Sat, 26 Jul 2008 08:09:10 BST CiteULike: zambujo's library [194 articles] http://www.citeulike.org/user/zambujo CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/zambujo/article/2865678 <i>Chemometrics and Intelligent Laboratory Systems, Vol. 2, No. 1. (1987), pp. 37-52.</i> Principal component analysis. S Wold Chemometrics and Intelligent Laboratory Systems, Vol. 2, No. 1. (1987), pp. 37-52. 2008-06-05T14:24:42-00:00 1987 Chemometrics and Intelligent Laboratory Systems 2 1 37 52 pca statistics http://www.citeulike.org/user/zambujo/article/118817 <i>J Mol Biol, Vol. 188, No. 3. (5 April 1986), pp. 415-431.</i><br /><br />Repressors, polymerases, ribosomes and other macromolecules bind to specific nucleic acid sequences. They can find a binding site only if the sequence has a recognizable pattern. We define a measure of the information (R sequence) in the sequence patterns at binding sites. It allows one to investigate how information is distributed across the sites and to compare one site to another. One can also calculate the amount of information (R frequency) that would be required to locate the sites, given that they occur with some frequency in the genome. Several Escherichia coli binding sites were analyzed using these two independent empirical measurements. The two amounts of information are similar for most of the sites we analyzed. In contrast, bacteriophage T7 RNA polymerase binding sites contain about twice as much information as is necessary for recognition by the T7 polymerase, suggesting that a second protein may bind at T7 promoters. The extra information can be accounted for by a strong symmetry element found at the T7 promoters. This element may be an operator. If this model is correct, these promoters and operators do not share much information. The comparisons between R sequence and R frequency suggest that the information at binding sites is just sufficient for the sites to be distinguished from the rest of the genome. Information content of binding sites on nucleotide sequences. TD Schneider GD Stormo L Gold A Ehrenfeucht J Mol Biol, Vol. 188, No. 3. (5 April 1986), pp. 415-431. 2005-03-09T21:21:57-00:00 1986 J Mol Biol 0022-2836 188 3 415 431 binding information http://www.citeulike.org/user/zambujo/article/2711454 <i>Trends in Biochemical Sciences, Vol. 23, No. 3. (1 March 1998), pp. 109-113.</i><br /><br />Site-specific DNA-protein interactions can be studied using experimental and computational methods. Experimental approaches typically analyze a protein-DNA interaction by measuring the free energy of binding under a variety of conditions. Computational methods focus on alignments of known binding sites for a protein, and, from these alignments, make estimates of the binding energy. Understanding the relationship between these two perspectives, and finding ways to improve both, is a major challenge of modern molecular biology. Specificity, free energy and information content in protein-DNA interactions Gary Stormo Dana Fields doi:10.1016/S0968-0004(98)01187-6 Trends in Biochemical Sciences, Vol. 23, No. 3. (1 March 1998), pp. 109-113. 2008-04-24T04:20:34-00:00 1998 Trends in Biochemical Sciences 23 3 109 113 binding information http://www.citeulike.org/user/zambujo/article/331510 <i>Science, Vol. 309, No. 5743. (25 August 2005), pp. 2075-2078.</i><br /><br />Organisms in fluctuating environments must adapt their behavior to survive. In clonal populations, this may be achieved through sensing followed by response, or through generation of diversity by stochastic phenotype switching. We show that stochastic switching can be favored over sensing when the environment changes infrequently. The optimal switching rates then mimic the statistics of environmental changes. We derive a relation between the long-term growth rate of the organism and the information available about its fluctuating environment. Phenotypic Diversity, Population Growth, and Information in Fluctuating Environments. Edo Kussell Stanislas Leibler doi:10.1126/science.1114383 Science, Vol. 309, No. 5743. (25 August 2005), pp. 2075-2078. 