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Items: 1 to 50 of 67

1.

Joining and splitting models with Markov melding.

Goudie RJB, Presanis AM, Lunn D, De Angelis D, Wernisch L.

Bayesian Anal. 2019 Jan;14(1):81-109. doi: 10.1214/18-BA1104.

2.

Branch-recombinant Gaussian processes for analysis of perturbations in biological time series.

Penfold CA, Sybirna A, Reid JE, Huang Y, Wernisch L, Ghahramani Z, Grant M, Surani MA.

Bioinformatics. 2018 Sep 1;34(17):i1005-i1013. doi: 10.1093/bioinformatics/bty603.

3.

Metabolic regulation of pluripotency and germ cell fate through α-ketoglutarate.

Tischler J, Gruhn WH, Reid J, Allgeyer E, Buettner F, Marr C, Theis F, Simons BD, Wernisch L, Surani MA.

EMBO J. 2019 Jan 3;38(1). pii: e99518. doi: 10.15252/embj.201899518. Epub 2018 Sep 26.

4.

Modelling of psychosocial and lifestyle predictors of peripartum depressive symptoms associated with distinct risk trajectories: a prospective cohort study.

English S, Steele A, Williams A, Blacklay J, Sorinola O, Wernisch L, Grammatopoulos DK.

Sci Rep. 2018 Aug 24;8(1):12799. doi: 10.1038/s41598-018-30874-z.

5.

GPseudoRank: a permutation sampler for single cell orderings.

Strauß ME, Reid JE, Wernisch L.

Bioinformatics. 2018 Jul 25. doi: 10.1093/bioinformatics/bty664. [Epub ahead of print]

PMID:
30052778
6.

Clusternomics: Integrative context-dependent clustering for heterogeneous datasets.

Gabasova E, Reid J, Wernisch L.

PLoS Comput Biol. 2017 Oct 16;13(10):e1005781. doi: 10.1371/journal.pcbi.1005781. eCollection 2017 Oct.

7.

A comparison of machine learning and Bayesian modelling for molecular serotyping.

Newton R, Wernisch L.

BMC Genomics. 2017 Aug 11;18(1):606. doi: 10.1186/s12864-017-3998-6.

8.

Platelet function is modified by common sequence variation in megakaryocyte super enhancers.

Petersen R, Lambourne JJ, Javierre BM, Grassi L, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP, Jiang T, Farrow S, Cairns J, Al-Subaie AM, Ashford S, Attwood A, Batista J, Bouman H, Burden F, Choudry FA, Clarke L, Flicek P, Garner SF, Haimel M, Kempster C, Ladopoulos V, Lenaerts AS, Materek PM, McKinney H, Meacham S, Mead D, Nagy M, Penkett CJ, Rendon A, Seyres D, Sun B, Tuna S, van der Weide ME, Wingett SW, Martens JH, Stegle O, Richardson S, Vallier L, Roberts DJ, Freson K, Wernisch L, Stunnenberg HG, Danesh J, Fraser P, Soranzo N, Butterworth AS, Heemskerk JW, Turro E, Spivakov M, Ouwehand WH, Astle WJ, Downes K, Kostadima M, Frontini M.

Nat Commun. 2017 Jul 13;8:16058. doi: 10.1038/ncomms16058.

9.

A graphical model approach visualizes regulatory relationships between genome-wide transcription factor binding profiles.

Ng FSL, Ruau D, Wernisch L, Göttgens B.

Brief Bioinform. 2018 Jan 1;19(1):162-173. doi: 10.1093/bib/bbw102.

10.

BTR: training asynchronous Boolean models using single-cell expression data.

Lim CY, Wang H, Woodhouse S, Piterman N, Wernisch L, Fisher J, Göttgens B.

BMC Bioinformatics. 2016 Sep 6;17(1):355. doi: 10.1186/s12859-016-1235-y.

11.

Pseudotime estimation: deconfounding single cell time series.

Reid JE, Wernisch L.

Bioinformatics. 2016 Oct 1;32(19):2973-80. doi: 10.1093/bioinformatics/btw372. Epub 2016 Jun 17.

12.

The Discovery and Validation of Biomarkers for the Diagnosis of Esophageal Squamous Dysplasia and Squamous Cell Carcinoma.

Couch G, Redman JE, Wernisch L, Newton R, Malhotra S, Dawsey SM, Lao-Sirieix P, Fitzgerald RC.

Cancer Prev Res (Phila). 2016 Jul;9(7):558-66. doi: 10.1158/1940-6207.CAPR-15-0379. Epub 2016 Apr 12.

13.

An optimal stratified Simon two-stage design.

