Publications

Publications of specific relevance to Applied Data Science
2020

Hijazi M, Smith R, Rajeeve V,
Bessant C and
Cutillas PR (2020).
Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring. Nature Research Nature Biotechnology 10.1038/s41587-019-0391-92018

Saha S, Matthews DA and
Bessant C (2018).
High throughput discovery of protein variants using proteomics informed by transcriptomics. Nucleic Acids Research vol. 46, (10) 4893-4902.
10.1093/nar/gky2952017

Pearce OMT, Delaine-Smith R, Maniati E, Nichols S, Wang J, Böhm S, Rajeeve V, Ullah D, Chakravarty P, Jones RR, Montfort A, Dowe T, Gribben J, Jones JL, Kocher HM, Serody JS, Vincent BG, Connelly J, Brenton JD,
Chelala C,
Cutillas PR, Lockley M,
Bessant C, Knight M and Balkwill FR (2017).
Deconstruction of a metastatic tumor microenvironment reveals a common matrix response in human cancers. Cancer Discov 10.1158/2159-8290.CD-17-0284
SAHA S, Chatzimichali E, Matthews D and
Bessant C (2017).
PITDB: a database of translated genomic elements. Oxford University Press Nucleic Acids Research 10.1093/nar/gkx906
Maringer K, Yousuf A, Heesom KJ, Fan J, Lee D, Fernandez-Sesma A,
Bessant C, Matthews DA and Davidson AD (2017).
Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti. Bmc Genomics vol. 18, (1) 101-101.
10.1186/s12864-016-3432-52016

Cauchi M, Weber CM, Bolt BJ, Spratt PB,
Bessant C, Turner DC, Willis CM, Britton LE, Turner C and Morgan G (2016).
Evaluation of gas chromatography mass spectrometry and pattern recognition for the identification of bladder cancer from urine headspace. Analytical Methods vol. 8, (20) 4037-4046.
10.1039/c6ay00400h
Mohareb F, Papadopoulou O, Panagou E, Nychas GJ and
Bessant C (2016).
Ensemble-based support vector machine classifiers as an efficient tool for quality assessment of beef fillets from electronic nose data. Analytical Methods vol. 8, (18) 3711-3721.
10.1039/c6ay00147e
Walton C, Montoya MPB, Fowler DP, Turner C, Jia W, Whitehead RN, Griffiths L, Waring RH, Ramsden DB, Cole JA, Cauchi M,
Bessant C, Naylor SJ and Hunter JO (2016).
Enteral feeding reduces metabolic activity of the intestinal microbiome in Crohn’s disease: an observational study. Nature Publishing Group: Open Access Hybrid Model Option B European Journal of Clinical Nutrition vol. 70, 1052-1056.
10.1038/ejcn.2016.74
Chatzimichali EA and
Bessant C (2016).
Novel application of heuristic optimisation enables the creation and thorough evaluation of robust support vector machine ensembles for machine learning applications. Metabolomics vol. 12, (1) 1-10.
10.1007/s11306-015-0894-4
(2016).
Proteome Informatics., Editors: Bessant C.
Royal Society of Chemistry 2015

Fan J, Saha S, Barker G, Heesom KJ, Ghali F, Jones AR, Matthews DA and
Bessant C (2015).
Galaxy integrated omics: Web-based standards-compliant workflows for proteomics informed by transcriptomics. Molecular and Cellular Proteomics vol. 14, (11) 3087-3093.
10.1074/mcp.O115.048777
Qi D, Zhang H, Fan J, Perkins S, Pisconti A, Simpson DM,
Bessant C, Hubbard S and Jones AR (2015).
The mzqLibrary - An open source Java library supporting the HUPO-PSI quantitative proteomics standard. Proteomics 10.1002/pmic.201400535
Cauchi M, Fowler DP, Walton C, Turner C, Waring RH, Ramsden DB, Hunter JO, Teale P, Cole JA and
Bessant C (2015).
Comparison of GC-MS, HPLC-MS and SIFT-MS in conjunction with multivariate classification for the diagnosis of Crohn's disease in urine. Analytical Methods vol. 7, (19) 8379-8385.
10.1039/c5ay01322d2014

