Christine A. Orengo

94 papers B 2Journal 83Unranked 8
YearRankTypeTitle / Venue / Authors
2026 J jnl
Leveraging protein language models and a scoring function for indel characterization and transfer learning.
Patterns
Oriol Gracia Carmona, Vilde Leipart, Gro V. Amdam, Christine A. Orengo, Franca Fraternali
2024 J jnl
Chainsaw: protein domain segmentation with fully convolutional neural networks.
Bioinform.
Jude Wells, Alex Hawkins-Hooker, Nicola Bordin, Ian Sillitoe, Brooks Paige, Christine A. Orengo
2023 J jnl
CATHe: detection of remote homologues for CATH superfamilies using embeddings from protein language models.
Bioinform.
Vamsi Nallapareddy, Nicola Bordin, Ian Sillitoe, Michael Heinzinger, Maria Littmann, Vaishali P. Waman, Neeladri Sen, Burkhard Rost, Christine A. Orengo
2023 J jnl
InterPro in 2022.
Nucleic Acids Res.
Typhaine Paysan-Lafosse, Matthias Blum, Sara Chuguransky, Tiago Grego, Beatriz Lázaro Pinto, Gustavo A. Salazar, Maxwell L. Bileschi, Peer Bork, Alan J. Bridge, Lucy J. Colwell, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Christine A. Orengo, Arun Prasad Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman
2022 J jnl
A roadmap for the functional annotation of protein families: a community perspective.
Database J. Biol. Databases Curation
Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J. Bridge, Stephen K. Burley, Stacey Cleveland, Lucy J. Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher S. Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria Jesus Martin, Claire D. McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Seán I. O'Donoghue, Christine A. Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey DePons, Lana Saleh, Gloria M. Sheynkman, Françoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu
2022 J jnl
Assigning protein function from domain-function associations using DomFun.
BMC Bioinform.
Elena Rojano, Fernando Moreno Jabato, James Richard Perkins, José Córdoba-Caballero, Federico García-Criado, Ian Sillitoe, Christine A. Orengo, Juan A. G. Ranea, Pedro Seoane-Zonjic
2022 J jnl
Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs.
Briefings Bioinform.
Neeladri Sen, Ivan Anishchenko, Nicola Bordin, Ian Sillitoe, Sameer Velankar, David Baker, Christine A. Orengo
2022 J jnl
Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia.
Bioinform.
Alastair M. Kilpatrick, Farzana Rahman, Audra Anjum, Sayane Shome, K. M. Salim Andalib, Shrabonti Banik, Sanjana F. Chowdhury, Peter Coombe, Yesid Cuesta Astroz, J. Maxwell Douglas, Pradeep Eranti, Aleyna D. Kiran, Sachendra Kumar, Hyeri Lim, Valentina Lorenzi, Tiago Lubiana, Sakib Mahmud, Rafael Puche, Agnieszka Rybarczyk, Syed Muktadir Al Sium, David Twesigomwe, Tomasz Zok, Christine A. Orengo, Iddo Friedberg, Janet Kelso, Lonnie R. Welch
2022 J jnl
Dissecting peripheral protein-membrane interfaces.
PLoS Comput. Biol.
Thibault Tubiana, Ian Sillitoe, Christine A. Orengo, Nathalie Reuter
2022 J jnl
PDBe-KB: collaboratively defining the biological context of structural data.
Nucleic Acids Res.
Mihaly Varadi, Stephen Anyango, David R. Armstrong, John M. Berrisford, Preeti Choudhary, Mandar S. Deshpande, Nurul Nadzirin, Sreenath Nair, Lukás Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom L. Blundell, Kelly Brock, José María Carazo, Jirí Damborský, Alessia David, Sucharita Dey, Roland L. Dunbrack Jr., Juan Fernández-Recio, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas A. Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José Ramón Macías, Mallur Srivatsan Madhusudhan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Pawel Rubach, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar Sánchez Sorzano, Jan Stourac, Joanna I. Sulkowska, Radka Svobodová Vareková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim F. Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar
2022 J jnl
Srinivasan (1962-2021) in Bioinformatics and beyond.
Bioinform.
M. Michael Gromiha, Christine A. Orengo, Ramanathan Sowdhamini, Janet M. Thornton
2021 J jnl
Biological impact of mutually exclusive exon switching.
