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Bayesian Detection of Piecewise Linear Trends in Replicated Time-Series with Application to Growth Data Modelling.

Papastamoulis P, Furukawa T, van Rhijn N, Bromley M, Bignell E, Rattray M.

Int J Biostat. 2019 Jul 25. pii: /j/ijb.ahead-of-print/ijb-2018-0052/ijb-2018-0052.xml. doi: 10.1515/ijb-2018-0052. [Epub ahead of print]


Endoplasmic Reticulum Stress Signalling Induces Casein Kinase 1-Dependent Formation of Cytosolic TDP-43 Inclusions in Motor Neuron-Like Cells.

Hicks DA, Cross LL, Williamson R, Rattray M.

Neurochem Res. 2019 Jul 6. doi: 10.1007/s11064-019-02832-2. [Epub ahead of print]


Quantitative single-cell live imaging links HES5 dynamics with cell-state and fate in murine neurogenesis.

Manning CS, Biga V, Boyd J, Kursawe J, Ymisson B, Spiller DG, Sanderson CM, Galla T, Rattray M, Papalopulu N.

Nat Commun. 2019 Jun 27;10(1):2835. doi: 10.1038/s41467-019-10734-8.


Hospital Staffs' Perceptions of Postoperative Nutrition Among Colorectal Patients: A Qualitative Study.

Rattray M, Roberts S, Desbrow B, Marshall AP.

Nutr Clin Pract. 2019 May 29. doi: 10.1002/ncp.10315. [Epub ahead of print]


A qualitative exploration of factors influencing medical staffs' decision-making around nutrition prescription after colorectal surgery.

Rattray M, Roberts S, Desbrow B, Wullschleger M, Robertson T, Hickman I, Marshall AP.

BMC Health Serv Res. 2019 Mar 19;19(1):178. doi: 10.1186/s12913-019-4011-7.


Genome-wide effect of pulmonary airway epithelial cell-specific Bmal1 deletion.

Zhang Z, Hunter L, Wu G, Maidstone R, Mizoro Y, Vonslow R, Fife M, Hopwood T, Begley N, Saer B, Wang P, Cunningham P, Baxter M, Durrington H, Blaikley JF, Hussell T, Rattray M, Hogenesch JB, Gibbs J, Ray DW, Loudon ASI.

FASEB J. 2019 May;33(5):6226-6238. doi: 10.1096/fj.201801682R. Epub 2019 Feb 22.


Rheumatoid arthritis reprograms circadian output pathways.

Poolman TM, Gibbs J, Walker AL, Dickson S, Farrell L, Hensman J, Kendall AC, Maidstone R, Warwood S, Loudon A, Rattray M, Bruce IN, Nicolaou A, Ray DW.

Arthritis Res Ther. 2019 Feb 6;21(1):47. doi: 10.1186/s13075-019-1825-y.


GrandPrix: scaling up the Bayesian GPLVM for single-cell data.

Ahmed S, Rattray M, Boukouvalas A.

Bioinformatics. 2019 Jan 1;35(1):47-54. doi: 10.1093/bioinformatics/bty533.


Classifying cells with Scasat, a single-cell ATAC-seq analysis tool.

Baker SM, Rogerson C, Hayes A, Sharrocks AD, Rattray M.

Nucleic Acids Res. 2019 Jan 25;47(2):e10. doi: 10.1093/nar/gky950.


Early oral feeding after colorectal surgery: A mixed methods study of knowledge translation.

Robertson TR, Eldridge NE, Rattray ME, Roberts SJ, Desbrow B, Marshall AP, Ali AB, Hickman IJ.

Nutr Diet. 2018 Sep;75(4):345-352. doi: 10.1111/1747-0080.12473. Epub 2018 Sep 5.


REVERBa couples the circadian clock to hepatic glucocorticoid action.

Caratti G, Iqbal M, Hunter L, Kim D, Wang P, Vonslow RM, Begley N, Tetley AJ, Woodburn JL, Pariollaud M, Maidstone R, Donaldson IJ, Zhang Z, Ince LM, Kitchen G, Baxter M, Poolman TM, Daniels DA, Stirling DR, Brocker C, Gonzalez F, Loudon AS, Bechtold DA, Rattray M, Matthews LC, Ray DW.