2005-09-23T21:32:25-00:00 2005 Science 1095-9203 309 5743 2075 2078 diversity fitness information population http://www.citeulike.org/user/zambujo/article/2222884 <i>(28 Dec 2007)</i><br /><br />The growth rate of organisms depends both on external conditions and on internal states, such as the expression levels of various genes. We show that to achieve a criterion mean growth rate over an ensemble of conditions, the internal variables must carry a minimum number of bits of information about those conditions. Evolutionary competition thus can select for cellular mechanisms that are more efficient in an abstract, information theoretic sense. Estimates based on recent experiments suggest that the minimum information required for reasonable growth rates is close to the maximum information that can be conveyed through biologically realistic regulatory mechanisms. These ideas are applicable most directly to unicellular organisms, but there are analogies to problems in higher organisms, and we suggest new experiments for both cases. Information and fitness Samuel Taylor Naftali Tishby William Bialek (28 Dec 2007) 2008-01-12T16:07:37-00:00 2007 fitness information http://www.citeulike.org/user/zambujo/article/1274217 <i>J Mol Biol, Vol. 193, No. 4. (20 February 1987), pp. 723-750.</i><br /><br />We present a statistical-mechanical selection theory for the sequence analysis of a set of specific DNA regulatory sites that makes it possible to predict the relationship between individual base-pair choices in the site and specific activity (affinity). The theory is based on the assumption that specific DNA sequences have been selected to conform to some requirement for protein binding (or activity), and that all sequences that can fulfil this requirement are equally likely to occur. In most cases, the number of specific DNA sequences that are known for a certain DNA-binding protein is very small, and we discuss in detail the small-sample uncertainties that this leads to. When applied to the binding sites for cro repressor in phage lambda, the theory can predict, from the sequence statistics alone, their rank order binding affinities in reasonable agreement with measured values. However, the statistical uncertainty generated by such a small sample (only 6 sites known) limits the result to order-of-magnitude comparisons. When applied to the much larger sample of Escherichia coli promoter sequences, the theory predicts the correlation between in vitro activity (k2KB values) and homology score (closeness to the consensus sequence) observed by Mulligan et al. (1984). The analysis of base-pair frequencies in the promoter sample is consistent with the assumption that base-pairs at different positions in the sites contribute independently to the specific activity, except in a few marginal cases that are discussed. When the promoter sites are ordered according to predicted activities, they seem to conform to the Gaussian distribution that results from a requirement for maximal sequence variability within the constraint of providing a certain average activity. The theory allows us to compare the number of specific sites with a certain activity to the number that would be expected from random occurrence in the genome. While strong promoters are "overspecified", in the sense that their probability of random occurrence is very low, random sequences with weak promoter-like properties are expected to occur in very large numbers. This leads to the conclusion that functional specificity is based on other properties in addition to primary sequence recognition; some possibilities are discussed. Finally, we show that the sequence information, as defined by Schneider et al. (1986), can be used directly (at least in the case of equilibrium binding sites) to estimate the number of protein molecules that are specifically bound at random "pseudosites" in the genome.