PLoS Comput. Biol.
Su Datt Lam, M. Madan Babu, Jonathan G. Lees, Christine A. Orengo
2021 J jnl
CATH functional families predict functional sites in proteins.
Bioinform.
Sayoni Das, Harry M. Scholes, Neeladri Sen, Christine A. Orengo
2021 J jnl
CATH: increased structural coverage of functional space.
Nucleic Acids Res.
Ian Sillitoe, Nicola Bordin, Natalie L. Dawson, Vaishali P. Waman, Paul Ashford, Harry M. Scholes, Camilla S. M. Pang, Laurel Woodridge, Clemens Rauer, Neeladri Sen, Mahnaz Abbasian, Sean Le Cornu, Su Datt Lam, Karel Berka, Ivana Hutarová Vareková, Radka Svobodová Vareková, Jonathan G. Lees, Christine A. Orengo
2021 J jnl
Clustering FunFams using sequence embeddings improves EC purity.
Bioinform.
Maria Littmann, Nicola Bordin, Michael Heinzinger, Konstantin Schütze, Christian Dallago, Christine A. Orengo, Burkhard Rost
2021 J jnl
The InterPro protein families and domains database: 20 years on.
Nucleic Acids Res.
Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasamy, Alex L. Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj, Lorna J. Richardson, Gustavo A. Salazar, Lowri Williams, Peer Bork, Alan J. Bridge, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Marco Necci, Christine A. Orengo, Arun Prasad Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman, Robert D. Finn
2021 J jnl
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies.
Briefings Bioinform.
Vaishali P. Waman, Neeladri Sen, Mihaly Varadi, Antoine Daina, Shoshana J. Wodak, Vincent Zoete, Sameer Velankar, Christine A. Orengo
2020 J jnl
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation.
Nucleic Acids Res.
Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Robert D. Finn, Julian Gough, David T. Jones, Lawrence A. Kelley, Typhaine Paysan-Lafosse, Su Datt Lam, Alexey G. Murzin, Arun Prasad Pandurangan, Gustavo A. Salazar, Marcin J. Skwark, Michael J. E. Sternberg, Sameer Velankar, Christine A. Orengo
2020 J jnl
PDBe-KB: a community-driven resource for structural and functional annotations.
Nucleic Acids Res.
Mihaly Varadi, John M. Berrisford, Mandar S. Deshpande, Sreenath Nair, Aleksandras Gutmanas, David R. Armstrong, Lukás Pravda, Bissan Al-Lazikani, Stephen Anyango, Geoffrey J. Barton, Karel Berka, Tom L. Blundell, Neera Borkakoti, Jose M. Dana, Sayoni Das, Sucharita Dey, Patrizio Di Micco, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Liang-Chin Huang, Rishabh Jain, Harry Jubb, Christos C. Kannas, Natarajan Kannan, Jaroslav Koca, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Fábio Madeira, M. S. Madhusudhan, Henry J. Martell, Stuart A. MacGowan, Jake E. McGreig, Saqib Mir, Abhik Mukhopadhyay, Luca Parca, Typhaine Paysan-Lafosse, Leandro G. Radusky, António J. M. Ribeiro, Luis Serrano, Ian Sillitoe, Gulzar Singh, Petr Skoda, Radka Svobodová Vareková, Jonathan D. Tyzack, Alfonso Valencia, Eloy D. Villasclaras-Fernández, Wim F. Vranken, Mark N. Wass, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar
2020 J jnl
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences.
Bioinform.
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 J. 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, J. 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
2019 — conf
Associating Protein Domains with Biological Functions: A Tripartite Network Approach.
IWBBIO (2)
Elena Rojano, James Richard Perkins, Ian Sillitoe, Christine A. Orengo, Juan Antonio Garcia-Ranea, Pedro Seoane
2019 J jnl
CATH: expanding the horizons of structure-based functional annotations for genome sequences.
Nucleic Acids Res.
Ian Sillitoe, Natalie L. Dawson, Tony E. Lewis, Sayoni Das, Jonathan G. Lees, Paul Ashford, Adeyelu Tolulope, Harry M. Scholes, Ilya Senatorov, Andra Bujan, Fatima Ceballos Rodriguez-Conde, Benjamin Dowling, Janet M. Thornton, Christine A. Orengo
2019 J jnl
FunFam protein families improve residue level molecular function prediction.
