by Matthew Cobb
Peyrieras, N. and Morange, M., ‘The study of lysogeny at the Pasteur Institute (1950–1960): an epistemologically open system’, Studies in History and Philosophy of Biology and Biomedical Sciences, vol. 33, 2002, pp. 419–30.
Pfeiffer, J. E., ‘Woods Hole in 1949’, Scientific American, vol. 181 (3), 1949, pp. 13–17.
Philippe, H., Brinkmann, H., Lavrov, D. V. et al., ‘Resolving difficult phylogenetic questions: why more sequences are not enough’, PLoS Biology, vol. 9, 2011, article e1000602.
Piccirilli, J. A., Krauch, T., Moroney, S. E. and Benner, S. A., ‘Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet’, Nature, vol. 343, 1990, pp. 33–7.
Pichot, A., Histoire de la notion de gène, Paris, Flammarion, 1999.
Pickering, A., The Cybernetic Brain: Sketches of Another Future, London, University of Chicago Press, 2010.
Pickstone, J. V., Ways of Knowing: A New History of Science, Technology and Medicine, Manchester, Manchester University Press, 2001.
Pinheiro, V. B., Taylor, A. I., Cozens, C. et al., ‘Synthetic genetic polymers capable of heredity and evolution’, Science, vol. 336, 2012, pp. 341–4.
Piper, A., ‘Light on a dark lady’, Trends in Biochemical Sciences, vol. 23, 1998, pp. 151–4.
Planer, R. J., ‘Replacement of the “genetic program” program’, Biology and Philosophy, vol. 29, 2014, pp. 33–53.
Poczai, P., Bell, N. and Hyvönen, J., ‘Imre Festetics and the Sheep Breeders’ Society of Moravia: Mendel’s forgotten “research network”‘, PLoS Biology, vol. 12, 2014, article e1001772.
Pollister, A. W., Hewson, S. and Alfert, M., ‘Studies on the desoxypentose nucleic acid content of animal nuclei’, Journal of Cellular Physiology, vol. 38 (Suppl. 1), 1951, pp. 101–19.
Pollock, M. R., ‘The discovery of DNA: An ironic tale of chance, prejudice and insight’, Journal of General Microbiology, vol. 63, 1970, pp. 1–20.
Polyanski, A, A., Hlevnjal, M. and Zagrovic, B., ‘Proteome-wide analysis reveals clues of complementary interactions between mRNAs and their cognate proteins as the physicochemical foundation of the genetic code’, RNA Biology, vol. 10, 2013, pp. 1248–54.
Pontecorvo, G., ‘Genetic formulation of gene structure and gene action’, Advances in Enzymology, vol. 13, 1952, pp. 121–49.
Powner, M. W., Gerland, B. and Sutherland, J. D., ‘Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions’, Nature, vol. 459, 2009, pp. 239–42.
Pringle, P., The Murder of Nikolai Vavilov, New York, Simon & Schuster, 2008.
Pross, A., What is Life? How Chemistry Becomes Biology, Oxford, Oxford University Press, 2012.
Prüfer, K., Racimo, F., Patterson, N. et al., ‘The complete genome sequence of a Neanderthal from the Altai Mountains’, Nature, vol. 505, 2014, pp. 43–9.
Prusiner, S. B., ‘Novel proteinaceous infectious particles cause scrapie’, Science, vol. 216, 1982, pp. 136–44.
Prusiner, S. B., ‘Prions’, Proceedings of the National Academy of Sciences USA, vol. 95, 1998, pp. 13363–83.
Prusiner, S. B. and McCarty, M., ‘Discovering DNA encodes heredity and prions are infectious proteins’, Annual Review of Genetics, vol. 40, 2006, pp. 25–45.
Ptashne, M., ‘François Jacob (1920–2013)’, Cell, vol. 253, 2013, pp. 1180–2.
Quastler, H., ‘A primer on information theory’, in H. P. Yockey, R. L. Platzman and H. Quastler (eds), Symposium on Information Theory in Biology, London, Pergamon, 1958a, pp. 3–49.
