Browse by UCL people
Group by: Type | Date
Number of items: 115.
Article
Adeyelu, Tolulope Tosin;
Moya-Garcia, Aurelio A;
Orengo, Christine;
(2022)
Exploiting protein family and protein network data to identify novel drug targets for bladder cancer.
Oncotarget
, 13
(1)
pp. 105-117.
10.18632/oncotarget.28175.
|
 |
|
Alba, MM;
Lee, D;
Pearl, FMG;
Shepherd, AJ;
Martin, N;
Orengo, CA;
Kellam, P;
(2001)
VIDA: a virus database system for the organization of animal virus genome open reading frames.
Nucleic Acids Research
, 29
(1)
133 - 136.
10.1093/nar/29.1.133.
|
 |
|
Alvarez-Carreno, Claudia;
Huynh, Angela T;
Petrov, Anton S;
Orengo, Christine;
Williams, Loren Dean;
(2024)
BEAN and HABAS: Polyphyletic insertions in the DNA-directed RNA polymerase.
Protein Science
, 33
(11)
, Article e5194. 10.1002/pro.5194.
|
|
|
Ashford, P;
Pang, CSM;
Moya-García, AA;
Adeyelu, T;
Orengo, CA;
(2019)
A CATH domain functional family based approach to identify putative cancer driver genes and driver mutations.
Scientific Reports
, 9
, Article 263. 10.1038/s41598-018-36401-4.
|
|
|
Baskozos, G;
Dawes, JM;
Austin, JS;
Antunes-Martins, A;
McDermott, L;
Clark, AJ;
Trendafilova, T;
... Bennett, DL; + view all
(2019)
Comprehensive analysis of Long non-coding RNA expression in dorsal root ganglion reveals cell type specificity and dysregulation following nerve injury.
Pain
, 160
(2)
pp. 463-485.
10.1097/j.pain.0000000000001416.
|
|
Bertoni, Damian;
Tsenkov, Maxim;
Magana, Paulyna;
Nair, Sreenath;
Pidruchna, Ivanna;
Querino Lima Afonso, Marcelo;
Midlik, Adam;
... Velankar, Sameer; + view all
(2025)
AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage.
Nucleic Acids Research
, Article gkaf1226. 10.1093/nar/gkaf1226.
(In press).
|
|
|
Blum, Matthias;
Andreeva, Antonina;
Florentino, Laise Cavalcanti;
Chuguransky, Sara Rocio;
Grego, Tiago;
Hobbs, Emma;
Pinto, Beatriz Lazaro;
... Bateman, Alex; + view all
(2024)
InterPro: the protein sequence classification resource in 2025.
Nucleic Acids Research
, Article gkae1082. 10.1093/nar/gkae1082.
(In press).
|
|
|
Blum, M;
Chang, H-Y;
Chuguransky, S;
Grego, T;
Kandasaamy, S;
Mitchell, A;
Nuka, G;
... Finn, RD; + view all
(2020)
The InterPro protein families and domains database: 20 years on.
Nucleic Acids Research
10.1093/nar/gkaa977.
(In press).
|
|
|
Bonello, Joseph;
Orengo, Christine;
(2024)
FunPredCATH: An ensemble method for predicting protein function using CATH.
Biochim Biophys Acta Proteins Proteom
, 1872
(2)
, Article 140985. 10.1016/j.bbapap.2023.140985.
|
|
Bordin, Nicola;
Dallago, Christian;
Heinzinger, Michael;
Kim, Stephanie;
Littmann, Maria;
Rauer, Clemens;
Steinegger, Martin;
... Orengo, Christine; + view all
(2022)
Novel machine learning approaches revolutionize protein knowledge.
Trends in Biochemical Sciences
10.1016/j.tibs.2022.11.001.
(In press).
|
|
Bordin, Nicola;
Lau, Andy M;
Orengo, Christine;
(2023)
Large-scale clustering of AlphaFold2 3D models shines light on the structure and function of proteins.
Molecular Cell
, 83
(22)
pp. 3950-3952.
10.1016/j.molcel.2023.10.039.
|
|
Bordin, Nicola;
Sillitoe, Ian;
Nallapareddy, Vamsi;
Rauer, Clemens;
Lam, Su Datt;
Waman, Vaishali P;
Sen, Neeladri;
... Orengo, Christine; + view all
(2023)
AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms.
Communications Biology
, 6
(1)
, Article 160. 10.1038/s42003-023-04488-9.
|
|
Bordin, N;
Sillitoe, I;
Lees, JG;
Orengo, C;
(2021)
Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds.
