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ORCIDSuzanna Lewis
Suzanna E. Lewis
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- affiliation: Lawrence Berkeley National Laboratory, CA, USA
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2020 – today
- 2021
[j32]Rebecca C. Jackson
, Nicolas Matentzoglu, James A. Overton, Randi Vita, James P. Balhoff, Pier Luigi Buttigieg, Seth Carbon, Mélanie Courtot, Alexander D. Diehl, Damion M. Dooley, William D. Duncan, Nomi L. Harris, Melissa A. Haendel, Suzanna E. Lewis, Darren A. Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M. Schriml, Barry Smith, Christian J. Stoeckert Jr., Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall, Bjoern Peters:
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. Database J. Biol. Databases Curation 2021 (2021)- 2020
- [j31]Kent A. Shefchek, Nomi L. Harris, Michael A. Gargano, Nicolas Matentzoglu, Deepak R. Unni, Matthew H. Brush, Dan Keith, Tom Conlin, Nicole A. Vasilevsky, Xingmin Aaron Zhang, James P. Balhoff, Larry Babb, Susan M. Bello, Hannah Blau, Yvonne M. Bradford, Seth Carbon, Leigh Carmody, Lauren E. Chan, Valentina Cipriani, Alayne Cuzick, Maria G. Della Rocca, Nathan A. Dunn, Shahim Essaid, Petra Fey, Christian A. Grove, Jean-Philippe F. Gourdine, Ada Hamosh, Midori A. Harris, Ingo Helbig, Maureen E. Hoatlin, Marcin P. Joachimiak, Simon Jupp, Kenneth B. Lett, Suzanna E. Lewis, Craig McNamara, Zoë May Pendlington, Clare Pilgrim, Tim E. Putman, Vida Ravanmehr, Justin T. Reese, Erin Rooney Riggs, Sofia M. C. Robb, Paola Roncaglia, James Seager, Erik Segerdell, Morgan Similuk, Andrea L. Storm, Courtney Thaxon, Anne E. Thessen, Julius O. B. Jacobsen, Julie A. McMurry, Tudor Groza, Sebastian Köhler, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel, Monica C. Munoz-Torres, David Osumi-Sutherland:
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 48(Database-Issue): D704-D715 (2020)
2010 – 2019
- 2019
- [j30]Nathan A. Dunn, Deepak R. Unni, Colin M. Diesh, Monica C. Munoz-Torres, Nomi L. Harris, Eric Yao, Helena Rasche, Ian H. Holmes, Christine G. Elsik, Suzanna E. Lewis:
Apollo: Democratizing genome annotation. PLoS Comput. Biol. 15(2) (2019) - 2018
- [j29]Kristoffer Forslund, Cécile Pereira, Salvador Capella-Gutiérrez, Alan W. Sousa da Silva, Adrian M. Altenhoff, Jaime Huerta-Cepas, Matthieu Muffato, Mateus Patricio, Klaas Vandepoele, Ingo Ebersberger, Judith A. Blake, Jesualdo Tomás Fernández-Breis, The Quest for Orthologs Consortium, Brigitte Boeckmann, Toni Gabaldón, Erik L. L. Sonnhammer, Christophe Dessimoz, Suzanna Lewis:
Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinform. 34(2): 323-329 (2018) - 2017
- [j28]Christopher J. Mungall, Julie A. McMurry, Sebastian Köhler, James P. Balhoff, Charles D. Borromeo, Matthew H. Brush, Seth Carbon, Tom Conlin, Nathan A. Dunn, Mark Engelstad, Erin Foster, Jean-Philippe F. Gourdine, Julius O. B. Jacobsen, Dan Keith, Bryan Laraway, Suzanna E. Lewis, Jeremy NguyenXuan, Kent A. Shefchek, Nicole A. Vasilevsky, Zhou Yuan, Nicole L. Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N. Robinson, Melissa A. Haendel:
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 45(Database-Issue): D712-D722 (2017) - [i3]Philippa C. Griffin, Jyoti Khadake, Kate S. LeMay, Suzanna E. Lewis, Sandra E. Orchard, Andrew Pask, Bernard J. Pope, Ute Roessner, Keith Russell, Torsten Seemann, Andrew E. Treloar, Sonika Tyagi, Jeffrey H. Christiansen, Saravanan Dayalan, Simon Gladman, Sandra B. Hangartner, Helen L. Hayden, William W. H. Ho, Gabriel Keeble-Gagnère, Pasi K. Korhonen, Peter Neish, Priscilla R. Prestes, Mark F. Richardson, Nathan S. Watson-Haigh, Kelly L. Wyres, Neil D. Young, Maria Victoria Schneider:
Best practice data life cycle approaches for the life sciences. F1000Research 6: 1618- (2017) - 2016
- [j27]Marc Feuermann, Pascale Gaudet, Huaiyu Mi, Suzanna E. Lewis, Paul D. Thomas:
Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes. Database J. Biol. Databases Curation 2016 (2016) - [j26]Guy Yachdav, Sebastian Wilzbach, Benedikt Rauscher, Robert Sheridan, Ian Sillitoe, James B. Procter, Suzanna E. Lewis, Burkhard Rost, Tatyana Goldberg:
MSAViewer: interactive JavaScript visualization of multiple sequence alignments. Bioinform. 32(22): 3501-3503 (2016) - [j25]Pier Luigi Buttigieg, Evangelos Pafilis, Suzanna E. Lewis, Mark P. Schildhauer, Ramona L. Walls, Christopher J. Mungall:
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. J. Biomed. Semant. 7: 57 (2016) - 2015
- [j24]Frederic B. Bastian, Marcus C. Chibucos, Pascale Gaudet, Michelle G. Giglio, Gemma L. Holliday, Hong Huang, Suzanna E. Lewis, Anne Niknejad, Sandra E. Orchard, Sylvain Poux, Nives Skunca, Marc Robinson-Rechavi:
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database J. Biol. Databases Curation 2015 (2015) - 2014
- [j23]Marcus C. Chibucos, Christopher J. Mungall, Rama Balakrishnan, Karen R. Christie, Rachael P. Huntley, Owen White, Judith A. Blake, Suzanna E. Lewis, Michelle G. Giglio:
Standardized description of scientific evidence using the Evidence Ontology (ECO). Database J. Biol. Databases Curation 2014 (2014) - [j22]Melissa A. Haendel, James P. Balhoff, Frederic B. Bastian, David C. Blackburn, Judith A. Blake, Yvonne M. Bradford, Aurélie Comte, Wasila M. Dahdul, Thomas Dececchi, Robert E. Druzinsky, Terry F. Hayamizu, Nizar Ibrahim, Suzanna E. Lewis, Paula M. Mabee, Anne Niknejad, Marc Robinson-Rechavi, Paul C. Sereno, Christopher J. Mungall:
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J. Biomed. Semant. 5: 21 (2014) - [j21]Anika Oellrich, Sebastian Köhler, Nicole L. Washington, Chris Mungall, Suzanna Lewis, Melissa A. Haendel, Peter N. Robinson, Damian Smedley:
The influence of disease categories on gene candidate predictions from model organism phenotypes. J. Biomed. Semant. 5(S-1): S4 (2014) - [j20]Sebastian Köhler, Sandra C. Doelken, Christopher J. Mungall, Sebastian Bauer, Helen V. Firth, Isabelle Bailleul-Forestier, Graeme C. M. Black, Danielle L. Brown, Michael Brudno, Jennifer Campbell, David R. FitzPatrick, Janan T. Eppig, Andrew P. Jackson, Kathleen Freson, Marta Gîrdea, Ingo Helbig, Jane A. Hurst, Johanna Jähn, Laird G. Jackson, Anne M. Kelly, David H. Ledbetter, Sahar Mansour, Christa L. Martin, Celia Moss, Andrew D. Mumford, Willem H. Ouwehand, Soo-Mi Park, Erin Rooney Riggs, Richard H. Scott, Sanjay Sisodiya, Steven Van Vooren, Ronald J. Wapner, Andrew O. M. Wilkie, Caroline F. Wright, Anneke T. Vulto-van Silfhout, Nicole de Leeuw, Bert B. A. de Vries, Nicole L. Washington, Cynthia L. Smith, Monte Westerfield, Paul N. Schofield, Barbara J. Ruef, Georgios V. Gkoutos, Melissa A. Haendel, Damian Smedley, Suzanna E. Lewis, Peter N. Robinson:
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 42(Database-Issue): 966-974 (2014) - [i2]Manuel Corpas, Rafael C. Jiménez, Seth Carbon, Alexander García Castro, Leyla Jael Castro, Tatyana Goldberg, John Gómez, Alex Kalderimis, Suzanna E. Lewis, Ian Mulvany, Aleksandra Pawlik, Francis Rowland, Gustavo A. Salazar, Fabian Schreiber, Ian Sillitoe, William Spooner, Anil S. Thanki, Jose M. Villaveces, Guy Yachdav, Henning Hermjakob:
BioJS: an open source standard for biological visualisation - its status in 2014. F1000Research 3: 55 (2014) - 2013
- [j19]Damian Smedley, Anika Oellrich, Sebastian Köhler, Barbara J. Ruef, Monte Westerfield, Peter N. Robinson, Suzanna Lewis, Christopher J. Mungall:
PhenoDigm: analyzing curated annotations to associate animal models with human diseases. Database J. Biol. Databases Curation 2013 (2013) - [j18]Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J. Mungall, Suzanna E. Lewis:
The environment ontology: contextualising biological and biomedical entities. J. Biomed. Semant. 4: 43 (2013) - [j17]Sarah Maynard, Christopher J. Mungall, Suzanna E. Lewis, Fahim T. Imam, Maryann E. Martone:
A knowledge based approach to matching human neurodegenerative disease and animal models. Frontiers Neuroinformatics 7: 7 (2013) - 2012
- [j16]Sergio Contrino, Richard N. Smith, Daniela Butano, Adrian Carr, Fengyuan Hu, Rachel Lyne, Kim Rutherford, Alex Kalderimis, Julie M. Sullivan, Seth Carbon, Ellen T. Kephart, Paul Lloyd, E. O. Stinson, Nicole L. Washington, Marc D. Perry, Peter Ruzanov, Zheng Zha, Suzanna E. Lewis, Lincoln D. Stein, Gos Micklem:
modMine: flexible access to modENCODE data. Nucleic Acids Res. 40(Database-Issue): 1082-1088 (2012) - [j15]Paul D. Thomas, Valerie Wood, Christopher J. Mungall, Suzanna E. Lewis, Judith A. Blake:
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS Comput. Biol. 8(2) (2012) - 2011
- [j14]Pascale Gaudet, Michael S. Livstone, Suzanna E. Lewis, Paul D. Thomas:
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings Bioinform. 12(5): 449-462 (2011) - [j13]Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris F. Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane, Charles E. Cook, Janan T. Eppig, Michael Y. Galperin, Robert Gentleman, Carole A. Goble, Takashi Gojobori, John M. Hancock, Douglas G. Howe, Tadashi Imanishi, Janet Kelso, David Landsman, Suzanna E. Lewis, Ilene Karsch-Mizrachi, Sandra E. Orchard, B. F. Francis Ouellette, Shoba Ranganathan, Lorna J. Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana A. Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki:
Towards BioDBcore: a community-defined information specification for biological databases. Database J. Biol. Databases Curation 2011 (2011) - [j12]Nicole L. Washington, E. O. Stinson, Marc D. Perry, Peter Ruzanov, Sergio Contrino, Richard N. Smith, Zheng Zha, Rachel Lyne, Adrian Carr, Paul Lloyd, Ellen T. Kephart, Sheldon J. McKay, Gos Micklem, Lincoln D. Stein, Suzanna E. Lewis:
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. Database J. Biol. Databases Curation 2011 (2011) - [j11]Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris F. Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane, Charles E. Cook, Janan T. Eppig, Michael Y. Galperin, Robert Gentleman, Carole A. Goble, Takashi Gojobori, John M. Hancock, Douglas G. Howe, Tadashi Imanishi, Janet Kelso, David Landsman, Suzanna E. Lewis, Ilene Karsch-Mizrachi, Sandra E. Orchard, B. F. Francis Ouellette, Shoba Ranganathan, Lorna J. Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana A. Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki:
Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res. 39(Database-Issue): 7-10 (2011) - 2010
- [j10]Huaiyu Mi, Qing Dong, Anushya Muruganujan, Pascale Gaudet, Suzanna Lewis, Paul D. Thomas:
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 38(Database-Issue): 204-210 (2010)
