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141.
?zgün Babur Mithat G?nen Bülent Arman Aksoy Nikolaus Schultz Giovanni Ciriello Chris Sander Emek Demir 《Genome biology》2015,16(1)
We present a novel method for the identification of sets of mutually exclusive gene alterations in a given set of genomic profiles. We scan the groups of genes with a common downstream effect on the signaling network, using a mutual exclusivity criterion that ensures that each gene in the group significantly contributes to the mutual exclusivity pattern. We test the method on all available TCGA cancer genomics datasets, and detect multiple previously unreported alterations that show significant mutual exclusivity and are likely to be driver events.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-015-0612-6) contains supplementary material, which is available to authorized users. 相似文献142.
Roel Hermsen Joep de Ligt Wim Spee Francis Blokzijl Sebastian Sch?fer Eleonora Adami Sander Boymans Stephen Flink Ruben van Boxtel Robin H van der Weide Tim Aitman Norbert Hübner Marieke Simonis Boris Tabakoff Victor Guryev Edwin Cuppen 《BMC genomics》2015,16(1)
Background
Since the completion of the rat reference genome in 2003, whole-genome sequencing data from more than 40 rat strains have become available. These data represent the broad range of strains that are used in rat research including commonly used substrains. Currently, this wealth of information cannot be used to its full extent, because the variety of different variant calling algorithms employed by different groups impairs comparison between strains. In addition, all rat whole genome sequencing studies to date used an outdated reference genome for analysis (RGSC3.4 released in 2004).Results
Here we present a comprehensive, multi-sample and uniformly called set of genetic variants in 40 rat strains, including 19 substrains. We reanalyzed all primary data using a recent version of the rat reference assembly (RGSC5.0 released in 2012) and identified over 12 million genomic variants (SNVs, indels and structural variants) among the 40 strains. 28,318 SNVs are specific to individual substrains, which may be explained by introgression from other unsequenced strains and ongoing evolution by genetic drift. Substrain SNVs may have a larger predicted functional impact compared to older shared SNVs.Conclusions
In summary we present a comprehensive catalog of uniformly analyzed genetic variants among 40 widely used rat inbred strains based on the RGSC5.0 assembly. This represents a valuable resource, which will facilitate rat functional genomic research. In line with previous observations, our genome-wide analyses do not show evidence for contribution of multiple ancestral founder rat subspecies to the currently used rat inbred strains, as is the case for mouse. In addition, we find that the degree of substrain variation is highly variable between strains, which is of importance for the correct interpretation of experimental data from different labs.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1594-1) contains supplementary material, which is available to authorized users. 相似文献143.
Widdick DA Hicks MG Thompson BJ Tschumi A Chandra G Sutcliffe IC Brülle JK Sander P Palmer T Hutchings MI 《Molecular microbiology》2011,80(5):1395-1412
Following translocation, bacterial lipoproteins are lipidated by lipoprotein diacylglycerol transferase (Lgt) and cleaved of their signal peptides by lipoprotein signal peptidase (Lsp). In Gram-negative bacteria and mycobacteria, lipoproteins are further lipidated by lipoprotein N-acyl transferase (Lnt), to give triacylated lipoproteins. Streptomyces are unusual amongst Gram-positive bacteria because they export large numbers of lipoproteins via the twin arginine protein transport (Tat) pathway. Furthermore, some Streptomyces species encode two Lgt homologues and all Streptomyces species encode two homologues of Lnt. Here we characterize lipoprotein biogenesis in the plant pathogen Streptomyces scabies and report that lgt and lsp mutants are defective in growth and development while only moderately affected in virulence. Lipoproteins are lost from the membrane in an S. scabies lgt mutant but restored by expression of Streptomyces coelicolor lgt1 or lgt2 confirming that both encode functional Lgt enzymes. Furthermore, lipoproteins are N-acylated in Streptomyces with efficient N-acylation dependent on Lnt1 and Lnt2. However, deletion of lnt1 and lnt2 has no effect on growth, development or virulence. We thus present a detailed study of lipoprotein biogenesis in Streptomyces, the first study of Lnt function in a monoderm bacterium and the first study of bacterial lipoproteins as virulence factors in a plant pathogen. 相似文献
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Hazen AL Diks SH Wahle JA Fuhler GM Peppelenbosch MP Kerr WG 《Journal of proteome research》2011,10(8):3542-3550
The changes in signal transduction associated with the acquisition of specific cell fates remain poorly understood. We performed massive parallel assessment of kinase signatures of the radiations of the hematopoietic system, including long-term repopulating hematopoietic stem cells (LT-HSC), short-term repopulating HSC (ST-HSC), immature natural killer (iNK) cells, NK cells, B cells, T cells, and myeloid cells. The LT-HSC kinome is characterized by noncanonical Wnt, Ca(2+) and classical protein kinase C (PKC)-driven signaling, which is lost upon the transition to ST-HSC, whose kinome signature prominently features receptor tyrosine kinase (RTK) activation of the Ras/MAPK signaling cassette. Further differentiation to iNK maintains signaling through this cassette but simultaneously leads to activation of a PI3K/PKB/Rac signaling, which becomes the dominant trait in the kinase signature following full differentiation toward NK cells. Differentiation along the myeloid and B cell lineages is accompanied by hyperactivation of both the Ras/MAPK and PI3K/PKB/Rac signaling cassette. T cells, however, deactivate signaling and only display residual G protein-coupled pathways. Thus, differentiation along the hematopoietic lineage is associated with major remodelling of cellular kinase signature. 相似文献
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149.
Jasmina Hugi Torsten M. Scheyer P. Martin Sander Nicole Klein Marcelo R. Sánchez-Villagra 《Comptes Rendus Palevol》2011,10(5-6):413-426
The long bone microstructure of four pachypleurosaurid taxa from Monte San Giorgio (Switzerland/Italy) was studied. Pachypleurosaurids are secondarily aquatic reptiles that lived during the Middle Triassic in varying marine environments of the Tethys. All four pachypleurosaurids show high compactness values in their long bones based on a thick cortex and a calcified cartilaginous core, which remains in the medullary region throughout the ontogeny. Parts or even the entire embryonic bone layer composed of a mixture of woven-fibered bone tissue and parallel-fibered bone tissue is preserved in both pachypleurosaurid genera. The rest of the cortex consists of lamellar-zonal bone tissue type. Differences in the microstructure of the bones between the pachypleurosaurids are reflected in the occurrence of remodelling processes, which, if present, affect the innermost growth marks of the cortex or the calcified cartilaginous core. Further variation is present in the spacing pattern of the growth cycles, as well as in the degree of vascularisation of the lamellar-zonal bone tissue type. Our data on the microstructure of the long bones support previous studies on morphology and facies distribution, which indicated different habitats and adaptation to a secondary aquatic lifestyle for each pachypleurosaurid taxon. Life history data furthermore reflect different longevities and ages at sexual maturity. The bone histological data of the stratigraphically youngest and oldest pachypleurosaurid species might indicate possible climate-dependant reproductive seasons similar to Recent lacertilian squamates. 相似文献
150.