Francesc Coll

Digital CSIC: ver perfil
ORCID: 0000-0002-7882-2325
WOS Research ID: V-1980-2019
Google Scholar: ver perfil

Currículum Vitae

Formación Académica

• 2010: Licenciatura en Biotecnología, Universidad Politécnica de Valencia, España
• 2011: Máster en Bioinformática Aplicada, Universidad de Cranfield, Reino Unido
• 2014: Doctorado en Genómica Microbiana, London School of Hygiene & Tropical Medicine, Reino Unido

 Formación Profesional

• 2011 – 2014 Investigador predoctoral (The Bloomsbury Colleges studentship), London School of Hygiene & Tropical Medicine, Reino Unido
• 2014 – 2016 Research Associate (posdoc), Universidad de Cambridge, Reino Unido
• 2016 – 2021 Sir Henry Wellcome Postdoctoral fellow (posdoc), London School of Hygiene & Tropical Medicine, Reino Unido
• 2021 – 2023 Assistant Professor (ISSF fellow), London School of Hygiene & Tropical Medicine, Reino Unido
• 2023 – 2024 Senior Staff Scientist, Wellcome Sanger Institute, Reino Unido
• 2023 – Honorary Assistant Professor, London School of Hygiene & Tropical Medicine, Reino Unido
• 2024 – Visiting Worker, Wellcome Sanger Institute, Reino Unido
• 2024 – Científico Titular, IBV-CSIC, Valencia, España

 Méritos

• 2021 – Institutional Strategic Support Fund (ISSF) Fellowship
• 2016 – Sir Henry Wellcome Postdoctoral Fellowship
• 2014 – Garnham Award (LSHTM) al mejor estudiante predoctoral

Publicaciones

Coll F, Gouliouris T, Blane B, Yeats CA, Raven KE, Ludden C, Khokhar FA, Wilson HJ, Roberts LW, Harrison EM, Horner CS, Le TH, Nguyen TH, Nguyen VT, Brown NM, Holmes MA, Parkhill J, Estee Török M, Peacock SJ.
Antibiot c resistance determination using Enterococcus faecium whole-genome sequences: a diagnostic accuracy study using genotypic and phenotypic data.
Lancet Microbe. 2024 Feb;5(2):e151-e163. doi: 10.1016/S2666-5247(23)00297-5. Epub 2024 Jan 11. PMID: 38219758.

Coll F.
Key variables affecting genetic distance calculations in genomic epidemiology.
Lancet Microbe. 2021 Oct;2(10):e486-e487. doi: 10.1016/S2666-5247(21)00183-X. Epub 2021 Aug 6. PMID: 35544172.

Walker TM, Miotto P, Köser CU, Fowler PW, Knaggs J, Iqbal Z, Hunt M Chindelevitch L, Farhat M, Cirillo DM, Comas I, Posey J, Omar SV, Peto TE, Suresh A, Uplekar S, Laurent S, Colman RE, Nathanson CM, Zignol M, Walker AS; CRyPTIC Consortium; Seq&Treat Consortium; Crook DW, Ismail N, Rodwell TC.
The 2021 WHO catalogue of <i>Mycobacterium tuberculosis</i> complex mutations associated with drug resistance: A genotypic analysis.
Lancet Microbe.2022 Apr;3(4):e265-e273. doi: 10.1016/S2666-5247(21)00301-3. PMID: 35373160; PMCID: PMC7612554.

Coll F, Gouliouris T, Bruchmann S, Phelan J, Raven KE, Clark TG, Parkhill J, Peacock SJ.
PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies.
Commun Biol. 2022 Mar 25;5(1):266.doi: 10.1038/s42003-022-03194-2.PMID: 35338232; PMCID: PMC8956664.

Ludden C, Coll F, Gouliouris T, Restif O, Blane B, Blackwell GA, Kumar N, Naydenova P, Crawley C, Brown NM, Parkhill J, Peacock SJ.
Defining nosocomial transmission of <i>Escherichia coli</i> and antimicrobial resistance genes: a genomic surveillance study.
Lancet Microbe.2021 Sep;2(9):e472-e480.doi: 10.1016/S2666-5247(21)00117-8.PMID: 34485958; PMCID: PMC8410606.

Stirrup O, Hughes J, Parker M, Partridge DG, Shepherd JG, Blackstone J, Coll F, Keeley A, Lindsey BB, Marek A, Peters C, Singer JB; COVID-19 Genomics UK (COG-UK) consortium; Tamuri A, de Silva TI, Thomson EC, Breuer J.
Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data.
Elife.2021 Jun 29;10:e65828.doi: 10.7554/eLife.65828. PMID: 34184637; PMCID: PMC8285103.

Coll F, Raven KE, Knight GM, Blane B, Harrison EM, Leek D, Enoch DA, Brown NM, Parkhill J, Peacock SJ.
Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant <i>Staphylococcus aureus</i>: a genomic epidemiology analysis.
Lancet Microbe.2020 Dec;1(8):e328-e335.doi: 10.1016/S2666-5247(20)30149-X.PMID: 33313577; PMCID: PMC7721685.

Gouliouris T, Coll F, Ludden C, Blane B, Raven KE, Naydenova P, Crawley C, Török ME, Enoch DA, Brown NM, Harrison EM, Parkhill J, Peacock S .
Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance.
Nat Microbiol.2021 Jan;6(1):103-111.doi: 10.1038/s41564-020-00806-7.Epub 2020 Oct 26.PMID: 33106672; PMCID: PMC7610418.

Leclerc QJ, Naylor NR, Aiken AM, Coll F, Knight GM.
Feasibility of informing syndrome-level empiric antibiotic recommendations using publicly available antibiotic resistance datasets.
Wellcome Open Res.2020 Jun 24;4:140.doi: 10.12688/wellcomeopenres.15477.2.PMID: 32656364; PMCID: PMC7327722.

Kime L, Randall CP, Banda FI, Coll F, Wright J, Richardson J, Empel J, Parkhill J, O’Neill AJ.
Transient Silencing of Antibiotic Resistance by Mutation Represents a Significant Potential Source of Unanticipated Therapeutic Failure.
mBio.2019 Oct 29;10(5):e01755-19.doi: 10.1128/mBio.01755-19.PMID: 31662453; PMCID: PMC6819657.

Harrison EM, Ba X, Coll F, Blane B, Restif O, Carvell H, Köser CU, Jamroz D, Reuter S, Lovering A, Gleadall N, Bellis KL, Uhlemann AC, Lowy FD, Massey RC, Grilo IR, Sobral R, Larsen J, Rhod Larsen A, Vingsbo Lundberg C, Parkhill J, Paterson GK, Holden MTG, Peacock SJ, Holmes MA.
Genomic identification of cryptic susceptibility to penicillins and β-lactamas inhibitors in methicillin- resistant Staphylococcus aureus.
Nat Microbiol. 2019 Oct;4(10):1680-1691. doi: 10.1038/s41564-019-0471-0. Epub 2019 Jun 24. PMID: 31235959; PMCID: PMC7611363.

Wailan AM, Coll F, Heinz E, Tonkin-Hill G, Corander J, Feasey NA, Thomson NR.
rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree.
Microb Genom. 2019 Apr;5(4):e000264. doi: 10.1099/mgen.0.000264. Epub 2019 Mar 28. PMID: 30920366; PMCID: PMC6521585.

Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K, Ali S, Abdallah AM, Alghamdi S, Alsomali M, Ahmed AO, Portelli S, Oppong Y, Alves A, Bessa TB, Campino S, Caws M, Chatterjee A, Crampin AC, Dheda K, Furnham N, Glynn JR, Grandjean L, Minh Ha D, Hasan R, Hasan Z, Hibberd ML, Joloba M, Jones-Lópe EC, Matsumoto T, Miranda A, Moore DJ, Mocillo N, Panaiotov S, Parkhill J, Penha C, Perdigão J, Portugal I, Rchiad Z, Robledo J, Sheen P, Shesha NT Sirgel FA, Sola C, Oliveira Sousa E, Streicher EM, Helden PV, Viveiros M, Warren RM, McNerney R, Pain A, Clark TG.
Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis.
Nat Genet. 2018 Feb;50(2):307-316. doi: 10.1038/s41588-017-0029-0. Epub 2018 Jan 22. Erratum in: Nat Genet. 2018 Apr 19;: PMID: 29358649.

Coll F, Harrison EM, Toleman MS, Reuter S, Raven KE, Blane B, Palmer B, Kappeler ARM, Brown NM, Török ME, Parkhill J, Peacock SJ.
Longitudin l genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community.
Sci Transl Med. 2017 Oct 25;9(413):eaak9745. doi: 10.1126/scitranslmed.aak9745. Epub 2017 Oct 25. PMID: 29070701; PMCID: PMC5683347.

Jamrozy D, Coll F, Mather AE, Harris SR, Harrison EM, MacGowan A, Karas A, Elston T, Estée Török M, Parkhill J, Peacock SJ.
Evolution of mobile gene ic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events.
BMC Genomics. 2017 Sep 4;18(1):684. doi: 10.1186/s12864-017-4065-z. PMID: 28870171; PMCID: PMC5584012.

