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131.
Vinga S Carvalho AM Francisco AP Russo LM Almeida JS 《Algorithms for molecular biology : AMB》2012,7(1):10-12
Background
Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2 -L distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations.Results
The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE) queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm.Conclusions
The analysis of biological sequences relies on algorithmic foundations facing mounting challenges, both logistic (performance) and analytical (lack of unifying mathematical framework). CGR is found to provide the latter and to promise the former: graph-based data structures for sequence analysis operations are entailed by numerical-based data structures produced by CGR maps, providing a unifying analytical framework for a diversity of pattern matching problems. 相似文献132.
Mireille A. Edens Peter M.A. van Ooijen Wendy J. Post Mark J.F. Haagmans Wisnumurti Kristanto Paul E. Sijens Erik J. van der Jagt Ronald P. Stolk 《Obesity (Silver Spring, Md.)》2009,17(12):2239-2244
An abundance of fat stored within the liver, or steatosis, is the beginning of a broad hepatological spectrum, usually referred to as fatty liver disease (FLD). For studies on FLD, quantitative hepatic fat ultrasonography would be an appealing study modality. Objective of this study was to develop a technique for quantifying hepatic fat content by ultrasonography and validate this using proton magnetic resonance spectroscopy (1H MRS) as gold standard. Eighteen white volunteers (BMI range 21.0–42.9) were scanned by both ultrasonography and 1H MRS. Altered ultrasound characteristics, present in the case of FLD, were assessed using a specially developed software program. Various attenuation and textural based indices of FLD were extracted from ultrasound images. Using linear regression analysis, the predictive power of several models (consisting of both attenuation and textural based measures) on log 10–transformed hepatic fat content by 1H MRS were investigated. The best quantitative model was compared with a qualitative ultrasonography method, as used in clinical care. A model with four ultrasound characteristics could modestly predict the amount of liver fat (adjusted explained variance 43.2%, P = 0.021). Expanding the model to seven ultrasound characteristics increased adjusted explained variance to 60% (P = 0.015), with r = 0.789 (P < 0.001). Comparing this quantitative model with qualitative ultrasonography revealed a significant advantage of the quantitative model in predicting hepatic fat content (P < 0.001). This validation study shows that a combination of computer‐assessed ultrasound measures from routine ultrasound images can be used to quantitatively assess hepatic fat content. 相似文献
133.
Edens WA Sharling L Cheng G Shapira R Kinkade JM Lee T Edens HA Tang X Sullards C Flaherty DB Benian GM Lambeth JD 《The Journal of cell biology》2001,154(4):879-891
High molecular weight homologues of gp91phox, the superoxide-generating subunit of phagocyte nicotinamide adenine dinucleotide phosphate (NADPH)-oxidase, have been identified in human (h) and Caenorhabditis elegans (Ce), and are termed Duox for "dual oxidase" because they have both a peroxidase homology domain and a gp91phox domain. A topology model predicts that the enzyme will utilize cytosolic NADPH to generate reactive oxygen, but the function of the ecto peroxidase domain was unknown. Ce-Duox1 is expressed in hypodermal cells underlying the cuticle of larval animals. To investigate function, RNA interference (RNAi) was carried out in C. elegans. RNAi animals showed complex phenotypes similar to those described previously in mutations in collagen biosynthesis that are known to affect the cuticle, an extracellular matrix. Electron micrographs showed gross abnormalities in the cuticle of RNAi animals. In cuticle, collagen and other proteins are cross-linked via di- and trityrosine linkages, and these linkages were absent in RNAi animals. The expressed peroxidase domains of both Ce-Duox1 and h-Duox showed peroxidase activity and catalyzed cross-linking of free tyrosine ethyl ester. Thus, Ce-Duox catalyzes the cross-linking of tyrosine residues involved in the stabilization of cuticular extracellular matrix. 相似文献
134.
135.
Xerophyllum tenax is a mass-flowering, nectarless herb in which self-pollination is unavoidable as anthers shed pollen onto the three, receptive stigmatic ridges attached to each pistil within a few hours after expansion of the perianth. We compared the pollination system with reproductive success in this species through controlled, hand-pollination experiments. Ovaries of flowers sampled from unbagged inflorescences were visited by pollen-eating flies (primarily members of the family Syrphidae), beetles (primarily Cosmosalia and Epicauta spp.), and small bees, and produced normal-sized capsules and mature seeds. Ovaries of flowers from inflorescences bagged to prevent insect pollination produced small capsules containing undeveloped or no seeds. Epifluorescence analyses suggest that 0.95 of the uncovered flowers are cross-pollinated by insects with pollen tubes penetrating style and ovary tissue. Flowers show a "leaky" but early-acting self-incompatibility system. While hundreds of pollen tubes germinate on each stigmatic surface following self-pollination, few pollen tubes penetrate the stigmatic surface and none penetrate the ovary. In contrast, when stigmas are cross-pollinated by hand with pollen from a second inflorescence pollen tubes were seen penetrating style and ovary. Self-incompatibility in X. tenax parallels that of some species of Trillium, a sister genus within the Melanthiaceae. 相似文献
136.