Gonzalez-Galarza FF, Qi D, Fan J,
Bessant C and Jones AR (2014).
A tutorial for software development in quantitative proteomics using PSI standard formats. Biochim Biophys Acta vol. 1844, (1 Pt A) 88-97.
10.1016/j.bbapap.2013.04.004
Bessant C, Oakley D and Shadforth I (2014).
Building Bioinformatics Solutions. Oxford University Press 
Cauchi M, Fowler DP, Walton C, Turner C, Jia W, Whitehead RN, Griffiths L, Dawson C, Bai H, Waring RH and others (2014).
Application of gas chromatography mass spectrometry (GC–MS) in conjunction with multivariate classification for the diagnosis of gastrointestinal diseases. Springer Us Metabolomics vol. 10, (6) 1113-1120.
10.1007/s11306-014-0650-1
Sattlecker M, Stone N and
Bessant C (2014).
Current trends in machine-learning methods applied to spectroscopic cancer diagnosis. Elsevier/Science Direct Trac Trends in Analytical Chemistry vol. 59, 17-25.
10.1016/j.trac.2014.02.016
Bessant C, Oakley D and Shadforth I (2014).
Building Bioinformatics Solutions 2nd Edition. Oxford University Press 
Gonzalez-Galarza FF, Qi D, Fan J,
Bessant C and Jones AR (2014).
A tutorial for software development in quantitative proteomics using PSI standard formats. Biochimica Et Biophysica Acta-Proteins and Proteomics vol. 1844, (1) 88-97.
10.1016/j.bbapap.2013.04.0042013

Walton C, Fowler DP, Turner C, Jia W, Whitehead RN, Griffiths L, Dawson C, Waring RH, Ramsden DB, Cole JA, Cauchi M,
Bessant C and Hunter JO (2013).
Analysis of volatile organic compounds of bacterial origin in chronic gastrointestinal diseases. Inflamm Bowel Dis vol. 19, (10) 2069-2078.
10.1097/MIB.0b013e31829a91f6
Walzer M, Qi D, Mayer G, Uszkoreit J, Eisenacher M, Sachsenberg T, Gonzalez-Galarza FF, Fan J,
Bessant C, Deutsch EW, Reisinger F, Vizcaíno JA, Medina-Aunon JA, Albar JP, Kohlbacher O and Jones AR (2013).
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Mol Cell Proteomics vol. 12, (8) 2332-2340.
10.1074/mcp.O113.0285062012

Evans VC, Barker G, Heesom KJ, Fan J,
Bessant C and Matthews DA (2012).
De novo derivation of proteomes from transcriptomes for transcript and protein identification. Nat Methods vol. 9, (12) 1207-1211.
10.1038/nmeth.2227
Gonzalez-Galarza FF, Lawless C, Hubbard SJ, Fan J,
Bessant C, Hermjakob H and Jones AR (2012).
A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis. Omics vol. 16, (9) 431-442.
10.1089/omi.2012.0022
Fan J, Mohareb F, Bond NJ, Lilley KS and
Bessant C (2012).
MRMaid 2.0: mining PRIDE for evidence-based SRM transitions. Omics vol. 16, (9) 483-488.
10.1089/omi.2011.0143
Jia W, Whitehead RN, Griffiths L, Dawson C, Bai H, Waring RH, Ramsden DB, Hunter JO, Cauchi M,
Bessant C, Fowler DP, Walton C, Turner C and Cole JA (2012).
Diversity and distribution of sulphate-reducing bacteria in human faeces from healthy subjects and patients with inflammatory bowel disease. Fems Immunol Med Microbiol vol. 65, (1) 55-68.
10.1111/j.1574-695X.2012.00935.x
Fan J, Mohareb F, Jones AME and
Bessant C (2012).
MRMaid: The SRM Assay Design Tool for Arabidopsis and Other Species. Front Plant Sci vol. 3,
10.3389/fpls.2012.001642011

Thiollet S,
Bessant C and Morgan SL (2011).
Application of multiple response optimization design to quantum dot-encoded microsphere bioconjugates hybridization assay. Anal Biochem vol. 414, (1) 23-30.
10.1016/j.ab.2011.02.024
Johnson PE, Baumgartner S, Aldick T, Bessant C#31514#, Giosafatto V, Heick J, Mamone G, O'Connor G, Poms R, Popping B, Reuter A, Ulberth F, Watson A, Monaci L and Mills ENC (2011).
Current perspectives and recommendations for the development of mass spectrometry methods for the determination of allergens in foods. J Aoac Int vol. 94, (4) 1026-1033.

