
Sandra E. Orchard
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2020 – today
- 2021
- [j33]Vasundra Touré, Steven Vercruysse, Marcio Luis Acencio, Ruth C. Lovering, Sandra E. Orchard, Glyn Bradley, Cristina Casals-Casas, Claudine Chaouiya, Noemi del-Toro, Åsmund Flobak, Pascale Gaudet, Henning Hermjakob, Charles Tapley Hoyt, Luana Licata, Astrid Lægreid, Christopher J. Mungall, Anne Niknejad, Simona Panni, Livia Perfetto, Pablo Porras, Dexter Pratt, Julio Saez-Rodriguez, Denis Thieffry, Paul D. Thomas, Dénes Türei, Martin Kuiper:
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). Bioinform. 36(24): 5712-5718 (2021) - 2020
- [j32]Livia Perfetto, Chiara Pastrello, Noemi del-Toro
, Margaret Duesbury, Marta Iannuccelli, Max Kotlyar, Luana Licata
, Birgit Meldal
, K. Panneerselvam, Simona Panni, N. Rahimzadeh, Sylvie Ricard-Blum, Lukasz Salwínski, A. Shrivastava
, Gianni Cesareni, M. Pellegrini, Sandra E. Orchard
, Igor Jurisica, Henning Hermjakob
, Pablo Porras
:
The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. Database J. Biol. Databases Curation 2020 (2020) - [j31]Rachel Drysdale, Charles E. Cook, Robert Petryszak, Vivienne Baillie Gerritsen, Mary Barlow, Elisabeth Gasteiger, Franziska Gruhl, Jürgen Haas, Jerry Lanfear, Rodrigo Lopez
, Nicole Redaschi
, Heinz Stockinger, Daniel Teixeira, Aravind Venkatesan, Alex Bateman
, Alan Bridge, Guy Cochrane
, Robert D. Finn
, Frank Oliver Glöckner, Marc Hanauer, Thomas M. Keane, Andrew Leach, Luana Licata
, Per Oksvold, Sandra E. Orchard
, Christine A. Orengo, Helen E. Parkinson
, Bengt Persson, Pablo Porras
, Jordi Rambla, Ana Rath, Charlotte Rodwell, Ugis Sarkans
, Dietmar Schomburg, Ian Sillitoe, Dylan Spalding
, Mathias Uhlén, Sameer Velankar
, Juan Antonio Vizcaíno
, Kalle von Feilitzen, Christian von Mering, Andrew D. Yates
, Niklas Blomberg
, Christine Durinx, Johanna R. McEntyre
:
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. Bioinform. 36(8): 2636-2642 (2020)
2010 – 2019
- 2019
- [j30]Edith D. Wong
, Marek S. Skrzypek, Shuai Weng
, Gail Binkley, Birgit H. M. Meldal
, Livia Perfetto
, Sandra E. Orchard
, Stacia R. Engel
, J. Michael Cherry
, SGD Project:
Integration of macromolecular complex data into the Saccharomyces Genome Database. Database J. Biol. Databases Curation 2019: baz008 (2019) - [j29]Livia Perfetto
, Marcio Luis Acencio
, Glyn Bradley, Gianni Cesareni, Noemi del-Toro
, Dávid Fazekas, Henning Hermjakob
, Tamás Korcsmáros, Martin Kuiper, Astrid Lægreid, Prisca Lo Surdo, Ruth C. Lovering
, Sandra E. Orchard
, Pablo Porras
, Paul D. Thomas
, Vasundra Touré, John Zobolas
, Luana Licata
:
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. Bioinform. 35(19): 3779-3785 (2019) - [j28]Birgit H. M. Meldal
, Hema Bye-A-Jee
, Lukás Gajdos, Zuzana Hammerová, Aneta Horácková, Filip Melicher, Livia Perfetto
, Daniel Pokorný
, Milagros Rodriguez-Lopez
, Alzbeta Türková, Edith D. Wong, Zengyan Xie, Elisabeth Barrera Casanova
, Noemi del-Toro
, Maximilian Koch
, Pablo Porras
, Henning Hermjakob
