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Items: 1 to 50 of 61

1.

Developing a simple method to enhance the generation of cone and rod photoreceptors in pluripotent stem cell-derived retinal organoids.

Zerti D, Dorgau B, Felemban M, Ghareeb AE, Yu M, Ding Y, Krasnogor N, Lako M.

Stem Cells. 2019 Oct 31. doi: 10.1002/stem.3082. [Epub ahead of print]

PMID:
31670434
2.

Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq.

Mutha NVR, Mohammed WK, Krasnogor N, Tan GYA, Wee WY, Li Y, Choo SW, Jakubovics NS.

Sci Rep. 2019 May 21;9(1):7664. doi: 10.1038/s41598-019-43979-w.

3.

Immunodeficiency, autoimmune thrombocytopenia and enterocolitis caused by autosomal recessive deficiency of PIK3CD-encoded phosphoinositide 3-kinase δ.

Swan DJ, Aschenbrenner D, Lamb CA, Chakraborty K, Clark J, Pandey S, Engelhardt KR, Chen R, Cavounidis A, Ding Y, Krasnogor N, Carey CD, Acres M, Needham S, Cant AJ, Arkwright PD, Chandra A, Okkenhaug K, Uhlig HH, Hambleton S.

Haematologica. 2019 Oct;104(10):e483-e486. doi: 10.3324/haematol.2018.208397. Epub 2019 May 9. No abstract available.

4.

Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations.

Naylor J, Fellermann H, Krasnogor N.

Bioinformatics. 2019 Oct 1;35(19):3859-3860. doi: 10.1093/bioinformatics/btz131.

PMID:
30796819
5.

A Scalable Test Suite for Continuous Dynamic Multiobjective Optimization.

Jiang S, Kaiser M, Yang S, Kollias S, Krasnogor N.

IEEE Trans Cybern. 2019 Feb 15. doi: 10.1109/TCYB.2019.2896021. [Epub ahead of print]

PMID:
30794198
6.

Decellularised extracellular matrix-derived peptides from neural retina and retinal pigment epithelium enhance the expression of synaptic markers and light responsiveness of human pluripotent stem cell derived retinal organoids.

Dorgau B, Felemban M, Hilgen G, Kiening M, Zerti D, Hunt NC, Doherty M, Whitfield P, Hallam D, White K, Ding Y, Krasnogor N, Al-Aama J, Asfour HZ, Sernagor E, Lako M.

Biomaterials. 2019 Apr;199:63-75. doi: 10.1016/j.biomaterials.2019.01.028. Epub 2019 Jan 22.

7.

Transcriptional responses of Streptococcus gordonii and Fusobacterium nucleatum to coaggregation.

Mutha NVR, Mohammed WK, Krasnogor N, Tan GYA, Choo SW, Jakubovics NS.

Mol Oral Microbiol. 2018 Dec;33(6):450-464. doi: 10.1111/omi.12248.

PMID:
30329223
8.

Disrupted alternative splicing for genes implicated in splicing and ciliogenesis causes PRPF31 retinitis pigmentosa.

Buskin A, Zhu L, Chichagova V, Basu B, Mozaffari-Jovin S, Dolan D, Droop A, Collin J, Bronstein R, Mehrotra S, Farkas M, Hilgen G, White K, Pan KT, Treumann A, Hallam D, Bialas K, Chung G, Mellough C, Ding Y, Krasnogor N, Przyborski S, Zwolinski S, Al-Aama J, Alharthi S, Xu Y, Wheway G, Szymanska K, McKibbin M, Inglehearn CF, Elliott DJ, Lindsay S, Ali RR, Steel DH, Armstrong L, Sernagor E, Urlaub H, Pierce E, Lührmann R, Grellscheid SN, Johnson CA, Lako M.

Nat Commun. 2018 Oct 12;9(1):4234. doi: 10.1038/s41467-018-06448-y.

9.

Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World.

Hordijk W, Naylor J, Krasnogor N, Fellermann H.

Life (Basel). 2018 Aug 18;8(3). pii: E33. doi: 10.3390/life8030033.

10.

Extracellular matrix component expression in human pluripotent stem cell-derived retinal organoids recapitulates retinogenesis in vivo and reveals an important role for IMPG1 and CD44 in the development of photoreceptors and interphotoreceptor matrix.

Felemban M, Dorgau B, Hunt NC, Hallam D, Zerti D, Bauer R, Ding Y, Collin J, Steel D, Krasnogor N, Al-Aama J, Lindsay S, Mellough C, Lako M.

Acta Biomater. 2018 Jul 1;74:207-221. doi: 10.1016/j.actbio.2018.05.023. Epub 2018 May 17.

11.

Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon.

Torelli E, Kozyra JW, Gu JY, Stimming U, Piantanida L, Voïtchovsky K, Krasnogor N.

Sci Rep. 2018 May 3;8(1):6989. doi: 10.1038/s41598-018-25270-6.

12.

Automatic selection of verification tools for efficient analysis of biochemical models.

Bakir ME, Konur S, Gheorghe M, Krasnogor N, Stannett M.

Bioinformatics. 2018 Sep 15;34(18):3187-3195. doi: 10.1093/bioinformatics/bty282.

13.

Streptococcus gordonii Challisin protease is required for sensing cell--cell contact with Actinomyces oris.

Mohammed WK, Krasnogor N, Jakubovics NS.

FEMS Microbiol Ecol. 2018 May 1;94(5). doi: 10.1093/femsec/fiy043.

PMID:
29547886
14.

Correction to Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations.

Naylor J, Fellermann H, Ding Y, Mohammed WK, Jakubovics NS, Dafhnis-Calas F, Heeb S, Cámara M, Mukherjee J, Biggs CA, Wright PC, Krasnogor N.

ACS Synth Biol. 2018 Mar 16;7(3):952. doi: 10.1021/acssynbio.8b00077. Epub 2018 Mar 1. No abstract available.

15.

Predicting species emergence in simulated complex pre-biotic networks.

Markovitch O, Krasnogor N.

PLoS One. 2018 Feb 15;13(2):e0192871. doi: 10.1371/journal.pone.0192871. eCollection 2018.

16.

CSBB: synthetic biology research at Newcastle University.

Goñi-Moreno A, Wipat A, Krasnogor N.

Biochem Soc Trans. 2017 Jun 15;45(3):781-783. doi: 10.1042/BST20160437.

17.

Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations.

Naylor J, Fellermann H, Ding Y, Mohammed WK, Jakubovics NS, Mukherjee J, Biggs CA, Wright PC, Krasnogor N.

ACS Synth Biol. 2017 Jul 21;6(7):1194-1210. doi: 10.1021/acssynbio.6b00315. Epub 2017 May 22. Erratum in: ACS Synth Biol. 2018 Mar 16;7(3):952.

18.

Designing Uniquely Addressable Bio-orthogonal Synthetic Scaffolds for DNA and RNA Origami.

Kozyra J, Ceccarelli A, Torelli E, Lopiccolo A, Gu JY, Fellermann H, Stimming U, Krasnogor N.

ACS Synth Biol. 2017 Jul 21;6(7):1140-1149. doi: 10.1021/acssynbio.6b00271. Epub 2017 Apr 25.

19.

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.

20.

Synthesis and cell-free cloning of DNA libraries using programmable microfluidics.

Ben Yehezkel T, Rival A, Raz O, Cohen R, Marx Z, Camara M, Dubern JF, Koch B, Heeb S, Krasnogor N, Delattre C, Shapiro E.

Nucleic Acids Res. 2016 Feb 29;44(4):e35. doi: 10.1093/nar/gkv1087. Epub 2015 Oct 19.

21.

Complexity measurement based on information theory and kolmogorov complexity.

Lui LT, Terrazas G, Zenil H, Alexander C, Krasnogor N.