Panagou EZ, Mohareb FR, Argyri AA,
Bessant CM and Nychas G-JE (2011).
A comparison of artificial neural networks and partial least squares modelling for the rapid detection of the microbial spoilage of beef fillets based on Fourier transform infrared spectral fingerprints. Food Microbiol vol. 28, (4) 782-790.
10.1016/j.fm.2010.05.014
Weber CM, Cauchi M, Patel M,
Bessant C, Turner C, Britton LE and Willis CM (2011).
Evaluation of a gas sensor array and pattern recognition for the identification of bladder cancer from urine headspace. Analyst vol. 136, (2) 359-364.
10.1039/c0an00382d
Cauchi M, Bianco L and
Bessant C (2011).
The quantification of pollutants in drinking water by use of artificial neural networks. Nat. Comput. vol. 10, 77-90.
10.1007/s11047-010-9185-1
Sattlecker M, Baker R, Stone N and
Bessant C (2011).
Support vector machine ensembles for breast cancer type prediction from mid-FTIR micro-calcification spectra. Elsevier Chemometrics and Intelligent Laboratory Systems vol. 107, 363-370.
10.1016/j.chemolab.2011.05.007
Sattlecker M, Stone N, Smith J and
Bessant C (2011).
Assessment of robustness and transferability of classification models built for cancer diagnostics using Raman spectroscopy. Wiley Online Library Journal of Raman Spectroscopy vol. 42, 897-903.
10.1002/jrs.2798
Bessant C (2011).
Data Mining for Genomics and Proteomics: Analysis of Gene and Protein Expression Data Darius M. Dziuda John Wiley and Sons, 2010, p. 327 ISBN: 978-0-470-16373-3. Wiley-Vch Verlag Proteomics vol. 11, 3768-3768.
2010

Kolk A, Hoelscher M, Maboko L, Jung J, Kuijper S, Cauchi M,
Bessant C, van Beers S, Dutta R, Gibson T and Reither K (2010).
Electronic-nose technology using sputum samples in diagnosis of patients with tuberculosis. J Clin Microbiol vol. 48, (11) 4235-4238.
10.1128/JCM.00569-10
Sattlecker M,
Bessant C, Smith J and Stone N (2010).
Investigation of support vector machines and Raman spectroscopy for lymph node diagnostics. Analyst vol. 135, (5) 895-901.
10.1039/b920229c
Cham Mead JA, Bianco L and
Bessant C (2010).
Free computational resources for designing selected reaction monitoring transitions. Proteomics vol. 10, (6) 1106-1126.
10.1002/pmic.200900396
Cham JA, Bianco L, Barton C and
Bessant C (2010).
MRMaid-DB: a repository of published SRM transitions. J Proteome Res vol. 9, (1) 620-625.
10.1021/pr900713u
Tetsuya H (2010).
Discerning data analysis methods to clarify agonistic/antagonistic actions on the ion flux assay of ligand-gated ionotropic glutamate receptor on engineered post-synapse model cells. Journal of Biosensors & Bioelectronics 
Tanoue C, Asakawa H, Cauchi M,
Bessant C, Ikeno S and Haruyama T (2010).
Tissular model/sensor seamless system for qualified analysis and its characterization. Elsevier Biochemical Engineering Journal vol. 52, 110-115.
10.1016/j.bej.2010.07.015
Kolk A, Hoelscher M, Maboko L, Jung J, Kuijper S, Cauchi M,
Bessant C, van Beers S, Dutta R, Gibson T and others (2010).
Electronic-nose technology in diagnosis of TB patients using sputum samples. Am Soc Microbiol Journal of Clinical Microbiology 2009

