[1]    L. Gold, D. Pribnow, T. Schneider, S. Shinedling, B. S. Singer, and G. Stormo. Translational initiation in prokaryotes. Annu. Rev. Microbiol., 35:365–403, 1981.

[2]    T. D. Schneider, G. D. Stormo, J. S. Haemer, and L. Gold. A design for computer nucleic-acid-sequence storage, retrieval, and manipulation. Nucleic Acids Res., 10:3013–3024, 1982. https://doi.org/10.1093/nar/10.9.3013, http://www.ncbi.nlm.nih.gov/pubmed/7099972.

[3]    G. D. Stormo, T. D. Schneider, and L. M. Gold. Characterization of translational initiation sites in E. coli. Nucleic Acids Res., 10:2971–2996, 1982. https://doi.org/10.1093/nar/10.9.2971.

[4]    G. D. Stormo, T. D. Schneider, L. Gold, and A. Ehrenfeucht. Use of the ’Perceptron’ algorithm to distinguish translational initiation sites in E. coli. Nucleic Acids Res., 10:2997–3011, 1982. https://doi.org/10.1093/nar/10.9.2997.

[5]    L. Gold, M. Inman, E. Miller, D. Pribnow, T. D. Schneider, S. Shinedling, and G. Stormo. Translational regulation during bacteriophage T4 development. In B. F. C. Clark and H. U. Petersen, editors, Gene Expression, Alfred Benzon Symposium 19, pages 379–394, Copenhagen, 1984. Munksgaard.

[6]    T. D. Schneider, G. D. Stormo, M. A. Yarus, and L. Gold. Delila system tools. Nucleic Acids Res., 12:129–140, 1984. https://doi.org/10.1093/nar/12.1Part1.129, http://www.ncbi.nlm.nih.gov/pubmed/6694897.

[7]    J. Childs, K. Villanueba, D. Barrick, T. D. Schneider, G. D. Stormo, L. Gold, M. Leitner, and M. Caruthers. Ribosome binding site sequences and function. In R. Calendar and L. Gold, editors, Sequence Specificity in Transcription and Translation, UCLA Symposia on Molecular and Cellular Biology, Vol. 30, pages 341–350, New York, 1985. Alan R. Liss, Inc.

[8]    B. Clift, D. Haussler, R. McConnell, T. D. Schneider, and G. D. Stormo. Sequence landscapes. Nucleic Acids Res, 14:141–158, 1986. https://doi.org/10.1093/nar/14.1.141.

[9]    T. D. Schneider, G. D. Stormo, L. Gold, and A. Ehrenfeucht. Information content of binding sites on nucleotide sequences. J. Mol. Biol., 188:415–431, 1986. https://doi.org/10.1016/0022-2836(86)90165-8, https://alum.mit.edu/www/toms/papers/schneider1986/.

[10]    G. D. Stormo, T. D. Schneider, and L. Gold. Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res., 14:6661–6679, 1986. https://doi.org/10.1093/nar/14.16.6661.

[11]    T. D. Schneider. Information and entropy of patterns in genetic switches. In G. J. Erickson and C. R. Smith, editors, Maximum-Entropy and Bayesian Methods in Science and Engineering, volume 2, pages 147–154, Dordrecht, The Netherlands, 1988. Kluwer Academic Publishers.

[12]    T. D. Schneider and G. D. Stormo. Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique. Nucleic Acids Res., 17:659–674, 1989.

[13]    T. D. Schneider and R. M. Stephens. Sequence logos: A new way to display consensus sequences. Nucleic Acids Res., 18:6097–6100, 1990. https://doi.org/10.1093/nar/18.20.6097, https://alum.mit.edu/www/toms/papers/logopaper/.

[14]    D. N. Arvidson, P. Youderian, T. D. Schneider, and G. D. Stormo. Automated kinetic assay of β-galactosidase activity. BioTechniques, 11(6):733–738, December 1991.

[15]    T. D. Schneider. Theory of molecular machines. I. Channel capacity of molecular machines. J. Theor. Biol., 148:83–123, 1991. https://doi.org/10.1016/S0022-5193(05)80466-7, https://alum.mit.edu/www/toms/papers/ccmm/.