Artif Life. Spring 2015;21(2):205-24. doi: 10.1162/ARTL_a_00157. Epub 2015 Jan 26.

PMID:
25622014
22.

Photochromic molecular implementations of universal computation.

Chaplin JC, Krasnogor N, Russell NA.

Biosystems. 2014 Dec;126:12-26. doi: 10.1016/j.biosystems.2014.09.004. Epub 2014 Oct 3.

23.

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.

24.

Meta-stochastic simulation of biochemical models for systems and synthetic biology.

Sanassy D, Widera P, Krasnogor N.

ACS Synth Biol. 2015 Jan 16;4(1):39-47. doi: 10.1021/sb5001406. Epub 2014 Oct 7.

PMID:
25152014
25.

Qualitative and quantitative analysis of systems and synthetic biology constructs using P systems.

Konur S, Gheorghe M, Dragomir C, Mierla L, Ipate F, Krasnogor N.

ACS Synth Biol. 2015 Jan 16;4(1):83-92. doi: 10.1021/sb500134w. Epub 2014 Aug 14.

PMID:
25090609
26.

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
27.

JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks.

Winterhalter C, Widera P, Krasnogor N.

Bioinformatics. 2014 Apr 1;30(7):1029-30. doi: 10.1093/bioinformatics/btt732. Epub 2013 Dec 19.

28.

Bacteria clustering by polymers induces the expression of quorum-sensing-controlled phenotypes.

Lui LT, Xue X, Sui C, Brown A, Pritchard DI, Halliday N, Winzer K, Howdle SM, Fernandez-Trillo F, Krasnogor N, Alexander C.

Nat Chem. 2013 Dec;5(12):1058-65. doi: 10.1038/nchem.1793. Epub 2013 Nov 10.

29.

Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination.

Dekkers BJ, Pearce S, van Bolderen-Veldkamp RP, Marshall A, Widera P, Gilbert J, Drost HG, Bassel GW, Müller K, King JR, Wood AT, Grosse I, Quint M, Krasnogor N, Leubner-Metzger G, Holdsworth MJ, Bentsink L.

Plant Physiol. 2013 Sep;163(1):205-15. doi: 10.1104/pp.113.223511. Epub 2013 Jul 15.

30.

Is there an optimal level of open-endedness in prebiotic evolution?

Markovitch O, Sorek D, Lui LT, Lancet D, Krasnogor N.

Orig Life Evol Biosph. 2012 Oct;42(5):469-73; discussion 474. doi: 10.1007/s11084-012-9309-y.

PMID:
23114973
31.

EnrichNet: network-based gene set enrichment analysis.

Glaab E, Baudot A, Krasnogor N, Schneider R, Valencia A.

Bioinformatics. 2012 Sep 15;28(18):i451-i457. doi: 10.1093/bioinformatics/bts389.

32.

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
33.

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.

34.

An intelligent multi-restart memetic algorithm for box constrained global optimisation.

Sun J, Garibaldi JM, Krasnogor N, Zhang Q.

Evol Comput. 2013 Spring;21(1):107-47. doi: 10.1162/EVCO_a_00068. Epub 2012 Mar 12.

PMID:
22335546
35.

Implementing conventional logic unconventionally: photochromic molecular populations as registers and logic gates.

Chaplin JC, Russell NA, Krasnogor N.

Biosystems. 2012 Jul;109(1):35-51. doi: 10.1016/j.biosystems.2011.12.005. Epub 2012 Jan 5.

PMID:
22240019
36.

The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology.

Blakes J, Twycross J, Romero-Campero FJ, Krasnogor N.

Bioinformatics. 2011 Dec 1;27(23):3323-4. doi: 10.1093/bioinformatics/btr571. Epub 2011 Oct 12.

37.

The ten grand challenges of synthetic life.

Porcar M, Danchin A, de Lorenzo V, Dos Santos VA, Krasnogor N, Rasmussen S, Moya A.