Quastler, H., ‘The domain of information theory in biology’, in H. P. Yockey, R. L. Platzman and H. Quastler (eds), Symposium on Information Theory in Biology, London, Pergamon, 1958b, pp. 187–96.
Quastler, H., ‘The status of information theory in biology: a round table discussion’, in H. P. Yockey, R. L. Platzman and H. Quastler (eds), Symposium on Information Theory in Biology, London, Pergamon, 1958c, pp. 399–402.
Rabinow, P., Making PCR: A Story of Biotechnology, Chicago, University of Chicago Press, 1996.
Radford, E. J., Ito, M., Shi, H. et al., ‘In utero undernourishment perturbs the adult sperm methylome and intergenerational metabolism’, Science, vol. 345, 2014, article 1255903.
Rasmussen, N., Gene Jockeys: Life Science and the Rise of Biotech Enterprise, Baltimore, Johns Hopkins University Press, 2014.
Reaves, M. L., Sinha, S., Rabinowitz, J. D. et al., ‘Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells’, Science, vol. 337, 2012, pp. 470–3.
Rechavi, O., Minevich, G. and Hobert, O., ‘Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans‘, Cell, vol. 147, 2011, pp. 1248–56.
Regier, J. C., Shultz, J. W., Zwick, A. et al., ‘Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences’, Nature, vol. 463, 2010, pp. 1079–83.
Reich, D., Green, R. E., Kircher, M. et al., ‘Genetic history of an archaic hominin group from Denisova Cave in Siberia’, Nature, vol. 468, 2010, pp. 1053–60.
Relyea, R. A., ‘New effects of Roundup on amphibians: Predators reduce herbicide mortality; herbicides induce antipredator morphology’, Ecological Applications, vol. 22, 2012, pp. 634–47.
Remigi, P., Capela, D., Clerissi, C. et al., ‘Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer’, PLoS Biology, vol. 12, 2014, article e1001942.
Rheinberger, H.-J., Towards a History of Epistemic Things: Synthesizing Proteins in the Test Tube, Stanford, Stanford University Press, 1997.
Rich, A., ‘An introduction to intra-cellular information transfer’, in R. Bellman (ed.), Proceedings of Symposia in Applied Mathematics XIV: Mathematical Problems in the Biological Sciences, Providence, RI, American Mathematical Society, 1962, pp. 205–13.
Rich, A., ‘Gamow and the genetic code’, in E. Harper, W. C. Parke and D. Anderson (eds), George Gamow Symposium, ASP Conference Series, Vol. 129), 1997, pp. 114–22.
Rich, A., ‘The excitement of discovery’, Annual Review of Biochemistry, vol. 73, 2004, pp. 1–37.
Rich, A. and Zhang, S., ‘Timeline. Z-DNA, the long road to biological function’, Nature Reviews Genetics, vol. 4, 2003, pp. 566–72.
Rich, A., Davies, D. R., Crick, F. H. and Watson, J. D., ‘The molecular structure of polyadenylic acid’, Journal of Molecular Biology, vol. 3, 1961, pp. 71–86.
Ridley, M., Francis Crick: Discoverer of the Genetic Code, London, Harper Perennial, 2006.
Rietveld, C. A., Esko, T., Davies, G. et al., ‘Common genetic variants associated with cognitive performance identified using the proxy-phenotype method’, Proceedings of the National Academy of Sciences USA, vol. 111, 2014, pp. 13790–4.
RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) and the FANTOM Consortium, ‘Antisense transcription in the mammalian transcriptome’, Science, vol. 309, 2005, pp. 1564–6.
Ring, K. L. and Cavalcanti, A. R. O., ‘Consequences of stop codon reassignment on protein evolution in ciliates with alternative genetic codes’, Molecular Biology and Evolution, vol. 25, 2007, pp. 179–86.
Rinke, C., Schwientek, P., Sczyrba, A. et al., ‘Insights into the phylogeny and coding potential of microbial dark matter’, Nature, vol. 499, 2013, pp. 431–7.
Roberts, R. B. (ed.), Microsomal Particles and Protein Synthesis, London, Pergamon, 1958.
Roberts, R. B., ‘Alternative codes and templates’, Proceedings of the National Academy of Sciences USA, vol. 48, 1962, pp. 897–900.
