The theme of this semester is “New frontiers in sequencing technology” and “Algorithmic advances in bioinformatics”. Please join us for the talks below , either in person (room A319, FI MU) or using the MSTeams platform. Click on the title of the talk below to access the virtual room. Contact lexa @ fi.muni.cz for additional information.

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20.9. 4 PM

FI MU
Introduction to the seminar

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27.9. 4 PM

Invited Talk (FI)
Monika Cechova
UCSC, USA
Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance
Dr. Cechova is a FI alumnus and an author of a groundbreaking study resulting in the first complete sequence of the human Y chromosome, see a recent Pop Mech opinion piece

Multi-generational pedigrees offer an opportunity to study transgenerational inheritance, including in biologically critical regions that are highly repetitive and are copy number variable within the population. Here, we present work aimed to release complete, T2T diploid assemblies of four individuals, representing a three-generational pedigree of African-American ancestry. To reach this goal, we utilize a combination of high-coverage, long-read (averaging 51x HiFi, PacBio, and 71x Nanopore Ultra-long data 100kb+, Oxford Nanopore Technologies) and short-read paired technologies for haplotype phasing (averaging including 76x coverage Omni-C, Cantata Genomics, 39x paired read parental data for trio-based phasing, as well as Strand-seq and Pore-C data). The use of two iterative, graph-based methods with ONT-UL integration—Verkko (Rautiainen et al. 2023) and hifiasm-UL (Cheng et al. 2022)—revealed a large number (e.g. 22/46) of automated telomere-to-telomere (T2T) chromosome assemblies, with additional improvements in finishing with the two assembly methods combined. As expected, breakpoints in automated assemblies were enriched for highly repetitive regions, such as segmental duplications, centromeric satellite DNAs, and repeat classes across the acrocentric short arms. A study of these assemblies allowed us to predict shared haplotypes and sites of meiotic exchange. We identified a subset of inconsistent breakpoints across shared haplotypes between family members, allowing us to explore methods to further automate T2T genomes using pedigree-pangenomes or leveraging the shared haplotype information from one family member to finalize the assembly in another.

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4.10. 4 PM

Invited Talk (CEITEC)
Brona Brejova
Comenius University, Bratislava
Use of graph representations in pangenomics and plasmid detection

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11.10. 4 PM

Invited Talk (FI)
Jan Kotrs
DNA Nexus, Brno (also FI alumnus) The current state of bioinformatics industry

Jan will talk about his path that brought him to DNAnexus, what bioinformatics skills are relevant inside the company, and what other entities are active in the Czech market, possibly beyond.

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15.11. 4 PM

Invited Talk (CEITEC)
Adam Krejci
Myllia, Vienna, Austria
Pooled CRISPR screens with single-cell readout - applications & challenges

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29.11. 4 PM

Invited Talk (CEITEC)
Jan Oppelt
!! CANCELLED !!
Title

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13.12. 4 PM

Invited Talk or Student Presentation
Vlastimil Martinek CEITEC
Predicting RNA decay with artificial neural networks

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