Judith Fonville

Associate Fellow and Biomedical Informatician, PAMM laboratories (The Netherlands)
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Dr Judy Fonville has a research background in multivariate data analysis and modelling of (bio)medical data. Upon completion of her PhD at Imperial College London in the department of Surgery and Cancer, she performed research at the Centre for Pathogen Evolution, University of Cambridge. As a Junior Research Fellow at Homerton College she studied the antibody response to influenza vaccination and infection, and modelled the risk posed by avian H5N1 influenza viruses. She is currently working as a data scientist at PAMM laboratories in The Netherlands, analysing data generated in medical microbiology and pathology diagnostics. These data are used in, for example, infection prevention and antibiotic therapy policy. She is also involved in the application of novel molecular techniques (such as next generation sequencing and bioinformatics), and developments in digital pathology. 


Development and application of chemometric methods for modelling metabolic spectral profiles, Imperial college London


Genetic diversity and host adaptation of avian H5N1 influenza viruses during human infection. Welkers MRA, Pawestri HA, Fonville JM, Sampurno OD, Pater M, Holwerda M, Han AX, Russell CA, Jeeninga RE, Setiawaty V, de Jong MD, Eggink D. Emerg Microbes Infect. 2019;8(1):262-271. doi: 10.1080/22221751.2019.1575700.

A Single Negative Result for van Quantitative PCR on Enrichment Broth Can Replace Five Rectal Swab Cultures in Screening for Vancomycin-Resistant Enterococci. Fonville JM, van Herk CMC, Das PHAC, van de Bovenkamp JHB, van Dommelen L. J Clin Microbiol. 2017 Jul;55(7):2261-2267. doi: 10.1128/JCM.00258-17. Epub 2017 May 10.

The global antigenic diversity of swine influenza A viruses. Lewis NS, Russell CA, Langat P, Anderson TK, Berger K, Bielejec F, Burke DF, Dudas G, Fonville JM, Fouchier RA, Kellam P, Koel BF, Lemey P, Nguyen T, Nuansrichy B, Peiris JM, Saito T, Simon G, Skepner E, Takemae N; ESNIP3 consortium, Webby RJ, Van Reeth K, Brookes SM, Larsen L, Watson SJ, Brown IH, Vincent AL. Elife. 2016 Apr 15;5:e12217. doi: 10.7554/eLife.12217.

Influenza B vaccine lineage selection--an optimized trivalent vaccine. Mosterín Höpping A, Fonville JM, Russell CA, James S, Smith DJ. Vaccine. 2016 Mar 18;34(13):1617-1622. doi: 10.1016/j.vaccine.2016.01.042. Epub 2016 Feb 16.

The confounded effects of age and exposure history in response to influenza vaccination. Mosterín Höpping A, McElhaney J, Fonville JM, Powers DC, Beyer WEP, Smith DJ. Vaccine. 2016 Jan 20;34(4):540-546. doi: 10.1016/j.vaccine.2015.11.058. Epub 2015 Dec 5.

Influenza Virus Reassortment Is Enhanced by Semi-infectious Particles but Can Be Suppressed by Defective Interfering Particles. Fonville JM, Marshall N, Tao H, Steel J, Lowen AC. PLoS Pathog. 2015 Oct 6;11(10):e1005204. doi: 10.1371/journal.ppat.1005204. eCollection 2015 Oct.

Dengue viruses cluster antigenically but not as discrete serotypes. Katzelnick LC, Fonville JM, Gromowski GD, Bustos Arriaga J, Green A, James SL, Lau L, Montoya M, Wang C, VanBlargan LA, Russell CA, Thu HM, Pierson TC, Buchy P, Aaskov JG, Muñoz-Jordán JL, Vasilakis N, Gibbons RV, Tesh RB, Osterhaus AD, Fouchier RA, Durbin A, Simmons CP, Holmes EC, Harris E, Whitehead SS, Smith DJ. Science. 2015 Sep 18;349(6254):1338-43. doi: 10.1126/science.aac5017.

Mapping Enterovirus A71 Antigenic Determinants from Viral Evolution. Huang SW, Tai CH, Fonville JM, Lin CH, Wang SM, Liu CC, Su IJ, Smith DJ, Wang JR. J Virol. 2015 Nov;89(22):11500-6. doi: 10.1128/JVI.02035-15. Epub 2015 Sep 2.

Antigenic Maps of Influenza A(H3N2) Produced With Human Antisera Obtained After Primary Infection. Fonville JM, Fraaij PL, de Mutsert G, Wilks SH, van Beek R, Fouchier RA, Rimmelzwaan GF. J Infect Dis. 2016 Jan 1;213(1):31-8. doi: 10.1093/infdis/jiv367. Epub 2015 Jul 3.