Robertson, M. P. and Joyce, G. F., ‘The origins of the RNA world’, Cold Spring Harbor Perspectives in Biology, vol. 4, 2012, article a003608.
Roch, A., ‘Die Geschichte der Computermaus’, Telepolis, 28 August 1998. [English translation at http://www-sul.stanford.edu/siliconbase/wip/control.html.]
Roch, A., ‘Biopolitics and intuitive algebra in the mathematization of cryptology? A review of Shannon’s ‘A
mathematical theory of cryptography’ from 1945’, Cryptologia, vol. 23, 1999, pp. 261–6.
Roche, J., ‘Notice nécrologique: André Boivin (1895–1949)’, Bulletin de la Société de Chimie Biologique, vol. 31, 1949, pp. 1564–7.
Rogers, E. M., ‘Claude Shannon’s cryptography research during World War II and the mathematical theory of communication’, Proceedings, IEEE 28th International Carnaham Conference on Security Technology, 1994, pp. 1–5.
Rogozin, I. B., Carmel, L., Csuros, M. and Koonin, E. V., ‘Origin and evolution of spliceosomal introns’, Biology Direct, vol. 7, 2012, p. 11.
Romiguier, J., Ranwez, V., Douzery, E. J. P. and Galtier, N., ‘Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes’, Genome Research, vol. 20, 2010, pp. 1001–9.
Rosenblith, W. A., ‘Cybernetics, or Control and communication in the animal and the machine by Norbert Wiener’, Annals of the American Academy of Political and Social Science, vol. 264, 1949, pp. 287–8.
Rosenblueth, A., Wiener, N. and Bigelow, J., ‘Behavior, purpose and teleology’, Philosophy of Science, vol. 10, 1943, pp. 18–24.
Rovner, A. J., Haimovich, A. D., Katz, S. R., et al., ‘Recoded organisms engineered to depend on synthetic amino acids’, Nature, vol. XXX, 2015, pp. 89–93.
Rowen, J. W., Eden, M. and Kahler, H., ‘Molecular characteristics of sodium desoxyribonucleate’, Biochimica et Biophysica Acta, vol. 10, 1953, pp. 89–92.
Rutherford, A., Creation, London, Penguin, 2013.
Safaee, N., Noronha, A. M., Rodionov, D. et al., ‘Structure of the parallel duplex of poly(A) RNA: evaluation of a 50 year-old prediction’, Angewandte Chemie International Edition, vol. 52, 2013, pp. 10370–3.
Salas, M., Smith M. A., Stanley, W. M. Jr. et al., ‘Direction of reading of the genetic message’, Journal of Biological Chemistry, vol. 240, 1965, pp. 3988–95.
Sánchez-Silva, R., Villalobo, E., Morin, L. and Torres A., ‘A new noncanonical nuclear genetic code: Translation of UAA into glutamate’, Current Biology, vol. 13, 2003, pp. 442–7.
Sanger F., ‘Sequences, sequences, and sequences’, Annual Review of Biochemistry, vol. 57, 1988, pp. 1–28.
Sanger, F. and Thompson, E. O. P., ‘The amino-acid sequence in the glycyl chain of insulin. 1. The investigation of lower peptides from partial hydrolysates’, Biochemical Journal, vol. 53, 1953a, pp. 353–66.
Sanger, F. and Thompson, E. O. P., ‘The amino-acid sequence in the glycyl chain of insulin. 2. The investigation of peptides from enzymic hydrolysates’, Biochemical Journal, vol. 53, 1953b, pp. 366–74.
Sanger, F. and Tuppy, H., ‘The amino-acid sequence in the phenylalanyl chain of insulin. I. The investigation of lower peptides from partial hydrolysates’, Biochemical Journal, vol. 49, 1951a, pp. 463–81.
Sanger, F. and Tuppy, H., ‘The amino-acid sequence in the phenylalanyl chain of insulin. II. The investigation of peptides from enzymic hydrolysates’, Biochemical Journal, vol. 49, 1951b, pp. 481–90.
