Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 45

1.

The Dark Proteome Database.

Perdigão N, Rosa AC, O'Donoghue SI.

BioData Min. 2017 Jul 20;10:24. doi: 10.1186/s13040-017-0144-6. eCollection 2017.

2.

SnapShot: Phosphoregulation of Mitosis.

Burgess A, Vuong J, Rogers S, Malumbres M, O'Donoghue SI.

Cell. 2017 Jun 15;169(7):1358-1358.e1. doi: 10.1016/j.cell.2017.06.003.

PMID:
28622516
3.

Monogenic and polygenic determinants of sarcoma risk: an international genetic study.

Ballinger ML, Goode DL, Ray-Coquard I, James PA, Mitchell G, Niedermayr E, Puri A, Schiffman JD, Dite GS, Cipponi A, Maki RG, Brohl AS, Myklebost O, Stratford EW, Lorenz S, Ahn SM, Ahn JH, Kim JE, Shanley S, Beshay V, Randall RL, Judson I, Seddon B, Campbell IG, Young MA, Sarin R, Blay JY, O'Donoghue SI, Thomas DM; International Sarcoma Kindred Study.

Lancet Oncol. 2016 Sep;17(9):1261-71. doi: 10.1016/S1470-2045(16)30147-4. Epub 2016 Aug 4.

PMID:
27498913
4.

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations.

Taberlay PC, Achinger-Kawecka J, Lun AT, Buske FA, Sabir K, Gould CM, Zotenko E, Bert SA, Giles KA, Bauer DC, Smyth GK, Stirzaker C, O'Donoghue SI, Clark SJ.

Genome Res. 2016 Jun;26(6):719-31. doi: 10.1101/gr.201517.115. Epub 2016 Apr 6.

5.

Unexpected features of the dark proteome.

Perdigão N, Heinrich J, Stolte C, Sabir KS, Buckley MJ, Tabor B, Signal B, Gloss BS, Hammang CJ, Rost B, Schafferhans A, O'Donoghue SI.

Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):15898-903. doi: 10.1073/pnas.1508380112. Epub 2015 Nov 17.

6.

Integrated visual analysis of protein structures, sequences, and feature data.

Stolte C, Sabir KS, Heinrich J, Hammang CJ, Schafferhans A, O'Donoghue SI.

BMC Bioinformatics. 2015;16 Suppl 11:S7. doi: 10.1186/1471-2105-16-S11-S7. Epub 2015 Aug 13.

7.

Comprehensive comparison of large-scale tissue expression datasets.

Santos A, Tsafou K, Stolte C, Pletscher-Frankild S, O'Donoghue SI, Jensen LJ.

PeerJ. 2015 Jun 30;3:e1054. doi: 10.7717/peerj.1054. eCollection 2015.

8.

SnapShot: Insulin/IGF1 Signaling.

Ma DK, Stolte C, Krycer JR, James DE, O'Donoghue SI.

Cell. 2015 May 7;161(4):948-948.e1. doi: 10.1016/j.cell.2015.04.041. Erratum in: Cell. 2015 Jul 30;162(3):689.

9.

Aquaria: simplifying discovery and insight from protein structures.

O'Donoghue SI, Sabir KS, Kalemanov M, Stolte C, Wellmann B, Ho V, Roos M, Perdigão N, Buske FA, Heinrich J, Rost B, Schafferhans A.

Nat Methods. 2015 Feb;12(2):98-9. doi: 10.1038/nmeth.3258. No abstract available.

PMID:
25633501
10.

Visual analytics of signalling pathways using time profiles.

Ma DK, Stolte C, Kaur S, Bain M, O'Donoghue SI.

Adv Exp Med Biol. 2015;823:3-22. doi: 10.1007/978-3-319-10984-8_1.

PMID:
25381099
11.

Visualising intrinsic disorder and conformational variation in protein ensembles.

Heinrich J, Krone M, O'Donoghue SI, Weiskopf D.

Faraday Discuss. 2014;169:179-93. doi: 10.1039/c3fd00138e. Epub 2014 Jun 12.

