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Items: 25

1.

A Combined Deep Learning GRU-Autoencoder for the Early Detection of Respiratory Disease in Pigs Using Multiple Environmental Sensors.

Cowton J, Kyriazakis I, Plötz T, Bacardit J.

Sensors (Basel). 2018 Aug 2;18(8). pii: E2521. doi: 10.3390/s18082521.

2.

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.

Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Giełdoń A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Ślusarz M, Ślusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popović Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Ołdziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D; Foldit Players consortium, Crivelli SN.

Sci Rep. 2018 Jul 2;8(1):9939. doi: 10.1038/s41598-018-26812-8.

3.

A machine learning approach for the identification of new biomarkers for knee osteoarthritis development in overweight and obese women.

Lazzarini N, Runhaar J, Bay-Jensen AC, Thudium CS, Bierma-Zeinstra SMA, Henrotin Y, Bacardit J.

Osteoarthritis Cartilage. 2017 Dec;25(12):2014-2021. doi: 10.1016/j.joca.2017.09.001. Epub 2017 Sep 9.

4.

RGIFE: a ranked guided iterative feature elimination heuristic for the identification of biomarkers.

Lazzarini N, Bacardit J.

BMC Bioinformatics. 2017 Jun 30;18(1):322. doi: 10.1186/s12859-017-1729-2.

5.

Functional networks inference from rule-based machine learning models.

Lazzarini N, Widera P, Williamson S, Heer R, Krasnogor N, Bacardit J.

BioData Min. 2016 Sep 5;9(1):28. doi: 10.1186/s13040-016-0106-4. eCollection 2016.

6.

High salinity effect on bioremediation of pretreated pesticide lixiviates from greenhouses.

Micó MM, González Ó, Bacardit J, Malfeito J, Sans C.

Environ Technol. 2015;36(24):3221-31. doi: 10.1080/09593330.2015.1057541. Epub 2015 Jun 29.

PMID:
26041507
7.

A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data.

Swan AL, Stekel DJ, Hodgman C, Allaway D, Alqahtani MH, Mobasheri A, Bacardit J.

BMC Genomics. 2015;16 Suppl 1:S2. doi: 10.1186/1471-2164-16-S1-S2. Epub 2015 Jan 15.

8.

Susceptibility to experimental infection of the invertebrate locusts (Schistocerca gregaria) with the apicomplexan parasite Neospora caninum.

Alkurashi MM, May ST, Kong K, Bacardit J, Haig D, Elsheikha HM.

PeerJ. 2014 Dec 2;2:e674. doi: 10.7717/peerj.674. eCollection 2014.

9.

Hard Data Analytics Problems Make for Better Data Analysis Algorithms: Bioinformatics as an Example.

Bacardit J, Widera P, Lazzarini N, Krasnogor N.

Big Data. 2014 Sep 1;2(3):164-176.

10.

The eukaryotic N-end rule pathway: conserved mechanisms and diverse functions.

Gibbs DJ, Bacardit J, Bachmair A, Holdsworth MJ.

Trends Cell Biol. 2014 Oct;24(10):603-11. doi: 10.1016/j.tcb.2014.05.001. Epub 2014 May 26. Review.

PMID:
24874449
11.

Heuristic for maximizing DNA reuse in synthetic DNA library assembly.

Blakes J, Raz O, Feige U, Bacardit J, Widera P, Ben-Yehezkel T, Shapiro E, Krasnogor N.

ACS Synth Biol. 2014 Aug 15;3(8):529-42. doi: 10.1021/sb400161v. Epub 2014 Apr 14.

PMID:
24730371
12.

WeFold: a coopetition for protein structure prediction.

Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA, Deng X, He Y, Krupa P, Li J, Mozolewska MA, Sieradzan AK, Smadbeck J, Wirecki T, Cooper S, Flatten J, Xu K, Baker D, Cheng J, Delbem AC, Floudas CA, Keasar C, Levitt M, Popović Z, Scheraga HA, Skolnick J, Crivelli SN; Foldit Players.

Proteins. 2014 Sep;82(9):1850-68. doi: 10.1002/prot.24538. Epub 2014 Jul 8.

