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171.
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Norman Sachs Joep de Ligt Oded Kopper Ewa Gogola Gergana Bounova Fleur Weeber Anjali Vanita Balgobind Karin Wind Ana Gracanin Harry Begthel Jeroen Korving Ruben van Boxtel Alexandra Alves Duarte Daphne Lelieveld Arne van Hoeck Robert Frans Ernst Francis Blokzijl Isaac Johannes Nijman Hans Clevers 《Cell》2018,172(1-2):373-386.e10
174.
Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion 总被引:32,自引:4,他引:28
Simple but exact statistical tests for detecting a cluster of associated
nucleotide changes in DNA are presented. The tests are based on the linear
distribution of a set of s sites among a total of n sites, where the s
sites may be the variable sites, sites of insertion/deletion, or
categorized in some other way. These tests are especially useful for
detecting gene conversion and intragenic recombination in a sample of DNA
sequences. In this case, the sites of interest are those that correspond to
particular ways of splitting the sequences into two groups (e.g., sequences
A and D vs. sequences B, C, and E-J). Each such split is termed a
phylogenetic partition. Application of these methods to a well-documented
case of gene conversion in human gamma-globin genes shows that sites
corresponding to two of the three observed partitions are significantly
clustered, whereas application to hominoid mitochondrial DNA
sequences--among which no recombination is expected to occur--shows no
evidence of such clustering. This indicates that clustering of
partition-specific sites is largely due to intragenic recombination or gene
conversion. Alternative hypotheses explaining the observed clustering of
sites, such as biased selection or mutation, are discussed.
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175.
The nucleotide sequences of the cow epsilon 2 and epsilon 4 globin genes
were determined. The sequences were 95% identical. These genes arose via a
four-gene block duplication that also gave rise to the bovine fetal (gamma)
and adult (beta) genes. Their deduced amino acid sequences are unlike any
previously reported fetal or adult globins; rather, comparison to other
mammalian globin genes indicates that they are embryonic in nature. The
sequence data indicate that these two genes have converted each other
during evolution. Pairwise comparison to the corresponding goat genes shows
greater similarity between paralogues than between more directly related
orthologues. This is in direct contrast to the situation between the cow
and goat fetal and adult genes. These observations suggest that the
frequency of DNA conversion or the fixation of conversion events may vary
in different locations of the cow beta-globin cluster.
相似文献
176.
Evidence for the involvement of the 16kD gene promoter in initiation of chromosomal replication of Escherichia coli strains carrying a B/r-derived replication origin. 总被引:4,自引:1,他引:3
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Initiation of chromosomal DNA replication of several Escherichia coli dnaA (Ts) strains is diminished in cell harbouring pBR322 hybrid plasmids carrying both oriC and the adjacent 16kD gene promoter of E. coli K12. This perturbance, resulting in very slow growth, is caused both by the dnaA allele and the E. coli B/r-derived region of the replication origin of these strains. Cloning and DNA sequence analysis of the E. coli B/r replication origin revealed several base differences as compared to the E. coli K12 sequence. The replication origin of temperature sensitive fast growing mutants, originating from a homologous exchange between chromosomal and plasmid DNA sequences were also cloned. Sequence data showed that a single base change within the promoter of the 16kD gene of these dnaA (Ts) strains is able to suppress the inhibition of chromosomal DNA replication by the mentioned pBR322 hybrid plasmids. Our results strongly indicate a role of the 16kD gene promoter in control of initiation of chromosomal DNA replication. 相似文献
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Human responses to propionic acid. I. Quantification of within- and between-participant variation in perception by normosmics and anosmics 总被引:4,自引:3,他引:1
The objective of this study was to fully characterize normosmic perception
of stimuli expected to cause widely varying degrees of olfactory and nasal
trigeminal stimulation and to directly evaluate the possible role of
olfactory nerve stimulation in nasal irritation sensitivity. During each of
four identical test sessions, four anosmic and 31 normosmic participants
were presented with a range of concentrations extending from peri-threshold
for normosmics to supra- threshold for anosmics. For each session, odor (O)
and nasal irritation (NI) sensitivities were summarized in terms of the
concentrations required to produce four sensation levels ('iso-response'
concentrations). Within-participant variation in these iso-response
concentrations was < 10-fold for 95% of normosmics, for both O and NI.
For O but not NI, these apparent fluctuations in sensitivity were largely
accounted for by the uncertainty surrounding the iso-response
concentrations calculated for each session. Anosmics exhibited minimal
within- and between-participant variation in NI and required, for all but
the highest perceptual level, a higher concentration than almost all
normosmics. Between-participant variation, expressed in terms of 90%
confidence interval widths, was approximately 0.5 log units for both O and
NI for the highest perceptual level, but increased to approximately 0.8 and
1.8 log units, respectively, for the lowest (peri- threshold) level. Our
findings suggest that: (i) most apparent variation over time in O
sensitivity is actually a reflection of the uncertainty surrounding
estimates of sensitivity obtained for each session; (ii) within- and
between-participant variation in O sensitivity is far less than is commonly
reported; and (iii) low to moderate levels of NI in normosmics are the
result of relatively weak trigeminal stimulation combined with much greater
olfactory activation.
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