2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2019
Zoznam článkov
- Pierre Marijon, Rayan Chikhi, Jean-Stephane Varre.
Graph analysis of fragmented long-read bacterial genome assemblies.
Bioinformatics,
35(21):4239-4246.
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 ]
- Michal Levy-Sakin, Steven Pastor, Yulia Mostovoy, Le Li, Alden K. Y. Leung, Jennifer McCaffrey, Eleanor Young, Ernest T. Lam, Alex R. Hastie, Karen H. Y. Wong, Claire Y. L. Chung, Walfred Ma, Justin Sibert, Ramakrishnan Rajagopalan, Nana Jin, Eugene Y. C. Chow, Catherine Chu, Annie Poon, Chin Lin, Ahmed Naguib, Wei-Ping Wang, Han Cao, Ting-Fung Chan, Kevin Y. Yip, Ming Xiao, Pui-Yan Kwok.
Genome maps across 26 human populations reveal population-specific patterns ofstructural variation.
Nat Commun,
10(1):1025.
2019.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Almodaresi F , Pandey P , Ferdman M , Johnson R , Patro R .
An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search.
In RECOMB 2019,
2019.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Lee I , Razaghi R , Gilpatrick T , Sadowski N , Sedlazeck FJ , Timp W .
Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing.
Technical Report https://doi.org/10.1101/504993, bioRxiv,
2018.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Amaiur Esnaola, Aitor Arrizabalaga-Escudero, Jorge Gonzalez-Esteban, Arturo Elosegi, Joxerra Aihartza.
Determining diet from faeces: Selection of metabarcoding primers for the insectivore Pyrenean desman (Galemys pyrenaicus).
PLoS One,
13(12):e0208986.
2018.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Ryan R. Wick, Louise M. Judd, Kathryn E. Holt.
Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutionalneural networks.
PLoS Comput Biol,
14(11):e1006583.
2018.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Satoshi Koide, Keisuke Kawano, Takuro Kutsuna.
Neural Edit Operations for Biological Sequences.
In NIPS 2018,
2018.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- 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 ]
- Jared T. Simpson, Rachael E. Workman, P. C. Zuzarte, Matei David, L. J. Dursi, Winston Timp.
Detecting DNA cytosine methylation using nanopore sequencing.
Nature methods,
14(4):407-410.
2017.
Supplement https://media.nature.com/original/nature-assets/nmeth/journal/v14/n4/extref/nmeth.4184-S1.pdf.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Mark R. Christie, Melanie L. Marine, Samuel E. Fox, Rod A. French, Michael S. Blouin.
A single generation of domestication heritably alters the expression of hundreds of genes.
Nat Commun,
7:10676.
2016.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Veronika B. Dubinkina, Dmitry S. Ischenko, Vladimir I. Ulyantsev, Alexander V. Tyakht, Dmitry G. Alexeev.
Assessment of k-mer spectrum applicability for metagenomic dissimilarityanalysis.
BMC bioinformatics,
17:38.
2016.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
