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101.
Adonney Allan de Oliveira Veras Pablo Henrique Caracciolo Gomes de Sá Vasco Azevedo Artur Silva Rommel Thiago Jucá Ramos 《Bioinformation》2013,9(16):840-841
Next-generation sequencing technologies have increased the amount of biological data generated. Thus, bioinformatics has become
important because new methods and algorithms are necessary to manipulate and process such data. However, certain challenges
have emerged, such as genome assembly using short reads and high-throughput platforms. In this context, several algorithms have
been developed, such as Velvet, Abyss, Euler-SR, Mira, Edna, Maq, SHRiMP, Newbler, ALLPATHS, Bowtie and BWA. However,
most such assemblers do not have a graphical interface, which makes their use difficult for users without computing experience
given the complexity of the assembler syntax. Thus, to make the operation of such assemblers accessible to users without a
computing background, we developed AutoAssemblyD, which is a graphical tool for genome assembly submission and remote
management by multiple assemblers through XML templates.
Availability
AssemblyD is freely available at https://sourceforge.net/projects/autoassemblyd. It requires Sun jdk 6 or higher. 相似文献102.
103.
Brigida TL Lucena Billy M dos Santos João LS Moreira Ana Paula B Moreira Alvaro C Nunes Vasco Azevedo Anderson Miyoshi Fabiano L Thompson Marcos Antonio de MoraisJunior 《BMC microbiology》2010,10(1):298
Background
Bacteria may compete with yeast for nutrients during bioethanol production process, potentially causing economic losses. This is the first study aiming at the quantification and identification of Lactic Acid Bacteria (LAB) present in the bioethanol industrial processes in different distilleries of Brazil. 相似文献104.
R. G. Loor A. M. Risterucci B. Courtois O. Fouet M. Jeanneau E. Rosenquist F. Amores A. Vasco M. Medina C. Lanaud 《Tree Genetics & Genomes》2009,5(3):421-433
The native Theobroma cacao L. population from Ecuador, known as Nacional, is famous for its fine cocoa flavour. From the beginning of the twentieth
century, however, it has been subjected to genetic erosion due principally to successive introductions of foreign germplasm
whose hybrid descendants gradually replaced the native plantations, implying a decrease in cocoa quality. We attempted to
trace this native cacao within a wide pool of modern Ecuadorian cacao population. Three hundred and twenty-two cacao accessions
collected from different geographical areas along the pacific coast of Ecuador and maintained in two living collections were
analysed using 40 simple-sequence repeat markers. Most of Ecuadorian cacao accessions displayed a high diversity and heterozygosity
level. A factorial analysis of correspondence (FAC) showed a continuous variation among them, with a few ones, grouped at
an extreme side of the FAC cloud, showing higher levels of homozygosity and lower introgression level by foreign cacaos. A
paternity analysis revealed that these highly homozygous individuals are the most probable ancestors of the modern Nacional
hybrid pool. These particular accessions studied could represent the native Nacional cacao present in Ecuador before the foreign
introductions. Their identification will help to conserve valuable genetic material and to improve cocoa quality in new cacao
varieties. 相似文献
105.
FE Pethick AF Lainson R Yaga A Flockhart DG Smith W Donachie LT Cerdeira A Silva E Bol TS Lopes MS Barbosa AC Pinto AR Dos Santos SC Soares SS Almeida LC Guimaraes FF Aburjaile VA Abreu D Ribeiro KK Fiaux CA Diniz EG Barbosa UP Pereira SS Hassan A Ali SM Bakhtiar FA Dorella AR Carneiro RT Ramos FS Rocha MP Schneider A Miyoshi V Azevedo MC Fontaine 《Journal of bacteriology》2012,194(17):4736-4737
Here, we report the whole-genome sequences of two ovine-pathogenic Corynebacterium pseudotuberculosis isolates: strain 3/99-5, which represents the first C. pseudotuberculosis genome originating from the United Kingdom, and 42/02-A, the second from Australia. These genome sequences will contribute to the objective of determining the global pan-genome of this bacterium. 相似文献
106.
