Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 382

1.

Emerging concepts in pseudoenzyme classification, evolution, and signaling.

Ribeiro AJM, Das S, Dawson N, Zaru R, Orchard S, Thornton JM, Orengo C, Zeqiraj E, Murphy JM, Eyers PA.

Sci Signal. 2019 Aug 13;12(594). pii: eaat9797. doi: 10.1126/scisignal.aat9797. Review.

PMID:
31409758
2.

Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1.

Martin-Herranz DE, Aref-Eshghi E, Bonder MJ, Stubbs TM, Choufani S, Weksberg R, Stegle O, Sadikovic B, Reik W, Thornton JM.

Genome Biol. 2019 Aug 14;20(1):146. doi: 10.1186/s13059-019-1753-9.

3.

VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations.

Stephenson JD, Laskowski RA, Nightingale A, Hurles ME, Thornton JM.

Bioinformatics. 2019 Jun 13. pii: btz482. doi: 10.1093/bioinformatics/btz482. [Epub ahead of print]

PMID:
31192369
4.

The widespread increase in inter-individual variability of gene expression in the human brain with age.

Kedlian VR, Donertas HM, Thornton JM.

Aging (Albany NY). 2019 Apr 19;11(8):2253-2280. doi: 10.18632/aging.101912.

5.

Finding enzyme cofactors in Protein Data Bank.

Mukhopadhyay A, Borkakoti N, Pravda L, Tyzack JD, Thornton JM, Velankar S.

Bioinformatics. 2019 Feb 13. doi: 10.1093/bioinformatics/btz115. [Epub ahead of print]

PMID:
30759194
6.

Using the drug-protein interactome to identify anti-ageing compounds for humans.

Fuentealba M, Dönertaş HM, Williams R, Labbadia J, Thornton JM, Partridge L.

PLoS Comput Biol. 2019 Jan 9;15(1):e1006639. doi: 10.1371/journal.pcbi.1006639. eCollection 2019 Jan.

7.

Identifying Potential Ageing-Modulating Drugs In Silico.

Dönertaş HM, Fuentealba M, Partridge L, Thornton JM.

Trends Endocrinol Metab. 2019 Feb;30(2):118-131. doi: 10.1016/j.tem.2018.11.005. Epub 2018 Dec 20. Review.

8.

A 3D geological model of a structurally complex Alpine region as a basis for interdisciplinary research.

Thornton JM, Mariethoz G, Brunner P.

Sci Data. 2018 Oct 30;5:180238. doi: 10.1038/sdata.2018.238.

9.

Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function.

Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM.

Methods Mol Biol. 2019;1851:263-275. doi: 10.1007/978-1-4939-8736-8_14.

PMID:
30298402
10.

Gene expression-based drug repurposing to target aging.

Dönertaş HM, Fuentealba Valenzuela M, Partridge L, Thornton JM.

Aging Cell. 2018 Oct;17(5):e12819. doi: 10.1111/acel.12819. Epub 2018 Aug 9.

11.

Transform-MinER: transforming molecules in enzyme reactions.

Tyzack JD, Ribeiro AJM, Borkakoti N, Thornton JM.

Bioinformatics. 2018 Oct 15;34(20):3597-3599. doi: 10.1093/bioinformatics/bty394.

12.

Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates.

Tyzack JD, Fernando L, Ribeiro AJM, Borkakoti N, Thornton JM.

Structure. 2018 Apr 3;26(4):565-571.e3. doi: 10.1016/j.str.2018.02.009. Epub 2018 Mar 15.

13.

To what extent do structural changes in catalytic metal sites affect enzyme function?

Valasatava Y, Rosato A, Furnham N, Thornton JM, Andreini C.

J Inorg Biochem. 2018 Feb;179:40-53. doi: 10.1016/j.jinorgbio.2017.11.002. Epub 2017 Nov 8.

14.

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.

Ribeiro AJM, Holliday GL, Furnham N, Tyzack JD, Ferris K, Thornton JM.

Nucleic Acids Res. 2018 Jan 4;46(D1):D618-D623. doi: 10.1093/nar/gkx1012.

