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41.
Maria-Ines Fariello Bertrand Servin Gwenola Tosser-Klopp Rachel Rupp Carole Moreno International Sheep Genomics Consortium Magali San Cristobal Simon Boitard 《PloS one》2014,9(8)
The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinpointing several new selection signatures in the sheep genome and distinguishing those related to modern breeding objectives and to earlier post-domestication constraints. The newly identified regions, together with the ones previously identified, reveal the extensive genome response to selection on morphology, color and adaptation to new environments. 相似文献
42.
43.
Linkage disequilibrium over short physical distances measured in sheep using a high‐density SNP chip
James W. Kijas Laercio Porto‐Neto Sonja Dominik Antonio Reverter Rowan Bunch Russell McCulloch Ben J. Hayes Rudiger Brauning John McEwan the International Sheep Genomics Consortium 《Animal genetics》2014,45(5):754-757
The extent of linkage disequilibrium (LD) between genetic loci has implications for both association studies and the accuracy of genomic prediction. To characterise the persistence of LD in diverse sheep breeds, two SNP genotyping platforms were used. First, existing SNP genotypes from 63 breeds obtained using the ovine SNP50 BeadChip (49 034 loci) were used to estimate LD decay in populations with contrasting levels of genetic diversity. Given the paucity of marker pairs separated by short physical distances on the SNP50 BeadChip, genotyping was subsequently performed for four breeds using the recently developed ovine HD BeadChip that assays approximately 600 000 SNPs with an average genomic spacing of 5 kb. This facilitated a highly accurate estimate of LD over short genomic distances (<30 kb) and revealed LD varies considerably between sheep breeds. Further, sheep appear to contain generally lower levels of LD than do other domestic species, likely a reflection of aspects of their past population history. 相似文献
44.
本研究通过用农药农蒙特(25×10~(-6))和氯氰菊酯(20×10~(-6))处理,采用生命表技术和控制效应来评判农药亚致死剂量对田间小菜蛾和优姬蜂种群动力学的影响。结果表明,农蒙特和氯氰菊酯对优姬蜂种群的控制效应大于对小菜蛾种群的控制效应,寄生在农蒙特处理的小菜蛾幼虫体内的优姬蜂幼虫的死亡率显著地高于氯氰菊酯处理的和对照的,表现出农蒙特对寄生蜂影响的深远性。 相似文献
45.
Gwenola Tosser-Klopp Philippe Bardou Olivier Bouchez Cédric Cabau Richard Crooijmans Yang Dong Cécile Donnadieu-Tonon André Eggen Henri C. M. Heuven Saadiah Jamli Abdullah Johari Jiken Christophe Klopp Cynthia T. Lawley John McEwan Patrice Martin Carole R. Moreno Philippe Mulsant Ibouniyamine Nabihoudine Eric Pailhoux Isabelle Palhière Rachel Rupp Julien Sarry Brian L. Sayre Aurélie Tircazes Jun Wang Wen Wang Wenguang Zhang International Goat Genome Consortium 《PloS one》2016,11(3)
46.
Mufaro Kanyangarara Edmore Mamini Sungano Mharakurwa Shungu Munyati Lovemore Gwanzura Tamaki Kobayashi Timothy Shields Luke C. Mullany Susan Mutambu Peter R. Mason Frank C. Curriero William J. Moss Southern Africa International Centers of Excellence for Malaria Research 《PloS one》2016,11(3)
Background
More than half of malaria cases in Zimbabwe are concentrated in Manicaland Province, where seasonal malaria epidemics occur despite intensified control strategies. Recently, high levels of pyrethroid and carbamate resistance were detected in Anopheles funestus, the major malaria vector in eastern Zimbabwe. In response, a single round of indoor residual spraying (IRS) using pirimiphos-methyl (an organophosphate) was implemented in four high burden districts of Manicaland Province from November 1, 2014 to December 19, 2014. The objective of this study was to evaluate the effect of this programmatic switch in insecticides on malaria morbidity reported from health care facilities in Mutasa District, one of the worst affected districts in Manicaland Province.Methods
The number of weekly malaria cases for each health facility 24 months prior to the 2014 IRS campaign and in the subsequent high transmission season were obtained from passive case surveillance. Environmental variables were extracted from remote-sensing data sources and linked to each health care facility. Negative binomial regression was used to model the weekly number of malaria cases, adjusted for seasonality and environmental variables.Results
From December 2012 to May 2015, 124,206 malaria cases were reported from 42 health care facilities in Mutasa District. Based on a higher burden of malaria, 20 out of 31 municipal wards were sprayed in the district. Overall, 87.3% of target structures were sprayed and 92.1% of the target population protected. During the 6 months after the 2014 IRS campaign, a period when transmission would have otherwise peaked, the incidence of malaria was 38% lower than the preceding 24 months at health facilities in the sprayed wards.Conclusions
Pirimiphos-methyl had a measurable impact on malaria incidence and is an effective insecticide for the control of An. funestus in eastern Zimbabwe. 相似文献47.
The International Sheep Genomics Consortium A. L. Archibald N. E. Cockett B. P. Dalrymple T. Faraut J. W. Kijas J. F Maddox J. C. McEwan V. Hutton Oddy H. W. Raadsma C. Wade J. Wang W. Wang X. Xun 《Animal genetics》2010,41(5):449-453
Until recently, the construction of a reference genome was performed using Sanger sequencing alone. The emergence of next-generation sequencing platforms now means reference genomes may incorporate sequence data generated from a range of sequencing platforms, each of which have different read length, systematic biases and mate-pair characteristics. The objective of this review is to inform the mammalian genomics community about the experimental strategy being pursued by the International Sheep Genomics Consortium (ISGC) to construct the draft reference genome of sheep (Ovis aries). Component activities such as data generation, sequence assembly and annotation are described, along with information concerning the key researchers performing the work. This aims to foster future participation from across the research community through the coordinated activities of the consortium. The review also serves as a ‘marker paper’ by providing information concerning the pre-publication release of the reference genome. This ensures the ISGC adheres to the framework for data sharing established at the recent Toronto International Data Release Workshop and provides guidelines for data users. 相似文献
48.
