Publications by authors named "Simon C Lovell"

65Publications

Using an integrative machine learning approach utilising homology modelling to clinically interpret genetic variants: CACNA1F as an exemplar.

Eur J Hum Genet 2020 Sep 20;28(9):1274-1282. Epub 2020 Apr 20.

Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.

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http://dx.doi.org/10.1038/s41431-020-0623-yDOI Listing
September 2020

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

Genes (Basel) 2020 02 9;11(2). Epub 2020 Feb 9.

Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester M13 9PT, UK.

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http://dx.doi.org/10.3390/genes11020179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7074066PMC
February 2020

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

Biomolecules 2019 10 15;9(10). Epub 2019 Oct 15.

Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK.

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http://dx.doi.org/10.3390/biom9100612DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6843117PMC
October 2019

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

Sci Rep 2018 09 12;8(1):13694. Epub 2018 Sep 12.

Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, United Kingdom.

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http://dx.doi.org/10.1038/s41598-018-31891-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6135816PMC
September 2018

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

PLoS Genet 2017 Oct 30;13(10):e1007068. Epub 2017 Oct 30.

Division of Evolution and Genome Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1007068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5697871PMC
October 2017

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

Virus Evol 2017 Jul 1;3(2):vex019. Epub 2017 Aug 1.

Evolution & Genomic Sciences, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, UK.

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http://dx.doi.org/10.1093/ve/vex019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570062PMC
July 2017

Rapid functional and evolutionary changes follow gene duplication in yeast.

Proc Biol Sci 2017 Aug;284(1861)

School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK

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http://dx.doi.org/10.1098/rspb.2017.1393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5577496PMC
August 2017

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

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

Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK

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http://dx.doi.org/10.1162/EVCO_a_00176DOI Listing
May 2017

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

BMC Evol Biol 2016 Feb 18;16:40. Epub 2016 Feb 18.

Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.

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http://www.biomedcentral.com/1471-2148/16/40
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http://dx.doi.org/10.1186/s12862-016-0608-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758157PMC
February 2016

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

Proteins 2016 Apr 23;84(4):411-26. Epub 2016 Feb 23.

Faculty of Life Sciences, the University of Manchester, Manchester, M13 9PL, United Kingdom.

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http://dx.doi.org/10.1002/prot.24987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4982100PMC
April 2016

Covariation Is a Poor Measure of Molecular Coevolution.

Mol Biol Evol 2015 Sep 4;32(9):2456-68. Epub 2015 May 4.

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom Evolutionary Biology Centre, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/molbev/msv109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4540965PMC
September 2015

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

Virology 2015 Aug 14;482:202-7. Epub 2015 Apr 14.

Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00426822150016
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http://dx.doi.org/10.1016/j.virol.2015.03.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4503884PMC
August 2015

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

J Hum Genet 2015 Apr 15;60(4):199-202. Epub 2015 Jan 15.

1] Institute of Human Development, University of Manchester, Manchester, UK [2] Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK.

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http://dx.doi.org/10.1038/jhg.2014.122DOI Listing
April 2015

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

Invest Ophthalmol Vis Sci 2015 Jan 8;56(2):883-91. Epub 2015 Jan 8.

Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Saint Mary's Hospital, Manchester, United Kingdom Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Saint Mary's Hospital, Manchester, United Kingdom.

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http://iovs.arvojournals.org/Article.aspx?doi=10.1167/iovs.1
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http://dx.doi.org/10.1167/iovs.14-15861DOI Listing
January 2015

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

Bioinformatics 2015 Feb 7;31(3):416-7. Epub 2014 Oct 7.

Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK.

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http://dx.doi.org/10.1093/bioinformatics/btu645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4308661PMC
February 2015

Inferring gene family histories in yeast identifies lineage specific expansions.

PLoS One 2014 12;9(6):e99480. Epub 2014 Jun 12.