Sohrab?P?Shah Yong?Huang Tao?Xu Macaire?MS?Yuen John?Ling BF?Francis?OuelletteEmail author 《BMC bioinformatics》2005,6(1):34
Background
We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. 相似文献137.
138.
OI Klychnikov AV Drabkin OV Vasilenko YS Pavlov MS Trofimova IN Smolenskaya AA Rozenkranz AS Sobolev AV Babakov 《Biochemistry. Biokhimii?a》1998,63(9):1083-1089
Higher plant plasma membranes carry receptors of different affinity for the phytotoxin fusicoccin. Reception of fusicoccin involves proteins belonging to the highly conserved 14-3-3 family, but the complete structure of the fusicoccin receptor (FCR) is unknown. Using radiation inactivation analysis, we estimated the molecular masses of low-affinity and high-affinity FCR at 63 +/- 7 and 130 +/- 15 kD, respectively. The dose dependences of receptor inactivation indicate that microsomal specimens contain "silent" FCRs of 420 +/- 90 kD in amounts commensurate with that of the active FCRs. Both low- and high-affinity FCRs are inactivated by hydrolytic enzymes from the outer surface of the plasma membrane, and impairment of protoplast integrity causes an irreversible transition of the low-affinity binding site into the high-affinity one. A scheme is proposed for the organization of different types of FCR in the plasma membrane, implying that the membrane affinity for fusicoccin reflects the interaction between proteins in the FCR complex. 相似文献
139.
Biotinyl-oligosaccharides are a relatively new generation of saccharide
probes that enable immobilization of desired oligosaccharides on
streptavidin matrices for studies of carbohydrate-protein interactions.
Here we describe the facile preparation of biotinyl-l-3-(2-naphthyl)-
alanine hydrazide (BNAH) derivatives of oligosaccharides, containing a
strong UV absorbing and fluorescent group, in which the ring of the
reducing-end monosaccharide is nonreduced. We evaluate reactivities of
immobilized BNAH- N -glycans with plant lectins that recognize aspects of
the oligosaccharide core or outer-arms. We make some comparisons with
2-amino-6-amidobiotinyl-pyridine (BAP) derivatives obtained by reductive
amination, and 6-(biotinyl)-aminocaproyl-hydrazide (BACH) derivatives which
have a longer spacer-arm. N -Glycan-BNAH and-BAP derivatives have, overall,
comparable reactivities with lectins which recognize N -glycan outer-arms
or the trimannosyl core, but only BNAH and BACH derivatives are bound by
lectins which recognize the non- reduced core. Moreover, with Pisum sativum
agglutinin (PSA) which additionally requires the fucosyl- N-
glycan-asparaginyl core for high affinity binding, the immobilized BNAH
derivative (which is an alanine hydrazide beta-glycoside) can substitute
for the natural beta- glycosylasparaginyl core, whereas the BACH derivative
(aminocaproyl- hydrazide-beta-glycoside) is less effective. BNAH is a
derivatization reagent of choice, therefore, for solid phase
carbohydrate-binding experiments with immobilized N -glycans.
相似文献
140.
The core domain of retrotransposon integrase in Hordeum: predicted structure and evolution 总被引:1,自引:0,他引:1
Suoniemi A; Tanskanen J; Pentikainen O; Johnson MS; Schulman AH 《Molecular biology and evolution》1998,15(9):1135-1144
Propagation of long terminal repeat (LTR)-bearing retrotransposons and
retroviruses requires integrase (IN, EC 2.7.7.-), encoded by the
retroelements themselves, which mediates the insertion of cDNA copies back
into the genome. An active retrotransposon family, BARE-1, comprises
approximately 7% of the barley (Hordeum vulgare subsp. vulgare) genome. We
have generated models for the secondary and tertiary structure of BARE-1 IN
and demonstrate their similarity to structures for human immunodeficiency
virus 1 and avian sarcoma virus INs. The IN core domains were compared for
80 clones from 28 Hordeum accessions representative of the diversity of the
genus. Based on the structural model, variations in the predicted, aligned
translations from these clones would have minimal structural and functional
effects on the encoded enzymes. This indicates that Hordeum retrotransposon
IN has been under purifying selection to maintain a structure typical of
retroviral INs. These represent the first such analyses for plant INs.
相似文献