15.

Intestinal Fork Head Regulates Nutrient Absorption and Promotes Longevity.

Bolukbasi E, Khericha M, Regan JC, Ivanov DK, Adcott J, Dyson MC, Nespital T, Thornton JM, Alic N, Partridge L.

Cell Rep. 2017 Oct 17;21(3):641-653. doi: 10.1016/j.celrep.2017.09.042.

16.

cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.

Martin-Herranz DE, Ribeiro AJM, Krueger F, Thornton JM, Reik W, Stubbs TM.

Nucleic Acids Res. 2017 Nov 16;45(20):11559-11569. doi: 10.1093/nar/gkx814.

17.

Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1.

Suri M, Evers JMG, Laskowski RA, O'Brien S, Baker K, Clayton-Smith J, Dabir T, Josifova D, Joss S, Kerr B, Kraus A, McEntagart M, Morton J, Smith A, Splitt M, Thornton JM; DDD Study, Wright CF.

Mol Genet Genomic Med. 2017 Jun 20;5(5):495-507. doi: 10.1002/mgg3.304. eCollection 2017 Sep.

18.

Understanding enzyme function evolution from a computational perspective.

Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM.

Curr Opin Struct Biol. 2017 Dec;47:131-139. doi: 10.1016/j.sbi.2017.08.003. Epub 2017 Sep 8. Review.

19.

PDBsum: Structural summaries of PDB entries.

Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM.

Protein Sci. 2018 Jan;27(1):129-134. doi: 10.1002/pro.3289. Epub 2017 Oct 27.

20.

Drug repurposing for aging research using model organisms.

Ziehm M, Kaur S, Ivanov DK, Ballester PJ, Marcus D, Partridge L, Thornton JM.

Aging Cell. 2017 Oct;16(5):1006-1015. doi: 10.1111/acel.12626. Epub 2017 Jun 16.

21.

Anna Tramontano 1957-2017.

Thornton JM, Valencia A, Schwede T.

Nat Struct Mol Biol. 2017 May 4;24(5):431-432. doi: 10.1038/nsmb.3410. No abstract available.

PMID:
28471426
22.

Incorporation of autopsy case-based learning into PhD graduate education: a novel approach to bridging the "bench-to-bedside" gap.

Brooks EG, Thornton JM, Ranheim EA, Fabry Z.

Hum Pathol. 2017 Oct;68:1-6. doi: 10.1016/j.humpath.2017.03.006. Epub 2017 Mar 16.

PMID:
28315694
23.

Clinical management of Brucella suis infection in dogs and implications for public health.

James DR, Golovsky G, Thornton JM, Goodchild L, Havlicek M, Martin P, Krockenberger MB, Marriott D, Ahuja V, Malik R, Mor SM.

Aust Vet J. 2017 Jan;95(1-2):19-25. doi: 10.1111/avj.12550.

PMID:
28124423
24.

Structural analysis of pathogenic mutations in the DYRK1A gene in patients with developmental disorders.

Evers JM, Laskowski RA, Bertolli M, Clayton-Smith J, Deshpande C, Eason J, Elmslie F, Flinter F, Gardiner C, Hurst JA, Kingston H, Kini U, Lampe AK, Lim D, Male A, Naik S, Parker MJ, Price S, Robert L, Sarkar A, Straub V, Woods G, Thornton JM; DDD Study, Wright CF.

Hum Mol Genet. 2017 Feb 1;26(3):519-526. doi: 10.1093/hmg/ddw409.

25.

Modeling birds on wires.

Aydoğdu A, Frasca P, D'Apice C, Manzo R, Thornton JM, Gachomo B, Wilson T, Cheung B, Tariq U, Saidel W, Piccoli B.

J Theor Biol. 2017 Feb 21;415:102-112. doi: 10.1016/j.jtbi.2016.11.026. Epub 2016 Dec 5.

PMID:
27932298
26.

Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases.

Mascotti ML, Juri Ayub M, Furnham N, Thornton JM, Laskowski RA.

