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

• Jouni Siren, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin. Haplotype-aware graph indexes. Bioinformatics, 36(2):400-407. 2020.
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• 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, pp. 63-76, 2020.
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• 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.
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• Mikko Rautiainen, Tobias Marschall. MBG: Minimizer-based Sparse de Bruijn Graph Construction. Technical Report doi:10.1101/2020.09.18.303156v1, bioRxiv, 2020.
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• 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, 10(1):5402. 2019.
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• Cynthia Maria Chibani, Anton Farr, Sandra Klama, Sascha Dietrich, Heiko Liesegang. Classifying the Unclassified: A Phage Classification Method. Viruses, 11(2). 2019.
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• Katelyn McNair, Carol Zhou, Elizabeth A. Dinsdale, Brian Souza, Robert A. Edwards. PHANOTATE: a novel approach to gene identification in phage genomes. Bioinformatics, 35(22):4537-4542. 2019.
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• 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, 37(12):1478-1481. 2019.
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• Yang Yang, Yang Zhang, Bing Ren, Jesse R. Dixon, Jian Ma. Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. Cell Syst, 8(6):494-505. 2019. Also at https://www.biorxiv.org/content/10.1101/552505v1.full-text.
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• Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A. Pevzner. Assembly of long, error-prone reads using repeat graphs. Nature biotechnology, 37(5):540-546. 2019.
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• 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, 16(1):88-94. 2019.
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• Egor Dolzhenko, Viraj Deshpande, Felix Schlesinger, Peter Krusche, Roman Petrovski, Sai Chen, Dorothea Emig-Agius, Andrew Gross, Giuseppe Narzisi, Brett Bowman, Konrad Scheffler, Joke J. F. A. {van Vugt}, Courtney French, Alba Sanchis-Juan, Kristina Ibanez, Arianna Tucci, Bryan Lajoie, Jan H. Veldink, F. Lucy Raymond, Ryan J. Taft, David R. Bentley, Michael A. Eberle. ExpansionHunter: A sequence-graph based tool to analyze variation in short tandemrepeat regions. Bioinformatics, 2019.
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• Rory Bowden, Robert W. Davies, Andreas Heger, Alistair T. Pagnamenta, Mariateresa {de Cesare}, Laura E. Oikkonen, Duncan Parkes, Colin Freeman, Fatima Dhalla, Smita Y. Patel, Niko Popitsch, Camilla L. C. Ip, Hannah E. Roberts, Silvia Salatino, Helen Lockstone, Gerton Lunter, Jenny C. Taylor, David Buck, Michael A. Simpson, Peter Donnelly. Sequencing of human genomes with nanopore technology. Nat Commun, 10(1):1869. 2019.
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• B. Llamas, G. Narzisi, V. Schneider, PA Audano, E Biederstedt, L Blauvelt, P Bradbury, X Chang, CS Chin, A Fungtammasan, WE Clarke et al. A strategy for building and using a human reference pangenome. F1000Research, 8:1751. 2019.
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• Zev N. Kronenberg, Ian T. Fiddes, David Gordon, Shwetha Murali, Stuart Cantsilieris, Olivia S. Meyerson, Jason G. Underwood, Bradley J. Nelson, Mark J. P. Chaisson, Max L. Dougherty, Katherine M. Munson, Alex R. Hastie, Mark Diekhans, Fereydoun Hormozdiari, Nicola Lorusso, Kendra Hoekzema, Ruolan Qiu, Karen Clark, Archana Raja, AnneMarie E. Welch, Melanie Sorensen, Carl Baker, Robert S. Fulton, Joel Armstrong, Tina A. Graves-Lindsay, Ahmet M. Denli, Emma R. Hoppe, PingHsun Hsieh, Christopher M. Hill, Andy Wing Chun Pang, Joyce Lee, Ernest T. Lam, Susan K. Dutcher, Fred H. Gage, Wesley C. Warren, Jay Shendure, David Haussler, Valerie A. Schneider, Han Cao, Mario Ventura, Richard K. Wilson, Benedict Paten, Alex Pollen, Evan E. Eichler. High-resolution comparative analysis of great ape genomes. Science, 360(6393). 2018.
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• 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, 49(11):1654-1660. 2017.
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• 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, 5(1):69. 2017.
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• Benjamin A. Logsdon, Jason Mezey. Gene expression network reconstruction by convex feature selection whenincorporating genetic perturbations. PLoS Comput Biol, 6(12):e1001014. 2010.
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