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Dr Emma Laing

Lecturer in Bioinformatics

Qualifications: BSc, MSc, PhD, PGCAP

Email:
Phone: Work: 01483 68 9626
Room no: 13 AY 04

Office hours

Mon-Fri by appointment 

Further information

Biography

2009 -             Lecturer in Bioinformatics. University of Surrey, Guildford, UK.
2005 - 2009   Research Associate in Bioinformatics. University of Surrey, Guildford, UK.
2002 - 2005   PhD Bioinformatics: Operon prediction in Streptomyces coelicolor. University of Manchester, Manchester,UK.
2001 - 2002   MSc Bioinformatics. University of East Anglia, Norwich, UK.
1997 - 2001   BSc Molecular Biology and Genetics. University of East Anglia, Norwich, UK.

Research Interests

My research lies within the broad area of identifying and constructing transcriptional networks and their integration with other networks, such as metabolic and molecular interaction networks. Such approaches are central to ‘Systems biology’ which is concerned with the development of in silico cell/organism models.

Particular areas of interest to me are:

Development of novel algorithms for data analysis

Development of bioinformatic tools for data interpretation

The integration of multi-omic large scale data sets

Construction of transcriptional networks

Data mining 
 

I am currently involved in research in Streptomyces coelicolor, Escherichia coli, Mycobacterium tuberculosis, Campylobacter jejuni, Viruses, microbial communities, Human cancers (prostate, ovarian, colon) and sleep in Humans and mice.

 

Useful links

Rank Products analysis online

Operon prediction viewer online

 

Grants

£620k BBSRC (BB/J01916X/1), 2012- present. 'A study of metagenomics-informed biochemical functionality of microbial fuel cells using DDGS as a substrate'. M Bushell (PI), CA Avignone-Rossa, AM Kierzek, EE Laing, RCT Slade & J Varcoe.

£1.2 million AFOSR, 2008-2011. 'Cognitive vulnerabiliy following extended wakefullness in defined genotyps'. D-J Dijk (PI), J Groeger, S N Archer, M von Schantz, C P Smith & EE Laing

£1.76 million BBSRC (BB/F022883/1),  2008-2011. 'Circadian and homeostatic contributions to physiology, cognition and genome-wide expression in human and mouse variants of the PER3 VNTR polymorphism.' Named investigator.

PhD projects

Irene Freire-Martin (Principal supervisor, collaboration with Prof. Roberto La Ragione, Dr. Simon Park and Prof. Martin Woodward.):
Characterisation of CTX-M plasmids conferring ß-lactam resistance in the Enterobacteriaceae.
Funded by Defra/AHVLA

Spencer Thomas (Co-supervisor, collaboration with Prof. Yaochu Jin and Prof. Colin Smith):
Gene Regulatory Networks and Evolutionary Algorithms: Modelling Genetic Oscillations, Mechanisms for Evolution and the Production of Antibiotics from Bacteria.
Funded by EPSRC DTC.

Tameera Rahman (Co-supervisor, collaboration with Prof. Yaochu Jin):
Modelling for Predicting Antigenic Variability in Foot-and-Mouth Disease.
Jointly funded by the Department of Computing and FHMS (University of Surrey).

Rebecca Clarke (Principal supervisor, collaboration with Roberto La Ragione):
Understanding the factors involved in Campylobacter biofilm formation and survival
Jointly funded by Leatherhead Food Research and FHMS (University of Surrey).

PhD vacancies to be advertised shortly:

BBSRC funded project, in collaboration with Dr. Claudio Avignone-Rossa and Symbio :
The development of a microbial community for increasing wheat crop yield.

Publications

Highlights

  • Bucca G, Laing E, Mersinias V, Allenby N, Hurd D, Holdstock J, Brenner V, Harrison M, Smith CP. (2009) 'Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon'. BIOMED CENTRAL LTD GENOME BIOLOGY, 10 (1) Article number ARTN R5
    doi: 10.1186/gb-2009-10-1-r5
    Full text is available at: http://epubs.surrey.ac.uk/203295/
  • Laing E, Sidhu K, Hubbard SJ. (2008) 'Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor'. BIOMED CENTRAL LTD BMC GENOMICS, 9 Article number ARTN 79
    doi: 10.1186/1471-2164-9-79
    Full text is available at: http://epubs.surrey.ac.uk/203302/

