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851.
Rivière JB Mirzaa GM O'Roak BJ Beddaoui M Alcantara D Conway RL St-Onge J Schwartzentruber JA Gripp KW Nikkel SM Worthylake T Sullivan CT Ward TR Butler HE Kramer NA Albrecht B Armour CM Armstrong L Caluseriu O Cytrynbaum C Drolet BA Innes AM Lauzon JL Lin AE Mancini GM Meschino WS Reggin JD Saggar AK Lerman-Sagie T Uyanik G Weksberg R Zirn B Beaulieu CL;Finding of Rare Disease Genes 《Nature genetics》2012,44(8):934-940
Megalencephaly-capillary malformation (MCAP) and megalencephaly-polymicrogyria-polydactyly-hydrocephalus (MPPH) syndromes are sporadic overgrowth disorders associated with markedly enlarged brain size and other recognizable features. We performed exome sequencing in 3 families with MCAP or MPPH, and our initial observations were confirmed in exomes from 7 individuals with MCAP and 174 control individuals, as well as in 40 additional subjects with megalencephaly, using a combination of Sanger sequencing, restriction enzyme assays and targeted deep sequencing. We identified de novo germline or postzygotic mutations in three core components of the phosphatidylinositol 3-kinase (PI3K)-AKT pathway. These include 2 mutations in AKT3, 1 recurrent mutation in PIK3R2 in 11 unrelated families with MPPH and 15 mostly postzygotic mutations in PIK3CA in 23 individuals with MCAP and 1 with MPPH. Our data highlight the central role of PI3K-AKT signaling in vascular, limb and brain development and emphasize the power of massively parallel sequencing in a challenging context of phenotypic and genetic heterogeneity combined with postzygotic mosaicism. 相似文献
852.
853.
Sung WK Zheng H Li S Chen R Liu X Li Y Lee NP Lee WH Ariyaratne PN Tennakoon C Mulawadi FH Wong KF Liu AM Poon RT Fan ST Chan KL Gong Z Hu Y Lin Z Wang G Zhang Q Barber TD Chou WC Aggarwal A Hao K Zhou W Zhang C Hardwick J Buser C Xu J Kan Z Dai H Mao M Reinhard C Wang J Luk JM 《Nature genetics》2012,44(7):765-769
To survey hepatitis B virus (HBV) integration in liver cancer genomes, we conducted massively parallel sequencing of 81 HBV-positive and 7 HBV-negative hepatocellular carcinomas (HCCs) and adjacent normal tissues. We found that HBV integration is observed more frequently in the tumors (86.4%) than in adjacent liver tissues (30.7%). Copy-number variations (CNVs) were significantly increased at HBV breakpoint locations where chromosomal instability was likely induced. Approximately 40% of HBV breakpoints within the HBV genome were located within a 1,800-bp region where the viral enhancer, X gene and core gene are located. We also identified recurrent HBV integration events (in ≥ 4 HCCs) that were validated by RNA sequencing (RNA-seq) and Sanger sequencing at the known and putative cancer-related TERT, MLL4 and CCNE1 genes, which showed upregulated gene expression in tumor versus normal tissue. We also report evidence that suggests that the number of HBV integrations is associated with patient survival. 相似文献
854.
855.
Sloan JL Johnston JJ Manoli I Chandler RJ Krause C Carrillo-Carrasco N Chandrasekaran SD Sysol JR O'Brien K Hauser NS Sapp JC Dorward HM Huizing M;NIH Intramural Sequencing Center Group Barshop BA Berry SA James PM Champaigne NL de Lonlay P Valayannopoulos V Geschwind MD Gavrilov DK Nyhan WL Biesecker LG Venditti CP 《Nature genetics》2011,43(9):883-886
We used exome sequencing to identify the genetic basis of combined malonic and methylmalonic aciduria (CMAMMA). We sequenced the exome of an individual with CMAMMA and followed up with sequencing of eight additional affected individuals (cases). This included one individual who was identified and diagnosed by searching an exome database. We identify mutations in ACSF3, encoding a putative methylmalonyl-CoA and malonyl-CoA synthetase as a cause of CMAMMA. We also examined a canine model of CMAMMA, which showed pathogenic mutations in a predicted ACSF3 ortholog. ACSF3 mutant alleles occur with a minor allele frequency of 0.0058 in ~1,000 control individuals, predicting a CMAMMA population incidence of ~1:30,000. ACSF3 deficiency is the first human disorder identified as caused by mutations in a gene encoding a member of the acyl-CoA synthetase family, a diverse group of evolutionarily conserved proteins, and may emerge as one of the more common human metabolic disorders. 相似文献
856.
