Mads Albertsen

2024

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 others, Jain, M., Salomaa, V., Lahti, L., Mirarab, S. & Knight, R., May 2024, In: Nature Biotechnology. 42, 5, p. 715–718 4 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Open Access

54 Citations (Scopus)

High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing

Jensen, T. B. N., Dall, S. M., Knutsson, S., Karst, S. M. & Albertsen, M., Apr 2024, In: PLOS ONE. 19, 4 April, e0301446.

Research output: Contribution to journal › Journal article › Research › peer-review

Open Access

1 Citation (Scopus)

Integrating Multi-Modal Spatial Data using Knowledge Graphs – a Case Study of Microflora Danica

Corfixen, M., Heede, T., Sagi, T., Albertsen, M., Nielsen, T. D. & Hose, K., 2024, In: CEUR Workshop Proceedings. 3726, 10 p.

Research output: Contribution to journal › Conference article in Journal › Research › peer-review

Open Access

12 Downloads (Pure)

Microflora Danica: the atlas of Danish environmental microbiomes

Singleton, C., Jensen, T., Delogu, F., Sørensen, E., Jørgensen, V., Karst, S., Yang, Y., Knudsen, K., Sereika, M., Petriglieri, F., Knutsson, S., Dall, S., Kirkegaard, R., Kristensen, J., Woodcroft, B., Speth, D., Aroney, S., Wagner, M., Dueholm, M. & Nielsen, P. & 1 others, Albertsen, M., 27 Jun 2024

Research output: Other contribution › Research

The effect of non-pooled multi-donor faecal microbiota transplantation for inducing clinical remission in patients with chronic pouchitis: Results from a multicentre randomised double-blinded placebo-controlled trial (MicroPouch)

Kousgaard, S. J., Cold, F., Halkjær, S. I., Petersen, A. M., Kjeldsen, J., Møller Hansen, J., Dall, S. M., Albertsen, M., Nielsen, H. L., Kirk, K. F., Duch, K., Sønderkær, M. & Thorlacius-Ussing, O., 6 May 2024, (E-pub ahead of print) In: Journal of Crohn's and Colitis. jjae066.

Research output: Contribution to journal › Journal article › Research › peer-review

2023

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria

Sereika, M., Petriglieri, F., Jensen, T. B. N., Sannikov, A., Hoppe, M., Nielsen, P. H., Marshall, I. P. G., Schramm, A. & Albertsen, M., Apr 2023, In: ISME Journal. 17, 4, p. 561-569 9 p.

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16 Citations (Scopus)

58 Downloads (Pure)

Enabling detection of ecological patterns in 10.000 samples representing the Danish soil microbiome

Albertsen, M., Nymann, T., Jørgensen, V. R., Sørensen, E. A., Mølvang Dall, S., Karst, S. M., Knutsson, S. & Nielsen, P. H., 18 Aug 2023.

Research output: Contribution to conference without publisher/journal › Poster › Communication

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110 Downloads (Pure)

Fast DNA-analyses for surveillance of microbial communities in full-scale deammonification tanks: Potential for control and troubleshooting

Andersen, M. H., Thomsen, L., Stokholm-Bjerregaard, M., Eriksen, S., Hansen, S. H., Albertsen, M. & Nielsen, P. H., 1 Jun 2023, In: Water Research. 236, 119919.

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3 Citations (Scopus)

16 Downloads (Pure)

Graph Neural Networks for Metagenomic Binning

Lamurias, A., Tibo, A., Hose, K., Albertsen, M. & Nielsen, T. D., 2023, The 2023 ICML Workshop on Computational Biology. 7 p. 81

Research output: Contribution to book/anthology/report/conference proceeding › Article in proceeding › Research › peer-review

Open Access

High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing

Jensen, T. B., Dall, S. M., Knutsson, S., Karst, S. M. & Albertsen, M., 4 Sept 2023, bioRxiv, 28 p.

Research output: Working paper/Preprint › Preprint

Open Access

Long-read metagenomics paves the way toward a complete microbial tree of life

Albertsen, M., Jan 2023, In: Nature Methods. 20, 1, p. 30-31 2 p.

Research output: Contribution to journal › Comment/debate › Research › peer-review

13 Citations (Scopus)

Metagenomic Binning using Connectivity-constrained Variational Autoencoders

Lamurias, A., Tibo, A., Hose, K., Nielsen, T. D. & Albertsen, M., 2023, Proceedings of the 40th International Conference on Machine Learning. Krause, A. & Brunskill, E. (eds.). p. 18471–18481 762. (The Proceedings of Machine Learning Research, Vol. 202).

Research output: Contribution to book/anthology/report/conference proceeding › Article in proceeding › Research › peer-review

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SpikeSeq: A rapid, cost efficient and simple method to identify SARS-CoV-2 variants of concern by Sanger sequencing part of the spike protein gene

Jørgensen, T. S., Pedersen, M. S., Blin, K., Kuntke, F., Salling, H. K., Marvig, R. L., Michaelsen, T. Y., Albertsen, M. & Larsen, H., Feb 2023, In: Journal of Virological Methods. 312, 114648.

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2 Citations (Scopus)

38 Downloads (Pure)

Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta

Moeller, F. U., Herbold, C. W., Schintlmeister, A., Mooshammer, M., Motti, C., Glasl, B., Kitzinger, K., Behnam, F., Watzka, M., Schweder, T., Albertsen, M., Richter, A., Webster, N. S. & Wagner, M., Aug 2023, In: ISME Journal. 17, 8, p. 1208-1223 16 p.

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5 Citations (Scopus)

6 Downloads (Pure)

Uncovering Methane Sink Potential and Habitat Preferences of Methanotrophs in Denmark

Knudsen, K. S., Nymann, T., Sereika, M., Nielsen, P. H., Albertsen, M. & Singleton, C. M., 2023, the Local Pangenome: Abstracts Book. p. 66

Research output: Contribution to book/anthology/report/conference proceeding › Conference abstract in proceeding › Research

2022

Author Correction: MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants (Nature Communications, (2022), 13, 1, (1908), 10.1038/s41467-022-29438-7)

Dueholm, M. K. D., Nierychlo, M., Andersen, K. S., Rudkjøbing, V., Knutsson, S., MiDAS Global Consortium, Albertsen, M. & Nielsen, P. H., 11 Jul 2022, In: Nature Communications. 13, 1, 4017.

Research output: Contribution to journal › Comment/debate › Research › peer-review

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4 Citations (Scopus)

38 Downloads (Pure)

Development of metagenomic DNA-sequencing in clinical microbiology diagnostics

Nielsen, M. E., Søgaard, K. K., Nielsen, H. L. & Albertsen, M., 14 Aug 2022.

Research output: Contribution to conference without publisher/journal › Conference abstract for conference › Research

Graph Neural Networks for Microbial Genome Recovery

Lamurias, A., Tibo, A., Hose, K., Albertsen, M. & Nielsen, T. D., 2022, arXiv.

Research output: Working paper/Preprint › Preprint

Open Access

Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark

Michaelsen, T. Y., Bennedbæk, M., Christiansen, L. E., Jørgensen, M. S. F., Møller, C. H., Sørensen, E. A., Knutsson, S., Brandt, J., Jensen, T. B. N., Chiche-Lapierre, C., Collados, E. F., Sørensen, T., Petersen, C., Le-Quy, V., Sereika, M., Hansen, F. T., Rasmussen, M., Fonager, J., Karst, S. M. & Marvig, R. L. & 70 others, Stegger, M., Sieber, R. N., Skov, R., Legarth, R., Krause, T. G., Fomsgaard, A., The Danish COVID-19 Genome Consortium (DCGC), Andersen, K. S. (Member of study group), Andersen, M. H. (Member of study group), Berg, A. (Member of study group), Bielidt, S. R. (Member of study group), Dall, S. M. (Member of study group), Dvarionaite, E. (Member of study group), Hansen, S. H. (Member of study group), Jørgensen, V. R. (Member of study group), Kirkegaard, R. H. (Member of study group), Saei, W. (Member of study group), Nicolajsen, T. B. (Member of study group), Østergaard, S. K. (Member of study group), Brøndum, R. F. (Member of study group), Bøgsted, M. (Member of study group), Hose, K. (Member of study group), Sagi, T. (Member of study group), Pakanec, M. (Member of study group), Fuglsang-Damgaard, D. (Member of study group), Mølvadgaard, M. (Member of study group), Krarup, H. (Member of study group), Svarrer, C. W. (Member of study group), Christiansen, M. T. (Member of study group), Ingham, A. C. (Member of study group), Johannesen, T. B. (Member of study group), Basterrechea, M. (Member of study group), Lilje, B. (Member of study group), Ellegaard, K. (Member of study group), Matusevicius, P. (Member of study group), Christoffersen, L. B. (Member of study group), Tang, M. H. E. (Member of study group), Ng, K. L. (Member of study group), Edslev, S. M. (Member of study group), Baig, S. (Member of study group), Larsen, O. H. (Member of study group), Skipper, K. A. (Member of study group), Vang, S. (Member of study group), Handberg, K. J. (Member of study group), Nielsen, M. T. K. (Member of study group), Kobel, C. M. (Member of study group), Andersen, C. (Member of study group), Tarpgaard, I. H. (Member of study group), Ellermann-Eriksen, S. (Member of study group), Castruita, J. A. S. (Member of study group), Schneider, U. V. (Member of study group), Jacobsen, N. G. (Member of study group), Andersen, C. (Member of study group), Pedersen, M. S. (Member of study group), Schønning, K. (Member of study group), Kirkby, N. (Member of study group), Nielsen, L. (Member of study group), Nilsson, L. L. (Member of study group), Friis, M. B. (Member of study group), Sundelin, T. (Member of study group), Hansen, T. A. (Member of study group), Skov, M. N. (Member of study group), Sydenham, T. V. (Member of study group), Nielsen, X. C. (Member of study group), Schouw, C. H. (Member of study group), Jensen, A. (Member of study group), Marmolin, E. S. (Member of study group), Coia, J. E. (Member of study group), Andersen, D. T. (Member of study group) & Albertsen, M., 4 May 2022, In: Genome Medicine. 14, 1, 47.

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10 Citations (Scopus)

45 Downloads (Pure)

Long-Read Metagenome-Assembled Genomes Improve Identification of Novel Complete Biosynthetic Gene Clusters in a Complex Microbial Activated Sludge Ecosystem

Sanchez Navarro, R., Nuhamunada, M., Mohite, O., Wasmund, K., Albertsen, M., Gram, L., Nielsen, P. H., Weber, T. & Singleton, C. M., 29 Nov 2022, In: mSystems. 7, 6, e00632-22.

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15 Citations (Scopus)

42 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.

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16 Citations (Scopus)

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Metagenomic binning with assembly graph embeddings

Lamurias, A., Sereika, M., Albertsen, M., Hose, K. & Nielsen, T. D., 25 Feb 2022.

Research output: Contribution to conference without publisher/journal › Paper without publisher/journal › Research

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Microflora Danica - The Microbiome of Denmark

Albertsen, M., Jørgensen, V. R., Nymann, T., Sørensen, E. A., Sereika, M., Mølvang Dall, S., Knutsson, S., Petriglieri, F., Dottorini, G., Singleton, C. M., Karst, S. M., Dueholm, M. K. D. & Nielsen, P. H., 14 Aug 2022.

Research output: Contribution to conference without publisher/journal › Poster › Research › peer-review

Microflora Danica - The Microbiome of Denmark

Nymann, T., Sørensen, E. A., Sereika, M., Jørgensen, V. R., Mølvang Dall, S., Knutsson, S., Petriglieri, F., Dottorini, G., Singleton, C. M., Karst, S. M., Dueholm, M. K. D., Nielsen, P. H. & Albertsen, M., 14 Nov 2022, p. P52.

Research output: Contribution to conference without publisher/journal › Poster › Research

Microflora Danica – the Microbiome of Denmark, including the inter-connecting water ways

Nymann, T., Sørensen, E. A., Sereika, M., Petriglieri, F., Dottorini, G., Vestergaard, S. Z., Jørgensen, V. R., Albertsen, M. & Nielsen, P. H., 14 Nov 2022.

Research output: Contribution to conference without publisher/journal › Poster › Research

Microflora Danica – the Microbiome of Denmark, including the inter-connecting water ways

Nymann, T., Sørensen, E. A., Sereika, M., Petriglieri, F., Dottorini, G., Vestergaard, S. Z., Jørgensen, V. R., Albertsen, M. & Nielsen, P. H., Sept 2022.

