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991.
We present a novel approach for analyzing biological time-series data using a context-free language (CFL) representation that allows the extraction and quantification of important features from the time-series. This representation results in Hierarchically AdaPtive (HAP) analysis, a suite of multiple complementary techniques that enable rapid analysis of data and does not require the user to set parameters. HAP analysis generates hierarchically organized parameter distributions that allow multi-scale components of the time-series to be quantified and includes a data analysis pipeline that applies recursive analyses to generate hierarchically organized results that extend traditional outcome measures such as pharmacokinetics and inter-pulse interval. Pulsicons, a novel text-based time-series representation also derived from the CFL approach, are introduced as an objective qualitative comparison nomenclature. We apply HAP to the analysis of 24 hours of frequently sampled pulsatile cortisol hormone data, which has known analysis challenges, from 14 healthy women. HAP analysis generated results in seconds and produced dozens of figures for each participant. The results quantify the observed qualitative features of cortisol data as a series of pulse clusters, each consisting of one or more embedded pulses, and identify two ultradian phenotypes in this dataset. HAP analysis is designed to be robust to individual differences and to missing data and may be applied to other pulsatile hormones. Future work can extend HAP analysis to other time-series data types, including oscillatory and other periodic physiological signals. 相似文献
992.
Colin Ruprecht Takayuki Tohge Alisdair Fernie Cara L. Mortimer Amanda Kozlo Paul D. Fraser Norma Funke Igor Cesarino Ruben Vanholme Wout Boerjan Kris Morreel Ingo Burgert Notburga Gierlinger Vincent Bulone Vera Schneider Andrea Stockero Juan Pedro Navarro Frank Pudel Bart Tambuyser James Hygate Jon Bumstead Louis Notley Staffan Persson 《Journal of visualized experiments : JoVE》2014,(87)
993.
We developed a new computational algorithm for the accurate identification of ligand binding envelopes rather than surface binding sites. We performed a large scale classification of the identified envelopes according to their shape and physicochemical properties. The predicting algorithm, called PocketFinder, uses a transformation of the Lennard-Jones potential calculated from a three-dimensional protein structure and does not require any knowledge about a potential ligand molecule. We validated this algorithm using two systematically collected data sets of ligand binding pockets from complexed (bound) and uncomplexed (apo) structures from the Protein Data Bank, 5616 and 11,510, respectively. As many as 96.8% of experimental binding sites were predicted at better than 50% overlap level. Furthermore 95.0% of the asserted sites from the apo receptors were predicted at the same level. We demonstrate that conformational differences between the apo and bound pockets do not dramatically affect the prediction results. The algorithm can be used to predict ligand binding pockets of uncharacterized protein structures, suggest new allosteric pockets, evaluate feasibility of protein-protein interaction inhibition, and prioritize molecular targets. Finally the data base of the known and predicted binding pockets for the human proteome structures, the human pocketome, was collected and classified. The pocketome can be used for rapid evaluation of possible binding partners of a given chemical compound. 相似文献
994.
Nicolaou KC Roecker AJ Hughes R van Summeren R Pfefferkorn JA Winssinger N 《Bioorganic & medicinal chemistry》2003,11(3):465-476
Using a polymer-bound selenenyl bromide resin, o-allyl and o-prenyl anilines were cycloaded to afford a series of solid-supported indoline and indole scaffolds. These scaffolds were then functionalized and cleaved via four distinct methods, namely traceless reduction, radical cyclization, radical rearrangement, and oxidative elimination, to afford 2-methyl indolines, polycyclic indolines, 2-methyl indoles, and 2-propenyl indolines, respectively. A number of small combinatorial libraries of compounds reminiscent of certain designed ligands of biological interest were constructed demonstrating the potential utility of the developed methodology to chemical biology studies and the drug discovery process. 相似文献
995.
996.
The polarity of sensory bristles on the thorax of Drosophila is linked to the orientation of the asymmetric cell divisions that partition cell fate determinants in this lineage. The orientation of these divisions is under the control of the Frizzled pathway that generates planar polarity in a number of cell types. 相似文献
997.
Vindhya Palagani Mona El Khatib Uta Kossatz Przemyslaw Bozko Martin R. Müller Michael P. Manns Till Krech Nisar P. Malek Ruben R. Plentz 《PloS one》2012,7(10)
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease with a high rate of metastasis. Recent studies have indicated that the Notch signalling pathway is important in PDAC initiation and maintenance, although the specific cell biological roles of the pathway remain to be established. Here we sought to examine this question in established pancreatic cancer cell lines using the γ-secretase inhibitor IX (GSI IX) to inactivate Notch. Based on the known roles of Notch in development and stem cell biology, we focused on effects on epithelial mesenchymal transition (EMT) and on pancreatic tumor initiating CD44+/EpCAM+ cells. We analyzed the effect of the GSI IX on growth and epithelial plasticity of human pancreatic cancer cell lines, and on the tumorigenicity of pancreatic tumor initiating CD44+/EpCAM+ cells. Notably, apoptosis was induced after GSI IX treatment and EMT markers were selectively targeted. Furthermore, under GSI IX treatment, decline in the growth of pancreatic tumor initiating CD44+/EpCAM+ cells was observed in vitro and in a xenograft mouse model. This study demonstrates a central role of Notch signalling pathway in pancreatic cancer pathogenesis and identifies an effective approach to inhibit selectively EMT and suppress tumorigenesis by eliminating pancreatic tumor initiating CD44+/EpCAM+ cells. 相似文献
998.
