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SYSTEMS MEDICINE / Human Immunology

+++ Open positions in the Schultze group in Bonn +++

 

We have several open, fully funded positions (Postdoc and PhD level) in the Schultze group and are looking for enthusiastic new colleagues to join our team!

We are an interdisciplinary group affiliated with the University of Bonn and the German Center for Neurodegenerative Diseases working in the field of systems medicine, genomics and immunoregulation encompassing wet lab work, sequencing, computation and bioinformatics.

We are applying omics techniques, esp. scRNA-seq, to study human immunology and are thriving to learn more about the molecular mechanisms governing health and disease with a focus on inflammation and inflammaging.

We are looking for passionately curious scientists with diverse backgrounds for wet lab, bioinformatic and computational projects.

More detailed information can be found here:
PhD (wet lab): bit.ly/2RmCRvY  

PhD (bioinfo): bit.ly/3s7B4aY
Postdoc (computational): bit.ly/2RqC7pD 


Deadline: Apr 30, 2021

viruses in silico | the EVBC lecture series

To keep you up to date with the latest developments in virus bioinformatics, especially new tools that might help you in your research, the European Virus Bioinformatics Center is organising a monthly lecture series entitled viruses in silico.

Upcoming lectures:
 
CIAlign, a tool to clean, interpret and visualise multiple sequence alignments, and its application to virus discovery.
26. April 2021 | 02-03 pm CEST
Dr. Katy Brown, Cambridge University, UK

Genomic surveillance of SARS-CoV-2 at the Robert Koch Institute: an overview and bioinformatics edge cases
17. Mai 2021 | 04-05 pm CEST
Dr. Martin Hölzer, Robert-Koch-Institute, Germany
The lectures take place online as Zoom Meetings. Participation is free.
Registration and further information via: http://evbc.uni-jena.de/events/viruses-in-silico/


Women in Bioinformatics: Prof. Dr. Nadine Ziemert, 18.05.21, 12:30

Are you interested in a scientific career as a woman in bioinformatics? But you have questions and worries regarding how to get there?

The online lecture series "Women in Bioinformatics" provides the answers. Successful female scientists present their research, their career path and answer your questions.

The series continues with

Prof. Dr. Nadine Ziemert

on 18.05.21 at 12:30-14:00.

Prof. Ziemert is professor for Natural Product Genome Mining at the University of Tübingen. Her work focuses on developing bioinformatic tools for the discovery of natural products from microbial genomes, elucidating the evolutionary history of their biosynthetic gene clusters and tracing their distribution in the environment.

Participation is free but registration is required for every talk. Registration starts 6 weeks before each talk.

Details and registration: https://www.bio.ifi.lmu.de/wib

Schedule:

27.04.21          12:30-14:00    Prof. Dr. Ina Koch

18.05.21          12:30-14:00    Prof. Dr. Nadine Ziemert

08.06.21          17:00-18:30    Prof. Dr. Kay Nieselt

29.06.21          16:00-17:30    Prof. Dr. Birte Kehr

20.07.21          12:30-14:00    Prof. Dr. Sabine Fischer

For further updates register for our Newsletter: https://lists.lrz.de/mailman/listinfo/wbioinformatics

Follow us on Twitter: https://twitter.com/WBioinformatics

 

 

5th Berlin Summer School 2021

  • Learn the essential computing skills for NGS bioinformatics
  • Understand NGS analysis algorithms (e.g. read alignment) and data formats
  • Use bioinformatics tools for handling NGS data
  • Perform first downstream analyses for studying genetic variation
  • Compare different approaches for differential expression analysis

The purpose of this intense one week summer course is to get a deep understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. You will be trained on understanding NGS data formats and handling potential problems/errors therein. In the summer school we will use a real-life RNA-seq dataset from the current market leader illumina.

All students will be enabled to perform important first tasks of NGS data analysis themselves. The layout of the summer school has been adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this new and fast evolving research topic.

In the evenings there will be social events, like a conference dinner, or a guided city tour through Berlin. These are always great networking possibilities.

Link: https://www.ecseq.com/workshops/workshop_2021-01-5th-Berlin-Summer-School-NGS-Data-Analysis

Bioinformatics Pipeline Development with Nextflow [May 3-6, 2021]

Streamline your research through the development of reproducible analysis pipelines

In a nutshell

  • Learn the fundamental best-practices of bioinformatic pipeline development
  • Understand how workflow management systems can accelerate your research
  • Use state-of-the-art, open source software to make complex analyses routine
  • Perform your own custom analysis pipelines using Nextflow

The purpose of the workshop is to introduce the concepts of bioinformatic pipeline development through the context of the open source Workflow Management System (WMS) Nextflow. The participants will be trained in the scripting, configuration and execution of example analysis pipelines based on current industry best-practices, and learn how to share them with other users. Finally, the participants will apply everything they have learned by implementing their own analysis pipelines from the ground up.

By the end of the workshop all attendees will be enabled to build their own scalable, reproducible bioinformatic pipelines which can be run locally, on high-performance computing clusters or even in the cloud. The course layout has been adapted to the needs of beginners in the field of computational biology and allows scientists with little or no background in software development to get a first hands-on experience in this new and fast-evolving area of expertise. This instructor-led live online workshop has been newly designed for an engaging, interactive online learning experience.