Frontiers in Molecular Neuroscience
, 8
, Article 668184. 10.3389/fmolb.2021.668184.
|
|
|
Das, S;
Dawson, NL;
Orengo, CA;
(2015)
Diversity in protein domain superfamilies.
Current Opinion in Genetics & Development
, 35
pp. 40-49.
10.1016/j.gde.2015.09.005.
|
|
|
Das, S;
Lee, D;
Sillitoe, I;
Dawson, NL;
Lees, JG;
Orengo, CA;
(2015)
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.
Bioinformatics
, 31
(21)
pp. 3460-3467.
10.1093/bioinformatics/btv398.
|
|
Das, S;
Orengo, C;
(2018)
Choosing the Best Enzyme Complex Structure Made Easy.
Structure
, 26
(4)
pp. 528-530.
10.1016/j.str.2018.03.009.
|
|
Das, S;
Orengo, CA;
(2016)
Protein function annotation using protein domain family resources.
Methods
, 93
pp. 24-34.
10.1016/j.ymeth.2015.09.029.
|
|
Das, S;
Scholes, HM;
Sen, N;
Orengo, C;
(2020)
CATH functional families predict functional sites in proteins.
Bioinformatics
10.1093/bioinformatics/btaa937.
(In press).
|
|
|
Das, S;
Sillitoe, I;
Lee, D;
Lees, JG;
Dawson, NL;
Ward, J;
Orengo, CA;
(2015)
CATH FunFHMMer web server: protein functional annotations using functional family assignments.
Nucleic Acids Res
, 43
(W1)
W148-W153.
10.1093/nar/gkv488.
|
|
|
Dawson, NL;
Lewis, TE;
Das, S;
Lees, JG;
Lee, D;
Ashford, P;
Orengo, CA;
(2017)
CATH: an expanded resource to predict protein function through structure and sequence.
Nucleic Acids Research
, 45
(D1)
D289-D295.
10.1093/nar/gkw1098.
|
|
de Crécy-Lagard, Valérie;
Amorin de Hegedus, Rocio;
Arighi, Cecilia;
Babor, Jill;
Bateman, Alex;
Blaby, Ian;
Blaby-Haas, Crysten;
... Xu, Jin; + view all
(2022)
A roadmap for the functional annotation of protein families: a community perspective.
Database
10.1093/database/baac062.
(In press).
|
|
|
Diboun, I;
Wernisch, L;
Orengo, CA;
Koltzenburg, M;
(2006)
Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma.
BMC GENOMICS
, 7
, Article 252. 10.1186/1471-2164-7-252.
|
|
|
Dobrijevic, D;
Benhamou, L;
Aliev, AE;
Méndez-Sánchez, D;
Dawson, N;
Baud, D;
Tappertzhofen, N;
... Ward, JM; + view all
(2019)
Metagenomic ene-reductases for the bioreduction of sterically challenging enones.
RSC Advances
, 9
(63)
pp. 36608-36614.
10.1039/c9ra06088j.
|
|
|
Finn, RD;
Attwood, TK;
Babbitt, PC;
Bateman, A;
Bork, P;
Bridge, AJ;
Chang, HY;
... Mitchell, AL; + view all
(2016)
InterPro in 2017-beyond protein family and domain annotations.
Nucleic Acids Research
10.1093/nar/gkw1107.
(In press).
|
|
|
Furnham, N;
Sillitoe, I;
Holliday, GL;
Cuff, AL;
Laskowski, RA;
Orengo, CA;
Thornton, JM;
(2012)
Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
PLoS Comput Biol
, 8
(3)
, Article e1002403. 10.1371/journal.pcbi.1002403.
|
|
|
Goldtzvik, Yonathan;
Sen, Neeladri;
Lam, Su Datt;
Orengo, Christine;
(2023)
Protein diversification through post-translational modifications, alternative splicing, and gene duplication.
Current Opinion in Structural Biology
, 81
, Article 102640. 10.1016/j.sbi.2023.102640.
|
|
Gromiha, M Michael;
Orengo, Christine;
Sowdhamini, Ramanathan;
Thornton, Janet;
(2022)
Srinivasan (1962-2021) in Bioinformatics and beyond.
Bioinformatics
10.1093/bioinformatics/btac054.
(In press).
|
|
|
Harrison, AP;
Johnston, CE;
Orengo, CA;
(2007)
Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips.
BMC BIOINFORMATICS
, 8
, Article 195. 10.1186/1471-2105-8-195.
|
|
|
Hasenahuer, Marcia A;
Sanchis-Juan, Alba;
Laskowski, Roman A;
Baker, James A;
Stephenson, James D;
Orengo, Christine A;
Lucy Raymond, F;
(2022)
Mapping the Constrained Coding Regions in the human genome to their corresponding proteins.