Spooner AD,
Bessant C, Turner C, Knobloch H and Chambers M (2009).
Evaluation of a combination of SIFT-MS and multivariate data analysis for the diagnosis of Mycobacterium bovis in wild badgers. Analyst vol. 134, (9) 1922-1927.
10.1039/b905627k
Blanco L, Mead JA and
Bessant C (2009).
Comparison of novel decoy database designs for optimizing protein identification searches using ABRF sPRG2006 standard MS/MS data sets. J Proteome Res vol. 8, (4) 1782-1791.
10.1021/pr800792z
Babrah J, McCarthy K, Lush RJ, Rye AD,
Bessant C and Stone N (2009).
Fourier transform infrared spectroscopic studies of T-cell lymphoma, B-cell lymphoid and myeloid leukaemia cell lines. Analyst vol. 134, (4) 763-768.
10.1039/b807967f
Mead JA, Bianco L, Ottone V, Barton C, Kay RG, Lilley KS, Bond NJ and
Bessant C (2009).
MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions. Mol Cell Proteomics vol. 8, (4) 696-705.
10.1074/mcp.M800192-MCP200
Moczko E, Meglinski IV,
Bessant C and Piletsky SA (2009).
Dyes assay for measuring physicochemical parameters. Anal Chem vol. 81, (6) 2311-2316.
10.1021/ac802482h
Mead JA, Bianco L and
Bessant C (2009).
Recent developments in public proteomic MS repositories and pipelines. Proteomics vol. 9, (4) 861-881.
10.1002/pmic.200800553
Thanaraj T, Terry LA and
Bessant C (2009).
Chemometric profiling of pre-climacteric Sri Lankan mango fruit (< i> Mangifera indica L.). Elsevier Food Chemistry vol. 112, 786-794.
10.1016/j.foodchem.2008.06.040
Tottey S, Robinson N, Waldron K, Firbank S and
Bessant C (2009).
Protein folding location determines binding of manganese versus copper. Pergamon Comparative Biochemistry and Physiology Part a: Molecular & Integrative Physiology vol. 153, S159-S159.
10.1016/j.cbpa.2009.04.3202008

Tottey S, Waldron KJ, Firbank SJ, Reale B,
Bessant C, Sato K, Cheek TR, Gray J, Banfield MJ, Dennison C and Robinson NJ (2008).
Protein-folding location can regulate manganese-binding versus copper- or zinc-binding. Nature vol. 455, (7216) 1138-1142.
10.1038/nature07340
Stott W, Ryan A, Jacobs IJ, Menon U,
Bessant C and Jones C (2008).
OSPACS: Ultrasound image management system. Source Code Biol Med vol. 3,
10.1186/1751-0473-3-11
Cauchi M,
Bessant C and Setford S (2008).
Simultaneous Quantitative Determination of Cadmium, Lead, and Copper on Carbon-Ink Screen-Printed Electrodes by Differential Pulse Anodic Stripping Voltammetry and Partial Least Squares Regression. Wiley Online Library Electroanalysis vol. 20, 2571-2577.
10.1002/elan.200804363
Mead J, Bianco L and
Bessant C (2008).
Using Bioinformatics to Increase Speed and Reduce Uncertainty in Protein Biomarker Discovery. Cranfield Multi-Strand Conference: Creating Wealth Through Research and Innovation vol. 6, 118-118.
2007

Mead JA, Shadforth IP and
Bessant C (2007).
Public proteomic MS repositories and pipelines: available tools and biological applications. Proteomics vol. 7, (16) 2769-2786.
10.1002/pmic.200700152
Goodacre R, Broadhurst D, Smilde AK, Kristal BS, Baker JD, Beger R,
Bessant C, Connor S, Capuani G, Craig A and others (2007).
Proposed minimum reporting standards for data analysis in metabolomics. Springer Us Metabolomics vol. 3, 231-241.
10.1007/s11306-007-0081-3
Bessant C (2007).
Microarray Analysis Software and its Applications. John Wiley & Sons, Ltd Handbook of Biosensors and Biochips 
Babrah J, McCarthy KP, Lush R, Rye AD,
Bessant C and Stone N (2007).
FT-infrared spectroscopic studies of lymphoma, lymphoid, and myeloid leukemia cell lines [6628-28]. International Society For Optical Engineering; 1999 Proceedings-Spie The International Society For Optical Engineering vol. 6628, 6628-6628.

