selected papers

Published: 2021 Feb 5

Pöntinen, A.K., Top, J., Arredondo-Alonso, S. et al. Nat Commun 12, 1523 (2021). https://doi.org/10.1038/s41467-021-21749-5

Published: 2020 Aug 28

Hernando-Amado S, Coque TM, Baquero F, Martínez JL.

Front Microbiol. 2020 Aug 28;11:1914. doi: 10.3389/fmicb.2020.01914. eCollection 2020.

PMID: 32983000 Free PMC article. Review.

Published: 2018 Jan 15

Lanza VF, Baquero F, Martínez JL, Ramos-Ruíz R, González-Zorn B, Andremont A, Sánchez-Valenzuela A, Ehrlich SD, Kennedy S, Ruppé E, van Schaik W, Willems RJ, de la Cruz F, Coque TM.

Microbiome. 2018 Jan 15;6(1):11. doi: 10.1186/s40168-017-0387-y.

PMID: 29335005 Free PMC article.

Published: 2018

Angers-Loustau A, Petrillo M, Bengtsson-Palme J, Berendonk T, Blais B, Chan KG, Coque TM, Hammer P, Heß S, Kagkli DM, Krumbiegel C, Lanza VF, Madec JY, Naas T, O'Grady J, Paracchini V, Rossen JWA, Ruppé E, Vamathevan J, Venturi V, Van den Eede G.

F1000Res. 2018 Apr 13;7:ISCB Comm J-459. doi: 10.12688/f1000research.14509.2. eCollection 2018.

PMID: 30026930 Free PMC article. Review.

Published: 2019 Jun 21

León-Sampedro R, Fernández-de-Bobadilla MD, San Millán Á, Baquero F, Coque TM*. J Antimicrob Chemother. doi: 10.1093/jac/dkz239. PMID: 31225883.

Published: 2017 Dec 7

Freitas AR, Tedim AP, Francia MV, Jensen LB, Novais C, Peixe L, Sánchez-Valenzuela A, Sundsfjord A, Hegstad K, Werner G, Sadowy E, Hammerum AM, Garcia-Migura L, Willems RJ, Baquero F, Coque TM.

J Antimicrob Chemother. 2016 Dec;71(12):3351-3366. doi: 10.1093/jac/dkw312. Epub 2016 Aug 15.

PMID: 27530756

Published: 201

Lanza VF, Tedim AP, Martínez JL, Baquero F, Coque TM.

Microbiol Spectr. 2015 Apr;3(2):PLAS-0039-2014. doi: 10.1128/microbiolspec.PLAS-0039-2014.

PMID: 26104702 Review.

Published: 2015 Mar 30

Curiao T, Marchi E, Viti C, Oggioni MR, Baquero F, Martinez JL, Coque TM.

Antimicrob Agents Chemother. 2015;59(6):3413-23. doi: 10.1128/AAC.00187-15. Epub 2015 Mar 30.

PMID: 25824225 Free PMC article.

Published: 2014 Dec 15

Martínez JL, Coque TM, Baquero F.

Nat Rev Microbiol. 2015 Feb;13(2):116-23. doi: 10.1038/nrmicro3399. Epub 2014 Dec 15.

PMID: 25534811 Review.

Published: 2016 Sep 23

Lanza VF, Baquero F, de la Cruz F, Coque TM.

Bioinformatics. 2017 Jan 15;33(2):283-285. doi: 10.1093/bioinformatics/btw601. Epub 2016 Sep 23.

PMID: 27663497

Published: 2021

Miguel D. Fernández-de-Bobadilla, Alba Talavera-Rodríguez, Lucía Chacón, Fernando Baquero, Teresa M. Coque, Val F. Lanza

bioRxiv 2021.01.30.428878; doi: https://doi.org/10.1101/2021.01.30.428878

Published: 2021

Petrillo M, Fabbri M, Kagkli DM et al. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing [version 1; peer review: awaiting peer review]. F1000Research 2021, 10:80 (https://doi.org/10.12688/f1000research.39214.1)

Published 2019 Sep 4

Hernando-Amado S, Coque TM, Baquero F, Martínez JL.

Nat Microbiol. 2019 Sep;4(9):1432-1442. doi: 10.1038/s41564-019-0503-9. Epub 2019 Aug 22.

PMID: 31439928 Review.