Journal of Molecular Biology
, Article 167892. 10.1016/j.jmb.2022.167892.
(In press).
|
|
Heinzinger, Michael;
Littmann, Maria;
Sillitoe, Ian;
Bordin, Nicola;
Orengo, Christine;
Rost, Burkhard;
(2022)
Contrastive learning on protein embeddings enlightens midnight zone.
NAR Genomics and Bioinformatics
, 4
(2)
, Article lqac043. 10.1093/nargab/lqac043.
|
|
Izarzugaza, JMG;
Baresic, A;
McMillan, LEM;
Yeats, C;
Clegg, AB;
Orengo, CA;
Martin, ACR;
(2009)
An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D.
BMC BIOINFORMATICS
, 10
, Article S5. 10.1186/1471-2105-10-S8-S5.
|
|
|
Jeffries, JWE;
Dawson, N;
Orengo, C;
Moody, TS;
Quinn, DJ;
Hailes, HC;
Ward, JM;
(2016)
Metagenome Mining: A Sequence Directed Strategy for the Retrieval of Enzymes for Biocatalysis.
ChemistrySelect
, 1
(10)
pp. 2217-2220.
10.1002/slct.201600515.
|
|
Jiang, Y;
Oron, TR;
Clark, WT;
Bankapur, AR;
D'Andrea, D;
Lepore, R;
Funk, CS;
... Radivojac, P; + view all
(2016)
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Genome Biology
, 17
, Article 184. 10.1186/s13059-016-1037-6.
|
|
|
Kilpatrick, AM;
Rahman, F;
Anjum, A;
Shome, S;
Andalib, KMS;
Banik, S;
Chowdhury, SF;
... Welch, L; + view all
(2022)
Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia.
Bioinformatics
, 38
(1)
i19-i27.
10.1093/bioinformatics/btac236.
|
|
Lam, SD;
Waman, VP;
Fraternali, F;
Orengo, C;
Lees, J;
(2022)
Structural and energetic analyses of SARS-CoV-2 N-terminal domain characterise sugar binding pockets and suggest putative impacts of variants on COVID-19 transmission.
Computational and Structural Biotechnology Journal
, 20
pp. 6302-6316.
10.1016/j.csbj.2022.11.004.
|
|
Lam, SD;
Ashford, P;
Díaz-Sánchez, S;
Villar, M;
Gortázar, C;
de la Fuente, J;
Orengo, C;
(2021)
Arthropod Ectoparasites Have Potential to Bind SARS-CoV-2 via ACE.
Viruses
, 13
(4)
, Article 708. 10.3390/v13040708.
|
|
|
Lam, SD;
Babu, MM;
Lees, J;
Orengo, CA;
(2021)
Biological impact of mutually exclusive exon switching.
PLoS Computational Biology
, 17
(3)
, Article e1008708. 10.1371/journal.pcbi.1008708.
|
|
|
Lam, SD;
Bordin, N;
Waman, VP;
Scholes, HM;
Ashford, P;
Sen, N;
van Dorp, L;
... Orengo, CA; + view all
(2020)
SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals.
Scientific Reports
, 10
, Article 16471. 10.1038/s41598-020-71936-5.
|
|
|
Lam, SD;
Das, S;
Sillitoe, I;
Orengo, C;
(2017)
An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences.
Acta Crystallographica Section D
, 73
pp. 628-640.
10.1107/S2059798317008920.
|
|
|
Lam, SD;
Dawson, NL;
Das, S;
Sillitoe, I;
Ashford, P;
Lee, D;
Lehtinen, S;
... Lees, JG; + view all
(2016)
Gene3D: expanding the utility of domain assignments.
Nucleic Acids Res
, 44
(D1)
D404-D409.
10.1093/nar/gkv1231.
|
|
|
Larcombe, L;
Hendricusdottir, R;
Attwood, TK;
Bacall, F;
Beard, N;
Bellis, LJ;
Dunn, WB;
... Rustici, G; + view all
(2017)
ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.
F1000Research
, 6
, Article 952. 10.12688/f1000research.11837.1.
|
|
|
Laskowski, RA;
Stephenson, JD;
Sillitoe, I;
Orengo, CA;
Thornton, JM;
(2020)
VarSite: disease variants and protein structure.
Protein Science
, 29
(1)
pp. 111-119.
10.1002/pro.3746.
|
|
|
Lee, D;
Das, S;
Dawson, NL;
Dobrijevic, D;
Ward, J;
Orengo, C;
(2016)
Novel computational protocols for functionally classifying and characterising serine beta-lactamases.
