2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2013
Zoznam článkov
- Joe Parker, Georgia Tsagkogeorga, James A. Cotton, Yuan Liu, Paolo Provero, Elia Stupka, Stephen J. Rossiter.
Genome-wide signatures of convergent evolution in echolocating mammals.
Nature,
502(7470):228-231.
2013.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Viraj Deshpande, Eric D. K. Fung, Son Pham, Vineet Bafna.
Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads.
In WABI 2013,
pp. 349-363,
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Gustavo Sacomoto, Vincent Lacroix, Marie-France Sagot.
A Polynomial Delay Algorithm for the Enumeration of Bubbles with Length Constraints in Directed Graphs and Its Application to the Detection of Alternative Splicing in RNA-seq Data.
In WABI 2013,
pp. 99-111, 2013.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Ming Li.
Towards Reliable Automatic Protein Structure Alignment.
In WABI 2013,
pp. 18-32, 2013.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Makinen.
A novel min-cost flow method for estimating transcript expression with RNA-Seq.
BMC bioinformatics,
14 Suppl 5:S15.
2013.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Stefano Lonardi, Denisa Duma, Matthew Alpert, Francesca Cordero, Marco Beccuti, Prasanna R. Bhat, Yonghui Wu, Gianfranco Ciardo, Burair Alsaihati, Yaqin Ma, Steve Wanamaker, Josh Resnik, Serdar Bozdag, Ming-Cheng Luo, Timothy J. Close.
Combinatorial pooling enables selective sequencing of the barley gene space.
PLoS Comput Biol,
9(4):e1003010.
2013.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Kui Zhang, Degui Zhi.
Joint haplotype phasing and genotype calling of multiple individuals usinghaplotype informative reads.
Bioinformatics,
29(19):2427-2434.
2013.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Jaebum Kim, Denis M. Larkin, Qingle Cai, ., Yongfen Zhang, Ri-Li Ge, Loretta Auvil, Boris Capitanu, Guojie Zhang, Harris A. Lewin, Jian Ma.
Reference-assisted chromosome assembly.
Proceedings of the National Academy of Sciences of the United States of America,
110(5):1785-1790.
2013.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Mohammadreza Ghodsi, Christopher M. Hill, Irina Astrovskaya, Henry Lin, Dan D. Sommer, Sergey Koren, Mihai Pop.
De novo likelihood-based measures for comparing genome assemblies.
BMC Res Notes,
6(1):334.
2013.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Iulian Pruteanu-Malinici, William H. Majoros, Uwe Ohler.
Automated annotation of gene expression image sequences via non-parametric factoranalysis and conditional random fields.
Bioinformatics,
29(13):i27-35.
2013.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Rayan Chikhi, Paul Medvedev.
Informed and automated k-mer size selection for genome assembly.
Bioinformatics,
2013.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- David Golan, Paul Medvedev.
Using state machines to model the Ion Torrent sequencing process and to improveread error rates.
Bioinformatics,
29(13):i344-351.
2013.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Noah M. Daniels, Andrew Gallant, Jian Peng, Lenore J. Cowen, Michael Baym, Bonnie Berger.
Compressive genomics for protein databases.
Bioinformatics,
29(13):i283-290.
2013.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Lin Huang, Victoria Popic, Serafim Batzoglou.
Short read alignment with populations of genomes.
Bioinformatics,
29(13):i361-370.
2013.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Salim Akhter Chowdhury, Stanley E. Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schaffer, Russell Schwartz.
Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations.
Bioinformatics,
29(13):i189-198.
2013.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Jared T. Simpson, Richard Durbin.
Efficient de novo assembly of large genomes using compressed data structures.
Genome research,
22(3):549-556.
2012.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Peter Glaus, Antti Honkela, Magnus Rattray.
Identifying differentially expressed transcripts from RNA-seq data withbiological variation.
Bioinformatics,
28(13):1721-1728.
2012.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Serita Nelesen, Kevin Liu, Li-San Wang, C. Randal Linder, Tandy Warnow.
DACTAL: divide-and-conquer trees (almost) without alignments.
Bioinformatics,
28(12):i274-282.
2012.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Jan Manuch, Murray Patterson, Roland Wittler, Cedric Chauve, Eric Tannier.
Linearization of ancestral multichromosomal genomes.
BMC bioinformatics,
13 Suppl 19:S11.
2012.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