Research output: Contribution to conference without publisher/journal › Poster › Research

MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

Dueholm, M. K. D., Nierychlo, M., Andersen, K. S., Rudkjøbing, V., Knutsson, S., MiDAS Global Consortium, Albertsen, M. & Nielsen, P. H., 7 Apr 2022, In: Nature Communications. 13, 1, 1908.

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161 Citations (Scopus)

76 Downloads (Pure)

Nanopore metagenomic sequencing of spiked donor blood plasma

Nielsen, M. E., Søgaard, K. K., Nielsen, H. L. & Albertsen, M., Sept 2022.

Research output: Contribution to conference without publisher/journal › Conference abstract for conference › Research

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

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158 Citations (Scopus)

80 Downloads (Pure)

Recovery of circular and high quality cable bacteria genomes from complex microbial communities

Sereika, M., Petriglieri, F., Nymann, T., P. G. Marshall, I., Schramm, A., Nielsen, P. H. & Albertsen, M., 16 Aug 2022.

Research output: Contribution to conference without publisher/journal › Poster › Communication

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Spatial separation of ribosomes and DNA in Asgard archaeal cells

Avcı, B., Brandt, J., Nachmias, D., Elia, N., Albertsen, M., Ettema, T. J. G., Schramm, A. & Kjeldsen, K. U., Feb 2022, In: ISME Journal. 16, 2, p. 606-610 5 p.

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16 Citations (Scopus)

36 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 others, Minich, 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.

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52 Citations (Scopus)

31 Downloads (Pure)

2021

Assessing Illumina, Nanopore and PacBio sequencing platforms at recovering high quality genomes from complex microbial communities

Sereika, M., Kirkegaard, R. H., Sørensen, E. A., Karst, S. M., Yssing Michaelsen, T. & Albertsen, M., 15 Nov 2021.

Research output: Contribution to conference without publisher/journal › Poster › Communication

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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.

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162 Citations (Scopus)

179 Downloads (Pure)

Deciphering the diversity of filamentous bacteria across the world

Nierychlo, M. A., Thomsen, L., Petriglieri, F., Kondrotaite, Z., Singleton, C. M., Dueholm, M. K. D., Andersen, K. S., Albertsen, M., Jørgensen, V. R. & Nielsen, P. H., 2021.

Research output: Contribution to conference without publisher/journal › Poster › Research

5 Downloads (Pure)

Developing new bioinformatic methods to supercharge genome-centric metagenomics using machine learning

Heidelbach, S., Lamurias, A., Sereika, M., Nielsen, T. D., Hose, K. & Albertsen, M., 15 Nov 2021.

Research output: Contribution to conference without publisher/journal › Conference abstract for conference › Communication

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From days to hours: Development and implementation of metagenomic DNA- sequencing in clinical microbiology diagnostics

Nielsen, M. E., Søgaard, K. K., Nielsen, H. L. & Albertsen, M., 15 Nov 2021. 1 p.

Research output: Contribution to conference without publisher/journal › Conference abstract for conference › Research

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42 Downloads (Pure)

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

173 Citations (Scopus)

Hospitalisation associated with SARS-CoV-2 delta variant in Denmark

Bager, P., Wohlfahrt, J., Rasmussen, M., Albertsen, M. & Krause, T. G., Oct 2021, In: The Lancet Infectious Diseases. 21, 10, p. 1351 1 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Open Access