PLoS Computational Biology
, 12
(6)
, Article e1004926. 10.1371/journal.pcbi.1004926.
|
|
Lee, D;
de Beer, TAP;
Laskowski, RA;
Thornton, JM;
Orengo, CA;
(2011)
1,000 structures and more from the MCSG.
BMC STRUCT BIOL
, 11
, Article 2. 10.1186/1472-6807-11-2.
|
|
|
Lees, JG;
Dawson, NL;
Sillitoe, I;
Orengo, CA;
(2016)
Functional innovation from changes in protein domains and their combinations.
Current Opinion in Structural Biology
, 38
pp. 44-52.
10.1016/j.sbi.2016.05.016.
|
|
|
Lees, JG;
Lee, D;
Studer, RA;
Dawson, NL;
Sillitoe, I;
Das, S;
Yeats, C;
... Orengo, CA; + view all
(2013)
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis.
Nucleic Acids Research
, 42
(D1)
D240-D245.
10.1093/nar/gkt1205.
|
|
|
Lees, JG;
Ranea, JA;
Orengo, CA;
(2015)
Identifying and characterising key alternative splicing events in Drosophila development.
BMC Genomics
, 16
, Article 608. 10.1186/s12864-015-1674-2.
|
|
|
Lehtinen, S;
Bähler, J;
Orengo, C;
(2015)
Co-Expression Network Models Suggest that Stress Increases Tolerance to Mutations.
Scientific Reports
, 5
, Article 16726. 10.1038/srep16726.
|
|
|
Lehtinen, S;
Lees, J;
Bähler, J;
Shawe-Taylor, J;
Orengo, C;
(2015)
Gene Function Prediction from Functional Association Networks Using Kernel Partial Least Squares Regression.
PLoS One
, 10
(8)
, Article e0134668. 10.1371/journal.pone.0134668.
|
|
|
Lewis, T;
Sillitoe, I;
Dawson, N;
Lam, SD;
Clarke, T;
Lee, D;
Orengo, C;
(2017)
Gene3D: Extensive prediction of globular domains in proteins.
Nucleic Acids Research
, Article gkx1069. 10.1093/nar/gkx1069/4588111.
|
|
|
Lewis, TE;
Sillitoe, I;
Andreeva, A;
Blundell, TL;
Buchan, DW;
Chothia, C;
Cozzetto, D;
... Orengo, C; + view all
(2014)
Genome3D: exploiting structure to help users understand their sequences.
Nucleic Acids Research
, 43
(D1)
D382-D386.
10.1093/nar/gku973.
|
|
|
Lewis, TE;
Sillitoe, I;
Andreeva, A;
Blundell, TL;
Buchan, DW;
Chothia, C;
Cuff, A;
... Orengo, C; + view all
(2013)
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.
Nucleic Acids Research
, 41
(Databa)
D499 - D507.
10.1093/nar/gks1266.
|
|
|
Lewis, TE;
Sillitoe, I;
Dawson, N;
Lam, SD;
Clarke, T;
Lee, D;
Orengo, C;
(2017)
Gene3D: Extensive prediction of globular domains in proteins.
[Corrigendum].
Nucleic Acids Research
10.1093/nar/gkx1187.
|
|
|
Lin, W;
Wells, J;
Wang, Z;
Orengo, C;
Martin, ACR;
(2024)
Enhancing missense variant pathogenicity prediction with protein language models using VariPred.
Scientific Reports
, 14
(1)
, Article 8136. 10.1038/s41598-024-51489-7.
|
|
Littmann, M;
Bordin, N;
Heinzinger, M;
Schütze, K;
Dallago, C;
Orengo, C;
Rost, B;
(2021)
Clustering FunFams using sequence embeddings improves EC purity.
Bioinformatics
, 37
(20)
pp. 3449-3455.
10.1093/bioinformatics/btab371.
|
|
|
Lobley, A;
Swindells, MB;
Orengo, CA;
Jones, DT;
(2007)
Inferring function using patterns of native disorder in proteins.
PLOS COMPUT BIOL
, 3
(8)
, Article e162. 10.1371/journal.pcbi.0030162.
|
|
|
Lombardi, B;
Ashford, P;
Moya-Garcia, AA;
Rust, A;
Crawford, M;
Williams, SV;
Knowles, MA;
... Godovac-Zimmermann, J; + view all
(2017)
Unique signalling connectivity of FGFR3-TACC3 oncoprotein revealed by quantitative phosphoproteomics and differential network analysis.
Oncotarget
, 8
(61)
pp. 102898-102911.
10.18632/oncotarget.22048.
|
|
|
Maréchal, A;
Meunier, B;
Lee, D;
Orengo, C;
Rich, PR;
(2012)
Yeast cytochrome c oxidase: a model system to study mitochondrial forms of the haem-copper oxidase superfamily.