(ABSTRACT TRUNCATED AT 400 WORDS) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. OG Berg PH von Hippel J Mol Biol, Vol. 193, No. 4. (20 February 1987), pp. 723-750. 2007-05-03T16:39:34-00:00 1987 J Mol Biol 0022-2836 193 4 723 750 interactions protein http://www.citeulike.org/user/zambujo/article/114199 <i>Science, Vol. 162, No. 3859. (13 December 1968), pp. 1243-1248.</i> The Tragedy of the Commons Garrett Hardin Science, Vol. 162, No. 3859. (13 December 1968), pp. 1243-1248. 2005-03-04T20:10:16-00:00 1968 Science 162 3859 1243 1248 clima rationality http://www.citeulike.org/user/zambujo/article/2137828 <i>Complexity, Vol. 2, No. 1. (1996), pp. 44-52.</i><br /><br />This article defines the concept of an information measure and shows how common information measures such as entropy, Shannon information, and algorithmic information content can be combined to solve problems of characterization, inference, and learning for complex systems. Particularly useful quantities are the effective complexity, which is roughly the length of a compact description of the identified regularities of an entity, and total information, which is effective complexity plus an entropy term that measures the information required to describe the random aspects of the entity. Mathematical definitions are given for both quantities and some applications are discussed. In particular, it is pointed out that if one compares different sets of identified regularities of an entity, the ?best? set minimizes the total information, and then, subject to that constraint, minimizes the effective complexity; the resulting effective complexity is then in many respects independent of the observer. © 1996 John Wiley & Sons, Inc. Information measures, effective complexity, and total information Murray Gell-Mann Seth Lloyd doi:10.1002/(SICI)1099-0526(199609/10)2:1<44::AID-CPLX10>3.0.CO;2-X Complexity, Vol. 2, No. 1. (1996), pp. 44-52. 2007-12-17T18:36:29-00:00 1996 Complexity 2 1 44 52 complexity information http://www.citeulike.org/user/zambujo/article/2492402 <i>Nature Biotechnology, Vol. 26, No. 3., pp. 303-304.</i> What is principal component analysis? Markus Ringnér doi:10.1038/nbt0308-303 Nature Biotechnology, Vol. 26, No. 3., pp. 303-304. 2008-03-09T04:13:08-00:00 Nature Biotechnology 1087-0156 26 3 303 304 Nature Publishing Group pca statistics http://www.citeulike.org/user/zambujo/article/81492 <i>Phys Rev E Stat Nonlin Soft Matter Phys, Vol. 69, No. 6 Pt 2. (June 2004)</i><br /><br />We present two classes of improved estimators for mutual information M(X,Y), from samples of random points distributed according to some joint probability density mu(x,y). In contrast to conventional estimators based on binnings, they are based on entropy estimates from k -nearest neighbor distances. This means that they are data efficient (with k=1 we resolve structures down to the smallest possible scales), adaptive (the resolution is higher where data are more numerous), and have minimal bias. Indeed, the bias of the underlying entropy estimates is mainly due to nonuniformity of the density at the smallest resolved scale, giving typically systematic errors which scale as functions of k/N for N points. Numerically, we find that both families become exact for independent distributions, i.e. the estimator M(X,Y) vanishes (up to statistical fluctuations) if mu(x,y)=mu(x)mu(y). This holds for all tested marginal distributions and for all dimensions of x and y. In addition, we give estimators for redundancies between more than two random variables. We compare our algorithms in detail with existing algorithms. Finally, we demonstrate the usefulness of our estimators for assessing the actual independence of components obtained from independent component analysis (ICA), for improving ICA, and for estimating the reliability of blind source separation. Estimating mutual information. A Kraskov H Stögbauer P Grassberger Phys Rev E Stat Nonlin Soft Matter Phys, Vol. 69, No. 6 Pt 2. (June 2004) 2005-01-21T15:52:08-00:00 2004 Phys Rev E Stat Nonlin Soft Matter Phys 1539-3755 69 6 Pt 2 estimation information http://www.citeulike.org/user/zambujo/article/332173 <i>Science, Vol. 286, No. 5438. (08 October 1999), pp. 295-299.