Bibliography

Akmaev and Wang, 2004: Akmaev, V. R. and Wang, C. J. (2004).
Correction of sequence-based artifacts in serial analysis of gene expression.
Bioinformatics, 20(8):1254-1263.
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.
Altshuler et al., 2000: Altshuler, D., Pollara, V. J., Cowles, C. R., Etten, W. J. V., Baldwin, J., Linton, L., and Lander, E. S. (2000).
An snp map of the human genome generated by reduced representation shotgun sequencing.
Nature, 407(6803):513-516.
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. L., Studholme, D. J., Yeats, C., and Eddy, S. R. (2004).
The Pfam protein families database.
Nucleic Acids Res, 32(Database issue):D138-D141.
Bendtsen et al., 2004a: Bendtsen, J. D., Jensen, L. J., Blom, N., Heijne, G. V., and Brunak, S. (2004a).
Feature-based prediction of non-classical and leaderless protein secretion.
Protein Eng Des Sel, 17(4):349-356.
Bendtsen et al., 2005: Bendtsen, J. D., Kiemer, L., Fausbøll, A., and Brunak, S. (2005).
Non-classical protein secretion in bacteria.
BMC Microbiol, 5:58.
Bendtsen et al., 2004b: Bendtsen, J. D., Nielsen, H., von Heijne, G., and Brunak, S. (2004b).
Improved prediction of signal peptides: SignalP 3.0.
J Mol Biol, 340(4):783-795.
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.
Blobel, 2000: Blobel, G. (2000).
Protein targeting (Nobel lecture).
Chembiochem., 1:86-102.
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.
Brockman et al., 2008: Brockman, W., Alvarez, P., Young, S., Garber, M., Giannoukos, G., Lee, W. L., Russ, C., Lander, E. S., Nusbaum, C., and Jaffe, D. B. (2008).
Quality scores and snp detection in sequencing-by-synthesis systems.
Genome Res, 18(5):763-770.
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.
Creighton et al., 2009: Creighton, C. J., Reid, J. G., and Gunaratne, P. H. (2009).
Expression profiling of micrornas by deep sequencing.
Brief Bioinform, 10(5):490-497.
Cronn et al., 2008: Cronn, R., Liston, A., Parks, M., Gernandt, D. S., Shen, R., and Mockler, T. (2008).
Multiplex sequencing of plant chloroplast genomes using solexa sequencing-by-synthesis technology.
Nucleic Acids Res, 36(19):e122.
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.
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.
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.
Gnerre et al., 2011: Gnerre, S., Maccallum, I., Przybylski, D., Ribeiro, F. J., Burton, J. N., Walker, B. J., Sharpe, T., Hall, G., Shea, T. P., Sykes, S., Berlin, A. M., Aird, D., Costello, M., Daza, R., Williams, L., Nicol, R., Gnirke, A., Nusbaum, C., Lander, E. S., and Jaffe, D. B. (2011).
High-quality draft assemblies of mammalian genomes from massively parallel sequence data.
Proceedings of the National Academy of Sciences of the United States of America, 108(4):1513-8.
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.
Hein, 2001: Hein, J. (2001).
An algorithm for statistical alignment of sequences related by a binary tree.
In Pacific Symposium on Biocomputing, page 179.
Hein et al., 2000: Hein, J., Wiuf, C., Knudsen, B., Møller, M. B., and Wibling, G. (2000).
Statistical alignment: computational properties, homology testing and goodness-of-fit.
J Mol Biol, 302(1):265-279.
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.
Homer N, 2010: Homer N, N. S. (2010).
Improved variant discovery through local re-alignment of short-read next-generation sequencing data using srma.
Genome Biol., 11(10):R99.
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.
Ji et al., 2008: Ji, H., Jiang, H., Ma, W., Johnson, D., Myers, R., and Wong, W. (2008).
An integrated software system for analyzing ChIP-chip and ChIP-seq data.
Nature Biotechnology, 26(11):1293-1300.
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.
Klee and Ellis, 2005: Klee, E. W. and Ellis, L. B. M. (2005).
Evaluating eukaryotic secreted protein prediction.
BMC Bioinformatics, 6:256.
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.
Krogh et al., 2001: Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E. L. (2001).
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
J Mol Biol, 305(3):567-580.
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.
Larget and Simon, 1999: Larget, B. and Simon, D. (1999).
Markov chain monte carlo algorithms for the bayesian analysis of phylogenetic trees.
Mol Biol Evol, 16:750-759.
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.
Li et al., 2010: Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., Li, S., Yang, H., Wang, J., and Wang, J. (2010).
De novo assembly of human genomes with massively parallel short read sequencing.
Genome research, 20(2):265-72.
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.