, Sandra E. Orchard
:
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. Nucleic Acids Res. 47(Database-Issue): D550-D558 (2019) - 2018
- [j27]M. Sivade Dumousseau, Maximilian Koch
, A. Shrivastava
, Diego Alonso-López
, Javier De Las Rivas
, Noemi del-Toro
, Colin W. Combe
, Birgit H. M. Meldal
, Joshua Heimbach, Juri Rappsilber
, Julie M. Sullivan, Yo Yehudi
, Sandra E. Orchard
:
JAMI: a Java library for molecular interactions and data interoperability. BMC Bioinform. 19(1): 133:1-133:9 (2018) - [j26]M. Sivade Dumousseau, Diego Alonso-López
, Mais G. Ammari, Glyn Bradley, Nancy H. Campbell
, Arnaud Céol
, Gianni Cesareni, Colin W. Combe
, Javier De Las Rivas
, Noemi del-Toro
, Joshua Heimbach, Henning Hermjakob
, Igor Jurisica, Maximilian Koch
, Luana Licata
, Ruth C. Lovering
, David J. Lynn, Birgit H. M. Meldal
, Gos Micklem, Simona Panni, Pablo Porras
, Sylvie Ricard-Blum, Bernd Roechert, Lukasz Salwínski
, A. Shrivastava
, Julie M. Sullivan, Nicolas Thierry-Mieg
, Yo Yehudi
, Kim Van Roey, Sandra E. Orchard
:
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. BMC Bioinform. 19(1): 134:1-134:8 (2018) - 2017
- [j25]Colin W. Combe
, Marine Sivade, Henning Hermjakob
, Joshua Heimbach, Birgit H. M. Meldal
, Gos Micklem, Sandra E. Orchard, Juri Rappsilber
:
ComplexViewer: visualization of curated macromolecular complexes. Bioinform. 33(22): 3673-3675 (2017) - 2016
- [j24]Sushil Tripathi, Steven Vercruysse
, Konika Chawla, Karen R. Christie, Judith A. Blake
, Rachael P. Huntley
, Sandra E. Orchard
, Henning Hermjakob
, Liv Thommesen, Astrid Lægreid, Martin Kuiper:
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. Database J. Biol. Databases Curation 2016 (2016) - [j23]Qinghua Wang, Shabbir S. Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez
, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai, Barbra Ferrell, Juliane Fluck
, Socorro Gama-Castro, Nancy George, Georgios V. Gkoutos
, Afroza Khanam Irin, Lars Juhl Jensen
, Silvia Jimenez, Toni Rose Jue
, Ingrid M. Keseler, Sumit Madan, Sérgio Matos
, Peter McQuilton
, Marija Milacic
, Matthew E. Mort, Jeyakumar Natarajan, Evangelos Pafilis, Emiliano Pereira, Shruti Rao
, Fabio Rinaldi
, Karen Rothfels, David Salgado
, Raquel M. Silva
, Onkar Singh, Raymund Stefancsik
, Chu-Hsien Su, Suresh Subramani, Hamsa D. Tadepally, Loukia Tsaprouni, Nicole A. Vasilevsky
, Xiaodong Wang, Andrew Chatr-aryamontri, Stanley J. F. Laulederkind, Sherri Matis-Mitchell, Johanna R. McEntyre
, Sandra E. Orchard
, Sangya Pundir
, Raul Rodriguez-Esteban
, Kimberly Van Auken, Zhiyong Lu, Mary L. Schaeffer, Cathy H. Wu, Lynette Hirschman, Cecilia N. Arighi
:
Overview of the interactive task in BioCreative V. Database J. Biol. Databases Curation 2016 (2016) - 2015
- [j22]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) - [j21]Sandra E. Orchard
, Henning Hermjakob
:
Shared resources, shared costs - leveraging biocuration resources. Database J. Biol. Databases Curation 2015 (2015) - [j20]Jose M. Villaveces, Rafael C. Jimenez