BMC Bioinform.
Linus Scheibenreif, Maria Littmann, Christine A. Orengo, Burkhard Rost
2019 J jnl
InterPro in 2019: improving coverage, classification and access to protein sequence annotations.
Nucleic Acids Res.
Alex L. Mitchell, Teresa K. Attwood, Patricia C. Babbitt, Matthias Blum, Peer Bork, Alan J. Bridge, Shoshana D. Brown, Hsin-Yu Chang, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Hongzhan Huang, Ivica Letunic, Rodrigo Lopez, Aurelien Luciani, Fábio Madeira, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Arun Prasad Pandurangan, Typhaine Paysan-Lafosse, Sebastien Pesseat, Simon C. Potter, Matloob Qureshi, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Gustavo A. Salazar, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Siew-Yit Yong, Robert D. Finn
2019 — ch.
Protein Structure Classification.
Encyclopedia of Bioinformatics and Computational Biology (2)
Natalie L. Dawson, Sayoni Das, Jonathan G. Lees, Christine A. Orengo
2018 J jnl
Gene3D: Extensive prediction of globular domains in proteins.
Nucleic Acids Res.
Tony E. Lewis, Ian Sillitoe, Natalie L. Dawson, Su Datt Lam, Tristan Clarke, David A. Lee, Christine A. Orengo, Jonathan G. Lees
2018 J jnl
Gene3D: Extensive prediction of globular domains in proteins.
Nucleic Acids Res.
Tony E. Lewis, Ian Sillitoe, Natalie L. Dawson, Su Datt Lam, Tristan Clarke, David A. Lee, Christine A. Orengo, Jonathan G. Lees
2017 J jnl
Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster.
PLoS Comput. Biol.
Cen Wan, Jonathan G. Lees, Federico Minneci, Christine A. Orengo, David T. Jones
2017 J jnl
CATH: an expanded resource to predict protein function through structure and sequence.
Nucleic Acids Res.
Natalie L. Dawson, Tony E. Lewis, Sayoni Das, Jonathan G. Lees, David A. Lee, Paul Ashford, Christine A. Orengo, Ian Sillitoe
2017 J jnl
ISCB's initial reaction to New England Journal of Medicine editorial on data sharing.
Bioinform.
Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia
2017 J jnl
InterPro in 2017 - beyond protein family and domain annotations.
Nucleic Acids Res.
Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan J. Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L. Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Young Mi Park, Sebastien Pesseat, Damiano Piovesan, Simon C. Potter, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Ioannis Xenarios, Lai-Su L. Yeh, Siew-Yit Yong, Alex L. Mitchell
2016 J jnl
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.
Bioinform.
Sayoni Das, David A. Lee, Ian Sillitoe, Natalie L. Dawson, Jonathan G. Lees, Christine A. Orengo
2016 J jnl
Gene3D: expanding the utility of domain assignments.
Nucleic Acids Res.
Su Datt Lam, Natalie L. Dawson, Sayoni Das, Ian Sillitoe, Paul Ashford, David A. Lee, Sonja Lehtinen, Christine A. Orengo, Jonathan G. Lees
2016 J jnl
ISCB's Initial Reaction to
PLoS Comput. Biol.
Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia
2016 J jnl
Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases.
PLoS Comput. Biol.
David A. Lee, Sayoni Das, Natalie L. Dawson, Dragana Dobrijevic, John Ward, Christine A. Orengo
2015 J jnl
CATH FunFHMMer web server: protein functional annotations using functional family assignments.
Nucleic Acids Res.
Sayoni Das, Ian Sillitoe, David A. Lee, Jonathan G. Lees, Natalie L. Dawson, John Ward, Christine A. Orengo
2015 J jnl
CATH: comprehensive structural and functional annotations for genome sequences.
Nucleic Acids Res.
Ian Sillitoe, Tony E. Lewis, Alison L. Cuff, Sayoni Das, Paul Ashford, Natalie L. Dawson, Nicholas Furnham, Roman A. Laskowski, David A. Lee, Jonathan G. Lees, Sonja Lehtinen, Romain A. Studer, Janet M. Thornton, Christine A. Orengo
2015 J jnl
FUN-L: gene prioritization for RNAi screens.
