2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2012
Zoznam článkov
- Heng Li, Richard Durbin.
Inference of human population history from individual whole-genome sequences.
Nature,
475(7357):493-496.
2011.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Hai Yang Hu, Liu He, Kseniya Fominykh, Zheng Yan, Song Guo, Xiaoyu Zhang, Martin S. Taylor, Lin Tang, Jie Li, Jianmei Liu, Wen Wang, Haijing Yu, Philipp Khaitovich.
Evolution of the human-specific microRNA miR-941.
Nat Commun,
3:1145.
2012.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Webb Miller, Stephan C. Schuster, Andreanna J. Welch, Aakrosh Ratan, Oscar C. Bedoya-Reina, Fangqing Zhao, Hie Lim Kim, Richard C. Burhans, Daniela I. Drautz, Nicola E. Wittekindt, Lynn P. Tomsho, Enrique Ibarra-Laclette, Luis Herrera-Estrella, Elizabeth Peacock, Sean Farley, George K. Sage, Karyn Rode, Martyn Obbard, Rafael Montiel, Lutz Bachmann, Olafur Ingolfsson, Jon Aars, Thomas Mailund, Oystein Wiig, Sandra L. Talbot, Charlotte Lindqvist.
Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change.
Proceedings of the National Academy of Sciences of the United States of America,
109(36):E2382-2390.
2012.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Thomas A. Hopf, Lucy J. Colwell, Robert Sheridan, Burkhard Rost, Chris Sander, Debora S. Marks.
Three-dimensional structures of membrane proteins from genomic sequencing.
Cell,
149(7):1607-1611.
2012.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Kevin Y. Yip, Chao Cheng, Nitin Bhardwaj, James B. Brown, Jing Leng, Anshul Kundaje, Joel Rozowsky, Ewan Birney, Peter Bickel, Michael Snyder, Mark Gerstein.
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors.
Genome biology,
13(9):R48.
2012.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Debora S. Marks, Lucy J. Colwell, Robert Sheridan, Thomas A. Hopf, Andrea Pagnani, Riccardo Zecchina, Chris Sander.
Protein 3D structure computed from evolutionary sequence variation.
PLoS One,
6(12):e28766.
2011.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Steffen Heyne, Fabrizio Costa, Dominic Rose, Rolf Backofen.
GraphClust: alignment-free structural clustering of local RNA secondarystructures.
Bioinformatics,
28(12):i224-232.
2012.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Giltae Song, Cathy Riemer, Benjamin Dickins, Hie Lim Kim, Louxin Zhang, Yu Zhang, Chih-Hao Hsu, Ross C. Hardison, {Nisc Comparative Sequencing Program}, Eric D. Green, Webb Miller.
Revealing mammalian evolutionary relationships by comparative analysis of gene clusters.
Genome Biol Evol,
4(4):586-601.
2012.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Luqman Hodgkinson, Richard M. Karp.
Algorithms to detect multiprotein modularity conserved during evolution.
IEEE/ACM Trans Comput Biol Bioinform,
9(4):1046-1048.
2012.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Yu Lin, Vaibhav Rajan, Bernard M. E. Moret.
Bootstrapping phylogenies inferred from rearrangement data.
Algorithms Mol Biol,
7(1):21.
2012.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Son K. Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, Max A. Alekseyev.
Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly.
Journal of computational biology,
2012.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Pierre Peterlongo, Rayan Chikhi.
Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer.
BMC bioinformatics,
13(1):48.
2012.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Anthony J. Cox, Tobias Jakobi, Giovanna Rosone, Ole B. Schulz-Trieglaff.
Comparing DNA Sequence Collections by Direct Comparison of Compressed Text Indexes .
In WABI 2012,
7534 volume of LNBI,
pp. 214-224, 2012.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Manuel Lafond, Krister M. Swenson, Nadia El-Mabrouk.
An Optimal Reconciliation Algorithm for Gene Trees with Polytomies.
In WABI 2012,
7534 volume of LNBI,
pp. 106-122, 2012.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Nikolay Vyahhi, Alex Pyshkin, Son Pham, Pavel A. Pevzner.
From de Bruijn Graphs to Rectangle Graphs for Genome Assembly.
In WABI 2012,
7534 volume of LNBI,
2012.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Elizabeth P. Murchison et al..
Genome sequencing and analysis of the Tasmanian devil and its transmissiblecancer.
Cell,
148(4):780-781.
2012.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Angelique D'Hont et al..
The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.
Nature,
488(7410):213-217.
2012.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Olivier {Tremblay Savard}, Denis Bertrand, Nadia El-Mabrouk.
Evolution of orthologous tandemly arrayed gene clusters.
BMC bioinformatics,
12 Suppl 9:S2.
2011.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Jimmy Yang, Tandy Warnow.
Fast and accurate methods for phylogenomic analyses.
BMC bioinformatics,
12 Suppl 9:S4.
2011.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Ilan Gronau, Melissa J. Hubisz, Brad Gulko, Charles G. Danko, Adam Siepel.
Bayesian inference of ancient human demography from individual genome sequences.
Nature genetics,
43(10):1031-1034.
2011.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Hosein Mohimani, Wei-Ting Liu, Joshua S. Mylne, Aaron G. Poth, Michelle L. Colgrave, Dat Tran, Michael E. Selsted, Pieter C. Dorrestein, Pavel A. Pevzner.
Cycloquest: identification of cyclopeptides via database search of their massspectra against genome databases.
Journal of proteome research,
10(10):4505-4512.
2011.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Andrew McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab Shah, Colin Collins, S. Cenk Sahinalp.
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seqand low coverage genome sequence data.
Bioinformatics,
27(11):1481-1488.
2011.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Yu Lin, Bernard M. E. Moret.
A new genomic evolutionary model for rearrangements, duplications, and lossesthat applies across eukaryotes and prokaryotes.
Journal of computational biology,
18(9):1055-1064.
2011.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Paul Medvedev, Son Pham, Mark Chaisson, Glenn Tesler, Pavel Pevzner.
Paired de bruijn graphs: a novel approach for incorporating mate pair informationinto genome assemblers.
Journal of computational biology : a journal of computational molecular cell biology,
18(11):1625-1634.
2011.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Marilia D. V. Braga, Eyla Willing, Jens Stoye.
Double cut and join with insertions and deletions.
Journal of computational biology,
18(9):1167-1174.
2011.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Rene L. Warren, Robert A. Holt.
Targeted assembly of short sequence reads.
PLoS One,
6(5):e19816.
2011.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson.
Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach.
Algorithms Mol Biol,
6(1):20.
2011.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Patrick Ng, Uri Keich.
Alignment constrained sampling.
Journal of computational biology,
18(2):155-158.
2011.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Jr-Shiuan Yang, Michael D. Phillips, Doron Betel, Ping Mu, Andrea Ventura, Adam C. Siepel, Kevin C. Chen, Eric C. Lai.
Widespread regulatory activity of vertebrate microRNA* species.
RNA,
17(2):312-316.
2011.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Ryan E. Mills, Klaudia Walter, Chip Stewart, et al..
Mapping copy number variation by population-scale genome sequencing.
Nature,
470(7332):59-65.
2011.
Clanok poskytneme zaujemcom.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Katherine S. Pollard, Melissa J. Hubisz, Kate R. Rosenbloom, Adam Siepel.
Detection of nonneutral substitution rates on mammalian phylogenies.
Genome research,
20(1):110-111.
2010.
[ Abstract ] [ BibTeX ] [ PubMed ]
