Software tools in Bioinformatics

Olga Zolotareva and Konstantinos Tzanakis
Seminar: Monday 10:00-12:00
Classroom: U10-146


In this seminar, students will choose, study and present one of the recent bioinformatic software tools published in peer-reviewed journals. The students are encouraged to suggest topics and tools of their interest or choose one of the following topics (shortlists of tools and a review article for topics will be provided):

  • Biclustering
  • Read Alignment
  • SNP Calling
  • Gene Expression Quantification
  • Gene Prioritization
  • Noise filtering and Baseline Correction
  • Peak detection
  • Peak alignment
  • Metabolite identification
  • Metabolomics data pre-treatment (normalization, scaling, transformation)
Topic Review Recommended tools
- Noise filtering and Baseline Correction
- Peak detection
- Metabolite identification
- Metabolomics data pre-treatment
(normalization, scaling, transformation)
Piasecka et al., 2019
Spicer et al., 2017
Lazar et al., 2015
OpenMs, XCMS, Workflow4Metabolomics, MeltDB, MetAlign
Peak alignment Lange et al., 2008 XCMS, OpenMs, MZmine
De novo transcriptome assembly Hölzer & Marz, 2019 Trinity, SPAdes
Read Mapping Canzar & Salzberg, 2015
Reinert et al., 2015
bwa, bowtie2, HISAT, STAR, GMAP
Single Nucleotide Variant Calling Xu 2018 VarScan2, Strelka, MuTect, DeepVariant
Expression Quantification and
differential expression analysis
Lowe et al., 2017
Finotello & Di Camillo, 2016
kallisto, limma-voom, DESeq2, EdgeR
Biclustering Pontes et al., 2015 QUBIC, DeBi, COALESCE, FABIA
Gene prioritization Zolotareva & Kleine 2019 Endeavour, PhenoRank, pBrit

The participants will give oral presentations (20-45 min’s, optimally about 25 min's) and prepare short summaries (5 to 10 pages) based on original research papers. In their reports, students must (i) briefly explain the problem solved by a selected tool (ii) describe the algorithm(s) implemented in this tool (iii) explain the choice of the tool among its analogs. At the end of the course, the students will peer-review their essays and revise them based on the received feedback.

Goals of the seminar

In this seminar students will develop skills necessary for:

  • independent reading and understanding of scientific texts (in English)
  • composition of a short written report (as a practice for the bachelor thesis)
  • oral presentation
  • peer-reviewing


Title Date
Preliminaries, topic selection (Kostas) 07.10.2019
Example presentation (Olga) 14.10.2019
Best Practices for Scientific Writing (Kostas) 21.10.2019
(preparing presentations) 28.10.2019
Jonas Waas - De novo transcriptome assembly, SPAdes 04.11.2019
Aya Bezine - Single Nucleotide Variant Calling, VarScan2 11.11.2019
Fabian Kolesch - Biclustering, QUBIC 18.11.2019
(preparing reports) 25.11.2019
(preparing reports) 02.12.2019
Lukas Schulte - Expression quantification and DE analysis,DeSeq2 16.12.2019
Submitting reports (1st version) 20.12.2019
Submitting reviews of essays 13.01.2020
Submitting revised essays 20.01.2020
teaching/2019winter/softwaretoolsinbioinformatics.txt · Last modified: 2019/12/16 09:56 by ktzanakis