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Identifying novel constrained elements by exploiting biased substitution patterns.
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Clanok je uz rezervovany.
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John Hawkins, Charles Grant, William Stafford Noble, Timothy L. Bailey.
Assessing phylogenetic motif models for predicting transcription factor binding sites.
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Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai.
Predictions of RNA secondary structure by combining homologous sequence information.
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25(12):i330-338.
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Mikhail Zaslavskiy, Francis Bach, Jean-Philippe Vert.
Global alignment of protein-protein interaction networks by graph matching methods.
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25(12):i259-267.
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Minmei Hou, Cathy Riemer, Piotr Berman, Ross Hardison, Webb Miller.
Aligning two genomic sequences that contain duplications .
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Heng Li, Richard Durbin.
Fast and accurate short read alignment with Burrows-Wheeler transform.
Bioinformatics,
25(14):1754-1760.
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Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann.
Proteome coverage prediction with infinite Markov models.
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25(12):i154-160.
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Todd A. Gibson and Debra S. Goldberg.
Reverse Engineering the Evolution of Protein Interaction Networks.
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Z. Khan, J. S. Bloom, B. A. Garcia, M. Singh, L. Kruglyak.
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Proceedings of the National Academy of Sciences of the United States of America,
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Tara A. Gianoulis, Jeroen Raes, Prianka V. Patel, Robert Bjornson, Jan O. Korbel, Ivica Letunic, Takuji Yamada, Alberto Paccanaro, Lars J. Jensen, Michael Snyder, Peer Bork, Mark B. Gerstein.
Quantifying environmental adaptation of metabolic pathways in metagenomics.
Proceedings of the National Academy of Sciences of the United States of America,
106(5):1374-1379.
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Elhanan Borenstein, Marcus W. Feldman.
Topological signatures of species interactions in metabolic networks.
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Nan Song, Jacob M. Joseph, George B. Davis, Dannie Durand.
Sequence similarity network reveals common ancestry of multidomain proteins.
PLoS Comput Biol,
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2008.
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Anthony P. Fejes, Gordon Robertson, Mikhail Bilenky, Richard Varhol, Matthew Bainbridge, Steven J. M. Jones.
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology.
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Daniel R. Zerbino, Ewan Birney.
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Heng Li, Jue Ruan, Richard Durbin.
Mapping short DNA sequencing reads and calling variants using mapping quality scores.
Genome research,
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Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler.
Using native and syntenically mapped cDNA alignments to improve de novo gene finding.
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Niranjan Nagarajan, Carl Kingsford.
Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques.
In Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine (BIBM),
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Vidushi S. Patel, Steven J. B. Cooper, Janine E. Deakin, Bob Fulton, Tina Graves, Wesley C. Warren, Richard K. Wilson, Jennifer A. M. Graves.
Platypus globin genes and flanking loci suggest a new insertional model for beta-globin evolution in birds and mammals.
BMC biology,
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2008.
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C. Gissi, F. Iannelli, G. Pesole.
Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species.
Heredity,
101(4):301-310.
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