Bibliography
- Allison et al., 2006
-
Allison, D., Cui, X., Page, G., and Sabripour, M. (2006).
Microarray data analysis: from disarray to consolidation and consensus.
NATURE REVIEWS GENETICS, 7(1):55. - Altschul and Gish, 1996
-
Altschul, S. F. and Gish, W. (1996).
Local alignment statistics.
Methods Enzymol, 266:460-480. - Altschul et al., 1990
-
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990).
Basic local alignment search tool.
J Mol Biol, 215(3):403-410. - Andrade et al., 1998
-
Andrade, M. A., O'Donoghue, S. I., and Rost, B. (1998).
Adaptation of protein surfaces to subcellular location.
J Mol Biol, 276(2):517-525. - Bachmair et al., 1986
-
Bachmair, A., Finley, D., and Varshavsky, A. (1986).
In vivo half-life of a protein is a function of its amino-terminal residue.
Science, 234(4773):179-186. - Baggerly et al., 2003
-
Baggerly, K., Deng, L., Morris, J., and Aldaz, C. (2003).
Differential expression in SAGE: accounting for normal between-library variation.
Bioinformatics, 19(12):1477-1483. - Bateman et al., 2004
-
Bateman, A., Coin, L., Durbin, R., Finn, R. D., Hollich, V., Griffiths-Jones,
S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E. L., Studholme, D. J.,
Yeats, C., and Eddy, S. R. (2004).
The Pfam protein families database.
Nucleic Acids Res., 32(Database issue):D138-D141. - Benjamini and Hochberg, 1995
-
Benjamini, Y. and Hochberg, Y. (1995).
Controlling the false discovery rate: a practical and powerful approach to multiple testing.
JOURNAL-ROYAL STATISTICAL SOCIETY SERIES B, 57:289-289. - Bishop and Friday, 1985
-
Bishop, M. J. and Friday, A. E. (1985).
Evolutionary trees from nucleic acid and protein sequences.
Proceeding of the Royal Society of London, B 226:271-302. - Blaisdell, 1989
-
Blaisdell, B. E. (1989).
Average values of a dissimilarity measure not requiring sequence alignment are twice the averages of conventional mismatch counts requiring sequence alignment for a computer-generated model system.
J Mol Evol, 29(6):538-47. - Bolstad et al., 2003
-
Bolstad, B., Irizarry, R., Astrand, M., and Speed, T. (2003).
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.
Bioinformatics, 19(2):185-193. - Bommarito et al., 2000
-
Bommarito, S., Peyret, N., and SantaLucia, J. (2000).
Thermodynamic parameters for DNA sequences with dangling ends.
Nucleic Acids Res, 28(9):1929-1934. - Chen et al., 2004
-
Chen, G., Znosko, B. M., Jiao, X., and Turner, D. H. (2004).
Factors affecting thermodynamic stabilities of RNA 3 x 3 internal loops.
Biochemistry, 43(40):12865-12876. - Clote et al., 2005
-
Clote, P., Ferré, F., Kranakis, E., and Krizanc, D. (2005).
Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency.
RNA, 11(5):578-591. - Cornette et al., 1987
-
Cornette, J. L., Cease, K. B., Margalit, H., Spouge, J. L., Berzofsky, J. A.,
and DeLisi, C. (1987).
Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins.
J Mol Biol, 195(3):659-685. - Costa, 2007
-
Costa, F. F. (2007).
Non-coding RNAs: lost in translation?
Gene, 386(1-2):1-10. - Crooks et al., 2004
-
Crooks, G. E., Hon, G., Chandonia, J.-M., and Brenner, S. E. (2004).
WebLogo: a sequence logo generator.
Genome Res, 14(6):1188-1190. - Dayhoff and Schwartz, 1978
-
Dayhoff, M. O. and Schwartz, R. M. (1978).
Atlas of Protein Sequence and Structure, volume 3 of 5 suppl., pages 353-358.
Nat. Biomed. Res. Found., Washington D.C. - Dayhoff et al., 1978
-
Dayhoff, M. O., Schwartz, R. M., and Orcutt, B. C. (1978).
A model of evolutionary change in protein.
Atlas of Protein Sequence and Structure, 5(3):345-352. - Dempster et al., 1977
-
Dempster, A., Laird, N., Rubin, D., et al. (1977).
Maximum likelihood from incomplete data via the EM algorithm.
