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MATCH-UP/MATRIX is a program designed to aid the investigatorinterested in determining primary protein structure. It is writtenin Applesoft BASIC for the Apple lle microcomputer. MATCH-UPwill survey any set of proteinaceous materials for amino acidsequence homology; however, it is primarily intended to comparethe structures of newly sequenced peptides with the establishedstructure of a protein with suspected homology. Any peptide-to-proteinalignment which shows a homology greater than or equal to thepercentage specified by the user will result in output. MATRIXwill compare the sequences of two proteins (peptides) in whateveralignment specified by the user and is intended to spot insertionsand/or deletions between structures.
Received on December 2, 1985; accepted on March 10, 1986 相似文献
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Antonia Piazzesi Yiru Wang Joshua Jackson Lena Wischhof Viktoria ZeislerDiehl Enzo Scifo Ina Oganezova Thorben Hoffmann Pablo Gmez Martín Fabio Bertan Chester J J Wrobel Frank C Schroeder Dan Ehninger Kristian Hndler Joachim L Schultze Lukas Schreiber Gerhild van EchtenDeckert Pierluigi Nicotera Daniele Bano 《EMBO reports》2022,23(5)
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Christoph?ScheichEmail author Dietmar?Leitner Volker?Sievert Martina?Leidert Brigitte?Schlegel Bernd?Simon Ivica?Letunic Konrad?Büssow Anne?Diehl 《BMC structural biology》2004,4(1):4
Background
High-throughput protein structure analysis of individual protein domains requires analysis of large numbers of expression clones to identify suitable constructs for structure determination. For this purpose, methods need to be implemented for fast and reliable screening of the expressed proteins as early as possible in the overall process from cloning to structure determination. 相似文献7.
Valentina Diehl Martin Wegner Paolo Grumati Koraljka Husnjak Simone Schaubeck Andrea Gubas Varun
Jayeshkumar Shah Ibrahim
H Polat Felix Langschied Cristian Prieto-Garcia Konstantin Müller Alkmini Kalousi Ingo Ebersberger Christian
H Brandts Ivan Dikic Manuel Kaulich 《Nucleic acids research》2021,49(10):5684
Combinatorial CRISPR-Cas screens have advanced the mapping of genetic interactions, but their experimental scale limits the number of targetable gene combinations. Here, we describe 3Cs multiplexing, a rapid and scalable method to generate highly diverse and uniformly distributed combinatorial CRISPR libraries. We demonstrate that the library distribution skew is the critical determinant of its required screening coverage. By circumventing iterative cloning of PCR-amplified oligonucleotides, 3Cs multiplexing facilitates the generation of combinatorial CRISPR libraries with low distribution skews. We show that combinatorial 3Cs libraries can be screened with minimal coverages, reducing associated efforts and costs at least 10-fold. We apply a 3Cs multiplexing library targeting 12,736 autophagy gene combinations with 247,032 paired gRNAs in viability and reporter-based enrichment screens. In the viability screen, we identify, among others, the synthetic lethal WDR45B-PIK3R4 and the proliferation-enhancing ATG7-KEAP1 genetic interactions. In the reporter-based screen, we identify over 1,570 essential genetic interactions for autophagy flux, including interactions among paralogous genes, namely ATG2A-ATG2B, GABARAP-MAP1LC3B and GABARAP-GABARAPL2. However, we only observe few genetic interactions within paralogous gene families of more than two members, indicating functional compensation between them. This work establishes 3Cs multiplexing as a platform for genetic interaction screens at scale. 相似文献
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Jessel R Haertel S Socaciu C Tykhonova S Diehl HA 《Journal of cellular and molecular medicine》2002,6(1):82-92