Sanger, F., Nicklen, S. and Coulson, A. R., ‘DNA sequencing with chain-terminating inhibitors’, Proceedings of the National Academy of Sciences USA, vol. 74, 1977, pp. 5463–7.
Sanger, F., Coulson, A. R., Friedmann, T. et al., ‘The nucleotide sequence of bacteriophage phiX174’, Journal of Molecular Biology, vol. 125, 1978, pp. 225–46.
Sankararaman, S., Mallick, S., Dannemann, M. et al., ‘The genomic landscape of Neanderthal ancestry in present-day humans’, Nature, vol. 507, 2014, pp. 354–7.
Sapp, J. The New Foundations of Evolution: On the Tree of Life, Oxford, Oxford University Press, 2009.
Sarkar, S., ‘What is Life? revisited’, BioScience, vol. 41, 1991, pp. 631–4.
Sarkar, S., ‘Biological information: a skeptical look at some central dogmas of molecular biology’, in S. Sarkar (ed.), The Philosophy and History of Molecular Biology: New Perspectives, Dordrecht, Kluwer, 1996a, pp. 187–231.
Sarkar, S., ‘Decoding “coding” – information and DNA’, BioScience, vol. 46, 1996b, pp. 857–64.
Sarkar, S., ‘Information in genetics and developmental biology: Comments on Maynard Smith’, Philosophy of Science, vol. 67, 2000, pp. 208–13.
Sarkar, S., ‘Erwin Schrödinger’s excursus on genetics’, in O. Harman and M. R. Dietrich (eds), Outsider Scientists: Routes to Innovation in Biology, Chicago, Chicago University Press, 2013, pp. 93–109.
Sasidharan, R. and Gerstein, M., ‘Genomics: Protein fossils live on as RNA’, Nature, vol. 453, 2008, pp. 729–31.
Sayre, A., Rosalind Franklin and DNA, London, Norton, 1975.
Schaffner, K., ‘Logic of discovery and justification in regulatory genetics’, Studies in History and Philosophy of Science, vol. 4, 1974, pp. 349–85.
Schlatter, M. and Aizawa, K., ‘Walter Pitts and “A Logical Calculus”’, Synthese, vol. 162, 2008, pp. 235–50.
Schmucker D., Clemens, J. C., Shu, H. et al., ‘Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity’, Cell, vol. 101, 2000, pp. 671–84.
Schneider, T. D., Stormo, G. D., Gold, L. and Ehrenfeucht, A., ‘Information content of binding sites on nucleotide sequences’, Journal of Molecular Biology, vol. 188, 1986, pp. 415–31.
Schrödinger, E., What is Life?, Cambridge, Cambridge University Press, 2000.
Schultz, J., ‘Aspects of the relation between genes and development in Drosophila‘, The American Naturalist, vol. 69, 1935, pp. 30–54.
Schultz, J., ‘The evidence of the nucleoprotein nature of the gene’, Cold Spring Harbor Symposia on Quantitative Biology, vol. 9, 1941, pp. 55–65.
Schultz, J., ‘The nature of heterochromatin’, Cold Spring Harbor Symposia on Quantitative Biology, vol. 12, 1947, pp. 179–91.
Schuster, S. C., ‘Next-generation sequencing transforms today’s biology’, Nature Methods, vol. 5, 2008, pp. 16–18.
Schwartz, D., ‘Speculations on gene action and protein specificity’, Proceedings of the National Academy of Sciences USA, vol. 41, 1955, pp. 300–7.
Schwartz, J., In Pursuit of the Gene: From Darwin to DNA, Cambridge, MA, Harvard University Press, 2008.
Shama, L. N. S. and Wegner, K. W., ‘Grandparental effects in marine sticklebacks: transgenerational plasticity across multiple generations’, Journal of Evolutionary Biology, vol. 27, 2014, pp. 2297–307.
Shannon, C. E., An Algebra for Theoretical Genetics, unpublished PhD thesis, Massachusetts Institute of Technology, 1940.
Shannon, C. E., ‘A mathematical theory of communication’, The Bell System Technical Journal, vol. 227, 1948a, pp. 379–423.