Bioinform.
Jonathan G. Lees, Jean-Karim Hériché, Ian Morilla, José María Fernández, Priit Adler, Martin Krallinger, Jaak Vilo, Alfonso Valencia, Jan Ellenberg, Juan A. G. Ranea, Christine A. Orengo
2015 J jnl
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.
Bioinform.
Sayoni Das, David A. Lee, Ian Sillitoe, Natalie L. Dawson, Jonathan G. Lees, Christine A. Orengo
2015 J jnl
Genome3D: exploiting structure to help users understand their sequences.
Nucleic Acids Res.
Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Cyrus Chothia, Domenico Cozzetto, Jose M. Dana, Ioannis Filippis, Julian Gough, David T. Jones, Lawrence A. Kelley, Gerard J. Kleywegt, Federico Minneci, Jaina Mistry, Alexey G. Murzin, Bernardo Ochoa-Montaño, Matt E. Oates, Marco Punta, Owen J. L. Rackham, Jonathan Stahlhacke, Michael J. E. Sternberg, Sameer Velankar, Christine A. Orengo
2015 J jnl
The InterPro protein families database: the classification resource after 15 years.
Nucleic Acids Res.
Alex L. Mitchell, Hsin-Yu Chang, Louise C. Daugherty, Matthew Fraser, Sarah Hunter, Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat, Amaia Sangrador-Vegas, Maxim Scheremetjew, Claudia Rato, Siew-Yit Yong, Alex Bateman, Marco Punta, Teresa K. Attwood, Christian J. A. Sigrist, Nicole Redaschi, Catherine Rivoire, Ioannis Xenarios, Daniel Kahn, Dominique Guyot, Peer Bork, Ivica Letunic, Julian Gough, Matt E. Oates, Daniel H. Haft, Hongzhan Huang, Darren A. Natale, Cathy H. Wu, Christine A. Orengo, Ian Sillitoe, Huaiyu Mi, Paul D. Thomas, Robert D. Finn
2014 J jnl
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis.
Nucleic Acids Res.
Jonathan G. Lees, David A. Lee, Romain A. Studer, Natalie L. Dawson, Ian Sillitoe, Sayoni Das, Corin Yeats, Benoit H. Dessailly, Robert Rentzsch, Christine A. Orengo
2013 J jnl
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.
Nucleic Acids Res.
Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Cyrus Chothia, Alison L. Cuff, Jose M. Dana, Ioannis Filippis, Julian Gough, Sarah Hunter, David T. Jones, Lawrence A. Kelley, Gerard J. Kleywegt, Federico Minneci, Alex L. Mitchell, Alexey G. Murzin, Bernardo Ochoa-Montaño, Owen J. L. Rackham, James Smith, Michael J. E. Sternberg, Sameer Velankar, Corin Yeats, Christine A. Orengo
2013 J jnl
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.
Nucleic Acids Res.
Ian Sillitoe, Alison L. Cuff, Benoit H. Dessailly, Natalie L. Dawson, Nicholas Furnham, David A. Lee, Jonathan G. Lees, Tony E. Lewis, Romain A. Studer, Robert Rentzsch, Corin Yeats, Janet M. Thornton, Christine A. Orengo
2013 J jnl
Protein function prediction using domain families.
BMC Bioinform.
Robert Rentzsch, Christine A. Orengo
2012 J jnl
Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies.
PLoS Comput. Biol.
Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton
2012 J jnl
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.
Nucleic Acids Res.
Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Syed Asad Rahman, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton
2012 J jnl
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis.
Nucleic Acids Res.
Jonathan G. Lees, Corin Yeats, James Richard Perkins, Ian Sillitoe, Robert Rentzsch, Benoit H. Dessailly, Christine A. Orengo
2012 J jnl
InterPro in 2011: new developments in the family and domain prediction database.
Nucleic Acids Res.
