Posts by Tags

A. baumanii

An ML classifier for A. baumanii plasmids

less than 1 minute read

Published:

Alessia Carrara, an Erasmus exchange master student from the University of Milan, did her internship with Sergio Arredondo Alonso and me. The topic of her thesis was “A Machine Learning classifier for A. baumanii plasmids”. She gave a presentation about her work at the Utrecht Bioinformatics Center (UBC) seminar.

ABPHM17

Poster ABPHM17

less than 1 minute read

Published:

Here’s the poster presented at ‘Applied Bioinformatics and Public Health Microbiology 2017’ at the Wellcome Genome Campus, Hinxton, Cambridge, UK on the Enterococcus faecium plasmidome

E. coli

mlplasmids FAQ

2 minute read

Published:

mlplasmids is an R package to predict if assembled short-read contigs from E. coli, K. pneunomiae or E. faecium originated from a plasmid or a chromosome. It uses species-specific machine learning classifiers which results in high precision and accuracy. mlplasmids can be used to predict the location of, for example, antibiotic resistance genes and the plasmidome content of a population of a bacterial species. The full description of mlplasmids is available as a preprint at bioRxiv.

E. faecium

How to separate the nesting dolls

less than 1 minute read

Published:

Mobile genetic elements can be nested, like russian dolls. This is also the case for the vanA gene cluster in Enterococcus faecium, which is located on a Tn1546 transposon, which, in turn, is often located on plasmids.

mlplasmids FAQ

2 minute read

Published:

mlplasmids is an R package to predict if assembled short-read contigs from E. coli, K. pneunomiae or E. faecium originated from a plasmid or a chromosome. It uses species-specific machine learning classifiers which results in high precision and accuracy. mlplasmids can be used to predict the location of, for example, antibiotic resistance genes and the plasmidome content of a population of a bacterial species. The full description of mlplasmids is available as a preprint at bioRxiv.

K. pneumoniae

mlplasmids FAQ

2 minute read

Published:

mlplasmids is an R package to predict if assembled short-read contigs from E. coli, K. pneunomiae or E. faecium originated from a plasmid or a chromosome. It uses species-specific machine learning classifiers which results in high precision and accuracy. mlplasmids can be used to predict the location of, for example, antibiotic resistance genes and the plasmidome content of a population of a bacterial species. The full description of mlplasmids is available as a preprint at bioRxiv.

R

mlplasmids FAQ

2 minute read

Published:

mlplasmids is an R package to predict if assembled short-read contigs from E. coli, K. pneunomiae or E. faecium originated from a plasmid or a chromosome. It uses species-specific machine learning classifiers which results in high precision and accuracy. mlplasmids can be used to predict the location of, for example, antibiotic resistance genes and the plasmidome content of a population of a bacterial species. The full description of mlplasmids is available as a preprint at bioRxiv.

Drawing a tree with colored tips in R (ggtree)

1 minute read

Published:

ggtree is a R package designed for viewing and annotating phylogenetic trees. It is based on the ggplot2 package. Here I will show step-by-step how to draw a tree with colored tips, because, even thought the bioconductor documentation is clear and complete, I did not read about this very common visualization.

SNP pipelines

Popularity of SNP pipelines

2 minute read

Published:

Recently we got back a round of reviews on a small review paper. There was one sentence in the text were I listed some SNP pipelines that I thought were good examples. The topic of the review is not pipelines so the intention was not to list all, just one or two. However reviewer 2 did not agree with my choice of examples. He suggested to omit the name of the pipeline that was unpublished and name a few other published ones instead.

assembly graph

How to separate the nesting dolls

less than 1 minute read

Published:

Mobile genetic elements can be nested, like russian dolls. This is also the case for the vanA gene cluster in Enterococcus faecium, which is located on a Tn1546 transposon, which, in turn, is often located on plasmids.

bioinformatics

How to separate the nesting dolls

less than 1 minute read

Published:

Mobile genetic elements can be nested, like russian dolls. This is also the case for the vanA gene cluster in Enterococcus faecium, which is located on a Tn1546 transposon, which, in turn, is often located on plasmids.