Shannon, C. E., ‘A mathematical theory of communication’, The Bell System Technical Journal, vol. 227, 1948b, pp. 623–56.
Shannon, C. E. and Weaver, W., The Mathematical Theory of Communication, Urbana, University of Illinois Press, 1949.
Shapiro, B. and Hofreiter, M., ‘A paleogenomic perspective on evolution and gene function: new insights from ancient DNA’, Science, vol. 343, 2014, article 1236573.
Shapiro, J. A., ‘Revisiting the Central Dogma in the twenty-first century’, Annals of the New York Academy of Sciences, vol. 1178, 2009, pp. 6–28.
shCherbak, V. I. and Makukov, M. A., ‘The “Wow! signal” of the terrestrial genetic code’, Icarus, vol. 224, 2013, pp. 228–42.
Shea, N., ‘What’s transmitted? Inherited information’, Biology and Philosophy, vol. 26, 2011, pp. 183–9.
Shen, P. S., Park, J., Qin, Y., et al., ‘Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains’, Science, vol. 347, 2015, pp. 75–8.
Sheridan, C., ‘First CRISPR-Cas patent opens race to stake out intellectual property’, Nature Biotechnology, vol. 32, 2014, pp. 599–601.
Shine, I. and Wrobel, S., Thomas Hunt Morgan: Pioneer of Genetics, Lexington, University of Kentucky Press, 1976.
Shreeve, J., The Genome War, New York, Knopf, 2004.
Singer, M., ‘Leon Heppel and the early days of
RNA biochemistry’, Journal of Biological Chemistry, vol. 278, 2003, pp. 47351–6.
Slater, E. C., ’1961 Moscow, USSR: The Fifth International Congress of Biochemistry’, IUBMB Life, vol. 55, 2003, pp. 185–7.
Sloan, P. R. and Fogel, B., Creating a Physical Biology. The Three-Man Paper and Early Molecular Biology, London, University of Chicago Press, 2011.
Smith, Z. D., Chan, M. M., Humm, K. C. et al., ‘DNA methylation dynamics of the human preimplantation embryo’, Nature, vol. 511, 2014, pp. 611–15.
Sofyer, V. N., ‘The consequences of political dictatorship for Russian science’, Nature Reviews Genetics, vol. 2, 2001, pp. 723–9.
Söll, D., Ohtsuka, E., Jones, D. S. et al., ‘Studies on polynucleotides, XLIX. Stimulation of the binding of aminoacyl-sRNAs to ribosomes by ribotrinucleotides and a survey of codon assignments for 20 amino acids’, Proceedings of the National Academy of Sciences USA, vol. 54, 1965, pp. 1378–85.
Sonneborn, T. M., ‘Molecular biology of the gene’, Science, vol. 150, 1965, p. 1282.
Spetner, L. M., ‘Information transmission in evolution’, IEEE Transactions on Information Theory, vol. 14, 1968, pp. 3–6.
Speyer, J. F., Lengyel, P., Basilio, C. and Ochoa, S., ‘Synthetic polynucleotides and the amino acid code, II’, Proceedings of the National Academy of Sciences USA, vol. 48, 1962a, pp. 63–8.
Speyer, J. F., Lengyel, P., Basilio, C. and Ochoa, S., ‘Synthetic polynucleotides and the amino acid code, IV’, Proceedings of the National Academy of Sciences USA, vol. 48, 1962b, pp. 441–8.
Speyer, J. F., Lengyel, P., Basilio, C. et al., ‘Synthetic polynucleotides and the amino acid code’, Cold Spring Harbor Symposia on Quantitative Biology, vol. 28, 1963, pp. 559–68.
Spiegelman, S., ‘Nuclear and cytoplasmic factors controlling enzymatic constitution’, Cold Spring Harbor Symposia on Quantitative Biology, vol. 11, 1946, pp. 256–77.
Spiegelman, S. and Landman, O. E., ‘Genetics of microorganisms’, Annual Review of Microbiology, vol. 8, 1954, pp. 181–236.
Srinivasan, G., James, C. M. and Krzycki, J. A., ‘Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA’, Science, vol. 296, 2002, pp. 1459–62.