J Clin Invest. 2018 Oct 1;128(10):4454-4471. doi: 10.1172/JCI96138. Epub 2018 Sep 4.


A qualitative exploration of patients' experiences with and perceptions of recommencing feeding after colorectal surgery.

Rattray M, Marshall AP, Desbrow B, Roberts S.

J Hum Nutr Diet. 2019 Feb;32(1):63-71. doi: 10.1111/jhn.12596. Epub 2018 Aug 27.


Trajectory inference and parameter estimation in stochastic models with temporally aggregated data.

Folia MM, Rattray M.

Stat Comput. 2018;28(5):1053-1072. doi: 10.1007/s11222-017-9779-x. Epub 2017 Oct 24.


Riluzole-Triazole Hybrids as Novel Chemical Probes for Neuroprotection in Amyotrophic Lateral Sclerosis.

Sweeney JB, Rattray M, Pugh V, Powell LA.

ACS Med Chem Lett. 2018 May 30;9(6):552-556. doi: 10.1021/acsmedchemlett.8b00103. eCollection 2018 Jun 14.


Feeding Practices and Nutrition Intakes Among Non-Critically Ill, Postoperative Adult Patients: An Observational Study.

Rattray M, Marshall A, Desbrow B, Roberts S.

Nutr Clin Pract. 2019 Jun;34(3):371-380. doi: 10.1002/ncp.10103. Epub 2018 Jun 7.


BGP: identifying gene-specific branching dynamics from single-cell data with a branching Gaussian process.

Boukouvalas A, Hensman J, Rattray M.

Genome Biol. 2018 May 29;19(1):65. doi: 10.1186/s13059-018-1440-2.


Identifying errors in meals provided to and sourced by patients on therapeutic diets in hospital.

Rattray M, Desbrow B, Roberts S.

Asia Pac J Clin Nutr. 2018;27(3):533-539. doi: 10.6133/apjcn.072017.10.


Cytokine Responses to Rhinovirus and Development of Asthma, Allergic Sensitization, and Respiratory Infections during Childhood.

Custovic A, Belgrave D, Lin L, Bakhsoliani E, Telcian AG, Solari R, Murray CS, Walton RP, Curtin J, Edwards MR, Simpson A, Rattray M, Johnston SL.

Am J Respir Crit Care Med. 2018 May 15;197(10):1265-1274. doi: 10.1164/rccm.201708-1762OC.


Evolution of IgE responses to multiple allergen components throughout childhood.

Howard R, Belgrave D, Papastamoulis P, Simpson A, Rattray M, Custovic A.

J Allergy Clin Immunol. 2018 Oct;142(4):1322-1330. doi: 10.1016/j.jaci.2017.11.064. Epub 2018 Feb 9.


A Bayesian model selection approach for identifying differentially expressed transcripts from RNA sequencing data.

Papastamoulis P, Rattray M.

J R Stat Soc Ser C Appl Stat. 2018 Jan;67(1):3-23. doi: 10.1111/rssc.12213. Epub 2017 Feb 7.


Bayesian estimation of differential transcript usage from RNA-seq data.

Papastamoulis P, Rattray M.

Stat Appl Genet Mol Biol. 2017 Nov 27;16(5-6):367-386. doi: 10.1515/sagmb-2017-0005.


Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data.

Dzida T, Iqbal M, Charapitsa I, Reid G, Stunnenberg H, Matarese F, Grote K, Honkela A, Rattray M.

PeerJ. 2017 Sep 28;5:e3742. doi: 10.7717/peerj.3742. eCollection 2017.


Efficient inference for sparse latent variable models of transcriptional regulation.

Dai Z, Iqbal M, Lawrence ND, Rattray M.

Bioinformatics. 2017 Dec 1;33(23):3776-3783. doi: 10.1093/bioinformatics/btx508.


A non-transcriptional role for the glucocorticoid receptor in mediating the cell stress response.

Ptushkina M, Poolman T, Iqbal M, Ashe M, Petersen J, Woodburn J, Rattray M, Whetton A, Ray D.

Sci Rep. 2017 Sep 21;7(1):12101. doi: 10.1038/s41598-017-09722-z.



Beart P, Robinson M, Rattray M, Maragakis NJ.

Adv Neurobiol. 2017;15:E1. doi: 10.1007/978-3-319-57193-5_21. No abstract available.


Comparing nutritional requirements, provision and intakes among patients prescribed therapeutic diets in hospital: An observational study.

Rattray M, Desbrow B, Roberts S.

Nutrition. 2017 Jul - Aug;39-40:50-56. doi: 10.1016/j.nut.2017.03.006. Epub 2017 Mar 23.


A systematic review of feeding practices among postoperative patients: is practice in-line with evidenced-based guidelines?

Rattray M, Roberts S, Marshall A, Desbrow B.

J Hum Nutr Diet. 2018 Apr;31(2):151-167. doi: 10.1111/jhn.12486. Epub 2017 Jun 6.


Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes.

Phillips NE, Manning C, Papalopulu N, Rattray M.

PLoS Comput Biol. 2017 May 11;13(5):e1005479. doi: 10.1371/journal.pcbi.1005479. eCollection 2017 May.


Sonic hedgehog signalling mediates astrocyte crosstalk with neurons to confer neuroprotection.

Ugbode CI, Smith I, Whalley BJ, Hirst WD, Rattray M.

J Neurochem. 2017 Aug;142(3):429-443. doi: 10.1111/jnc.14064. Epub 2017 Jun 20.


Astrocytic transporters in Alzheimer's disease.

Ugbode C, Hu Y, Whalley B, Peers C, Rattray M, Dallas ML.

Biochem J. 2017 Feb 1;474(3):333-355. doi: 10.1042/BCJ20160505. Review.


Erratum to: Making sense of big data in health research: towards an EU action plan.

Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G.

Genome Med. 2016 Nov 7;8(1):118. No abstract available.


Stochasticity in the miR-9/Hes1 oscillatory network can account for clonal heterogeneity in the timing of differentiation.

Phillips NE, Manning CS, Pettini T, Biga V, Marinopoulou E, Stanley P, Boyd J, Bagnall J, Paszek P, Spiller DG, White MR, Goodfellow M, Galla T, Rattray M, Papalopulu N.

Elife. 2016 Oct 4;5. pii: e16118. doi: 10.7554/eLife.16118.


Making sense of big data in health research: Towards an EU action plan.

Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G.

Genome Med. 2016 Jun 23;8(1):71. doi: 10.1186/s13073-016-0323-y. Erratum in: Genome Med. 2016 Nov 7;8(1):118.


Inferring the perturbation time from biological time course data.

Yang J, Penfold CA, Grant MR, Rattray M.

Bioinformatics. 2016 Oct 1;32(19):2956-64. doi: 10.1093/bioinformatics/btw329. Epub 2016 Jun 10.


Astrocytes Grown in Alvetex(®) Three Dimensional Scaffolds Retain a Non-reactive Phenotype.

Ugbode CI, Hirst WD, Rattray M.

Neurochem Res. 2016 Aug;41(8):1857-67. doi: 10.1007/s11064-016-1911-3. Epub 2016 Apr 21.


Neuronal-glial populations form functional networks in a biocompatible 3D scaffold.

Smith I, Haag M, Ugbode C, Tams D, Rattray M, Przyborski S, Bithell A, Whalley BJ.

Neurosci Lett. 2015 Nov 16;609:198-202. doi: 10.1016/j.neulet.2015.10.044. Epub 2015 Oct 19.


Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays.

Honkela A, Peltonen J, Topa H, Charapitsa I, Matarese F, Grote K, Stunnenberg HG, Reid G, Lawrence ND, Rattray M.

Proc Natl Acad Sci U S A. 2015 Oct 20;112(42):13115-20. doi: 10.1073/pnas.1420404112. Epub 2015 Oct 5.


Fast Nonparametric Clustering of Structured Time-Series.

Hensman J, Rattray M, Lawrence ND.

IEEE Trans Pattern Anal Mach Intell. 2015 Feb;37(2):383-93. doi: 10.1109/TPAMI.2014.2318711.


Fast and accurate approximate inference of transcript expression from RNA-seq data.

Hensman J, Papastamoulis P, Glaus P, Honkela A, Rattray M.

Bioinformatics. 2015 Dec 15;31(24):3881-9. doi: 10.1093/bioinformatics/btv483. Epub 2015 Aug 26.


Distinguishing Asthma Phenotypes Using Machine Learning Approaches.

Howard R, Rattray M, Prosperi M, Custovic A.

