The Microbiome of Denmark

Albertsen, Mads (PI)
Nielsen, Per Halkjær (PI)
Jensen, Thomas Bygh Nymann (Project Participant)
Sørensen, Emil Aarre (Project Participant)
Sereika, Mantas (Project Participant)
Dottorini, Giulia (Project Participant)
Petriglieri, Francesca (Project Participant)
Jørgensen, Vibeke Rudkjøbing (Project Participant)
Kirkegaard, Rasmus Hansen (Project Participant)
Yang, Yu (Project Participant)
Karst, Søren Michael (Project Participant)
Giguere, Andrew Tyler (Project Participant)
Knutsson, Simon (Project Participant)
Singleton, Caitlin Margaret (Project Participant)
Dueholm, Morten Kam Dahl (Project Participant)
Mølvang Dall, Sebastian (Project Participant)
Kristensen, Jannie Munk (Project Participant)
Delogu, Francesco (Project Participant)

9 Poster
7 Journal article
1 Conference abstract for conference
1 Comment/debate

7 results

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Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing
Singleton, C. M., Petriglieri, F., Kristensen, J. M., Kirkegaard, R. H., Michaelsen, T. Y., Andersen, M. H., Kondrotaite, Z., Karst, S. M., Dueholm, M. S., Nielsen, P. H. & Albertsen, M., 31 Mar 2021, In: Nature Communications. 12, 1, 13 p., 2009.
Research output: Contribution to journal › Journal article › Research › peer-review

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132 Citations (Scopus)

138 Downloads (Pure)
Greengenes2 unifies microbial data in a single reference tree
McDonald, D., Jiang, Y., Balaban, M., Cantrell, K., Zhu, Q., Gonzalez, A., Morton, J. T., Nicolaou, G., Parks, D. H., Karst, S. M., Albertsen, M., Hugenholtz, P., DeSantis, T., Song, S. J., Bartko, A., Havulinna, A. S., Jousilahti, P., Cheng, S., Inouye, M., Niiranen, T., & 5 othersJain, M., Salomaa, V., Lahti, L., Mirarab, S. & Knight, R., 27 Jul 2023, (E-pub ahead of print) In: Nature Biotechnology.
Research output: Contribution to journal › Journal article › Research › peer-review

Open Access
17 Citations (Scopus)
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing
Karst, S. M., Ziels, R. M., Kirkegaard, R. H., Sørensen, E. A., McDonald, D., Zhu, Q., Knight, R. & Albertsen, M., Feb 2021, In: Nature Methods. 18, 2, p. 165-169 5 p.
Research output: Contribution to journal › Journal article › Research › peer-review
145 Citations (Scopus)
Improved description of terrestrial habitat types by including microbial communities as indicators
Danielsen, A-C. S., Nielsen, P. H., Hermansen, C., Weber, P. L., de Jonge, L. W., Jørgensen, V. R., Greve, M. H., Corcoran, D., Dueholm, M. K. D. & Bruhn, D., 15 Oct 2023, In: Journal of Environmental Management. 344, 118677.
Research output: Contribution to journal › Journal article › Research › peer-review

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43 Downloads (Pure)
Metagenomic binning with assembly graph embeddings
Lamurias, A., Sereika, M., Albertsen, M., Hose, K. & Nielsen, T. D., Oct 2022, In: Bioinformatics. 38, 19, p. 4481-4487 7 p.
Research output: Contribution to journal › Journal article › Research › peer-review

Open Access
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9 Citations (Scopus)

87 Downloads (Pure)
Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing
Sereika, M., Kirkegaard, R. H., Karst, S. M., Yssing Michaelsen, T., Sørensen, E. A., Wollenberg, R. D. & Albertsen, M., 4 Jul 2022, In: Nature Methods. 19, 7, p. 823-826 4 p.
Research output: Contribution to journal › Journal article › Communication

Open Access
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108 Citations (Scopus)

56 Downloads (Pure)
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
Shaffer, J. P., Nothias, L. F., Thompson, L. R., Sanders, J. G., Salido, R. A., Couvillion, S. P., Brejnrod, A. D., Lejzerowicz, F., Haiminen, N., Lutz, H. L., Zhu, Q., Martino, C., Morton, J. T., Karthikeyan, S., Nothias-Esposito, M., Dührkop, K., Böcker, S., Kim, H. W., Aksenov, A. A., Bittremieux, W., & 31 othersMinich, J. J., Marotz, C., Bryant, M. K. M., Sanders, K., Schwartz, T., Humphrey, G., Vásquez-Baeza, Y., Tripathi, A., Parida, L., Carrieri, A. P., Beck, K. L., Das, P., González, A., McDonald, D., Ladau, J., Karst, S. M., Albertsen, M., Ackermann, G., DeReus, J., Thomas, T., Petras, D., Shade, A., Stegen, J., Song, S. J., Metz, T. O., Swafford, A. D., Dorrestein, P. C., Jansson, J. K., Gilbert, J. A., Knight, R. & the Earth Microbiome Project 500 (EMP500) Consortium, Dec 2022, In: Nature Microbiology. 7, 12, p. 2128-2150 23 p.
Research output: Contribution to journal › Journal article › Research › peer-review

Open Access
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34 Citations (Scopus)

23 Downloads (Pure)

The Microbiome of Denmark

Research output

Search results

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

Greengenes2 unifies microbial data in a single reference tree

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

Improved description of terrestrial habitat types by including microbial communities as indicators

Metagenomic binning with assembly graph embeddings

Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing

Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity