Bioinformatics Journal Club
Due to the Covid-19 outbreak the journal club is suspended until further notice.
We help run a biweekly gathering of bioinformaticians on Mondays 16:00 at the meeting room on the 2nd floor at Institute of Molecular Genetics at Krč (we setup signs to make it easy to find). The presentation/discussion takes about an hour and some informal chat follows. Everybody is welcome to come. If you have a paper you want to share, you are also welcome. In any case, contact Martin Modrák (This email address is being protected from spambots. You need JavaScript enabled to view it.) for further details.
Upcoming sessions
- ??, 16:00 Vojtěch Tláskal (MBU CAS), Bacterial taxonomy and the tree of life
- ??, 16:00 Pavel Abaffy (IBT CAS), Martin Modrák (MBU CAS), Bulk RNA-seq deconvolution using single-cell reference
Past Sessions
Fall '19 - Spring '20
- Jun 22th, (virtual) Martin Modrák (MBU CAS), scVelo: Trajectory inference from single-cell RNA-seq, Video recording
- Mar 9th, 16:00 Petra Svatoňová (IMG CAS), False discovery rates: a new deal
- Feb 24th, 16:00 Veronika Niederlová (IMG CAS), Detection of doublets in scRNA-seq data: Veronika's slides; DoubletDecon, scds, DoubletFinder
- Feb 10th, 16:00 Daniel Morais (MBU CAS), Protax-fungi: fungal taxonomic placement
- Jan 27th, 16:00 Tijana Martinovic (MBU CAS), How choice of pipeline affects metagenomic analysis
- Jan 13th, 16:00 Marek Schwarz, (MBU CAS), Finding gapped binding motifs
- Dec 2nd, 16:00 Martin Modrák, (MBU CAS), Science and statistics
- Nov 18th, 16:00 Jan Kubovčiak, Juraj Michálik (IMG CAS), Lessons learned from single-cell RNA-seq workshop
- Nov 4th, 16:00 Michal Kolář (IMG CAS), Applied single-cell transcriptomics in head and neck cancer
Fall '18 - Spring '19
- May 21st, 16:30 Tijana Martinovic (MBU CAS), Correcting for protocol bias in metagenomic data
- May 7th, 16:30 Jochen Krattenmacher (IBT CAS), A free energy principle for the brain
- Apr 23rd, 16:30 Tatyana Kobets (IMG CAS), Selecting a ChIP-seq peak caller
- Apr 9th, 16:30 Iñaki Odriozola (MBU CAS), Dissimilarity coefficients and analysis of beta-diversity.
- Mar 26th, 16:30 Problem solving session vol I, Josef Pasulka and his RNA-seq
- Mar 12th, 16:30 Martin Modrák (MBU CAS), Compositional Data Analysis is necessary for simulating and analyzing RNA-Seq data (version with figures embedded in text here)
- Feb 26th, 16:30 Tijana Martinovic (MBU CAS), Rarefying microbiome data prior to analysis: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
- Feb 14h, 16:30, Michal Kolář (IMG CAS), A comprehensive comparison of tools for differential ChIP-seq analysis
- Jan 31st, 16:30, Daniel Morais (MBU CAS), Microbiome surveys with amplicon sequencing - should we normalize by 16S?
- Jan 17th, 15:30, Marek Schwarz (MBU CAS), False-positives in ChIP-Seq
- Nov 8th, 15:30 Martin Modrák (MBU CAS), How to handle semi-arbitrary choices in data analysis: Increasing Transparency Through a Multiverse Analysis
- Oct 25th, 15:30, Jiří Novotný (IMG CAS), sequencing of T cell–receptors and subsequent analysis with focus on MIGEC
Fall '17 - Spring '18
- Jun 21st, 15:30, Why most published research findings are false, Martin Modrák (MBU CAS) Season Finale!
- May 10th, A communal catalogue reveals Earth's multiscale microbial diversity, Daniel Morais (MBU CAS)
- Apr 12th, Statistics, p-values, their misinterpretation with examples in differential expression (DESeq2), loosely inspired by Measurement error and the replication crisis, slides, code for simulations, Martin Modrák (MBU CAS)
- Mar 15th, Computing energy landscape maps and structural excursions of proteins, Emanuel Karl Peter (IBT, BIOCEV)
- Mar 1st, Nextflow: building workflows for bioinformatics. An example RNA-seq pipeline, Jan Kubovčiak (IMG CAS)
- Feb 15th, Digital normalization for genome assembly and its limitations, Tomáš Větrovský (MBU CAS)
- Feb 1st, t-SNE - dimensionality reduction and its pitfalls, Michal Kolář (IMG CAS)
- Jan 18th, R-Scape - determining evolutionary support for RNA structures, Marek Schwarz (MBU CAS)
- Jan 4th, Salmon - RNA-seq quantification and pseudoalignment, Martin Modrák (MBU CAS)
- Dec 7th, DADA2 - analysing amplicon metagenomic data , Daniel Morais (MBU CAS)