Parashar D, Bowden J, Starr C, Wernisch L, Mander A.

Pharm Stat. 2016 Jul;15(4):333-40. doi: 10.1002/pst.1742. Epub 2016 Mar 2.

14.
15.

Analysis of dysplasia in patients with Barrett's esophagus based on expression pattern of 90 genes.

Varghese S, Newton R, Ross-Innes CS, Lao-Sirieix P, Krishnadath KK, O'Donovan M, Novelli M, Wernisch L, Bergman J, Fitzgerald RC.

Gastroenterology. 2015 Nov;149(6):1511-1518.e5. doi: 10.1053/j.gastro.2015.07.053. Epub 2015 Aug 3.

PMID:
26248086
16.

A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships.

Newton R, Wernisch L.

PLoS One. 2014 Aug 22;9(8):e105522. doi: 10.1371/journal.pone.0105522. eCollection 2014.

17.

Key regulators control distinct transcriptional programmes in blood progenitor and mast cells.

Calero-Nieto FJ, Ng FS, Wilson NK, Hannah R, Moignard V, Leal-Cervantes AI, Jimenez-Madrid I, Diamanti E, Wernisch L, Göttgens B.

EMBO J. 2014 Jun 2;33(11):1212-26. doi: 10.1002/embj.201386825. Epub 2014 Apr 23.

18.

The combination of autofluorescence endoscopy and molecular biomarkers is a novel diagnostic tool for dysplasia in Barrett's oesophagus.

di Pietro M, Boerwinkel DF, Shariff MK, Liu X, Telakis E, Lao-Sirieix P, Walker E, Couch G, Mills L, Nuckcheddy-Grant T, Slininger S, O'Donovan M, Visser M, Meijer SL, Kaye PV, Wernisch L, Ragunath K, Bergman JJ, Fitzgerald RC.

Gut. 2015 Jan;64(1):49-56. doi: 10.1136/gutjnl-2013-305975. Epub 2014 Apr 10.

19.

STEME: a robust, accurate motif finder for large data sets.

Reid JE, Wernisch L.

PLoS One. 2014 Mar 13;9(3):e90735. doi: 10.1371/journal.pone.0090735. eCollection 2014.

20.

Non-replicating Mycobacterium tuberculosis elicits a reduced infectivity profile with corresponding modifications to the cell wall and extracellular matrix.

Bacon J, Alderwick LJ, Allnutt JA, Gabasova E, Watson R, Hatch KA, Clark SO, Jeeves RE, Marriott A, Rayner E, Tolley H, Pearson G, Hall G, Besra GS, Wernisch L, Williams A, Marsh PD.

PLoS One. 2014 Feb 6;9(2):e87329. doi: 10.1371/journal.pone.0087329. eCollection 2014.

21.

Two novel pathway analysis methods based on a hierarchical model.

Evangelou M, Dudbridge F, Wernisch L.

Bioinformatics. 2014 Mar 1;30(5):690-7. doi: 10.1093/bioinformatics/btt583. Epub 2013 Oct 11.

22.

Testing the utility of an integrated analysis of copy number and transcriptomics datasets for inferring gene regulatory relationships.

Goh XY, Newton R, Wernisch L, Fitzgerald R.

PLoS One. 2013 May 30;8(5):e63780. doi: 10.1371/journal.pone.0063780. Print 2013.

23.

Transcription factor and chromatin features predict genes associated with eQTLs.

Wang D, Rendon A, Wernisch L.

Nucleic Acids Res. 2013 Feb 1;41(3):1450-63. doi: 10.1093/nar/gks1339. Epub 2012 Dec 28.

24.

DNA methylation as an adjunct to histopathology to detect prevalent, inconspicuous dysplasia and early-stage neoplasia in Barrett's esophagus.

Alvi MA, Liu X, O'Donovan M, Newton R, Wernisch L, Shannon NB, Shariff K, di Pietro M, Bergman JJ, Ragunath K, Fitzgerald RC.

Clin Cancer Res. 2013 Feb 15;19(4):878-88. doi: 10.1158/1078-0432.CCR-12-2880. Epub 2012 Dec 14.

25.

Cell signalling regulates dynamics of Nanog distribution in embryonic stem cell populations.

Luo Y, Lim CL, Nichols J, Martinez-Arias A, Wernisch L.

J R Soc Interface. 2013 Jan 6;10(78):20120525. doi: 10.1098/rsif.2012.0525. Epub 2012 Nov 8.

26.

Displaying R spatial statistics on Google dynamic maps with web applications created by Rwui.

Newton R, Deonarine A, Wernisch L.