Journal articles

  • Allenby NE, Laing E, Bucca G, Kierzek AM, Smith CP. (2012) 'Diverse control of metabolism and other cellular processes in Streptomyces coelicolor by the PhoP transcription factor: genome-wide identification of in vivo targets.'. Nucleic Acids Res, England: 40 (19), pp. 9543-9556.
    doi: 10.1093/nar/gks766
    Full text is available at: http://epubs.surrey.ac.uk/725768/

    Abstract

    Streptomycetes sense and respond to the stress of phosphate starvation via the two-component PhoR-PhoP signal transduction system. To identify the in vivo targets of PhoP we have undertaken a chromatin-immunoprecipitation-on-microarray analysis of wild-type and phoP mutant cultures and, in parallel, have quantified their transcriptomes. Most (ca. 80%) of the previously in vitro characterized PhoP targets were identified in this study among several hundred other putative novel PhoP targets. In addition to activating genes for phosphate scavenging systems PhoP was shown to target two gene clusters for cell wall/extracellular polymer biosynthesis. Furthermore PhoP was found to repress an unprecedented range of pathways upon entering phosphate limitation including nitrogen assimilation, oxidative phosphorylation, nucleotide biosynthesis and glycogen catabolism. Moreover, PhoP was shown to target many key genes involved in antibiotic production and morphological differentiation, including afsS, atrA, bldA, bldC, bldD, bldK, bldM, cdaR, cdgA, cdgB and scbR-scbA. Intriguingly, in the PhoP-dependent cpk polyketide gene cluster, PhoP accumulates substantially at three specific sites within the giant polyketide synthase-encoding genes. This study suggests that, following phosphate limitation, Streptomyces coelicolor PhoP functions as a 'master' regulator, suppressing central metabolism, secondary metabolism and developmental pathways until sufficient phosphate is salvaged to support further growth and, ultimately, morphological development.

  • Bonde BK, Beste DJV, Laing E, Kierzek AM, McFadden J. (2011) 'Differential Producibility Analysis (DPA) of Transcriptomic Data with Metabolic Networks: Deconstructing the Metabolic Response of M. tuberculosis'. PUBLIC LIBRARY SCIENCE PLOS COMPUTATIONAL BIOLOGY, 7 (6) Article number ARTN e1002060
    doi: 10.1371/journal.pcbi.1002060
    Full text is available at: http://epubs.surrey.ac.uk/184902/
  • Lewis RA, Shahi SK, Laing E, Bucca G, Efthimiou G, Bushell M, Smith CP. (2011) 'Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2).'. BMC Res Notes, England: 4
    doi: 10.1186/1756-0500-4-78
    Full text is available at: http://epubs.surrey.ac.uk/203297/

    Abstract

    The present study represents a genome-wide transcriptomic analysis of the response of the model streptomycete Streptomyces coelicolor A3(2) M145 to fermentor culture in Modified Evans Media limited, respectively, for nitrogen, phosphate and carbon undertaken as part of the ActinoGEN consortium to provide a publicly available reference microarray dataset.

  • Laing E, Smith CP. (2010) 'RankProdIt: A web-interactive Rank Products analysis tool.'. BMC Res Notes, England: 3
    doi: 10.1186/1756-0500-3-221
    Full text is available at: http://epubs.surrey.ac.uk/203303/

    Abstract

    The first objective of a DNA microarray experiment is typically to generate a list of genes or probes that are found to be differentially expressed or represented (in the case of comparative genomic hybridizations and/or copy number variation) between two conditions or strains. Rank Products analysis comprises a robust algorithm for deriving such lists from microarray experiments that comprise small numbers of replicates, for example, less than the number required for the commonly used t-test. Currently, users wishing to apply Rank Products analysis to their own microarray data sets have been restricted to the use of command line-based software which can limit its usage within the biological community.

  • Lewis RA, Laing E, Allenby N, Bucca G, Brenner V, Harrison M, Kierzek AM, Smith CP. (2010) 'Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization'. BIOMED CENTRAL LTD BMC GENOMICS, 11 Article number ARTN 682
    doi: 10.1186/1471-2164-11-682
    Full text is available at: http://epubs.surrey.ac.uk/203299/
  • Salerno P, Larsson J, Bucca G, Laing E, Smith CP, Flardh K. (2009) 'One of the Two Genes Encoding Nucleoid-Associated HU Proteins in Streptomyces coelicolor Is Developmentally Regulated and Specifically Involved in Spore Maturation'. AMER SOC MICROBIOLOGY J BACTERIOL, 191 (21), pp. 6489-6500.
    doi: 10.1128/JB.00709-09
  • Sooriakumaran P, Macanas-Pirard P, Bucca G, Henderson A, Langley SE, Laing RW, Smith CP, Laing EE, Coley HM. (2009) 'A gene expression profiling approach assessing celecoxib in a randomized controlled trial in prostate cancer.'. International Institute of Anticancer Research (IIAR) Cancer Genomics Proteomics, Greece: 6 (2), pp. 93-99.
    Full text is available at: http://epubs.surrey.ac.uk/203293/

    Abstract

    We performed a pilot study, looking at the COX-2 inhibitor celecoxib, on newly diagnosed prostate cancer patients in the neo-adjuvant setting using DNA microarray analysis.

