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41.
Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics 总被引:3,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42.
A novel mutator of Escherichia coli carrying a defect in the dgt gene, encoding a dGTP triphosphohydrolase 下载免费PDF全文
A novel mutator locus in Escherichia coli was identified from a collection of random transposon insertion mutants. Several mutators in this collection were found to have an insertion in the dgt gene, encoding a previously characterized dGTP triphosphohydrolase. The mutator activity of the dgt mutants displays an unusual specificity. Among the six possible base pair substitutions in a lacZ reversion system, the G·C→C·G transversion and A·T→G·C transition are strongly enhanced (10- to 50-fold), while a modest effect (two- to threefold) is also observed for the G·C→A·T transition. Interestingly, a two- to threefold reduction in mutant frequency (antimutator effect) is observed for the G·C→T·A transversion. In the absence of DNA mismatch repair (mutL) some of these effects are reduced or abolished, while other effects remain unchanged. Analysis of these effects, combined with the DNA sequence contexts in which the reversions take place, suggests that alterations of the dGTP pools as well as alterations in the level of some modified dNTP derivatives could affect the fidelity of in vivo DNA replication and, hence, account for the overall mutator effects. 相似文献
43.
Sylvanne M Daniels Carlos E Melendez-Peña Robert J Scarborough Aïcha Daher Helen S Christensen Mohamed El Far Damian FJ Purcell Sébastien Lainé Anne Gatignol 《BMC molecular biology》2009,10(1):38-13
Background
Dicer, Ago2 and TRBP are the minimum components of the human RNA-induced silencing complex (RISC). While Dicer and Ago2 are RNases, TRBP is the double-stranded RNA binding protein (dsRBP) that loads small interfering RNA into the RISC. TRBP binds directly to Dicer through its C-terminal domain. 相似文献44.
Electron Paramagnetic Resonance (EPR) was used to investigate the Tempyo spin label (3-carbamoyl-2,2,5,5-tetramethyl-3-pyrrolin-1-yloxy) as a report group for the interactions and the conformational changes of lyophilized bovine serum albumin (BSA) and bovine hemoglobin (BH), as function of pH values in the range 2.5-11. The EPR spectra are similar with those of other non-covalently spin label porphyrins in frozen solution at very low temperatures. This behavior indicated a possible spin-spin interaction between the hemic iron and the nitroxide group. The changes in the EPR spectra as function of the pH are discussed in terms of conformational changes of the proteins. Spectral simulations and magnetic EPR parameters reveal the following: (i) one single paramagnetic species, with Gaussian line shape, was used for the best fits of experimental spectra in the case of serum albumin samples; and (ii) a weighted sum of Lorentzian and Gaussian line shape in the case of hemoglobin samples. The representation of correlation time vs. pH, reveals a dependence of degree of immobilization of spin label on the conformational changes of proteins in acidic and basic environment. 相似文献
45.
Yui Osanai Damian S. Bougoure Helen L. Hayden Mark J. Hovenden 《Plant and Soil》2013,368(1-2):419-431
Background and aims
Specific associations exist between plant species and the soil microbial community and these associations vary between habitat types and different plant groups. However, there is evidence that the associations are highly specific. Hence, we aimed to determine the specificity of plant-microbe relationships amongst co-occurring grass species in a temperate grassland.Methods and results
We examined the broad microbial groups of bacteria and fungi as well as a specific fungal group, the arbuscular mycorrhizal community amongst two dominant C3 and C4 species and one sub-dominant C3 species using terminal restriction fragment length polymorphism (T-RFLP) analysis. We found that the two dominant species were more similar to each other in their bacterial and arbuscular mycorrhizal community composition than either was to the sub-dominant species, but not in their fungal community composition. We also found no clear evidence that those differences were directly linked to soil chemical properties.Conclusions
Our results demonstrate that co-occurring grass species have a distinct soil microbial community and T-RFLP analysis is able to detect plant species effect on the microbial community composition on an extremely local scale, providing an insight into the differences in the response of bacterial, fungal and arbuscular mycorrhizal communities to different, but similar and co-occurring, plant species. 相似文献46.