Harrison EM, Coll F, Toleman MS, Blane B, Brown NM, Török ME, Parkhill, Peacock SJ.
Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England.
Sci Rep. 2017 Aug 7;7(1):7406. doi: 10.1038/s41598-017-07662-2. PMID: 28785112; PMCID: PMC5547075.

Toleman MS, Reuter S, Coll F, Harrison EM, Peacock SJ.
Local Persistence of Novel MRSA Lineage after Hospital Ward Outbreak, Cambridge, UK, 2011-2013.
Emerg Infect Dis. 2016 Sep;22(9):1658-9. doi: 10.3201/eid2209.151100. Epub 2016 Sep 15. PMID: 27268128; PMCID: PMC4994339.

Toleman MS, Reuter S, Coll F, Harrison EM, Blane B, Brown NM, Török M , Parkhill J, Peacock SJ.
Systematic Surveillance Detects Multiple Silent Introductions and Household Transmission of Methicillin-Resistant Staphylococcus aureus USA300 in the East of England.
J Infect Dis. 2016 Aug 1;214(3):447-53. doi: 10.1093/infdis/jiw166. Epub 2016 Apr 27. PMID: 27122590; PMCID: PMC4936647.

Phelan J, Coll F, McNerney R, Ascher DB, Pires DE, Furnham N, Coeck N, Hill-Cawthorne GA, Nair MB, Mallard K, Ramsay A, Campino S, Hibberd ML, Pain A, Rigouts L, Clark TG.
Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance.
BMC Med. 2016 Mar 23;14:31. doi: 10.1186/s12916-016-0575-9. PMID: 27005572; PMCID: PMC4804620.

Coll F, McNerney R, Preston MD, Guerra-Assunção JA, Warry A, Hill-Cawthor e G, Mallard K, Nair M, Miranda A, Alves A, Perdigão J, Viveiros M, Portuga I, Hasan Z, Hasan R, Glynn JR, Martin N, Pain A, Clark TG.
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences.
Genome Med. 2015 May 27;7(1):51. doi: 10.1186/s13073-015-0164-0. PMID: 26019726; PMCID: PMC4446134.

Benavente ED, Coll F, Furnham N, McNerney R, Glynn JR, Campino S, Pain A, Mohareb FR, Clark TG.
PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis.
BMC Bioinformatics. 2015 May 13;16(1):155. doi: 10.1186/s12859-015-0603-3. PMID: 25968323; PMCID: PMC4429496.

Samad H, Coll F, Preston MD, Ocholla H, Fairhurst RM, Clark TG.
Imputation- based population genetics analysis of Plasmodium falciparum malaria parasites.
PLoS Genet. 2015 Apr 30;11(4):e1005131. doi: 10.1371/journal.pgen.1005131. PLoS Genet. 2016 Aug;12(8):e1006300. PMID: 25928499; PMCID: PMC4415759.

Bergval I, Coll F, Schuitema A, de Ronde H, Mallard K, Pain A, McNerney R, Clark TG, Anthony RM.
A proportion of mutations fixed in the genomes of in vitro selected isogenic drug-resistant Mycobacterium tuberculosis mutants can be detected as minority variants in the parent culture.
FEMS Microbiol Lett. 2015 Jan;362(2):1-7. doi: 10.1093/femsle/fnu037. Epub 2014 Dec 4. PMID: 25670707.

Coll F, McNerney R, Guerra-Assunção JA, Glynn JR, Perdigão J, Viveiros M, Portugal I, Pain A, Martin N, Clark TG.
A robust SNP barcode for typing Mycobacterium tuberculosis complex strains.
Nat Commun. 2014 Sep 1;5:4812. doi: 10.1038/ncomms5812. PMID: 25176035; PMCID: PMC4166679.

Coll F, Preston M, Guerra-Assunção JA, Hill-Cawthorn G, Harris D, Perdig £o J, Viveiros M, Portugal I, Drobniewski F, Gagneux S, Glynn JR, Pain A, Parkhill J, McNerney R, Martin N, Clark TG.
PolyTB: a genomic variation map for Mycobacterium tuberculosis.
Tuberculosis (Edinb). 2014 May;94(3):346-54. doi: 10.1016/j.tube.2014.02.005. Epub 2014 Feb 15. PMID: 24637013; PMCID: PMC4066953.

Coll F, Mallard K, Preston MD, Bentley S, Parkhill J, McNerney R, Martin N, Clark TG.
SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences.
Bioinformatics. 2012 Nov 15;28(22):2991-3. doi: 10.1093/bioinformatics/bts544. Epub 2012 Sep 26. PMID: 23014632; PMCID: PMC3496340.