- 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 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.
- Berman et al., 2003
-
Berman, H., Henrick, K., and Nakamura, H. (2003).
Announcing the worldwide protein data bank.
Nat Struct Biol, 10(12):980.
- 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.
- Knudsen and Miyamoto, 2003
-
Knudsen, B. and Miyamoto, M. M. (2003).
Sequence alignments and pair hidden markov models using evolutionary
history.
Journal of Molecular Biology, 333(2):453 - 460.
- 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.
- Lu et al., 2008
-
Lu, M., Dousis, A. D., and Ma, J. (2008).
Opus-rota: A fast and accurate method for side-chain modeling.
Protein Science, 17(9):1576-1585.
- 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.
- Miao et al., 2011
-
Miao, Z., Cao, Y., and Jiang, T. (2011).
Rasp: rapid modeling of protein side chain conformations.
Bioinformatics, 27(22):3117-3122.
- 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.
- Pace et al., 1995
-
Pace, C. N., Vajdos, F., Fee, L., Grimsley, G., and Gray, T. (1995).
How to measure and predict the molar absorption coefficient of a
protein.
Protein science, 4(11):2411-2423.
- 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.
- 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.