Journal of the Royal Statistical Society, 39(1):1-38. - Dudoit et al., 2003
-
Dudoit, S., Shaffer, J., and Boldrick, J. (2003).
Multiple Hypothesis Testing in Microarray Experiments.
STATISTICAL SCIENCE, 18(1):71-103. - Eddy, 2004
-
Eddy, S. R. (2004).
Where did the BLOSUM62 alignment score matrix come from?
Nat Biotechnol, 22(8):1035-1036. - Edgar, 2004
-
Edgar, R. C. (2004).
Muscle: a multiple sequence alignment method with reduced time and space complexity.
BMC Bioinformatics, 5:113. - Efron, 1982
-
Efron, B. (1982).
The jackknife, the bootstrap and other resampling plans, volume 38.
SIAM. - Eisen et al., 1998
-
Eisen, M., Spellman, P., Brown, P., and Botstein, D. (1998).
Cluster analysis and display of genome-wide expression patterns.
Proceedings of the National Academy of Sciences, 95(25):14863-14868. - Eisenberg et al., 1984
-
Eisenberg, D., Schwarz, E., Komaromy, M., and Wall, R. (1984).
Analysis of membrane and surface protein sequences with the hydrophobic moment plot.
J Mol Biol, 179(1):125-142. - Emini et al., 1985
-
Emini, E. A., Hughes, J. V., Perlow, D. S., and Boger, J. (1985).
Induction of hepatitis a virus-neutralizing antibody by a virus-specific synthetic peptide.
J Virol, 55(3):836-839. - Engelman et al., 1986
-
Engelman, D. M., Steitz, T. A., and Goldman, A. (1986).
Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins.
Annu Rev Biophys Biophys Chem, 15:321-353. - Falcon and Gentleman, 2007
-
Falcon, S. and Gentleman, R. (2007).
Using GOstats to test gene lists for GO term association.
Bioinformatics, 23(2):257. - Felsenstein, 1981
-
Felsenstein, J. (1981).
Evolutionary trees from DNA sequences: a maximum likelihood approach.
J Mol Evol, 17(6):368-376. - Felsenstein, 1985
-
Felsenstein, J. (1985).
Confidence limits on phylogenies: An approach using the bootstrap.
Journal of Molecular Evolution, 39:783-791. - Feng and Doolittle, 1987
-
Feng, D. F. and Doolittle, R. F. (1987).
Progressive sequence alignment as a prerequisite to correct phylogenetic trees.
J Mol Evol, 25(4):351-360. - Forsberg et al., 2001
-
Forsberg, R., Oleksiewicz, M. B., Petersen, A. M., Hein, J., Bøtner, A., and
Storgaard, T. (2001).
A molecular clock dates the common ancestor of European-type porcine reproductive and respiratory syndrome virus at more than 10 years before the emergence of disease.
Virology, 289(2):174-179. - Galperin and Koonin, 1998
-
Galperin, M. Y. and Koonin, E. V. (1998).
Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption.
In Silico Biol, 1(1):55-67. - Gentleman and Mullin, 1989
-
Gentleman, J. F. and Mullin, R. (1989).
The distribution of the frequency of occurrence of nucleotide subsequences, based on their overlap capability.
Biometrics, 45(1):35-52. - Gill and von Hippel, 1989
-
Gill, S. C. and von Hippel, P. H. (1989).
Calculation of protein extinction coefficients from amino acid sequence data.
Anal Biochem, 182(2):319-326. - Gonda et al., 1989
-
Gonda, D. K., Bachmair, A., Wünning, I., Tobias, J. W., Lane, W. S., and
Varshavsky, A. (1989).
Universality and structure of the N-end rule.
J Biol Chem, 264(28):16700-16712. - Guindon and Gascuel, 2003
-
Guindon, S. and Gascuel, O. (2003).
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood.
Systematic Biology, 52(5):696-704. - Guo et al., 2006
-
Guo, L., Lobenhofer, E. K., Wang, C., Shippy, R., Harris, S. C., Zhang, L.,
Mei, N., Chen, T., Herman, D., Goodsaid, F. M., Hurban, P., Phillips, K. L.,
Xu, J., Deng, X., Sun, Y. A., Tong, W., Dragan, Y. P., and Shi, L. (2006).
Rat toxicogenomic study reveals analytical consistency across microarray platforms.
