2-AIN-505, 2-AIN-251: Seminar in Bioinformatics (1), (3)
Winter 2021

Time and place:
Tuesday 17:20, I-23 or online
doc. Mgr. Tomáš Vinař, PhD M-163,
doc. Mgr. Broňa Brejová, PhD M-163,
The seminar starts on September 21 by the first presentation. The seminar will be in a hybrid form both in person and online at Google Meet.
List of presentations:
Alessia Petescia

Paola Bonizzoni, Clelia De Felice, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza. Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning. In AlCoB 2021: Algorithms for Computational Biology, 2021. link

Askar Gafurov

Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel. Viral population estimation using pyrosequencing. PLoS Comput Biol, 2008. link

Lukáš Kiss

Xuran Wang, Jihwan Park, Katalin Susztak, Nancy R. Zhang, Mingyao Li. Bulk tissue cell type deconvolution with multi-subject single-cell expressionreference. Nat Commun, 2019. link

13.10.2021 (Wednesday!)
Seminar link will be sent by email.

Vladimír Boža

Vladimír Boža, Peter Perešíni, Broňa Brejová, Tomáš Vinař. Dynamic Pooling Improves Nanopore Base Calling Accuracy. Technical Report https://arxiv.org/abs/2105.07520, arXiv, link

Peter Peresini, Vladimir Boza, Brona Brejova, Tomas Vinar. Nanopore Base Calling on the Edge. Bioinformatics, 2021. link

Jozef Sitarčík

Pay Giesselmann, Bjorn Brandl, Etienne Raimondeau, Rebecca Bowen, Christian Rohrandt, Rashmi Tandon, Helene Kretzmer, Gunter Assum, Christina Galonska, Reiner Siebert, Ole Ammerpohl, Andrew Heron, Susanne A. Schneider, Julia Ladewig, Philipp Koch, Bernhard M. Schuldt, James E. Graham, Alexander Meissner, Franz-Josef Muller. Analysis of short tandem repeat expansions and their methylation state withnanopore sequencing. Nature biotechnology, 2019. link

Matej Fedor

Omar Ahmed, Massimiliano Rossi, Sam Kovaka, Michael C. Schatz, Travis Gagie, Christina Boucher, Ben Langmead. Pan-genomic matching statistics for targeted nanopore sequencing. iScience, 2021. link

Filip Kerák

Dhaivat Joshi, Shunfu Mao, Sreeram Kannan, Suhas Diggavi. QAlign: aligning nanopore reads accurately using current-level modeling. Bioinformatics, 2021. link

Andrej Baláž

Jouni Sirén et al.. Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit. Technical Report 2020.12.04.412486, bioRxiv, 2021. link

Adrián Goga

Thomas Buchler, Caroline Rather, Pascal Weber, Enno Ohlebusch. Coordinate Systems for Pangenome Graphs based on the Level Function and Minimum Path Covers. In Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2021) - Volume 3: BIOINFORMATICS, pages 21-29, 2021. link

Eva Herencsárová

Nicholas J. Croucher, Andrew J. Page, Thomas R. Connor, Aidan J. Delaney, Jacqueline A. Keane, Stephen D. Bentley, Julian Parkhill, Simon R. Harris. Rapid phylogenetic analysis of large samples of recombinant bacterial wholegenome sequences using Gubbins. Nucleic acids research, 2015. link

seminár nebude
Veronika Tordová

Rafal Mostowy, Nicholas J. Croucher, Cheryl P. Andam, Jukka Corander, William P. Hanage, Pekka Marttinen. Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations. Molecular biology and evolution, 2017. link

Tomáš Jarábek

Xian Chang, Jordan Eizenga, Adam M. Novak, Jouni Siren, Benedict Paten. Distance indexing and seed clustering in sequence graphs. Bioinformatics, 2020. link