Computational and Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099480PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4055711PMC
January 2015

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

Virology 2014 Apr 22;454-455:34-9. Epub 2014 Feb 22.

Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK. Electronic address:

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http://dx.doi.org/10.1016/j.virol.2014.01.029DOI Listing
April 2014

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

PLoS One 2013 3;8(5):e62670. Epub 2013 May 3.

Computational and Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062670PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3643936PMC
November 2013

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

PLoS One 2013 29;8(4):e62866. Epub 2013 Apr 29.

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062866PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3639263PMC
November 2013

Alternative splicing and protein interaction data sets.

Nat Biotechnol 2013 Apr;31(4):292-3

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http://dx.doi.org/10.1038/nbt.2540DOI Listing
April 2013

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

BMC Evol Biol 2012 Dec 6;12:238. Epub 2012 Dec 6.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.

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http://dx.doi.org/10.1186/1471-2148-12-238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537733PMC
December 2012

Evolvability of yeast protein-protein interaction interfaces.

J Mol Biol 2012 Jun 1;419(5):387-96. Epub 2012 Apr 1.

Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1016/j.jmb.2012.03.021DOI Listing
June 2012

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

Proteins 2012 Feb 17;80(2):490-504. Epub 2011 Nov 17.

Manchester Business School, The University of Manchester, United Kingdom.

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http://dx.doi.org/10.1002/prot.23215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849216PMC
February 2012

Determining the evolutionary history of gene families.

Bioinformatics 2012 Jan 28;28(1):48-55. Epub 2011 Oct 28.

Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK.

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http://dx.doi.org/10.1093/bioinformatics/btr592DOI Listing
January 2012

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

J Mol Biol 2011 Jul;410(5):1023-34

Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1016/j.jmb.2011.04.037DOI Listing
July 2011

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

PLoS One 2011 27;6(6):e21053. Epub 2011 Jun 27.

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021053PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3124478PMC
December 2011

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

Mol Biol Evol 2011 Dec 20;28(12):3331-44. Epub 2011 Jun 20.

University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msr167DOI Listing
December 2011

Constraints on HIV-1 diversity from protein structure.

J Virol 2010 Dec 29;84(24):12995-3003. Epub 2010 Sep 29.

Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom.

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http://jvi.asm.org/cgi/doi/10.1128/JVI.00702-10
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http://dx.doi.org/10.1128/JVI.00702-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3004343PMC
December 2010

Gene duplication and environmental adaptation within yeast populations.

Genome Biol Evol 2010 21;2:591-601. Epub 2010 Jul 21.

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1093/gbe/evq043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997561PMC
December 2010

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

Mol Biol Evol 2010 Nov 14;27(11):2567-75. Epub 2010 Jun 14.

Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msq144DOI Listing
November 2010

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

J Biol Chem 2010 Jul 29;285(28):21600-6. Epub 2010 Apr 29.

Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, United Kingdom.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M110.111211
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http://dx.doi.org/10.1074/jbc.M110.111211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898433PMC
July 2010

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

BMC Genomics 2009 Nov 12;10:521. Epub 2009 Nov 12.

Faculty of Life Sciences, University of Manchester, Manchester M139PT, UK.

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http://dx.doi.org/10.1186/1471-2164-10-521DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779822PMC
November 2009

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

Biochem Soc Trans 2009 Aug;37(Pt 4):768-71

Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1042/BST0370768DOI Listing
August 2009

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

Proteins 2009 Nov;77(2):342-58

Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1002/prot.22440DOI Listing
November 2009

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

Bioinformatics 2009 May 17;25(10):1271-9. Epub 2009 Mar 17.

Faculty of Life Sciences, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/bioinformatics/btp150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677743PMC
May 2009

The effect of sequence evolution on protein structural divergence.

Mol Biol Evol 2009 May 4;26(5):1055-65. Epub 2009 Feb 4.

