Author

S. J. Pamp

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 7

Signature Assays, Organisms & Methods

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Assay:metagenomics· 6 Approach:statistical model· 4 Organism:human· 3 Research Focus:benchmarking· 2 Research Focus:cell type annotation· 2 Approach:deep learning· 2 Research Focus:differential expression· 2 Approach:biophysical modeling· 1

Frequent Co-Authors

F. M. Aarestrup· 7 shared P. Kirstahler· 3 shared C. S. Poulsen· 2 shared O. Lund· 2 shared A. Battisti· 1 shared A. Bossers· 1 shared A. C. Masche· 1 shared A. Caprioli· 1 shared

Activity by Year

2017-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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7 shared papersMicrobiology

F. M. Aarestrup

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Author profile →

7 papers

Recent·Most cited

Detection of Parasites in Microbiomes using Metagenomics

P. Kirstahler, F. M. Aarestrup, S. J. Pamp

This study detects parasites in microbiomes using metagenomics, finding Blastocystis sp. and Eimeria in livestock and various subtypes in humans, with prevalence patterns linked to income level and age.

bioRxiv · Mar 27, 2022 · PreprintMicrobiology

Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes

C. S. Poulsen, C. T. Ekstrom, F. M. Aarestrup, S. J. Pamp

This study shows that library preparation and sequencing platforms introduce systematic biases in metagenomic microbiome analysis, emphasizing the need for standardization.

bioRxiv · Jan 11, 2022Microbiology

Standard Sample Storage Conditions Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns

C. S. Poulsen, R. S. Kaas, F. M. Aarestrup, S. J. Pamp

This study evaluates how storage conditions affect microbiome composition and antimicrobial resistance in metagenomics data, finding significant effects from temperature, time, and freeze-thaw cycles.

bioRxiv · May 24, 2021Microbiology

A Peek into the Plasmidome of Global Sewage

P. Kirstahler, F. Teudt, S. Otani, F. M. Aarestrup, S. J. Pamp

This study analyzes the plasmidome of global sewage samples to identify plasmid-encoded traits, revealing novel plasmids and AMR gene distribution.

bioRxiv · Mar 8, 2021Microbiology

Specific Gut Microbiome Members are Associated with Distinct Immune Markers in Allogeneic Hematopoietic Stem Cell Transplantation

A. C. Masche, K. Kielsen, M. S. Cilieborg, O. Lund, S. Holmes, F. M. Aarestrup, K. G. Muller, S. J. Pamp

The paper identifies associations between gut microbiome taxa and immune markers in HSCT patients, linking specific microbial profiles to clinical outcomes like aGvHD and mortality.

bioRxiv · Mar 28, 2019 · PreprintMicrobiology

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid

P. Kirstahler, S. Solborg Bjerrum, A. Friis-Moller, M. la Cour, F. M. Aarestrup, H. Westh, S. J. Pamp

This study develops a genomics-based approach to identify microorganisms in human ocular body fluids, showing high concordance with traditional methods.

bioRxiv · Jan 31, 2018Microbiology

Abundance and diversity of the fecal resistome in slaughter pigs and broilers in nine European countries

P. Munk, B. E. Knudsen, O. Lukjacenko, A. S. R. Duarte, R. E. C. Luiken, L. Van Gompel, L. A. M. Smit, H. Schmitt, A. D. Garcia, R. B. Hansen, T. N. Petersen, A. Bossers, E. Ruppe, H. Graveland, A. van Essen, , F. M. Aarestrup

The paper quantifies and compares the resistomes of slaughter pigs and broilers across nine European countries, finding differences in AMR gene abundance and diversity linked to country-specific antimicrobial usage.

bioRxiv · Sep 28, 2017Microbiology