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131.
David March Lars Boehme Joaquín Tintor Pedro Joaquín Vlez‐Belchi Brendan J. Godley 《Global Change Biology》2020,26(2):586-596
Marine animals are increasingly instrumented with environmental sensors that provide large volumes of oceanographic data. Here, we conduct an innovative and comprehensive global analysis to determine the potential contribution of animal‐borne instruments (ABI) into ocean observing systems (OOSs) and provide a foundation to establish future integrated ocean monitoring programmes. We analyse the current gaps of the long‐term Argo observing system (>1.5 million profiles) and assess its spatial overlap with the distribution of marine animals across eight major species groups (tuna and billfishes, sharks and rays, marine turtles, pinnipeds, cetaceans, sirenians, flying seabirds and penguins). We combine distribution ranges of 183 species and satellite tracking observations from >3,000 animals. Our analyses identify potential areas where ABI could complement OOS. Specifically, ABI have the potential to fill gaps in marginal seas, upwelling areas, the upper 10 m of the water column, shelf regions and polewards of 60° latitude. Our approach provides the global baseline required to plan the integration of ABI into global and regional OOS while integrating conservation and ocean monitoring priorities. 相似文献
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Karsten Schnatbaum Victor Solis‐Mezarino Daniil Pokrovsky Frederike Schfer Dennis Nagl Lars Hornberger Johannes Zerweck Tobias Knaute Julia Avramova‐Nehmer Mike Schutkowski Veit Hornung Holger Wenschuh Moritz Carl Vlker‐Albert Axel Imhof Ulf Reimer 《Proteomics》2020,20(10)
Targeted proteomics depends on the availability of stable isotope labeled (SIL) peptide standards, which for absolute protein quantification need to be absolutely quantified. In the present study, three new approaches for absolute quantification of SIL peptides are developed. All approaches rely on a quantification tag (Qtag) with a specific UV absorption. The Qtag is attached to the peptide during synthesis and is removed by tryptic digestion under standard proteomics workflow conditions. While one quantification method (method A) is designed to allow the fast and economic production of absolutely quantified SIL peptides, two other methods (methods B and C) are developed to enable the straightforward re‐quantification of SIL peptides after reconstitution to control and monitor known problems related to peptide solubility, precipitation, and adhesion to vials. All methods yield consistent results when compared to each other and when compared to quantification by amino acid analysis. The precise quantitation methods are used to characterize the in vivo specificity of the H3 specific histone methyltransferase EZH2. 相似文献
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Max Lundberg Xiuqin Zhong Anna Konrad Remi‐Andr Olsen Lars Rberg 《Molecular ecology》2020,29(11):1990-2003
Pathogen‐mediated balancing selection is commonly considered to play an important role in the maintenance of genetic diversity, in particular in immune genes. However, the factors that may influence which immune genes are the targets of such selection are largely unknown. To address this, here we focus on Pattern Recognition Receptor (PRR) signalling pathways, which play a key role in innate immunity. We used whole‐genome resequencing data from a population of bank voles (Myodes glareolus) to test for associations between balancing selection, pleiotropy and gene function in a set of 123 PRR signalling pathway genes. To investigate the effect of gene function, we compared genes encoding (a) receptors for microbial ligands versus downstream signalling proteins, and (b) receptors recognizing components of microbial cell walls, flagella and capsids versus receptors recognizing features of microbial nucleic acids. Analyses based on the nucleotide diversity of full coding sequences showed that balancing selection primarily targeted receptor genes with a low degree of pleiotropy. Moreover, genes encoding receptors recognizing components of microbial cell walls etc. were more important targets of balancing selection than receptors recognizing nucleic acids. Tests for localized signatures of balancing selection in coding and noncoding sequences showed that such signatures were mostly located in introns, and more evenly distributed among different functional categories of PRR pathway genes. The finding that signatures of balancing selection in full coding sequences primarily occur in receptor genes, in particular those encoding receptors for components of microbial cell walls etc., is consistent with the idea that coevolution between hosts and pathogens is an important cause of balancing selection on immune genes. 相似文献
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Background and AimsHorizontal gene transfer (HGT) is an important evolutionary mechanism because it transfers genetic material that may code for traits or functions between species or genomes. It is frequent in mitochondrial and nuclear genomes but has not been demonstrated between plastid genomes of different green land plant species.MethodsWe Sanger-sequenced the nuclear internal transcribed spacers (ITS1 and 2) and the plastid rpl16 G2 intron (rpl16). In five individuals with foreign rpl16 we also sequenced atpB-rbcL and trnLUAA-trnFGAA.Key ResultsWe discovered 14 individuals of a moss species with typical nuclear ITSs but foreign plastid rpl16 from a species of a distant lineage. None of the individuals with three plastid markers sequenced contained all foreign markers, demonstrating the transfer of plastid fragments rather than the entire plastid genome, i.e. entire plastids were not transferred. The two lineages diverged 165–185 Myr BP. The extended time interval since lineage divergence suggests that the foreign rpl16 is more likely explained by HGT than by hybridization or incomplete lineage sorting.ConclusionsWe provide the first conclusive evidence of interspecific plastid-to-plastid HGT among land plants. Two aspects are critical: it occurred at several localities during the massive colonization of recently disturbed open habitats that were created by large-scale liming as a freshwater biodiversity conservation measure; and it involved mosses whose unique life cycle includes spores that first develop a filamentous protonema phase. We hypothesize that gene transfer is facilitated when protonema filaments of different species intermix intimately when colonizing disturbed early succession habitats. 相似文献
138.
Tolar Tjaša Galik Alfred Le Bailly Matthieu Dufour Benjamin Caf Nina Toškan Borut Bužan Elena Zver Lars Janžekovič Franc Velušček Anton 《Vegetation History and Archaeobotany》2021,30(1):107-118
Vegetation History and Archaeobotany - Multi-proxy analysis of the coprolites which were found during excavations at two Late Neolithic (fourth millennium bc) pile-dwelling sites (Črnelnik and... 相似文献
139.
Barry J. Grant Lars Skjrven Xin‐Qiu Yao 《Protein science : a publication of the Protein Society》2021,30(1):20-30
Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D‐eddm package supports both experimental and theoretical simulation‐generated structures, is integrated with other methods for dissecting sequence‐structure–function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: http://thegrantlab.org/bio3d/ . 相似文献
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