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601.
Gautam P Jha P Kumar D Tyagi S Varma B Dash D Mukhopadhyay A;Indian Genome Variation Consortium Mukerji M 《Human genetics》2012,131(1):131-143
Copy number variations (CNVs) have provided a dynamic aspect to the apparently static human genome. We have analyzed CNVs
larger than 100 kb in 477 healthy individuals from 26 diverse Indian populations of different linguistic, ethnic and geographic
backgrounds. These CNVRs were identified using the Affymetrix 50K Xba 240 Array. We observed 1,425 and 1,337 CNVRs in the
deletion and amplification sets, respectively, after pooling data from all the populations. More than 50% of the genes encompassed
entirely in CNVs had both deletions and amplifications. There was wide variability across populations not only with respect
to CNV extent (ranging from 0.04–1.14% of genome under deletion and 0.11–0.86% under amplification) but also in terms of functional
enrichments of processes like keratinization, serine proteases and their inhibitors, cadherins, homeobox, olfactory receptors
etc. These did not correlate with linguistic, ethnic, geographic backgrounds and size of populations. Certain processes were
near exclusive to deletion (serine proteases, keratinization, olfactory receptors, GPCRs) or duplication (homeobox, serine
protease inhibitors, embryonic limb morphogenesis) datasets. Populations having same enriched processes were observed to contain
genes from different genomic loci. Comparison of polymorphic CNVRs (5% or more) with those cataloged in Database of Genomic
Variants revealed that 78% (2473) of the genes in CNVRs in Indian populations are novel. Validation of CNVs using Sequenom
MassARRAY revealed extensive heterogeneity in CNV boundaries. Exploration of CNV profiles in such diverse populations would
provide a widely valuable resource for understanding diversity in phenotypes and disease. 相似文献
602.
Javed A Melé M Pybus M Zalloua P Haber M Comas D Netea MG Balanovsky O Balanovska E Jin L Yang Y Arunkumar G Pitchappan R Bertranpetit J Calafell F Parida L;Genographic Consortium 《Human genetics》2012,131(4):601-613
We have analyzed human genetic diversity in 33 Old World populations including 23 populations obtained through Genographic Project studies. A set of 1,536 SNPs in five X chromosome regions were genotyped in 1,288 individuals (mostly males). We use a novel analysis employing subARG network construction with recombining chromosomal segments. Here, a subARG is constructed independently for each of five gene-free regions across the X chromosome, and the results are aggregated across them. For PCA, MDS and ancestry inference with STRUCTURE, the subARG is processed to obtain feature vectors of samples and pairwise distances between samples. The observed population structure, estimated from the five short X chromosomal segments, supports genome-wide frequency-based analyses: African populations show higher genetic diversity, and the general trend of shared variation is seen across the globe from Africa through Middle East, Europe, Central Asia, Southeast Asia, and East Asia in broad patterns. The recombinational analysis was also compared with established methods based on SNPs and haplotypes. For haplotypes, we also employed a fixed-length approach based on information-content optimization. Our recombinational analysis suggested a southern migration route out of Africa, and it also supports a single, rapid human expansion from Africa to East Asia through South Asia. 相似文献
603.
604.
Johannes Werner Manuel Ferrer Gurvan Michel Alexander J. Mann Sixing Huang Silvia Juarez Sergio Ciordia Juan P. Albar María Alcaide Violetta La Cono Michail M. Yakimov André Antunes Marco Taborda Milton S. da Costa Tran Hai Frank Oliver Glöckner Olga V. Golyshina Peter N. Golyshin Hanno Teeling The MAMBA Consortium 《Environmental microbiology》2014,16(8):2525-2537
Euryarchaea from the genus Halorhabdus have been found in hypersaline habitats worldwide, yet are represented by only two isolates: Halorhabdus utahensis AX‐2T from the shallow Great Salt Lake of Utah, and Halorhabdus tiamatea SARL4BT from the Shaban deep‐sea hypersaline anoxic lake (DHAL) in the Red Sea. We sequenced the H. tiamatea genome to elucidate its niche adaptations. Among sequenced archaea, H. tiamatea features the highest number of glycoside hydrolases, the majority of which were expressed in proteome experiments. Annotations and glycosidase activity measurements suggested an adaptation towards recalcitrant algal and plant‐derived hemicelluloses. Glycosidase activities were higher at 2% than at 0% or 5% oxygen, supporting a preference for low‐oxygen conditions. Likewise, proteomics indicated quinone‐mediated electron transport at 2% oxygen, but a notable stress response at 5% oxygen. Halorhabdus tiamatea furthermore encodes proteins characteristic for thermophiles and light‐dependent enzymes (e.g. bacteriorhodopsin), suggesting that H. tiamatea evolution was mostly not governed by a cold, dark, anoxic deep‐sea habitat. Using enrichment and metagenomics, we could demonstrate presence of similar glycoside hydrolase‐rich Halorhabdus members in the Mediterranean DHAL Medee, which supports that Halorhabdus species can occupy a distinct niche as polysaccharide degraders in hypersaline environments. 相似文献
605.