Nat Biotechnol, 24(9):1162-1169. - Han et al., 1999
-
Han, K., Kim, D., and Kim, H. (1999).
A vector-based method for drawing RNA secondary structure.
Bioinformatics, 15(4):286-297. - Hasegawa et al., 1985
-
Hasegawa, M., Kishino, H., and Yano, T. (1985).
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA.
Journal of Molecular Evolution, 22(2):160-174. - Henikoff and Henikoff, 1992
-
Henikoff, S. and Henikoff, J. G. (1992).
Amino acid substitution matrices from protein blocks.
Proc Natl Acad Sci U S A, 89(22):10915-10919. - Höhl et al., 2007
-
Höhl, M., Rigoutsos, I., and Ragan, M. A. (2007).
Pattern-based phylogenetic distance estimation and tree reconstruction.
Evolutionary Bioinformatics, 2:0-0. - Hopp and Woods, 1983
-
Hopp, T. P. and Woods, K. R. (1983).
A computer program for predicting protein antigenic determinants.
Mol Immunol, 20(4):483-489. - Ikai, 1980
-
Ikai, A. (1980).
Thermostability and aliphatic index of globular proteins.
J Biochem (Tokyo), 88(6):1895-1898. - Janin, 1979
-
Janin, J. (1979).
Surface and inside volumes in globular proteins.
Nature, 277(5696):491-492. - Jones et al., 1992
-
Jones, D., Taylor, W., and Thornton, J. (1992).
The rapid generation of mutation data matrices from protein sequences.
Computer Applications in the Biosciences (CABIOS), 8:275-282. - Jukes and Cantor, 1969
-
Jukes, T. and Cantor, C. (1969).
Mammalian Protein Metabolism, chapter Evolution of protein molecules, pages 21-32.
New York: Academic Press. - Kal et al., 1999
-
Kal, A. J., van Zonneveld, A. J., Benes, V., van den Berg, M., Koerkamp, M. G.,
Albermann, K., Strack, N., Ruijter, J. M., Richter, A., Dujon, B., Ansorge,
W., and Tabak, H. F. (1999).
Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources.
Mol Biol Cell, 10(6):1859-1872. - Karplus and Schulz, 1985
-
Karplus, P. A. and Schulz, G. E. (1985).
Prediction of chain flexibility in proteins.
Naturwissenschaften, 72:212-213. - Kaufman and Rousseeuw, 1990
-
Kaufman, L. and Rousseeuw, P. (1990).
Finding groups in data. an introduction to cluster analysis.
Wiley Series in Probability and Mathematical Statistics. Applied Probability and Statistics, New York: Wiley, 1990. - Kierzek et al., 1999
-
Kierzek, R., Burkard, M. E., and Turner, D. H. (1999).
Thermodynamics of single mismatches in RNA duplexes.
Biochemistry, 38(43):14214-14223. - Kimura, 1980
-
Kimura, M. (1980).
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
J Mol Evol, 16(2):111-120. - Knudsen and Miyamoto, 2001
-
Knudsen, B. and Miyamoto, M. M. (2001).
A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins.
Proc Natl Acad Sci U S A, 98(25):14512-14517. - Kolaskar and Tongaonkar, 1990
-
Kolaskar, A. S. and Tongaonkar, P. C. (1990).
A semi-empirical method for prediction of antigenic determinants on protein antigens.
FEBS Lett, 276(1-2):172-174. - Kyte and Doolittle, 1982
-
Kyte, J. and Doolittle, R. F. (1982).
A simple method for displaying the hydropathic character of a protein.
J Mol Biol, 157(1):105-132. - Leitner and Albert, 1999
-
Leitner, T. and Albert, J. (1999).
The molecular clock of HIV-1 unveiled through analysis of a known transmission history.
Proc Natl Acad Sci U S A, 96(19):10752-10757. - Lloyd, 1982
-
Lloyd, S. (1982).
Least squares quantization in PCM.
Information Theory, IEEE Transactions on, 28(2):129-137. - Longfellow et al., 1990
-
Longfellow, C. E., Kierzek, R., and Turner, D. H. (1990).
Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides.
Biochemistry, 29(1):278-285. - Maizel and Lenk, 1981
-
Maizel, J. V. and Lenk, R. P. (1981).
Enhanced graphic matrix analysis of nucleic acid and protein sequences.