, Pablo Porras, Noemi del-Toro
, Margaret Duesbury
, Marine Dumousseau, Sandra E. Orchard
, H. Choi, Peipei Ping, N. C. Zong, Manor Askenazi
, Bianca Habermann
, Henning Hermjakob
:
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. Database J. Biol. Databases Curation 2015 (2015) - [j19]Eric W. Deutsch, Juan P. Albar, Pierre-Alain Binz, Martin Eisenacher, Andrew R. Jones
, Gerhard Mayer
, Gilbert S. Omenn
, Sandra E. Orchard
, Juan Antonio Vizcaíno
, Henning Hermjakob
:
Development of data representation standards by the human proteome organization proteomics standards initiative. J. Am. Medical Informatics Assoc. 22(3): 495-506 (2015) - [j18]Birgit H. M. Meldal
, Oscar Forner-Martinez
, Maria C. Costanzo, Jose M. Dana
, Janos Demeter
, Marine Dumousseau, Selina S. Dwight, Anna Gaulton
, Luana Licata
, Anna N. Melidoni
, Sylvie Ricard-Blum, Bernd Roechert, Marek S. Skrzypek, Manu Tiwari
, Sameer Velankar
, Edith D. Wong, Henning Hermjakob
, Sandra E. Orchard:
The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database-Issue): 479-484 (2015) - 2014
- [j17]Sandra E. Orchard
, Mais G. Ammari, Bruno Aranda, Lionel Breuza
, Leonardo Briganti, Fiona Broackes-Carter, Nancy H. Campbell
, Gayatri Chavali, Carol Chen, Noemi del-Toro
, Margaret Duesbury
, Marine Dumousseau, Eugenia Galeota
, Ursula Hinz, Marta Iannuccelli, Sruthi Jagannathan, Rafael C. Jimenez
, Jyoti Khadake, Astrid Lægreid, Luana Licata
, Ruth C. Lovering
, Birgit Meldal
, Anna N. Melidoni
, Mila Milagros, Daniele Peluso, Livia Perfetto
, Pablo Porras, Arathi Raghunath, Sylvie Ricard-Blum, Bernd Roechert, Andre Stutz, Michael Tognolli
, Kim Van Roey, Gianni Cesareni
, Henning Hermjakob
:
The MIntAct project - IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. 42(Database-Issue): 358-363 (2014) - 2013
- [j16]Gerhard Mayer
, Luisa Montecchi-Palazzi, David Ovelleiro, Andrew R. Jones
, Pierre-Alain Binz
, Eric W. Deutsch, Matthew Chambers, Marius Kallhardt, Fredrik Levander
, James Shofstahl, Sandra E. Orchard
, Juan Antonio Vizcaíno
, Henning Hermjakob
, Christian Stephan, Helmut E. Meyer, Martin Eisenacher:
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database J. Biol. Databases Curation 2013 (2013) - [j15]Kim Van Roey, Sandra E. Orchard
, Samuel Kerrien
, Marine Dumousseau, Sylvie Ricard-Blum, Henning Hermjakob
, Toby J. Gibson
:
Capturing cooperative interactions with the PSI-MI format. Database J. Biol. Databases Curation 2013 (2013) - [j14]John Gómez, Leyla J. Garcia
, Gustavo A. Salazar
, Jose M. Villaveces, Swanand P. Gore
, Alexander García Castro
, Maria Jesus Martin
, Guillaume Launay
, Rafael Alcántara
, Noemi del-Toro
, Marine Dumousseau, Sandra E. Orchard
, Sameer Velankar
, Henning Hermjakob
, Chenggong Zong, Peipei Ping
, Manuel Corpas
, Rafael C. Jimenez
:
BioJS: an open source JavaScript framework for biological data visualization. Bioinform. 29(8): 1103-1104 (2013) - [j13]Noemi del-Toro
, Marine Dumousseau, Sandra E. Orchard
, Rafael C. Jimenez
, Eugenia Galeota
, Guillaume Launay
