Courses and Workshops

We organize and teach courses aimed at beginners, as well as those who are more advanced in bioinformatic analyses. Course subjects are related to various aspects of bioinformatics, mostly connected with next generation sequencing (NGS) data analysis. We also offer courses focused on statistic analysis in R and on programming. Our courses will inform you about the current state of knowledge in particular topics, let you practice individually discussed issues, and help you become more familiar with nomenclature.

Currently we offer the following courses

• Introduction to NGS Processing and Analysis of NGS Data
• NGS in Gene Regulation Studies
• Introduction to RNA-Seq Data Analysis
• Basics of Bioinformatics
• Do it yourself! Practical Approaches to Molecular Data Analysis
• Fundamentals of Programming in Python
• Programming for Biologists in Python
• Building Biological Databases and Websites
• Biological Data Analysis and Visualization in R
• Introduction to Genomics Data Analysis in R
• Environmental Biology. Biological Data Analysis in R
• Basics of Machine Learning

Our courses usually last one, two, or&nbp;three days. We&nbp;offer mostly practical hands-on courses with some elements of&nbp;lectures organized in&nbp;computer classrooms, usually from 9.00&nbp;a.m. till 5.00&nbp;p.m. (including coffee and lunch breaks). Teaching materials, computers with appropriate software, catering, and certificates of&nbp;attendance are&nbp;provided and&nbp;included in&nbp;the registration fee.

We also co-organize an event called Poznan Summer School of Bioinformatics

It&nbp;is&nbp;worth mentioning that we&nbp;are&nbp;open for&nbp;any&nbp;other suggestions and propositions and we&nbp;do&nbp;our best to&nbp;find proper topics and&nbp;courses to&nbp;fulfill your needs. We also organize courses outside of&nbp;Poznań, at&nbp;your location. Please feel free to&nbp;contact&nbp;us.

NGS (next-generation sequencing) data analysis

Data quality control, processing and filtering

RNA-Seq

• Gene and transcript expression estimation
• Differential expression analysis
• Ab initio transcriptome assembly (genome-based) and annotation; detection of novel genes and splicing isoforms
• De novo transcriptome assembly (genome-independent) and annotation

Small RNA Analysis

• Identification of miRNAs and phased siRNAs
• Quantification and differential expression
• IsomiR and miRNA editing analysis
• Degradome-Seq data processing
• Identification of sRNA targets
• Data upload to miRBase

Genome Variants Calling

• SNPs, small INDELs, structural variants
• Germline and somatic alterations (e.g. tumor vs normal tissue)
• Whole Genome Sequencing (WGS), Exome-Seq, targeted sequencing

De novo genome assembly and annotation

ChIP-Seq: Pol II, histone modifications

Data upload to NGS databases (Sequence Read Archive, Gene Expression Omnibus)

Setting up stand-alone (IGV) and online (JBrowse) genome browsers

Genome annotation

Automated annotation of prokaryotic and eukaryotic genomes

Genome annotation with RNA-Seq data

Identification of non-coding RNAs (long non-coding RNAs, microRNAs and other ncRNAs)

Identification of repetitive elements

Setting up stand-alone (IGV) and online (JBrowse) genome browsers

Building online databases with genomic and transcriptomic data

Other

Manipulating customers' large-scale data

Sequence- and HMM-based database searches

Customized data analysis with Python

Data analysis in Bioconductor (R environment)

Building analytical pipelines

Primer design

And even more: ask us!