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101.
102.
Masuya H Yoshikawa S Heida N Toyoda T Wakana S Shiroishi T 《Journal of bioinformatics and computational biology》2007,5(6):1173-1191
Recently, a number of collaborative large-scale mouse mutagenesis programs have been launched. These programs aim for a better understanding of the roles of all individual coding genes and the biological systems in which these genes participate. In international efforts to share phenotypic data among facilities/institutes, it is desirable to integrate information obtained from different phenotypic platforms reliably. Since the definitions of specific phenotypes often depend on a tacit understanding of concepts that tends to vary among different facilities, it is necessary to define phenotypes based on the explicit evidence of assay results. We have developed a website termed PhenoSITE (Phenome Semantics Information with Terminology of Experiments: http://www.gsc.riken.jp/Mouse/), in which we are trying to integrate phenotype-related information using an experimental-evidence-based approach. The site's features include (1) a baseline database for our phenotyping platform; (2) an ontology associating international phenotypic definitions with experimental terminologies used in our phenotyping platform; (3) a database for standardized operation procedures of the phenotyping platform; and (4) a database for mouse mutants using data produced from the large-scale mutagenesis program at RIKEN GSC. We have developed two types of integrated viewers to enhance the accessibility to mutant resource information. One viewer depicts a matrix view of the ontology-based classification and chromosomal location of each gene; the other depicts ontology-mediated integration of experimental protocols, baseline data, and mutant information. These approaches rely entirely upon experiment-based evidence, ensuring the reliability of the integrated data from different phenotyping platforms. 相似文献
103.
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. 总被引:10,自引:1,他引:9
Ken Kurokawa Takehiko Itoh Tomomi Kuwahara Kenshiro Oshima Hidehiro Toh Atsushi Toyoda Hideto Takami Hidetoshi Morita Vineet K Sharma Tulika P Srivastava Todd D Taylor Hideki Noguchi Hiroshi Mori Yoshitoshi Ogura Dusko S Ehrlich Kikuji Itoh Toshihisa Takagi Yoshiyuki Sakaki Tetsuya Hayashi Masahira Hattori 《DNA research》2007,14(4):169-181
Numerous microbes inhabit the human intestine, many of which are uncharacterized or uncultivable. They form a complex microbial community that deeply affects human physiology. To identify the genomic features common to all human gut microbiomes as well as those variable among them, we performed a large-scale comparative metagenomic analysis of fecal samples from 13 healthy individuals of various ages, including unweaned infants. We found that, while the gut microbiota from unweaned infants were simple and showed a high inter-individual variation in taxonomic and gene composition, those from adults and weaned children were more complex but showed a high functional uniformity regardless of age or sex. In searching for the genes over-represented in gut microbiomes, we identified 237 gene families commonly enriched in adult-type and 136 families in infant-type microbiomes, with a small overlap. An analysis of their predicted functions revealed various strategies employed by each type of microbiota to adapt to its intestinal environment, suggesting that these gene sets encode the core functions of adult and infant-type gut microbiota. By analysing the orphan genes, 647 new gene families were identified to be exclusively present in human intestinal microbiomes. In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a 'hot spot' for horizontal gene transfer between microbes. 相似文献
104.
Toyoda T Mochizuki Y Player K Heida N Kobayashi N Sakaki Y 《Bioinformatics (Oxford, England)》2007,23(4):524-526
OmicBrowse is a browser to explore multiple datasets coordinated in the multidimensional omic space integrating omics knowledge ranging from genomes to phenomes and connecting evolutional correspondences among multiple species. OmicBrowse integrates multiple data servers into a single omic space through secure peer-to-peer server communications, so that a user can easily obtain an integrated view of distributed data servers, e.g. an integrated view of numerous whole-genome tiling-array data retrieved from a user's in-house private-data server, along with various genomic annotations from public internet servers. OmicBrowse is especially appropriate for positional-cloning purposes. It displays both genetic maps and genomic annotations within wide chromosomal intervals and assists a user to select candidate genes by filtering their annotations or associated documents against user-specified keywords or ontology terms. We also show that an omic-space chart effectively represents schemes for integrating multiple datasets of multiple species. Availability: OmicBrowse is developed by the Genome-Phenome Superbrain Project and is released as free open-source software under the GNU General Public License at http://omicspace.riken.jp. 相似文献
105.