Sarah Hunter, Philip Jones, Alex L. Mitchell, Rolf Apweiler, Teresa K. Attwood, Alex Bateman, Thomas Bernard, David Binns, Peer Bork, Sarah W. Burge, Edouard De Castro, Penny C. Coggill, Matthew Corbett, Ujjwal Das, Louise C. Daugherty, Lauranne Duquenne, Robert D. Finn, Matthew Fraser, Julian Gough, Daniel H. Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Conor McMenamin, Huaiyu Mi, Prudence Mutowo-Meullenet, Nicola J. Mulder, Darren A. Natale, Christine A. Orengo, Sebastien Pesseat, Marco Punta, Antony F. Quinn, Catherine Rivoire, Amaia Sangrador-Vegas, Jeremy D. Selengut, Christian J. A. Sigrist, Maxim Scheremetjew, John G. Tate, Manjulapramila Thimmajanarthanan, Paul D. Thomas, Cathy H. Wu, Corin Yeats, Siew-Yit Yong
2011 J jnl
Characterization of pathogenic germline mutations in human Protein Kinases.
BMC Bioinform.
José M. G. Izarzugaza, Lisa E. M. Hopcroft, Anja Baresic, Christine A. Orengo, Andrew C. R. Martin, Alfonso Valencia
2011 J jnl
Extending CATH: increasing coverage of the protein structure universe and linking structure with function.
Nucleic Acids Res.
Alison L. Cuff, Ian Sillitoe, Tony E. Lewis, Andrew B. Clegg, Robert Rentzsch, Nicholas Furnham, Marialuisa Pellegrini-Calace, David T. Jones, Janet M. Thornton, Christine A. Orengo
2011 J jnl
The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences.
Nucleic Acids Res.
Corin Yeats, Jonathan G. Lees, Phil Carter, Ian Sillitoe, Christine A. Orengo
2010 J jnl
A fast and automated solution for accurately resolving protein domain architectures.
Bioinform.
Corin Yeats, Oliver Redfern, Christine A. Orengo
2010 J jnl
Finding the "Dark Matter" in Human and Yeast Protein Network Prediction and Modelling.
PLoS Comput. Biol.
Juan A. G. Ranea, Ian Morilla, Jonathan G. Lees, Adam James Reid, Corin Yeats, Andrew B. Clegg, Francisca Sánchez-Jiménez, Christine A. Orengo
2010 J jnl
Gene3D: merging structure and function for a Thousand genomes.
Nucleic Acids Res.
Jonathan G. Lees, Corin Yeats, Oliver Redfern, Andrew B. Clegg, Christine A. Orengo
2009 J jnl
An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D.
BMC Bioinform.
José M. G. Izarzugaza, Anja Baresic, Lisa E. M. McMillan, Corin Yeats, Andrew B. Clegg, Christine A. Orengo, Andrew C. R. Martin, Alfonso Valencia
2009 J jnl
FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies.
PLoS Comput. Biol.
Oliver Redfern, Benoit H. Dessailly, Timothy Dallman, Ian Sillitoe, Christine A. Orengo
2009 J jnl
InterPro: the integrative protein signature database.
Nucleic Acids Res.
Sarah Hunter, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Ujjwal Das, Louise C. Daugherty, Lauranne Duquenne, Robert D. Finn, Julian Gough, Daniel H. Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Aurélie Laugraud, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex L. Mitchell, Nicola J. Mulder, Darren A. Natale, Christine A. Orengo, Antony F. Quinn, Jeremy D. Selengut, Christian J. A. Sigrist, Manjula Thimma, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, Corin Yeats
2009 J jnl
The CATH classification revisited - architectures reviewed and new ways to characterize structural divergence in superfamilies.
Nucleic Acids Res.
Alison L. Cuff, Ian Sillitoe, Tony E. Lewis, Oliver Redfern, Richard Garratt, Janet M. Thornton, Christine A. Orengo
2008 J jnl
FFPred: an integrated feature-based function prediction server for vertebrate proteomes.
Nucleic Acids Res.
Anna E. Lobley, Timothy Nugent, Christine A. Orengo, David T. Jones
2008 J jnl
Gene3D: comprehensive structural and functional annotation of genomes.
Nucleic Acids Res.
Corin Yeats, Jonathan G. Lees, Adam James Reid, Paul Kellam, Nigel J. Martin, Xinhui Liu, Christine A. Orengo
2008 J jnl
ISPIDER Central: an integrated database web-server for proteomics.
