Dr Mark D. Preston


Research

Bioinformatics processing of biological medicines for the National Institute for Biological Standards and Control.

Statistical and population genomics in the areas of infectious and tropical diseases (C. difficile, MRSA, malaria and TB), formerly at the London School of Hygiene and Tropical Medicine.

Numerical and functional analysis solving water wave problems with integral equations and Navier-Stokes equations working with Prof. Edward Fraenkel FRS at the University of Bath.

Mathematical biology/theoretical ecology, including fragmentation, foraging and population dynamics with collaborators at University of York, University of Tennessee (US) and University of Nevada (US).


Selected Publications

On a singular initial-value problem for the Navier-Stokes equations
L.E. Fraenkel, M.D. Preston
2015 Mathematika 10.1112/S0025579314000333

A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains
M.D. Preston, et al.
2014 Nature Communications 10.1038/ncomms5052

PlasmoView: A web-based resourse to visualise global Plasmodium falciparum genomic variation
M.D. Preston, et al.
2013 J. Infectious Diseases 10.1093/infdis/jit812

GGV/PlasmoView
An AJAX based web tool for genetic polymorphism and geographical data visualisation written using PHP, GD, HTML, CSS, JavaScript and Perl. A live instance with over 600 samples/600k SNPs is hosted on the PathogenSeq website using the latest malaria genotyping data.
Preston et al, 2013 J. Infectious Diseases

Varb
Varb is a variant display and analysis tool for VCF files. The basic inputs are a reference genome (fasta format), variants (VCF) and annotation (GFF format) files. In real-time, the software filters variants and updates calculated population genetic matrics (Tajima's D, Weir's Fst). The latest version is available for download Google Code repository. See SVAMP for an alternative version.
Preston et al, 2013 Bioinformatics

Dwarf
An extensible, scriptable genomic analysis tool. The source code is available for download dwarf-1.0.tar.gz.
Preston et al, 2013 Annals of Human Genetics

TBDR
A web tool, although able to be run from the command line, that enables the rapid assessment of short read sequence data for mutations associated with drug resistance in Mycobacterium tuberculosis. Written by me to utilise Francesc's analysis for the community. Code available on the pathogenseq website and from this website rapiddr.zip.
Coll et al, 2015 Genome Medicine

SVAMP
An iteration of Varb led by Raeece Naeem and Lailatul Hidayah at KAUST to increase its functionality including phylogeny and PCoA analyses.
Naeem et al, 2014 Bioinformatics

PolyTB
Related to PlamsoView, Francesc Coll and I produced an website to visualise and query TB variation, through matrix, phylogenic and geographic views.
Coll et al, 2014 Tuberculosis; External Link

EstMoi
A bioinformatic interpretation of PCR methods for estimating multiplicity of infection using whole genome deep sequence data.
Assefa et al, 2013 Bioinformatics; External Link

SpolPred
SpolPred performs in silico spoligotyping, a strain-type identification method for TB, from raw sequence data.
Coll et al, 2012 Bioinformatics; External Link

Analysis of Porcine Rotavirus after Serial Passage through Modified MA104 Cell Lines
N. Meade, R. Chandler-Bostock, J. Mitchell, M.D. Preston, N. Rose, R. Emes, K. Mellits
2017 Submitted/Heliyon

Pathways-wide genetic risks in Chlamydial infections overlap between tissue tropisms: A genome-wide association scan
C.h. Roberts, S. Ouberg, M.D. Preston, H.J.C. de Vries, M.J. Holland, S.A. Morre
2017 Submitted/biorxiv 10.1101/205286

Comparative genome analysis and global phylogeny of the toxin variant Clostridium difficile PCR ribotype 017 reveals the evolution of two independent sublineages
M.D. Cairns, M.D. Preston, C.L. Hall, D.N. Gerding, P.M. Hawkey, H. Kato, H. Kim, E.J. Kuijper, T.D. Lawley, H. Pituch, S. Reid, B. Kullin, T.V. Riley, K. Solomon, P.J. Tsai, J.S. Weese, R.A. Stabler, B.W. Wren
2017 J. Clinical Microbiology 10.1128/JCM.01296-16

The nature of the conserved basic amino acid sequences found among 437 heparin binding proteins determined by network analysis
T.R. Rudd, M.D. Preston, E.A. Yates
2017 Molecular BioSystems 10.1039/C6MB00857G

From FASTQ to Function: In Silico Methods for Processing Next-Generation Sequencing Data
M.D. Preston, R.A. Stabler
2016 Clostridium difficile: Methods and Protocols 10.1007/978-1-4939-6361-4_3

Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing
E.T. Mee, M.D. Preston, P.D. Minor, S. Schepelmann, CSS Participants
2016 Vaccine 10.1016/j.vaccine.2015.12.020

Conjunctival fibrosis and the innate barriers to Chlamydia trachomatis intracellular infection: a genome wide association study
C.h. Roberts, C. S. Franklin, P. Makalo, H. Joof, I. Sarr, O.S. Mahdi, A. Sillah, M. Bah, F. Payne, A.E. Jeffreys, W. Bottomley, A. Natividad, S. Molina-Gonzalez, S.E. Burr, M.D. Preston, D. Kwiatkowski, K.A. Rockett, T.G. Clark, M.J. Burton, D.C.W. Mabey, R. Bailey, I.S. Barros, . J. Holland
2015 Nature Scientific Reports 10.1038/srep17447

Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi
S.A. Assefa, C. Lim, M.D. Preston, C.W. Duffy, M.B. Nair, S.A. Adroub, K.A. Kadir, J.M. Goldberg, D.E. Neafsey, P. Divis, T.G. Clark, M.T. Duraisingh, D.J. Conway, A. Pain, B. Singh
2015 Proceedings of the National Academy of Sciences 10.1073/pnas.1509534112

Impact of individual movement and changing resource availability on male-female encounter rates in an herbivorous insect
M.D. Preston, M.L. Forister, J.W. Pitchford, P.A. Armsworth
2015 Ecological Complexity 10.1016/j.ecocom.2015.07.004

Genomic epidemiology of a protracted hospital outbreak caused by a toxin A negative, Clostridium difficile sublineage PCR Ribotype 017 strain in London, England.
M.D. Cairns, M.D. Preston, T.D. Lawley, T.G. Clark, R.A. Stabler, B.W. Wren
2015 J. Clinical Microbiology 10.1128/JCM.00648-15

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences
F. Coll, R. McNerney, M.D. Preston, J.A. Guerra-Assuncaol, A. Warry, G. Hill-Cawthrone, K. Mallard, M. Nair, A. Miranda, A. Alves, J. Perdigao, M. Voveoros, I. Portugal, Z. Hasan, R. Hasan, J.R. Glynn, N. Martin, A. Pain, T.G. Clark
2015 Genome Medicine 10.1186/s13073-015-0164-0

Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites
H. Samad, F. Coll, M.D. Preston, H. Ocholla, R.M. Fairhurst, T.G. Clark
2015 PLoS Genetic 10.1371/journal.pgen.1005131

On a singular initial-value problem for the Navier-Stokes equations
L.E. Fraenkel, M.D. Preston
2015 Mathematika 10.1112/S0025579314000333

Whole-genome scans provide evidence of adaptive evolution in Malawian Plasmodium falciparum isolates
H. Ocholla, M.D. Preston, M. Mipando, A.T. Jensen, S. Campino, B. MacInnis, D. Alcock, A. Terlouw, I. Zongo, J-B. Oudraogo, A. Djimda, S.A. Assefa, O. Doumbo, S. Borrmann, A. Nzila, K. Marsh, R.M. Fairhurst, F. Nosten, T.J. Anderson, D.P. Kwiatkowski, A. Craig, T.G. Clark, J. Montgomery
2014 J. Infectious Diseases 10.1093/infdis/jiu349

A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains
M.D. Preston, S. Campino, S.A. Assefa, D. Echeverry, H. Ocholla, A. Amambua-Ngwa, L.B. Stewart, D.J. Conway, S. Borrmann, P. Michon, I. Zongo, J-B. Ouedraogo, A. Djimda, O. Doumbo, F. Nosten, A. Pain, T. Bousema, C.J. Drakeley, R.M. Fairhurst, C.J. Sutherland, C. Roper T.G. Clark
2014 Nature Communications 10.1038/ncomms5052

SVAMP: Sequence variation analysis, maps and phylogeny
R. Naeem, L. Hidayah, M.D. Preston, T.G. Clark, A. Pain
2014 Bioinformatics 10.1093/bioinformatics/btu176

PolyTB: A genomic variation map for Mycobacterium tuberculosis
F. Coll, M.D. Preston, J.A. Guerra-Assuncao, G. Hill-Cawthorn, D. Harris, J. Perdigao, M. Viveiros, I. Portugal, F. Drobniewski, S. Gagneux, J.R. Glynn, A. Pain, J. Parkhill, R. McNerney, N. Martin, T.G. Clark
2014 Tuberculosis 10.1016/j.tube.2014.02.005

