2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2020
Rozvrh

Seminár:
Utorok 17:20, M-VIII
Vyučujúci:
doc. Mgr. Tomáš Vinař, PhD	M-163,

doc. Mgr. Broňa Brejová, PhD	M-163,

Oznamy:
Seminár začína 22.9.2020 prvou prezentáciou. Semináre budú prebiehať online na linke https://meet.google.com/czn-mpfg-ipx
Zoznam prezentácií:

22.9.2020 Tomáš Vinař	Mikko Rautiainen, Tobias Marschall. MBG: Minimizer-based Sparse de Bruijn Graph Construction. Technical Report doi:10.1101/2020.09.18.303156v1, bioRxiv, 2020. link
29.9.2020 Aďo Goga	Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A. Pevzner. Assembly of long, error-prone reads using repeat graphs. Nature biotechnology, 2019. link
6.10.2020 Dominika Szabová	Mitchell R. Vollger, Philip C. Dishuck, Melanie Sorensen, AnneMarie E. Welch, Vy Dang, Max L. Dougherty, Tina A. Graves-Lindsay, Richard K. Wilson, Mark J. P. Chaisson, Evan E. Eichler. Long-read sequence and assembly of segmental duplications. Nature methods, 2019. link
13.10.2020 Askar Gafurov	Robert C. Edgar. Syncmers are more sensitive than minimizers for selecting conserved k-mers in biological sequences. Technical Report doi:10.1101/2020.09.29.319095, bioRxiv, 2020. link
20.10.2020 Peter Perešíni	Hannah Brown, Lei Zuo, Dan Gusfield. Comparing Integer Linear Programming to SAT-Solving for Hard Problems in Computational and Systems Biology. In AlCoB 2020: Algorithms for Computational Biology, 2020. link
27.10.2020 Samo Molčan	Benjamin A. Logsdon, Jason Mezey. Gene expression network reconstruction by convex feature selection whenincorporating genetic perturbations. PLoS Comput Biol, 2010. link
3.11.2020 Dominika Mihálová	Katelyn McNair, Carol Zhou, Elizabeth A. Dinsdale, Brian Souza, Robert A. Edwards. PHANOTATE: a novel approach to gene identification in phage genomes. Bioinformatics, 2019. link
10.11.2020 Andrej Baláž	Jie Ren, Nathan A. Ahlgren, Yang Young Lu, Jed A. Fuhrman, Fengzhu Sun. VirFinder: a novel k-mer based tool for identifying viral sequences fromassembled metagenomic data. Microbiome, 2017. link
17.11.2020 seminár nebude
24.11.2020 Lukáš Kiss	Cynthia Maria Chibani, Anton Farr, Sandra Klama, Sascha Dietrich, Heiko Liesegang. Classifying the Unclassified: A Phage Classification Method. Viruses, 2019. link
1.12.2020 Tomáš Jarábek	Jordan M Eizenga, Adam M Novak, Emily Kobayashi, Flavia Villani, Cecilia Cisar, Simon Heumos, Glenn Hickey, Vincenza Colonna, Benedict Paten, Erik Garrison. Efficient dynamic variation graphs. link
8.12.2020 Jozef Sitarčík	Jouni Siren, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin. Haplotype-aware graph indexes. Bioinformatics, 2020. link
15.12.2020 Broňa Brejová	Hannes P. Eggertsson, Snaedis Kristmundsdottir, Doruk Beyter, Hakon Jonsson, Astros Skuladottir, Marteinn T. Hardarson, Daniel F. Gudbjartsson, Kari Stefansson, Bjarni V. Halldorsson, Pall Melsted. GraphTyper2 enables population-scale genotyping of structural variation usingpangenome graphs. Nat Commun, 2019. link Hannes P. Eggertsson, Hakon Jonsson, Snaedis Kristmundsdottir, Eirikur Hjartarson, Birte Kehr, Gisli Masson, Florian Zink, Kristjan E. Hjorleifsson, Aslaug Jonasdottir, Adalbjorg Jonasdottir, Ingileif Jonsdottir, Daniel F. Gudbjartsson, Pall Melsted, Kari Stefansson, Bjarni V. Halldorsson. Graphtyper enables population-scale genotyping using pangenome graphs. Nature genetics, 2017. link