[16]    T. D. Schneider. Theory of molecular machines. II. Energy dissipation from molecular machines. J. Theor. Biol., 148:125–137, 1991. https://doi.org/10.1016/S0022-5193(05)80467-9, https://alum.mit.edu/www/toms/papers/edmm/.

[17]    N. D. Herman and T. D. Schneider. High information conservation implies that at least three proteins bind independently to F plasmid incD repeats. J. Bacteriol., 174:3558–3560, 1992.

[18]    K. E. Rudd and T. D. Schneider. Compilation of E. coli ribosome binding sites. In Jeffrey H. Miller, editor, A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria, pages 17.19–17.45, Cold Spring Harbor, New York, 1992. Cold Spring Harbor Laboratory Press.

[19]    R. M. Stephens and T. D. Schneider. Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. J. Mol. Biol., 228:1124–1136, 1992. https://doi.org/10.1016/0022-2836(92)90320-J, https://alum.mit.edu/www/toms/papers/splice/.

[20]    M. C. Shaner, I. M. Blair, and T. D. Schneider. Sequence logos: A powerful, yet simple, tool. In T. N. Mudge, V. Milutinovic, and L. Hunter, editors, Proceedings of the Twenty-Sixth Annual Hawaii International Conference on System Sciences, Volume 1: Architecture and Biotechnology Computing, pages 813–821, Los Alamitos, CA, 1993. IEEE Computer Society Press. https://alum.mit.edu/www/toms/papers/hawaii/.

[21]    T. D. Schneider. Use of information theory in molecular biology. In D. J. Matzke, editor, Workshop on Physics and Computation PhysComp ’92, Proceedings of the Workshop on Physics and computation October 2-4, Dallas, Texas, pages 102–110, Los Alamitos, CA, 1993. IEEE Computer Society Press.

[22]    P. P. Papp, D. K. Chattoraj, and T. D. Schneider. Information analysis of sequences that bind the replication initiator RepA. J. Mol. Biol., 233:219–230, 1993. https://doi.org/10.1006/jmbi.1993.1501 https://alum.mit.edu/www/toms/papers/helixrepa/.

[23]    T. D. Schneider. Protein patterns as shown by sequence logos. In P. R. Keller and Mary M. Keller, editors, Visual Cues - Practical Data Visualization, page 64, Piscataway, NJ, 1993. IEEE Press.

[24]    D. Barrick, K. Villanueba, J. Childs, R. Kalil, T. D. Schneider, C. E. Lawrence, L. Gold, and G. D. Stormo. Quantitative analysis of ribosome binding sites in E. coli. Nucleic Acids Res., 22:1287–1295, 1994. https://doi.org/10.1093/nar/22.7.1287.

[25]    T. D. Schneider. Sequence logos, machine/channel capacity, Maxwell’s demon, and molecular computers: a review of the theory of molecular machines. Nanotechnology, 5:1–18, 1994. https://doi.org/10.1088/0957-4484/5/1/001, https://alum.mit.edu/www/toms/papers/nano2/.

[26]    M. B. Toledano, I. Kullik, F. Trinh, P. T. Baird, T. D. Schneider, and G. Storz. Redox-dependent shift of OxyR-DNA contacts along an extended DNA binding site: A mechanism for differential promoter selection. Cell, 78:897–909, 1994.

[27]    P. K. Rogan and T. D. Schneider. Using information content and base frequencies to distinguish mutations from genetic polymorphisms in splice junction recognition sites. Human Mutation, 6:74–76, 1995. https://doi.org/10.1002/humu.1380060114, https://alum.mit.edu/www/toms/papers/colonsplice/.

[28]    P. K. Rogan, J. J. Salvo, R. M. Stephens, and T. D. Schneider. Visual display of sequence conservation as an aid to taxonomic classification using PCR amplification. In Clifford A. Pickover, editor, Visualizing Biological Information, pages 21–32, Singapore, 1995. World Scientific.

