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.

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.

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.

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.

Eddy, 2004
Eddy, S. R. (2004).
Where did the BLOSUM62 alignment score matrix come from?
Nat Biotechnol, 22(8):1035-1036.

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.

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.

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.

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.

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.