</i> Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families Steve Lockless Rama Ranganathan doi:10.1126/science.286.5438.295 Science, Vol. 286, No. 5438. (08 October 1999), pp. 295-299. 2005-09-25T12:48:05-00:00 1999 Science 286 5438 295 299 evolution protein stability thermostability http://www.citeulike.org/user/zambujo/article/2515843 <i>Multivariate Behavioral Research, Vol. 34, No. 3., pp. 367-96.</i> Nonsymmetric correspondence analysis: a tool for analysing contingency tables with a dependence structure PM Kroonenberg R Lombardo Multivariate Behavioral Research, Vol. 34, No. 3., pp. 367-96. 2008-03-11T17:25:36-00:00 Multivariate Behavioral Research 34 3 367 96 Lawrence Earlbaum pca statistics http://www.citeulike.org/user/zambujo/article/2369819 <i>Journal of the American Statistical Association, Vol. 75, No. 369. (1980), pp. 74-81.</i> A Critique of Some Ridge Regression Methods G Smith F Campbell Journal of the American Statistical Association, Vol. 75, No. 369. (1980), pp. 74-81. 2008-02-13T13:08:15-00:00 1980 Journal of the American Statistical Association 75 369 74 81 JSTOR kernel http://www.citeulike.org/user/zambujo/article/350841 <i>Statistica Neerlandica, Vol. 59, No. 4. (November 2005), pp. 498-505.</i> Ridge regression revisited Paul Boer Christian Hafner doi:10.1111/j.1467-9574.2005.00304.x Statistica Neerlandica, Vol. 59, No. 4. (November 2005), pp. 498-505. 2005-10-14T12:41:14-00:00 2005 Statistica Neerlandica 0039-0402 59 4 498 505 Blackwell Publishing kernel http://www.citeulike.org/user/zambujo/article/352522 <i>(3 Mar 2003)</i><br /><br />This chapter describes gene expression analysis by Singular Value Decomposition (SVD), emphasizing initial characterization of the data. We describe SVD methods for visualization of gene expression data, representation of the data using a smaller number of variables, and detection of patterns in noisy gene expression data. In addition, we describe the precise relation between SVD analysis and Principal Component Analysis (PCA) when PCA is calculated using the covariance matrix, enabling our descriptions to apply equally well to either method. Our aim is to provide definitions, interpretations, examples, and references that will serve as resources for understanding and extending the application of SVD and PCA to gene expression analysis. Singular Value Decomposition and Principal Component Analysis Michael Wall Andreas Rechtsteiner Luis Rocha (3 Mar 2003) 2005-10-17T02:36:40-00:00 2003 statistics http://www.citeulike.org/user/zambujo/article/2259488 <i></i> Calculating the Singular Values and Pseudo-Inverse of a Matrix G Golub W Kahan 2008-01-20T01:55:42-00:00 statistics http://www.citeulike.org/user/zambujo/article/2369691 <i>Technometrics, Vol. 42, No. 1. (2000), pp. 80-86.</i> Ridge Regression: Biased Estimation for Nonorthogonal Problems AE Hoerl RW Kennard Technometrics, Vol. 42, No. 1. (2000), pp. 80-86. 2008-02-13T12:43:39-00:00 2000 Technometrics 42 1 80 86 JSTOR kernel http://www.citeulike.org/user/zambujo/article/2289037 <i>Transactions on Pattern Analysis and Machine Intelligence, Vol. 22, No. 1. (2000), pp. 4-37.</i> Statistical pattern recognition: a review AK Jain RPWJ Mao Transactions on Pattern Analysis and Machine Intelligence, Vol. 22, No. 1. (2000), pp. 4-37. 2008-01-25T11:08:00-00:00 2000 Transactions on Pattern Analysis and Machine Intelligence 22 1 4 37 statistics http://www.citeulike.org/user/zambujo/article/2289020 <i>Psychometrika, Vol. 50, No. 1. (1985), pp. 91-119.