Biochimica et Biophysica Acta (BBA) - Bioenergetics
, 1817
(4)
620 - 628.
10.1016/j.bbabio.2011.08.011.
|
|
|
Marsden, RL;
Lewis, TA;
Orengo, CA;
(2007)
Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint.
BMC BIOINFORMATICS
, 8
, Article 86. 10.1186/1471-2105-8-86.
|
|
|
Mitchell, AL;
Attwood, TK;
Babbitt, PC;
Blum, M;
Bork, P;
Bridge, A;
Brown, SD;
... Finn, RD; + view all
(2018)
InterPro in 2019: improving coverage, classification and access to protein sequence annotations.
Nucleic Acids Research
10.1093/nar/gky1100.
|
|
|
Moya-García, A;
Adeyelu, T;
Kruger, FA;
Dawson, NL;
Lees, JG;
Overington, JP;
Orengo, C;
(2017)
Structural and Functional View of Polypharmacology.
Scientific Reports
, 7
, Article 10102. 10.1038/s41598-017-10012-x.
|
 |
|
Mulder, NJ;
Apweiler, R;
Attwood, TK;
Bairoch, A;
Bateman, A;
Binns, D;
Bork, P;
... Yeats, C; + view all
(2007)
New developments in the InterPro database.
Nucleic Acids Research
, 35
(Supple)
, Article D224-D228. 10.1093/nar/gkl841.
|
|
|
Nallapareddy, Vamsi;
Bordin, Nicola;
Sillitoe, Ian;
Heinzinger, Michael;
Littmann, Maria;
Waman, Vaishali P;
Sen, Neeladri;
... Orengo, Christine; + view all
(2023)
CATHe: Detection of remote homologues for CATH superfamilies using embeddings from protein language models.
Bioinformatics
, 39
(1)
, Article btad029. 10.1093/bioinformatics/btad029.
|
|
Orengo, C;
Velankar, S;
Wodak, S;
Zoete, V;
Bonvin, AMJJ;
Elofsson, A;
Feenstra, KA;
... Schneider, B; + view all
(2020)
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community).
F1000Research
, 9
, Article 278. 10.12688/f1000research.20559.1.
|
|
|
Patani, H;
Bunney, TD;
Thiyagarajan, N;
Norman, RA;
Ogg, D;
Breed, J;
Ashford, P;
... Katan, M; + view all
(2016)
Landscape of activating cancer mutations in FGFR kinases and their differential responses to inhibitors in clinical use.
Oncotarget
, 7
(17)
pp. 24252-24268.
10.18632/oncotarget.8132.
|
|
|
Paysan-Lafosse, Typhaine;
Blum, Matthias;
Chuguransky, Sara;
Grego, Tiago;
Pinto, Beatriz Lázaro;
Salazar, Gustavo A;
Bileschi, Maxwell L;
... Bateman, Alex; + view all
(2023)
InterPro in 2022.
Nucleic Acids Research
, 51
(D1)
D418-D427.
10.1093/nar/gkac993.
|
|
PDBe-KB consortium;
(2020)
PDBe-KB: a community-driven resource for structural and functional annotations.
Nucleic Acids Research
, 48
(D1)
D344-D353.
10.1093/nar/gkz853.
|
|
|
Perkins, JR;
Antunes-Martins, A;
Calvo, M;
Grist, J;
Rust, W;
Schmid, R;
Hildebrandt, T;
... Bennett, DLH; + view all
(2014)
A comparison of RNA-seq and exon arrays for whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat.
MOLECULAR PAIN
, 10
, Article ARTN 7. 10.1186/1744-8069-10-7.
|
|
|
Perkins, JR;
Dawes, JM;
McMahon, SB;
Bennett, DL;
Orengo, C;
Kohl, M;
(2012)
ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data.
BMC Genomics
, 13
, Article 296. 10.1186/1471-2164-13-296.
|
 |
|
Perkins, JR;
Dawes, JM;
McMahon, SB;
Bennett, DL;
Orengo, C;
Kohl, M;
(2012)
ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data.
BMC Genomics
, 13
, Article 296. 10.1186/1471-2164-13-296.
|
|
|
Perkins, JR;
Lees, J;
Antunes-Martins, A;
Diboun, I;
McMahon, SB;
Bennett, DL;
Orengo, C;
(2013)
PainNetworks: a web-based resource for the visualisation of pain-related genes in the context of their network associations.
Pain
, 154
(12)
2586.e1-2586.12.
10.1016/j.pain.2013.09.003.
|
|
Radivojac, P;
Clark, WT;
Oron, TR;
Schnoes, AM;
Wittkop, T;
Sokolov, A;
Graim, K;
... Friedberg, I; + view all
(2013)
A large-scale evaluation of computational protein function prediction.
