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 (Tato e-mailová adresa je chráněna před spamboty. Pro její zobrazení musíte mít povolen Javascript.) 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)
