Successful preparation and analysis of a 5-site 2-variable DNA library

Adleman L (1994) Molecular computation of solutions of combinatorial problems. Science 266:1021–1024. doi: 10.1126/science.7973651

Andronescu M, Aguirre-Hernandez R, Condon A et al (2003) RNAsoft: a suite of RNA secondary structure prediction and design software tools. Nucleic Acids Res 31:3416–3422. doi: 10.1093/nar/gkg612

Bishop M, Macula A, Renz T (2006) SynDCode suite, http://syndcode.geneseo.edu/ , which has a link to run the SynDCode program as well as a manuscript describing the program and the parameters used; cited 19 Mar 2007

Bishop M, D’yachkov A, Macula A et al (2007) Free Energy Gap and Statistical Thermodynamic. J Comput Biol (in press)

Bracho MA, Moy A, Barrio E (1998) Contribution of Taq polymerase-induced errors to the estimation of RNA virus diversity. J Gen Virol 79:2921–2928

Braich S, Chelyapov N, Johnson C et al (2002) Solution of a 20-variable 3-SAT problem on a DNA computer. Science 296:499–502. doi: 10.1126/science.1069528

Cai H, White P, Torney D et al (2000) Flow cytometry-based minisequencing: a new platform for high throughput single nucleotide polymorphism scoring. Genomics 66:135–143. doi: 10.1006/geno.2000.6218

Chen J, Deaton R, Garzon M (2006) Characterization of non-crosshybridizing DNA oligonucleotides manufactured in vitro. Nat Comput 5:65–181. doi: 10.1007/s11047-005-4460-2

D’yachkov A, Erdös P, Macula AJ et al (2003) Exordium for DNA codes. J Comb Optim 7(4):369–380. doi: 10.1023/B:JOCO.0000017385.39168.0d

D’yachkov AG, Vilenkin PA, Ismagilov IK et al (2005) On DNA codes. Prob Inf Trans 41(4):349–367. doi: 10.1007/s11122-006-0004-3

Eason R, Pourmand N, Tongprasit W et al (2004) Characterization of synthetic DNA bar codes in Saccharomyces cerevisiae gene-deletion strains. Proc Natl Acad Sci USA 101:11046–11051. doi: 10.1073/pnas.0403672101

Fish D, Horne M, Searles R et al (2007) Multiplex SNP discrimination. Biophys J 92:L89–L92. doi: 10.1529/biophysj.107.105320

Hardenbol P, Baner J, Jain M et al (2003) Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat Biotechnol 6:673–678. doi: 10.1038/nbt821

Kaderali L, Deshpande A, Nolan J et al (2003) Primer-design for multiplexed genotyping. Nucleic Acids Res 31:1796–1802. doi: 10.1093/nar/gkg267

Kaplan PD, Ouyang Q, Thaler DS et al (1997) Parallel overlap assembly for the construction of computational DNA libraries. J Theor Biol 188:333–4116. doi: 10.1006/jtbi.1997.0475

Ouyang Q, Kaplan PD, Liu S et al (1997) DNA solution of the maximal clique problem. Science 278:446–449. doi: 10.1126/science.278.5337.446

Pagano A, Gal S (2007) An approach to using modified nucleotides in aqueous DNA computing. Lect Notes Comput Sci 4848:161–169

Penchovsky R, Ackermann J (2003) DNA library design for molecular computation. J Comput Biol 10:215–229. doi: 10.1089/106652703321825973

Pogozelski WK, Bernard MP, Priore SF et al (2006) Experimental validation of DNA sequences for DNA computing: Use of a SYBR green assay. Lect Notes Comput Sci 3892:322–331

Ritter T (1994) Estimating population from repetitions in accumulated random samples. Cryptologia 18(2):155–190. doi: 10.1080/0161-119491882847

Rose J, Deaton R, Suyama A (2004) Statistical thermodynamic analysis and design of DNA-based computers. Nat Comput 3:443–359. doi: 10.1007/s11047-004-2641-z

Shortreed M, Chang S, Hong D (2005) A thermodynamic approach to designing structure-free combinatorial DNA word sets. Nucleic Acids Res 33:4965–4977. doi: 10.1093/nar/gki812

Tulpan D, Andronescu M, Chang S et al (2005) Thermodynamically based DNA strand design. Nucleic Acids Res 33:4951–4964. doi: 10.1093/nar/gki773

Valignat M, Theodoly O, Crocker J et al (2005) Reversible self-assembly and directed assemblyof DNA-linked micrometer-sized colloids. Proc Natl Acad Sci USA 102:4225–4229. doi: 10.1073/pnas.0500507102