Nature Methods
, 10
(3)
pp. 221-227.
10.1038/NMETH.2340.
|
|
|
Rallapalli, PM;
Orengo, CA;
Studer, RA;
Perkins, SJ;
(2014)
Positive selection during the evolution of the blood coagulation factors in the context of their disease-causing mutations.
Molecular Biology and Evolution
, 31
(11)
pp. 3040-3056.
10.1093/molbev/msu248.
|
|
|
Ranea, JAG;
Morilla, I;
Lees, JG;
Reid, AJ;
Yeats, C;
Clegg, AB;
Sanchez-Jimenez, F;
(2010)
Finding the "Dark Matter'' in Human and Yeast Protein Network Prediction and Modelling.
PLOS COMPUT BIOL
, 6
(9)
, Article e1000945. 10.1371/journal.pcbi.1000945.
|
|
|
Ranea, JAG;
Yeats, C;
Grant, A;
Orengo, CA;
(2007)
Predicting protein function with hierarchical phylogenetic profiles: The Gene3D phylo-tuner method applied to eukaryotic Genomes.
PLoS Computational Biology
, 3
(11)
, Article e237. 10.1371/journal.pcbi.0030237.
|
|
|
Rauer, C;
Sen, N;
Waman, VP;
Abbasian, M;
Orengo, CA;
(2021)
Computational approaches to predict protein functional families and functional sites.
Current Opinion in Structural Biology
, 70
pp. 108-122.
10.1016/j.sbi.2021.05.012.
|
|
Redfern, OC;
Dessailly, BH;
Dallman, TJ;
Sillitoe, I;
Orengo, CA;
(2009)
FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies.
PLOS COMPUT BIOL
, 5
(8)
, Article e1000485. 10.1371/journal.pcbi.1000485.
|
|
|
Redfern, OC;
Harrison, A;
Dallman, T;
Pearl, FMG;
Orengo, CA;
(2007)
CATHEDRAL: A fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures.
PLOS COMPUT BIOL
, 3
(11)
, Article e232. 10.1371/journal.pcbi.0030232.
|
|
|
Reid, AJ;
Ranea, JAG;
Clegg, AB;
Orengo, CA;
(2010)
CODA: Accurate Detection of Functional Associations between Proteins in Eukaryotic Genomes Using Domain Fusion.
PLOS ONE
, 5
(6)
, Article e10908. 10.1371/journal.pone.0010908.
|
|
|
Reid, AJ;
Ranea, JAG;
Orengo, CA;
(2010)
Comparative evolutionary analysis of protein complexes in E. coli and yeast.
BMC GENOMICS
, 11
, Article 79. 10.1186/1471-2164-11-79.
|
|
|
Rodríguez-López, María;
Bordin, Nicola;
Lees, Jon;
Scholes, Harry;
Hassan, Shaimaa;
Saintain, Quentin;
Kamrad, Stephan;
... Bähler, Jürg; + view all
(2023)
Broad functional profiling of fission yeast proteins using phenomics and machine learning.
eLife
, 12
10.7554/elife.88229.3.
|
|
|
Rojano, Elena;
Jabato, Fernando M;
Perkins, James R;
Cordoba-Caballero, Jose;
Garcia-Criado, Federico;
Sillitoe, Ian;
Orengo, Christine;
... Seoane-Zonjic, Pedro; + view all
(2022)
Assigning protein function from domain-function associations using DomFun.
BMC Bioinformatics
, 23
(1)
, Article 43. 10.1186/s12859-022-04565-6.
|
|
|
Rojas, AM;
Santamaria, A;
Malik, R;
Jensen, TS;
Körner, R;
Morilla, I;
de Juan, D;
... Ranea, JA; + view all
(2012)
Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology.
PLoS One
, 7
(3)
, Article e31813. 10.1371/journal.pone.0031813.
|
|
|
Scheibenreif, L;
Littmann, M;
Orengo, C;
Rost, B;
(2019)
FunFam protein families improve residue level molecular function prediction.
BMC Bioinformatics
, 20
(1)
, Article 400. 10.1186/s12859-019-2988-x.
|
|
|
Scholes, HM;
Cryar, A;
Kerr, F;
Sutherland, D;
Gethings, LA;
Vissers, JPC;
Lees, JG;
... Thalassinos, K; + view all
(2020)
Dynamic changes in the brain protein interaction network correlates with progression of Aβ42 pathology in Drosophila.
Scientific Reports
, 10
, Article 18517. 10.1038/s41598-020-74748-9.
|
|
|
Sen, Neeladri;
Anishchenko, Ivan;
Bordin, Nicola;
Sillitoe, Ian;
Velankar, Sameer;
Baker, David;
Orengo, Christine;
(2022)
Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs.
