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dfg's Introduction

Hi there! 👋

I am a researcher and team lead at the Genome Competence Center of the Robert Koch Institute in Berlin, Germany. We study infectious diseases in a One Health context by applying real-time nanopore sequencing, pangenomics approaches, analyzing environmental samples such as wastewater, and studying microbial evolution using bioinformatics for genomic surveillance.

I studied Bioinformatics at the University of Jena, Germany and achieved my PhD by specializing in RNA Bioinformatics and High-Throughput Analysis. Following this, I moved to the European Bioinformatics Institute (EMBL-EBI), Hinxton (UK) to work in Microbiome Informatics. Since 2020, I have continued my academic journey at the RKI in Berlin, the national institute for public health in Germany, conducting research with my team and (inter)national colleagues in the following areas (further details can be found on my personal website):

Research interests 🔭

  • Microbial bioinformatics
  • Genomic surveillance
  • Pathogen detection and characterization
  • Nanopore real-time sequencing
  • Transcriptomics and gene expression
  • Metagenomics and metatranscriptomics
  • Cloud computing, automation, and reproducibility with Nextflow and containers

Skills ✔️

My Skillsnextflow

Top Langs

Bioinformatics tools 💾

My team and I develop bioinformatics tools and pipelines for microbial genomics, nanopore sequencing, metagenomics, and transcriptomics. I favor Nextflow pipelines with containerized dependencies for reproducibility. You can find my code on my personal GitHub, at github.com/hoelzer-lab (from my time leading a team at the University of Jena), and github.com/rki-mf1 (from the RKI Genome Competence Center). We also contribute to other repositories. Here are some examples:

  • VLQ-nf: SARS-CoV-2 lineage deconvolution from wastewater samples following Baaijens et al. [Paper]
  • RIBAP: A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs. [Paper]
  • POCP-nf: Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. [Paper]
  • RNAflow: A simple yet effective bulk RNA-Seq differential gene expression pipeline using Nextflow. [Paper]
  • VIRify: Detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies. [Paper]
  • WhatThePhage: Phage identification via nextflow and docker or singularity. [Paper]
  • poreCoV: SARS-CoV-2 genome reconstruction workflow for nanopore sequence data. [Paper]
  • CoVpipe2: SARS-CoV-2 genome reconstruction for Illumina data in Nextflow. [Paper]
  • CLEAN: A nextflow pipeline for decontamination of short reads, long reads and contigs. [Paper]

stats

Selected publications 📜

  • Eva Aßmann, Shelesh Agrawal, Laura Orschler, Sindy Böttcher, Susanne Lackner, Martin Hölzer (2024). "Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data". GigaScience. doi.org/10.1093/gigascience/giae051
  • Kevin Lamkiewicz, Lisa-Marie Barf, Konrad Sachse, Martin Hölzer (2024). "RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level". Genome Biology, 25 (1), 170. doi.org/10.1186/s13059-024-03312-9
  • Martin Hölzer (2024). "POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy". Bioinformatics, 40 (4), btae175. doi.org/10.1093/bioinformatics/btae175
  • Guillermo Rangel-Pineros, Alexandre Almeida, Martin Beracochea, Ekaterina Sakharova, Manja Marz, Alejandro Reyes Muñoz, Martin Hölzer, Robert D Finn (2023). "VIRify: an integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models." PLOS Computational Biology, 19 (8), e1011422. doi.org/10.1371/journal.pcbi.1011422
  • Sara Saheb Kashaf, Diana M Proctor, Clay Deming, Paul Saary, Martin Hölzer, Monica E Taylor, Heidi H Kong, Julia A Segre, Alexandre Almeida, Robert D Finn (2021). "Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions." Nature Microbiology, 7 (1), 169-179. nature.com/articles/s41564-021-01011-w
  • Christian Brandt, Sebastian Krautwurst, Riccardo Spott, Mara Lohde, Mateusz Jundzill, Mike Marquet, Martin Hölzer (2021). "poreCov - an easy to use, fast, and robust workflow for SARS-CoV-2 genome reconstruction via nanopore sequencing." Frontiers in Genetics, 12, 711437. doi.org/10.3389/fgene.2021.711437
  • Will A Overholt, Martin Hölzer, Patricia Geesink, Celia Diezel, Manja Marz, Kirsten Küsel (2020). "Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome‐assembled genomes from a complex aquifer system." Environmental microbiology, 22(9), 4000-4013. doi.org/10.1111/1462-2920.15186
  • Martin Hölzer, Manja Marz (2019). "De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers". GigaScience, 8 (5), giz039. doi.org/10.1093/gigascience/giz039

... Full list of publications

How to reach me 📫

linkedin researchgate

Further details can be found on my personal website.