Syst Synth Biol. 2011 Jun;5(1-2):1-9. doi: 10.1007/s11693-011-9084-5. Epub 2011 Aug 5.

38.

A computational study of liposome logic: towards cellular computing from the bottom up.

Smaldon J, Romero-Campero FJ, Fernández Trillo F, Gheorghe M, Alexander C, Krasnogor N.

Syst Synth Biol. 2010 Sep;4(3):157-79. doi: 10.1007/s11693-010-9060-5. Epub 2010 Jul 18.

39.

Synthetic biology gains momentum in Europe.

Gilbert D, Jaramillo A, Krasnogor N, de Lorenzo V.

Syst Synth Biol. 2010 Sep;4(3):145-7. doi: 10.1007/s11693-010-9065-0. Epub 2010 Oct 5. No abstract available.

40.

A thermodynamic switch modulates abscisic acid receptor sensitivity.

Dupeux F, Santiago J, Betz K, Twycross J, Park SY, Rodriguez L, Gonzalez-Guzman M, Jensen MR, Krasnogor N, Blackledge M, Holdsworth M, Cutler SR, Rodriguez PL, Márquez JA.

EMBO J. 2011 Aug 16;30(20):4171-84. doi: 10.1038/emboj.2011.294.

41.

Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions.

Bassel GW, Lan H, Glaab E, Gibbs DJ, Gerjets T, Krasnogor N, Bonner AJ, Holdsworth MJ, Provart NJ.

Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9709-14. doi: 10.1073/pnas.1100958108. Epub 2011 May 18.

42.

Extending pathways and processes using molecular interaction networks to analyse cancer genome data.

Glaab E, Baudot A, Krasnogor N, Valencia A.

BMC Bioinformatics. 2010 Dec 13;11:597. doi: 10.1186/1471-2105-11-597.

43.

RERG (Ras-like, oestrogen-regulated, growth-inhibitor) expression in breast cancer: a marker of ER-positive luminal-like subtype.

Habashy HO, Powe DG, Glaab E, Ball G, Spiteri I, Krasnogor N, Garibaldi JM, Rakha EA, Green AR, Caldas C, Ellis IO.

Breast Cancer Res Treat. 2011 Jul;128(2):315-26. doi: 10.1007/s10549-010-1073-y. Epub 2010 Aug 10.

PMID:
20697807
44.

Toward high-throughput, multicriteria protein-structure comparison and analysis.

Shah AA, Folino G, Krasnogor N.

IEEE Trans Nanobioscience. 2010 Jun;9(2):144-55. doi: 10.1109/TNB.2010.2043851.

PMID:
20650704
45.

Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study.

Twycross J, Band LR, Bennett MJ, King JR, Krasnogor N.

BMC Syst Biol. 2010 Mar 26;4:34. doi: 10.1186/1752-0509-4-34.

46.

TopoGSA: network topological gene set analysis.

Glaab E, Baudot A, Krasnogor N, Valencia A.

Bioinformatics. 2010 May 1;26(9):1271-2. doi: 10.1093/bioinformatics/btq131. Epub 2010 Mar 24.

47.

Evolving cell models for systems and synthetic biology.

Cao H, Romero-Campero FJ, Heeb S, Cámara M, Krasnogor N.

Syst Synth Biol. 2010 Mar;4(1):55-84. doi: 10.1007/s11693-009-9050-7. Epub 2010 Jan 22.

48.

Controlled polymer synthesis--from biomimicry towards synthetic biology.

Pasparakis G, Krasnogor N, Cronin L, Davis BG, Alexander C.

Chem Soc Rev. 2010 Jan;39(1):286-300. doi: 10.1039/b809333b. Epub 2009 Oct 6. Review.

PMID:
20023853
49.

ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization.

Glaab E, Garibaldi JM, Krasnogor N.

BMC Bioinformatics. 2009 Oct 28;10:358. doi: 10.1186/1471-2105-10-358.

50.

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

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