Bioinformatics Core Facility

Bioinformatics Core Facility

The aim of the Bioinformatics Core Facility is to assist wet-lab researchers in our institute for their bioinformatics data analysis. Our facility is tightly embedded in the Computational Systems Biochemistry and works in close contact with the researchers at the Max-Planck Institute of Biochemistry and Neurobiology. These close links ensure that our services remain state-of-the-art, not only by keeping up with novel developments in the field, but also by offering bioinformatics assistance that goes beyond publicly available analysis methods.

One-day Workshop on<br />Computational Mass Spectrometry-based Proteomics

One-day Workshop on
Computational Mass Spectrometry-based Proteomics

29 April 2020, Munich
Max-Planck-Institute of Biochemistry, Deutschland

We will soon provide more details

How to contact us?



Service

Our Bioinformatics core facility has several tasks to help the researchers at the Max-Planck Institute of Biochemistry and Neurobiology:

  • Preliminary discussion about experimental design together with other core facilities, such as sequencing facility. This crucial step assures to obtain high quality results from your projects.
  • Consultation for the bioinformatics methods, available computational tools and statistical data analysis
  • Preparation of data sets to submit in public repositories, such as PRIDE, GEO or SRA, as requested by many journals upon manuscript submission
  • Provide bioinformatics trainings

Some selected topics from our bioinformatics core facility:

Genomics
Next-Generation sequencing (NGS) data analysis
Comparative genomics
Combining chromatin immunoprecipitation assays with sequencing (ChIP-seq)
Whole genome sequencing (WGS)

Metabolomics

Proteomics

Shot-gun proteomics analysis (both identification and quantification)
De novo sequencing
Chemical crosslinking combined with mass spectrometry
Proteogenomics
Protein-protein interactions
Ion-mobility mass spectrometry data analysis
Multiple sequence alignment
Alternative splicing
Protein functional annotation and prediction
Pathway enrichment analysis

Phylogenetic analysis
Motif search
Sequence similarities (BLAST)

Transcriptomics

Single cell transcriptomics
RNA-seq for mRNA, or long non-coding RNA
tRNA-Seq
Ribosome profiling
RNAi screening
Single guide RNA for CRISPR

Multi-omics

 



Courses

We are organizing a one-day workshop on Computational Mass Spectrometry-based Proteomics that includes hands-on training on how to run MaxQuant and Persesus on the 29th of April, 2020. The further details will be posted here.


Useful Links

You can find some links for several useful links about Bioinformatics and programming.

Protein structure visualization, prediction & analysis PyMol, UCSF-Chimera, HADDOCK, I-TASSER
Genomics

lENCODE, UCSC genome browser

Programming tutorials

learn programming: R, R studio python and documentation for python 2.7, python 3.7.1and jupyter

Johns Hopkins Data Science Lab: courses, books

programming exercises: coding-bat for python or coding-bat for java

Annual MaxQuant summer school the largest workshop in computational proteomics, details and how to register here
Proteomics analysis MaxQuant, Perseus
Databases GEO, DAVID, HumanProteinAtlas Uniprot, Ensembl
Public repositories PRIDE, ProteomeXchange Consortium
Statistics Bioconductor, Perseus

 

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