15 posts · 6,526 views
We research viral evolution via computational biology so that we can stop them. Our main topics are phylogenies and network epidemiology. We primarily work with HIV. Science pirates. Because open access isn't always open enough. We document the scientific process, the papers we read and the background context.
The authors propose that the main factor limiting people's perception of climate change is the natural variability of the weather, citing a recent USA survey evidencing that public opinion on the existence and importance of global warming is heavily influenced by recent local climatic variation. The paper focus on summer heat, asserting that variation in [...]... Read more »
Phylogenetic trees are a specialization of hierarchical clustering which elegantly capture relatedness between observations, grouping like with like. Yet hierarchical clusterings have one common complaint, as compared to density/distribution based clustering, the ability to classify the data into different types. Finding a meaningful cut of the tree into subtrees remains an open question in the [...]... Read more »
Prosperi MC, Ciccozzi M, Fanti I, Saladini F, Pecorari M, Borghi V, Di Giambenedetto S, Bruzzone B, Capetti A, Vivarelli A.... (2011) A novel methodology for large-scale phylogeny partition. Nature communications, 321. PMID: 21610724
The authors compare 136 isolates of V. Cholerae, 113 of which are from the 7th (El Tor) pandemic and 18 previously published genomes. The consensus tree identified eight distinct lineages, and shows that the El Tor clades seem to have origin independent of the classic 01 clinical isolates. A supplemental tree of the El Tor [...]... Read more »
Mutreja A, Kim DW, Thomson NR, Connor TR, Lee JH, Kariuki S, Croucher NJ, Choi SY, Harris SR, Lebens M.... (2011) Evidence for several waves of global transmission in the seventh cholera pandemic. Nature, 477(7365), 462-5. PMID: 21866102
Our dispersal from Africa was rapid. The dispersal began 60-70 kya, reaching SE Asia/Australia 45 kya, and northern Europe 42 kya. Previous to this, the arid climate of NE Africa and Arabia would have been a formidible barrier. Likewise, dispersal into the Americas appears to have been blocked until 15 kya by the massive ice [...]... Read more »
Eriksson A, Betti L, Friend AD, Lycett SJ, Singarayer JS, von Cramon-Taubadel N, Valdes PJ, Balloux F, & Manica A. (2012) Late Pleistocene climate change and the global expansion of anatomically modern humans. Proceedings of the National Academy of Sciences of the United States of America, 109(40), 16089-94. PMID: 22988099
A heterogeneous model of the reproductive number shows that most diseases have superspreaders.... Read more »
The authors determine that superspreading is a normal feature of disease spread, and provide both a model and a definition for superspreading. Define the individual reproductive number v (the expected number of secondary cases from the infected individual) as a random gamma distributed variable with mean R0 and dispersion k. Modeling transmission as a Poisson [...]... Read more »
One of the earlier papers on the subject, dating from 1996. Phylogenetic analysis powerfully describes evolutionary patterns, but until this paper its accuracy had not been tested in a real-world case. Such testing is still impossible for multicellular life. Virus, however, evolve so rapidly they can be monitored in real time. The authors analyze a [...]... Read more »
Leitner T, Escanilla D, Franzén C, Uhlén M, & Albert J. (1996) Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis. Proceedings of the National Academy of Sciences of the United States of America, 93(20), 10864-9. PMID: 8855273
Phylo-MCOA is a method for comparing a large number of phylogenetic trees in order to identify outliers, either genes or species. Genes which have radically different evolutionary history than the consensus suggest: significantly faster or slower evolutionary rate, under positive selection, horizontal transfer, paralogous Outlier species might be experience gene transfer passed through bottlenecks have [...]... Read more »
de Vienne DM, Ollier S, & Aguileta G. (2012) Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis. Molecular biology and evolution, 29(6), 1587-98. PMID: 22319162
The authors present an alignment-free method for estimating the number of pair-wise mismatches between two sequences. Distance between a Query sequence Q and a subject sequence S is given by shustrings. A shustring starting at position i for Q is the shortest substring Q[i...i+x] that does not appear in S. This is a shustring of length x. [...]... Read more »
Haubold B, & Pfaffelhuber P. (2012) Alignment-free population genomics: an efficient estimator of sequence diversity. G3 (Bethesda, Md.), 2(8), 883-9. PMID: 22908037
editors note: I have mixed feelings about posting this article. I am not opposed to GM food per se, but have many reservations about its use in practice. Since GM is protected by patents, it takes our common heritage and makes it the property of one company. GM as currently practiced supports mass monoculture agriculture, [...]... Read more »
Séralini GE, Clair E, Mesnage R, Gress S, Defarge N, Malatesta M, Hennequin D, & de Vendômois JS. (2012) Long term toxicity of a Roundup herbicide and a Roundup-tolerant genetically modified maize. Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association. PMID: 22999595
Altruism is widespread in nature, both in occurance and in how it is expressed. This work claims to be one of the first which classifies altruism into different types. Using the three canonical functional responses of ecological modeling to map resource supply onto reproductive output, the authors identify four distinct types of altruism. Survival. Defense, [...]... Read more »
Van Dyken JD, & Wade MJ. (2012) Origins of altruism diversity I: the diverse ecological roles of altruistic strategies and their evolutionary responses to local competition. Evolution; international journal of organic evolution, 66(8), 2484-97. PMID: 22834747
The author previously distinguish between four distinct altruistic stratetigies: “r-strategies” (survival and fecundity altruism) and “K-strategies” (resource enhancement and resource efficiency altruism). R-strategies increase growth rate and are counterselected by intense local resource competition, K-strategies increase growth yeild and are favored by intense resource competition. Organisms do not evolve to fit a static environment, but [...]... Read more »
Van Dyken JD, & Wade MJ. (2012) Origins of altruism diversity ii: runaway coevolution of altruistic strategies via "reciprocal niche construction". Evolution; international journal of organic evolution, 66(8), 2498-513. PMID: 22834748
Miniture sensors allow the authors to record the social networks of New Caledonian crows, logging both wide-range (21 meters) and close-range (less than 5.5 meters) encounters. They record 28,000 interactions in 7 days. The data shows that crow social networks do allow for tranmission of culutre between family groups. The average number of close-range interaction [...]... Read more »
Rutz C, Burns ZT, James R, Ismar SM, Burt J, Otis B, Bowen J, & St Clair JJ. (2012) Automated mapping of social networks in wild birds. Current biology : CB, 22(17). PMID: 22974988
Protein evolutionary rates, even within the same organism, can differ by several orders of magnitude.It is compelling to imagine that this is due to differences in the proportion of functional sites on the protein, but evidence for this hypothesis is weak. The authors try to solve the mystery by looking deeper, not at the rate [...]... Read more »
Tóth-Petróczy A, & Tawfik DS. (2011) Slow protein evolutionary rates are dictated by surface-core association. Proceedings of the National Academy of Sciences of the United States of America, 108(27), 11151-6. PMID: 21690394
We can combat HIV by introducing a competing infection with a therapeutic interfering particle (TIP). TIPs are minimal versions of the pathogen which lack envelope and structural genes of the wild-type. Typically, the resulting genome is an order of magnitude shorter. This means they are synthesized faster. They stop infection by co-opting the wild type [...]... Read more »
Metzger VT, Lloyd-Smith JO, & Weinberger LS. (2011) Autonomous targeting of infectious superspreaders using engineered transmissible therapies. PLoS computational biology, 7(3). PMID: 21483468
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