2-AIN-506 a 2-AIN-252: Seminár z bioinformatiky (2) a (4)
Leto 2020
Zoznam článkov
- Sophie Rohling, Alexander Linne, Jendrik Schellhorn, Morteza Hosseini, Thomas Dencker, Burkhard Morgenstern.
The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances.
PLoS One,
15(2):e0228070.
2020.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Zhenchang Liang, Shengchang Duan, Jun Sheng, Shusheng Zhu, Xuemei Ni, Jianhui Shao, Chonghuai Liu, Peter Nick, Fei Du, Peige Fan, Ruzhi Mao, Yifan Zhu, Weiping Deng, Min Yang, Huichuan Huang, Yixiang Liu, Yiqing Ding, Xianju Liu, Jianfu Jiang, Youyong Zhu, Shaohua Li, Xiahong He, Wei Chen, Yang Dong.
Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses.
Nat Commun,
10(1):1190.
2019.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- 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.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- 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.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- David C. Danko, Dmitry Meleshko, Daniela Bezdan, Christopher Mason, Iman Hajirasouliha.
Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads formetagenomics.
Genome research,
29(1):116-124.
2019.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Mohammed AlQuraishi.
AlphaFold at CASP13.
Bioinformatics,
35(22):4862-4865.
2019.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- 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.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- 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.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- 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.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Mohammed AlQuraishi.
End-to-End Differentiable Learning of Protein Structure.
Cell Syst,
8(4):292-301.
2019.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- 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.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Pavel Sagulenko, Vadim Puller, Richard A. Neher.
TreeTime: Maximum-likelihood phylodynamic analysis.
Virus Evol,
4(1):vex042.
2018.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- James Hadfield, Colin Megill, Sidney M. Bell, John Huddleston, Barney Potter, Charlton Callender, Pavel Sagulenko, Trevor Bedford, Richard A. Neher.
Nextstrain: real-time tracking of pathogen evolution.
Bioinformatics,
34(23):4121-4123.
2018.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- 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.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Tanja Stadler, Denise Kuhnert, Sebastian Bonhoeffer, Alexei J. Drummond.
Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV).
Proceedings of the National Academy of Sciences of the United States of America,
110(1):228-233.
2013.
The website links to a blog post applying this method to SARS-CoV-2.
[ Abstract ] [ Download from publisher ] [ Webpage ] [ BibTeX ] [ PubMed ]
