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排序方式: 共有706条查询结果,搜索用时 390 毫秒
31.
Florian Villegas Daphné Lehalle Daniela Mayer Melanie Rittirsch Michael B. Stadler Marietta Zinner Daniel Olivieri Pierre Vabres Laurence Duplomb-Jego Eveline S.J.M. De Bont Yannis Duffourd Floor Duijkers Magali Avila David Geneviève Nada Houcinat Thibaud Jouan Paul Kuentz Klaske D. Lichtenbelt Joerg Betschinger 《Cell Stem Cell》2019,24(2):257-270.e8
32.
Luo J Stadler PF He S Meyer A 《Journal of experimental zoology. Part B. Molecular and developmental evolution》2007,308(3):250-258
A tetraploidization event took place in the cyprinid lineage leading to goldfishes about 15 million years ago. A PCR survey for Hox genes in the goldfish Carassius auratus auratus (Actinopterygii: Cyprinidae) was performed to assess the consequences of this genome duplication. Not surprisingly, the genomic organization of the Hox gene clusters of goldfish is similar to that of the closely related zebrafish (Danio rerio). However, the goldfish exhibits a much larger number of recent pseudogenes, which are characterized by indels. These findings are consistent with the hypothesis that dosage effects cause selection pressure to rapidly silence crucial developmental regulators after a tetraploidization event. 相似文献
33.
Agatha A. van der Klaauw Sophie Croizier Edson Mendes de Oliveira Lukas K.J. Stadler Soyoung Park Youxin Kong Matthew C. Banton Panna Tandon Audrey E. Hendricks Julia M. Keogh Susanna E. Riley Sofia Papadia Elana Henning Rebecca Bounds Elena G. Bochukova Vanisha Mistry Stephen O’Rahilly Richard B. Simerly I. Sadaf Farooqi 《Cell》2019,176(4):729-742.e18
34.
Eminger M Gásková D Brodská B Holoubek A Stadler N Sigler K 《Folia microbiologica》1999,44(3):283-288
The rate and extent of uptake of the fluorescent probe diS-C3(3) reporting on membrane potential inS. cerevisiae is affected by the strain under study, cell-growth phase, starvation and by the concentration of glucose both in the growth
medium and in the monitored cell suspension under non-growth conditions. Killer toxin K1 brings about changes in membrane
potential. In all types of cells tested,viz. in glucose-supplied stationary or exponential cells of the killer-sensitive strain S6/1 or a conventional strain RXII, or
in glucose-free exponential cells of both strains, both active and heat-inactivated toxin slow down the potential-dependent
uptake of diS-C3(3) into the cells. This may reflect “clogging” of pores in the cell wall that hinders, but does not prevent, probe passage
to the plasma membrane and its equilibration. The clogging effect of heat-inactivated toxin is stronger than that exerted
by active toxin. In susceptible cells,i.e. in exponential-phase glucose-supplied cells of the sensitive strain S6/1, this phase of probe uptake retardation is followed
by an irreversible red shift in probe fluorescence maximumλ
max indicating damage to membrane integrity and cell permeabilization. A similar fast red shift inλ
max signifying lethal cell damage was found in heat-killed or nystatin-treated cells. 相似文献
35.
The secondary structures of nucleic acids form a particularly important class of contact structures. Many important RNA molecules,
however, contain pseudo-knots, a structural feature that is excluded explicitly from the conventional definition of secondary
structures. We propose here a generalization of secondary structures incorporating ‘non-nested’ pseudo-knots, which we call
bi-secondary structures, and discuss measures for the complexity of more general contact structures based on their graph-theoretical properties.
Bi-secondary structures are planar trivalent graphs that are characterized by special embedding properties. We derive exact
upper bounds on their number (as a function of the chain length n) implying that there are fewer different structures than sequences. Computational results show that the number of bi-secondary
structures grows approximately like 2.35n. Numerical studies based on kinetic folding and a simple extension of the standard energy model show that the global features
of the sequence-structure map of RNA do not change when pseudo-knots are introduced into the secondary structure picture.