Int J Health Geogr. 2012 Sep 24;11:41. doi: 10.1186/1476-072X-11-41.

27.

Comparison of methods for competitive tests of pathway analysis.

Evangelou M, Rendon A, Ouwehand WH, Wernisch L, Dudbridge F.

PLoS One. 2012;7(7):e41018. doi: 10.1371/journal.pone.0041018. Epub 2012 Jul 31.

28.

Transcription factor co-localization patterns affect human cell type-specific gene expression.

Wang D, Rendon A, Ouwehand W, Wernisch L.

BMC Genomics. 2012 Jun 21;13:263. doi: 10.1186/1471-2164-13-263.

29.

New gene functions in megakaryopoiesis and platelet formation.

Gieger C, Radhakrishnan A, Cvejic A, Tang W, Porcu E, Pistis G, Serbanovic-Canic J, Elling U, Goodall AH, Labrune Y, Lopez LM, Mägi R, Meacham S, Okada Y, Pirastu N, Sorice R, Teumer A, Voss K, Zhang W, Ramirez-Solis R, Bis JC, Ellinghaus D, Gögele M, Hottenga JJ, Langenberg C, Kovacs P, O'Reilly PF, Shin SY, Esko T, Hartiala J, Kanoni S, Murgia F, Parsa A, Stephens J, van der Harst P, Ellen van der Schoot C, Allayee H, Attwood A, Balkau B, Bastardot F, Basu S, Baumeister SE, Biino G, Bomba L, Bonnefond A, Cambien F, Chambers JC, Cucca F, D'Adamo P, Davies G, de Boer RA, de Geus EJ, Döring A, Elliott P, Erdmann J, Evans DM, Falchi M, Feng W, Folsom AR, Frazer IH, Gibson QD, Glazer NL, Hammond C, Hartikainen AL, Heckbert SR, Hengstenberg C, Hersch M, Illig T, Loos RJ, Jolley J, Khaw KT, Kühnel B, Kyrtsonis MC, Lagou V, Lloyd-Jones H, Lumley T, Mangino M, Maschio A, Mateo Leach I, McKnight B, Memari Y, Mitchell BD, Montgomery GW, Nakamura Y, Nauck M, Navis G, Nöthlings U, Nolte IM, Porteous DJ, Pouta A, Pramstaller PP, Pullat J, Ring SM, Rotter JI, Ruggiero D, Ruokonen A, Sala C, Samani NJ, Sambrook J, Schlessinger D, Schreiber S, Schunkert H, Scott J, Smith NL, Snieder H, Starr JM, Stumvoll M, Takahashi A, Tang WH, Taylor K, Tenesa A, Lay Thein S, Tönjes A, Uda M, Ulivi S, van Veldhuisen DJ, Visscher PM, Völker U, Wichmann HE, Wiggins KL, Willemsen G, Yang TP, Hua Zhao J, Zitting P, Bradley JR, Dedoussis GV, Gasparini P, Hazen SL, Metspalu A, Pirastu M, Shuldiner AR, Joost van Pelt L, Zwaginga JJ, Boomsma DI, Deary IJ, Franke A, Froguel P, Ganesh SK, Jarvelin MR, Martin NG, Meisinger C, Psaty BM, Spector TD, Wareham NJ, Akkerman JW, Ciullo M, Deloukas P, Greinacher A, Jupe S, Kamatani N, Khadake J, Kooner JS, Penninger J, Prokopenko I, Stemple D, Toniolo D, Wernisch L, Sanna S, Hicks AA, Rendon A, Ferreira MA, Ouwehand WH, Soranzo N.

Nature. 2011 Nov 30;480(7376):201-8. doi: 10.1038/nature10659.

30.

STEME: efficient EM to find motifs in large data sets.

Reid JE, Wernisch L.

Nucleic Acids Res. 2011 Oct;39(18):e126. doi: 10.1093/nar/gkr574. Epub 2011 Jul 23.

31.

Creating web applications for spatial epidemiological analysis and mapping in R using Rwui.

Newton R, Deonarine A, Wernisch L.

Source Code Biol Med. 2011 Apr 1;6(1):6. doi: 10.1186/1751-0473-6-6.

32.

Empirical Bayesian models for analysing molecular serotyping microarrays.

Newton R, Hinds J, Wernisch L.

BMC Bioinformatics. 2011 Mar 31;12:88. doi: 10.1186/1471-2105-12-88.

33.

An integrated machine learning approach for predicting DosR-regulated genes in Mycobacterium tuberculosis.

Zhang Y, Hatch KA, Bacon J, Wernisch L.

BMC Syst Biol. 2010 Mar 31;4:37. doi: 10.1186/1752-0509-4-37.

34.

Statistical model comparison applied to common network motifs.

Domedel-Puig N, Pournara I, Wernisch L.

BMC Syst Biol. 2010 Mar 3;4:18. doi: 10.1186/1752-0509-4-18.

35.

Variable structure motifs for transcription factor binding sites.

Reid JE, Evans KJ, Dyer N, Wernisch L, Ott S.

BMC Genomics. 2010 Jan 14;11:30. doi: 10.1186/1471-2164-11-30.

36.

Transcriptional programs: modelling higher order structure in transcriptional control.

Reid JE, Ott S, Wernisch L.

BMC Bioinformatics. 2009 Jul 16;10:218. doi: 10.1186/1471-2105-10-218.

37.

A HaemAtlas: characterizing gene expression in differentiated human blood cells.

Watkins NA, Gusnanto A, de Bono B, De S, Miranda-Saavedra D, Hardie DL, Angenent WG, Attwood AP, Ellis PD, Erber W, Foad NS, Garner SF, Isacke CM, Jolley J, Koch K, Macaulay IC, Morley SL, Rendon A, Rice KM, Taylor N, Thijssen-Timmer DC, Tijssen MR, van der Schoot CE, Wernisch L, Winzer T, Dudbridge F, Buckley CD, Langford CF, Teichmann S, Göttgens B, Ouwehand WH; Bloodomics Consortium.

Blood. 2009 May 7;113(19):e1-9. doi: 10.1182/blood-2008-06-162958. Epub 2009 Feb 19.

38.

Estimating translational selection in eukaryotic genomes.

dos Reis M, Wernisch L.

Mol Biol Evol. 2009 Feb;26(2):451-61. doi: 10.1093/molbev/msn272. Epub 2008 Nov 25.

39.

Can replication save noisy microarray data?

Wernisch L.

Comp Funct Genomics. 2002;3(4):372-4. doi: 10.1002/cfg.196.

40.

The heat shock response of Mycobacterium tuberculosis: linking gene expression, immunology and pathogenesis.

Stewart GR, Wernisch L, Stabler R, Mangan JA, Hinds J, Laing KG, Butcher PD, Young DB.

Comp Funct Genomics. 2002;3(4):348-51. doi: 10.1002/cfg.183.

41.

Using temporal correlation in factor analysis for reconstructing transcription factor activities.

Pournara I, Wernisch L.

EURASIP J Bioinform Syst Biol. 2008:172840. doi: 10.1155/2008/172840.

42.

A Bayesian Change point model for differential gene expression patterns of the DosR regulon of Mycobacterium tuberculosis.

Zhang Y, Hatch KA, Wernisch L, Bacon J.

BMC Genomics. 2008 Feb 22;9:87. doi: 10.1186/1471-2164-9-87.

43.

Quantification of global transcription patterns in prokaryotes using spotted microarrays.

Sidders B, Withers M, Kendall SL, Bacon J, Waddell SJ, Hinds J, Golby P, Movahedzadeh F, Cox RA, Frita R, Ten Bokum AM, Wernisch L, Stoker NG.

Genome Biol. 2007;8(12):R265.

44.

Lipid composition and transcriptional response of Mycobacterium tuberculosis grown under iron-limitation in continuous culture: identification of a novel wax ester.

Bacon J, Dover LG, Hatch KA, Zhang Y, Gomes JM, Kendall S, Wernisch L, Stoker NG, Butcher PD, Besra GS, Marsh PD.

Microbiology. 2007 May;153(Pt 5):1435-44.

45.

A comparative study of S/MAR prediction tools.

Evans K, Ott S, Hansen A, Koentges G, Wernisch L.

BMC Bioinformatics. 2007 Mar 2;8:71.

46.
47.

A Hidden Markov model web application for analysing bacterial genomotyping DNA microarray experiments.

Newton R, Hinds J, Wernisch L.

Appl Bioinformatics. 2006;5(4):211-8.

PMID:
17140267
48.

Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma.

Diboun I, Wernisch L, Orengo CA, Koltzenburg M.

BMC Genomics. 2006 Oct 9;7:252.

49.

Archaeology and evolution of transfer RNA genes in the Escherichia coli genome.

Withers M, Wernisch L, dos Reis M.

RNA. 2006 Jun;12(6):933-42. Epub 2006 Apr 17.

50.

Applying GIFT, a Gene Interactions Finder in Text, to fly literature.

Domedel-Puig N, Wernisch L.

Bioinformatics. 2005 Sep 1;21(17):3582-3. Epub 2005 Jul 12.

PMID:
16014369

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