J Mol Biol. 2016 Jul 31;428(15):3131-46. doi: 10.1016/j.jmb.2016.07.003. Epub 2016 Jul 14.

27.

Reaction Decoder Tool (RDT): extracting features from chemical reactions.

Rahman SA, Torrance G, Baldacci L, Martínez Cuesta S, Fenninger F, Gopal N, Choudhary S, May JW, Holliday GL, Steinbeck C, Thornton JM.

Bioinformatics. 2016 Jul 1;32(13):2065-6. doi: 10.1093/bioinformatics/btw096. Epub 2016 Feb 22.

28.

Exploring the chemistry and evolution of the isomerases.

Martínez Cuesta S, Rahman SA, Thornton JM.

Proc Natl Acad Sci U S A. 2016 Feb 16;113(7):1796-801. doi: 10.1073/pnas.1509494113. Epub 2016 Feb 3.

29.

Characterising Complex Enzyme Reaction Data.

Dönertaş HM, Martínez Cuesta S, Rahman SA, Thornton JM.

PLoS One. 2016 Feb 3;11(2):e0147952. doi: 10.1371/journal.pone.0147952. eCollection 2016.

30.

Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain.

Laskowski RA, Tyagi N, Johnson D, Joss S, Kinning E, McWilliam C, Splitt M, Thornton JM, Firth HV; DDD Study, Wright CF.

Hum Mol Genet. 2016 Mar 1;25(5):927-35. doi: 10.1093/hmg/ddv625. Epub 2016 Jan 5.

31.

Proteins: interaction at a distance.

Laskowski RA, Thornton JM.

IUCrJ. 2015 Oct 30;2(Pt 6):609-10. doi: 10.1107/S2052252515020217. eCollection 2015 Nov 1.

32.

Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.

Furnham N, Dawson NL, Rahman SA, Thornton JM, Orengo CA.

J Mol Biol. 2016 Jan 29;428(2 Pt A):253-267. doi: 10.1016/j.jmb.2015.11.010. Epub 2015 Nov 14.

33.

Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity.

Tyagi N, Farnell EJ, Fitzsimmons CM, Ryan S, Tukahebwa E, Maizels RM, Dunne DW, Thornton JM, Furnham N.

PLoS Comput Biol. 2015 Oct 29;11(10):e1004546. doi: 10.1371/journal.pcbi.1004546. eCollection 2015 Oct.

34.

Monitoring the health of the work environment with a daily assessment tool: the REAL - Relative Environment Assessment Lens - indicator.

Hinsley KE, Marshall AC, Hurtig MH, Thornton JM, O'Connell CA, Porter CL, Connor JA, Hickey PA.

Cardiol Young. 2016 Aug;26(6):1082-9. doi: 10.1017/S1047951115001808. Epub 2015 Oct 1.

PMID:
26423013
35.

SurvCurv database and online survival analysis platform update.

Ziehm M, Ivanov DK, Bhat A, Partridge L, Thornton JM.

Bioinformatics. 2015 Dec 1;31(23):3878-80. doi: 10.1093/bioinformatics/btv463. Epub 2015 Aug 6.

36.

The Classification and Evolution of Enzyme Function.

Martínez Cuesta S, Rahman SA, Furnham N, Thornton JM.

Biophys J. 2015 Sep 15;109(6):1082-6. doi: 10.1016/j.bpj.2015.04.020. Epub 2015 May 15. Review.

37.

Longevity GWAS Using the Drosophila Genetic Reference Panel.

Ivanov DK, Escott-Price V, Ziehm M, Magwire MM, Mackay TF, Partridge L, Thornton JM.

J Gerontol A Biol Sci Med Sci. 2015 Dec;70(12):1470-8. doi: 10.1093/gerona/glv047. Epub 2015 Apr 28.

38.

Endovascular treatment for Small Core and Anterior circulation Proximal occlusion with Emphasis on minimizing CT to recanalization times (ESCAPE) trial: methodology.