Acknowledgement 🌱

My GitHub landing page was heavily inspired by github.com/jonas-fuchs - also check out Jonas' page and the great bioinformatics tools he's developing for viruses!

dfg's People

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dfg's Issues

New DFG RTF template since May 2020

The DFG made changes that need to be integrated into the LaTeX template:

Bitte beachten Sie, dass die Strukturierung des Leitfadens ab Mai 2020 und somit auch die "Beschreibung des Vorhabens" geändert wurde. Übergangsweise können Anträge nach dem Link auf eine Office-Dateivorherigen Vordruck (53.01 - 02/20) eingereicht werden bis zum 30. Oktober 2020. Neuerungen finden Sie zusammengefasst in der Interner LinkInformation für die Wissenschaft

Neben dem wissenschaftlichen Kernbereich sind vielfältige Begleitinformationen Gegenstand eines Projektantrags. Angesichts des weiterhin beschränkten Seitenumfangs gibt es künftig eine geschützte Seitenanzahl für den wissenschaftlichen Kernbereich. Den begleitenden Informationen, deren einzelne Fragen projektabhängig und fachspezifisch sehr unterschiedliche Relevanz haben können, soll ein entsprechender Raum gegeben werden.

https://www.dfg.de/foerderung/info_wissenschaft/2020/info_wissenschaft_20_24/index.html

Die Beschreibung des Vorhabens ist vom Umfang her beschränkt, hierbei stehen für Kap. 1 bis 4maximal 15 Seiten zur Verfügung. Ab Kapitel 5 stehen zusätzlich 10 Seiten zur Verfügung. Die vorgegebene Formatierung ist beizubehalten, insbesondere soll die Schrift Arial 11 Punkt, Zeilenabstand 1,2 nicht unterschritten werden. Für die Kapitel Projektbezogenes Publikationsverzeichnis und Literaturverzeichnis soll die Schrift Arial 9 Punkt nicht unterschritten werden

https://www.dfg.de/formulare/54_01/54_01_de.pdf
http://www.dfg.de/formulare/53_01_elan/53_01_de_elan.rtf

Highlighting the author's publications in section 4

In the current template DFG states in the section "Project- and subject-related list of publications" to highlight the author's publications. Also highlighting is not a must the DFG strongly recommends doing so. Here is a short solution that can be added to the Header.tex:

%% Highlight entries
\usepackage[svgnames]{xcolor}
\DeclareBibliographyCategory{important}
\colorlet{impentry}{Maroon}% let 'impentry' = Maroon
\AtEveryBibitem{%
  \ifcategory{important}%
    {\bfseries\color{impentry}}%
    {}%
  }
\addtocategory{important}{%
Smith2023a,Smith2023b,Smith2023c,Smith2023d,MIller1900, % don't miss the comma after the last entry
}

Updated DFG template 54.01

There are some changes that should be incorporated into the template before further usage!

Die DFG hat den Leitfaden für Projektanträge (Vordruck 54.01) aktualisiert. Das betrifft die Beschreibung des Vorhabens bei Projektanträgen im Rahmen einer Sachbeihilfe, des Emmy Noether-Programms, einer Forschungsgruppe, einer Klinischen Forschungsgruppe oder eines Schwerpunktprogramms. Übergangsweise werden Anträge nach der alten Vorlage nur noch bis zum 31. Mai 2022 angenommen.

Folgendes hat sich geändert:
• Angaben zum Umgang mit Forschungsdaten sind nun verpflichtend (weitere Infos inklusive Checkliste).
• Die Kapitel „Umgang mit Forschungsdaten“ und „Relevanz von Geschlecht und/oder Vielfältigkeit“ sind nun im wissenschaftlichen Teil der Vorhabenbeschreibung angesiedelt.
• Im Kapitel 2.3 „Arbeitsprogramm“ können ggf. Qualitätssicherungsmaßnahmen erläutert werden.
• Das Kapitel 4.1.2 „Erläuterung zu den vorgesehenen Untersuchungen bei Versuchen am Menschen oder an vom Menschen entnommenem Material“ wurde um den Bereich Versuche mit „identifizierbaren Daten“ ergänzt.
• Die Hinweise zum „Dual Use Research of Concern“ (Kapitel 4.1.5) wurden aufgrund geänderter rechtlicher Normierungen aktualisiert. An dieser Stelle möchte ich an unsere eigene Hausverfügung zum Umgang mit DURC erinnern.

finalcompile boolean setting should precede Header input

dfg/dfg.tex

Line 17 in f9af0eb

\setboolean{finalcompile}{false}

The Header.tex file uses the finalcompile boolean to determine whether todo notes & section labels are shown... but the value of the variable is only set in dfg.tex after the Header.tex has been input. As such, setting the variable in dfg.tex has no effect on the compiled document.

To fix:

  • Declare the variable in proposal.sty
  • Move the \setboolean command to before \input{Header}

Numbering of own references

New DFG guidelines ask to number your references in Sec. 1.2.1. and 1.2.2 consecutively. For other references in the bibliography, it seems that one can arrange them alphabetically. Please suggest that how one should do this in your template?

todo package on the cover page

Thanks for sharing the template. I'm using it for my proposal and I'll let you know if my proposal is successful. In the meantime, I have a question:

the \todo box containing the text First-time should be shifted a bit to the left since it overflows to the right in my pdf generated. I have tried to shift it leftward but was not successful.

