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Items: 1 to 50 of 73

1.

Variability in Gene Expression is Associated with Incomplete Penetrance in Inherited Eye Disorders.

Green DJ, Sallah SR, Ellingford JM, Lovell SC, Sergouniotis PI.

Genes (Basel). 2020 Feb 9;11(2). pii: E179. doi: 10.3390/genes11020179.

2.

Severe type I interferonopathy and unrestrained interferon signaling due to a homozygous germline mutation in STAT2.

Duncan CJA, Thompson BJ, Chen R, Rice GI, Gothe F, Young DF, Lovell SC, Shuttleworth VG, Brocklebank V, Corner B, Skelton AJ, Bondet V, Coxhead J, Duffy D, Fourrage C, Livingston JH, Pavaine J, Cheesman E, Bitetti S, Grainger A, Acres M, Innes BA, Mikulasova A, Sun R, Hussain R, Wright R, Wynn R, Zarhrate M, Zeef LAH, Wood K, Hughes SM, Harris CL, Engelhardt KR, Crow YJ, Randall RE, Kavanagh D, Hambleton S, Briggs TA.

Sci Immunol. 2019 Dec 13;4(42). pii: eaav7501. doi: 10.1126/sciimmunol.aav7501.

PMID:
31836668
3.

Reliable Generation of Native-Like Decoys Limits Predictive Ability in Fragment-Based Protein Structure Prediction.

Kandathil SM, Garza-Fabre M, Handl J, Lovell SC.

Biomolecules. 2019 Oct 15;9(10). pii: E612. doi: 10.3390/biom9100612.

4.

Biochemical and structural analyses suggest that plasminogen activators coevolved with their cognate protein substrates and inhibitors.

Jendroszek A, Madsen JB, Chana-Muñoz A, Dupont DM, Christensen A, Panitz F, Füchtbauer EM, Lovell SC, Jensen JK.

J Biol Chem. 2019 Mar 8;294(10):3794-3805. doi: 10.1074/jbc.RA118.005419. Epub 2019 Jan 16.

PMID:
30651349
5.

Improved fragment-based protein structure prediction by redesign of search heuristics.

Kandathil SM, Garza-Fabre M, Handl J, Lovell SC.

Sci Rep. 2018 Sep 12;8(1):13694. doi: 10.1038/s41598-018-31891-8.

6.

Non-muscle myosin IIB (Myh10) is required for epicardial function and coronary vessel formation during mammalian development.

Ridge LA, Mitchell K, Al-Anbaki A, Shaikh Qureshi WM, Stephen LA, Tenin G, Lu Y, Lupu IE, Clowes C, Robertson A, Barnes E, Wright JA, Keavney B, Ehler E, Lovell SC, Kadler KE, Hentges KE.

PLoS Genet. 2017 Oct 30;13(10):e1007068. doi: 10.1371/journal.pgen.1007068. eCollection 2017 Oct.

7.

MolProbity: More and better reference data for improved all-atom structure validation.

Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB 3rd, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC.

Protein Sci. 2018 Jan;27(1):293-315. doi: 10.1002/pro.3330. Epub 2017 Nov 27.

8.

Adaptive HIV-1 evolutionary trajectories are constrained by protein stability.

Olabode AS, Kandathil SM, Lovell SC, Robertson DL.

Virus Evol. 2017 Aug 1;3(2):vex019. doi: 10.1093/ve/vex019. eCollection 2017 Jul.

9.

Rapid functional and evolutionary changes follow gene duplication in yeast.

Naseeb S, Ames RM, Delneri D, Lovell SC.

Proc Biol Sci. 2017 Aug 30;284(1861). pii: 20171393. doi: 10.1098/rspb.2017.1393.

10.

The role of small in-frame insertions/deletions in inherited eye disorders and how structural modelling can help estimate their pathogenicity.

Sergouniotis PI, Barton SJ, Waller S, Perveen R, Ellingford JM, Campbell C, Hall G, Gillespie RL, Bhaskar SS, Ramsden SC, Black GC, Lovell SC.

Orphanet J Rare Dis. 2016 Sep 14;11(1):125. doi: 10.1186/s13023-016-0505-0.

11.

Generating, Maintaining, and Exploiting Diversity in a Memetic Algorithm for Protein Structure Prediction.

Garza-Fabre M, Kandathil SM, Handl J, Knowles J, Lovell SC.

Evol Comput. 2016 Winter;24(4):577-607. Epub 2016 Feb 23.

PMID:
26908350
12.

Binding interface change and cryptic variation in the evolution of protein-protein interactions.

Ames RM, Talavera D, Williams SG, Robertson DL, Lovell SC.