Cooper JD Smyth DJ Smiles AM Plagnol V Walker NM Allen JE Downes K Barrett JC Healy BC Mychaleckyj JC Warram JH Todd JA 《Nature genetics》2008,40(12):1399-1401
We carried out a meta-analysis of data from three genome-wide association (GWA) studies of type 1 diabetes (T1D), testing 305,090 SNPs in 3,561 T1D cases and 4,646 controls of European ancestry. We obtained further support for 4q27 (IL2-IL21, P = 1.9 x 10(-8)) and, after genotyping an additional 6,225 cases, 6,946 controls and 2,828 families, convincing evidence for four previously unknown and distinct risk loci in chromosome regions 6q15 (BACH2, P = 4.7 x 10(-12)), 10p15 (PRKCQ, P = 3.7 x 10(-9)), 15q24 (CTSH, P = 3.2 x 10(-15)) and 22q13 (C1QTNF6, P = 2.0 x 10(-8)). 相似文献
857.
858.
International Consortium for Systemic Lupus Erythematosus Genetics 《Nature genetics》2008,40(2):204-210
Systemic lupus erythematosus (SLE) is a common systemic autoimmune disease with complex etiology but strong clustering in families (lambda(S) = approximately 30). We performed a genome-wide association scan using 317,501 SNPs in 720 women of European ancestry with SLE and in 2,337 controls, and we genotyped consistently associated SNPs in two additional independent sample sets totaling 1,846 affected women and 1,825 controls. Aside from the expected strong association between SLE and the HLA region on chromosome 6p21 and the previously confirmed non-HLA locus IRF5 on chromosome 7q32, we found evidence of association with replication (1.1 x 10(-7) < P(overall) < 1.6 x 10(-23); odds ratio = 0.82-1.62) in four regions: 16p11.2 (ITGAM), 11p15.5 (KIAA1542), 3p14.3 (PXK) and 1q25.1 (rs10798269). We also found evidence for association (P < 1 x 10(-5)) at FCGR2A, PTPN22 and STAT4, regions previously associated with SLE and other autoimmune diseases, as well as at > or =9 other loci (P < 2 x 10(-7)). Our results show that numerous genes, some with known immune-related functions, predispose to SLE. 相似文献
859.
Di Bernardo MC Crowther-Swanepoel D Broderick P Webb E Sellick G Wild R Sullivan K Vijayakrishnan J Wang Y Pittman AM Sunter NJ Hall AG Dyer MJ Matutes E Dearden C Mainou-Fowler T Jackson GH Summerfield G Harris RJ Pettitt AR Hillmen P Allsup DJ Bailey JR Pratt G Pepper C Fegan C Allan JM Catovsky D Houlston RS 《Nature genetics》2008,40(10):1204-1210
We conducted a genome-wide association study of 299,983 tagging SNPs for chronic lymphocytic leukemia (CLL) and performed validation in two additional series totaling 1,529 cases and 3,115 controls. We identified six previously unreported CLL risk loci at 2q13 (rs17483466; P = 2.36 x 10(-10)), 2q37.1 (rs13397985, SP140; P = 5.40 x 10(-10)), 6p25.3 (rs872071, IRF4; P = 1.91 x 10(-20)), 11q24.1 (rs735665; P = 3.78 x 10(-12)), 15q23 (rs7176508; P = 4.54 x 10(-12)) and 19q13.32 (rs11083846, PRKD2; P = 3.96 x 10(-9)). These data provide the first evidence for the existence of common, low-penetrance susceptibility to a hematological malignancy and new insights into disease causation in CLL. 相似文献
860.
Korn JM Kuruvilla FG McCarroll SA Wysoker A Nemesh J Cawley S Hubbell E Veitch J Collins PJ Darvishi K Lee C Nizzari MM Gabriel SB Purcell S Daly MJ Altshuler D 《Nature genetics》2008,40(10):1253-1260
Accurate and complete measurement of single nucleotide (SNP) and copy number (CNV) variants, both common and rare, will be required to understand the role of genetic variation in disease. We present Birdsuite, a four-stage analytical framework instantiated in software for deriving integrated and mutually consistent copy number and SNP genotypes. The method sequentially assigns copy number across regions of common copy number polymorphisms (CNPs), calls genotypes of SNPs, identifies rare CNVs via a hidden Markov model (HMM), and generates an integrated sequence and copy number genotype at every locus (for example, including genotypes such as A-null, AAB and BBB in addition to AA, AB and BB calls). Such genotypes more accurately depict the underlying sequence of each individual, reducing the rate of apparent mendelian inconsistencies. The Birdsuite software is applied here to data from the Affymetrix SNP 6.0 array. Additionally, we describe a method, implemented in PLINK, to utilize these combined SNP and CNV genotypes for association testing with a phenotype. 相似文献