Briefings in Bioinformatics
10.1093/bib/bbac187.
(In press).
|
|
Sillitoe, I;
Andreeva, A;
Blundell, TL;
Buchan, DWA;
Finn, RD;
Gough, J;
Jones, D;
... Orengo, C; + view all
(2019)
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation.
Nucleic Acids Research
10.1093/nar/gkz967.
(In press).
|
|
|
Sillitoe, I;
Bordin, N;
Dawson, N;
Waman, VP;
Ashford, P;
Scholes, HM;
Pang, CSM;
... Orengo, CA; + view all
(2020)
CATH: increased structural coverage of functional space.
Nucleic Acids Research
10.1093/nar/gkaa1079.
(In press).
|
|
|
Sillitoe, I;
Dawson, N;
Lewis, TE;
Das, S;
Lees, JG;
Ashford, P;
Tolulope, A;
... Orengo, CA; + view all
(2019)
CATH: expanding the horizons of structure-based functional annotations for genome sequences.
Nucleic Acids Research
, 47
(D1)
D280-D284.
10.1093/nar/gky1097.
|
|
Sillitoe, I;
Dawson, N;
Thornton, J;
Orengo, C;
(2015)
The history of the CATH structural classification of protein domains.
Biochimie
, 119
pp. 209-217.
10.1016/j.biochi.2015.08.004.
|
|
|
Sillitoe, I;
Lewis, TE;
Cuff, A;
Das, S;
Ashford, P;
Dawson, NL;
Furnham, N;
... Orengo, CA; + view all
(2014)
CATH: comprehensive structural and functional annotations for genome sequences.
Nucleic Acids Research
, 43
(D1)
D376-D381.
10.1093/nar/gku947.
|
|
|
Swift, S;
Tucker, A;
Vinciotti, V;
Martin, N;
Orengo, C;
Liu, XH;
Kellam, P;
(2004)
Consensus clustering and functional interpretation of gene-expression data.
GENOME BIOLOGY
, 5
, Article R94. 10.1186/gb-2004-5-11-r94.
|
|
|
Tan, Cedric CS;
Lam, Su Datt;
Richard, Damien;
Owen, Christopher J;
Berchtold, Dorothea;
Orengo, Christine;
Nair, Meera Surendran;
... Balloux, François; + view all
(2022)
Transmission of SARS-CoV-2 from humans to animals and potential host adaptation.
Nature Communications
, 13
(1)
, Article 2988. 10.1038/s41467-022-30698-6.
|
|
Thornton, J;
Orengo, C;
(2017)
Editorial overview: Catalysis and regulation.
[Editorial comment].
Current Opinion in Structural Biology
, 47
vi-viii.
10.1016/j.sbi.2017.11.005.
|
|
Tsuchiya, Y;
Zhyvoloup, A;
Bakovic, J;
Thomas, N;
Yi Kun Yu, B;
Das, S;
Orengo, C;
... Gout, I; + view all
(2018)
Protein CoAlation and antioxidant function of Coenzyme A in prokaryotic cells.
Biochemical Journal
, 475
(11)
pp. 1909-1937.
10.1042/BCJ20180043.
|
|
Tubiana, Thibault;
Sillitoe, Ian;
Orengo, Christine;
Reuter, Nathalie;
(2022)
Dissecting peripheral protein-membrane interfaces.
PLoS Computational Biology
, 18
(12)
, Article e1010346. 10.1371/journal.pcbi.1010346.
|
|
Tyzack, JD;
Furnham, N;
Sillitoe, I;
Orengo, CM;
Thornton, JM;
(2019)
Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function.
Methods in Molecular Biology
, 1851
pp. 263-275.
10.1007/978-1-4939-8736-8_14.
|
|
Tyzack, JD;
Furnham, N;
Sillitoe, I;
Orengo, CM;
Thornton, JM;
(2017)
Understanding enzyme function evolution from a computational perspective.
Curr Opin Struct Biol
, 47
pp. 131-139.
10.1016/j.sbi.2017.08.003.
|
|
|
Vallat, B;
Tauriello, G;
Bienert, S;
Haas, J;
Webb, BM;
Žídek, A;
Zheng, W;
... Westbrook, JD; + view all
(2023)
ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.
Journal of Molecular Biology
, Article 168021. 10.1016/j.jmb.2023.168021.
(In press).
|
|
Varadi, M;
Bordin, N;
Orengo, C;
Velankar, S;
(2023)
The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors.
Current Opinion in Structural Biology
, 79
, Article 102543. 10.1016/j.sbi.2023.102543.