PlasmoView: A web-based resourse to visualise global Plasmodium falciparum genomic variation
M.D. Preston, S.A. Assefa, H. Ocholla, C.J Sutherland, S. Borrmann, A. Nzila, P. Michon, TT Hien, T Bousema, C.J. Drakeley, I. Zongo, J.B. Ouedraogo, A.A. Djimde, O.K. Doumbo, F. Nosten, R.M. Fairhurst, D.J. Conway, C. Roper, T.G. Clark
2013 J. Infectious Diseases 10.1093/infdis/jit812

Using family-based designs for detecting rare variant disease associations
M.D. Preston, F. Dudbridge
2013 Annals of Human Genetics 10.1111/ahg.12051

EstMoi: Estimating multiplicity of infection using parasite deep sequencing data
S.A. Assefa, M.D. Preston, S. Campino, H. Ocholla, C.J. Sutherland, T.G. Clark
2013 Bioinformatics 10.1093/bioinformatics/btu005

Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing
T.G. Clark, K. Mallard, F. Coll, M.D. Preston, S.A. Assefa, D. Harris, S. Ogwang, F. Mumbowa, B. Kirenga, D.M. O'Sullivan, A. Okwera, K.D. Eisenach, M. Joloba, S.D. Bentley, J.J. Ellner, J. Parkhill, E.C. Jones-Lopez, R. McNerney
2013 Plos One 10.1371/journal.pone.0083012

Dystromirs as serum biomarkers for monitoring the disease severity in Duchenne Muscular Dystrophy
I.T. Zaharieva, M. Calissano, M. Scoto, M.D. Preston, S. Cirak, L. Feng, J. Collins, R. Kole, M. Guglieri, V. Straub, K. Bushby, A. Ferlini, J.E. Morgan, F. Muntoni
2013 Plos One 10.1371/journal.pone.0080263

SpolPred: Rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences
F. Coll, K. Mallard, M.D. Preston, S. Bentley, J. Parkhill, R. McNerney, N. Martin, T.G. Clark
2012 Bioinformatics 10.1093/bioinformatics/bts544

VarB: A variation browsing tool for polymorphisms derived from next-generation sequence data
M.D. Preston, H.M. Manske et al.
2012 Bioinformatics 10.1093/bioinformatics/bts557

A Nyström method for a boundary value problem arising in unsteady water wave problems
M.D. Preston, S.N. Chandler-Wilde, P.G. Chamberlain
2011 IMA: J. Numerical Analysis 10.1093/imanum/drq009

Evolutionary optimality in stochastic search problems
M.D. Preston, J.W. Pitchford, A.J. Wood
2010 J. Royal Society Interface 10.1098/rsif.2010.0090

An integral equation method for a boundary value problem arising in unsteady water wave problems
M.D. Preston, S.N. Chandler-Wilde, P.G. Chamberlain
2008 J. Integral Equations and Applications 10.1216/JIE-2008-20-1-121

Conferences

Poster: Butterfly mating, Won 3rd Prize in Poster Competition.
M.D. Preston, J.W. Pitchford, P.R. Armsworth, M. Forrister
2012 UCL Computational Life and Medical Sciences Network Annual Symposium, London

Paper: An integral equation method for a boundary value problem arising in unsteady water wave problems
M.D. Preston, S.N. Chandler-Wilde, P.G. Chamberlain
2005 Proc. of the UKBIM5, Liverpool

BSc Mathematics, MSc Multimedia Technology, PhD Mathematics

Experience

Head of Bioinformatics
National Institute for Biological Standards and Control
2015 -
Research Fellow
London School of Hygiene and Tropical Medicine
2011 - 2015
Research Assistant
University of Bath, Department of Mathematics
2009 - 2011
Research Associate
University of York, Department of Biology
2008 - 2011
Teaching Fellow
University of York, Department of Mathematics
2007 - 2008

IT Consultant
Self-employed
2000 -
IT Manager
SoftBrands Hospitality, USA
2002 - 2003
IT Programer
Madge Networks
1998 - 1999

PhD Mathematics
University of Reading, Department of Mathematics
2004 - 2007
MSc Multimedia Technology
University of Bath, Department of Computer Science
1999 - 2000
BSc Mathematics
University of Bath, Department of Mathematics
1994 - 1998

Funding

Leverhulme Emeritus Fellowship
University of Bath (awarded to Prof Edward Fraenkel FRS)
2009
Pump-prime Funding
University of York
2008 - 2009
Teaching Award
University of York
2007
EPSRC Doctoral Training
University of Reading
2004 - 2007
Panasonic Trust Fellowship
University of Bath
1999 - 2000