Proc Natl Acad Sci U S A, 78(12):7665-7669. - Mathews et al., 2004
-
Mathews, D. H., Disney, M. D., Childs, J. L., Schroeder, S. J., Zuker, M., and
Turner, D. H. (2004).
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of rna secondary structure.
Proc Natl Acad Sci U S A, 101(19):7287-7292. - Mathews et al., 1999
-
Mathews, D. H., Sabina, J., Zuker, M., and Turner, D. H. (1999).
Expanded sequence dependence of thermodynamic parameters improves prediction of rna secondary structure.
J Mol Biol, 288(5):911-940. - Mathews and Turner, 2002
-
Mathews, D. H. and Turner, D. H. (2002).
Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops.
Biochemistry, 41(3):869-880. - Mathews and Turner, 2006
-
Mathews, D. H. and Turner, D. H. (2006).
Prediction of RNA secondary structure by free energy minimization.
Curr Opin Struct Biol, 16(3):270-278. - McCaskill, 1990
-
McCaskill, J. S. (1990).
The equilibrium partition function and base pair binding probabilities for RNA secondary structure.
Biopolymers, 29(6-7):1105-1119. - McGinnis and Madden, 2004
-
McGinnis, S. and Madden, T. L. (2004).
BLAST: at the core of a powerful and diverse set of sequence analysis tools.
Nucleic Acids Res, 32(Web Server issue):W20-W25. - Michener and Sokal, 1957
-
Michener, C. and Sokal, R. (1957).
A quantitative approach to a problem in classification.
Evolution, 11:130-162. - Mortazavi et al., 2008
-
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008).
Mapping and quantifying mammalian transcriptomes by rna-seq.
Nat Methods, 5(7):621-628. - Mukherjee and Zhang, 2009
-
Mukherjee, S. and Zhang, Y. (2009).
MM-align: A quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming.
Nucleic Acids Res., 37. - Purvis, 1995
-
Purvis, A. (1995).
A composite estimate of primate phylogeny.
Philos Trans R Soc Lond B Biol Sci, 348(1326):405-421. - Rivas and Eddy, 2000
-
Rivas, E. and Eddy, S. R. (2000).
Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs.
Bioinformatics, 16(7):583-605. - Robinson et al., 2010
-
Robinson, M. D., McCarthy, D. J., and Smyth, G. K. (2010).
edger: a bioconductor package for differential expression analysis of digital gene expression data.
Bioinformatics, 26(1):139-140. - Robinson and Smyth, 2007
-
Robinson, M. D. and Smyth, G. K. (2007).
Moderated statistical tests for assessing differences in tag abundance.
Bioinformatics, 23(21):2881-2887. - Robinson and Smyth, 2008
-
Robinson, M. D. and Smyth, G. K. (2008).
Small-sample estimation of negative binomial dispersion, with applications to sage data.
Biostatistics, 9(2):321-332. - Rose et al., 1985
-
Rose, G. D., Geselowitz, A. R., Lesser, G. J., Lee, R. H., and Zehfus, M. H.
(1985).
Hydrophobicity of amino acid residues in globular proteins.
Science, 229(4716):834-838. - Rost, 2001
-
Rost, B. (2001).
Review: protein secondary structure prediction continues to rise.
J Struct Biol, 134(2-3):204-218. - Saitou and Nei, 1987
-
Saitou, N. and Nei, M. (1987).
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Mol Biol Evol, 4(4):406-425. - Sankoff et al., 1983
-
Sankoff, D., Kruskal, J., Mainville, S., and Cedergren, R. (1983).
Time Warps, String Edits, and Macromolecules: the Theory and Practice of Sequence Comparison, chapter Fast algorithms to determine RNA secondary structures containing multiple loops, pages 93-120.
Addison-Wesley, Reading, Ma. - SantaLucia, 1998
-
SantaLucia, J. (1998).
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.
Proc Natl Acad Sci U S A, 95(4):1460-1465. - Schechter and Berger, 1967
-
Schechter, I. and Berger, A. (1967).
On the size of the active site in proteases. I. Papain.
Biochem Biophys Res Commun, 27(2):157-162. - Schechter and Berger, 1968
-
Schechter, I. and Berger, A. (1968).
On the active site of proteases. 3. Mapping the active site of papain; specific peptide inhibitors of papain.