(In press).
|
|
Varadi, Mihaly;
Anyango, Stephen;
Armstrong, David;
Berrisford, John;
Choudhary, Preeti;
Deshpande, Mandar;
Nadzirin, Nurul;
... Velankar, Sameer; + view all
(2022)
PDBe-KB: collaboratively defining the biological context of structural data.
Nucleic Acids Research
, 50
(D1)
D534-D542.
10.1093/nar/gkab988.
|
|
|
Varadi, Mihaly;
Nair, Sreenath;
Sillitoe, Ian;
Tauriello, Gerardo;
Anyango, Stephen;
Bienert, Stefan;
Borges, Clemente;
... Velankar, Sameer; + view all
(2022)
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources.
Gigascience
, 11
, Article giac118. 10.1093/gigascience/giac118.
|
|
Waman, Vaishali P;
Bordin, Nicola;
Alcraft, Rachel;
Vickerstaff, Robert;
Rauer, Clemens;
Chan, Qian;
Sillitoe, Ian;
... Orengo, Christine; + view all
(2024)
CATH 2024: CATH-AlphaFlow Doubles the Number of Structures in CATH and Reveals Nearly 200 New Folds.
Journal of Molecular Biology
, Article 168551. 10.1016/j.jmb.2024.168551.
(In press).
|
|
Waman, VP;
Ashford, P;
Lam, SD;
Sen, N;
Abbasian, M;
Woodridge, L;
Goldtzvik, Y;
... Orengo, CA; + view all
(2024)
Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics.
Scientific Reports
, 14
, Article 14208. 10.1038/s41598-024-61541-1.
|
|
Waman, VP;
Orengo, C;
Kleywegt, GJ;
Lesk, AM;
(2021)
Three-dimensional Structure Databases of Biological Macromolecules.
Data Mining Techniques for the Life Sciences. Methods in Molecular Biology
, 2449
pp. 43-91.
10.1007/978-1-0716-2095-3_3.
|
|
Waman, VP;
Sen, N;
Varadi, M;
Daina, A;
Wodak, SJ;
Zoete, V;
Velankar, S;
(2021)
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies.
Briefings in Bioinformatics
, 22
(2)
pp. 742-768.
10.1093/bib/bbaa362.
|
|
Wan, C;
Lees, JG;
Minneci, F;
Orengo, CA;
Jones, DT;
(2017)
Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster.
PLoS Computational Biology
, 13
(10)
, Article e1005791. 10.1371/journal.pcbi.1005791.
|
|
|
Yeats, C;
Lees, J;
Carter, P;
Sillitoe, I;
Orengo, C;
(2011)
The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences.
Nucleic Acids Research
, 39
W546-W550.
10.1093/nar/gkr438.
|
|
|
Yeats, C;
Lees, J;
Reid, A;
Kellam, P;
Liu, X;
Orengo, C;
Martin, N;
(2008)
Gene3D: Comprehensive structural and functional annotation of genomes.
Nucleic Acids Research
, 36
(SUPPL.)
D414- D418.
10.1093/nar/gkm1019.
|
|
|
Yu-Wai-Man, C;
Owen, N;
Lees, J;
Tagalakis, AD;
Hart, SL;
Webster, AR;
Orengo, CA;
(2017)
Genome-wide RNA-Sequencing analysis identifies a distinct fibrosis gene signature in the conjunctiva after glaucoma surgery.
Scientific Reports
, 7
, Article 5644. 10.1038/s41598-017-05780-5.
|
|
|
Zhou, N;
Jiang, Y;
Bergquist, TR;
Lee, AJ;
Kacsoh, BZ;
Crocker, AW;
Lewis, KA;
... Friedberg, I; + view all
(2019)
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
Genome Biology
, 20
(1)
, Article 244. 10.1186/s13059-019-1835-8.
|
|
Working / discussion paper
|
Lam, SD;
Bordin, N;
Waman, VP;
Scholes, HM;
Ashford, P;
Sen, N;
van Dorp, L;
... Orengo, CA; + view all
(2020)
SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals.
BioRxiv: Cold Spring Harbor, NY, USA.
|
|
The CAFA Consortium;
Jones, D;
Wan, C;
Cozzetto, D;
Fa, R;
(2019)
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
Cold Spring Harbor Laboratory Press
(In press).
|
|
Thesis
|
Baskozos, G;
(2017)
Bioinformatics approaches to identify pain mediators, novel LncRNAs and distinct modalities of neuropathic pain.
Doctoral thesis , UCL (University College London).
|
|
|
Das, S;
(2016)
Functional classification of protein domain superfamilies for protein function annotation.
Doctoral thesis , UCL (University College London).
|