An ML classifier for A. baumanii plasmids

less than 1 minute read

Published:

Alessia Carrara, an Erasmus exchange master student from the University of Milan, did her internship with Sergio Arredondo Alonso and me. The topic of her thesis was “A Machine Learning classifier for A. baumanii plasmids”. She gave a presentation about her work at the Utrecht Bioinformatics Center (UBC) seminar.

mlplasmids FAQ

2 minute read

Published:

mlplasmids is an R package to predict if assembled short-read contigs from E. coli, K. pneunomiae or E. faecium originated from a plasmid or a chromosome. It uses species-specific machine learning classifiers which results in high precision and accuracy. mlplasmids can be used to predict the location of, for example, antibiotic resistance genes and the plasmidome content of a population of a bacterial species. The full description of mlplasmids is available as a preprint at bioRxiv.

Popularity of SNP pipelines

2 minute read

Published:

Recently we got back a round of reviews on a small review paper. There was one sentence in the text were I listed some SNP pipelines that I thought were good examples. The topic of the review is not pipelines so the intention was not to list all, just one or two. However reviewer 2 did not agree with my choice of examples. He suggested to omit the name of the pipeline that was unpublished and name a few other published ones instead.

Poster ABPHM17

less than 1 minute read

Published:

Here’s the poster presented at ‘Applied Bioinformatics and Public Health Microbiology 2017’ at the Wellcome Genome Campus, Hinxton, Cambridge, UK on the Enterococcus faecium plasmidome

Drawing a tree with colored tips in R (ggtree)

1 minute read

Published:

ggtree is a R package designed for viewing and annotating phylogenetic trees. It is based on the ggplot2 package. Here I will show step-by-step how to draw a tree with colored tips, because, even thought the bioconductor documentation is clear and complete, I did not read about this very common visualization.

chromosome

How to separate the nesting dolls

less than 1 minute read

Published:

Mobile genetic elements can be nested, like russian dolls. This is also the case for the vanA gene cluster in Enterococcus faecium, which is located on a Tn1546 transposon, which, in turn, is often located on plasmids.

An ML classifier for A. baumanii plasmids

less than 1 minute read

Published:

Alessia Carrara, an Erasmus exchange master student from the University of Milan, did her internship with Sergio Arredondo Alonso and me. The topic of her thesis was “A Machine Learning classifier for A. baumanii plasmids”. She gave a presentation about her work at the Utrecht Bioinformatics Center (UBC) seminar.

mlplasmids FAQ

2 minute read

Published:

mlplasmids is an R package to predict if assembled short-read contigs from E. coli, K. pneunomiae or E. faecium originated from a plasmid or a chromosome. It uses species-specific machine learning classifiers which results in high precision and accuracy. mlplasmids can be used to predict the location of, for example, antibiotic resistance genes and the plasmidome content of a population of a bacterial species. The full description of mlplasmids is available as a preprint at bioRxiv.

data carpentry

first post

Drawing a tree with colored tips in R (ggtree)

1 minute read

Published:

ggtree is a R package designed for viewing and annotating phylogenetic trees. It is based on the ggplot2 package. Here I will show step-by-step how to draw a tree with colored tips, because, even thought the bioconductor documentation is clear and complete, I did not read about this very common visualization.

ggtree

Drawing a tree with colored tips in R (ggtree)

1 minute read

Published:

ggtree is a R package designed for viewing and annotating phylogenetic trees. It is based on the ggplot2 package. Here I will show step-by-step how to draw a tree with colored tips, because, even thought the bioconductor documentation is clear and complete, I did not read about this very common visualization.

gplas

How to separate the nesting dolls

less than 1 minute read

Published:

Mobile genetic elements can be nested, like russian dolls. This is also the case for the vanA gene cluster in Enterococcus faecium, which is located on a Tn1546 transposon, which, in turn, is often located on plasmids.

machine learning

An ML classifier for A. baumanii plasmids

less than 1 minute read

Published:

Alessia Carrara, an Erasmus exchange master student from the University of Milan, did her internship with Sergio Arredondo Alonso and me. The topic of her thesis was “A Machine Learning classifier for A. baumanii plasmids”. She gave a presentation about her work at the Utrecht Bioinformatics Center (UBC) seminar.

mlplasmids FAQ

2 minute read

Published:

mlplasmids is an R package to predict if assembled short-read contigs from E. coli, K. pneunomiae or E. faecium originated from a plasmid or a chromosome. It uses species-specific machine learning classifiers which results in high precision and accuracy. mlplasmids can be used to predict the location of, for example, antibiotic resistance genes and the plasmidome content of a population of a bacterial species. The full description of mlplasmids is available as a preprint at bioRxiv.

