Daniel Mende

Research output

Research output per year 2020 2022 2023 2024

• 14 Article

Research output per year

Research output per year

Search results

• 2024

  Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre

  Beckett, S. J., Demory, D., Coenen, A. R., Casey, J. R., Dugenne, M., Follett, C. L., Connell, P., Carlson, M. C. G., Hu, S. K., Wilson, S. T., Muratore, D., Rodriguez-Gonzalez, R. A., Peng, S., Becker, K. W., Mende, D. R., Armbrust, E. V., Caron, D. A., Lindell, D., White, A. E., Ribalet, F., & 1 othersWeitz, J. S., 1 Dec 2024, In: Nature communications. 15, 1, 2105.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

• SPIRE: a Searchable, Planetary-scale mIcrobiome REsource

  Schmidt, T. S. B., Fullam, A., Ferretti, P., Orakov, A., Maistrenko, O. M., Ruscheweyh, H-J., Letunic, I., Duan, Y., van Rossum, T., Sunagawa, S., Mende, D. R., Finn, R. D., Kuhn, M., Pedro Coelho, L. & Bork, P., 5 Jan 2024, In: Nucleic Acids Research. 52, D1, p. D777-D783

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access
  2 Citations (Scopus)
• 2023

  eggNOG 6.0: enabling comparative genomics across 12 535 organisms

  Hernández-Plaza, A., Szklarczyk, D., Botas, J., Cantalapiedra, C. P., Giner-Lamia, J., Mende, D. R., Kirsch, R., Rattei, T., Letunic, I., Jensen, L. J., Bork, P., von Mering, C. & Huerta-Cepas, J., 6 Jan 2023, In: Nucleic Acids Research. 51, 1 D, p. D389-D394

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access
  47 Citations (Scopus)

• Impact of antibiotics on gut microbiome composition and resistome in the first years of life in low- to middle-income countries: A systematic review

  Luchen, C. C., Chibuye, M., Spijker, R., Simuyandi, M., Chisenga, C., Bosomprah, S., Chilengi, R., Schultsz, C., Mende, D. R. & Harris, V. C., 1 Jun 2023, In: PLoS medicine. 20, 6, p. e1004235 e1004235.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access
  4 Citations (Scopus)

• proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

  Fullam, A., Letunic, I., Schmidt, T. S. B., Ducarmon, Q. R., Karcher, N., Khedkar, S., Kuhn, M., Larralde, M., Maistrenko, O. M., Malfertheiner, L., Milanese, A., Rodrigues, J. F. M., Sanchis-López, C., Schudoma, C., Szklarczyk, D., Sunagawa, S., Zeller, G., Huerta-Cepas, J., von Mering, C., Bork, P., & 1 othersMende, D. R., 6 Jan 2023, In: Nucleic Acids Research. 51, D1, p. D760-D766

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access
  10 Citations (Scopus)
• 2022

  Benchmarking the topological accuracy of bacterial phylogenomic workflows using in silico evolution

  van der Putten, B. C. L., Huijsmans, N. A. H., Mende, D. R. & Schultsz, C., 1 Mar 2022, In: Microbial genomics. 8, 3, 000799.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access

• Complex marine microbial communities partition metabolism of scarce resources over the diel cycle

  Muratore, D., Boysen, A. K., Harke, M. J., Becker, K. W., Casey, J. R., Coesel, S. N., Mende, D. R., Wilson, S. T., Aylward, F. O., Eppley, J. M., Vislova, A., Peng, S., Rodriguez-Gonzalez, R. A., Beckett, S. J., Virginia Armbrust, E., DeLong, E. F., Karl, D. M., White, A. E., Zehr, J. P., van Mooy, B. A. S., & 3 othersDyhrman, S. T., Ingalls, A. E. & Weitz, J. S., 1 Feb 2022, In: Nature Ecology and Evolution. 6, 2, p. 218-229 12 p.