BMC Evol Biol. 2016 Feb 18;16:40. doi: 10.1186/s12862-016-0608-1.

13.

Toward a detailed understanding of search trajectories in fragment assembly approaches to protein structure prediction.

Kandathil SM, Handl J, Lovell SC.

Proteins. 2016 Apr;84(4):411-26. doi: 10.1002/prot.24987. Epub 2016 Feb 23.

14.

Covariation Is a Poor Measure of Molecular Coevolution.

Talavera D, Lovell SC, Whelan S.

Mol Biol Evol. 2015 Sep;32(9):2456-68. doi: 10.1093/molbev/msv109. Epub 2015 May 4.

15.

Ebolavirus is evolving but not changing: No evidence for functional change in EBOV from 1976 to the 2014 outbreak.

Olabode AS, Jiang X, Robertson DL, Lovell SC.

Virology. 2015 Aug;482:202-7. doi: 10.1016/j.virol.2015.03.029. Epub 2015 Apr 14.

16.

Agnathia-otocephaly complex and asymmetric velopharyngeal insufficiency due to an in-frame duplication in OTX2.

Sergouniotis PI, Urquhart JE, Williams SG, Bhaskar SS, Black GC, Lovell SC, Whitby DJ, Newman WG, Clayton-Smith J.

J Hum Genet. 2015 Apr;60(4):199-202. doi: 10.1038/jhg.2014.122. Epub 2015 Jan 15.

PMID:
25589041
17.

Abrogation of HMX1 function causes rare oculoauricular syndrome associated with congenital cataract, anterior segment dysgenesis, and retinal dystrophy.

Gillespie RL, Urquhart J, Lovell SC, Biswas S, Parry NR, Schorderet DF, Lloyd IC, Clayton-Smith J, Black GC.

Invest Ophthalmol Vis Sci. 2015 Jan 8;56(2):883-91. doi: 10.1167/iovs.14-15861.

PMID:
25574057
18.

DupliPHY-Web: a web server for DupliPHY and DupliPHY-ML.

Ames RM, Lovell SC.

Bioinformatics. 2015 Feb 1;31(3):416-7. doi: 10.1093/bioinformatics/btu645. Epub 2014 Oct 7.

19.

Erbb2 is required for cardiac atrial electrical activity during development.

Tenin G, Clowes C, Wolton K, Krejci E, Wright JA, Lovell SC, Sedmera D, Hentges KE.

PLoS One. 2014 Sep 30;9(9):e107041. doi: 10.1371/journal.pone.0107041. eCollection 2014.

20.

Inferring gene family histories in yeast identifies lineage specific expansions.

Ames RM, Money D, Lovell SC.

PLoS One. 2014 Jun 12;9(6):e99480. doi: 10.1371/journal.pone.0099480. eCollection 2014.

21.

Constraints from protein structure and intra-molecular coevolution influence the fitness of HIV-1 recombinants.

Woo J, Robertson DL, Lovell SC.

Virology. 2014 Apr;454-455:34-9. doi: 10.1016/j.virol.2014.01.029. Epub 2014 Feb 22.

22.

Sequencing and characterisation of rearrangements in three S. pastorianus strains reveals the presence of chimeric genes and gives evidence of breakpoint reuse.

Hewitt SK, Donaldson IJ, Lovell SC, Delneri D.

PLoS One. 2014 Mar 18;9(3):e92203. doi: 10.1371/journal.pone.0092203. eCollection 2014.

23.

Mutations in non-acid patch residues disrupt H2A.Z's association with chromatin through multiple mechanisms.

Wood TJ, Thistlethwaite A, Harris MR, Lovell SC, Millar CB.

PLoS One. 2013 Oct 1;8(10):e76394. doi: 10.1371/journal.pone.0076394. eCollection 2013.

24.

Modular biological function is most effectively captured by combining molecular interaction data types.

Ames RM, Macpherson JI, Pinney JW, Lovell SC, Robertson DL.

PLoS One. 2013 May 3;8(5):e62670. doi: 10.1371/journal.pone.0062670. Print 2013.

25.

The role of protein interactions in mediating essentiality and synthetic lethality.

Talavera D, Robertson DL, Lovell SC.

PLoS One. 2013 Apr 29;8(4):e62866. doi: 10.1371/journal.pone.0062866. Print 2013.

26.

Alternative splicing and protein interaction data sets.

Talavera D, Robertson DL, Lovell SC.

Nat Biotechnol. 2013 Apr;31(4):292-3. doi: 10.1038/nbt.2540. No abstract available.

PMID:
23563420
27.

Analysis of genetic interaction networks shows that alternatively spliced genes are highly versatile.

