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A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
Hello! Welcome to my page.
Postdoctoral researcher in microbial transcriptomics and RNA biology
Posts
Future Blog Post
Published:
This post will show up by default. To disable scheduling of future posts, edit config.yml and set future: false.
Blog Post number 4
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 3
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 2
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 1
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
portfolio
The joy of spreadsheets
Published:
To get straight to the point: This post is about data manipulation and visualization in R.
Obviously, that is something completely different from my first post and with more content coming up, I have to think about giving the blog a clearer structure 🤔
But for now, it should be fine. As you will definitely see some code during your read, please do not be intimidated! You will not miss the final statement, even if you are not familiar with programming. As some kind of a reminiscence to the previous topic, this post again deals with movies and the development of their duration over the years.
The power of interactive plots
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At the beginning of the year, I remember myself staring at the screen, sitting on a bunch of genomic data and thinking:
“Man, it would be really helpful to hover over my data points and check what properties they have…”
As this may seem a bit nerdy, nowadays dynamic content has become quite natural and offers a whole new range of possibilities especially when dealing with large, complex data sets.
Animated bar graphs in R
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Last week I saw this post on Twitter where Adam Spannbauer visualized an animated ‘growing’ bar graph in R. Pretty impressive!
Is an animated graph contributing to a better understanding?
From the comments and a related second post it became clear, that this animation was visually appealing, but in no way contributing to a better understanding of the data behind the graph. So I sat down and thought about requirements for an animated bar chart that can be embedded in a presentation and contribute (maybe) to a better understanding:
How I start a bioinformatics project
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I started analyzing sequencing data just over one year ago. In the beginning it was so exciting to finally receive the first reads, do some quality checks and start further analysis, that I didn´t think about reproducibility. I ended up with multiple distinct versions of mapped reads, adapter/quality trimmed reads from scripts using different parameters. It was bad…
So I had to force myself to rethink my workflow, which I will show you (in a simplifed way) in the following.
Write your first R package
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In my opinion packages are one of the main reasons why R is so successfull. They add a whole new level of functionality and reproducibility and also increase the productivity of every user by reusable R functions, their documentation and sample data.
publications
Next Generation DNA-Seq and differential RNA-Seq allow re-annotation of the Pyrococcus furiosus DSM 3638 genome and provide insights into archaeal antisense transcription
Published in Frontiers in Microbiology, 2019
RNA-supplemented re-annotation of the new Pyrococcus furiosus reference genome.
CopR, a global regulator of transcription to maintain copper homeostasis in Pyrococcus furiosus
Published in Frontiers in Microbiology, 2021
Integrating RNA-seq and ChiP-seq data we found out that CopR is the master regulator for copper homeostasis in Pyrococcus furiosus.
Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea
Published in Nucleic Acids Research, 2021
Study be the Ferreira-Cerca lab analyzing the in vivo role of the universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea.
Coupling of transcription and translation in Archaea: Cues from the bacterial world
Published in Frontiers in Microbiology, 2021
This perspective is about requirements and functional implications of transcription-translation coupling in archaea.
Nanopore sequencing of RNA and cDNA molecules in Escherichia coli
Published in RNA, 2022
Here we compared available Nanopore RNA-seq protocols for the analysis of multiple transcriptomic features in E. coli.
Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea
Published in RNA, 2023
We used Nanopore cDNA and direct RNA sequencing to explore rRNA processing and the stage-dependent installation of rRNA modifications in Archaea.
Transcriptional and translational dynamics underlying heat shock response in the thermophilic crenarchaeon Sulfolobus acidocaldarius
Published in mBio, 2023
In this study we assisted with data analysis of transcriptomics & proteomics data to look into the heat shock response of Sulfolobus
The archaeal Lsm protein from Pyrococcus furiosus binds co-transcriptionally to poly(U)-rich target RNAs
Published in Biological Chemistry, 2023
Study identifying how the archaeal Lsm protein interacts with RNA targets during transcription in Pyrococcus furiosus.
Uncovering the temporal dynamics and regulatory networks of thermal stress response in a hyperthermophile
Published in mBio, 2023
An integrated transcriptomics and proteomics study revealing stress response dynamics in a hyperthermophilic archaeon.
The transcriptional regulator EarA and intergenic terminator sequences modulate archaellation in Pyrococcus furiosus
Published in Frontiers in Microbiology, 2023
Study exploring how the regulator EarA and transcription terminators influence archaellum formation in Pyrococcus furiosus.
Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment
Published in Nucleic Acids Research, 2024
We characterized the transcription elongation complex and Spt4/5 recruitment in Archaea at the structural level.
MinD2 modulates cell shape and motility in the archaeon Haloferax volcanii
Published in Frontiers in Microbiology, 2024
Study exploring how MinD2 influences the cellular architecture and movement of the archaeon Haloferax volcanii.
Single-Molecule Sequencing of RNA
Published in American Chemical Society, ACS In Focus Series, 2025
Comprehensive introduction to single-molecule RNA sequencing, covering Nanopore and PacBio technologies and their applications in research and medicine.