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41.
Eva?FreyhultEmail author Peteris?Prusis Maris?Lapinsh Jarl?ES?Wikberg Vincent?Moulton Mats?G?GustafssonEmail author 《BMC bioinformatics》2005,6(1):50
Background
Proteochemometrics is a new methodology that allows prediction of protein function directly from real interaction measurement data without the need of 3D structure information. Several reported proteochemometric models of ligand-receptor interactions have already yielded significant insights into various forms of bio-molecular interactions. The proteochemometric models are multivariate regression models that predict binding affinity for a particular combination of features of the ligand and protein. Although proteochemometric models have already offered interesting results in various studies, no detailed statistical evaluation of their average predictive power has been performed. In particular, variable subset selection performed to date has always relied on using all available examples, a situation also encountered in microarray gene expression data analysis. 相似文献42.
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Association study and expression analysis of porcine ESR1 as a candidate gene for boar fertility and sperm quality 总被引:2,自引:0,他引:2
Gunawan A Kaewmala K Uddin MJ Cinar MU Tesfaye D Phatsara C Tholen E Looft C Schellander K 《Animal reproduction science》2011,128(1-4):11-21
Male fertility is impaired through the lack of ESR1 (Estrogen Receptor 1) but little is known about the ESR1 roles in boar spermatogenesis and fertility. Therefore, this research was aimed at investigating the association with sperm quality and boar fertility traits in a total of 300 boars both from purebred Pietrain and Pietrain × Hampshire crosses. A SNP in coding region of ESR1g.672C>T in exon 1 was associated with sperm motility (P<0.05) and plasma droplet rate (P<0.01) while the polymorphism in non-coding region of ESR1g.35756T>C in inton 1 was associated with non-return rate (P<0.05). Furthermore, to analyse the mRNA and protein expression of ESR1 in boar reproductive tissues, a total of six boars were divided into two groups [Group I (G-I) and Group II (G-II)], where G-I had relatively better sperm quality. ESR1 expression was higher in tissues collected from G-I boars than those of collected from G-II boars, and the difference in mRNA expression was significant (P<0.01) in head of epididymis. The ESR1 protein expression results from western blot coincided with the results of qRT-PCR. The ESR1 protein localization observed a strong staining in the cytoplasm of Sertoli cell in the testis, in the epithelial cells in head and tail of epididymis, in smooth muscle in tail of epididymis, and in the post acrosomal region and tail of the spermatozoa. These results will improve the understanding of the functions of the ESR1 in spermatogenesis within the reproductive tract and will shed light on ESR1 as a candidate in the selection of boar with good sperm quality and fertility. 相似文献
45.
Hani Susianti Atma Gunawan Jayarani Fatimah Putri Basuki B Purnomo Kusworini Handono Handono Kalim 《Bioinformation》2014,10(8):487-490
The TGF-β1 cytokine concentration is known to be higher in nephritis with implied Lupus Nephritis severity. The production of
TGF-β1 cytokine is associated with G915C polymorphism. Therefore, it is of interest to study G915C polymorphism. The G915C
polymorphism changes codon 25 which encodes arginine into proline in the signal peptide of TGF-β1. The amino acid substitution
affects signal peptide properties that may inhibit the transport of TGF-β1 into the endoplasmic reticulum and eventually decline
the cytokine production. Hence, the effect of G915C polymorphism on the properties of the signal peptide, the ability of TGF-β1
transport into the endoplasmic reticulum and the concentrations of urinary TGF-β1 in Lupus Nephritis patients was studied. The
arginine substitution into proline decreased the polarity of the signal peptide for TGF-β1. The increased hydrophobicity with
increased binding energy of the signal peptide for TGF-β1 to Signal Recognition Particle (SRP) and translocon is shown. This
implies decreased protein complex stability in potentially blocking the transport of TGF-β1 into the endoplasmic reticulum. This
transport retention possibly hampers the synthesis and maturation of TGF-β1 leading to decreased cytokine production. 相似文献
46.
XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services 总被引:1,自引:0,他引:1
Background
Life sciences make heavily use of the web for both data provision and analysis. However, the increasing amount of available data and the diversity of analysis tools call for machine accessible interfaces in order to be effective. HTTP-based Web service technologies, like the Simple Object Access Protocol (SOAP) and REpresentational State Transfer (REST) services, are today the most common technologies for this in bioinformatics. However, these methods have severe drawbacks, including lack of discoverability, and the inability for services to send status notifications. Several complementary workarounds have been proposed, but the results are ad-hoc solutions of varying quality that can be difficult to use. 相似文献47.
The red imported fire ant (RIFA) (Solenopsis invicta Buren), an exotic insect pest in Texas, has become well established throughout the eastern part of the state. More aggressive
than native ant species, RIFA gradually have enlarged their range and spread north and west despite intense efforts to stop
them. Symbiotic bacteria have an important relationship in the midgut of fourth instar RIFA larvae. However, the presence
of symbiotic bacteria in hemolymph has not been explored. In this study, symbiotic bacteria isolated from the hemolymph of
fourth instar larvae of RIFA were genetically identified in terms of genus using a partial sequence of the 16S rRNA gene. Using three different primer sets to amplify regions of the gyrA, gyrB, and SG850 genes, multiple species of the genus Bacillus were identified as inhabitants of fire ant hemolymph. Analysis of gyrA gene identified Bacillus cereus with a percentage match of 94.13–99.20% with DNA sequences from GenBank BLAST (). Using the gyrB gene, Bacillus species were identified with a percentage match of 95.48% to 100% using DNA sequences from GenBank. Finally, analysis of
the SG850 gene identified Bacillus cereus with a percentage match of 96.20% to 99.83% using DNA sequences from GenBank. 相似文献
48.
Morano LD Bextine BR Garcia DA Maddox SV Gunawan S Vitovsky NJ Black MC 《Current microbiology》2008,56(4):346-351
Xylella fastidiosa is the causative agent of Pierce’s Disease of grape. No published record of X. fastidiosa genetics in Texas exists despite growing financial risk to the U.S. grape industry, a Texas population of the glassy-winged
sharpshooter insect vector (Homalodisca
vitripennis) now spreading in California, and evidence that the bacterium is ubiquitous to southern states. Using sequences of conserved
gyrB and mopB genes, we have established at least two strains in Texas, grape strain and ragweed strain, corresponding genetically with
subsp. piercei and multiplex, respectively. The grape strain in Texas is found in Vitis vinifera varieties, hybrid vines, and wild Vitis near vineyards, whereas the ragweed strain in Texas is found in annuals, shrubs, and trees near vineyards or other areas.
RFLP and QRT PCR techniques were used to differentiate grape and ragweed strains with greater efficiency than sequencing and
are practical for screening numerous X. fastidiosa isolates for clade identity. 相似文献
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