44 Citations (Scopus)

Increased transmissibility of SARS-CoV-2 lineage B.1.1.7 by age and viral load

Lyngse, F. P., Mølbak, K., Skov, R. L., Christiansen, L. E., Mortensen, L. H., Albertsen, M., Møller, C. H., Krause, T. G., Rasmussen, M., Michaelsen, T. Y., Voldstedlund, M., Fonager, J., Steenhard, N., Danish Covid-19 Genome Consortium, Kirkeby, C. T., Albertsen, M. (Member of study group), Brandt, J. (Member of study group), Knutsson, S. (Member of study group), Sørensen, E. A. (Member of study group) & Nymann, T. (Member of study group) & 36 others, Petersen, C. (Member of study group), Chiche-Lapierre, C. E. (Member of study group), Hansen, F. T. (Member of study group), Collados, E. F. (Member of study group), Berg, A. (Member of study group), Remmer Bielidt, S. (Member of study group), Mølvang Dall, S. (Member of study group), Dvarionaite, E. (Member of study group), Hove Hansen, S. (Member of study group), Jørgensen, V. R. (Member of study group), Nicolajsen, T. B. (Member of study group), Saei, W. (Member of study group), Østergaard, S. K. (Member of study group), Yssing Michaelsen, T. (Member of study group), Le-Quy, V. (Member of study group), Sereika, M. (Member of study group), Kirkegaard, R. H. (Member of study group), Andersen, K. S. (Member of study group), Andersen, M. H. (Member of study group), Hansen, K. K. (Member of study group), Boye, M. (Member of study group), Bach, M. P. (Member of study group), Dissing, P. (Member of study group), Drastrup-Fjordbak, A. (Member of study group), Collin, M. (Member of study group), Büttner, F. (Member of study group), Andersen, S. (Member of study group), Otte, L. S. (Member of study group), Bøgsted, M. (Member of study group), Brøndum, R. F. (Member of study group), Hose, K. (Member of study group), Sagi, T. (Member of study group), Pakanec, M. (Member of study group), Krarup, H. B. (Member of study group), Fuglsang-Damgaard, D. (Member of study group) & Mølvadgaard, M. (Member of study group), 13 Dec 2021, In: Nature Communications. 12, 1, 7251.

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58 Citations (Scopus)

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102 Citations (Scopus)

Risk of hospitalisation associated with infection with SARS-CoV-2 lineage B.1.1.7 in Denmark: an observational cohort study

Danish Covid-19 Genome Consortium, Nov 2021, In: The Lancet Infectious Diseases. 21, 11, p. 1507-1517 11 p.

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83 Citations (Scopus)

The Importance of Taxonomic Classification Software and Machine Learning Algorithms for the Prediction of Colorectal Cancer

Mølvang Dall, S., Yssing Michaelsen, T. & Albertsen, M., 15 Nov 2021.

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The Microbiome of Nutrient Removal Plants Across the World

Dueholm, M. K. D., Andersen, K. S., Nierychlo, M. A., Albertsen, M., Jørgensen, V. R. & Nielsen, P. H., 24 May 2021.

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2020

Bacteria from the Genus Arcobacter Are Abundant in Effluent from Wastewater Treatment Plants

Kristensen, J. M., Nierychlo, M. A., Albertsen, M. & Nielsen, P. H., 17 Apr 2020, In: Applied and Environmental Microbiology. 86, 9, 13 p., e03044.

Research output: Contribution to journal › Journal article › Research › peer-review

Open Access

57 Citations (Scopus)

Clinical results and microbiota changes after faecal microbiota transplantation for chronic pouchitis: a pilot study

Kousgaard, S. J., Michaelsen, T. Y., Nielsen, H. L., Kirk, K. F., Brandt, J., Albertsen, M. & Thorlacius-Ussing, O., Apr 2020, In: Scandinavian Journal of Gastroenterology. 55, 4, p. 421-429 9 p.

Research output: Contribution to journal › Journal article › Research › peer-review

19 Citations (Scopus)

Comparative Genome-Centric Analysis of Freshwater and Marine ANAMMOX Cultures Suggests Functional Redundancy in Nitrogen Removal Processes

Ali, M., Shaw, D. R., Albertsen, M. & Saikaly, P. E., 7 Jul 2020, In: Frontiers in Microbiology. 11, 1637.

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38 Citations (Scopus)

62 Downloads (Pure)

Connecting structure to function with the recovery of over 1000 high-quality activated sludge metagenome-assembled genomes encoding full-length rRNA genes using long-read sequencing

Singleton, C. M., Petriglieri, F., Kristensen, J. M., Kirkegaard, R. H., Yssing Michaelsen, T., Andersen, M. H., Kondrotaite, Z., Karst, S. M., Dueholm, M. S., Nielsen, P. H. & Albertsen, M., 12 May 2020, In: bioRxiv.

Research output: Contribution to journal › Journal article › Research

Open Access

Mads Albertsen

Research output

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