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Dr Mike Smith

Dr Mike Smith

Research Associate, RADIANT FP7 project

CRUK Cambridge Institute,
Li Ka Shing Centre,
Robinson Way

Cambridge CB2 0RE

Research Interests

Much of Mike's work focuses on understanding properties of the raw data produced by microarrays and next-generation sequencing.  Although one hopes for perfect data from each and every experiment, this is rarely the case, and so accurate and thorough assessment of data quality is a vital step in any experimental analysis.

Software

Mike is involved in a number of software projects, primarily rooted in the R programming language.  These include the beadarray, BeadDataPackR and illuminaio packages for dealing with various aspects of Illumina BeadArray processing.  He has also contributed code to the snapCGH package for predicting DNA copy-number and break-points from arrayCGH data, and EBImage which provides general purpose image processing tools in the R environment.  More recently he has worked on the IONiseR package, for performing quality assessment on Oxford Nanopore MinION sequencing data.  Code for investigating the contents of .xad files produced by the Agilent 2100 Bioanalyzer can be obtained from BitBucket.

A copy of his CV can be downloaded here

Key Publications

  • Smith ML, Baggerly KA, Bengtsson H, Ritchie ME, Hansen KD "illuminaio: An open source IDAT parsing tool for Illumina microarrays"F1000Research (2013), 2:264
  • Smith ML and Lynch AG. "BeadDataPackR: A Tool to Facilitate the Sharing of Raw Data from Illumina BeadArray Studies", Cancer Informatics (2010) 9:217-227
  • Smith ML, Dunning MJ, Tavaré S, Lynch AG.  "Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data", BMC Bioinformatics (2010) 11:208

Other Publications

  • Weaver JMJ, Ross-Innes CS, Shannon N, Lynch AG, Forshew T, Barbera M, Murtaza M, Ong C-AJ, Lao-Sirieix P, Dunning M, Smith L, Smith ML, Anderson CM, Carvalho B, O'Donovan M, Underwood TJ, May AP, Grehan N, Hardwick R, Davies J, Oloumi A, Aparicio S, Caldas C, Eldridge MD, Edwards PAW, Rosenfeld N, Tavaré S, Fitzgerald RC, and the OCCAMS consortium. "Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis"Nature Genetics. (2014) 46:837–843
  • Ritchie ME, Dunning MJ, Smith ML, Shi W, Lynch AG. "BeadArray Expression Analysis Using Bioconductor", PLoS Comp. Biol. (2011) 7(12).
  • Cairns JM, Spyrou C, Stark R, Smith ML, Tavaré S, Lynch AG. "BayesPeak - An R package for analysing ChIP-seq data", Bioinformatics. (2011) 27(5):713-714.
  • Moskvina V, Smith M, Ivanov D, Blackwood D, Stclair D, Hultman C, Toncheva D, Gill M, Corvin A, O'Dushlaine C, Morris DW, Wray NR, Sullivan P, Pato C, Pato MT, Sklar P, Purcell S, Holmans P, O'Donovan MC, Owen MJ, Kirov G. "Genetic Differences between Five European Populations", Human Heredity (2010) 70(2):141-149
  • Lynch AG, Smith ML, Dunning MJ, Cairns JM, Barbosa-Morais NL, Tavaré S. "beadarray, BASH and HULK - tools to increase the value of Illumina BeadArray experiments". In A. Gusnato, K.V. Mardia, & C.J. Fallaize (eds), Statistical Tools for Challenges in Bioinformatics. 2009 pp. 33-37. Leeds, Leeds University Press.
  • Dunning MJ, Smith ML, Ritchie ME, Tavaré S. "beadarray: R classes and methods for Illumina bead-based data"Bioinformatics. (2007) 23(16):2183-2184.
  • Dunning M, Smith ML, Thorne NP, Tavaré S. "beadarray: An R package to analyse Illumina BeadArrays"R News. (2006) 6(5):17-23.
  • Dunning M, Thorne NP, Camilier I, Smith ML , Tavaré S. "Quality control and low-level statistical analysis of Illumina BeadArrays"REVSTAT. (2006) 4:1-30.