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61.
62.
ABSTRACT: Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have been designed over the last few years and have found use in comparative genomics and phylogenetic inference. However, the assessment of phylogenies built from such data has not been properly addressed to date. The standard method used in sequence-based phylogenetic inference is the bootstrap, but it relies on a large number of homologous characters that can be resampled; yet in the case of rearrangements, the entire genome is a single character. Alternatives such as the jackknife suffer from the same problem, while likelihood tests cannot be applied in the absence of well established probabilistic models. We present a new approach to the assessment of distance-based phylogenetic inference from whole-genome data; our approach combines features of the jackknife and the bootstrap and remains nonparametric. For each feature of our method, we give an equivalent feature in the sequence-based framework; we also present the results of extensive experimental testing, in both sequence-based and genome-based frameworks. Through the feature-by-feature comparison and the experimental results, we show that our bootstrapping approach is on par with the classic phylogenetic bootstrap used in sequence-based reconstruction, and we establish the clear superiority of the classic bootstrap for sequence data and of our corresponding new approach for rearrangement data over proposed variants. Finally, we test our approach on a small dataset of mammalian genomes, verifying that the support values match current thinking about the respective branches. Our method is the first to provide a standard of assessment to match that of the classic phylogenetic bootstrap for aligned sequences. Its support values follow a similar scale and its receiver-operating characteristics are nearly identical, indicating that it provides similar levels of sensitivity and specificity. Thus our assessment method makes it possible to conduct phylogenetic analyses on whole genomes with the same degree of confidence as for analyses on aligned sequences. Extensions to search-based inference methods such as maximum parsimony and maximum likelihood are possible, but remain to be thoroughly tested. 相似文献
63.
64.
Contribution of sucrose synthase, ADP-glucose pyrophosphorylase and starch synthase to starch synthesis in developing pea seeds 总被引:11,自引:0,他引:11
Using genetic variability existing amongst nine pea genotypes (Pisum sativum L.), the biochemical basis of sink strength in developing pea seeds was investigated. Sink strength was considered to be reflected by the rate of starch synthesis (RSS) in the embryo, and sink activity in the seed was reflected by the relative rate of starch synthesis (RRSS). These rates were compared to the activities of three enzymes of the starch biosynthetic pathway [sucrose synthase (Sus), ADP-glucose pyrophosphorylase and starch synthase] at three developmental stages during seed filling (25, 50 and 75% of the dry seed weight). Complete sets of data collected during seed filling for the nine genotypes showed that, for all enzyme activities (expressed on a protein basis), only Sus in the embryo and seed coat was linearly and significantly correlated to RRSS. The contribution of the three enzyme activities to the variability in RSS and RRSS was evaluated by multiple regression analysis for the first two developmental stages. Only Sus activity in the embryo could explain, at least in part, the significant variability observed for both the RSS and the RRSS at each developmental stage. We conclude that Sus activity is a reliable marker of sink activity in developing pea seeds. 相似文献
65.
Patricia Bustos María Inés Gajardo Claudio Gómez Hughes Goldie Emilio Cardemil Ana María Jabalquinto 《The protein journal》1996,15(5):467-472
The reaction of Woordward's reagent K (WRK) with model amino acids and proteins has been analyzed. Our results indicate that WRK forms 340-nm-absorbing adducts with sulfhydryl- and imidazol-containing compounds, but not with carboxylic acid derivatives, in agreement with Llamaset al. [(1986),J. Am. Chem. Soc. 108, 5543–5548], but not with Sinha and Brewer [(1985),Anal. Biochem. 151, 327–333]. The chemical modification ofEscherichia coli andSaccharomyces cerevisiae phosphoenolpyruvate carboxykinases with WRK leads to an increase in the absorption at 340 nm, and we have demonstrated its reaction with His and Cys residues in these proteins. These results caution against claims of glutamic or aspartic acid modification by WRK based on the absorption at 340 nm of protein-WRK adducts. 相似文献
66.
