Author

S. Arredondo-Alonso

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· 6 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Organism:E. coli· 4 Assay:whole-genome sequencing· 4 Approach:statistical model· 3 Organism:bacteria (other)· 2 Approach:experimental assay· 2 Organism:human· 2 Assay:long-read sequencing· 2 Research Focus:variant calling· 2

Frequent Co-Authors

J. Corander· 5 shared R. A. Gladstone· 3 shared A. C. Schurch· 2 shared A. K. Pontinen· 2 shared A. K. Pöntinen· 2 shared G. Tonkin-Hill· 2 shared J. Top· 2 shared O. Samuelsen· 2 shared

Activity by Year

2017-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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5 shared papersMicrobiology

J. Corander

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Author profile →

7 papers

Recent·Most cited

Plasmid-driven strategies for clone success in Escherichia coli

S. Arredondo-Alonso, A. K. Pontinen, J. Gama, R. A. Gladstone, K. Harms, G. Tonkin-Hill, H. A. Thorpe, G. S. Simonsen, O. Samuelsen, P. J. Johnsen, J. Corander

The paper uses long-read sequencing to analyze plasmids and chromosomes in E. coli over two decades, revealing long-term plasmid-lineage associations and success strategies.

bioRxiv · Oct 14, 2023 · PreprintMicrobiology

The population-level impact of Enterococcus faecalis genetics on intestinal colonisation and extraintestinal infection

C. Chaguza, A. K. Pöntinen, J. Top, S. Arredondo-Alonso, A. R. Freitas, C. Novais, C. Torres, S. D. Bentley, L. Peixe, T. M. Coque, R. J. L. Willems, J. Corander

This study investigates the genetic factors influencing E. faecalis intestinal colonization and extraintestinal infection using GWAS and heritability analysis across 750 isolates.

bioRxiv · Sep 26, 2022 · PreprintMicrobiology

Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe

G. Tonkin-Hill, R. A. Gladstone, A. K. Pontinen, S. Arredondo-Alonso, S. D. Bentley, J. Corander

The paper introduces Panstripe, a method to robustly analyze gene gain and loss rates in prokaryotic pangenomes, accounting for sampling bias and annotation errors.

bioRxiv · Apr 23, 2022Evolutionary Biology

A high-throughput multiplexing and selection strategy to complete bacterial genomes

S. Arredondo-Alonso, A. K. Pöntinen, F. Cleon, R. A. Gladstone, A. C. Schürch, P. J. Johnsen, O. Samuelsen, J. Corander

This paper evaluates a high-throughput multiplexing strategy using Oxford Nanopore Technologies to complete bacterial genomes, showing improved assembly contiguity and completeness.

bioRxiv · Jun 14, 2021Microbiology

Conditionally essential genes for survival during starvation in Enterococcus faecium E745

V. de Maat, S. Arredondo-Alonso, R. Willems, W. van Schaik

This study identifies genes essential for Enterococcus faecium survival during starvation using Tn-seq, highlighting usp as a key gene for environmental robustness.

bioRxiv · Apr 10, 2020Microbiology

mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species

S. Arredondo-Alonso, M. R. C. Rogers, J. C. Braat, T. D. Verschuuren, J. Top, J. Corander, R. J. L. Willems, A. C. Schurch

The paper introduces mlplasmids, an SVM-based tool to classify short-read WGS contigs as plasmid- or chromosome-derived in bacterial species, achieving high accuracy across three species.

bioRxiv · May 23, 2018Microbiology

On the (im)possibility to reconstruct plasmids from whole genome short-read sequencing data

S. Arredondo-Alonso, W. van Schaik, R. J. Willems, A. C. Schurch

This study evaluates plasmid reconstruction algorithms from short-read sequencing data using reference genomes, finding that none fully and unambiguously predict plasmid sequences, with performance varying by plasmid size and assembly quality.

bioRxiv · Mar 28, 2017Microbiology