Julie Chesné Richard Danger Karine Botturi Martine Reynaud-Gaubert Sacha Mussot Marc Stern Isabelle Danner-Boucher Jean-Fran?ois Mornex Christophe Pison Claire Dromer Romain Kessler Marcel Dahan Olivier Brugière Jér?me Le Pavec Frédéric Perros Marc Humbert Carine Gomez Sophie Brouard Antoine Magnan the COLT Consortium 《PloS one》2014,9(10)
606.
Lauren N. Ayton Peter J. Blamey Robyn H. Guymer Chi D. Luu David A. X. Nayagam Nicholas C. Sinclair Mohit N. Shivdasani Jonathan Yeoh Mark F. McCombe Robert J. Briggs Nicholas L. Opie Joel Villalobos Peter N. Dimitrov Mary Varsamidis Matthew A. Petoe Chris D. McCarthy Janine G. Walker Nick Barnes Anthony N. Burkitt Chris E. Williams Robert K. Shepherd Penelope J. Allen for the Bionic Vision Australia Research Consortium 《PloS one》2014,9(12)
Retinal visual prostheses (“bionic eyes”) have the potential to restore vision to blind or profoundly vision-impaired patients. The medical bionic technology used to design, manufacture and implant such prostheses is still in its relative infancy, with various technologies and surgical approaches being evaluated. We hypothesised that a suprachoroidal implant location (between the sclera and choroid of the eye) would provide significant surgical and safety benefits for patients, allowing them to maintain preoperative residual vision as well as gaining prosthetic vision input from the device. This report details the first-in-human Phase 1 trial to investigate the use of retinal implants in the suprachoroidal space in three human subjects with end-stage retinitis pigmentosa. The success of the suprachoroidal surgical approach and its associated safety benefits, coupled with twelve-month post-operative efficacy data, holds promise for the field of vision restoration.
Trial Registration
Clinicaltrials.gov NCT01603576相似文献607.
Jonas Carlsson Alml?f Per Lundmark Anders Lundmark Bing Ge Tomi Pastinen Cardiogenics Consortium Alison H. Goodall Fran?ois Cambien Panos Deloukas Willem H. Ouwehand Ann-Christine Syv?nen 《PloS one》2014,9(7)
We applied genome-wide allele-specific expression analysis of monocytes from 188 samples. Monocytes were purified from white blood cells of healthy blood donors to detect cis-acting genetic variation that regulates the expression of long non-coding RNAs. We analysed 8929 regions harboring genes for potential long non-coding RNA that were retrieved from data from the ENCODE project. Of these regions, 60% were annotated as intergenic, which implies that they do not overlap with protein-coding genes. Focusing on the intergenic regions, and using stringent analysis of the allele-specific expression data, we detected robust cis-regulatory SNPs in 258 out of 489 informative intergenic regions included in the analysis. The cis-regulatory SNPs that were significantly associated with allele-specific expression of long non-coding RNAs were enriched to enhancer regions marked for active or bivalent, poised chromatin by histone modifications. Out of the lncRNA regions regulated by cis-acting regulatory SNPs, 20% (n = 52) were co-regulated with the closest protein coding gene. We compared the identified cis-regulatory SNPs with those in the catalog of SNPs identified by genome-wide association studies of human diseases and traits. This comparison identified 32 SNPs in loci from genome-wide association studies that displayed a strong association signal with allele-specific expression of non-coding RNAs in monocytes, with p-values ranging from 6.7×10−7 to 9.5×10−89. The identified cis-regulatory SNPs are associated with diseases of the immune system, like multiple sclerosis and rheumatoid arthritis. 相似文献
608.
Jennifer M. Fettweis Myrna G. Serrano Bernice Huang J. Paul Brooks Abigail L. Glascock Nihar U. Sheth Vaginal Microbiome Consortium Jerome F. Strauss III Kimberly K. Jefferson Gregory A. Buck 《PloS one》2014,9(10)
Humans are colonized by thousands of bacterial species, but it is difficult to assess the metabolic and pathogenic potential of the majority of these because they have yet to be cultured. Here, we characterize an uncultivated vaginal mycoplasma tightly associated with trichomoniasis that was previously known by its 16S rRNA sequence as “Mnola.” In this study, the mycoplasma was found almost exclusively in women infected with the sexually transmitted pathogen Trichomonas vaginalis, but rarely observed in women with no diagnosed disease. The genomes of four strains of this species were reconstructed using metagenome sequencing and assembly of DNA from four discrete mid-vaginal samples, one of which was obtained from a pregnant woman with trichomoniasis who delivered prematurely. These bacteria harbor several putative virulence factors and display unique metabolic strategies. Genes encoding proteins with high similarity to potential virulence factors include two collagenases, a hemolysin, an O-sialoglycoprotein endopeptidase and a feoB-type ferrous iron transport system. We propose the name “Candidatus Mycoplasma girerdii” for this potential new pathogen. 相似文献
609.
Genomic Resources Development Consortium Stephen R. Keller David M. Nelson Cortney Pylant Scott R. Santos Regina Trott 《Molecular ecology resources》2014,14(2):435-436
This article documents the public availability of (i) genomic sequence data and 43 microsatellite loci for the bat species, Lasiurus borealis and Lasiurus cinereus, and (ii) complete mitochondrial and partial nuclear genomes for two jack species, Caranx ignobilis, Caranx melampygus. 相似文献
610.