</i> An analysis and synthesis of multiple correspondence analysis, optimal scaling, dual scaling, homogeneity analysis and other methods for quantifying categorical multivariate data M Tenenhaus FW Young Psychometrika, Vol. 50, No. 1. (1985), pp. 91-119. 2008-01-25T10:57:20-00:00 1985 Psychometrika 50 1 91 119 Springer statistics http://www.citeulike.org/user/zambujo/article/2289013 <i>ACM Computing Surveys (CSUR), Vol. 31, No. 3. (1999), pp. 264-323.</i> Data clustering: a review AK Jain MN Murty PJ Flynn ACM Computing Surveys (CSUR), Vol. 31, No. 3. (1999), pp. 264-323. 2008-01-25T10:53:15-00:00 1999 ACM Computing Surveys (CSUR) 31 3 264 323 ACM Press New York, NY, USA statistics http://www.citeulike.org/user/zambujo/article/2280122 <i>Bioinformatics for Geneticists, Vol. 317 (2003)</i> Amino acid properties and consequences of substitutions MJ Betts RB Russell Bioinformatics for Geneticists, Vol. 317 (2003) 2008-01-23T11:04:20-00:00 2003 Bioinformatics for Geneticists 317 protein http://www.citeulike.org/user/zambujo/article/2244382 <i>R News, Vol. 4, No. 1. (2004), pp. 5-10.</i> The ade4 Package--I: One-table Methods D Chessel AB Dufour J Thioulouse R News, Vol. 4, No. 1. 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(2007) 2007-12-22T19:57:47-00:00 2007 PLoS Comput Biol 3 11 hiv http://www.citeulike.org/user/zambujo/article/2141170 <i>Journal of the American Society for Information Science, Vol. 44, No. 4. (1993), pp. 204-211.</i> Shannon revisited: Information in terms of uncertainty C Cole Journal of the American Society for Information Science, Vol. 44, No. 4. (1993), pp. 204-211. 2007-12-18T14:39:56-00:00 1993 Journal of the American Society for Information Science 44 4 204 211 entropy information review http://www.citeulike.org/user/zambujo/article/2141165 <i>Behav Sci, Vol. 10, No. 3. (1965), pp. 193-237.</i> Living systems: basic concepts. JG Miller Behav Sci, Vol. 10, No. 3. (1965), pp. 193-237. 2007-12-18T14:37:53-00:00 1965 Behav Sci 10 3 193 237 review http://www.citeulike.org/user/zambujo/article/2141152 <i>Evolution, Vol. 42, No. 3. (1988), pp. 433-440.</i> Experimental Studies of Pleiotropy and Epistasis in Escherichia coli. II. Compensation for Maldaptive Effects Associated with Resistance to Virus T4 RE Lenski Evolution, Vol. 42, No. 3. (1988), pp. 433-440. 2007-12-18T14:33:02-00:00 1988 Evolution 42 3 433 440 JSTOR epistasis resistance http://www.citeulike.org/user/zambujo/article/2141131 <i>Int. Microbiol, Vol. 1 (1998), pp. 265-270.</i> Bacterial evolution and the cost of antibiotic resistance RE Lenski Int. Microbiol, Vol. 1 (1998), pp. 265-270. 2007-12-18T14:26:12-00:00 1998 Int. Microbiol 1 265 270 evolution resistance thermostability http://www.citeulike.org/user/zambujo/article/2141128 <i>Genet. Mol. Res, Vol. 2, No. 4. (2003), pp. 383-393.</i> Preferred amino acids and thermostability ST Farias MC Bonato Genet. Mol. Res, Vol. 2, No. 4. (2003), pp. 383-393. 2007-12-18T14:24:31-00:00 2003 Genet. Mol. Res 2 4 383 393 protein thermostability http://www.citeulike.org/user/zambujo/article/2098757 <i>Science, Vol. 174, No. 4013. 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(2007) 2007-10-25T16:58:40-00:00 2007 The Journal of Cell Biology 177 1 Rockefeller Univ Press statistics http://www.citeulike.org/user/zambujo/article/2048467 <i>Genet Res, Vol. 65, No. 2. (1995), pp. 123-45.</i> A general model for the evolution of recombination. NH Barton Genet Res, Vol. 65, No. 2. (1995), pp. 123-45. 2007-12-03T09:02:31-00:00 1995 Genet Res 65 2 123 45 recombination http://www.citeulike.org/user/zambujo/article/2013414 <i>Philosophical Magazine, Vol. 2, No. 6. (1901), pp. 559-572.</i> On lines and planes of closest fit to systems of points in space K Pearson Philosophical Magazine, Vol. 2, No. 6. (1901), pp. 559-572. 