  Research output: Contribution to journal › Article › Academic › peer-review
  16 Citations (Scopus)

• Critical Assessment of Metagenome Interpretation: the second round of challenges

  Meyer, F., Fritz, A., Deng, Z-L., Koslicki, D., Lesker, T. R., Gurevich, A., Robertson, G., Alser, M., Antipov, D., Beghini, F., Bertrand, D., Brito, J. J., Brown, C. T., Buchmann, J., Buluç, A., Chen, B., Chikhi, R., Clausen, P. T. L. C., Cristian, A., Dabrowski, P. W., & 83 othersDarling, A. E., Egan, R., Eskin, E., Georganas, E., Goltsman, E., Gray, M. A., Hansen, L. H., Hofmeyr, S., Huang, P., Irber, L., Jia, H., Jørgensen, T. S., Kieser, S. D., Klemetsen, T., Kola, A., Kolmogorov, M., Korobeynikov, A., Kwan, J., LaPierre, N., Lemaitre, C., Li, C., Limasset, A., Malcher-Miranda, F., Mangul, S., Marcelino, V. R., Marchet, C., Marijon, P., Meleshko, D., Mende, D. R., Milanese, A., Nagarajan, N., Nissen, J., Nurk, S., Oliker, L., Paoli, L., Peterlongo, P., Piro, V. C., Porter, J. S., Rasmussen, S., Rees, E. R., Reinert, K., Renard, B., Robertsen, E. M., Rosen, G. L., Ruscheweyh, H-J., Sarwal, V., Segata, N., Seiler, E., Shi, L., Sun, F., Sunagawa, S., Sørensen, S. R. J., Thomas, A., Tong, C., Trajkovski, M., Tremblay, J., Uritskiy, G., Vicedomini, R., Wang, Z., Wang, Z., Wang, Z., Warren, A., Willassen, N. P., Yelick, K., You, R., Zeller, G., Zhao, Z., Zhu, S., Zhu, J., Garrido-Oter, R., Gastmeier, P., Hacquard, S., Häußler, S., Khaledi, A., Maechler, F., Mesny, F., Radutoiu, S., Schulze-Lefert, P., Smit, N., Strowig, T., Bremges, A., Sczyrba, A. & McHardy, A. C., Apr 2022, In: Nature methods. 19, 4, p. 429-440 12 p.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access
  98 Citations (Scopus)

• Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study

  Janes, V. A., Matamoros, S. B., Munk, P., Clausen, P. T. L. C., Koekkoek, S. M., Koster, L. A. M., Jakobs, M. E., de Wever, B., Visser, C. E., Aarestrup, F. M., Lund, O., de Jong, M. D., Bossuyt, P. M. M., Mende, D. R. & Schultsz, C., 1 Aug 2022, In: The Lancet. Microbe. 3, 8, p. e588-e597

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access
  7 Citations (Scopus)

• Towards the biogeography of prokaryotic genes

  Coelho, L. P., Alves, R., del Río, Á. R., Myers, P. N., Cantalapiedra, C. P., Giner-Lamia, J., Schmidt, T. S., Mende, D. R., Orakov, A., Letunic, I., Hildebrand, F., van Rossum, T., Forslund, S. K., Khedkar, S., Maistrenko, O. M., Pan, S., Jia, L., Ferretti, P., Sunagawa, S., Zhao, X-M., & 3 othersNielsen, H. B., Huerta-Cepas, J. & Bork, P., 13 Jan 2022, In: NATURE. 601, 7892, p. 252-256

  Research output: Contribution to journal › Article › Academic › peer-review
  56 Citations (Scopus)
• 2021

  Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean

  Becker, K. W., Harke, M. J., Mende, D. R., Muratore, D., Weitz, J. S., DeLong, E. F., Dyhrman, S. T. & van Mooy, B. A. S., Feb 2021, In: ISME journal. 15, 2, p. 520-533 14 p.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access
  25 Citations (Scopus)

• GUNC: detection of chimerism and contamination in prokaryotic genomes

  Orakov, A., Fullam, A., Coelho, L. P., Khedkar, S., Szklarczyk, D., Mende, D. R., Schmidt, T. S. B. & Bork, P., 1 Dec 2021, In: Genome Biology. 22, 1, 178.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access
  72 Citations (Scopus)
• 2020

  Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

  Maistrenko, O. M., Mende, D. R., Luetge, M., Hildebrand, F., Schmidt, T. S. B., Li, S. S., Rodrigues, J. F. M., von Mering, C., Pedro Coelho, L., Huerta-Cepas, J., Sunagawa, S. & Bork, P., 1 May 2020, In: ISME journal. 14, 5, p. 1247-1259 13 p.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access
  53 Citations (Scopus)

• Thermus thermophilus DNA can be used as internal control for process monitoring of clinical metagenomic next-generation sequencing of urine samples

  Janes, V. A., van der Laan, J. S., Matamoros, S. B., Mende, D. R., de Jong, M. D. & Schultsz, C., 1 Sept 2020, In: Journal of Microbiological Methods. 176, 106005.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access
  6 Citations (Scopus)