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Keith J. Edwards Alex L. Reid Jane A. Coghill Simon T. Berry Gary L. A. Barker 《Plant biotechnology journal》2009,7(4):375-390
Single nucleotide polymorphisms are the most common polymorphism in plant and animal genomes and, as such, are the logical choice for marker-assisted selection. However, many plants are also polyploid, and marker-assisted selection can be complicated by the presence of highly similar, but non-allelic, homoeologous sequences. Despite this, there is practical and academic demand for high-throughput genotyping in several polyploid crop species, such as allohexaploid wheat. In this paper, we present such a system, which utilizes public single nucleotide polymorphisms previously identified in both agronomically important genes and in randomly selected, mapped, expressed sequence tags developed by the wheat community. To achieve relatively high levels of multiplexing, we used non-amplified genomic DNA and padlock probe pairs, together with high annealing temperatures, to differentiate between similar sequences in the wheat genome. Our results suggest that padlock probes are capable of discriminating between homoeologous sequences and hence can be used to efficiently genotype wheat varieties. 相似文献
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A parsimony analysis was performed on restriction sites at the Hba-ps4
pseudogene locus within one of four inversions associated with mouse t
haplotypes. The results suggest that all t haplotypes form a monophyletic
group and that the in (17)4 inversion originated before the radiation of
the Mus musculus species complex but after the divergence of the lineages
leading to M. spretus, M. abbotti, and M. hortulanus. A time frame based on
the evolutionary rate of mouse pseudogenes places the origin of this t
haplotype inversion at 1.5 Mya, or approximately 1.5 Myr after the origin
of the more proximal t complex inversion, in (17)2. The accumulated
evidence indicates that complete t haplotypes have been assembled in a
stepwise manner, with each of these inversions occurring on separate
chromosomal lineages and at different evolutionary times. In addition, the
evolutionary relationships of pseudogene sequences resulting from genetic
exchange between wild-type and t haplotype alleles were examined. Analysis
of sequences from the 5' and 3' sides of a putative site of recombination
resulted in cladograms with different topologies. The implications for
hypotheses concerning the evolutionary forces acting on t haplotypes and
their rapid propagation throughout worldwide populations of mice are
discussed.
相似文献
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D. Hopwood Kathleen R. Logan G. Coghill I. A. D. Bouchier 《The Histochemical journal》1977,9(2):153-161
Synopsis The histochemistry of lipids and mucosubstances in normal human oesophageal epithelium were studies in biopsies obtained from 24 patients undergoing investigations of the upper gastro-intestinal tract. Neutral fat droplets, 1–2 gmm in diameter, were present in all layers, the greatest number being in the functional layer cells. No unsaturated lipids or fatty acids were demonstrable. Much glycogen was present in the cytoplasm of the prickle and functional cell layers as demonstrated by PAS (and diastase digestion) techniques. The intercellular space of the most superfical of the functional cell layer contained neutral and sialic acid-rich acid mucopolysaccharides. These may be important in protecting the epithelium against physical and chemical trauma. 相似文献
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Robert King Nicholas Bird Ricardo Ramirez-Gonzalez Jane A. Coghill Archana Patil Keywan Hassani-Pak Cristobal Uauy Andrew L. Phillips 《PloS one》2015,10(9)
Targeted Induced Local Lesions in Genomes (TILLING) is a reverse genetics approach to identify novel sequence variation in genomes, with the aims of investigating gene function and/or developing useful alleles for breeding. Despite recent advances in wheat genomics, most current TILLING methods are low to medium in throughput, being based on PCR amplification of the target genes. We performed a pilot-scale evaluation of TILLING in wheat by next-generation sequencing through exon capture. An oligonucleotide-based enrichment array covering ~2 Mbp of wheat coding sequence was used to carry out exon capture and sequencing on three mutagenised lines of wheat containing previously-identified mutations in the TaGA20ox1 homoeologous genes. After testing different mapping algorithms and settings, candidate SNPs were identified by mapping to the IWGSC wheat Chromosome Survey Sequences. Where sequence data for all three homoeologues were found in the reference, mutant calls were unambiguous; however, where the reference lacked one or two of the homoeologues, captured reads from these genes were mis-mapped to other homoeologues, resulting either in dilution of the variant allele frequency or assignment of mutations to the wrong homoeologue. Competitive PCR assays were used to validate the putative SNPs and estimate cut-off levels for SNP filtering. At least 464 high-confidence SNPs were detected across the three mutagenized lines, including the three known alleles in TaGA20ox1, indicating a mutation rate of ~35 SNPs per Mb, similar to that estimated by PCR-based TILLING. This demonstrates the feasibility of using exon capture for genome re-sequencing as a method of mutation detection in polyploid wheat, but accurate mutation calling will require an improved genomic reference with more comprehensive coverage of homoeologues. 相似文献
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Claribel Cruz-García Alison E Murray Jorge LM Rodrigues Jeffrey A Gralnick Lee Ann McCue Margaret F Romine Frank E Löffler James M Tiedje 《BMC microbiology》2011,11(1):64