[29]    T. D. Schneider. Genetic patterns as shown by sequence logos. In C. Pickover, editor, The Pattern Book: Fractals, Art and Nature, pages 44–45, River Edge, NJ, 1995. World Scientific.

[30]    T. D. Schneider. New approaches in mathematical biology: Information theory and molecular machines. In Julian Chela-Flores and Francois Raulin, editors, Chemical Evolution: Physics of the Origin and Evolution of Life, pages 313–321, Dordrecht, The Netherlands, 1996. Kluwer Academic Publishers. https://doi.org/10.1007/978-94-009-1712-5_28.

[31]    T. D. Schneider. Reading of DNA sequence logos: Prediction of major groove binding by information theory. Meth. Enzym., 274:445–455, 1996. https://alum.mit.edu/www/toms/papers/oxyr/.

[32]    T. D. Schneider and D. N. Mastronarde. Fast multiple alignment of ungapped DNA sequences using information theory and a relaxation method. Discrete Applied Mathematics, 71:259–268, 1996. https://alum.mit.edu/www/toms/papers/malign, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2785095/, https://doi.org/10.1016/S0166-218X(96)00068-6.

[33]    D. K. Chattoraj and T. D. Schneider. Replication control of plasmid P1 and its host chromosome: the common ground. Prog. Nucl. Acid Res. Mol. Biol., 57:145–186, 1997. http://www.sciencedirect.com/science/article/pii/S0079660308602809, https://doi.org/10.1016/S0079-6603(08)60280-9.

[34]    T. D. Schneider and J. Spouge. Information content of individual genetic sequences. J. Theor. Biol., 189:427–441, 1997. https://doi.org/10.1006/jtbi.1997.0540, https://alum.mit.edu/www/toms/papers/ri/.

[35]    T. D. Schneider. Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences. Nucleic Acids Res., 25:4408–4415, 1997. https://doi.org/10.1093/nar/25.21.4408, https://alum.mit.edu/www/toms/papers/walker/, erratum: NAR 26(4): 1135, 1998.

[36]    P. N. Hengen, S. L. Bartram, L. E. Stewart, and T. D. Schneider. Information analysis of Fis binding sites. Nucleic Acids Res., 25:4994–5002, 1997. https://doi.org/10.1093/nar/25.24.4994, https://alum.mit.edu/www/toms/papers/fisinfo/.

[37]    P. K. Rogan, B. M. Faux, and T. D. Schneider. Information analysis of human splice site mutations. Human Mutation, 12:153–171, 1998. Erratum in: Hum Mutat 1999;13(1):82. https://doi.org/10.1002/(SICI)1098-1004(1998)12:3\%3C153::AID-HUMU3\%3E3.0.CO;2-I, https://alum.mit.edu/www/toms/papers/rfs/, https://schneider.ncifcrf.gov/papers/rfs/.

[38]    R. Allikmets, W. W. Wasserman, A. Hutchinson, P. Smallwood, J. Nathans, P. K. Rogan, T. D. Schneider, and M. Dean. Organization of the ABCR gene: analysis of promoter and splice junction sequences. Gene, 215:111–122, 1998. https://alum.mit.edu/www/toms/papers/abcr/.

[39]    S. R. Matten, T. D. Schneider, S. Ringquist, and W. S. A. Brusilow. Identification of an intragenic ribosome binding site that affects expression of the uncB gene of the Escherichia coli proton-translocating ATPase (unc) operon. J. Bacteriol., 180:3940–3945, 1998.

[40]    P. W. Tooley, J. J. Salvo, T. D. Schneider, and P. K. Rogan. Phylogenetic inference based on information theory-based PCR amplification. Journal of Phytopathology, 146:427–430, 1998. https://doi.org/10.1111/j.1439-0434.1998.tb04776.x.

[41]    S. G. Khan, H. L. Levy, R. Legerski, E. Quackenbush, J. T. Reardon, S. Emmert, A. Sancar, L. Li, T. D. Schneider, J. E. Cleaver, and K. H. Kraemer. Xeroderma pigmentosum group C splice mutation associated with autism and hypoglycinemia. J. Investigative Dermatology, 111:791–796, 1998. http://www.nature.com/jid/journal/v111/n5/abs/5600180a.html, https://doi.org/10.1046/j.1523-1747.1998.00391.x.

[42]    R. K. Shultzaberger and T. D. Schneider. Using sequence logos and information analysis of Lrp DNA binding sites to investigate discrepancies between natural selection and SELEX. Nucleic Acids Res., 27:882–887, 1999. https://alum.mit.edu/www/toms/papers/lrp/, https://doi.org/10.1093/nar/27.3.882.

[43]    T. D. Schneider and P. K. Rogan. Computational analysis of nucleic acid information defines binding sites, United States Patent 5867402, 1999. https://alum.mit.edu/www/toms/patent/walker/.

[44]    M. Zheng, B. Doan, T. D. Schneider, and G. Storz. OxyR and SoxRS regulation of fur. J. Bacteriol., 181:4639–4643, 1999. https://alum.mit.edu/www/toms/papers/oxyrfur/.

[45]    T. I. Wood, K. L. Griffith, W. P. Fawcett, K.-W. Jair, T. D. Schneider, and R. E. Wolf. Interdependence of the position and orientation of SoxS binding sites in the transcriptional activation of the class I subset of Escherichia coli superoxide-inducible promoters. Mol. Microbiol., 34:414–430, 1999.

[46]    T. D. Schneider. Measuring molecular information. J. Theor. Biol., 201:87–92, 1999. https://alum.mit.edu/www/toms/papers/ridebate/.

[47]    T. D. Schneider. The bottle. Nature, 406:351, 2000.

[48]    N. Kannan, T. D. Schneider, and S. Vishveshwara. Logos for amino-acid preferences in different backbone packing density regions of protein structural classes. Acta Crystallogr D Biol Crystallogr, 56:1156–1165, 2000. https://alum.mit.edu/www/toms/papers/Kannan.Vishveshwara2000/.

[49]    S. R. Svojanovsky, T. D. Schneider, and P. K. Rogan. Redundant designations of BRCA1 intron 11 splicing mutation; c. 4216-2A>G; IVS11-2A>G; L78833, 37698, A>G. Human Mutation, 16:264, 2000. http://www3.interscience.wiley.com/cgi-bin/abstract/73001161/START.

[50]    T. D. Schneider. Evolution of biological information. Nucleic Acids Res., 28:2794–2799, 2000. https://doi.org/10.1093/nar/28.14.2794, https://alum.mit.edu/www/toms/papers/ev/.

[51]    S. Emmert, T. D. Schneider, S. G. Khan, and K. H. Kraemer. The human XPG gene: gene architecture, alternative splicing and single nucleotide polymorphisms. Nucleic Acids Res., 29:1443–1452, 2001.

[52]    M. Zheng, X. Wang, B. Doan, K. A. Lewis, T. D. Schneider, and G. Storz. Computation-Directed Identification of OxyR-DNA Binding Sites in Escherichia coli. J. Bacteriol., 183:4571–4579, 2001.

[53]    R. K. Shultzaberger, R. E. Bucheimer, K. E. Rudd, and T. D. Schneider. Anatomy of Escherichia coli Ribosome Binding Sites. J. Mol. Biol., 313:215–228, 2001. https://doi.org/10.1006/jmbi.2001.5040, https://alum.mit.edu/www/toms/papers/flexrbs/.

[54]    T. D. Schneider. Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation. Nucleic Acids Res., 29:4881–4891, 2001. https://doi.org/10.1093/nar/29.23.4881, https://alum.mit.edu/www/toms/papers/baseflip/.

[55]    I. G. Lyakhov, P. N. Hengen, D. Rubens, and T. D. Schneider. The P1 Phage Replication Protein RepA Contacts an Otherwise Inaccessible Thymine N3 Proton by DNA Distortion or Base Flipping. Nucleic Acids Res., 29:4892–4900, 2001. https://doi.org/10.1093/nar/29.23.4892, https://alum.mit.edu/www/toms/papers/repan3/.