, Johannes Goll, Karin Breuer, Keiichiro Ono, Lukasz Salwínski
, Henning Hermjakob
:
A new reference implementation of the PSICQUIC web service. Nucleic Acids Res. 41(Webserver-Issue): 601-606 (2013) - [c2]Pablo Porras, Paola Roncaglia, Emily Dimmer, Jane Lomax, Rachael P. Huntley, Sandra E. Orchard, Marine Dumousseau, Samuel Kerrien, Henning Hermjakob:
The Apoptosis Gene Ontology project and the IntAct-Apoptosis dataset: updating the conceptual representation of apoptosis. IWBBIO 2013: 757-758 - 2012
- [j12]Samuel Kerrien
, Bruno Aranda, Lionel Breuza
, Alan Bridge
, Fiona Broackes-Carter, Carol Chen, Margaret Duesbury
, Marine Dumousseau, Marc Feuermann, Ursula Hinz, Christine Jandrasits
, Rafael C. Jimenez
, Jyoti Khadake, Usha Mahadevan, Patrick Masson, Ivo Pedruzzi
, Eric Pfeiffenberger, Pablo Porras
, Arathi Raghunath, Bernd Roechert, Sandra E. Orchard
, Henning Hermjakob
:
The IntAct molecular interaction database in 2012. Nucleic Acids Res. 40(Database-Issue): 841-846 (2012) - 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 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) - [j10]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 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
- [j9]Bruno Aranda, P. Achuthan, Yasmin Alam-Faruque, Irina M. Armean
, Alan Bridge
, C. Derow, Marc Feuermann, A. T. Ghanbarian, Samuel Kerrien
, Jyoti Khadake, J. Kerssemakers
, C. Leroy, M. Menden, Magali Michaut
, Luisa Montecchi-Palazzi, S. N. Neuhauser, Sandra E. Orchard
, V. Perreau, Bernd Roechert, K. van Eijk, Henning Hermjakob
:
The IntAct molecular interaction database in 2010. Nucleic Acids Res. 38(Database-Issue): 525-531 (2010) - [p1]Sandra E. Orchard
, Samuel Kerrien
:
Molecular Interactions and Data Standardisation. Proteome Bioinformatics 2010: 309-318
2000 – 2009
- 2008
- [j8]Sandra E. Orchard
, Henning Hermjakob
:
The HUPO proteomics standards initiative - easing communication and minimizing data loss in a changing world. Briefings Bioinform. 9(2): 166-173 (2008) - [j7]Tony Chiang, Nianhua Li, Sandra E. Orchard
, Samuel Kerrien
, Henning Hermjakob
, Robert Gentleman, Wolfgang Huber
:
Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. Bioinform. 24(8): 1100-1101 (2008) - [j6]Gabrielle A. Reeves, Karen Eilbeck, Michele Magrane
, Claire O'Donovan
, Luisa Montecchi-Palazzi, Midori A. Harris
, Sandra E. Orchard
, Rafael C. Jimenez
, Andreas Prlic
, Tim J. P. Hubbard, Henning Hermjakob
, Janet M. Thornton
:
The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinform. 24(23): 2767-2772 (2008) - 2007
- [j5]Nicola J. Mulder
, Rolf Apweiler
, Teresa K. Attwood
, Amos Bairoch
, Alex Bateman
, David Binns, Peer Bork
, Virginie Buillard, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Louise C. Daugherty, Mark Dibley, Robert D. Finn
, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicolas Hulo, Sarah Hunter
, Daniel Kahn, Alexander Kanapin
, Anish Kejariwal, Alberto Labarga
, Petra S. Langendijk-Genevaux
, David Lonsdale, Rodrigo Lopez
