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11.
Specific binding of rat liver nuclear proteins to DNA 总被引:10,自引:0,他引:10
12.
Prud'homme B Gompel N Rokas A Kassner VA Williams TM Yeh SD True JR Carroll SB 《Nature》2006,440(7087):1050-1053
The independent evolution of morphological similarities is widespread. For simple traits, such as overall body colour, repeated transitions by means of mutations in the same gene may be common. However, for more complex traits, the possible genetic paths may be more numerous; the molecular mechanisms underlying their independent origins and the extent to which they are constrained to follow certain genetic paths are largely unknown. Here we show that a male wing pigmentation pattern involved in courtship display has been gained and lost multiple times in a Drosophila clade. Each of the cases we have analysed (two gains and two losses) involved regulatory changes at the pleiotropic pigmentation gene yellow. Losses involved the parallel inactivation of the same cis-regulatory element (CRE), with changes at a few nucleotides sufficient to account for the functional divergence of one element between two sibling species. Surprisingly, two independent gains of wing spots resulted from the co-option of distinct ancestral CREs. These results demonstrate how the functional diversification of the modular CREs of pleiotropic genes contributes to evolutionary novelty and the independent evolution of morphological similarities. 相似文献
13.
Dimensionality reduction techniques are used for representing higher dimensional data by a more parsimonious and meaningful
lower dimensional structure. In this paper we will study two such approaches, namely Carroll’s Parametric Mapping (abbreviated
PARAMAP) (Shepard and Carroll, 1966) and Tenenbaum’s Isometric Mapping (abbreviated Isomap) (Tenenbaum, de Silva, and Langford,
2000). The former relies on iterative minimization of a cost function while the latter applies classical MDS after a preprocessing
step involving the use of a shortest path algorithm to define approximate geodesic distances. We will develop a measure of
congruence based on preservation of local structure between the input data and the mapped low dimensional embedding, and compare
the different approaches on various sets of data, including points located on the surface of a sphere, some data called the
"Swiss Roll data", and truncated spheres. 相似文献
14.
A mathematical programming approach to fitting general graphs 总被引:1,自引:1,他引:0
We present an algorithm for fitting general graphs to proximity data. The algorithm utilizes a mathematical programming procedure based on a penalty function approach to impose additivity constraints upon parameters. For a user-specified number of links, the algorithm seeks to provide the connected network that gives the least-squares approximation to the proximity data with the specified number of links, allowing for linear transformations of the data. The network distance is the minimum-path-length metric for connected graphs. As a limiting case, the algorithm provides a tree where each node corresponds to an object, if the number of links is set equal to the number of objects minus one. A Monte Carlo investigation indicates that the resulting networks tend to fall within one percentage point of the least-squares solution in terms of the variance accounted for, but do not always attain this global optimum. The network model is discussed in relation to ordinal network representations (Klauer 1989) and NETSCAL (Hutchinson 1989), and applied to several well-known data sets. 相似文献
15.
Least squares algorithms for constructing constrained ultrametric and additive tree representations of symmetric proximity data 总被引:1,自引:1,他引:0
A mathematical programming algorithm is developed for fitting ultrametric or additive trees to proximity data where external constraints are imposed on the topology of the tree. The two procedures minimize a least squares loss function. The method is illustrated on both synthetic and real data. A constrained ultrametric tree analysis was performed on similarities between 32 subjects based on preferences for ten odors, while a constrained additive tree analysis was carried out on some proximity data between kinship terms. Finally, some extensions of the methodology to other tree fitting procedures are mentioned.The first author is supported as Bevoegdverklaard Navorser of the Belgian Nationaal Fonds voor Wetenschappelijk Onderzoek. 相似文献
16.
17.
A modified CANDECOMP algorithm is presented for fitting the metric version of the Extended INDSCAL model to three-way proximity
data. The Extended INDSCAL model assumes, in addition to the common dimensions, a unique dimension for each object. The modified
CANDECOMP algorithm fits the Extended INDSCAL model in a dimension-wise fashion and ensures that the subject weights for the
common and the unique dimensions are nonnegative. A Monte Carlo study is reported to illustrate that the method is fairly
insensitive to the choice of the initial parameter estimates. A second Monte Carlo study shows that the method is able to
recover an underlying Extended INDSCAL structure if present in the data. Finally, the method is applied for illustrative purposes
to some empirical data on pain relievers. In the final section, some other possible uses of the new method are discussed.
Geert De Soete is supported as “Bevoegdverklaard Navorser” of the Belgian “Nationaal Fonds voor Wetenschappelijik Onderzoek”. 相似文献
18.
Global analysis of protein localization in budding yeast 总被引:1,自引:0,他引:1
19.
Genetics and the making of Homo sapiens 总被引:4,自引:0,他引:4
Carroll SB 《Nature》2003,422(6934):849-857
Understanding the genetic basis of the physical and behavioural traits that distinguish humans from other primates presents one of the great new challenges in biology. Of the millions of base-pair differences between humans and chimpanzees, which particular changes contributed to the evolution of human features after the separation of the Pan and Homo lineages 5-7 million years ago? How can we identify the 'smoking guns' of human genetic evolution from neutral ticks of the molecular evolutionary clock? The magnitude and rate of morphological evolution in hominids suggests that many independent and incremental developmental changes have occurred that, on the basis of recent findings in model animals, are expected to be polygenic and regulatory in nature. Comparative genomics, population genetics, gene-expression analyses and medical genetics have begun to make complementary inroads into the complex genetic architecture of human evolution. 相似文献
20.
Genetic mechanisms and constraints governing the evolution of correlated traits in drosophilid flies
Some morphological traits differ greatly between related species, but it is not clear whether diversity evolves through changes in the same genes and whether similar, independent (that is, convergent) changes occur by the same mechanism. Pigmentation in fruitflies presents an attractive opportunity to explore these issues because pigmentation patterns are diverse, similar patterns have arisen in independent clades, and numerous genes governing their formation have been identified in Drosophila melanogaster. Here we show that both evolutionary diversification and convergence can be due to evolution at the same locus, by comparing abdominal pigmentation and trichome patterns and the expression of Bric-à-brac2 (Bab2), which regulates both traits in D. melanogaster, in 13 species representing the major clades of the subfamily Drosophilinae. Modifications of Bab2 expression are frequently correlated with diverse pigmentation and trichome patterns that evolved independently in multiple lineages. In a few species, Bab2 expression is not correlated with changes in pigmentation but is correlated with a conserved pattern of trichomes, indicating that this locus can be circumvented to evolve new patterns when a correlated trait is under different constraints. 相似文献