Published: 2019 Aug 21

León-Sampedro R, Del Campo R, Rodriguez-Baños M, Lanza VF, Pozuelo MJ, Francés-Cuesta C, Tedim AP, Freitas AR, Novais C, Peixe L, Willems RJL, Corander J, González Candelas F, Baquero F, Coque TM.

Environ Microbiol. 2019 Aug;21(8):3046-3062. doi: 10.1111/1462-2920.14702. Epub 2019 Jul 4.

PMID: 31162871

Published: 2019 Jan 4

Ruppé E, Ghozlane A, Tap J, Pons N, Alvarez AS, Maziers N, Cuesta T, Hernando-Amado S, Clares I, Martínez JL, Coque TM, Baquero F, Lanza VF, Máiz L, Goulenok T, de Lastours V, Amor N, Fantin B, Wieder I, Andremont A, van Schaik W, Rogers M, Zhang X, Willems RJL, de Brevern AG, Batto JM, Blottière HM, Léonard P, Léjard V, Letur A, Levenez F, Weiszer K, Haimet F, Doré J, Kennedy SP, Ehrlich SD.

Nat Microbiol. 2019 Jan;4(1):112-123. doi: 10.1038/s41564-018-0292-6. Epub 2018 Nov 26.

PMID: 30478291

Published: 2017 Jan

Tedim AP, Ruíz-Garbajosa P, Rodríguez MC, Rodríguez-Baños M, Lanza VF, Derdoy L, Cárdenas Zurita G, Loza E, Cantón R, Baquero F, Coque TM.

J Antimicrob Chemother. 2017 Jan;72(1):48-55. doi: 10.1093/jac/dkw366. Epub 2016 Sep 21.

PMID: 27655856

Published: 2016 Jan 13

Curiao T, Marchi E, Grandgirard D, León-Sampedro R, Viti C, Leib SL, Baquero F, Oggioni MR, Martinez JL, Coque TM.

BMC Genomics. 2016 Jul 13;17:491. doi: 10.1186/s12864-016-2778-z.

PMID: 27411385 Free PMC article.

Published: 2015 

Baquero F, Lanza VF, Cantón R, Coque TM.

Evol Appl. 2015 Mar;8(3):223-39. doi: 10.1111/eva.12235. Epub 2014 Dec 11.

PMID: 25861381 Free PMC article.

Published: 2014 Dec 29

Tedim AP, Ruiz-Garbajosa P, Corander J, Rodríguez CM, Cantón R, Willems RJ, Baquero F, Coque TM.

Appl Environ Microbiol. 2015 Mar;81(5):1820-31. doi: 10.1128/AEM.03661-14. Epub 2014 Dec 29.

PMID: 25548052 Free PMC article.

Published: 2011 Jul 19

Baquero F, Coque TM.

FEMS Microbiol Rev. 2011 Sep;35(5):705-6. doi: 10.1111/j.1574-6976.2011.00293.x. Epub 2011 Jul 19.

PMID: 21714793 No abstract available.

Published: 2017

Martínez JL, Coque TM, Lanza VF, de la Cruz F, Baquero F.

Ann N Y Acad Sci. 2017 Jan;1388(1):26-41. doi: 10.1111/nyas.13282. Epub 2016 Nov 10.

PMID: 27861983 Review.

Conference and Workshop Reports

  • 2021. Angers-Loustau A, Petrillo M, Bengtsson-Palme J, Berendonk T, Blais B, Chan KG, Coque TM, Hammer P, Heß S, Kagkli DM, Krumbiegel C, Lanza VF, Madec J-Y, Naas T, O’Grady J, Paracchini V, Rossen JWA, Ruppé E, Vamathevan J, Venturi V, Van den Eede G: The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies. F1000Research, 7, 459 (2018). doi: 10.12688/f1000research.14509.2 

  • 2017. European Comission. Joint Research Centre (JRC) Conference and Workshop Reports. The Role and Implementation of Next-Generation Sequencing Technologies in the Coordinated Action Plan against Antimicrobial Resistance. March 21th - 22nd, 2017 Villa Borghi, Italy. JRC Conference and Workshop Report, EUR 28619 (2017). doi: 10.2760/745099

TECHNOLOGICAL TRANSFERENCE

  • ResCap. Transference to Roche-Nimblegene. Application of SeqCapE