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71.
Different functional classes of genes are characterized by different compositional properties 总被引:1,自引:0,他引:1
A compositional analysis on a set of human genes classified in several functional classes was performed. We found out that the GC3, i.e. the GC level at the third codon positions, of the genes involved in cellular metabolism was significantly higher than those involved in information storage and processing. Analyses of human/Xenopus ortologous genes showed that: (i) the GC3 increment of the genes involved in cellular metabolism was significantly higher than those involved in information storage and processing; and (ii) a strong correlation between the GC3 and the corresponding GCi, i.e. the GC level of introns, was found in each functional class. The non-randomness of the GC increments favours the selective hypothesis of gene/genome evolution. 相似文献
72.
To achieve higher level expression of Interferon α2b (IFN-α2b) in methylotrophic yeast (Pichia pastoris), a cDNA fragment coding for the mature IFN-α2b was designed and synthesized based on the synonymous codon bias of P. pastoris and optimized G+C content. The synthetic IFN-α2b was inserted into the secreted expression vector pPICZαA, and then integrated
into P. pastoris GS115 genome by electroporation. Multi-copy integrants in the Mut+ recombinant P. pastoris strain were screened by high concentrations of Zeocin. 120 hours culturing allowed expression of the IFN-α2b transformant
up to 810 mg/L as detected by SDS-PAGE and quantitative methods. In addition, Western blot analysis showed that the recombinant
proteins had immunogenicity. The significant antiviral activity of the recombinant IFN-α2b protein was verified by WISH/ VSV
system, which was 3.3×105 IU/mL.
Foundation items: The National ‘973’ Basic Research Program (2002CB111302); The National Natural Science Foundation of China
(30370807) 相似文献
73.
Immobilized pH gradient isoelectric focusing (IPG-IEF) has emerged as a highly promising alternative to strong-cation exchange fractionation as the first dimension in shot-gun proteomics. Herein is shown the compatibility of this method with iTRAQ isotope labeling for relative quantitation and validation of sequence matches from database searching. 相似文献
74.
The BRCA1 gene is located on the human chromosome 17q21.31 and plays important role in biological processes. The aminoacyl-tRNA synthetases (AARS) are a family of heterogenous enzymes responsible protein synthesis and whose secondary functions include a role in autoimmune myositis. Our findings reveal that the compositional constraint and the preference of more A/T –ending codons determine the codon usage patterns in BRCA1 gene while more G/C-ending codons influence the codon usage pattern of AARS gene among mammals. The codon usage bias in BRCA1 and AARS genes is low. The codon CGC encoding arginine amino acid and the codon TTA encoding leucine were uniformly distributed in BRCA1 and AARS genes, respectively in mammals including human. Natural selection might have played a major role while mutation pressure might have played a minor role in shaping the codon usage pattern of BRCA1 and AARS genes. 相似文献
75.
Greenland S 《Biometrics》2001,57(1):182-188
Standard presentations of epidemiological results focus on incidence-ratio estimates derived from regression models fit to specialized study data. These data are often highly nonrepresentative of populations for which public-health impacts must be evaluated. Basic methods are provided for interval estimation of attributable fractions from model-based incidence-ratio estimates combined with independent survey estimates of the exposure distribution in the target population of interest. These methods are illustrated in estimation of the potential impact of magnetic-field exposures on childhood leukemia in the United States, based on pooled data from 11 case-control studies and a U.S. sample survey of magnetic-field exposures. 相似文献
76.
Greenland S 《Biometrics》2001,57(3):663-670
In Bayesian and empirical Bayes analyses of epidemiologic data, the most easily implemented prior specifications use a multivariate normal distribution for the log relative risks or a conjugate distribution for the discrete response vector. This article describes problems in translating background information about relative risks into conjugate priors and a solution. Traditionally, conjugate priors have been specified through flattening constants, an approach that leads to conflicts with the true prior covariance structure for the log relative risks. One can, however, derive a conjugate prior consistent with that structure by using a data-augmentation approximation to the true log relative-risk prior, although a rescaling step is needed to ensure the accuracy of the approximation. These points are illustrated with a logistic regression analysis of neonatal-death risk. 相似文献
77.
The traditional definition of a confidence interval requires the coverage probability at any value of the parameter to be at least the nominal confidence level. In constructing such intervals for parameters in discrete distributions, less conservative behavior results from inverting a single two-sided test than inverting two separate one-sided tests of half the nominal level each. We illustrate for a variety of discrete problems, including interval estimation of a binomial parameter, the difference and the ratio of two binomial parameters for independent samples, and the odds ratio. 相似文献
78.
Pavesi A 《Journal of molecular evolution》2001,53(2):104-113
The GB virus C/hepatitis G virus (GBV-C/HGV) is a newly identified human RNA virus, belonging to the Flaviviridae family. Persistent infection by GBV-C/HGV is common in humans, and genetically divergent isolates have been identified in
different parts of the world. Due to the absence of a real pathogenic role of GBV-C/HGV in liver disease and its extremely
low mutation rate, this virus is a potential marker to trace prehistoric links between human populations. In this study, origin
and evolution of GBV-C/HGV were examined using a set of fully sequenced strains of worldwide origin. A first phylogenetic
analysis, addressed to the short (255 nucleotides) NS5A overlapping coding region by the neighbor-joining method, suggested
an ancient African origin of GBV-C/HGV. This notion was confirmed when the same analysis was applied to the genomic regions
showing the lowest rate of synonymous substitutions, covering one-fourth (2184 nucleotides) of the total coding potential
of the virus genome. By using a multivariate statistical method and extending the analysis to the complete coding region,
fine details of the evolutionary history of GBV-C/HGV were further elucidated. By this approach, isolates from Southeast Asia
appeared to be the most closely related to those of African origin, consistent with a major route of ancient human migrations
from Africa to southeastern parts of the Asian continent.
Received: 26 October 2000 / Accepted: 28 February 2001 相似文献
79.
Natural selection favors certain synonymous codons which aid translation in Escherichia coli, yet codons not favored by translational selection persist. We use the frequency distributions of synonymous polymorphisms
to test three hypotheses for the existence of translationally sub-optimal codons: (1) selection is a relatively weak force,
so there is a balance between mutation, selection, and drift; (2) at some sites there is no selection on codon usage, so some
synonymous sites are unaffected by translational selection; and (3) translationally sub-optimal codons are favored by alternative
selection pressures at certain synonymous sites. We find that when all the data is considered, model 1 is supported and both
models 2 and 3 are rejected as sole explanations for the existence of translationally sub-optimal codons. However, we find
evidence in favor of both models 2 and 3 when the data is partitioned between groups of amino acids and between regions of
the genes. Thus, all three mechanisms appear to contribute to the existence of translationally sub-optimal codons in E. coli.
Received: 18 July 2000 / Accepted: 17 April 2001 相似文献
80.
A survey of the patterns of synonymous codon preference in the HIV env gene reveals a correlation between the codon bias and the mutability requirements of different regions of the protein. At
hypervariable regions in gp120 one finds a greater proportion of codons that tend to mutate nonsynonymously, but to a target
that is similar in hydrophobicity and volume. We argue that this strategy results from a compromise between the selective
pressure placed on the virus by the induced immune response, which favors amino acid substitutions in the complementarity
determining regions, and the negative selection against missense mutations that violate structural constraints of the env protein.
Received: 9 June 1997 / Accepted: 25 May 1998 相似文献