Also, enabling \setboolean{finalcompile}{true} before input the Header.tex file didn't change anything to my pdf generated.

~[Feature Request] Literature sorting improvement~ Literature in v54.01 DFG template

Summary
Is there a way to include literature sorting with different labels directly into the template?
e.g. own literature labeled as [E1], [E2], ...
others literature labeld as [1], [2], ...

Describing the Problem
There are mainly two different literature sections

  • own work (project specific and non-project specific) (Section 1.2, 1.2.1 and 1.2.2)
  • general literature in Section 3: state of research, project goals, working program

The general order is

  • state of research and own pre-research
  • own literature for pre-research (Section 1.2, 1.2.1 and 1.2.2)
  • Describing project goals
  • others literature, for state of research, own research and working program

The result is a unsorted mixture of literature in the text. Lets assume [1]-[10] are own literature, and [11-30] others.
In Chapter 1 in the text, there is a mixture of the literature, e.g.

txt [11], ..... [1] .... [12] ... [2,3] .... [13].... [14]....

Possible Solution
is there a way to label own literature with additonal sign directly into the template?

txt [1], ..... [E1] .... [2] ... [E2, E3] .... [3].... [4]....

New DFG Template

According to 1 there is a new chapter 7.8 "Module Standard Allowance for Gender Equality Measures" at the end.

I will look for other changes of the current template. If someone finds others, please write it down here. Then I can put all of them into this template at the end of this week.

ToDo Notes package

Now there are small macros like \todo, but we could add this package todonotes 1. I would include it. The macro \todo now can be reused, it would necessary to extend a small workaround when using externalize with tikz (i already have) to the behaviour of \todo will just be more fancy in the default config.

I can make a proposal here in a seperate branch by a pull request if you like.

BR Beckus

Remove sections "Signature" and "List of attachments"?

First of all, thank you very much for creating and sharing the so wonderful DFG LaTeX template! It helped me really a lot prepare my proposal. I'll definitely keep to use your template for my other future proposals:)

I got wondering that if sections 6 "Signature" and 7 "List of attachments" really exist in the present official DFG templates. Maybe ~4 years ago they were in the official template, but now as far as I see 53_01_en_elan.rtf of 11/20, 03/22, and 09/22 (yeah, this month they again updated it), there are no corresponding sections anymore. I also did a random survey for 53_05_en_elan.rtf, 53_09_en_elan.rtf, 53_15_en_elan.rtf, 53_24_en_elan.rtf, and 53_120_en_elan.rtf, none of which seems to have the corresponding sections.

I actually noticed this because, after submitting my proposal, the DFG office requested to remove these sections to comply the present template.

So, if you think reasonable, how about now removing these chapters? Or, if these sections are requested in some DFG proposal categories, how about indicating this in the template?

change in paragraph environment remain after the work package sections

After adding the "WP" prefix to the \paragraph headings in dfg.tex the following \subsubsubsection also contain the prefix, because the \subsubsubsection definition is based on \paragraph. As a result I see, for instance, travel expenses with the "WP" prefix.

Definition in the proposal.sty:

\newcommand{\subsubsubsection}[1]{\paragraph{#1} \mbox{} \par}
\setcounter{secnumdepth}{5}

Before the work package section in dfg.tex:
\renewcommand{\theparagraph}{WP\,\arabic{paragraph}}

After the work package section something like \renewcommand{\theparagraph}{\arabic{paragraph}} is missing. The letter code line adds numbering to the heading but only on the first level. If one needs section level 4 (e.g. 1.4.1.2 Foo Bar) another solution needs to be found.

German version?

Hi,
first, let me thank you for creating this LaTeX template!
I am thinking of translating it into a German version. Is there any interest for that?
If yes, the best way is probably to create it as a separate file 'dfg-german.tex', no?
Regards,
Nicolas

Move Header.txt to proposal.sty

I'd like to move all from Header.txt to proposal.sty. I see no things according to dfg.tex or dfg-german.tex which cannot be implemented in proposal.sty. I think this is more cleaner then. I also propose the following:

  • move all of the current Header.tex to proposal.sty
  • the paragraph styling is now like [parskip=full] of komascript. [parskip=half] which is the default of komascript will save space
  • the definition of \subparagraph{} will make new lines. Even a \paragraph{} usually does not.
  • \subparagraph{} and even ¸\paragraph{} (to be checked) has some space above itself, it can be reduced. Maybe a switch to quickly remove this when one gets in trouble of filling this 15 pages space?
  • define the DFG-Color als a color-code ready to be used in proposal.sty

If nothing stands against that, I will do this changes. Also some things which are defined in the single files dfg.tex and dfg-german.tex may come into this.

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