---
title: "IV106 Bionformatics seminar"
date: 2023-02-07T16:00:00+02:00
type: post
categories:
- Teaching
tags:
- talk
- seminar
- interdisciplinarity
draft: false
thumbnail: https://gitlab.fi.muni.cz/bioinf/bioinf.pages.fi.muni.cz/-/raw/master/images/A319.png

---

There is no specific theme for this semester, so anything that falls within the broader definition of Bioinformatics goes. We will be sharing several guests with a "sister seminar" at CEITEC, described here:

*The Bioinformatics Seminar is a seminar series organized together with the Faculty of Informatics in the interdisciplinary fields of Bioinformatics, Biostatistics, and Computational Biology. The seminar series aims to invite exciting speakers working on the current state-of-the-art bioinformatics problems. The goal is to broaden bioinformatics knowledge for scientists and students and promote mutual connections and interactions between bioinformaticians at MU. The seminars are held alternately at the CEITEC MU (E35/211) and FI MU (A319) and also streamed online every other Wednesday from 16:00.*

*Link to [CEITEC Bioinformatics Seminar webpage](https://www.ceitec.eu/bioinformatics-seminar-series/)*

Please join us for the talks below, either in person or using the MSTeams platform (click on the title). All times are Central European (Prague, Vienna, Budapest). Please, note, that not all seminars will be held jointly. Contact lexa @ fi.muni.cz or vojtech.bystry @ ceitec.muni.cz for additional information. 

#### 15.2. 4 PM
FI MU  
Introduction to the seminar  
**Students Only**  

#### 22.2. 4 PM
Invited Talk  
**Matej Trojak, Sybila, FI MU**  
*In systems biology, models play a crucial role in understanding studied systems. There are many modelling approaches, among which a rule-based framework provides a way for describing systems in a concise and understandable form. In this talk, the speaker will explain the key principles employed by the rule-based approach. It will be demonstrated using the so-called Biochemical Space Language, a representative of the languages with rule-based features. The talk will also include a brief demonstration of eBCSgen, a software tool to support modelling and analysis using BCSL, integrated within the Galaxy framework.*  
**[Biochemical Space Language: a rule-based modelling formalism for describing biochemical processes](https://is.muni.cz/go/online-vyuka-i2at1u)**

#### 1.3. 4 PM
Invited Talk  
**Sung won Lim, Binomica Labs, New York, USA**  
*SWL is an amateur researcher located in New York City, working with a small research group of like-minded independent researchers called [Binomica Labs](https://binomicalabs.org/). A warehouse worker with no formal academic training, he's sequenced and assembled a number of microbial genomes, including first complete genome of Deinococcus radiophilus and first genome of Halococcus dombrowskii, revealing another genus of Haloarchaea containing plasmid-carried rRNA operons. He's currently collaborating with a number of biology labs on different projects, focusing on microbial phylogeny and phage biology.*  
**[Independent research circa 2023; an amateur biology perspective](https://is.muni.cz/go/online-vyuka-9lhlcm)**  

#### 8.3. 4 PM
Invited Talk (CEITEC)  
**dr.Petr Simecek, Bioinformatics Core Facility, CEITEC MU**  
*The field of natural language processing (NLP) has undergone a significant transformation with the emergence of large language models, such as GPT3.5, OPT, and BLOOM. More recently, similar neural network architectures have been adapted to genomics and proteomics, paving the way for exciting developments in these domains.
During this presentation, we will examine the current protein language models, such as ProtDistillBert, ProtBertBFD, and ESM2, and illustrate how to fine-tune them to suit specific tasks. Moreover, we will elucidate how protein embeddings encapsulate both evolutionary and functional information.
To conclude, we will showcase this methodology on the problem of detection of knotted proteins, i.e. proteins whose backbones are intricately tangled in knots. To be specific, we will classify knotted proteins based solely on their protein sequence.*  
**[Could we have ChatGPT for proteins?](https://is.muni.cz/go/online-vyuka-4aundz)**  