Nucleic Acids Res.
Jennifer A. Siepen, Khalid Belhajjame, Julian N. Selley, Suzanne M. Embury, Norman W. Paton, Carole A. Goble, Stephen G. Oliver, Robert Stevens, Lucas Zamboulis, Nigel J. Martin, Alexandra Poulovassilis, Philip Jones, Richard G. Côté, Henning Hermjakob, Melissa M. Pentony, David T. Jones, Christine A. Orengo, Simon J. Hubbard
2008 J jnl
LigASite - a database of biologically relevant binding sites in proteins with known
Nucleic Acids Res.
Benoit H. Dessailly, Marc F. Lensink, Christine A. Orengo, Shoshana J. Wodak
2007 J jnl
CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures.
PLoS Comput. Biol.
Oliver Redfern, Andrew P. Harrison, Timothy Dallman, Frances M. G. Pearl, Christine A. Orengo
2007 J jnl
Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips.
BMC Bioinform.
Andrew P. Harrison, Caroline E. Johnston, Christine A. Orengo
2007 J jnl
Inferring Function Using Patterns of Native Disorder in Proteins.
PLoS Comput. Biol.
Anna E. Lobley, Mark B. Swindells, Christine A. Orengo, David T. Jones
2007 J jnl
Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone.
Bioinform.
Adam James Reid, Corin Yeats, Christine A. Orengo
2007 J jnl
New developments in the InterPro database.
Nucleic Acids Res.
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
2007 J jnl
Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic Genomes.
PLoS Comput. Biol.
Juan A. G. Ranea, Corin Yeats, Alastair Grant, Christine A. Orengo
2007 J jnl
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.
Nucleic Acids Res.
Lesley H. Greene, Tony E. Lewis, Sarah Addou, Alison L. Cuff, Timothy Dallman, Mark Dibley, Oliver Redfern, Frances M. G. Pearl, Rekha Nambudiry, Adam James Reid, Ian Sillitoe, Corin Yeats, Janet M. Thornton, Christine A. Orengo
2007 J jnl
Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint.
BMC Bioinform.
Russell L. Marsden, Tony A. Lewis, Christine A. Orengo
2006 J jnl
Gene3D: modelling protein structure, function and evolution.
Nucleic Acids Res.
Corin Yeats, Michael Maibaum, Russell L. Marsden, Mark Dibley, David A. Lee, Sarah Addou, Christine A. Orengo
2006 — conf
Improved Robustness in Time Series Analysis of Gene Expression Data by Polynomial Model Based Clustering.
CompLife
Michael Hirsch, Allan Tucker, Stephen Swift, Nigel J. Martin, Christine A. Orengo, Paul Kellam, Xiaohui Liu
2005 — conf
Cluster Based Integration of Heterogeneous Biological Databases Using the AutoMed Toolkit.
DILS
Michael Maibaum, Lucas Zamboulis, Galia Rimon, Christine A. Orengo, Nigel J. Martin, Alexandra Poulovassilis
2005 J jnl
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.
Nucleic Acids Res.
Frances M. G. Pearl, Annabel E. Todd, Ian Sillitoe, Mark Dibley, Oliver Redfern, Tony E. Lewis, Christopher Bennett, Russell L. Marsden, Alastair Grant, David A. Lee, Adrian Akpor, Michael Maibaum, Andrew P. Harrison, Timothy Dallman, Gabrielle A. Reeves, Ilhem Diboun, Sarah Addou, Stefano Lise, Caroline E. Johnston, Antonio Sillero, Janet M. Thornton, Christine A. Orengo
2004 J jnl
A practical and robust sequence search strategy for structural genomics target selection.
Bioinform.
James E. Bray, Russell L. Marsden, Stuart C. G. Rison, Alexei Savchenko, Aled M. Edwards, Janet M. Thornton, Christine A. Orengo
2004 B conf
A structural perspective on genome evolution.
RECOMB
David A. Lee, Alastair Grant, Ian Sillitoe, Mark Dibley, Juan Garcia Ranea, Christine A. Orengo
2004 — conf
BioMap: Gene Family based Integration of Heterogeneous Biological Databases Using AutoMed Metadata.