13.

Fosetyl-Al photo-Fenton degradation and its endogenous catalyst inhibition.

Micó MM, Zapata A, Maldonado MI, Bacardit J, Malfeito J, Sans C.

J Hazard Mater. 2014 Jan 30;265:177-84. doi: 10.1016/j.jhazmat.2013.11.064. Epub 2013 Dec 7.

PMID:
24361796
14.

Analysis of mass spectrometry data from the secretome of an explant model of articular cartilage exposed to pro-inflammatory and anti-inflammatory stimuli using machine learning.

Swan AL, Hillier KL, Smith JR, Allaway D, Liddell S, Bacardit J, Mobasheri A.

BMC Musculoskelet Disord. 2013 Dec 13;14:349. doi: 10.1186/1471-2474-14-349.

15.

Application of machine learning to proteomics data: classification and biomarker identification in postgenomics biology.

Swan AL, Mobasheri A, Allaway D, Liddell S, Bacardit J.

OMICS. 2013 Dec;17(12):595-610. doi: 10.1089/omi.2013.0017. Epub 2013 Oct 12. Review.

16.

Reduced neonatal mortality in Meishan piglets: a role for hepatic fatty acids?

Fainberg HP, Bodley K, Bacardit J, Li D, Wessely F, Mongan NP, Symonds ME, Clarke L, Mostyn A.

PLoS One. 2012;7(11):e49101. doi: 10.1371/journal.pone.0049101. Epub 2012 Nov 14.

17.

Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features.

Bacardit J, Widera P, Márquez-Chamorro A, Divina F, Aguilar-Ruiz JS, Krasnogor N.

Bioinformatics. 2012 Oct 1;28(19):2441-8. Epub 2012 Jul 25.

PMID:
22833524
18.

Using rule-based machine learning for candidate disease gene prioritization and sample classification of cancer gene expression data.

Glaab E, Bacardit J, Garibaldi JM, Krasnogor N.

PLoS One. 2012;7(7):e39932. doi: 10.1371/journal.pone.0039932. Epub 2012 Jul 11.

19.

Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets.

Bassel GW, Glaab E, Marquez J, Holdsworth MJ, Bacardit J.

Plant Cell. 2011 Sep;23(9):3101-16. doi: 10.1105/tpc.111.088153. Epub 2011 Sep 6.

20.

Experimental design applied to photo-Fenton treatment of highly methomyl-concentrated water.

Micó MM, Bacardit J, Sans C.

Water Sci Technol. 2010;62(9):2066-74. doi: 10.2166/wst.2010.522.

PMID:
21045333
21.

Performance and efficiency of memetic Pittsburgh learning classifier systems.

Bacardit J, Krasnogor N.

Evol Comput. 2009 Fall;17(3):307-42. doi: 10.1162/evco.2009.17.3.307.

PMID:
19708771
22.

Automated alphabet reduction for protein datasets.

Bacardit J, Stout M, Hirst JD, Valencia A, Smith RE, Krasnogor N.

BMC Bioinformatics. 2009 Jan 6;10:6. doi: 10.1186/1471-2105-10-6.

23.

Prediction of recursive convex hull class assignments for protein residues.

Stout M, Bacardit J, Hirst JD, Krasnogor N.

Bioinformatics. 2008 Apr 1;24(7):916-23. doi: 10.1093/bioinformatics/btn050. Epub 2008 Feb 5.

PMID:
18252738
24.

Coupled photochemical-biological system to treat biorecalcitrant wastewater.

Bacardit J, García-Molina V, Bayarri B, Giménez J, Chamarro E, Sans C, Esplugas S.

Water Sci Technol. 2007;55(12):95-100.

PMID:
17674833
25.

Two short peptides including segments of subunit A of Escherichia coli DNA gyrase as potential probes to evaluate the antibacterial activity of quinolones.

Marchetto R, Nicolás E, Castillo N, Bacardit J, Navia M, Vila J, Giralt E.

J Pept Sci. 2001 Jan;7(1):27-40.

PMID:
11245203

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