2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2011
Zoznam článkov

• S. Gao, W. K. Sung, N. Nagarajan. Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences. Journal of computational biology : a journal of computational molecular cell biology, 2011.
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• David Golan, Saharon Rosset. Accurate estimation of heritability in genome wide studies using random effects models. Bioinformatics, 27(13):i317-i323. 2011.
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• Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai. IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics, 27(13):i85-i93. 2011.
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• Michael Hirsch, Bernhard Scholkopf, Michael Habeck. A blind deconvolution approach for improving the resolution of cryo-EM density maps. Journal of computational biology, 18(3):335-336. 2011.
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• Karin Noy, Fadi Towfic, Gayle M. Wittenberg, Daniel Fasulo. Shape-Based Feature Matching Improves Protein Identification via LC-MS and Tandem MS. Journal of computational biology, 18(4):547-547. 2011.
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• Zasha Weinberg, Ronald R. Breaker. R2R - software to speed the depiction of aesthetic consensus RNA secondary structures. BMC bioinformatics, 12:3. 2011.
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• Christos Kozanitis, Chris Saunders, Semyon Kruglyak, Vineet Bafna, George Varghese. Compressing Genomic Sequence Fragments Using SlimGene. Journal of computational biology, 18(3):401-403. 2011.
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• Jianxing Feng, Wei Li, Tao Jiang. Inference of isoforms from short sequence reads. Journal of computational biology, 18(3):305-311. 2011.
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• Patrick Ng, Uri Keich. Alignment constrained sampling. Journal of computational biology, 18(2):155-158. 2011.
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• 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.
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• Can Alkan, Maria Francesca Cardone, Claudia Rita Catacchio, Francesca Antonacci, Stephen J. O'Brien, Oliver A. Ryder, Stefania Purgato, Monica Zoli, Giuliano Della Valle, Evan E. Eichler, Mario Ventura. Genome-wide characterization of centromeric satellites from multiple mammalian genomes. Genome research, 21(1):137-145. 2011.
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• 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.
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• Cedric Chauve, Haris Gavranovic, Aida Ouangraoua, Eric Tannier. Yeast ancestral genome reconstructions: the possibilities of computational methods II. Journal of computational biology, 17(9):1097-1102. 2010.
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• Tomislav Domazet-Loso, Diethard Tautz. A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature, 468(7325):815-818. 2010. Clanok poskytneme na poziadanie.
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• Florent Murat, Jian-Hong Xu, Eric Tannier, Michael Abrouk, Nicolas Guilhot, Caroline Pont, Joachim Messing, Jerome Salse. Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome research, 20(11):1545-1547. 2010.
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• Tamir Tuller, Asaf Carmi, Kalin Vestsigian, Sivan Navon, Yuval Dorfan, John Zaborske, Tao Pan, Orna Dahan, Itay Furman, Yitzhak Pilpel. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell, 141(2):344-344. 2010.
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• Yarden Katz, Eric T. Wang, Edoardo M. Airoldi, Christopher B. Burge. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature methods, 7(12):1009-1015. 2010.
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• Laxmi Parida. Ancestral recombinations graph: a reconstructability perspective using random-graphs framework. Journal of computational biology, 17(10):1345-1350. 2010.
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• David J. Witherspoon, Jinchuan Xing, Yuhua Zhang, W. Scott Watkins, Mark A. Batzer, Lynn B. Jorde. Mobile element scanning (ME-Scan) by targeted high-throughput sequencing. BMC genomics, 11:410. 2010.
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• Péter L. Erdős, Lajos Soukup, Jens Stoye. Balanced vertices in trees and a simpler algorithm to compute the genomic distance. Applied Mathematics Letters, 24(1):82-86. 2010.
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• Miklos Csuros. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics, 26(15):1910-1912. 2010.
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• Robert Giegerich, Christian {Honer zu Siederdissen}. Semantics and Ambiguity of Stochastic RNA Family Models. Transactions on Computational Biology and Bioinformatics, 8(2):499-516. 2010.
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• 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.
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• Mathieu Lajoie, Denis Bertrand, Nadia El-Mabrouk. Inferring the evolutionary history of gene clusters from phylogenetic and gene order data. Molecular biology and evolution, 27(4):761-762. 2010.
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• Samuel C. Flores, Yaqi Wan, Rick Russell, Russ B. Altman. Predicting RNA structure by multiple template homology modeling. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, :216-217. 2010.
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• Sushmita Roy, Jason Ernst, Peter V. Kharchenko, et al.. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science, 330(6012):1787-1787. 2010.
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• Alexander Schoenhuth, Raheleh Salari and S. Cenk Sahinalp. Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties. In WABI, 6293 volume of Lecture Notes in Bioinformatics, 2010. Springer.
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• Adam R. Boyko, Pascale Quignon, Lin Li, Jeffrey J. Schoenebeck, Jeremiah D. Degenhardt, Kirk E. Lohmueller, Keyan Zhao, Abra Brisbin, Heidi G. Parker, Bridgett M. vonHoldt, Michele Cargill, Adam Auton, Andy Reynolds, Abdel G. Elkahloun, Marta Castelhano, Dana S. Mosher, Nathan B. Sutter, Gary S. Johnson, John Novembre, Melissa J. Hubisz, Adam Siepel, Robert K. Wayne, Carlos D. Bustamante, Elaine A. Ostrander. A simple genetic architecture underlies morphological variation in dogs. PLoS Biology, 8(8):e1000451. 2010.
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• Ali Tofigh, Michael Hallett, Jens Lagergren. Simultaneous Identification of Duplications and Lateral Gene Transfers. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2010.
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• Alexander M. Tsankov, Dawn Anne Thompson, Amanda Socha, Aviv Regev, Oliver J. Rando. The role of nucleosome positioning in the evolution of gene regulation. PLoS Biology, 8(7):e1000414. 2010.
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• David C. Hess, Chad L. Myers, Curtis Huttenhower, Matthew A. Hibbs, Alicia P. Hayes, Jadine Paw, John J. Clore, Rosa M. Mendoza, Bryan San Luis, Corey Nislow, Guri Giaever, Michael Costanzo, Olga G. Troyanskaya, Amy A. Caudy. Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet, 5(3):e1000407. 2009.
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