2007-11-29T10:41:36-00:00 1901 Philosophical Magazine 2 6 559 572 pca http://www.citeulike.org/user/zambujo/article/2013405 <i>Journal of Mathematical Psychology, Vol. 47, No. 1. (2003), pp. 90-100.</i> Tutorial on maximum likelihood estimation IJ Myung Journal of Mathematical Psychology, Vol. 47, No. 1. (2003), pp. 90-100. 2007-11-29T10:40:26-00:00 2003 Journal of Mathematical Psychology 47 1 90 100 Elsevier likelihood http://www.citeulike.org/user/zambujo/article/2013382 <i>Statistical Science, Vol. 1, No. 1. (1986), pp. 54-75.</i> Bootstrap Methods for Standard Errors, Confidence Intervals, and Other Measures of Statistical Accuracy B Efron R Tibshirani Statistical Science, Vol. 1, No. 1. (1986), pp. 54-75. 2007-11-29T10:37:44-00:00 1986 Statistical Science 1 1 54 75 JSTOR bootstrap http://www.citeulike.org/user/zambujo/article/2013274 <i>HIV Sequence Compendium (2001), pp. 134-170.</i> HIV-1 fitness: implications for drug resistance, disease progression, and global epidemic evolution Quinones Mateu EJ Arts HIV Sequence Compendium (2001), pp. 134-170. 2007-11-29T10:33:09-00:00 2001 HIV Sequence Compendium 134 170 fitness hiv review http://www.citeulike.org/user/zambujo/article/2013256 <i>Antimicrobial Agents and Chemotherapy, Vol. 44, No. 4. (2000)</i> A Novel Phenotypic Drug Susceptibility Assay for Human Immunodeficiency Virus Type 1 CJ Petropoulos NT Parkin KL Limoli YS Lie T Wrin W Huang H Tian D Smith GA Winslow DJ Capon Others Antimicrobial Agents and Chemotherapy, Vol. 44, No. 4. (2000) 2007-11-29T10:30:48-00:00 2000 Antimicrobial Agents and Chemotherapy 44 4 Am Soc Microbiol hiv http://www.citeulike.org/user/zambujo/article/1984494 <i>Nat Rev Drug Discov (2007)</i> HIV drug development: the next 25 years. C Flexner Nat Rev Drug Discov (2007) 2007-11-26T10:08:52-00:00 2007 Nat Rev Drug Discov hiv http://www.citeulike.org/user/zambujo/article/1873874 <i>J. Virol., Vol. 73, No. 12. (1 December 1999), pp. 10489-10502.</i><br /><br />To understand the high variability of the asymptomatic interval between primary human immunodeficiency virus type 1 (HIV-1) infection and the development of AIDS, we studied the evolution of the C2-V5 region of the HIV-1 env gene and of T-cell subsets in nine men with a moderate or slow rate of disease progression. They were monitored from the time of seroconversion for a period of 6 to 12 years until the development of advanced disease in seven men. Based on the analysis of viral divergence from the founder strain, viral population diversity within sequential time points, and the outgrowth of viruses capable of utilizing the CXCR4 receptor (X4 viruses), the existence of three distinct phases within the asymptomatic interval is suggested: an early phase of variable duration during which linear increases (~1% per year) in both divergence and diversity were observed; an intermediate phase lasting an average of 1.8 years, characterized by a continued increase in divergence but with stabilization or decline in diversity; and a late phase characterized by a slowdown or stabilization of divergence and continued stability or decline in diversity. X4 variants emerged around the time of the early- to intermediate-phase transition and then achieved peak representation and began a decline around the transition between the intermediate and late phases. The late-phase transition was also associated with failure of T-cell homeostasis (defined by a downward inflection in CD3+ T cells) and decline of CD4+ T cells to [<=]200 cells/microl. The strength of these temporal associations between viral divergence and diversity, viral coreceptor specificity, and T-cell homeostasis and subset composition supports the concept that the phases described represent a consistent pattern of viral evolution during the course of HIV-1 infection in moderate progressors. Recognition of this pattern may help explain previous conflicting data on the relationship between viral evolution and disease progression and may provide a useful framework for evaluating immune damage and recovery in untreated and treated HIV-1 infections. Consistent Viral Evolutionary Changes Associated with the Progression of Human Immunodeficiency Virus Type 1 Infection Raj Shankarappa Joseph Margolick Stephen Gange Allen Rodrigo David Upchurch Homayoon Farzadegan Phalguni Gupta Charles Rinaldo Gerald Learn Xi He Xiao-Li Huang James Mullins J. Virol., Vol. 73, No. 12. (1 December 1999), pp. 10489-10502. 