Bioinformatics Research and Applications
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Takeo Kanade | Josef Kittler | David Hutchison | T. Kanade | J. Kittler | O. Eulenstein | David Hutchison | D. Janies | Zhipeng Cai
[1] Joshua E. Elias,et al. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. , 2003, Journal of proteome research.
[2] Noah J. Cowan,et al. Nodal Dynamics, Not Degree Distributions, Determine the Structural Controllability of Complex Networks , 2011, PloS one.
[3] N. Ahn,et al. Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies. , 2010, Journal of proteome research.
[4] X. Xia,et al. The rate heterogeneity of nonsynonymous substitutions in mammalian mitochondrial genes. , 1998, Molecular biology and evolution.
[5] J. Wiens,et al. Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling , 2012, PloS one.
[6] Yi-Kuo Yu,et al. Detection of co-eluted peptides using database search methods , 2008, Biology Direct.
[7] Hidetoshi Shimodaira,et al. Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference , 1999, Molecular Biology and Evolution.
[8] Yi Pan,et al. Essential Proteins Discovery from Weighted Protein Interaction Networks , 2010, ISBRA.
[9] L. Mirny,et al. Protein complexes and functional modules in molecular networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[10] P. Pevzner,et al. De novo peptide sequencing and identification with precision mass spectrometry. , 2007, Journal of proteome research.
[11] H. Kishino,et al. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea , 1989, Journal of Molecular Evolution.
[12] S. O’Brien,et al. A Molecular Phylogeny of Living Primates , 2011, PLoS genetics.
[13] P. D. Rijk,et al. Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: Calibration of the molecular clock , 1993, Journal of Molecular Evolution.
[14] J. Felsenstein. Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.
[15] James P Edwards,et al. Anti-Inflammatory Activity of a Potent, Selective Leukotriene A4 Hydrolase Inhibitor in Comparison with the 5-Lipoxygenase Inhibitor Zileuton , 2007, Journal of Pharmacology and Experimental Therapeutics.
[16] D. N. Perkins,et al. Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.
[17] Cynthia Parr,et al. Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)? , 2011, Systematic biology.
[18] Ming Li,et al. PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. , 2003, Rapid communications in mass spectrometry : RCM.
[19] Dmitrij Frishman,et al. MIPS: analysis and annotation of proteins from whole genomes in 2005 , 2006, Nucleic Acids Res..
[20] J. Wiens,et al. Missing data, incomplete taxa, and phylogenetic accuracy. , 2003, Systematic biology.
[21] Richard H. Ree,et al. Inferring Phylogenies from RAD Sequence Data , 2012, PloS one.
[22] R. Aebersold,et al. ProbIDtree: An automated software program capable of identifying multiple peptides from a single collision‐induced dissociation spectrum collected by a tandem mass spectrometer , 2005, Proteomics.
[23] Yan Lin,et al. DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes , 2008, Nucleic Acids Res..
[24] M. Mann,et al. Electrospray Ionization for Mass Spectrometry of Large Biomolecules , 1990 .
[25] J. Felsenstein,et al. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. , 1994, Molecular biology and evolution.
[26] Bin Song,et al. Mining Metabolic Networks for Optimal Drug Targets , 2007, Pacific Symposium on Biocomputing.
[27] J. McCaskill. The equilibrium partition function and base pair binding probabilities for RNA secondary structure , 1990, Biopolymers.
[28] N. L. Greenbaum,et al. A conserved pseudouridine modification in eukaryotic U2 snRNA induces a change in branch-site architecture. , 2001, RNA.
[29] Randy Goebel,et al. Approximation Algorithms for the Maximum Multiple RNA Interaction Problem , 2013, COCOA.
[30] J. Shultz,et al. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences , 2010, Nature.
[31] Vladimir I. Levenshtein,et al. Binary codes capable of correcting deletions, insertions, and reversals , 1965 .
[32] P. Pevzner,et al. PepNovo: de novo peptide sequencing via probabilistic network modeling. , 2005, Analytical chemistry.
[33] Hosna Jabbari,et al. An O(n5) Algorithm for MFE Prediction of Kissing Hairpins and 4-Chains in Nucleic Acids , 2009, J. Comput. Biol..
[34] Jeremy M. Brown,et al. The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference , 2009, Systematic biology.
[35] Xuhua Xia,et al. GC skew in protein-coding genes between the leading and lagging strands in bacterial genomes: new substitution models incorporating strand bias. , 2008, Journal of theoretical biology.
[36] Bin Ma,et al. PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification* , 2011, Molecular & Cellular Proteomics.
[37] M. Siddall,et al. Success of Parsimony in the Four‐Taxon Case: Long‐Branch Repulsion by Likelihood in the Farris Zone , 1998 .
[38] Nancy L. Greenbaum,et al. A Combinatorial Approach for Multiple RNA Interaction: Formulations, Approximations, and Heuristics , 2013, COCOON.
[39] Insuk Lee,et al. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality , 2007, BMC Bioinformatics.
[40] Xuhua Xia,et al. DNA Replication and Strand Asymmetry in Prokaryotic and Mitochondrial Genomes , 2012, Current genomics.
[41] Shi-Jie Chen,et al. Free energy landscapes of RNA/RNA complexes: with applications to snRNA complexes in spliceosomes. , 2006, Journal of molecular biology.
[42] Dipali G. Sashital,et al. U2–U6 RNA folding reveals a group II intron-like domain and a four-helix junction , 2004, Nature Structural &Molecular Biology.
[43] 中尾 光輝,et al. KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース) , 2000 .
[44] P. Mallick,et al. Peptide Identification from Mixture Tandem Mass Spectra* , 2010, Molecular & Cellular Proteomics.
[45] Yong Wang,et al. An index of substitution saturation and its application. , 2003, Molecular phylogenetics and evolution.
[46] John D. Venable,et al. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra , 2004, Nature Methods.
[47] Albert-László Barabási,et al. Control Centrality and Hierarchical Structure in Complex Networks , 2012, PloS one.
[48] W. A. Cox,et al. A Phylogenomic Study of Birds Reveals Their Evolutionary History , 2008, Science.
[49] K. Kjer,et al. Ribosomal RNA and Tetrapod Phylogeny , 2003 .
[50] X. Xia. DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution , 2013, Molecular biology and evolution.
[51] H. Philippe,et al. Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. , 2013, Molecular biology and evolution.
[52] T. Jukes. CHAPTER 24 – Evolution of Protein Molecules , 1969 .
[53] Ioannis Xenarios,et al. DIP: the Database of Interacting Proteins , 2000, Nucleic Acids Res..
[54] C. Ball,et al. Saccharomyces Genome Database. , 2002, Methods in enzymology.
[55] Joseph Felsenstein,et al. Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters , 1973 .
[56] Gary D Bader,et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.
[57] Xuhua Xia,et al. On transition bias in mitochondrial genes of pocket gophers , 1996, Journal of Molecular Evolution.
[58] Bin Ma,et al. An effective algorithm for peptide de novo sequencing from MS/MS spectra , 2005, J. Comput. Syst. Sci..
[59] Sean R. Collins,et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae , 2006, Nature.
[60] P. Bork,et al. Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.
[61] P. Bourne,et al. Peptide Identification by Database Search of Mixture Tandem Mass Spectra* , 2011, Molecular & Cellular Proteomics.
[62] Jason E Stajich,et al. Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. , 2008, Systematic biology.
[63] Shmuel Sattath,et al. How reliable are experimental protein-protein interaction data? , 2003, Journal of molecular biology.