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