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Lesbats P Botbol Y Chevereau G Vaillant C Calmels C Arneodo A Andreola ML Lavigne M Parissi V 《PLoS pathogens》2011,7(2):e1001280
Establishment of stable HIV-1 infection requires the efficient integration of the retroviral genome into the host DNA. The molecular mechanism underlying the control of this process by the chromatin structure has not yet been elucidated. We show here that stably associated nucleosomes strongly inhibit in vitro two viral-end integration by decreasing the accessibility of DNA to integrase. Remodeling of the chromatinized template by the SWI/SNF complex, whose INI1 major component interacts with IN, restores and redirects the full-site integration into the stable nucleosome region. These effects are not observed after remodeling by other human remodeling factors such as SNF2H or BRG1 lacking the integrase binding protein INI1. This suggests that the restoration process depends on the direct interaction between IN and the whole SWI/SNF complex, supporting a functional coupling between the remodeling and integration complexes. Furthermore, in silico comparison between more than 40,000 non-redundant cellular integration sites selected from literature and nucleosome occupancy predictions also supports that HIV-1 integration is promoted in the genomic region of weaker intrinsic nucleosome density in the infected cell. Our data indicate that some chromatin structures can be refractory for integration and that coupling between nucleosome remodeling and HIV-1 integration is required to overcome this natural barrier. 相似文献
954.
LeChasseur Y Dufour S Lavertu G Bories C Deschênes M Vallée R De Koninck Y 《Nature methods》2011,8(4):319-325
Recording electrical activity from identified neurons in intact tissue is key to understanding their role in information processing. Recent fluorescence labeling techniques have opened new possibilities to combine electrophysiological recording with optical detection of individual neurons deep in brain tissue. For this purpose we developed dual-core fiberoptics-based microprobes, with an optical core to locally excite and collect fluorescence, and an electrolyte-filled hollow core for extracellular single unit electrophysiology. This design provides microprobes with tips < 10 μm, enabling analyses with single-cell optical resolution. We demonstrate combined electrical and optical detection of single fluorescent neurons in rats and mice. We combined electrical recordings and optical Ca2(+) measurements from single thalamic relay neurons in rats, and achieved detection and activation of single channelrhodopsin-expressing neurons in Thy1::ChR2-YFP transgenic mice. The microprobe expands possibilities for in vivo electrophysiological recording, providing parallel access to single-cell optical monitoring and control. 相似文献
955.
Ficarro SB Zhang Y Carrasco-Alfonso MJ Garg B Adelmant G Webber JT Luckey CJ Marto JA 《Molecular & cellular proteomics : MCP》2011,10(11):O111.011064
Despite intense, continued interest in global analyses of signaling cascades through mass spectrometry-based studies, the large-scale, systematic production of phosphoproteomics data has been hampered in-part by inefficient fractionation strategies subsequent to phosphopeptide enrichment. Here we explore two novel multidimensional fractionation strategies for analysis of phosphopeptides. In the first technique we utilize aliphatic ion pairing agents to improve retention of phosphopeptides at high pH in the first dimension of a two-dimensional RP-RP. The second approach is based on the addition of strong anion exchange as the second dimension in a three-dimensional reversed phase (RP)-strong anion exchange (SAX)-RP configuration. Both techniques provide for automated, online data acquisition, with the 3-D platform providing the highest performance both in terms of separation peak capacity and the number of unique phosphopeptide sequences identified per μg of cell lysate consumed. Our integrated RP-SAX-RP platform provides several analytical figures of merit, including: (1) orthogonal separation mechanisms in each dimension; (2) high separation peak capacity (3) efficient retention of singly- and multiply-phosphorylated peptides; (4) compatibility with automated, online LC-MS analysis. We demonstrate the reproducibility of RP-SAX-RP and apply it to the analysis of phosphopeptides derived from multiple biological contexts, including an in vitro model of acute myeloid leukemia in addition to primary polyclonal CD8(+) T-cells activated in vivo through bacterial infection and then purified from a single mouse. 相似文献
956.
Guillaume Emaresi Jérôme Pellet Sylvain Dubey Alexandre H. Hirzel Luca Fumagalli 《Conservation Genetics》2011,12(1):41-50
Habitat destruction and fragmentation are known to strongly affect dispersal by altering the quality of the environment between
populations. As a consequence, lower landscape connectivity is expected to enhance extinction risks through a decrease in
gene flow and the resulting negative effects of genetic drift, accumulation of deleterious mutations and inbreeding depression.
Such phenomena are particularly harmful for amphibian species, characterized by disjunct breeding habitats. The dispersal
behaviour of amphibians being poorly understood, it is crucial to develop new tools, allowing us to determine the influence
of landscape connectivity on the persistence of populations. In this study, we developed a new landscape genetics approach
that aims at identifying land-uses affecting genetic differentiation, without a priori assumptions about associated ecological
costs. We surveyed genetic variation at seven microsatellite loci for 19 Alpine newt (Mesotriton alpestris) populations in western Switzerland. Using strips of varying widths that define a dispersal corridor between pairs of populations,
we were able to identify land-uses that act as dispersal barriers (i.e. urban areas) and corridors (i.e. forests). Our results
suggest that habitat destruction and landscape fragmentation might in the near future affect common species such as M. alpestris. In addition, by identifying relevant landscape variables influencing population structure without unrealistic assumptions
about dispersal, our method offers a simple and flexible tool of investigation as an alternative to least-cost models and
other approaches. 相似文献
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DNA sequencing has revolutionized yeast taxonomy. Although initially rDNA sequences proved to be universal and convenient for assigning phylogenetic relationships, it was eventually supplanted by multigene analysis, which provided more discriminating and robust results. This led to a new classification of the major yeast clades, which is still used as a reference today. More recently, the availability of a large number of complete genome sequences has given a new perspective on the molecular taxonomy of yeasts by providing a high number of genes to compare. It also highlighted an unexpected aspect of yeast genome evolution: the existence of interspecific hybrids outside of the industrial Saccharomyces clade. Together with the loss of heterozygosity in interspecific hybrids and a reduced sexuality leading to clonal propagation, this observation obliges us to reexamine the present concept of species. In parallel, the ongoing challenge is to find a universal molecular marker, to improve fast authentication and, if possible, phylogeny of yeasts. The future of yeast taxonomy will involve the sequencing of more genomes, thorough analysis of populations to obtain a good representation of the biodiversity and integration of these data into dedicated databases. 相似文献
959.
Protein S-prenylation is a lipid modification that regulates membrane-protein and protein-protein interactions in cell signaling. Though sites of protein S-prenylation can be predicted based upon conserved C-terminal CaaX or CC/CXC motifs, biochemical detection of protein S-prenylation in cells is still challenging. Herein, we report an alkynyl-isoprenol chemical reporter (alk-FOH) as an efficient substrate for prenyltransferases in mammalian cells that enables sensitive detection of S-farnesylated and S-geranylgeranylated proteins using bioorthogonal ligation methods. Fluorescent detection alleviates the need to deplete cellular isoprenoids for biochemical analysis of S-prenylated proteins and enables robust characterization of S-prenylated proteins, such as effectors that are injected into host cells by bacterial pathogens. This alkynyl-prenylation reporter provides a sensitive tool for biochemical analysis and rapid profiling of prenylated proteins in cells. 相似文献
960.
Corinne Lorenzo Céline Frongia Raphaël Jorand Jérôme Fehrenbach Pierre Weiss Amina Maandhui Guillaume Gay Bernard Ducommun Valérie Lobjois 《Cell division》2011,6(1):1-8