We investigated the time-dependence of apoptotic events in EL4 cells by monitoring plasma membrane changes in correlation to DNA fragmentation and cell shrinkage. We applied three apoptosis inducers (staurosporine, tubericidine and X-rays) and we looked at various markers to follow the early-to-late apoptotic events: phospholipid translocation (identified through annexin V-fluorescein assay and propidium iodide), lipid package (via merocyanine assay), membrane fluidity and anisotropy (via fluorescent measurements), DNA fragmentation by the fluorescence-labeling test and cell size measurements. The different apoptotic inducers caused different reactions of the cells: staurosporine induced apoptosis most rapidly in a high number of cells, tubercidine triggered apoptosis only in the S phase cells, while X-rays caused a G2/M arrest and subsequently apoptosis. Loss of lipid asymmetry is promptly detectable after one hour of incubation time. The phosphatidylserine translocation, decrease of lipid package and anisotropy, and the increase of membrane fluidity appeared to be based on the same process of lipid asymmetry loss. Therefore, the DNA fragmentation and the cell shrinkage appear to be parallel and independent processes running on different time scales but which are kinetically inter-related. The results indicate different signal steps to apoptosis dependent on inducer characteristics but the kinetics of \"early-to-late\" apoptosis appears to be a fixed program. 相似文献
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Locus Heterogeneity for Waardenburg Syndrome is Predictive of Clinical Subtypes 总被引:1,自引:4,他引:1
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Lindsay A. Farrer Kathleen S. Arnos James H. Asher Clinton T. Baldwin Scott R. Diehl Thomas B. Friedman Jacquie Greenberg Kenneth M. Grundfast Christopher Hoth Anil K. Lalwani Barbara Landa Kate Leverton Aubrey Milunsky Robert Morell Walter E. Nance Valerie Newton Rajkumar Ramesar Valluri S. Rao Jennifer E. Reynolds Theresa B. San Agustin Edward R. Wilcox Ingrid Winship Andrew P. Read 《American journal of human genetics》1994,55(4):728-737
Waardenburg syndrome (WS) is a dominantly inherited and clinically variable syndrome of deafness, pigmentary changes, and distinctive facial features. Clinically, WS type I (WS1) is differentiated from WS type II (WS2) by the high frequency of dystopia canthorum in the family. In some families, WS is caused by mutations in the PAX3 gene on chromosome 2q. We have typed microsatellite markers within and flanking PAX3 in 41 WS1 kindreds and 26 WS2 kindreds in order to estimate the proportion of families with probable mutations in PAX3 and to study the relationship between phenotypic and genotypic heterogeneity. Evaluation of heterogeneity in location scores obtained by multilocus analysis indicated that WS is linked to PAX3 in 60% of all WS families and in 100% of WS1 families. None of the WS2 families were linked. In those families in which equivocal lod scores (between −2 and +1) were found, PAX3 mutations have been identified in 5 of the 15 WS1 families but in none of the 4 WS2 families. Although preliminary studies do not suggest any association between the phenotype and the molecular pathology in 20 families with known PAX3 mutations and in four patients with chromosomal abnormalities in the vicinity of PAX3, the presence of dystopia in multiple family members is a reliable indicator for identifying families likely to have a defect in PAX3. 相似文献
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Topical application of different juvenile hormone analogs (JHA) or of a mixture of stereoisomers of insect juvenile hormone (JH) 1 and 3 to fed virgin female Ornithodoros moubata immediately after feeding induced vitellogenesis and egg-laying in up to 70% of treated females. In controls only 13.7% oviposited. The eggs were sterile, with abnormal shape, but their number versus the weight of engorged females was normal or sometimes greater than in mated females. However, preoviposition period was longer than in mated females. It was more difficult to induce egg-laying by similar topical applications 100 days after feeding of virgin females. A maximum of 58% of ovipositing females was obtained with a very high dosage of JH mixture (500 fig). Injection of this mixture into the females was more potent; 15 to 50 fig induced oviposition in about 60% of the females. The preoviposition period was also longer than in control females. Our results suggest the presence of a JH-like substance which is involved in the hormonal control of vitellogenesis. However, since natural isomers of JH were much less efficient than isomeric mixtures or JHA, we suppose that the natural tick hormone does not correspond to JH, but rather to a JH-like substance. 相似文献