microbial

Popularity of SNP pipelines

2 minute read

Published:

Recently we got back a round of reviews on a small review paper. There was one sentence in the text were I listed some SNP pipelines that I thought were good examples. The topic of the review is not pipelines so the intention was not to list all, just one or two. However reviewer 2 did not agree with my choice of examples. He suggested to omit the name of the pipeline that was unpublished and name a few other published ones instead.

mlplasmids

mlplasmids FAQ

2 minute read

Published:

mlplasmids is an R package to predict if assembled short-read contigs from E. coli, K. pneunomiae or E. faecium originated from a plasmid or a chromosome. It uses species-specific machine learning classifiers which results in high precision and accuracy. mlplasmids can be used to predict the location of, for example, antibiotic resistance genes and the plasmidome content of a population of a bacterial species. The full description of mlplasmids is available as a preprint at bioRxiv.

mplasmids

How to separate the nesting dolls

less than 1 minute read

Published:

Mobile genetic elements can be nested, like russian dolls. This is also the case for the vanA gene cluster in Enterococcus faecium, which is located on a Tn1546 transposon, which, in turn, is often located on plasmids.

network analysis

How to separate the nesting dolls

less than 1 minute read

Published:

Mobile genetic elements can be nested, like russian dolls. This is also the case for the vanA gene cluster in Enterococcus faecium, which is located on a Tn1546 transposon, which, in turn, is often located on plasmids.

phylogeny

Drawing a tree with colored tips in R (ggtree)

1 minute read

Published:

ggtree is a R package designed for viewing and annotating phylogenetic trees. It is based on the ggplot2 package. Here I will show step-by-step how to draw a tree with colored tips, because, even thought the bioconductor documentation is clear and complete, I did not read about this very common visualization.

plasmid

How to separate the nesting dolls

less than 1 minute read

Published:

Mobile genetic elements can be nested, like russian dolls. This is also the case for the vanA gene cluster in Enterococcus faecium, which is located on a Tn1546 transposon, which, in turn, is often located on plasmids.

An ML classifier for A. baumanii plasmids

less than 1 minute read

Published:

Alessia Carrara, an Erasmus exchange master student from the University of Milan, did her internship with Sergio Arredondo Alonso and me. The topic of her thesis was “A Machine Learning classifier for A. baumanii plasmids”. She gave a presentation about her work at the Utrecht Bioinformatics Center (UBC) seminar.

mlplasmids FAQ

2 minute read

Published:

mlplasmids is an R package to predict if assembled short-read contigs from E. coli, K. pneunomiae or E. faecium originated from a plasmid or a chromosome. It uses species-specific machine learning classifiers which results in high precision and accuracy. mlplasmids can be used to predict the location of, for example, antibiotic resistance genes and the plasmidome content of a population of a bacterial species. The full description of mlplasmids is available as a preprint at bioRxiv.

Poster ABPHM17

less than 1 minute read

Published:

Here’s the poster presented at ‘Applied Bioinformatics and Public Health Microbiology 2017’ at the Wellcome Genome Campus, Hinxton, Cambridge, UK on the Enterococcus faecium plasmidome

podcast

poster

Poster ABPHM17

less than 1 minute read

Published:

Here’s the poster presented at ‘Applied Bioinformatics and Public Health Microbiology 2017’ at the Wellcome Genome Campus, Hinxton, Cambridge, UK on the Enterococcus faecium plasmidome

teaching

tuberculosis

twitter

Popularity of SNP pipelines

2 minute read

Published:

Recently we got back a round of reviews on a small review paper. There was one sentence in the text were I listed some SNP pipelines that I thought were good examples. The topic of the review is not pipelines so the intention was not to list all, just one or two. However reviewer 2 did not agree with my choice of examples. He suggested to omit the name of the pipeline that was unpublished and name a few other published ones instead.

visualization

Drawing a tree with colored tips in R (ggtree)

1 minute read

Published:

ggtree is a R package designed for viewing and annotating phylogenetic trees. It is based on the ggplot2 package. Here I will show step-by-step how to draw a tree with colored tips, because, even thought the bioconductor documentation is clear and complete, I did not read about this very common visualization.

workflows