Biochem Biophys Res Commun, 32(5):898-902. - Schneider and Stephens, 1990
-
Schneider, T. D. and Stephens, R. M. (1990).
Sequence logos: a new way to display consensus sequences.
Nucleic Acids Res, 18(20):6097-6100. - Schroeder et al., 1999
-
Schroeder, S. J., Burkard, M. E., and Turner, D. H. (1999).
The energetics of small internal loops in RNA.
Biopolymers, 52(4):157-167. - Shapiro et al., 2007
-
Shapiro, B. A., Yingling, Y. G., Kasprzak, W., and Bindewald, E. (2007).
Bridging the gap in RNA structure prediction.
Curr Opin Struct Biol, 17(2):157-165. - Siepel and Haussler, 2004
-
Siepel, A. and Haussler, D. (2004).
Combining phylogenetic and hidden Markov models in biosequence analysis.
J Comput Biol, 11(2-3):413-428. - Smith and Waterman, 1981
-
Smith, T. F. and Waterman, M. S. (1981).
Identification of common molecular subsequences.
J Mol Biol, 147(1):195-197. - Sturges, 1926
-
Sturges, H. A. (1926).
The choice of a class interval.
Journal of the American Statistical Association, 21:65-66. - Tian et al., 2005
-
Tian, L., Greenberg, S., Kong, S., Altschuler, J., Kohane, I., and Park, P.
(2005).
Discovering statistically significant pathways in expression profiling studies.
Proceedings of the National Academy of Sciences, 102(38):13544-13549. - Tobias et al., 1991
-
Tobias, J. W., Shrader, T. E., Rocap, G., and Varshavsky, A. (1991).
The N-end rule in bacteria.
Science, 254(5036):1374-1377. - Tusher et al., 2001
-
Tusher, V. G., Tibshirani, R., and Chu, G. (2001).
Significance analysis of microarrays applied to the ionizing radiation response.
Proc Natl Acad Sci U S A, 98(9):5116-5121. - von Ahsen et al., 2001
-
von Ahsen, N., Wittwer, C. T., and Schütz, E. (2001).
Oligonucleotide melting temperatures under PCR conditions: nearest-neighbor corrections for Mg(2+), deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas.
Clin Chem, 47(11):1956-1961. - Welling et al., 1985
-
Welling, G. W., Weijer, W. J., van der Zee, R., and Welling-Wester, S. (1985).
Prediction of sequential antigenic regions in proteins.
FEBS Lett, 188(2):215-218. - Whelan and Goldman, 2001
-
Whelan, S. and Goldman, N. (2001).
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.
Molecular Biology and Evolution, 18:691-699. - Wootton and Federhen, 1993
-
Wootton, J. C. and Federhen, S. (1993).
Statistics of local complexity in amino acid sequences and sequence databases.
Computers in Chemistry, 17:149-163. - Workman and Krogh, 1999
-
Workman, C. and Krogh, A. (1999).
No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution.
Nucleic Acids Res, 27(24):4816-4822. - Xu and Zhang, 2010
-
Xu, J. and Zhang, Y. (2010).
How significant is a protein structure similarity with TM-score = 0.5?
Bioinformatics, 26(7):889-95. - Yang, 1994a
-
Yang, Z. (1994a).
Estimating the pattern of nucleotide substitution.
Journal of Molecular Evolution, 39(1):105-111. - Yang, 1994b
-
Yang, Z. (1994b).
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods.
Journal of Molecular Evolution, 39(3):306-314. - Zhang and Skolnick, 2004
-
Zhang, Y. and Skolnick, J. (2004).
Scoring function for automated assessment of protein structure template quality.
Proteins, 57(4):702-10. - Zuker, 1989a
-
Zuker, M. (1989a).
On finding all suboptimal foldings of an rna molecule.
Science, 244(4900):48-52. - Zuker, 1989b
-
Zuker, M. (1989b).
The use of dynamic programming algorithms in rna secondary structure prediction.
Mathematical Methods for DNA Sequences, pages 159-184. - Zuker and Sankoff, 1984
-
Zuker, M. and Sankoff, D. (1984).
Rna secondary structures and their prediction.
Bulletin of Mathemetical Biology, 46:591-621. - Zuker and Stiegler, 1981
-
Zuker, M. and Stiegler, P. (1981).
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.
Nucleic Acids Res, 9(1):133-148.
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