Faculty of Life Sciences, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/molbev/msp020DOI Listing
May 2009

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

Nat Biotechnol 2008 Jan;26(1):69-72

Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Rd., Manchester M13 9PT, UK.

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http://dx.doi.org/10.1038/nbt0108-69DOI Listing
January 2008

All duplicates are not equal: the difference between small-scale and genome duplication.

Genome Biol 2007 ;8(10):R209

Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1186/gb-2007-8-10-r209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246283PMC
May 2008

An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network.

BMC Bioinformatics 2007 Aug 6;8:289. Epub 2007 Aug 6.

Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, UK.

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http://dx.doi.org/10.1186/1471-2105-8-289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1963338PMC
August 2007

Protein interactions from complexes: a structural perspective.

Comp Funct Genomics 2007 20:49356. Epub 2006 Dec 20.

Centre for the Analysis of Biological Complexity, Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1155/2007/49356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1838958PMC
June 2010

Specificity in protein interactions and its relationship with sequence diversity and coevolution.

Proc Natl Acad Sci U S A 2007 May 27;104(19):7999-8004. Epub 2007 Apr 27.

Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, United Kingdom.

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http://dx.doi.org/10.1073/pnas.0609962104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1876561PMC
May 2007

Andante: reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities.

Bioinformatics 2007 May 6;23(9):1099-105. Epub 2007 Mar 6.

Department of Biochemistry, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btm073DOI Listing
May 2007

Bioinformatics: from molecules to systems. A discussion meeting held at The Royal Society on 4 and 5 April 2005.

J R Soc Interface 2005 Sep;2(4):397-400

Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1098/rsif.2005.0053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885864PMC
September 2005

Secondary structure assignment that accurately reflects physical and evolutionary characteristics.

BMC Bioinformatics 2005 Dec 1;6 Suppl 4:S8. Epub 2005 Dec 1.

Biochemistry Dept, University of Cambridge, Cambridge CB2 1GA, UK.

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http://dx.doi.org/10.1186/1471-2105-6-S4-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866377PMC
December 2005

CHORAL: a differential geometry approach to the prediction of the cores of protein structures.

Bioinformatics 2005 Oct 26;21(19):3719-25. Epub 2005 Jul 26.

Department of Biochemistry, University of Cambridge Tennis Court Road, Cambridge CB2 1GA, UK.

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http://dx.doi.org/10.1093/bioinformatics/bti595DOI Listing
October 2005

Distinguishing structural and functional restraints in evolution in order to identify interaction sites.

J Mol Biol 2004 Oct;342(5):1487-504

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.

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http://dx.doi.org/10.1016/j.jmb.2004.08.022DOI Listing
October 2004

Human glutaminyl cyclase and bacterial zinc aminopeptidase share a common fold and active site.

BMC Biol 2004 Feb 10;2. Epub 2004 Feb 10.

Department of Chemistry and Biochemistry, Texas State University-San Marcos, San Marcos, TX 78666, USA.

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http://dx.doi.org/10.1186/1741-7007-2-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC368447PMC
February 2004

Are non-functional, unfolded proteins ('junk proteins') common in the genome?

Authors:
Simon C Lovell

FEBS Lett 2003 Nov;554(3):237-9

School of Biological Science, University of Manchester, 2.205 Stopford Building, Oxford Rd, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1016/s0014-5793(03)01223-7DOI Listing
November 2003

Crystal structures of engrailed homeodomain mutants: implications for stability and dynamics.

J Biol Chem 2003 Oct 15;278(44):43699-708. Epub 2003 Aug 15.

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.

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http://dx.doi.org/10.1074/jbc.M308029200DOI Listing
October 2003

Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles.

Proteins 2003 Apr;51(1):41-55

Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.1002/prot.10285DOI Listing
April 2003

Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

Proteins 2003 Feb;50(3):437-50

Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

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http://doi.wiley.com/10.1002/prot.10286
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http://dx.doi.org/10.1002/prot.10286DOI Listing
February 2003