Bioinformatics (BIF)

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  • 2025

    A Non-Metaproteomics Researchers’ View on Metaproteomics in Microbiome Research

    Aho, V. T. E., Clerbaux, L. A., Kupczok, A., Tillett, B., Garg, N. & Henderickx, J. G. E., 27 Apr 2025, (E-pub ahead of print) In: Proteomics.

    Research output: Contribution to journal › Comment/Letter to the editor › Academic › peer-review

    Open Access

  • Discovery of metabolites prevails amid in-source fragmentation

    El Abiead, Y., Rutz, A., Zuffa, S., Amer, B., Xing, S., Brungs, C., Schmid, R., Correia, M. S. P., Caraballo-Rodriguez, A. M., Zarrinpar, A., Mannochio-Russo, H., Witting, M., Mohanty, I., Pluskal, T., Bittremieux, W., Knight, R., Patterson, A. D., van der Hooft, J. J. J., Böcker, S. & Dunn, W. B. & 6 others, Linington, R. G., Wishart, D. S., Wolfender, J. L., Fiehn, O., Zamboni, N. & Dorrestein, P. C., Mar 2025, In: Nature Metabolism. 7, 3, p. 435-437

    Research output: Contribution to journal › Comment/Letter to the editor › Academic

  • New solutions for antibiotic discovery: Prioritizing microbial biosynthetic space using ecology and machine learning

    Medema, M. H. & van Wezel, G. P., Feb 2025, In: PloS Biology. 23, 3 p., e3003058.

    Research output: Contribution to journal › Comment/Letter to the editor › Academic

    Open Access
  • 2024

    Reply to: On the statistical foundation of a recent single molecule FRET benchmark

    Götz, M., Barth, A., Bohr, S. S. R., Börner, R., Chen, J., Cordes, T., Erie, D. A., Gebhardt, C., Hadzic, M. C. A. S., Hamilton, G. L., Hatzakis, N. S., Hugel, T., Kisley, L., Lamb, D. C., de Lannoy, C., Mahn, C., Dunukara, D., de Ridder, D., Sanabria, H. & Schimpf, J. & 9 others, Seidel, C. A. M., Sigel, R. K. O., Sletfjerding, M. B., Thomsen, J., Vollmar, L., Wanninger, S., Weninger, K. R., Xu, P. & Schmid, S., 30 Apr 2024, In: Nature Communications. 15, 1, 3626.

    Research output: Contribution to journal › Comment/Letter to the editor › Academic

    Open Access
    2 Citations (Scopus)
  • 2022

    Author Correction: Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes

    Gavriilidou, A., Kautsar, S. A., Zaburannyi, N., Krug, D., Müller, R., Medema, M. H. & Ziemert, N., Aug 2022, In: Nature Microbiology. 7, 8, p. 1324-1324 1 p.

    Research output: Contribution to journal › Comment/Letter to the editor › Academic

    3 Citations (Scopus)

  • Freedom of expression: A synthetic route to metabolites

    Augustijn, H. E. & Medema, M. H., 28 Apr 2022, In: Cell. 185, 9, p. 1449-1451

    Research output: Contribution to journal › Comment/Letter to the editor › Academic

    1 Citation (Scopus)
  • 2021

    Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization

    Gauthier, J., Boulain, H., van Vugt, J. J. F. A., Baudry, L., Persyn, E., Aury, J. M., Noel, B., Bretaudeau, A., Legeai, F., Warris, S., Chebbi, M. A., Dubreuil, G., Duvic, B., Kremer, N., Gayral, P., Musset, K., Josse, T., Bigot, D., Bressac, C. & Moreau, S. & 31 others, Periquet, G., Harry, M., Montagné, N., Boulogne, I., Sabeti-Azad, M., Maïbèche, M., Chertemps, T., Hilliou, F., Siaussat, D., Amselem, J., Luyten, I., Capdevielle-Dulac, C., Labadie, K., Merlin, B. L., Barbe, V., de Boer, J. G., Marbouty, M., Cônsoli, F. L., Dupas, S., Hua-Van, A., Le Goff, G., Bézier, A., Jacquin-Joly, E., Whitfield, J. B., Vet, L. E. M., Smid, H. M., Kaiser, L., Koszul, R., Huguet, E., Herniou, E. A. & Drezen, J. M., 30 Jul 2021, In: Communications Biology. 4, 1, 940.