DEXA Workshops
Michael Maibaum, Galia Rimon, Christine A. Orengo, Nigel J. Martin, Alexandra Poulovassilis
2004 — conf
Consensus Clustering and Functional Interpretation of Gene Expression Data.
Spanish Bioinformatics Conference
Paul Kellam, Stephen Swift, Allan Tucker, Veronica Vinciotti, Nigel J. Martin, Christine A. Orengo, Xiaohui Liu
2004 J jnl
EyeSite: a semi-automated database of protein families in the eye.
Nucleic Acids Res.
David A. Lee, Sandrine Fefeu, Adrian A. Edo-Ukeh, Christine A. Orengo, Christine Slingsby
2004 — conf
Microeconomic Principles Explain an Optimal Genome Size in Bacteria.
Spanish Bioinformatics Conference
Juan Garcia Ranea, Alastair Grant, Janet M. Thornton, Christine A. Orengo
2003 — conf
A Structural Perspective on Genome Evolution(Invited Talk).
German Conference on Bioinformatics
Christine A. Orengo
2003 J jnl
Gene3D: structural assignments for the biologist and bioinformaticist alike.
Nucleic Acids Res.
Daniel W. A. Buchan, Stuart C. G. Rison, James E. Bray, David A. Lee, Frances M. G. Pearl, Janet M. Thornton, Christine A. Orengo
2003 J jnl
Recognizing the fold of a protein structure.
Bioinform.
Andrew P. Harrison, Frances M. G. Pearl, Ian Sillitoe, Tim Slidel, Richard Mott, Janet M. Thornton, Christine A. Orengo
2003 J jnl
The CATH database: an extended protein family resource for structural and functional genomics.
Nucleic Acids Res.
Frances M. G. Pearl, C. F. Bennett, James E. Bray, Andrew P. Harrison, Nigel J. Martin, Adrian J. Shepherd, Ian Sillitoe, Janet M. Thornton, Christine A. Orengo
2002 J jnl
A framework for modelling virus gene expression data.
Intell. Data Anal.
Paul Kellam, Xiaohui Liu, Nigel J. Martin, Christine A. Orengo, Stephen Swift, Allan Tucker
2002 J jnl
PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources.
Bioinform.
Adrian J. Shepherd, Nigel J. Martin, Roger G. Johnson, Paul Kellam, Christine A. Orengo
2001 B conf
A Framework for Modelling Short, High-Dimensional Multivariate Time Series: Preliminary Results in Virus Gene Expression Data Analysis.
IDA
Paul Kellam, Xiaohui Liu, Nigel J. Martin, Christine A. Orengo, Stephen Swift, Allan Tucker
2001 J jnl
A rapid classification protocol for the CATH Domain Database to support structural genomics.
Nucleic Acids Res.
Frances M. G. Pearl, Nigel J. Martin, James E. Bray, Daniel W. A. Buchan, Andrew P. Harrison, David A. Lee, Gabrielle A. Reeves, Adrian J. Shepherd, Ian Sillitoe, Annabel E. Todd, Janet M. Thornton, Christine A. Orengo
2001 J jnl
VIDA: a virus database system for the organization of animal virus genome open reading frames.
Nucleic Acids Res.
M. Mar Albà, David A. Lee, Frances M. G. Pearl, Adrian J. Shepherd, Nigel J. Martin, Christine A. Orengo, Paul Kellam
2000 J jnl
Assigning genomic sequences to CATH.
Nucleic Acids Res.
Frances M. G. Pearl, David A. Lee, James E. Bray, Ian Sillitoe, Annabel E. Todd, Andrew P. Harrison, Janet M. Thornton, Christine A. Orengo
1999 J jnl
The CATH Database provides insights into protein structure/function relationships.
Nucleic Acids Res.
Christine A. Orengo, Frances M. G. Pearl, James E. Bray, Annabel E. Todd, A. C. Martin, Loredana Lo Conte, Janet M. Thornton
1998 — conf
[Invited Lecture] Protein Folds and Functions.
German Conference on Bioinformatics
Janet M. Thornton, Andrew C. R. Martin, Christine A. Orengo, Duncan Milburn, Roman A. Laskowski
1996 J jnl
A Protein Structure Comparison Methodology.
Comput. Chem.
Nigel P. Brown, Christine A. Orengo, William R. Taylor