[56]    I. Arnould, L. M. Schriml, C. Prades, M. Lachtermachter-Triunfol, T. Schneider, C. Maintoux, C. Lemoine, D. Debono, C. Devaud, L. Naudin, S. Bauch, M. Annat, T. Annilo, R. Allikmets, B. Gold, P. Denfle, M. Rosier, and M. Dean. Identifying and characterizing a five-gene cluster of ATP-binding cassette transporters mapping to human chromosome 17q24: a new subgroup within the ABCA subfamily. GeneScreen, 1:157–164, 2001.

[57]    S. G. Khan, V. Muniz-Medina, T. Shahlavi, C. C. Baker, H. Inui, T. Ueda, S. Emmert, T. D. Schneider, and K. H. Kraemer. The human XPC DNA repair gene: arrangement, splice site information content and influence of a single nucleotide polymorphism in a splice acceptor site on alternative splicing and function. Nucleic Acids Res., 30:3624–3631, 2002.

[58]    T. D. Schneider. Consensus Sequence Zen. Applied Bioinformatics, 1:111–119, 2002. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852464/, https://alum.mit.edu/www/toms/papers/zen/.

[59]    P. N. Hengen, I. G. Lyakhov, L. E. Stewart, and T. D. Schneider. Molecular flip-flops formed by overlapping Fis sites. Nucleic Acids Res., 31(22):6663–6673, 2003. https://doi.org/10.1093/nar/gkg877.

[60]    T. D. Schneider. Some lessons for molecular biology from information theory. In Karmeshu, editor, Entropy Measures, Maximum Entropy Principle and Emerging Applications. Special Series on Studies in Fuzziness and Soft Computing. (Festschrift Volume in honour of Professor J.N. Kapour, Jawaharlal Nehru University, India), volume 119, pages 229–237, New York, 2003. Springer-Verlag. https://alum.mit.edu/www/toms/papers/lessons2003/.

[61]    T. D. Schneider and P. N. Hengen. MOLECULAR COMPUTING ELEMENTS: GATES AND FLIP-FLOPS, United States Patent 6,774,222, European Patent 1057118, 2004, 2004. US Patent WO 99/42929, PCT/US99/03469. https://alum.mit.edu/www/toms/patent/molecularcomputing/.

[62]    S. G. Khan, A. Metin, E. Gozukara, H. Inui, T. Shahlavi, V. Muniz-Medina, C. C. Baker, T. Ueda, J. R. Aiken, T. D. Schneider, and K. H. Kraemer. Two essential splice lariat branchpoint sequences in one intron in a xeroderma pigmentosum DNA repair gene: mutations result in reduced XPC mRNA levels that correlate with cancer risk. Hum Mol Genet, 13:343–352, 2004. http://hmg.oxfordjournals.org/cgi/content/full/13/3/343.

[63]    John M. Hancock and Marketa J. Zvelebil. Dictionary of Bioinformatics and Computational Biology. John Wiley & Sons, Inc., Hoboken, New Jersey, 2004. https://alum.mit.edu/www/toms/papers/Hancock.Zvelebil2004/. Thomas D. Schneider contributed 50 entries to the dictionary. The web links to Tom Schneider’s web site are incorrect but this has been handled on the server computer. See https://alum.mit.edu/www/toms/toms/. The entries in the book originated from the online page “A Glossary for Molecular Information Theory and the Delila System”, https://alum.mit.edu/www/toms/glossary.html.

[64]    I. G. Lyakhov, T. D. Schneider, G. A. Lyakhov, and N. V. Suyazov. Orientational ordering of protein micro- and nanoparticles in a nonuniform magnetic field. Physics of Wave Phenomena, 13(1):1–14, 2005.

[65]    Z. Chen and T. D. Schneider. Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases. Nucleic Acids Res., 33:6172–6187, 2005. https://doi.org/10.1093/nar/gki915, https://alum.mit.edu/www/toms/papers/t7like/.

[66]    T. D. Schneider. Claude Shannon: Biologist. IEEE Engineering in Medicine and Biology Magazine, 25(1):30–33, 2006. https://alum.mit.edu/www/toms/papers/shannonbiologist/, https://doi.org/10.1109/MEMB.2006.1578661.