Kumuthini J,
Bessant C, Wilson P and Crowther D (2007).
Gene regulatory network of human adipocyte differentiation. Biomed Central Ltd Bmc Systems Biology vol. 1, P57-P57.
10.1186/1752-0509-1-s1-p57
Kumuthini J, Jouffe L and
Bessant C (2007).
Session 1-Microarray and Systems Biology I (Networks)-A Novel Graph Optimisation Algorithm for the Extraction of Gene Regulatory Networks from Temporal Microarray Data. Lecture Notes in Computer Science vol. 4414, 28-28.
2006

Shadforth I, Xu W, Crowther D and
Bessant C (2006).
GAPP: a fully automated software for the confident identification of human peptides from tandem mass spectra. J Proteome Res vol. 5, (10) 2849-2852.
10.1021/pr060205s
Ernst W, Trummer E, Mead J,
Bessant C, Strelec H, Katinger H and Hesse F (2006).
Evaluation of a genomics platform for cross-species transcriptome analysis of recombinant CHO cells. Biotechnol J vol. 1, (6) 639-650.
10.1002/biot.200600010
Fend R, Kolk AHJ,
Bessant C, Buijtels P, Klatser PR and Woodman AC (2006).
Prospects for clinical application of electronic-nose technology to early detection of Mycobacterium tuberculosis in culture and sputum. J Clin Microbiol vol. 44, (6) 2039-2045.
10.1128/JCM.01591-05
Dunkley TPJ, Hester S, Shadforth IP, Runions J, Weimar T, Hanton SL, Griffin JL,
Bessant C, Brandizzi F, Hawes C, Watson RB, Dupree P and Lilley KS (2006).
Mapping the Arabidopsis organelle proteome. Proc Natl Acad Sci U S A vol. 103, (17) 6518-6523.
10.1073/pnas.0506958103
Saini S,
Bessant C, Lee-davey J and Malecha MM (2006).
VOLTAMMETRIC DETECTION OF METABOLITES IN PHYSIOLOGICAL FLUIDS.
Sadowski PG, Dunkley TPJ, Shadforth IP, Dupree P,
Bessant C, Griffin JL and Lilley KS (2006).
Quantitative proteomic approach to study subcellular localization of membrane proteins. Nat Protoc vol. 1, (4) 1778-1789.
10.1038/nprot.2006.254
Lilley KS, Hawes C, Hanton SL, Dunkley TPJ, Runions J, Hester S, Weimar T, Shadforth IP,
Bessant C, Dupree P and others (2006).
Mapping the Arabidopsis organelle proteome. Editor No Identificado Proceedings of The National Academy of Sciences of The United States of America 6518-6523.
2005

Shadforth I, Crowther D and
Bessant C (2005).
Protein and peptide identification algorithms using MS for use in high-throughput, automated pipelines. Proteomics vol. 5, (16) 4082-4095.
10.1002/pmic.200402091
Shadforth I, Todd K, Crowther D and
Bessant C (2005).
Determination of partial amino acid composition from tandem mass spectra for use in peptide identification strategies. Proteomics vol. 5, (7) 1787-1796.
10.1002/pmic.200401058
SAINI S,
BESSANT C, LEE-DAVEY J, MALECHA M and others (2005).
VOLTAMMETRIC DETECTION OF METABOLITES IN PHYSIOLOGICAL FLUIDS.
Shadforth I, Dunkley T, Lilley K, Crowther D and
Bessant C (2005).
Confident protein identification using the average peptide score method coupled with search-specific, ab initio thresholds. Rapid Commun Mass Spectrom vol. 19, (22) 3363-3368.
10.1002/rcm.2203
Mead JA, Bianco L and
Bessant C (2005).
the focus of attention in financial reporting. Abacus 2004