Patricia Bustos María Inés Gajardo Claudio Gómez Hughes Goldie Emilio Cardemil Ana María Jabalquinto 《Journal of Protein Chemistry》1996,15(5):467-472
The reaction of Woordward's reagent K (WRK) with model amino acids and proteins has been analyzed. Our results indicate that WRK forms 340-nm-absorbing adducts with sulfhydryl- and imidazol-containing compounds, but not with carboxylic acid derivatives, in agreement with Llamaset al. [(1986),J. Am. Chem. Soc.
108, 5543–5548], but not with Sinha and Brewer [(1985),Anal. Biochem.
151, 327–333]. The chemical modification ofEscherichia coli andSaccharomyces cerevisiae phosphoenolpyruvate carboxykinases with WRK leads to an increase in the absorption at 340 nm, and we have demonstrated its reaction with His and Cys residues in these proteins. These results caution against claims of glutamic or aspartic acid modification by WRK based on the absorption at 340 nm of protein-WRK adducts.Abbreviations HPLC
high-performance liquid chromatography
- MES
2-(N-morpholino)ethanesulfonic acid
- PEP
phosphoenolpyruvate
- PEPCK
phosphoenolpyruvate carboxykinase
- PTH
phenylthiohydantoin
- WRK
Woordward's reagent K (2-ethyl-5-phenylisoxazolium-3-sulfonate) 相似文献
67.
Sea urchin Hox genes: insights into the ancestral Hox cluster 总被引:3,自引:0,他引:3
We describe the Hox cluster in the radially symmetric sea urchin and
compare our findings to what is known from clusters in bilaterally
symmetric animals. Several Hox genes from the direct-developing sea urchin
Heliocidaris erythrogramma are described. CHEF gel analysis shows that the
Hox genes are clustered on a < or = 300 kilobase (kb) fragment of DNA,
and only a single cluster is present, as in lower chordates and other
nonvertebrate metazoans. Phylogenetic analyses of sea urchin, amphioxus,
Drosophila, and selected vertebrate Hox genes confirm that the H.
erythrogramma genes, and others previously cloned from other sea urchins,
belong to anterior, central, and posterior groups. Despite their radial
body plan and lack of cephalization, echinoderms retain at least one of the
anterior group Hox genes, an orthologue of Hox3. The structure of the
echinoderm Hox cluster suggests that the ancestral deuterostome had a Hox
cluster more similar to the current chordate cluster than was expected Sea
urchins have at least three Abd-B type genes, suggesting that Abd-B
expansion began before the radiation of deuterostomes.
相似文献
68.
Protein interacting with NIMA (never in mitosis A)‐1 regulates axonal growth cone adhesion and spreading through myristoylated alanine‐rich C kinase substrate isomerization 下载免费PDF全文
69.
70.
Excitatory amino acids such asl-glutamate (Glu) and quisqualate (QUIS) markedly potentiated K+-evoked release of exogeneous [3H]dopamine (DA) from rat striatal slices. Intranstriatal kainic acid injections resulted in a total disappearance of the stimulatory effects of Glu on evoked-release of [3H]DA as well as in a parallel reduction in the maximal number (Bmax) of ad-aspartate-insensitivel-[3H]Glu binding site in striatal particulate fractions. Following cortical ablation, the potentiating effect of Glu on [3H]DA release in decorticated striatal slices lasted longer, compared to normal slices, and occured during the 2nd min following K+-depolarization. However, the extent (%) of Glu stimulation on [3H]DA release remained the same in decorticated and normal striatal slices. Cortical ablation produced also a significant decrease in the Bmax and in theK
d
of thed-aspartateinsensitive binding site towardsl[3H]Glu. These results support the proposal that thed-aspartate-insensitive Glu binding site is somehow related to an amino acid receptor-mediated modulation of dopaminergic transmission in the rat corpus striatum. 相似文献