We find a large fraction of neutral mutations and, in particular, networks of sequences that fold into the same shape. These
neutral networks percolate through the entire sequence space. 相似文献
36.
A sucrose (Suc) transporter cDNA has been cloned from Alonsoa meridionalis, a member of the Scrophulariaceae. This plant species has an open minor vein configuration and translocates mainly raffinose and stachyose in addition to Suc in the phloem (C. Knop, O. Voitsekhovskaja, G. Lohaus [2001] Planta 213: 80-91). These are typical properties of symplastic phloem loaders. For functional characterization, AmSUT1 cDNA was expressed in bakers' yeast (Saccharomyces cerevisiae). Substrate and inhibitor specificities, energy dependence, and Km value of the protein agree well with the properties measured for other Suc transporters of apoplastic phloem loaders. A polyclonal antiserum against the 17 N-terminal amino acids of the A. meridionalis Suc transporter AmSUT1 was used to determine the cellular localization of the AmSUT1 protein. Using fluorescence labeling on sections from A. meridionalis leaves and stems, AmSUT1 was localized exclusively in phloem cells. Further histological characterization identified these cells as companion cells and sieve elements. p-Chloromercuribenzenesulfonic acid affected the sugar exudation of cut leaves in such a way that the exudation rates of Suc and hexoses decreased, whereas those of raffinose and stachyose increased. The data presented indicate that phloem loading of Suc and retrieval of Suc in A. meridionalis are at least partly mediated by the activity of AmSUT1 in addition to symplastic phloem loading. 相似文献
37.
Alignment of RNA base pairing probability matrices 总被引:6,自引:0,他引:6
MOTIVATION: Many classes of functional RNA molecules are characterized by highly conserved secondary structures but little detectable sequence similarity. Reliable multiple alignments can therefore be constructed only when the shared structural features are taken into account. Since multiple alignments are used as input for many subsequent methods of data analysis, structure-based alignments are an indispensable necessity in RNA bioinformatics. RESULTS: We present here a method to compute pairwise and progressive multiple alignments from the direct comparison of base pairing probability matrices. Instead of attempting to solve the folding and the alignment problem simultaneously as in the classical Sankoff's algorithm, we use McCaskill's approach to compute base pairing probability matrices which effectively incorporate the information on the energetics of each sequences. A novel, simplified variant of Sankoff's algorithms can then be employed to extract the maximum-weight common secondary structure and an associated alignment. AVAILABILITY: The programs pmcomp and pmmulti described in this contribution are implemented in Perl and can be downloaded together with the example datasets from http://www.tbi.univie.ac.at/RNA/PMcomp/. A web server is available at http://rna.tbi.univie.ac.at/cgi-bin/pmcgi.pl 相似文献
38.
Witwer C Hofacker IL Stadler PF 《IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM》2004,1(2):66-77
Most functional RNA molecules have characteristic structures that are highly conserved in evolution. Many of them contain pseudoknots. Here, we present a method for computing the consensus structures including pseudoknots based on alignments of a few sequences. The algorithm combines thermodynamic and covariation information to assign scores to all possible base pairs, the base pairs are chosen with the help of the maximum weighted matching algorithm. We applied our algorithm to a number of different types of RNA known to contain pseudoknots. All pseudoknots were predicted correctly and more than 85 percent of the base pairs were identified. 相似文献
39.
Fried C Prohaska SJ Stadler PF 《Journal of experimental zoology. Part B. Molecular and developmental evolution》2004,302(2):165-173
Despite their homology and analogous function, the Hox gene clusters of vertebrates and invertebrates are subject to different constraints on their structural organization. This is demonstrated by a drastically different distribution of repetitive DNA elements in the Hox cluster regions. While gnathostomes have a strong tendency to exclude repetitive DNA elements from the inside of their Hox clusters, no such trend can be detected in the Hox gene clusters of protostomes. Repeats "invade" the gnathostome Hox clusters from the 5' and 3' ends while the core of the clusters remains virtually free of repetitive DNA. This invasion appears to be correlated with relaxed constraints associated with gene loss after cluster duplications. 相似文献
40.