Fend R,
Bessant C, Williams AJ and Woodman AC (2004).
Monitoring haemodialysis using electronic nose and chemometrics. Biosens Bioelectron vol. 19, (12) 1581-1590.
10.1016/j.bios.2003.12.010
Saini S,
Bessant C, Lee-Davey J and Malecha MM (2004).
Voltammetric detection of metabolites in physiological fluids. Google Patents 
Richards E,
Bessant C and Saini S (2004).
Simultaneous quantification of analytes in quaternary mixtures using dual pulse staircase voltammetry and genetically optimised neural networks. Analyst vol. 129, (4) 355-358.
10.1039/b400577p
Saini S,
Bessant C, Liedtke C and Leiferkus J (2004).
DIAGNOSIS BY SENSING VOLATILE COMPONENTS.2003

Malecha M,
Bessant C and Saini S (2003).
Identification of oil contaminants on polymer coated beverage cans using fluorescence spectroscopy. Appl Spectrosc vol. 57, (8) 1042-1048.
10.1366/000370203322259020
Richards E,
Bessant C and Saini S (2003).
A liquid handling system for the automated acquisition of data for training, validating and testing calibration models. Elsevier Sensors and Actuators B: Chemical vol. 88, 149-154.
10.1016/S0925-4005(02)00318-0
Bessant C and Richards E (2003).
Neural networks for the calibration of voltammetric data. Elsevier Nature-Inspired Methods in Chemometrics: Genetic Algorithms and Artificial Neural Networks: Genetic Algorithms and Artificial NE vol. 23, 257-257.
10.1016/S0922-3487(03)23009-42002

SAINI S,
BESSANT C, LIEDTKE C, LEIFERKUS J and others (2002).
DIAGNOSIS BY SENSING VOLATILE COMPONENTS.
Malecha M,
Bessant C and Saini S (2002).
Principal components analysis for the visualisation of multidimensional chemical data acquired by scanning Raman microspectroscopy. Analyst vol. 127, (9) 1261-1266.
10.1039/b203281c
Saini S,
Bessant C, Liedtke C and Leiferkus J (2002).
Diagnosis by sensing volatile components. Google Patents 
Richards E,
Bessant C and Saini S (2002).
Optimisation of a neural network model for calibration of voltammetric data. Elsevier Chemometrics and Intelligent Laboratory Systems vol. 61, 35-49.
10.1016/S0169-7439(01)00170-8
Malecha M,
Bessant C, Perry D and Saini S (2002).
Identification of oil contaminants on polymer coated beverage cans using Raman spectroscopy. Royal Society of Chemistry Analyst vol. 127, 297-303.
10.1039/b108801g2001

Saini S, Barr H and
Bessant C (2001).
Sniffing out disease using the artificial nose. Biologist (London) vol. 48, (5) 229-233.
Bessant C, Ritchie L, Saini S, Pahlavanpour B and Wilson G (2001).
Chemometric evaluation of synchronous scan fluorescence spectroscopy for the determination of regulatory conformance and usage history of insulation oils. Society For Applied Spectroscopy Applied Spectroscopy vol. 55, 840-846.
10.1366/00037020119528662000

Ritchie LJ, Ferguson CP,
Bessant C and Saini S (2000).
A ten channel fibre-optic device for distributed sensing of underground hydrocarbon leakage. J Environ Monit vol. 2, (6) 670-673.
10.1039/b008210o
SAINI S and
BESSANT C (2000).
ANALYSIS OF MIXTURES.
Bessant C and Saini S (2000).
A chemometric analysis of dual pulse staircase voltammograms obtained in mixtures of ethanol, fructose and glucose. Elsevier Journal of Electroanalytical Chemistry vol. 489, 76-83.
10.1016/S0022-0728(00)00229-11999
Bessant C and Saini S (1999).
Simultaneous determination of ethanol, fructose, and glucose at an unmodified platinum electrode using artificial neural networks. Acs Publications Analytical Chemistry vol. 71, 2806-2813.
10.1021/ac9901790
Brereton R and others (1999).
Integrated processing of triply coupled diode array liquid chromatography electrospray mass spectrometric signals by chemometric methods. Royal Society of Chemistry Analyst vol. 124, 1733-1744.
10.1039/a907089c1997
Bessant C and Saini S (1997).
An object oriented approach to electroanalytical technique implementation. Wiley Online Library Electroanalysis vol. 9, 926-931.
10.1002/elan.1140091212