[67]    T. D. Schneider and D. Rubens. HIGH SPEED PARALLEL MOLECULAR NUCLEIC ACID SEQUENCING, 2006. US Patent 6,982,146, https://alum.mit.edu/www/toms/patent/dnasequencing/.

[68]    Z. Chen and T. D. Schneider. Comparative analysis of tandem T7-like promoter containing regions in enterobacterial genomes reveals a novel group of genetic islands. Nucleic Acids Res., 34:1133–1147, 2006. https://doi.org/10.1093/nar/gkj511, https://alum.mit.edu/www/toms/papers/t7island/.

[69]    E. Bindewald, T. D. Schneider, and B. A. Shapiro. CorreLogo: An online server for 3D sequence logos of RNA and DNA alignments. Nucleic Acids Res., 34:w405–w411, 2006. https://doi.org/10.1093/nar/gkl269, https://alum.mit.edu/www/toms/papers/correlogo/.

[70]    T. D. Schneider. Twenty years of Delila and molecular information theory. Biological Theory: Integrating Development, Evolution, and Cognition, 1(3):250–260, 2006.

[71]    R. K. Shultzaberger, Zehua Chen, Karen A. Lewis, and T. D. Schneider. Anatomy of Escherichia coli σ70 promoters. Nucleic Acids Res., 35:771–788, 2007. https://doi.org/10.1093/nar/gkl956, https://alum.mit.edu/www/toms/papers/flexprom/.

[72]    R. K. Shultzaberger, L. R. Roberts, I. G. Lyakhov, I. A. Sidorov, A. G. Stephen, R. J. Fisher, and T. D. Schneider. Correlation between binding rate constants and individual information of E. coli Fis binding sites. Nucleic Acids Res., 35:5275–5283, 2007. https://doi.org/10.1093/nar/gkm471, https://alum.mit.edu/www/toms/papers/fisbc/.

[73]    Z. Chen, K. A. Lewis, R. K. Shultzaberger, I. G. Lyakhov, M. Zheng, B. Doan, G. Storz, and T. D. Schneider. Discovery of Fur binding site clusters in Escherichia coli by information theory models. Nucleic Acids Res., 35:6762–6777, 2007. https://alum.mit.edu/www/toms/papers/fur/.

[74]    H. Inui, K. S. Oh, C. Nadem, T. Ueda, S. G. Khan, A. Metin, E. Gozukara, S. Emmert, H. Slor, D. B. Busch, C. C. Baker, J. J. Digiovanna, D. Tamura, C. S. Seitz, A. Gratchev, W. H. Wu, K. Y. Chung, H. J. Chung, E. Azizi, R. Woodgate, T. D. Schneider, and K. H. Kraemer. Xeroderma Pigmentosum-Variant Patients from America, Europe, and Asia. J Invest Dermatol, 128:2055–2068, 2008. https://alum.mit.edu/www/toms/papers/xpv/.

[75]    T. D. Schneider and I. G. Lyakhov. MOLECULAR MOTOR, 2008. US Patent 7,349,834, Australian Patent 784085, European Patent 1204680, Canadian Patent 2380611, June 8, 2010. https://alum.mit.edu/www/toms/patent/molecularrotationengine/.

[76]    I. Lyakhov, K. Annangarachari, and T. D. Schneider. Discovery of Novel Tumor Suppressor p53 Response Elements Using Information Theory. Nucleic Acids Res., 36:3828–3833, 2008. https://alum.mit.edu/www/toms/papers/p53/.

[77]    M. R. Hemm, B. J. Paul, T. D. Schneider, G. Storz, and K. E. Rudd. Small membrane proteins found by comparative genomics and ribosome binding site models. Mol. Microbiol., 70:1487–1501, 2008. https://doi.org/10.1111/j.1365-2958.2008.06495.x, https://alum.mit.edu/www/toms/papers/smallproteins/.

[78]    T. D. Schneider. 70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence. Nucleic Acids Res., 38:5995–6006, 2010. https://doi.org/doi:10.1093/nar/gkq389, https://alum.mit.edu/www/toms/papers/emmgeo/.

