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ORCIDChristine A. Orengo
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- affiliation: University College London, Institute of Structural and Molecular Biology, UK
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2020 – today
- 2023
[j80]Vamsi Nallapareddy
, Nicola Bordin, Ian Sillitoe, Michael Heinzinger, Maria Littmann, Vaishali P. Waman, Neeladri Sen, Burkhard Rost, Christine A. Orengo:
CATHe: detection of remote homologues for CATH superfamilies using embeddings from protein language models. Bioinform. 39(1) (2023)- [j79]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:
InterPro in 2022. Nucleic Acids Res. 51(D1): 418-427 (2023) - 2022
- [j78]Neeladri Sen, Ivan Anishchenko, Nicola Bordin, Ian Sillitoe, Sameer Velankar, David Baker, Christine A. Orengo:
Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs. Briefings Bioinform. 23(4) (2022) - [j77]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:
A roadmap for the functional annotation of protein families: a community perspective. Database J. Biol. Databases Curation 2022(2022) (2022) - [j76]M. Michael Gromiha, Christine A. Orengo, Ramanathan Sowdhamini, Janet M. Thornton:
Srinivasan (1962-2021) in Bioinformatics and beyond. Bioinform. 38(8): 2377-2379 (2022) - [j75]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:
Assigning protein function from domain-function associations using DomFun. BMC Bioinform. 23(1): 43 (2022) - [j74]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:
PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res. 50(D1): 534-542 (2022) - [j73]Thibault Tubiana, Ian Sillitoe, Christine A. Orengo, Nathalie Reuter:
Dissecting peripheral protein-membrane interfaces. PLoS Comput. Biol. 18(12): 1010346 (2022) - 2021
- [j72]Vaishali P. Waman, Neeladri Sen, Mihaly Varadi, Antoine Daina, Shoshana J. Wodak, Vincent Zoete, Sameer Velankar, Christine A. Orengo:
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. Briefings Bioinform. 22(2): 742-768 (2021) - [j71]Sayoni Das, Harry M. Scholes, Neeladri Sen, Christine A. Orengo:
CATH functional families predict functional sites in proteins. Bioinform. 37(8): 1099-1106 (2021) - [j70]Maria Littmann, Nicola Bordin, Michael Heinzinger, Konstantin Schütze, Christian Dallago, Christine A. Orengo, Burkhard Rost:
Clustering FunFams using sequence embeddings improves EC purity. Bioinform. 37(20): 3449-3455 (2021) - [j69]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:
CATH: increased structural coverage of functional space. Nucleic Acids Res. 49(Database-Issue): D266-D273 (2021) - [j68]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:
The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 49(Database-Issue): D344-D354 (2021) - [j67]Su Datt Lam, M. Madan Babu, Jonathan G. Lees, Christine A. Orengo:
Biological impact of mutually exclusive exon switching. PLoS Comput. Biol. 17(3) (2021) - 2020
- [j66]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:
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. Bioinform. 36(8): 2636-2642 (2020) - [j65]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:
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. Nucleic Acids Res. 48(Database-Issue): D314-D319 (2020) - [j64]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:
PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 48(Database-Issue): D344-D353 (2020)
2010 – 2019
- 2019
- [j63]Linus Scheibenreif, Maria Littmann, Christine A. Orengo, Burkhard Rost:
FunFam protein families improve residue level molecular function prediction. BMC Bioinform. 20(1): 400:1-400:9 (2019) - [j62]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:
CATH: expanding the horizons of structure-based functional annotations for genome sequences. Nucleic Acids Res. 47(Database-Issue): D280-D284 (2019) - [j61]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:
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 47(Database-Issue): D351-D360 (2019) - [c10]Elena Rojano, James Richard Perkins, Ian Sillitoe, Christine A. Orengo, Juan Antonio Garcia-Ranea, Pedro Seoane:
Associating Protein Domains with Biological Functions: A Tripartite Network Approach. IWBBIO (2) 2019: 155-164 - [r1]Natalie L. Dawson, Sayoni Das, Jonathan G. Lees, Christine A. Orengo:
Protein Structure Classification. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 472-487 - 2018
- [j60]Tony E. Lewis, Ian Sillitoe, Natalie L. Dawson, Su Datt Lam, Tristan Clarke, David A. Lee, Christine A. Orengo, Jonathan G. Lees:
Gene3D: Extensive prediction of globular domains in proteins. Nucleic Acids Res. 46(Database-Issue): D1282 (2018) - [j59]Tony E. Lewis, Ian Sillitoe, Natalie L. Dawson, Su Datt Lam, Tristan Clarke, David A. Lee, Christine A. Orengo, Jonathan G. Lees:
Gene3D: Extensive prediction of globular domains in proteins. Nucleic Acids Res. 46(Database-Issue): D435-D439 (2018) - 2017
- [j58]Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia:
ISCB's initial reaction to New England Journal of Medicine editorial on data sharing. Bioinform. 33(18): 2968 (2017) - [j57]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:
InterPro in 2017 - beyond protein family and domain annotations. Nucleic Acids Res. 45(Database-Issue): D190-D199 (2017) - [j56]Natalie L. Dawson, Tony E. Lewis, Sayoni Das, Jonathan G. Lees, David A. Lee, Paul Ashford, Christine A. Orengo, Ian Sillitoe:
CATH: an expanded resource to predict protein function through structure and sequence. Nucleic Acids Res. 45(Database-Issue): D289-D295 (2017) - [j55]Cen Wan, Jonathan G. Lees, Federico Minneci, Christine A. Orengo, David T. Jones:
Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster. PLoS Comput. Biol. 13(10) (2017) - 2016
- [j54]Sayoni Das, David A. Lee, Ian Sillitoe, Natalie L. Dawson, Jonathan G. Lees, Christine A. Orengo:
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. Bioinform. 32(18): 2889 (2016) - [j53]Su Datt Lam, Natalie L. Dawson, Sayoni Das, Ian Sillitoe, Paul Ashford, David A. Lee, Sonja Lehtinen, Christine A. Orengo, Jonathan G. Lees:
Gene3D: expanding the utility of domain assignments. Nucleic Acids Res. 44(Database-Issue): 404-409 (2016) - [j52]Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia:
ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing. PLoS Comput. Biol. 12(3) (2016) - [j51]David A. Lee, Sayoni Das, Natalie L. Dawson, Dragana Dobrijevic, John Ward, Christine A. Orengo:
Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases. PLoS Comput. Biol. 12(6) (2016) - 2015
- [j50]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:
FUN-L: gene prioritization for RNAi screens. Bioinform. 31(12): 2052-2053 (2015) - [j49]Sayoni Das, David A. Lee, Ian Sillitoe, Natalie L. Dawson, Jonathan G. Lees, Christine A. Orengo:
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. Bioinform. 31(21): 3460-3467 (2015) - [j48]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:
The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 43(Database-Issue): 213-221 (2015) - [j47]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:
CATH: comprehensive structural and functional annotations for genome sequences. Nucleic Acids Res. 43(Database-Issue): 376-381 (2015) - [j46]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:
Genome3D: exploiting structure to help users understand their sequences. Nucleic Acids Res. 43(Database-Issue): 382-386 (2015) - [j45]Sayoni Das, Ian Sillitoe, David A. Lee, Jonathan G. Lees, Natalie L. Dawson, John Ward, Christine A. Orengo:
CATH FunFHMMer web server: protein functional annotations using functional family assignments. Nucleic Acids Res. 43(Webserver-Issue): W148-W153 (2015) - 2014
- [j44]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:
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis. Nucleic Acids Res. 42(Database-Issue): 240-245 (2014) - 2013
- [j43]Robert Rentzsch, Christine A. Orengo:
Protein function prediction using domain families. BMC Bioinform. 14(S-3): S5 (2013) - [j42]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:
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res. 41(Database-Issue): 490-498 (2013) - [j41]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:
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res. 41(Database-Issue): 499-507 (2013) - 2012
- [j40]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:
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 40(Database-Issue): 306-312 (2012) - [j39]Jonathan G. Lees, Corin Yeats, James Richard Perkins, Ian Sillitoe, Robert Rentzsch, Benoit H. Dessailly, Christine A. Orengo:
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. Nucleic Acids Res. 40(Database-Issue): 465-471 (2012) - [j38]Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Syed Asad Rahman, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton:
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. Nucleic Acids Res. 40(Database-Issue): 776-782 (2012) - [j37]Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton:
Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies. PLoS Comput. Biol. 8(3) (2012) - 2011
- [j36]José M. G. Izarzugaza, Lisa E. M. Hopcroft, Anja Baresic, Christine A. Orengo, Andrew C. R. Martin, Alfonso Valencia:
Characterization of pathogenic germline mutations in human Protein Kinases. BMC Bioinform. 12(S-4): S1 (2011) - [j35]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:
Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Res. 39(Database-Issue): 420-426 (2011) - [j34]Corin Yeats, Jonathan G. Lees, Phil Carter, Ian Sillitoe, Christine A. Orengo:
The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences. Nucleic Acids Res. 39(Web-Server-Issue): 546-550 (2011) - 2010
- [j33]Corin Yeats, Oliver Redfern, Christine A. Orengo:
A fast and automated solution for accurately resolving protein domain architectures. Bioinform. 26(6): 745-751 (2010) - [j32]Jonathan G. Lees, Corin Yeats, Oliver Redfern, Andrew B. Clegg, Christine A. Orengo:
Gene3D: merging structure and function for a Thousand genomes. Nucleic Acids Res. 38(Database-Issue): 296-300 (2010) - [j31]Juan A. G. Ranea, Ian Morilla, Jonathan G. Lees, Adam James Reid, Corin Yeats, Andrew B. Clegg, Francisca Sánchez-Jiménez, Christine A. Orengo:
Finding the "Dark Matter" in Human and Yeast Protein Network Prediction and Modelling. PLoS Comput. Biol. 6(9) (2010)
2000 – 2009
- 2009
- [j30]José M. G. Izarzugaza, Anja Baresic, Lisa E. M. McMillan, Corin Yeats, Andrew B. Clegg, Christine A. Orengo, Andrew C. R. Martin, Alfonso Valencia:
An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D. BMC Bioinform. 10(S-8): 5 (2009) - [j29]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:
InterPro: the integrative protein signature database. Nucleic Acids Res. 37(Database-Issue): 211-215 (2009) - [j28]Alison L. Cuff, Ian Sillitoe, Tony E. Lewis, Oliver Redfern, Richard Garratt, Janet M. Thornton, Christine A. Orengo:
The CATH classification revisited - architectures reviewed and new ways to characterize structural divergence in superfamilies. Nucleic Acids Res. 37(Database-Issue): 310-314 (2009) - [j27]Oliver Redfern, Benoit H. Dessailly, Timothy Dallman, Ian Sillitoe, Christine A. Orengo:
FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies. PLoS Comput. Biol. 5(8) (2009) - 2008
- [j26]Corin Yeats, Jonathan G. Lees, Adam James Reid, Paul Kellam, Nigel J. Martin, Xinhui Liu, Christine A. Orengo:
Gene3D: comprehensive structural and functional annotation of genomes. Nucleic Acids Res. 36(Database-Issue): 414-418 (2008) - [j25]Benoit H. Dessailly, Marc F. Lensink, Christine A. Orengo, Shoshana J. Wodak:
LigASite - a database of biologically relevant binding sites in proteins with known apo-structures. Nucleic Acids Res. 36(Database-Issue): 667-673 (2008) - [j24]Anna E. Lobley, Timothy Nugent, Christine A. Orengo, David T. Jones:
FFPred: an integrated feature-based function prediction server for vertebrate proteomes. Nucleic Acids Res. 36(Web-Server-Issue): 297-302 (2008) - [j23]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:
ISPIDER Central: an integrated database web-server for proteomics. Nucleic Acids Res. 36(Web-Server-Issue): 485-490 (2008) - 2007
- [j22]Adam James Reid, Corin Yeats, Christine A. Orengo:
Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone. Bioinform. 23(18): 2353-2360 (2007) - [j21]Andrew P. Harrison, Caroline E. Johnston, Christine A. Orengo:
Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips. BMC Bioinform. 8 (2007) - [j20]Russell L. Marsden, Tony A. Lewis, Christine A. Orengo:
Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint. BMC Bioinform. 8 (2007) - [j19]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) - [j18]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:
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res. 35(Database-Issue): 291-297 (2007) - [j17]Anna E. Lobley, Mark B. Swindells, Christine A. Orengo, David T. Jones:
Inferring Function Using Patterns of Native Disorder in Proteins. PLoS Comput. Biol. 3(8) (2007) - [j16]Juan A. G. Ranea, Corin Yeats, Alastair Grant, Christine A. Orengo:
Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic Genomes. PLoS Comput. Biol. 3(11) (2007) - [j15]Oliver Redfern, Andrew P. Harrison, Timothy Dallman, Frances M. G. Pearl, Christine A. Orengo:
CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures. PLoS Comput. Biol. 3(11) (2007) - 2006
- [j14]Corin Yeats, Michael Maibaum, Russell L. Marsden, Mark Dibley, David A. Lee, Sarah Addou, Christine A. Orengo:
Gene3D: modelling protein structure, function and evolution. Nucleic Acids Res. 34(Database-Issue): 281-284 (2006) - [c9]Michael Hirsch, Allan Tucker, Stephen Swift, Nigel J. Martin, Christine A. Orengo, Paul Kellam, Xiaohui Liu:
Improved Robustness in Time Series Analysis of Gene Expression Data by Polynomial Model Based Clustering. CompLife 2006: 1-10 - 2005
- [j13]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:
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res. 33(Database-Issue): 247-251 (2005) - [c8]Michael Maibaum, Lucas Zamboulis, Galia Rimon, Christine A. Orengo, Nigel J. Martin, Alexandra Poulovassilis:
Cluster Based Integration of Heterogeneous Biological Databases Using the AutoMed Toolkit. DILS 2005: 191-207 - 2004
- [j12]James E. Bray, Russell L. Marsden, Stuart C. G. Rison, Alexei Savchenko, Aled M. Edwards, Janet M. Thornton, Christine A. Orengo:
A practical and robust sequence search strategy for structural genomics target selection. Bioinform. 20(14): 2288-2295 (2004) - [j11]David A. Lee, Sandrine Fefeu, Adrian A. Edo-Ukeh, Christine A. Orengo, Christine Slingsby:
EyeSite: a semi-automated database of protein families in the eye. Nucleic Acids Res. 32(Database-Issue): 148-152 (2004) - [c7]Michael Maibaum, Galia Rimon, Christine A. Orengo, Nigel J. Martin, Alexandra Poulovassilis:
BioMap: Gene Family based Integration of Heterogeneous Biological Databases Using AutoMed Metadata. DEXA Workshops 2004: 384-388 - [c6]Paul Kellam, Stephen Swift, Allan Tucker, Veronica Vinciotti, Nigel J. Martin, Christine A. Orengo, Xiaohui Liu:
Consensus Clustering and Functional Interpretation of Gene Expression Data. Spanish Bioinformatics Conference 2004: 6 - [c5]Juan Garcia Ranea, Alastair Grant, Janet M. Thornton, Christine A. Orengo:
Microeconomic Principles Explain an Optimal Genome Size in Bacteria. Spanish Bioinformatics Conference 2004: 43 - [c4]David A. Lee, Alastair Grant, Ian Sillitoe, Mark Dibley, Juan Garcia Ranea, Christine A. Orengo:
A structural perspective on genome evolution. RECOMB 2004: 336 - 2003
- [j10]Andrew P. Harrison, Frances M. G. Pearl, Ian Sillitoe, Tim Slidel, Richard Mott, Janet M. Thornton, Christine A. Orengo:
Recognizing the fold of a protein structure. Bioinform. 19(14): 1748-1759 (2003) - [j9]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:
The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Res. 31(1): 452-455 (2003) - [j8]Daniel W. A. Buchan, Stuart C. G. Rison, James E. Bray, David A. Lee, Frances M. G. Pearl, Janet M. Thornton, Christine A. Orengo:
Gene3D: structural assignments for the biologist and bioinformaticist alike. Nucleic Acids Res. 31(1): 469-473 (2003) - [c3]Christine A. Orengo:
A Structural Perspective on Genome Evolution(Invited Talk). German Conference on Bioinformatics 2003: 109-110 - 2002
- [j7]Adrian J. Shepherd, Nigel J. Martin, Roger G. Johnson, Paul Kellam, Christine A. Orengo:
PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources. Bioinform. 18(12): 1666-1672 (2002) - [j6]Paul Kellam, Xiaohui Liu, Nigel J. Martin, Christine A. Orengo, Stephen Swift, Allan Tucker:
A framework for modelling virus gene expression data. Intell. Data Anal. 6(3): 267-279 (2002) - 2001
- [j5]M. Mar Albà, David A. Lee, Frances M. G. Pearl, Adrian J. Shepherd, Nigel J. Martin, Christine A. Orengo, Paul Kellam:
VIDA: a virus database system for the organization of animal virus genome open reading frames. Nucleic Acids Res. 29(1): 133-136 (2001) - [j4]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:
A rapid classification protocol for the CATH Domain Database to support structural genomics. Nucleic Acids Res. 29(1): 223-227 (2001) - [c2]Paul Kellam, Xiaohui Liu, Nigel J. Martin, Christine A. Orengo, Stephen Swift, Allan Tucker:
A Framework for Modelling Short, High-Dimensional Multivariate Time Series: Preliminary Results in Virus Gene Expression Data Analysis. IDA 2001: 218-227 - 2000
- [j3]Frances M. G. Pearl, David A. Lee, James E. Bray, Ian Sillitoe, Annabel E. Todd, Andrew P. Harrison, Janet M. Thornton, Christine A. Orengo:
Assigning genomic sequences to CATH. Nucleic Acids Res. 28(1): 277-282 (2000)
1990 – 1999
- 1999
- [j2]Christine A. Orengo, Frances M. G. Pearl, James E. Bray, Annabel E. Todd, A. C. Martin, Loredana Lo Conte, Janet M. Thornton:
The CATH Database provides insights into protein structure/function relationships. Nucleic Acids Res. 27(1): 275-279 (1999) - 1998
- [c1]Janet M. Thornton, Andrew C. R. Martin, Christine A. Orengo, Duncan Milburn, Roman A. Laskowski:
[Invited Lecture] Protein Folds and Functions. German Conference on Bioinformatics 1998 - 1996
- [j1]Nigel P. Brown, Christine A. Orengo, William R. Taylor:
A Protein Structure Comparison Methodology. Comput. Chem. 20(3): 359-380 (1996)
Coauthor Index
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