DNA Methylation Data Analysis Workshop [April 12-15, 2021]

Advance your epigenetics research with NGS methods.

In a nutshell

  • Learn how bisulfite sequencing works
  • Understand how bisulfite-treated reads are mapped to a reference genome
  • Perform basic analyses (call methylated regions, perform basic downstream analyses)
  • Use shell scripting to create reusable data pipelines
  • Visualize results (ready-to-publish)

The purpose of this workshop is to get a deeper understanding of the use of bisulfite-treated DNA in order to analyze the epigenetic layer of DNA methylation. Advantages and disadvantages of the so-called 'bisulfite sequencing' and its implications on data analyses will be covered. The participants will be trained to understand bisulfite-treated NGS data, to detect potential problems/errors and finally to implement their own pipelines. After this course they will be able to analyze DNA methylation and create ready-to-publish graphics.

By the end of this workshop the participants will:

  • be familiar with the sequencing method of Illumina
  • understand how bisulfite sequencing works
  • be aware of the mapping problem of bisulfite-treated data
  • understand how bisulfite-treated reads are mapped to a reference genome
  • be familiar with common data formats and standards
  • know relevant tools for data processing
  • automate tasks with shell scripting to create reusable data pipelines
  • perform basic analyses (call methylated regions, perform basic downstream analyses)
  • plot and visualize results (ready-to-publish)
  • be able to reuse all analyses

Link: https://www.ecseq.com/workshops/workshop_2021-04-NGS-DNA-Methylation-Data-Analysis

Online Course - A Practical Introduction to NGS Data Analysis [March 1-3, 2021]

Advance your research. Understand NGS and analyze sequenced data yourself.
In a nutshell

  •     Learn the essential computing skills for NGS bioinformatics
  •     Understand NGS technology, algorithms and data formats
  •     Use bioinformatics tools for handling sequencing data
  •     Perform first downstream analyses for studying genetic variation

The purpose of this workshop is to get a deeper understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. The participants will be trained on understanding their own NGS data, finding potential problems/errors therein and finally perform their first downstream analysis (variant calling). In the course we will use a real-life NGS dataset from the current market leader illumina.

All workshop attendees will be enabled to perform important first tasks of NGS data analysis themselves. The course layout has been adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this fast evolving research topic.

The online course will make use of a web conferencing system. Hands-on NGS analysis will be performed in an interactive browser-based data analysis platform. Before the course, you will get a printed manuscript.

 



DNA Methylation Data Analysis Workshop [2.-5. November 2020]

The purpose of this workshop is to get a deeper understanding of the use of bisulfite-treated DNA in order to analyze the epigenetic layer of DNA methylation. Advantages and disadvantages of the so-called 'bisulfite sequencing' and its implications on data analyses will be covered. The participants will be trained to understand bisulfite-treated NGS data, to detect potential problems/errors and finally to implement their own pipelines. After this course they will be able to analyze DNA methylation and create ready-to-publish graphics.

By the end of this workshop the participants will:

  •     be familiar with the sequencing method of Illumina
  •     understand how bisulfite sequencing works
  •     be aware of the mapping problem of bisulfite-treated data
  •     understand how bisulfite-treated reads are mapped to a reference genome
  •     be familiar with common data formats and standards
  •     know relevant tools for data processing
  •     automate tasks with shell scripting to create reusable data pipelines
  •     perform basic analyses (call methylated regions, perform basic downstream analyses)
  •     plot and visualize results (ready-to-publish)
  •     be able to reuse all analyses


Links: https://www.ecseq.com/workshops/workshop_2020-06-NGS-DNA-Methylation-Data-Analysis

 

Online Course - A Practical Introduction to NGS Data Analysis [9. - 11. Dezember 2020]

The purpose of this workshop is to get a deeper understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. The participants will be trained on understanding their own NGS data, finding potential problems/errors therein and finally perform their first downstream analysis (variant calling). In the course we will use a real-life NGS dataset from the current market leader illumina.

All workshop attendees will be enabled to perform important first tasks of NGS data analysis themselves. The course layout has been adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this fast evolving research topic.

The online course will make use of a web conferencing system. Hands-on NGS analysis will be performed in an interactive browser-based platform. Before the course, you will get a printed manuscript and a USB key by mail.

Links: https://www.ecseq.com/workshops/workshop_2020-07-A-Practical-Introduction-to-NGS-Data-Analysis-Online-Course

Online Course - A Practical Introduction to NGS Data Analysis [14. - 16. Oktober 2020]

The purpose of this workshop is to get a deeper understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. The participants will be trained on understanding their own NGS data, finding potential problems/errors therein and finally perform their first downstream analysis (variant calling). In the course we will use a real-life NGS dataset from the current market leader illumina.

All workshop attendees will be enabled to perform important first tasks of NGS data analysis themselves. The course layout has been adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this fast evolving research topic.

The online course will make use of a web conferencing system. Hands-on NGS analysis will be performed in an interactive browser-based platform. Before the course, you will get a printed manuscript and a USB key by mail.

Links: https://www.ecseq.com/workshops/workshop_2020-05-A-Practical-Introduction-to-NGS-Data-Analysis-Online-Course.html

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