2000 – 2009
- 2009
- [j9]Seth Carbon, Amelia Ireland, Christopher J. Mungall, Shengqiang Shu, Brad Marshall, Suzanna Lewis:
AmiGO: online access to ontology and annotation data. Bioinform. 25(2): 288-289 (2009) - [j8]Ed Lee, Nomi L. Harris, Mark Gibson, Raymond Chetty, Suzanna Lewis:
Apollo: a community resource for genome annotation editing. Bioinform. 25(14): 1836-1837 (2009) - [j7]Daniel Schober, Barry Smith, Suzanna E. Lewis, Waclaw Kusnierczyk, Jane Lomax, Chris Mungall, Chris F. Taylor, Philippe Rocca-Serra, Susanna-Assunta Sansone:
Survey-based naming conventions for use in OBO Foundry ontology development. BMC Bioinform. 10 (2009) - [j6]Lisa Matthews, Gopal Gopinath, Marc Gillespie, Michael Caudy, David Croft, Bernard de Bono, Phani V. Garapati, Jill Hemish, Henning Hermjakob, Bijay Jassal, Alexander Kanapin, Suzanna Lewis, Shahana Mahajan, Bruce May, Esther Schmidt, Imre Vastrik, Guanming Wu, Ewan Birney, Lincoln Stein, Peter D'Eustachio:
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 37(Database-Issue): 619-622 (2009) - 2008
- [i1]Nicole L. Washington, M. Gibson, Chris Mungall, Michael Ashburner, Georgios V. Gkoutos, Monte Westerfield, Melissa A. Haendel, Suzanna E. Lewis:
NLP and Phenotypes: using Ontologies to link Human Diseases to Animal Models. Ontologies and Text Mining for Life Sciences 2008 - 2007
- [j5]John Day-Richter, Midori A. Harris, Melissa A. Haendel, Suzanna Lewis:
OBO-Edit - an ontology editor for biologists. Bioinform. 23(16): 2198-2200 (2007) - [j4]Bernard de Bono, Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Gopal Gopinath, David Croft, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein:
Reactome: An integrated expert model of human molecular processes and access toolkit. J. Integr. Bioinform. 4(3) (2007) - 2006
- [j3]Mark Yandell, Chris Mungall, Chris Smith, Simon Prochnik, Joshua S. Kaminker, George Hartzell, Suzanna Lewis, Gerald M. Rubin:
Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes. PLoS Comput. Biol. 2(3) (2006) - [c3]Esther Schmidt, Ewan Birney, David Croft, Bernard de Bono, Peter D'Eustachio, Marc Gillespie, Gopal Gopinath, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Lincoln Stein, Imre Vastrik, Guanming Wu:
Reactome - A Knowledgebase of Biological Pathways. OTM Workshops (1) 2006: 710-719 - 2005
- [j2]G. Joshi-Tope, Marc Gillespie, Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Bernard de Bono, Bijay Jassal, Gopal R. Gopinath, G. R. Wu, Lisa Matthews, Suzanna Lewis, Ewan Birney, Lincoln Stein:
Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 33(Database-Issue): 428-432 (2005) - 2004
- [j1]Michael Bada, Robert Stevens, Carole A. Goble, Yolanda Gil, Michael Ashburner, Judith A. Blake, J. Michael Cherry, Midori A. Harris, Suzanna Lewis:
A short study on the success of the Gene Ontology. J. Web Semant. 1(2): 235-240 (2004) - 2000
- [c2]Robin McEntire, Peter D. Karp, Neil F. Abernethy, David Benton, Gregg Helt, Matt DeJongh, Robert Kent, Anthony Kosky, Suzanna Lewis, Dan Hodnett, Eric P. Neumann, Frank Olken, Dhiraj K. Pathak, Peter Tarczy-Hornoch, Luca Toldo, Thodoros Topaloglou:
An Evaluation of Ontology Exchange Languages for Bioinformatics. ISMB 2000: 239-250
1990 – 1999
- 1992
- [c1]Victor M. Markowitz, Suzanna Lewis, John L. McCarthy, Frank Olken, Manfred Zorn:
Data Management for Genomic Mapping Applications: A Case Study. SSDBM 1992: 45-57
Coauthor Index
Chris Mungall
aka: Christopher J. Mungall
aka: Christopher J. Mungall
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