The power to separate the variance of a quantitative trait locus (QTL) from the polygenic variance is determined by the variability
of genes identical by descent (IBD) at the QTL. This variability may increase with inbreeding. Selfing, the most extreme form
of inbreeding, increases the variability of the IBD value shared by siblings, and thus has a higher efficiency for QTL mapping
than random mating. In self-incompatible organisms, sib mating is the closest form of inbreeding. Similar to selfing, sib
mating may also increase the power of QTL detection relative to random mating. In this study, we develop an IBD-based method
under sib mating designs for QTL mapping. The efficiency of sib mating is then compared with random mating. Monte Carlo simulations
show that sib mating designs notably increase the power for QTL detection. When power is intermediate, the power to detect
a QTL using full-sib mating is, on average, 7% higher than under random mating. In addition, the IBD-based method proposed
in this paper can be used to combine data from multiple families. As a result, the estimated QTL parameters can be applied
to a wide statistical inference space relating to the entire reference population.
This revised version was published online in July 2006 with corrections to the Cover Date. 相似文献
47.
Alternatively spliced RNAs encode several isoforms of CD46 (MCP), a regulator of complement activation 总被引:2,自引:0,他引:2
Damian F. J. Purcell Sarah M. Russell Nicholas J. Deacon Melissa A. Brown David J. Hooker Ian F. C. McKenzie 《Immunogenetics》1991,33(5-6):335-344
Five alternative cDNA clones were isolated for CD46, also known as the membrane cofactor protein (MCP) for the factor I-mediated cleavage of the complement convertases. One of these cDNA clones (a) was identical to an earlier MCP clone. The other four CD46 clones 3ontained the four NH2-terminanl short consensus repeat (SCR) units of MCP, but differed at the region encoding the carboxyl-terminal of the protein which includes an extracellular segment rich in Ser, Thr, and Pro residues, a hydrophobic membrane-spanning domain, and a 33 amino acid cytoplasmic tail. The different CD46 cDNAs have variously: (b) inserted a 93 base pair (bp) exon resulting in a new cytoplasmic tail of 26 amino acids; (c) deleted a 42 bp exon from the extracellular Ser/Thr rich region; (d) used a cryptic splice acceptor sequence to delete 37 bp from an exon encoding transmembrane sequence; or (e) failed to splice the intron after the four SCR units. These were shown by northern blot and polymerase chain reaction to arise by alternative splicing of CD46 RNA. Forms (a), (b), and (c) of CD46 RNA are common in placental RNA, but (d) was rare, and (e) was incompletely processed and therefore aberrant. The polymerase chain reaction (PCR) was used to map the sites of the intron/exon junctions and demonstrate further possible splice variants of CD46. The alternative RNAs for CD46 may correlate to the different isoforms of CD46 found in different tissues, tumors, and in serum.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number M58050.
Address correspondence and offprint requests to: D. F. J. Purcell. 相似文献
48.
49.
The additive genetic effects of traits can be used to predict evolutionary trajectories,
such as responses to selection. Non-additive genetic and maternal environmental effects
can also change evolutionary trajectories and influence phenotypes, but these effects have
received less attention by researchers. We partitioned the phenotypic variance of survival
and fitness-related traits into additive genetic, non-additive genetic and maternal
environmental effects using a full-factorial breeding design within two allopatric
populations of Atlantic salmon (Salmo salar). Maternal environmental effects were
large at early life stages, but decreased during development, with non-additive genetic
effects being most significant at later juvenile stages (alevin and fry). Non-additive
genetic effects were also, on average, larger than additive genetic effects. The
populations, generally, did not differ in the trait values or inferred genetic
architecture of the traits. Any differences between the populations for trait values could
be explained by maternal environmental effects. We discuss whether the similarities in
architectures of these populations is the result of natural selection across a common
juvenile environment. 相似文献
50.