Talavera D, Sheoran R, Lovell SC.

PLoS One. 2013;8(2):e55671. doi: 10.1371/journal.pone.0055671. Epub 2013 Feb 7.

28.

The origins of the evolutionary signal used to predict protein-protein interactions.

Swapna LS, Srinivasan N, Robertson DL, Lovell SC.

BMC Evol Biol. 2012 Dec 6;12:238. doi: 10.1186/1471-2148-12-238.

29.

Mutations in ADAR1 cause Aicardi-Goutières syndrome associated with a type I interferon signature.

Rice GI, Kasher PR, Forte GM, Mannion NM, Greenwood SM, Szynkiewicz M, Dickerson JE, Bhaskar SS, Zampini M, Briggs TA, Jenkinson EM, Bacino CA, Battini R, Bertini E, Brogan PA, Brueton LA, Carpanelli M, De Laet C, de Lonlay P, del Toro M, Desguerre I, Fazzi E, Garcia-Cazorla A, Heiberg A, Kawaguchi M, Kumar R, Lin JP, Lourenco CM, Male AM, Marques W Jr, Mignot C, Olivieri I, Orcesi S, Prabhakar P, Rasmussen M, Robinson RA, Rozenberg F, Schmidt JL, Steindl K, Tan TY, van der Merwe WG, Vanderver A, Vassallo G, Wakeling EL, Wassmer E, Whittaker E, Livingston JH, Lebon P, Suzuki T, McLaughlin PJ, Keegan LP, O'Connell MA, Lovell SC, Crow YJ.

Nat Genet. 2012 Nov;44(11):1243-8. doi: 10.1038/ng.2414. Epub 2012 Sep 23.

30.

The interface of protein structure, protein biophysics, and molecular evolution.

Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S.

Protein Sci. 2012 Jun;21(6):769-85. doi: 10.1002/pro.2071. Epub 2012 Apr 23. Review.

31.

Evolvability of yeast protein-protein interaction interfaces.

Talavera D, Williams SG, Norris MG, Robertson DL, Lovell SC.

J Mol Biol. 2012 Jun 22;419(5):387-96. doi: 10.1016/j.jmb.2012.03.021. Epub 2012 Apr 1.

PMID:
22472422
32.

Mutations in CTC1, encoding conserved telomere maintenance component 1, cause Coats plus.

Anderson BH, Kasher PR, Mayer J, Szynkiewicz M, Jenkinson EM, Bhaskar SS, Urquhart JE, Daly SB, Dickerson JE, O'Sullivan J, Leibundgut EO, Muter J, Abdel-Salem GM, Babul-Hirji R, Baxter P, Berger A, Bonafé L, Brunstom-Hernandez JE, Buckard JA, Chitayat D, Chong WK, Cordelli DM, Ferreira P, Fluss J, Forrest EH, Franzoni E, Garone C, Hammans SR, Houge G, Hughes I, Jacquemont S, Jeannet PY, Jefferson RJ, Kumar R, Kutschke G, Lundberg S, Lourenço CM, Mehta R, Naidu S, Nischal KK, Nunes L, Ounap K, Philippart M, Prabhakar P, Risen SR, Schiffmann R, Soh C, Stephenson JB, Stewart H, Stone J, Tolmie JL, van der Knaap MS, Vieira JP, Vilain CN, Wakeling EL, Wermenbol V, Whitney A, Lovell SC, Meyer S, Livingston JH, Baerlocher GM, Black GC, Rice GI, Crow YJ.

Nat Genet. 2012 Jan 22;44(3):338-42. doi: 10.1038/ng.1084.

PMID:
22267198
33.

The dual role of fragments in fragment-assembly methods for de novo protein structure prediction.

Handl J, Knowles J, Vernon R, Baker D, Lovell SC.

Proteins. 2012 Feb;80(2):490-504. doi: 10.1002/prot.23215. Epub 2011 Nov 17.

34.

Determining the evolutionary history of gene families.

Ames RM, Money D, Ghatge VP, Whelan S, Lovell SC.

Bioinformatics. 2012 Jan 1;28(1):48-55. doi: 10.1093/bioinformatics/btr592. Epub 2011 Oct 28.

PMID:
22039210
35.

Using knowledge of protein structural constraints to predict the evolution of HIV-1.

Williams SG, Madan R, Norris MG, Archer J, Mizuguchi K, Robertson DL, Lovell SC.

J Mol Biol. 2011 Jul 29;410(5):1023-34. doi: 10.1016/j.jmb.2011.04.037.

PMID:
21763504
36.

Characterization of protein-protein interaction interfaces from a single species.

Talavera D, Robertson DL, Lovell SC.