PMID:
25340810
12.

How to learn about gene function: text-mining or ontologies?

Soldatos TG, Perdigão N, Brown NP, Sabir KS, O'Donoghue SI.

Methods. 2015 Mar;74:3-15. doi: 10.1016/j.ymeth.2014.07.004. Epub 2014 Aug 1. Review.

PMID:
25088781
13.

COMPARTMENTS: unification and visualization of protein subcellular localization evidence.

Binder JX, Pletscher-Frankild S, Tsafou K, Stolte C, O'Donoghue SI, Schneider R, Jensen LJ.

Database (Oxford). 2014 Feb 25;2014:bau012. doi: 10.1093/database/bau012. Print 2014.

14.

Caipirini: using gene sets to rank literature.

Soldatos TG, O'Donoghue SI, Satagopam VP, Barbosa-Silva A, Pavlopoulos GA, Wanderley-Nogueira AC, Soares-Cavalcanti NM, Schneider R.

BioData Min. 2012 Feb 1;5(1):1. doi: 10.1186/1756-0381-5-1.

15.

Defective lamin A-Rb signaling in Hutchinson-Gilford Progeria Syndrome and reversal by farnesyltransferase inhibition.

Marji J, O'Donoghue SI, McClintock D, Satagopam VP, Schneider R, Ratner D, Worman HJ, Gordon LB, Djabali K.

PLoS One. 2010 Jun 15;5(6):e11132. doi: 10.1371/journal.pone.0011132.

16.

Visualization of omics data for systems biology.

Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC.

Nat Methods. 2010 Mar;7(3 Suppl):S56-68. doi: 10.1038/nmeth.1436. Review.

PMID:
20195258
17.

Visualization of macromolecular structures.

O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ.

Nat Methods. 2010 Mar;7(3 Suppl):S42-55. doi: 10.1038/nmeth.1427. Epub 2010 Mar 1. Review.

PMID:
20195256
18.

Visualizing biological data-now and in the future.

O'Donoghue SI, Gavin AC, Gehlenborg N, Goodsell DS, Hériché JK, Nielsen CB, North C, Olson AJ, Procter JB, Shattuck DW, Walter T, Wong B.

Nat Methods. 2010 Mar;7(3 Suppl):S2-4. doi: 10.1038/nmeth.f.301.

PMID:
20195254
19.

Martini: using literature keywords to compare gene sets.

Soldatos TG, O'Donoghue SI, Satagopam VP, Jensen LJ, Brown NP, Barbosa-Silva A, Schneider R.

Nucleic Acids Res. 2010 Jan;38(1):26-38. doi: 10.1093/nar/gkp876. Epub 2009 Oct 25.

20.

Reflect: augmented browsing for the life scientist.

Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R.

Nat Biotechnol. 2009 Jun;27(6):508-10. doi: 10.1038/nbt0609-508. No abstract available.

PMID:
19513049
21.

Arena3D: visualization of biological networks in 3D.

Pavlopoulos GA, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R.

BMC Syst Biol. 2008 Nov 28;2:104. doi: 10.1186/1752-0509-2-104.

22.

Text mining for biology--the way forward: opinions from leading scientists.

Altman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, Krallinger M, Mons B, O'Donoghue SI, Peitsch MC, Rebholz-Schuhmann D, Shatkay H, Valencia A.

Genome Biol. 2008;9 Suppl 2:S7. doi: 10.1186/gb-2008-9-s2-s7. Epub 2008 Sep 1.

23.

Error distribution derived NOE distance restraints.

Nilges M, Habeck M, O'Donoghue SI, Rieping W.

Proteins. 2006 Aug 15;64(3):652-64.

PMID:
16729263
24.

The SRS 3D module: integrating structures, sequences and features.

O'Donoghue SI, Meyer JE, Schafferhans A, Fries K.

Bioinformatics. 2004 Oct 12;20(15):2476-8. Epub 2004 Apr 15.

PMID:
15087318
25.

The PSSH database of alignments between protein sequences and tertiary structures.