Expected Effect of Deleterious Mutations on Within-Host Adaptation of Pathogens. Fonville JM. J Virol. 2015 Sep;89(18):9242-51. doi: 10.1128/JVI.00832-15. Epub 2015 Jun 24.

Antibody landscapes after influenza virus infection or vaccination. Fonville JM, Wilks SH, James SL, Fox A, Ventresca M, Aban M, Xue L, Jones TC, Le NMH, Pham QT, Tran ND, Wong Y, Mosterin A, Katzelnick LC, Labonte D, Le TT, van der Net G, Skepner E, Russell CA, Kaplan TD, Rimmelzwaan GF, Masurel N, de Jong JC, Palache A, Beyer WEP, Le QM, Nguyen TH, Wertheim HFL, Hurt AC, Osterhaus ADME, Barr IG, Fouchier RAM, Horby PW, Smith DJ. Science. 2014 Nov 21;346(6212):996-1000. doi: 10.1126/science.1256427.

Quantifying the fitness advantage of polymerase substitutions in Influenza A/H7N9 viruses during adaptation to humans. Fonville JM, Burke DF, Lewis NS, Katzelnick LC, Russell CA. PLoS One. 2013 Sep 27;8(9):e76047. doi: 10.1371/journal.pone.0076047. eCollection 2013.

Hyperspectral visualization of mass spectrometry imaging data. Fonville JM, Carter CL, Pizarro L, Steven RT, Palmer AD, Griffiths RL, Lalor PF, Lindon JC, Nicholson JK, Holmes E, Bunch J. Anal Chem. 2013 Feb 5;85(3):1415-23. doi: 10.1021/ac302330a. Epub 2013 Jan 15.

Direct detection of peptides and small proteins in fingermarks and determination of sex by MALDI mass spectrometry profiling. Ferguson LS, Wulfert F, Wolstenholme R, Fonville JM, Clench MR, Carolan VA, Francese S. Analyst. 2012 Oct 21;137(20):4686-92. doi: 10.1039/c2an36074h.

Chemical shifts in nucleic acids studied by density functional theory calculations and comparison with experiment. Fonville JM, Swart M, Vokáčová Z, Sychrovský V, Šponer JE, Šponer J, Hilbers CW, Bickelhaupt FM, Wijmenga SS. Chemistry. 2012 Sep 24;18(39):12372-87. doi: 10.1002/chem.201103593. Epub 2012 Aug 16.

The potential for respiratory droplet-transmissible A/H5N1 influenza virus to evolve in a mammalian host. Russell CA, Fonville JM, Brown AE, Burke DF, Smith DL, James SL, Herfst S, van Boheemen S, Linster M, Schrauwen EJ, Katzelnick L, Mosterín A, Kuiken T, Maher E, Neumann G, Osterhaus AD, Kawaoka Y, Fouchier RA, Smith DJ. Science. 2012 Jun 22;336(6088):1541-7. doi: 10.1126/science.1222526.

Robust data processing and normalization strategy for MALDI mass spectrometric imaging. Fonville JM, Carter C, Cloarec O, Nicholson JK, Lindon JC, Bunch J, Holmes E. Anal Chem. 2012 Feb 7;84(3):1310-9. doi: 10.1021/ac201767g. Epub 2012 Jan 10.

Statistical total correlation spectroscopy scaling for enhancement of metabolic information recovery in biological NMR spectra. Maher AD, Fonville JM, Coen M, Lindon JC, Rae CD, Nicholson JK. Anal Chem. 2012 Jan 17;84(2):1083-91. doi: 10.1021/ac202720f. Epub 2011 Dec 27.

Non-linear modeling of 1H NMR metabonomic data using kernel-based orthogonal projections to latent structures optimized by simulated annealing. Fonville JM, Bylesjö M, Coen M, Nicholson JK, Holmes E, Lindon JC, Rantalainen M. Anal Chim Acta. 2011 Oct 31;705(1-2):72-80. doi: 10.1016/j.aca.2011.04.016. Epub 2011 Apr 20.

Systems parasitology: effects of Fasciola hepatica on the neurochemical profile in the rat brain. Saric J, Li JV, Utzinger J, Wang Y, Keiser J, Dirnhofer S, Beckonert O, Sharabiani MT, Fonville JM, Nicholson JK, Holmes E. Mol Syst Biol. 2010 Jul;6:396. doi: 10.1038/msb.2010.49.

Evaluation of full-resolution J-resolved 1H NMR projections of biofluids for metabonomics information retrieval and biomarker identification. Fonville JM, Maher AD, Coen M, Holmes E, Lindon JC, Nicholson JK. Anal Chem. 2010 Mar 1;82(5):1811-21. doi: 10.1021/ac902443k.