[79]    T. D. Schneider. A brief review of molecular information theory. Nano Communication Networks, 1:173–180, 2010. https://doi.org/10.1016/j.nancom.2010.09.002, https://alum.mit.edu/www/toms/papers/brmit/.

[80]    J. H. Jeong, H. J. Kim, K. H. Kim, M. Shin, Y. Hong, J. H. Rhee, T. D. Schneider, and H. E. Choy. An unusual feature associated with LEE1 P1 promoters in enteropathogenic Escherichia coli (EPEC). Mol. Microbiol., 83:612–622, 2012. https://alum.mit.edu/www/toms/papers/leeprom/.

[81]    H. Lou, H. Li, M. Yeager, K. Im, B. Gold, T. D. Schneider, J. F. Fraumeni Jr, S. J. Chanock, S. K. Anderson, and M. Dean. Promoter variants in the MSMB gene associated with prostate cancer regulate MSMB/NCOA4 fusion transcripts. Hum. Genet., 131:1453–1466, 2012.

[82]    Ilya Lyakhov, Thomas D. Schneider, and Danielle Needle. NANOPROBES FOR DETECTION OR MODIFICATION OF MOLECULES, 2013. US Patent 8,344,121 issued January 1, 2013 https://alum.mit.edu/www/toms/patent/nanoprobe/.

[83]    Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson, and Jane B. Reece. Instructor’s Review Copy for Campbell Biology in Focus. Pearson Education Ltd, Boston, 9th edition, 2014. Sequence logos are explained on page 284. Thomas Schneider supplied the figures.

[84]    T. D. Schneider. (various entries). In John M. Hancock and Marketa J. Zvelebil, editors, Concise Encyclopaedia of Bioinformatics and Computational Biology, 2nd Edition, West Sussex, UK, 2014. Wiley-Blackwell. http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470978716.html, http://www.amazon.com/Concise-Encyclopaedia-Bioinformatics-Computational-Biology/dp/0470978716.

[85]    Ilya Lyakhov, Thomas D. Schneider, and Danielle Needle. NANOPROBES FOR DETECTION OR MODIFICATION OF MOLECULES, 2013. US Patent 8,703,734 issued April 22, 2014 https://alum.mit.edu/www/toms/patent/nanoprobe/.

[86]    K. M. Pluchino, D. Esposito, J. K. Moen, M. D. Hall, J. P. Madigan, S. Shukla, L. V. Procter, V. E. Wall, T. D. Schneider, I. Pringle, S. V. Ambudkar, D. R. Gill, S. C. Hyde, and M. M. Gottesman. Identification of a Cryptic Bacterial Promoter in Mouse (mdr1a) P-Glycoprotein cDNA. PLoS One, 10:e0136396, 2015.

[87]    Z. Qian, A. Trostel, D. E. A. Lewis, S. J. Lee, X. He, A. M. Stringer, J. T. Wade, T. D. Schneider, T. Durfee, and S. Adhya. Genome-Wide Transcriptional Regulation and Chromosome Structural Arrangement by GalR in E. coli. Front Mol Biosci, 3:74, 2016. https://doi.org/10.3389/fmolb.2016.00074.

[88]    K. J. Fenstermacher, V. Achuthan, T. D. Schneider, and J. J. DeStefano. An Evolutionary/Biochemical Connection Between Promoter- and Primer-Dependent Polymerases Revealed by Selective Evolution of Ligands by Exponential Enrichment (SELEX). J Bacteriol, MISSING:MISSING, 2018. https://doi.org/10.1128/JB.00579-17.

[89]    T. D. Schneider. Information theory primer, with an appendix on logarithms. Published on the web, 2013, 2013. https://doi.org/10.13140/2.1.2607.2000, https://alum.mit.edu/www/toms/papers/primer/.

[90]    Thomas D. Schneider, Ilya Lyakhov, and Danielle Needle. PROBE FOR NUCLEIC ACID SEQUENCING AND METHODS OF USE, 2010. US patent claims allowed; European patent number 1960550 granted on 2010 September 15. US patent number 7,871,777 granted on 2011 January 18. https://alum.mit.edu/www/toms/patent/medusa/.

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