2007-11-06T13:13:16-00:00 1999 J. Virol. 73 12 10489 10502 hiv http://www.citeulike.org/user/zambujo/article/1855407 <i>Nature, Vol. 404, No. 6775. (16 March 2000), pp. 281-285.</i> The ecological cost of sex Patrick Doncaster Graeme Pound Simon Cox doi:10.1038/35005078 Nature, Vol. 404, No. 6775. (16 March 2000), pp. 281-285. 2007-11-02T09:03:18-00:00 2000 Nature 404 6775 281 285 sex http://www.citeulike.org/user/zambujo/article/1851705 <i>networks, Vol. 63, No. 57. (2001)</i> Informational Complexity and Functional Activity of RNA Structures JM Carothers SC Oestreich JH Davis JW Szostak networks, Vol. 63, No. 57. (2001) 2007-11-01T16:41:33-00:00 2001 networks 63 57 information protein http://www.citeulike.org/user/zambujo/article/1851670 <i>Protein Science, Vol. 4, No. 11. (1995), pp. 2269-2278.</i> Covariation of residues in the homeodomain sequence family ND Clarke Protein Science, Vol. 4, No. 11. (1995), pp. 2269-2278. 2007-11-01T16:30:46-00:00 1995 Protein Science 4 11 2269 2278 Cold Spring Harbor Lab information protein http://www.citeulike.org/user/zambujo/article/788462 <i>Trends in Ecology & Evolution, Vol. 21, No. 6. (June 2006), pp. 296-302.</i><br /><br />The past two decades have seen extensive growth of sexual selection research. Theoretical and empirical work has clarified many components of pre- and postcopulatory sexual selection, such as aggressive competition, mate choice, sperm utilization and sexual conflict. Genetic mechanisms of mate choice evolution have been less amenable to empirical testing, but molecular genetic analyses can now be used for incisive experimentation. Here, we highlight some of the currently debated areas in pre- and postcopulatory sexual selection. We identify where new techniques can help estimate the relative roles of the various selection mechanisms that might work together in the evolution of mating preferences and attractive traits, and in sperm-egg interactions. Sexual selection and mate choice Malte Andersson Leigh Simmons doi:10.1016/j.tree.2006.03.015 Trends in Ecology & Evolution, Vol. 21, No. 6. (June 2006), pp. 296-302. 2006-08-07T06:27:25-00:00 2006 Trends in Ecology & Evolution 21 6 296 302 sex http://www.citeulike.org/user/zambujo/article/547060 <i>Nature, Vol. 411, No. 6838. (7 June 2001), pp. 692-695.</i><br /><br />The maintenance of sexual reproduction is a problem in evolutionary theory because, all else being equal, asexual populations have a twofold fitness advantage over their sexual counterparts and should rapidly outnumber a sexual population because every individual has the potential to reproduce. The twofold cost of sex exists because of anisogamy or gamete dimorphism-egg-producing females make a larger contribution to the zygote compared with the small contribution made by the sperm of males, but both males and females contribute 50% of the genes. Anisogamy also generates the conditions for sexual selection, a powerful evolutionary force that does not exist in asexual populations. The continued prevalence of sexual reproduction indicates that the 'all else being equal' assumption is incorrect. Here I show that sexual selection can mitigate or even eliminate the cost of sex. If sexual selection causes deleterious mutations to be more deleterious in males than females, then deleterious mutations are maintained at lower equilibrium frequency in sexual populations relative to asexual populations. The fitness of sexual females is higher than asexuals because there is no difference in the fecundity of sexual females and asexuals of the same genotype, but the equilibrium frequency of deleterious mutations is lower in sexual populations. The results are not altered by synergistic epistasis in males. Sexual selection and the maintenance of sexual reproduction. AF Agrawal doi:10.1038/35079590 Nature, Vol. 411, No. 6838. (7 June 2001), pp. 692-695. 