Sugiki T Uyama T Toyoda M Morioka H Kume S Miyado K Matsumoto K Saito H Tsumaki N Takahashi Y Toyama Y Umezawa A 《Journal of cellular biochemistry》2007,100(5):1240-1254
What is it that defines a bone marrow‐derived chondrocyte? We attempted to identify marrow‐derived cells with chondrogenic nature and immortality without transformation, defining “immortality” simply as indefinite cell division. KUM5 mesenchymal cells, a marrow stromal cell line, generated hyaline cartilage in vivo and exhibited enchondral ossification at a later stage after implantation. Selection of KUM5 chondroblasts based on the activity of the chondrocyte‐specific cis‐regulatory element of the collagen α2(XI) gene resulted in enhancement of their chondrogenic nature. Gene chip analysis revealed that OP9 cells, another marrow stromal cell line, derived from macrophage colony‐stimulating factor‐deficient osteopetrotic mice and also known to be niche‐constituting cells for hematopoietic stem cells expressed chondrocyte‐specific or ‐associated genes such as type II collagen α1, Sox9, and cartilage oligomeric matrix protein at an extremely high level, as did KUM5 cells. After cultured OP9 micromasses exposed to TGF‐β3 and BMP2 were implanted in mice, they produced abundant metachromatic matrix with the toluidine blue stain and formed type II collagen‐positive hyaline cartilage within 2 weeks in vivo. Hierarchical clustering and principal component analysis based on microarray data of the expression of cell surface markers and cell‐type‐specific genes resulted in grouping of KUM5 and OP9 cells into the same subcategory of “chondroblast,” that is, a distinct cell type group. We here show that these two cell lines exhibit the unique characteristics of hyaline cartilage formation and enchondral ossification in vitro and in vivo. J. Cell. Biochem. 100: 1240–1254, 2007. © 2006 Wiley‐Liss, Inc. 相似文献
106.
107.
Tsunemi K Taguchi F Marutani M Watanabe-Sugimoto M Inagaki Y Toyoda K Shiraishi T Ichinose Y 《Molecular Plant Pathology》2011,12(7):709-714
The HrpZ harpin of Pseudomonas syringae is known to induce a hypersensitive response (HR) in some plants. In P. syringae pv. tabaci (Pta), the harpin gene hrpZ has been spontaneously disrupted by an internal deletion in its open reading frame and a frame shift. The loss of the ability of the recombinant harpin polypeptide of Pta to induce HR despite the high sensitivity of tobacco plants to harpin led us to investigate the meaning of the disrupted hrpZ gene in the virulence of Pta 6605. The hrpZ gene from P. syringae pv. pisi was introduced into wild-type (WT) Pta. The hrpZ-complemented Pta secreted harpin into the culture medium, but failed to cause disease symptoms by both infiltration and spray inoculation. Inoculation with the hrpZ-complemented Pta induced defence responses in tobacco plants, whereas the defence responses of tobacco plants were not prominent on inoculation with WT Pta. These results indicate that an ancestor of Pta might have disrupted hrpZ by an internal deletion to evade plant defences and confer the ability to cause disease in tobacco plants. 相似文献
108.
Takahashi S Toyoda A Sekiyama Y Takagi H Nogawa T Uramoto M Suzuki R Koshino H Kumano T Panthee S Dairi T Ishikawa J Ikeda H Sakaki Y Osada H 《Nature chemical biology》2011,7(7):461-468
Spiroacetal compounds are ubiquitous in nature, and their stereospecific structures are responsible for diverse pharmaceutical activities. Elucidation of the biosynthetic mechanisms that are involved in spiroacetal formation will open the door to efficient generation of stereospecific structures that are otherwise hard to synthesize chemically. However, the biosynthesis of these compounds is poorly understood, owing to difficulties in identifying the responsible enzymes and analyzing unstable intermediates. Here we comprehensively describe the spiroacetal formation involved in the biosynthesis of reveromycin A, which inhibits bone resorption and bone metastases of tumor cells by inducing apoptosis in osteoclasts. We performed gene disruption, systematic metabolite analysis, feeding of labeled precursors and conversion studies with recombinant enzymes. We identified two key enzymes, dihydroxy ketone synthase and spiroacetal synthase, and showed in vitro reconstruction of the stereospecific spiroacetal structure from a stable acyclic precursor. Our findings provide insights into the creation of a variety of biologically active spiroacetal compounds for drug leads. 相似文献
109.
Ryuichi Ono Yoko Kuroki Mie Naruse Masayuki Ishii Sawa Iwasaki Atsushi Toyoda Asao Fujiyama Geoff Shaw Marilyn B. Renfree Tomoko Kaneko-Ishino Fumitoshi Ishino 《DNA research》2011,18(4):211-219
In humans and mice, there are 11 genes derived from sushi-ichi related retrotransposons, some of which are known to play essential roles in placental development. Interestingly, this family of retrotransposons was thought to exist only in eutherian mammals, indicating their significant contributions to the eutherian evolution, but at least one, PEG10, is conserved between marsupials and eutherians. Here we report a novel sushi-ichi retrotransposon-derived gene, SIRH12, in the tammar wallaby, an Australian marsupial species of the kangaroo family. SIRH12 encodes a protein highly homologous to the sushi-ichi retrotransposon Gag protein in the tammar wallaby, while SIRH12 in the South American short-tailed grey opossum is a pseudogene degenerated by accumulation of multiple nonsense mutations. This suggests that SIRH12 retrotransposition occurred only in the marsupial lineage but acquired and retained some as yet unidentified novel function, at least in the lineage of the tammar wallaby. 相似文献
110.
Onomoto K Morimoto S Kawaguchi T Toyoda H Tanaka M Kuroda M Uno K Kumada T Matsuda F Shimotohno K Fujita T Murakami Y 《PloS one》2011,6(5):e19799