  • Bucca G, Laing E, Mersinias V, Allenby N, Hurd D, Holdstock J, Brenner V, Harrison M, Smith CP. (2009) 'Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon'. BIOMED CENTRAL LTD GENOME BIOLOGY, 10 (1) Article number ARTN R5
    doi: 10.1186/gb-2009-10-1-r5
    Full text is available at: http://epubs.surrey.ac.uk/203295/
  • Laing E, Sidhu K, Hubbard SJ. (2008) 'Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor'. BIOMED CENTRAL LTD BMC GENOMICS, 9 Article number ARTN 79
    doi: 10.1186/1471-2164-9-79
    Full text is available at: http://epubs.surrey.ac.uk/203302/
  • Hesketh A, Bucca G, Laing E, Flett F, Hotchkiss G, Smith CP, Chater KF. (2007) 'New pleiotropic effects of eliminating a rare tRNA from Streptomyces coelicolor, revealed by combined proteomic and transcriptomic analysis of liquid cultures'. BIOMED CENTRAL LTD BMC GENOMICS, 8 Article number ARTN 261
    doi: 10.1186/1471-2164-8-261
    Full text is available at: http://epubs.surrey.ac.uk/203300/
  • Beste DJV, Laing E, Bonde B, Avignone-Rossa C, Bushell ME, McFadden JJ. (2007) 'Transcriptomic analysis identifies growth rate modulation as a component of the adaptation of mycobacteria to survival inside the macrophage'. AMER SOC MICROBIOLOGY JOURNAL OF BACTERIOLOGY, 189 (11), pp. 3969-3976.
    doi: 10.1128/JB.01787-06
    Full text is available at: http://epubs.surrey.ac.uk/184935/
  • Noens EE, Mersinias V, Willemse J, Traag BA, Laing E, Chater KF, Smith CP, Koerten HK, van Wezel GP. (2007) 'Loss of the controlled localization of growth stage-specific cell-wall synthesis pleiotropically affects developmental gene expression in an ssgA mutant of Streptomyces coelicolor'. BLACKWELL PUBLISHING MOLECULAR MICROBIOLOGY, 64 (5), pp. 1244-1259.
    doi: 10.1111/j.1365-2958.2007.05732.x
  • Tellez JO, Dobrzynski H, Greener ID, Graham GM, Laing E, Honjo H, Hubbard SJ, Boyett MR, Billeter R. (2006) 'Differential expression of ion channel transcripts in atrial muscle and sinoatrial node in rabbit'. LIPPINCOTT WILLIAMS & WILKINS CIRCULATION RESEARCH, 99 (12), pp. 1384-1393.
    doi: 10.1161/01.RES.0000251717.98379.69
  • Laing E, Mersinias V, Smith CP, Hubbard SJ. (2006) 'Analysis of gene expression in operons of Streptomyces coelicolor'. BIOMED CENTRAL LTD GENOME BIOLOGY, 7 (6) Article number ARTN R46
    doi: 10.1186/gb-2006-7-6-r46
    Full text is available at: http://epubs.surrey.ac.uk/203294/

Conference papers

  • Lordan J, Karanjia N, Bucca G, Laing E, Smith C. (2010) 'Prospective analysis of the gene expression signature of peri-metastasis 'halo' tissue following neo-adjuvant chemotherapy-induced tumour reduction of colorectal liver metastasis'. WILEY-BLACKWELL BRITISH JOURNAL OF SURGERY, Liverpool, ENGLAND: Electronic Poster of Distinction in Association-of-Surgeons-of-Great-Britain-and-Ireland-International-Surgical-Congress 97, pp. 61-62.

Teaching

BMS2036 Molecular Biology and Genetics 2

BMS3072 Systems Biology

 

MSc Computational Intelligence and Computational Biology

MSc Systems Biology

MSc Veterinary Microbiology

Departmental Duties

Module organiser BMS1026

Senior PTY tutor for Microbiology and Veterinary Biosciences

Exams officer for MSc Veterinary Biosciences

Programme Director MSc Systems Biology