#### 15.3. 4 PM
Invited Talk  
**dr.Karel Sedlář, Institut für Informatik, Ludwig-Maximilians-University of Munich, Germany**  
*White biotechnology, i.e., a technology that uses living cells to synthesize easily degradable products, is the key to the transition from a linear oil-based to a circular bio-based economy. Suitable microbes are selected by their potential functional capacity revealed by computational analyses of their genomes. Nevertheless, bioinformatics analyses of non-model organisms are specific because many computational tools require the use of datasets that are unavailable for novel bacteria due to non-existing microbiological kits to perform desired experiments or simply due to missing knowledge of required input data. As there are hundreds of computational tools and packages to perform various kinds of bioinformatics analyses providing different results, their combination is usually needed to infer novel knowledge. In this talk, we’ll go through some basic steps in analyses of bacterial genomes, we’ll show how to combine multiple tools, and we’ll try to adjust current methods to datasets they were not originally designed for.*  
**[Computational Analyses and Functional Annotations of Non-Model Bacteria for White Biotechnology](https://is.muni.cz/go/online-vyuka-iycohs)**  

#### 22.3. 4 PM
FI MU Journal Club.  
Guman, Kubin+Olajec 
**Student presentations (Students Only)**  

#### 29.3. 4 PM
Invited Talk (CEITEC)  
**Tomáš Pluskal, IOCB Prague**  
*Although plants are an incredibly rich source of pharmaceutically relevant specialized
metabolites, biosynthetic pathway elucidation in plants has proven challenging. Unlike bacteria
and many fungal species that contain biosynthetic operons, the genes of a given plant typically
scatter randomly across the genome, making pathway discovery via genome mining nearly
impossible. My lab is developing generalized workflows for connecting biosynthetic gene
sequences (RNAseq data) to their downstream metabolites (LC-MS data). For this, I will
demonstrate a top-down approach, which is based on correlating expression levels of enzymes
with metabolite abundance across a plant family, and a bottom-up approach, which is based on
predicting the substrate specificity and function of individual biosynthetic enzymes directly
from their sequences using deep learning.*  
**[Decoding the chemical language of plants](https://is.muni.cz/go/online-vyuka-j96b47)**  

#### 5.4. 4 PM
Invited Talk  
**Jordan M Eizenga, University of Santa Cruz, Genomics Institute, USA**  
*Many bioinformatics pipelines crucially depend on a reference genome: an assembly that stands in for the genome of a species. However, due to genomic variation, there is a limit to how well a single assembly can represent an entire species. This introduces a pervasive reference bias where analyses become less accurate whenever a sample's genome differs from the reference. The field of pangenomics has emerged to combat this bias, mostly by using sequence graphs that incorporate genomic variation as an alternative to conventional reference genomes. This talk will survey some of the recent developments in human pangenomics, including the Human Pangenome Reference Consortium's creation of high-quality pangenome data resources. It will also discuss some of the applications of pangenomes, with an emphasis on the presenter's research into pantranscriptomics: methods that incorporate pangenomic techniques into transcriptomic analyses.*  
**[Sequence graph methods for the analysis of the human pangenome and pantranscriptome](https://is.muni.cz/go/online-vyuka-piwugq)**  

#### 12.4. 4 PM
FI MU Journal Club.  
Michalik+Sloup, Sramkova+Slany  
**Student presentations (Students Only)**  

#### 19.4. 4 PM
FI MU Journal Club.  
Melus+Varga, Charpentier+Lostak  
**Student presentations (Students Only)**  

#### 26.4. 4 PM
Invited Talk (CEITEC)  
**!!CANCELLED!! Adam Krejčí, Myllia Biotechnology, Vienna, Austria**  
**  
**Pooled CRISPR screens with single-cell readout - applications & challenges**  

#### 3.5. 4 PM
FI MU Journal Club.  
Kadasi+Pavlik, Ratajik  
**Student presentations (Students Only)**  

#### 10.5. 4 PM
Invited Talk  
**Monika Cechova, FI MUNI, currently University of Santa Cruz, Genomics Institute, USA**  
**  
**[TBA](https://is.muni.cz/go/online-vyuka-mz4xw9)**  

#### 17.5. 4 PM
Invited Talk (CEITEC)  
**Karolína Trachtová, Christian Doppler Laboratory for Applied Metabolomics, Medical University of Vienna**  
*TBD*  
**[TITLE](https://is.muni.cz/go/online-vyuka-kr03sz)**  

