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91.
Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales 总被引:21,自引:4,他引:21
Powerful analyses of population structure require information from multiple
genetic loci. To help develop a molecular toolbox for obtaining this
information, we have designed universal oligonucleotide primers that span
conserved intron-exon junctions in a wide variety of animal phyla. We test
the utility of exon-primed, intron-crossing amplifications by analyzing the
variability of actin intron sequences from humpback, blue, and bowhead
whales and comparing the results with mitochondrial DNA (mtDNA) haplotype
data. Humpback actin introns fall into two major clades that exist in
different frequencies in different oceanic populations. It is surprising
that Hawaii and California populations, which are very distinct in mtDNAs,
are similar in actin intron alleles. This discrepancy between mtDNA and
nuclear DNA results may be due either to differences in genetic drift in
mitochondrial and nuclear genes or to preferential movement of males, which
do not transmit mtDNA to offspring, between separate breeding grounds.
Opposing mtDNA and nuclear DNA results can help clarify otherwise hidden
patterns of structure in natural populations.
相似文献
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Robert J. Peace Kyle K. Biggar Kenneth B. Storey James R. Green 《Nucleic acids research》2015,43(20):e138
The prediction of novel pre-microRNA (miRNA) from genomic sequence has received considerable attention recently. However, the majority of studies have focused on the human genome. Previous studies have demonstrated that sensitivity (correctly detecting true miRNA) is sustained when human-trained methods are applied to other species, however they have failed to report the dramatic drop in specificity (the ability to correctly reject non-miRNA sequences) in non-human genomes. Considering the ratio of true miRNA sequences to pseudo-miRNA sequences is on the order of 1:1000, such low specificity prevents the application of most existing tools to non-human genomes, as the number of false positives overwhelms the true predictions. We here introduce a framework (SMIRP) for creating species-specific miRNA prediction systems, leveraging sequence conservation and phylogenetic distance information. Substantial improvements in specificity and precision are obtained for four non-human test species when our framework is applied to three different prediction systems representing two types of classifiers (support vector machine and Random Forest), based on three different feature sets, with both human-specific and taxon-wide training data. The SMIRP framework is potentially applicable to all miRNA prediction systems and we expect substantial improvement in precision and specificity, while sustaining sensitivity, independent of the machine learning technique chosen. 相似文献
95.
SYNOPSIS. Ochromonas danica in a complex natural growth medium dies at 6–10 C in 4 days; O. malhamensis in ∼2 days. O. danica grown in the medium supplemented with 4.0% glycerol survived at −10±2 C for 35 days, and with 8% glycerol 29 days. O. malhamensis lasted only to 5 days in these media supplemented with 4% glycerol. Ethylene glycol and dimethylsulfoxide were too toxic to be effective. Difficulties in freeze-preservation of certain other phagocytic cells, notably blood granulocytes having comparatively simple flexuous outer membranes, add interest to use of O. danica and O. malhamensis as test organisms for preservation methods, especially in the convenient, inexpensive -10 to -20 C range. Biphasic media with an overlay of distilled water serve for conservation at room temperature. Problems of mutational erosion of these photosynthetic phagotrophs are discussed. 相似文献