewis, Suzanna;
Rico, Tace

Publication type:

Article

Disease insights through cross-species phenotype comparisons.

Published in:

Mammalian Genome, 2015, v. 26, n. 9/10, p. 548, doi. 10.1007/s00335-015-9577-8

By:

Haendel, Melissa;
Vasilevsky, Nicole;
Brush, Matthew;
Hochheiser, Harry;
Jacobsen, Julius;
Oellrich, Anika;
Mungall, Christopher;
Washington, Nicole;
Köhler, Sebastian;
Lewis, Suzanna;
Robinson, Peter;
Smedley, Damian

Publication type:

Article

Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery.

Published in:

Human Mutation, 2015, v. 36, n. 10, p. 979, doi. 10.1002/humu.22857

By:

Mungall, Christopher J.;
Washington, Nicole L.;
Nguyen‐Xuan, Jeremy;
Condit, Christopher;
Smedley, Damian;
Köhler, Sebastian;
Groza, Tudor;
Shefchek, Kent;
Hochheiser, Harry;
Robinson, Peter N.;
Lewis, Suzanna E.;
Haendel, Melissa A.

Publication type:

Article

Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis.

Published in:

Human Molecular Genetics, 2010, v. 19, n. 4, p. 707, doi. 10.1093/hmg/ddp521

By:

Karp, David R.;
Marthandan, Nishanth;
Marsh, Steven G.E.;
Ahn, Chul;
Arnett, Frank C.;
DeLuca, David S.;
Diehl, Alexander D.;
Dunivin, Raymond;
Eilbeck, Karen;
Feolo, Michael;
Guidry, Paula A.;
Helmberg, Wolfgang;
Lewis, Suzanna;
Mayes, Maureen D.;
Mungall, Chris;
Natale, Darren A.;
Peters, Bjoern;
Petersdorf, Effie;
Reveille, John D.;
Smith, Barry

Publication type:

Article

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.

Published in:

Nature Biotechnology, 2007, v. 25, n. 11, p. 1251, doi. 10.1038/nbt1346

By:

Smith, Barry;
Ashburner, Michael;
Rosse, Cornelius;
Bard, Jonathan;
Bug, William;
Ceusters, Werner;
Goldberg, Louis J.;
Eilbeck, Karen;
Ireland, Amelia;
Mungall, Christopher J.;
Leontis, Neocles;
Rocca-Serra, Philippe;
Ruttenberg, Alan;
Sansone, Susanna-Assunta;
Scheuermann, Richard H.;
Nigam Shah;
Whetzel, Patricia L.;
Lewis, Suzanna

Publication type:

Article