International Arabidopsis Informatics Consortium 《The Plant cell》2012,24(6):2248-2256
The Arabidopsis information portal (AIP), a resource expected to provide access to all community data and combine outputs into a single user-friendly interface, has emerged from community discussions over the last 23 months. These discussions began during two closely linked workshops in early 2010 that established the International Arabidopsis Informatics Consortium (IAIC). The design of the AIP will provide core functionality while remaining flexible to encourage multiple contributors and constant innovation. An IAIC-hosted Design Workshop in December 2011 proposed a structure for the AIP to provide a framework for the minimal components of a functional community portal while retaining flexibility to rapidly extend the resource to other species. We now invite broader participation in the AIP development process so that the resource can be implemented in a timely manner. 相似文献
49.
Marchini J Cutler D Patterson N Stephens M Eskin E Halperin E Lin S Qin ZS Munro HM Abecasis GR Donnelly P;International HapMap Consortium 《American journal of human genetics》2006,78(3):437-450
Knowledge of haplotype phase is valuable for many analysis methods in the study of disease, population, and evolutionary genetics. Considerable research effort has been devoted to the development of statistical and computational methods that infer haplotype phase from genotype data. Although a substantial number of such methods have been developed, they have focused principally on inference from unrelated individuals, and comparisons between methods have been rather limited. Here, we describe the extension of five leading algorithms for phase inference for handling father-mother-child trios. We performed a comprehensive assessment of the methods applied to both trios and to unrelated individuals, with a focus on genomic-scale problems, using both simulated data and data from the HapMap project. The most accurate algorithm was PHASE (v2.1). For this method, the percentages of genotypes whose phase was incorrectly inferred were 0.12%, 0.05%, and 0.16% for trios from simulated data, HapMap Centre d'Etude du Polymorphisme Humain (CEPH) trios, and HapMap Yoruban trios, respectively, and 5.2% and 5.9% for unrelated individuals in simulated data and the HapMap CEPH data, respectively. The other methods considered in this work had comparable but slightly worse error rates. The error rates for trios are similar to the levels of genotyping error and missing data expected. We thus conclude that all the methods considered will provide highly accurate estimates of haplotypes when applied to trio data sets. Running times differ substantially between methods. Although it is one of the slowest methods, PHASE (v2.1) was used to infer haplotypes for the 1 million-SNP HapMap data set. Finally, we evaluated methods of estimating the value of r(2) between a pair of SNPs and concluded that all methods estimated r(2) well when the estimated value was >or=0.8. 相似文献
50.
Schaid DJ McDonnell SK Zarfas KE Cunningham JM Hebbring S Thibodeau SN Eeles RA Easton DF Foulkes WD Simard J Giles GG Hopper JL Mahle L Moller P Badzioch M Bishop DT Evans C Edwards S Meitz J Bullock S Hope Q Guy M Hsieh CL Halpern J Balise RR Oakley-Girvan I Whittemore AS Xu J Dimitrov L Chang BL Adams TS Turner AR Meyers DA Friedrichsen DM Deutsch K Kolb S Janer M Hood L Ostrander EA Stanford JL Ewing CM Gielzak M Isaacs SD Walsh PC Wiley KE Isaacs WB Lange EM Ho LA Beebe-Dimmer JL Wood DP 《Human genetics》2006,120(4):471-485
While it is widely appreciated that prostate cancers vary substantially in their propensity to progress to a life-threatening
stage, the molecular events responsible for this progression have not been identified. Understanding these molecular mechanisms
could provide important prognostic information relevant to more effective clinical management of this heterogeneous cancer.
Hence, through genetic linkage analyses, we examined the hypothesis that the tendency to develop aggressive prostate cancer may have an important genetic component. Starting with 1,233 familial prostate cancer families with genome
scan data available from the International Consortium for Prostate Cancer Genetics, we selected those that had at least three
members with the phenotype of clinically aggressive prostate cancer, as defined by either high tumor grade and/or stage, resulting
in 166 pedigrees (13%). Genome-wide linkage data were then pooled to perform a combined linkage analysis for these families.
Linkage signals reaching a suggestive level of significance were found on chromosomes 6p22.3 (LOD = 3.0), 11q14.1–14.3 (LOD = 2.4),
and 20p11.21–q11.21 (LOD = 2.5). For chromosome 11, stronger evidence of linkage (LOD = 3.3) was observed among pedigrees
with an average at diagnosis of 65 years or younger. Other chromosomes that showed evidence for heterogeneity in linkage across
strata were chromosome 7, with the strongest linkage signal among pedigrees without male-to-male disease transmission (7q21.11,
LOD = 4.1), and chromosome 21, with the strongest linkage signal among pedigrees that had African American ancestry (21q22.13–22.3;
LOD = 3.2). Our findings suggest several regions that may contain genes which, when mutated, predispose men to develop a more
aggressive prostate cancer phenotype. This provides a basis for attempts to identify these genes, with potential clinical
utility for men with aggressive prostate cancer and their relatives.
The names of all authors and their affiliations are listed in the Acknowledgements. The fact that Dr Schaid’s name is given
here for purposes of correspondence should not be taken to imply that he played the sole leading part in writing this article.
An erratum to this article can be found at 相似文献