Schafferhans A, Meyer JE, O'Donoghue SI.

Nucleic Acids Res. 2003 Jan 1;31(1):494-8.

26.

NMR studies of the aggregation of glucagon-like peptide-1: formation of a symmetric helical dimer.

Chang X, Keller D, O'Donoghue SI, Led JJ.

FEBS Lett. 2002 Mar 27;515(1-3):165-70.

27.

Comparison of ARM and HEAT protein repeats.

Andrade MA, Petosa C, O'Donoghue SI, Müller CW, Bork P.

J Mol Biol. 2001 May 25;309(1):1-18. Review.

PMID:
11491282
28.

Automated assignment of ambiguous nuclear overhauser effects with ARIA.

Linge JP, O'Donoghue SI, Nilges M.

Methods Enzymol. 2001;339:71-90. No abstract available.

PMID:
11462826
29.

Unraveling the symmetry ambiguity in a hexamer: calculation of the R6 human insulin structure.

O'Donoghue SI, Chang X, Abseher R, Nilges M, Led JJ.

J Biomol NMR. 2000 Feb;16(2):93-108.

PMID:
10723989
30.

Molecular dynamics and accuracy of NMR structures: effects of error bounds and data removal.

Chalaoux FR, O'Donoghue SI, Nilges M.

Proteins. 1999 Mar 1;34(4):453-63.

PMID:
10081958
31.

Adaptation of protein surfaces to subcellular location.

Andrade MA, O'Donoghue SI, Rost B.

J Mol Biol. 1998 Feb 20;276(2):517-25.

PMID:
9512720
32.

The structure of a novel insecticidal neurotoxin, omega-atracotoxin-HV1, from the venom of an Australian funnel web spider.

Fletcher JI, Smith R, O'Donoghue SI, Nilges M, Connor M, Howden ME, Christie MJ, King GF.

Nat Struct Biol. 1997 Jul;4(7):559-66.

PMID:
9228949
33.
36.

High resolution NMR solution structure of the leucine zipper domain of the c-Jun homodimer.

Junius FK, O'Donoghue SI, Nilges M, Weiss AS, King GF.

J Biol Chem. 1996 Jun 7;271(23):13663-7.

37.

Catalysis by hamster dihydroorotase: zinc binding, site-directed mutagenesis, and interaction with inhibitors.

Williams NK, Manthey MK, Hambley TW, O'Donoghue SI, Keegan M, Chapman BE, Christopherson RI.

Biochemistry. 1995 Sep 12;34(36):11344-52.

PMID:
7547862
38.
39.
40.

Determination of the solution structure of a platelet-adhesion peptide of von Willebrand factor.

Knott HM, Berndt MC, Kralicek AV, O'Donoghue SI, King GF.

Biochemistry. 1992 Nov 17;31(45):11152-8.

PMID:
1445855
41.

Solution structure of endothelin-3 determined using NMR spectroscopy.

Mills RG, O'Donoghue SI, Smith R, King GF.

Biochemistry. 1992 Jun 23;31(24):5640-5.

PMID:
1610811
42.

Models of the actin monomer and filament from fluorescence resonance-energy transfer.

O'Donoghue SI, Hambly BD, dos Remedios CG.

Eur J Biochem. 1992 Apr 15;205(2):591-601.

43.

Structure of actin observed by fluorescence resonance energy transfer spectroscopy.

Miki M, O'Donoghue SI, Dos Remedios CG.

J Muscle Res Cell Motil. 1992 Apr;13(2):132-45. Review. No abstract available.

PMID:
1534564
44.

Removing the two C-terminal residues of actin affects the filament structure.

O'Donoghue SI, Miki M, dos Remedios CG.

Arch Biochem Biophys. 1992 Feb 14;293(1):110-6.

PMID:
1731627
45.

Structural interpretation of fluorescence resonance-energy transfer measurements.

O'Donoghue SI.

Comput Appl Biosci. 1991 Oct;7(4):471-7.

PMID:
1747778

Supplemental Content

Loading ...
Support Center