, Ivica Letunic
, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry
, Alex L. Mitchell
, Anastasia N. Nikolskaya, Sandra E. Orchard
, Christine A. Orengo, Robert Petryszak
, Jeremy D. Selengut, Christian J. A. Sigrist
, Paul D. Thomas
, Franck Valentin, Derek Wilson, Cathy H. Wu, Corin Yeats:
New developments in the InterPro database. Nucleic Acids Res. 35(Database-Issue): 224-228 (2007) - [j4]Samuel Kerrien
, Yasmin Alam-Faruque, Bruno Aranda, I. Bancarz, Alan Bridge
, C. Derow, Emily Dimmer, Marc Feuermann, A. Friedrichsen, Rachael P. Huntley
, C. Kohler, Jyoti Khadake, C. Leroy, A. Liban, C. Lieftink, Luisa Montecchi-Palazzi, Sandra E. Orchard
, Judith E. Risse, Karine Robbe
, Bernd Roechert, David Thorneycroft, Y. Zhang, Rolf Apweiler
, Henning Hermjakob
:
IntAct - open source resource for molecular interaction data. Nucleic Acids Res. 35(Database-Issue): 561-565 (2007) - 2005
- [j3]Nicola J. Mulder
, Rolf Apweiler
, Teresa K. Attwood
, Amos Bairoch
, Alex Bateman
, David Binns, Paul Bradley, Peer Bork
, Phillip Bucher, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin
, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin
, Maria Krestyaninova
, David Lonsdale, Rodrigo Lopez
, Ivica Letunic
, Martin Madera, John Maslen, Jennifer McDowall, Alex L. Mitchell
, Anastasia N. Nikolskaya, Sandra E. Orchard
, Marco Pagni
, Chris P. Ponting
, Emmanuel Quevillon, Jeremy D. Selengut, Christian J. A. Sigrist
, Ville Silventoinen, David J. Studholme
, Robert Vaughan
, Cathy H. Wu:
InterPro, progress and status in 2005. Nucleic Acids Res. 33(Database-Issue): 201-205 (2005) - [c1]Sandra E. Orchard, Luisa Montecchi-Palazzi, Henning Hermjakob, Rolf Apweiler:
The Use of Common Ontologies and Controlled Vocabularies to Enable Data Exchange and Deposition for Complex Proteomic Experiments. Pacific Symposium on Biocomputing 2005 - 2004
- [j2]Henning Hermjakob
, Luisa Montecchi-Palazzi, Chris Lewington, Sugath Mudali, Samuel Kerrien
, Sandra E. Orchard
, Martin Vingron, Bernd Roechert, Peter Roepstorff, Alfonso Valencia, Hanah Margalit, John Armstrong, Amos Bairoch
, Gianni Cesareni, David James Sherman, Rolf Apweiler
:
IntAct: an open source molecular interaction database. Nucleic Acids Res. 32(Database-Issue): 452-455 (2004) - 2003
- [j1]Nicola J. Mulder, Rolf Apweiler
, Terri K. Attwood
, Amos Bairoch
, Daniel Barrell, Alex Bateman
, David Binns, Margaret Biswas, Paul Bradley, Peer Bork
, Philipp Bucher, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin
, Laurent Falquet, Wolfgang Fleischmann, Sam Griffiths-Jones
, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin
, Maria Krestyaninova
, Rodrigo Lopez
, Ivica Letunic
, David Lonsdale, Ville Silventoinen, Sandra E. Orchard
, Marco Pagni
, David Peyruc, Chris P. Ponting
, Jeremy D. Selengut, Florence Servant
, Christian J. A. Sigrist
, Robert Vaughan
, Evgeni M. Zdobnov:
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res. 31(1): 315-318 (2003)
Coauthor Index

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