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991.
Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species 总被引:1,自引:0,他引:1
Makedonka Mitreva Michael C Wendl John Martin Todd Wylie Yong Yin Allan Larson John Parkinson Robert H Waterston James P McCarter 《Genome biology》2006,7(8):R75-19
Background
Codon usage has direct utility in molecular characterization of species and is also a marker for molecular evolution. To understand codon usage within the diverse phylum Nematoda, we analyzed a total of 265,494 expressed sequence tags (ESTs) from 30 nematode species. The full genomes of Caenorhabditis elegans and C. briggsae were also examined. A total of 25,871,325 codons were analyzed and a comprehensive codon usage table for all species was generated. This is the first codon usage table available for 24 of these organisms. 相似文献992.
Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics 总被引:4,自引:1,他引:3
Fermin D Allen BB Blackwell TW Menon R Adamski M Xu Y Ulintz P Omenn GS States DJ 《Genome biology》2006,7(4):R35-13
Background
Defining the location of genes and the precise nature of gene products remains a fundamental challenge in genome annotation. Interrogating tandem mass spectrometry data using genomic sequence provides an unbiased method to identify novel translation products. A six-frame translation of the entire human genome was used as the query database to search for novel blood proteins in the data from the Human Proteome Organization Plasma Proteome Project. Because this target database is orders of magnitude larger than the databases traditionally employed in tandem mass spectra analysis, careful attention to significance testing is required. Confidence of identification is assessed using our previously described Poisson statistic, which estimates the significance of multi-peptide identifications incorporating the length of the matching sequence, number of spectra searched and size of the target sequence database. 相似文献993.
Background
In vitro maturation (IVM) of oocytes followed by fertilization in vitro (IVF) and embryo transfer offers an alternative to conventional IVF treatment that minimises drug administration and avoids ovarian hyperstimulation. However, the technique is less efficient than maturation in vivo. In the present study, a non-human primate model was used to address the hypothesis that the number of oocytes is increased and their nuclear and cytoplasmic maturity after IVM are improved when maturation is initiated in vivo by priming with hCG. 相似文献994.
Many studies have reported that polymorphisms of the mannose-binding lectin (MBL) gene are associated with autoimmune disease.
Here, we investigate the relationship between MBL gene polymorphisms and susceptibility to juvenile idiopathic arthritis (JIA)
in a Han-nationality population from the Hubei province of China. PCR-restriction fragment length polymorphism was used to
investigate polymorphisms of codons 54 and 57 in exon 1 of the MBL gene in 93 patients with JIA and 48 control children. Neither
group showed codon 57 polymorphisms. There was no significant difference in the genotypic frequencies of codon 54 between
patients with JIA and healthy controls (wild type, 71.0% versus 75.0%, respectively; heterozygous type, 25.8% versus 25.0%,
respectively; and homozygous type, 3.2% versus 0.0%, respectively). In addition, no association was found between the subgroups
of patients with JIA and control individuals. Our results provide no evidence for a relationship between MBL gene mutation
and susceptibility to JIA. 相似文献
995.
Over the past few years, there has been a dramatic increase in the identification of anti-angiogenic fragments from larger proteins with unrelated functions. These cryptic anti-angiogenic molecules are largely derived from matrix components such as collagen and fibronectin, as well as from circulating proteins and some intracellular proteins. Here, we discuss the relevance of these developments in terms of their physiological roles and possible therapeutic applications. 相似文献
996.
Triethylene tetraamine: a novel telomerase inhibitor 总被引:3,自引:0,他引:3
Telomerase inhibition can be achieved by stabilization of G-quadruplex structure. Triethylene tetraamine, a small linear molecule, has been identified as a potent telomerase inhibitor. It stabilizes both intra- and inter-molecular G-quadruplexes and shows a good differential between potent telomerase inhibition and acute cytotoxicity. 相似文献
997.
Si YX Yin SJ Oh S Wang ZJ Ye S Yan L Yang JM Park YD Lee J Qian GY 《Journal of biomolecular structure & dynamics》2012,29(5):999-1012
Tyrosinase inhibition studies have recently gained the attention of researchers due to their potential application values. We simulated docking (binding energies for AutoDock Vina: -9.1 kcal/mol) and performed a molecular dynamics simulation to verify docking results between tyrosinase and rutin. The docking results suggest that rutin mostly interacts with histidine residues located in the active site. A 10 ns molecular dynamics simulation showed that one copper ion at the tyrosinase active site was responsible for the interaction with rutin. Kinetic analyses showed that rutin-mediated inactivation followed a first-order reaction and mono- and biphasic rate constants occurred with rutin. The inhibition was a typical competitive type with K(i) = 1.10±0.25 mM. Measurements of intrinsic and ANS-binding fluorescences showed that rutin showed a relatively strong binding affinity for tyrosinase and one possible binding site that could be a copper was detected accompanying with a hydrophobic exposure of tyrosinase. Cell viability testing with rutin in HaCaT keratinocytes showed that no toxic effects were produced. Taken together, rutin has the potential to be a potent anti-pigment agent. The strategy of predicting tyrosinase inhibition based on hydroxyl group number and computational simulation may prove useful for the screening of potential tyrosinase inhibitors. 相似文献
998.
The movement of transposable elements (TE) in eukaryotic genomes can often result in the occurrence of nested TEs (the insertion of TEs into pre-existing TEs). We performed a general TE assessment using available databases to detect nested TEs and analyze their characteristics and putative functions in eukaryote genomes. A total of 802 TEs were found to be inserted into 690 host TEs from a total number of 11,329 TEs. We reveal that repetitive sequences are associated with an increased occurrence of nested TEs and sequence biased of TE insertion. A high proportion of the genes which were associated with nested TEs are predicted to localize to organelles and participate in nucleic acid and protein binding. Many of these function in metabolic processes, and encode important enzymes for transposition and integration. Therefore, nested TEs in eukaryotic genomes may negatively influence genome expansion, and enrich the diversity of gene expression or regulation. 相似文献
999.
1000.