Maeda et al., 2008: Maeda, N., Nishiyori, H., Nakamura, M., Kawazu, C., Murata, M., Sano, H., Hayashida, K., Fukuda, S., Tagami, M., Hasegawa, A., Murakami, K., Schroder, K., Irvine, K., Hume, D., Hayashizaki, Y., Carninci, P., and Suzuki, H. (2008).
Development of a dna barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer.
Biotechniques, 45(1):95-97.
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.
Menne et al., 2000: Menne, K. M., Hermjakob, H., and Apweiler, R. (2000).
A comparison of signal sequence prediction methods using a test set of signal peptides.
Bioinformatics, 16(8):741-742.
Meyer et al., 2007: Meyer, M., Stenzel, U., Myles, S., Prüfer, K., and Hofreiter, M. (2007).
Targeted high-throughput sequencing of tagged nucleic acid samples.
Nucleic Acids Res, 35(15):e97.
Michener and Sokal, 1957: Michener, C. and Sokal, R. (1957).
A quantitative approach to a problem in classification.
Evolution, 11:130-162.
Morin et al., 2008: Morin, R. D., O'Connor, M. D., Griffith, M., Kuchenbauer, F., Delaney, A., Prabhu, A.-L., Zhao, Y., McDonald, H., Zeng, T., Hirst, M., Eaves, C. J., and Marra, M. A. (2008).
Application of massively parallel sequencing to microrna profiling and discovery in human embryonic stem cells.
Genome Res, 18(4):610-621.
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.
Nguyen et al., 2011: Nguyen, P., Ma, J., Pei, D., Obert, C., Cheng, C., and Geiger, T. (2011).
Identification of errors introduced during high throughput sequencing of the t cell receptor repertoire.
BMC genomics, 12(1):106.
Nielsen et al., 1997: Nielsen, H., Engelbrecht, J., Brunak, S., and von Heijne, G. (1997).
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
Protein Eng, 10(1):1-6.
Nielsen, 2007: Nielsen, K. L., editor (2007).
Serial Analysis of Gene Expression (SAGE): Methods and Protocols, volume 387 of Methods in Molecular Biology.
Humana Press.
Parkhomchuk et al., 2009: Parkhomchuk, D., Borodina, T., Amstislavskiy, V., Banaru, M., Hallen, L., Krobitsch, S., Lehrach, H., and Soldatov, A. (2009).
Transcriptome analysis by strand-specific sequencing of complementary dna.
Nucleic Acids Res, 37(18):e123.
Purvis, 1995: Purvis, A. (1995).
A composite estimate of primate phylogeny.
Philos Trans R Soc Lond B Biol Sci, 348(1326):405-421.
Reinhardt and Hubbard, 1998: Reinhardt, A. and Hubbard, T. (1998).
Using neural networks for prediction of the subcellular location of proteins.
Nucleic Acids Res, 26(9):2230-2236.
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.
Sneath and Sokal, 1973: Sneath, P. and Sokal, R. (1973).
Numerical Taxonomy.
Freeman, San Francisco.
Stark et al., 2010: Stark, M. S., Tyagi, S., Nancarrow, D. J., Boyle, G. M., Cook, A. L., Whiteman, D. C., Parsons, P. G., Schmidt, C., Sturm, R. A., and Hayward, N. K. (2010).
Characterization of the melanoma mirnaome by deep sequencing.
PLoS One, 5(3):e9685.
Sturges, 1926: Sturges, H. A. (1926).
The choice of a class interval.
Journal of the American Statistical Association, 21:65-66.
't Hoen et al., 2008: 't Hoen, P. A. C., Ariyurek, Y., Thygesen, H. H., Vreugdenhil, E., Vossen, R. H. A. M., de Menezes, R. X., Boer, J. M., van Ommen, G.-J. B., and den Dunnen, J. T. (2008).
Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms.
Nucleic Acids Res, 36(21):e141.
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.
von Heijne, 1986: von Heijne, G. (1986).
A new method for predicting signal sequence cleavage sites.
Nucl. Acids Res., 14:4683-4690.
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.
Wyman et al., 2009: Wyman, S. K., Parkin, R. K., Mitchell, P. S., Fritz, B. R., O'Briant, K., Godwin, A. K., Urban, N., Drescher, C. W., Knudsen, B. S., and Tewari, M. (2009).
Repertoire of micrornas in epithelial ovarian cancer as determined by next generation sequencing of small rna cdna libraries.
PLoS One, 4(4):e5311.
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.
Yang and Rannala, 1997: Yang, Z. and Rannala, B. (1997).
Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.
Mol Biol Evol, 14(7):717-724.
Zerbino and Birney, 2008: Zerbino, D. R. and Birney, E. (2008).
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Genome Res, 18(5):821-829.
Zerbino et al., 2009: Zerbino, D. R., McEwen, G. K., Margulies, E. H., and Birney, E. (2009).
Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler.
PloS one, 4(12):e8407.
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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