Vasco Manuel Nobre de Carvalho da Silva Vieira Rui Orlando Pimenta Santos 《Journal of phycology》2010,46(6):1128-1137
Studies investigating the demographic traits that drive the patterns of phase dominance (the ploidy ratio) in isomorphic biphasic life cycles have not found an integrative solution. Either fertility or survival has been suggested independently as the main driver. Here, we provide a global theoretical framework on how demographic mechanisms determine the ploidy ratio, unifying previous numerical and observational attempts at this question. The analytical solutions of both the ploidy ratio and its elasticities to model parameters of a stage/size‐structured model patterned after the life cycle of a marine alga were derived and analyzed. A complex interaction among vital rates determines the patterns of phase dominance of biphasic life cycles. Three co‐occurring processes—growth, fertility, and looping—may dominate the dynamics of the population, determining both its growth rate and ploidy ratio. Our analyses show that in species where fertility is low, the ploidy ratio is highly elastic to looping transitions (survival, breakage, and clonal growth). Consequently, the subtle morphological, ecophysiological, and biochemistry phase differences that have been reported in isomorphic life cycles as not explaining the observed ploidy ratios, may, in fact, explain them if they translate into slight phase differences in looping transitions. In species where fertility is low, the looping dissimilarities between phases cannot be too high favoring simultaneously one phase, as the population structure would be completely dominated by that phase. In the case of ecological similarity between phases (equal looping and growth rates between phases), a ploidy ratio different from one can only be set by strong phase differences in fertility. 相似文献
107.
In spite of genome sequences of both human and N. gonorrhoeae in hand, vaccine for gonorrhea is yet not available. Due to availability of several host and pathogen genomes and numerous tools for in silico prediction of effective B-cell and T-cell epitopes; recent trend of vaccine designing has been shifted to peptide or epitope based vaccines that are more specific, safe, and easy to produce. In order to design and develop such a peptide vaccine against the pathogen, we adopted a novel computational approache based on sequence, structure, QSAR, and simulation methods along with fold level analysis to predict potential antigenic B-cell epitope derived T-cell epitopes from four vaccine targets of N. gonorrhoeae previously identified by us [Barh and Kumar (2009) In Silico Biology 9, 1-7]. Four epitopes, one from each protein, have been designed in such a way that each epitope is highly likely to bind maximum number of HLA molecules (comprising of both the MHC-I and II) and interacts with most frequent HLA alleles (A*0201, A*0204, B*2705, DRB1*0101, and DRB1*0401) in human population. Therefore our selected epitopes are highly potential to induce both the B-cell and T-cell mediated immune responses. Of course, these selected epitopes require further experimental validation. 相似文献
108.
109.
Wanderson M. Silva Núbia Seyffert Alessandra Ciprandi Agenor V. Santos Thiago L. P. Castro Luis G. C. Pacheco Debmalya Barh Yves Le Loir Adriano M. C. Pimenta Anderson Miyoshi Artur Silva Vasco Azevedo 《Current microbiology》2013,67(4):460-465
Corynebacterium pseudotuberculosis is the etiologic agent of caseous lymphadenitis a chronic infectious disease affecting small ruminants. The 2D-DIGE technique was used to compare the exoproteomes of two C. pseudotuberculosis biovar ovis strains isolated from goat (strain 1002) and sheep (strain C231). Seventeen proteins differentially produced were identified here. Nine proteins appeared over-produced in the exoproteome of 1002 goat strain and 8 in that of C231 sheep strain. These proteins were related to various biological functions, such as the cell envelope, respiratory metabolism and proteolysis. This proteomic analysis revealed strain-specific exoproteins although each of the corresponding genes was found in both strain genomes. Such differential expression pattern may reflect inter-strain differences in adaptation to a specific host, in pathogenicity and or in antigenicity of this pathogenic bacterium. 相似文献
110.
Cerdeira LT Pinto AC Schneider MP de Almeida SS dos Santos AR Barbosa EG Ali A Barbosa MS Carneiro AR Ramos RT de Oliveira RS Barh D Barve N Zambare V Belchior SE Guimarães LC de Castro Soares S Dorella FA Rocha FS de Abreu VA Tauch A Trost E Miyoshi A Azevedo V Silva A 《Journal of bacteriology》2011,193(22):6420-6421
In this work, we report the complete genome sequence of a Corynebacterium pseudotuberculosis PAT10 isolate, collected from a lung abscess in an Argentine sheep in Patagonia, whose pathogen also required an investigation of its pathogenesis. Thus, the analysis of the genome sequence offers a means to better understanding of the molecular and genetic basis of virulence of this bacterium. 相似文献