Curr Allergy Asthma Rep. 2015 Jul;15(7):38. doi: 10.1007/s11882-015-0542-0. Review.


Neuronal DNA damage response-associated dysregulation of signalling pathways and cholesterol metabolism at the earliest stages of Alzheimer-type pathology.

Simpson JE, Ince PG, Minett T, Matthews FE, Heath PR, Shaw PJ, Goodall E, Garwood CJ, Ratcliffe LE, Brayne C, Rattray M, Wharton SB; MRC Cognitive Function and Ageing Neuropathology Study Group.

Neuropathol Appl Neurobiol. 2016 Feb;42(2):167-79. doi: 10.1111/nan.12252. Epub 2015 Jul 7.


C9ORF72 GGGGCC Expanded Repeats Produce Splicing Dysregulation which Correlates with Disease Severity in Amyotrophic Lateral Sclerosis.

Cooper-Knock J, Bury JJ, Heath PR, Wyles M, Higginbottom A, Gelsthorpe C, Highley JR, Hautbergue G, Rattray M, Kirby J, Shaw PJ.

PLoS One. 2015 May 27;10(5):e0127376. doi: 10.1371/journal.pone.0127376. eCollection 2015.


Hoxa2 selectively enhances Meis binding to change a branchial arch ground state.

Amin S, Donaldson IJ, Zannino DA, Hensman J, Rattray M, Losa M, Spitz F, Ladam F, Sagerström C, Bobola N.

Dev Cell. 2015 Feb 9;32(3):265-77. doi: 10.1016/j.devcel.2014.12.024. Epub 2015 Jan 29.


Elucidating the mechanisms of TDP-43 aggregation in a cellular model of motor neuron disease.

Hicks D, Rattray M.

Springerplus. 2015 Jun 12;4(Suppl 1):L23. doi: 10.1186/2193-1801-4-S1-L23. eCollection 2015. No abstract available.


Relationship between genome and epigenome--challenges and requirements for future research.

Almouzni G, Altucci L, Amati B, Ashley N, Baulcombe D, Beaujean N, Bock C, Bongcam-Rudloff E, Bousquet J, Braun S, Bressac-de Paillerets B, Bussemakers M, Clarke L, Conesa A, Estivill X, Fazeli A, Grgurević N, Gut I, Heijmans BT, Hermouet S, Houwing-Duistermaat J, Iacobucci I, Ilaš J, Kandimalla R, Krauss-Etschmann S, Lasko P, Lehmann S, Lindroth A, Majdič G, Marcotte E, Martinelli G, Martinet N, Meyer E, Miceli C, Mills K, Moreno-Villanueva M, Morvan G, Nickel D, Niesler B, Nowacki M, Nowak J, Ossowski S, Pelizzola M, Pochet R, Potočnik U, Radwanska M, Raes J, Rattray M, Robinson MD, Roelen B, Sauer S, Schinzer D, Slagboom E, Spector T, Stunnenberg HG, Tiligada E, Torres-Padilla ME, Tsonaka R, Van Soom A, Vidaković M, Widschwendter M.

BMC Genomics. 2014 Jun 18;15:487. doi: 10.1186/1471-2164-15-487.


Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

wa Maina C, Honkela A, Matarese F, Grote K, Stunnenberg HG, Reid G, Lawrence ND, Rattray M.

PLoS Comput Biol. 2014 May 15;10(5):e1003598. doi: 10.1371/journal.pcbi.1003598. eCollection 2014 May.


Neuronal influences are necessary to produce mitochondrial co-localization with glutamate transporters in astrocytes.

Ugbode CI, Hirst WD, Rattray M.

J Neurochem. 2014 Sep;130(5):668-77. doi: 10.1111/jnc.12759. Epub 2014 Jun 16.


Improved variational Bayes inference for transcript expression estimation.

Papastamoulis P, Hensman J, Glaus P, Rattray M.

Stat Appl Genet Mol Biol. 2014 Apr 1;13(2):203-16. doi: 10.1515/sagmb-2013-0054.


Age-related changes in physical fall risk factors: results from a 3 year follow-up of community dwelling older adults in Tasmania, Australia.

Bird ML, Pittaway JK, Cuisick I, Rattray M, Ahuja KD.

Int J Environ Res Public Health. 2013 Nov 11;10(11):5989-97. doi: 10.3390/ijerph10115989.

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