PLoS One. 2011;6(6):e21053. doi: 10.1371/journal.pone.0021053. Epub 2011 Jun 27.

37.

Diversification at transcription factor binding sites within a species and the implications for environmental adaptation.

Ames RM, Lovell SC.

Mol Biol Evol. 2011 Dec;28(12):3331-44. doi: 10.1093/molbev/msr167. Epub 2011 Jun 20.

PMID:
21693437
38.

Tartrate-resistant acid phosphatase deficiency causes a bone dysplasia with autoimmunity and a type I interferon expression signature.

Briggs TA, Rice GI, Daly S, Urquhart J, Gornall H, Bader-Meunier B, Baskar K, Baskar S, Baudouin V, Beresford MW, Black GC, Dearman RJ, de Zegher F, Foster ES, Francès C, Hayman AR, Hilton E, Job-Deslandre C, Kulkarni ML, Le Merrer M, Linglart A, Lovell SC, Maurer K, Musset L, Navarro V, Picard C, Puel A, Rieux-Laucat F, Roifman CM, Scholl-Bürgi S, Smith N, Szynkiewicz M, Wiedeman A, Wouters C, Zeef LA, Casanova JL, Elkon KB, Janckila A, Lebon P, Crow YJ.

Nat Genet. 2011 Feb;43(2):127-31. doi: 10.1038/ng.748. Epub 2011 Jan 9.

39.

Constraints on HIV-1 diversity from protein structure.

Woo J, Robertson DL, Lovell SC.

J Virol. 2010 Dec;84(24):12995-3003. doi: 10.1128/JVI.00702-10. Epub 2010 Sep 29.

40.

Gene duplication and environmental adaptation within yeast populations.

Ames RM, Rash BM, Hentges KE, Robertson DL, Delneri D, Lovell SC.

Genome Biol Evol. 2010;2:591-601. doi: 10.1093/gbe/evq043. Epub 2010 Jul 21.

41.

An integrated view of molecular coevolution in protein-protein interactions.

Lovell SC, Robertson DL.

Mol Biol Evol. 2010 Nov;27(11):2567-75. doi: 10.1093/molbev/msq144. Epub 2010 Jun 14. Review.

PMID:
20551042
42.

Interactions between Kar2p and its nucleotide exchange factors Sil1p and Lhs1p are mechanistically distinct.

Hale SJ, Lovell SC, de Keyzer J, Stirling CJ.

J Biol Chem. 2010 Jul 9;285(28):21600-6. doi: 10.1074/jbc.M110.111211. Epub 2010 Apr 29.

43.

Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

Lovell SC, Li X, Weerasinghe NR, Hentges KE.

BMC Genomics. 2009 Nov 12;10:521. doi: 10.1186/1471-2164-10-521.

44.

Analysis of synthetic lethality reveals genetic interactions between the GTPase Snu114p and snRNAs in the catalytic core of the Saccharomyces cerevisiae spliceosome.

Frazer LN, Lovell SC, O'Keefe RT.

Genetics. 2009 Oct;183(2):497-515-1SI-4SI. doi: 10.1534/genetics.109.107243. Epub 2009 Jul 20.

45.

Evolution in protein interaction networks: co-evolution, rewiring and the role of duplication.

Robertson DL, Lovell SC.

Biochem Soc Trans. 2009 Aug;37(Pt 4):768-71. doi: 10.1042/BST0370768. Review.

PMID:
19614591
46.

Quantitative analysis and prediction of curvature in leucine-rich repeat proteins.

Hindle KL, Bella J, Lovell SC.

Proteins. 2009 Nov 1;77(2):342-58. doi: 10.1002/prot.22440.

PMID:
19452560
47.

Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction.

Handl J, Knowles J, Lovell SC.

Bioinformatics. 2009 May 15;25(10):1271-9. doi: 10.1093/bioinformatics/btp150. Epub 2009 Mar 17.

48.

The effect of sequence evolution on protein structural divergence.

Williams SG, Lovell SC.

Mol Biol Evol. 2009 May;26(5):1055-65. doi: 10.1093/molbev/msp020. Epub 2009 Feb 4.

PMID:
19193735
49.

The leucine-rich repeat structure.

Bella J, Hindle KL, McEwan PA, Lovell SC.

Cell Mol Life Sci. 2008 Aug;65(15):2307-33. doi: 10.1007/s00018-008-8019-0. Review.

PMID:
18408889
50.

Protein-protein interaction networks and biology--what's the connection?

Hakes L, Pinney JW, Robertson DL, Lovell SC.

Nat Biotechnol. 2008 Jan;26(1):69-72. doi: 10.1038/nbt0108-69. No abstract available.

PMID:
18183023

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