    Research output: Contribution to journal › Comment/Letter to the editor › Academic

    Open Access
    3 Citations (Scopus)
  • 2020

    Erratum: Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms (Communications biology (2020) 3 1 (303))

    Kallscheuer, N., Jeske, O., Sandargo, B., Boedeker, C., Wiegand, S., Bartling, P., Jogler, M., Rohde, M., Petersen, J., Medema, M. H., Surup, F. & Jogler, C., 21 Sept 2020, In: Communications Biology. 3, 531.

    Research output: Contribution to journal › Comment/Letter to the editor › Academic

    Open Access
    2 Citations (Scopus)

  • Erratum: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms

    Kallscheuer, N., Jeske, O., Sandargo, B., Boedeker, C., Wiegand, S., Bartling, P., Jogler, M., Rohde, M., Petersen, J., Medema, M. H., Surup, F. & Jogler, C., 31 Aug 2020, In: Communications Biology. 3, 1, 1 p., 487.

    Research output: Contribution to journal › Comment/Letter to the editor › Academic

    Open Access

  • Mass spectrometry searches using MASST

    Wang, M., Jarmusch, A. K., Vargas, F., Aksenov, A. A., Gauglitz, J. M., Weldon, K., Petras, D., da Silva, R., Quinn, R., Melnik, A. V., van der Hooft, J. J. J., Caraballo-Rodríguez, A. M., Nothias, L. F., Aceves, C. M., Panitchpakdi, M., Brown, E., Di Ottavio, F., Sikora, N., Elijah, E. O. & Labarta-Bajo, L. & 16 others, Gentry, E. C., Shalapour, S., Kyle, K. E., Puckett, S. P., Watrous, J. D., Carpenter, C. S., Bouslimani, A., Ernst, M., Swafford, A. D., Zúñiga, E. I., Balunas, M. J., Klassen, J. L., Loomba, R., Knight, R., Bandeira, N. & Dorrestein, P. C., 1 Jan 2020, In: Nature Biotechnology. 38, p. 23-26

    Research output: Contribution to journal › Comment/Letter to the editor › Academic › peer-review

    Open Access
    172 Citations (Scopus)
  • 2019

    Artificial intelligence in the lab: ask not what your computer can do for you

    de Ridder, D., Jan 2019, In: Microbial Biotechnology. 12, 1, p. 38-40

    Research output: Contribution to journal › Comment/Letter to the editor › Academic

    Open Access
    8 Citations (Scopus)

  • Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

    Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J. & Cope, E. K. & 92 others, Da Silva, R., Diener, C., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J. M., Gibbons, S. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G. A., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M. G. I., Lee, J., Ley, R., Liu, Y. X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B. D., McDonald, D., McIver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Navas-Molina, J. A., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R., Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaugh, P. J., Ul-Hasan, S., van der Hooft, J. J. J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H. D., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Zhu, Q., Knight, R. & Caporaso, J. G., 9 Aug 2019, In: Nature Biotechnology.

    Research output: Contribution to journal › Comment/Letter to the editor › Academic

    490 Citations (Scopus)

  • Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

    Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, T. C., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J. & Cope, E. K. & 92 others, da Silva, R., Diener, C., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J. M., Gibbons, S. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G. A., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M. G. I., Lee, J., Ley, R., Liu, Y. X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B. D., McDonald, D., McIver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Navas-Molina, J. A., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R., Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaugh, P. J., Ul-Hasan, S., van der Hooft, J. J. J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H. D., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Zhu, Q., Knight, R. & Caporaso, J. G., 1 Aug 2019, In: Nature Biotechnology. 37, 8, p. 852-857 6 p.

    Research output: Contribution to journal › Comment/Letter to the editor › Academic › peer-review

    14289 Citations (Scopus)