Demchuk AM, Goyal M, Menon BK, Eesa M, Ryckborst KJ, Kamal N, Patil S, Mishra S, Almekhlafi M, Randhawa PA, Roy D, Willinsky R, Montanera W, Silver FL, Shuaib A, Rempel J, Jovin T, Frei D, Sapkota B, Thornton JM, Poppe A, Tampieri D, Lum C, Weill A, Sajobi TT, Hill MD; ESCAPE Trial Investigators.

Int J Stroke. 2015 Apr;10(3):429-38. doi: 10.1111/ijs.12424. Epub 2014 Dec 25.

PMID:
25546514
39.

Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing.

Papatheodorou I, Petrovs R, Thornton JM.

Bioinformatics. 2014 Nov 1;30(21):2999-3003. doi: 10.1093/bioinformatics/btu493. Epub 2014 Jul 26.

40.

The evolution of enzyme function in the isomerases.

Martinez Cuesta S, Furnham N, Rahman SA, Sillitoe I, Thornton JM.

Curr Opin Struct Biol. 2014 Jun;26:121-30. doi: 10.1016/j.sbi.2014.06.002. Epub 2014 Jul 5. Review.

41.

Exploring the biological and chemical complexity of the ligases.

Holliday GL, Rahman SA, Furnham N, Thornton JM.

J Mol Biol. 2014 May 15;426(10):2098-111. doi: 10.1016/j.jmb.2014.03.008. Epub 2014 Mar 21. Review.

42.

MDL-1, a growth- and tumor-suppressor, slows aging and prevents germline hyperplasia and hypertrophy in C. elegans.

Riesen M, Feyst I, Rattanavirotkul N, Ezcurra M, Tullet JM, Papatheodorou I, Ziehm M, Au C, Gilliat AF, Hellberg J, Thornton JM, Gems D.

Aging (Albany NY). 2014 Feb;6(2):98-117.

43.

DAF-16/FoxO directly regulates an atypical AMP-activated protein kinase gamma isoform to mediate the effects of insulin/IGF-1 signaling on aging in Caenorhabditis elegans.

Tullet JM, Araiz C, Sanders MJ, Au C, Benedetto A, Papatheodorou I, Clark E, Schmeisser K, Jones D, Schuster EF, Thornton JM, Gems D.

PLoS Genet. 2014 Feb 6;10(2):e1004109. doi: 10.1371/journal.pgen.1004109. eCollection 2014 Feb.

44.

EC-BLAST: a tool to automatically search and compare enzyme reactions.

Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM.

Nat Methods. 2014 Feb;11(2):171-4. doi: 10.1038/nmeth.2803. Epub 2014 Jan 12.

45.

Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.

de Beer TA, Laskowski RA, Parks SL, Sipos B, Goldman N, Thornton JM.

PLoS Comput Biol. 2013;9(12):e1003382. doi: 10.1371/journal.pcbi.1003382. Epub 2013 Dec 12.

46.

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.

Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM.

Nucleic Acids Res. 2014 Jan;42(Database issue):D485-9. doi: 10.1093/nar/gkt1243. Epub 2013 Dec 6.

47.

LigSearch: a knowledge-based web server to identify likely ligands for a protein target.

de Beer TA, Laskowski RA, Duban ME, Chan AW, Anderson WF, Thornton JM.

Acta Crystallogr D Biol Crystallogr. 2013 Dec;69(Pt 12):2395-402. doi: 10.1107/S0907444913022294. Epub 2013 Nov 19.

48.

PDBsum additions.

de Beer TA, Berka K, Thornton JM, Laskowski RA.

Nucleic Acids Res. 2014 Jan;42(Database issue):D292-6. doi: 10.1093/nar/gkt940. Epub 2013 Oct 22.

49.

Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv.

Ziehm M, Thornton JM.

Aging Cell. 2013 Oct;12(5):910-6. doi: 10.1111/acel.12121. Epub 2013 Jul 22.

50.

Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data.

Ziehm M, Piper MD, Thornton JM.

Aging Cell. 2013 Oct;12(5):917-22. doi: 10.1111/acel.12123. Epub 2013 Jul 22.

Supplemental Content

Loading ...
Support Center