McEvoy CR Cloete R Müller B Schürch AC van Helden PD Gagneux S Warren RM Gey van Pittius NC 《PloS one》2012,7(4):e30593
Mycobacterium tuberculosis complex (MTBC) genomes contain 2 large gene families termed pe and ppe. The function of pe/ppe proteins remains enigmatic but studies suggest that they are secreted or cell surface associated and are involved in bacterial virulence. Previous studies have also shown that some pe/ppe genes are polymorphic, a finding that suggests involvement in antigenic variation. Using comparative sequence analysis of 18 publicly available MTBC whole genome sequences, we have performed alignments of 33 pe (excluding pe_pgrs) and 66 ppe genes in order to detect the frequency and nature of genetic variation. This work has been supplemented by whole gene sequencing of 14 pe/ppe (including 5 pe_pgrs) genes in a cohort of 40 diverse and well defined clinical isolates covering all the main lineages of the M. tuberculosis phylogenetic tree. We show that nsSNP's in pe (excluding pgrs) and ppe genes are 3.0 and 3.3 times higher than in non-pe/ppe genes respectively and that numerous other mutation types are also present at a high frequency. It has previously been shown that non-pe/ppe M. tuberculosis genes display a remarkably low level of purifying selection. Here, we also show that compared to these genes those of the pe/ppe families show a further reduction of selection pressure that suggests neutral evolution. This is inconsistent with the positive selection pressure of "classical" antigenic variation. Finally, by analyzing such a large number of genes we were able to detect large differences in mutation type and frequency between both individual genes and gene sub-families. The high variation rates and absence of selective constraints provides valuable insights into potential pe/ppe function. Since pe/ppe proteins are highly antigenic and have been studied as potential vaccine components these results should also prove informative for aspects of M. tuberculosis vaccine design. 相似文献
999.
I Valles MJ Pajares V Segura E Guruceaga J Gomez-Roman D Blanco A Tamura LM Montuenga R Pio 《PloS one》2012,7(8):e42086
Lung cancer is a leading cause of cancer death worldwide. Several alterations in RNA metabolism have been found in lung cancer cells; this suggests that RNA metabolism-related molecules are involved in the development of this pathology. In this study, we searched for RNA metabolism-related genes that exhibit different expression levels between normal and tumor lung tissues. We identified eight genes differentially expressed in lung adenocarcinoma microarray datasets. Of these, seven were up-regulated whereas one was down-regulated. Interestingly, most of these genes had not previously been associated with lung cancer. These genes play diverse roles in mRNA metabolism: three are associated with the spliceosome (ASCL3L1, SNRPB and SNRPE), whereas others participate in RNA-related processes such as translation (MARS and MRPL3), mRNA stability (PCBPC1), mRNA transport (RAE), or mRNA editing (ADAR2, also known as ADARB1). Moreover, we found a high incidence of loss of heterozygosity at chromosome 21q22.3, where the ADAR2 locus is located, in NSCLC cell lines and primary tissues, suggesting that the downregulation of ADAR2 in lung cancer is associated with specific genetic losses. Finally, in a series of adenocarcinoma patients, the expression of five of the deregulated genes (ADAR2, MARS, RAE, SNRPB and SNRPE) correlated with prognosis. Taken together, these results support the hypothesis that changes in RNA metabolism are involved in the pathogenesis of lung cancer, and identify new potential targets for the treatment of this disease. 相似文献
1000.
Amparo M. Martínez Luis T. Gama Javier Ca?ón Catarina Ginja Juan V. Delgado Susana Dunner Vincenzo Landi Inmaculada Martín-Burriel M. Cecilia T. Penedo Clementina Rodellar Jose Luis Vega-Pla Atzel Acosta Luz A. álvarez Esperanza Camacho Oscar Cortés Jose R. Marques Roberto Martínez Ruben D. Martínez Lilia Melucci Guillermo Martínez-Velázquez Jaime E. Mu?oz Alicia Postiglioni Jorge Quiroz Philip Sponenberg Odalys Uffo Axel Villalobos Delsito Zambrano Pilar Zaragoza 《PloS one》2012,7(11)