2006-03-11T00:55:52-00:00 2001 Nature 0028-0836 411 6838 692 695 sex http://www.citeulike.org/user/zambujo/article/547039 <i>Nature, Vol. 411, No. 6838. (7 June 2001), pp. 689-692.</i><br /><br />Sex is expensive. A population of females that reproduce asexually should prima facie have twice the growth rate of an otherwise equivalent anisogamous sexual population lacking paternal care, or a population with modes of paternal care that can be co-opted by parthenogenetic females. The two leading theories for the maintenance of sex require either synergistic interactions between deleterious mutations, or antagonistic epistasis between beneficial mutations. Current evidence is equivocal as to whether the required levels of epistasis exist. Here I show that a third factor, differential male mating success (or, more generally, higher variance in male than in female fitness), can drastically reduce mutational load in sexual populations with or without any form of epistasis. Differential mating success has the further advantage of being ubiquitous, and is likely to have preceded or evolved concurrently with anisogamy. Sexual selection and the maintenance of sex. S Siller doi:10.1038/35079578 Nature, Vol. 411, No. 6838. (7 June 2001), pp. 689-692. 2006-03-11T00:53:37-00:00 2001 Nature 0028-0836 411 6838 689 692 sex http://www.citeulike.org/user/zambujo/article/1846670 <i>Biology Letters, Vol. 2, No. 4. (22 December 2006), pp. 536-538.</i><br /><br />Sexual selection is a powerful and ubiquitous force in sexual populations. It has recently been argued that sexual selection can eliminate the twofold cost of sex even with low genomic mutation rates. By means of differential male mating success, deleterious mutations in males become more deleterious than in females, and it has been shown that sexual selection can drastically reduce the mutational load in a sexual population, with or without any form of epistasis. However, any mechanism that claims to maintain sexual reproduction must be able to prevent the fixation of an asexual mutant clone with a twofold fitness advantage. Here, I show that despite very strong sexual selection, the fixation of an asexual mutant cannot be prevented under reasonable genomic mutation rates. Sexual selection can have a strong effect on the average mutational load in a sexual population, but as it cannot prevent the fixation of an asexual mutant, it is unlikely to play a key role on the maintenance of sexual reproduction. Sexual selection and its effect on the fixation of an asexual clone Marcel Salathé doi:10.1098/rsbl.2006.0529 Biology Letters, Vol. 2, No. 4. (22 December 2006), pp. 536-538. 2007-10-31T11:22:51-00:00 2006 Biology Letters 2 4 536 538 sex http://www.citeulike.org/user/zambujo/article/1787756 <i>Antimicrobial Agents and Chemotherapy, Vol. 48, No. 8. (2003), pp. 3122-3126.</i> Distribution of Human Immunodeficiency Virus Type 1 Protease and Reverse Transcriptase Mutation Patterns in 4,183 Persons Undergoing Genotypic Resistance Testing SY Rhee T Liu J Ravela MJ Gonzales RW Shafer Antimicrobial Agents and Chemotherapy, Vol. 48, No. 8. (2003), pp. 3122-3126. 2007-10-19T07:36:33-00:00 2003 Antimicrobial Agents and Chemotherapy 48 8 3122 3126 Am Soc Microbiol hiv pr rt trevor http://www.citeulike.org/user/zambujo/article/1769733 <i>Cell, Vol. 82, No. 2. (1995), pp. 183-8.</i> Viral latency in HIV disease. JM Mccune Cell, Vol. 82, No. 2. (1995), pp. 183-8. 2007-10-15T10:39:26-00:00 1995 Cell 82 2 183 8 hiv review