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Items: 1 to 20 of 40

1.

Recommendations on e-infrastructures for next-generation sequencing.

Spjuth O, Bongcam-Rudloff E, Dahlberg J, Dahlö M, Kallio A, Pireddu L, Vezzi F, Korpelainen E.

Gigascience. 2016 Jun 7;5:26. doi: 10.1186/s13742-016-0132-7. Review.

2.

Origin of aromatase inhibitory activity via proteochemometric modeling.

Simeon S, Spjuth O, Lapins M, Nabu S, Anuwongcharoen N, Prachayasittikul V, Wikberg JE, Nantasenamat C.

PeerJ. 2016 May 12;4:e1979. doi: 10.7717/peerj.1979. eCollection 2016.

3.

Erratum to: A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data.

Siretskiy A, Sundqvist T, Voznesenskiy M, Spjuth O.

Gigascience. 2015 Dec 9;4:61. doi: 10.1186/s13742-015-0100-7. eCollection 2015.

4.

Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of 'Omics' Data from Human Cell Cultures.

Grafström RC, Nymark P, Hongisto V, Spjuth O, Ceder R, Willighagen E, Hardy B, Kaski S, Kohonen P.

Altern Lab Anim. 2015 Nov;43(5):325-32.

5.

BioImg.org: A Catalog of Virtual Machine Images for the Life Sciences.

Dahlö M, Haziza F, Kallio A, Korpelainen E, Bongcam-Rudloff E, Spjuth O.

Bioinform Biol Insights. 2015 Sep 10;9:125-8. doi: 10.4137/BBI.S28636. eCollection 2015.

6.

Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research.

Spjuth O, Krestyaninova M, Hastings J, Shen HY, Heikkinen J, Waldenberger M, Langhammer A, Ladenvall C, Esko T, Persson MÅ, Heggland J, Dietrich J, Ose S, Gieger C, Ried JS, Peters A, Fortier I, de Geus EJ, Klovins J, Zaharenko L, Willemsen G, Hottenga JJ, Litton JE, Karvanen J, Boomsma DI, Groop L, Rung J, Palmgren J, Pedersen NL, McCarthy MI, van Duijn CM, Hveem K, Metspalu A, Ripatti S, Prokopenko I, Harris JR.

Eur J Hum Genet. 2016 Apr;24(4):521-8. doi: 10.1038/ejhg.2015.165. Epub 2015 Aug 26.

PMID:
26306643
7.

Experiences with workflows for automating data-intensive bioinformatics.

Spjuth O, Bongcam-Rudloff E, Hernández GC, Forer L, Giovacchini M, Guimera RV, Kallio A, Korpelainen E, Kańduła MM, Krachunov M, Kreil DP, Kulev O, Łabaj PP, Lampa S, Pireddu L, Schönherr S, Siretskiy A, Vassilev D.

Biol Direct. 2015 Aug 19;10:43. doi: 10.1186/s13062-015-0071-8.

8.

A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data.

Siretskiy A, Sundqvist T, Voznesenskiy M, Spjuth O.

Gigascience. 2015 Jun 4;4:26. doi: 10.1186/s13742-015-0058-5. eCollection 2015. Erratum in: Gigascience. 2015;4:61.

9.

Scaling predictive modeling in drug development with cloud computing.

Moghadam BT, Alvarsson J, Holm M, Eklund M, Carlsson L, Spjuth O.

J Chem Inf Model. 2015 Jan 26;55(1):19-25. doi: 10.1021/ci500580y. Epub 2015 Jan 8.

PMID:
25493610
10.

Benchmarking study of parameter variation when using signature fingerprints together with support vector machines.

Alvarsson J, Eklund M, Andersson C, Carlsson L, Spjuth O, Wikberg JE.

J Chem Inf Model. 2014 Nov 24;54(11):3211-7. doi: 10.1021/ci500344v. Epub 2014 Oct 28.

PMID:
25318024
11.

Ligand-based target prediction with signature fingerprints.

Alvarsson J, Eklund M, Engkvist O, Spjuth O, Carlsson L, Wikberg JE, Noeske T.

J Chem Inf Model. 2014 Oct 27;54(10):2647-53. doi: 10.1021/ci500361u. Epub 2014 Oct 3.

PMID:
25230336
12.

Cancer biology, toxicology and alternative methods development go hand-in-hand.

Kohonen P, Ceder R, Smit I, Hongisto V, Myatt G, Hardy B, Spjuth O, Grafström R.

Basic Clin Pharmacol Toxicol. 2014 Jul;115(1):50-8. doi: 10.1111/bcpt.12257. Epub 2014 May 23. Review.

13.

Automated QuantMap for rapid quantitative molecular network topology analysis.

Schaal W, Hammerling U, Gustafsson MG, Spjuth O.

Bioinformatics. 2013 Sep 15;29(18):2369-70. doi: 10.1093/bioinformatics/btt390. Epub 2013 Jul 4.

14.

Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data.

Lampa S, Dahlö M, Olason PI, Hagberg J, Spjuth O.

Gigascience. 2013 Jun 25;2(1):9. doi: 10.1186/2047-217X-2-9.

15.

A unified proteochemometric model for prediction of inhibition of cytochrome p450 isoforms.

Lapins M, Worachartcheewan A, Spjuth O, Georgiev V, Prachayasittikul V, Nantasenamat C, Wikberg JE.

PLoS One. 2013 Jun 17;8(6):e66566. doi: 10.1371/journal.pone.0066566. Print 2013.

16.

WhichCyp: prediction of cytochromes P450 inhibition.

Rostkowski M, Spjuth O, Rydberg P.

Bioinformatics. 2013 Aug 15;29(16):2051-2. doi: 10.1093/bioinformatics/btt325. Epub 2013 Jun 5.

17.

The ChEMBL database as linked open data.

Willighagen EL, Waagmeester A, Spjuth O, Ansell P, Williams AJ, Tkachenko V, Hastings J, Chen B, Wild DJ.

J Cheminform. 2013 May 8;5(1):23. doi: 10.1186/1758-2946-5-23.

18.

Applications of the InChI in cheminformatics with the CDK and Bioclipse.

Spjuth O, Berg A, Adams S, Willighagen EL.

J Cheminform. 2013 Mar 13;5(1):14. doi: 10.1186/1758-2946-5-14.

19.

Bioclipse-R: integrating management and visualization of life science data with statistical analysis.

Spjuth O, Georgiev V, Carlsson L, Alvarsson J, Berg A, Willighagen E, Wikberg JE, Eklund M.

Bioinformatics. 2013 Jan 15;29(2):286-9. doi: 10.1093/bioinformatics/bts681. Epub 2012 Nov 23.

20.

Open source drug discovery with bioclipse.

Spjuth O, Carlsson L, Alvarsson J, Georgiev V, Willighagen E, Eklund M.

Curr Top Med Chem. 2012;12(18):1980-6.

PMID:
23110533
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