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21.
Noe Fernandez‐Pozo Fabian B. Haas Rabea Meyberg Kristian K. Ullrich Manuel Hiss Pierre‐Franois Perroud Sebastian Hanke Viktor Kratz Adrian F. Powell Eleanor F. Vesty Christopher G. Daum Matthew Zane Anna Lipzen Avinash Sreedasyam Jane Grimwood Juliet C. Coates Kerrie Barry Jeremy Schmutz Lukas A. Mueller Stefan A. Rensing 《The Plant journal : for cell and molecular biology》2020,102(1):165-177
Physcomitrella patens is a bryophyte model plant that is often used to study plant evolution and development. Its resources are of great importance for comparative genomics and evo‐devo approaches. However, expression data from Physcomitrella patens were so far generated using different gene annotation versions and three different platforms: CombiMatrix and NimbleGen expression microarrays and RNA sequencing. The currently available P. patens expression data are distributed across three tools with different visualization methods to access the data. Here, we introduce an interactive expression atlas, Physcomitrella Expression Atlas Tool (PEATmoss), that unifies publicly available expression data for P. patens and provides multiple visualization methods to query the data in a single web‐based tool. Moreover, PEATmoss includes 35 expression experiments not previously available in any other expression atlas. To facilitate gene expression queries across different gene annotation versions, and to access P. patens annotations and related resources, a lookup database and web tool linked to PEATmoss was implemented. PEATmoss can be accessed at https://peatmoss.online.uni-marburg.de 相似文献
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Andreas Lackner Robert Sehlke Marius Garmhausen Giuliano Giuseppe Stirparo Michelle Huth Fabian TitzTeixeira Petra van der Lelij Julia Ramesmayer Henry F Thomas Meryem Ralser Laura Santini Elena Galimberti Mihail Sarov A Francis Stewart Austin Smith Andreas Beyer Martin Leeb 《The EMBO journal》2021,40(8)
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Leonard Schmiester Yannik Schlte Frank T. Bergmann Tacio Camba Erika Dudkin Janine Egert Fabian Frhlich Lara Fuhrmann Adrian L. Hauber Svenja Kemmer Polina Lakrisenko Carolin Loos Simon Merkt Wolfgang Müller Dilan Pathirana Elba Raimúndez Lukas Refisch Marcus Rosenblatt Paul L. Stapor Philipp Stdter Dantong Wang Franz-Georg Wieland Julio R. Banga Jens Timmer Alejandro F. Villaverde Sven Sahle Clemens Kreutz Jan Hasenauer Daniel Weindl 《PLoS computational biology》2021,17(1)
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been—so far—no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing the observation model and experimental data as well as parameters to be estimated. We already implemented PEtab support into eight well-established model simulation and parameter estimation toolboxes with hundreds of users in total. We provide a Python library for validation and modification of a PEtab problem and currently 20 example parameter estimation problems based on recent studies. 相似文献
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J. Wikman-coffelt F. Fabian Dean T. Mason 《Preparative biochemistry & biotechnology》2013,43(2):97-101
Abstract Myosin can be frozen in liquid nitrogen (?70°C) and stored at this temperature for 5 months with no loss in K+, Ca2+, or actin + Mg2+ -stimulated ATPase activities. Furthermore, myosin can be refrozen and thawed in this manner for at least 5 consecutive times with no alteration in ATP ase activity. 相似文献
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Nicholas Johnson Sarah Ha?denteufel Melanie Theis Adrienne W. Paton James C. Paton Richard Zimmermann Stephen High 《PloS one》2013,8(10)
The metazoan Sec61 translocon transports polypeptides into and across the membrane of the endoplasmic reticulum via two major routes, a well-established co-translational pathway and a post-translational alternative. We have used two model substrates to explore the elements of a secretory protein precursor that preferentially direct it towards a co- or post-translational pathway for ER translocation. Having first determined the capacity of precursors to enter ER derived microsomes post-translationally, we then exploited semi-permeabilized mammalian cells specifically depleted of key membrane components using siRNA to address their contribution to the membrane translocation process. These studies suggest precursor chain length is a key factor in the post-translational translocation at the mammalian ER, and identify Sec62 and Sec63 as important components acting on this route. This role for Sec62 and Sec63 is independent of the signal sequence that delivers the precursor to the ER. However, the signal sequence can influence the subsequent membrane translocation process, conferring sensitivity to a small molecule inhibitor and dictating reliance on the molecular chaperone BiP. Our data support a model where secretory protein precursors that fail to engage the signal recognition particle, for example because they are short, are delivered to the ER membrane via a distinct route that is dependent upon both Sec62 and Sec63. Although this requirement for Sec62 and Sec63 is unaffected by the specific signal sequence that delivers a precursor to the ER, this region can influence subsequent events, including both Sec61 mediated transport and the importance of BiP for membrane translocation. Taken together, our data suggest that an ER signal sequence can regulate specific aspects of Sec61 mediated membrane translocation at a stage following Sec62/Sec63 dependent ER delivery. 相似文献
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Sakine Simsekyilmaz Fabian Schreiber Stefan Weinandy Felix Gremse Tolga Taha S?nmez Elisa A. Liehn 《Journal of visualized experiments : JoVE》2013,(75)
Despite the considerable progress made in the stent development in the last decades, cardiovascular diseases remain the main cause of death in western countries. Beside the benefits offered by the development of different drug-eluting stents, the coronary revascularization bears also the life-threatening risks of in-stent thrombosis and restenosis. Research on new therapeutic strategies is impaired by the lack of appropriate methods to study stent implantation and restenosis processes. Here, we describe a rapid and accessible procedure of stent implantation in mouse carotid artery, which offers the possibility to study in a convenient way the molecular mechanisms of vessel remodeling and the effects of different drug coatings. 相似文献