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991.
Molecular Ecology Resources Primer Development Consortium Abercrombie LG Anderson CM Baldwin BG Bang IC Beldade R Bernardi G Boubou A Branca A Bretagnolle F Bruford MW Buonamici A Burnett Jr RK Canal D Cárdenas H Caullet C Chen SY Chun YJ Cossu C Crane CF Cros-Arteil S Cudney-Bueno R Danti R Dávila JA Della Rocca G Dobata S Dunkle LD Dupas S Faure N Ferrero ME Fumanal B Gigot G González I Goodwin SB Groth D Hardesty BD Hasegawa E Hoffman EA Hou ML Jamsari AF Ji HJ Johnson DH Joseph L Justy F 《Molecular ecology resources》2009,9(5):1375-1379
This article documents the addition of 283 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Agalinis acuta; Ambrosia artemisiifolia; Berula erecta; Casuarius casuarius; Cercospora zeae-maydis; Chorthippus parallelus; Conyza canadensis; Cotesia sesamiae; Epinephelus acanthistius; Ficedula hypoleuca; Grindelia hirsutula; Guadua angustifolia; Leucadendron rubrum; Maritrema novaezealandensis; Meretrix meretrix; Nilaparvata lugens; Oxyeleotris marmoratus; Phoxinus neogaeus; Pristomyrmex punctatus; Pseudobagrus brevicorpus; Seiridium cardinale; Stenopsyche marmorata; Tetranychus evansi and Xerus inauris. These loci were cross-tested on the following species: Agalinis decemloba; Agalinis tenella; Agalinis obtusifolia; Agalinis setacea; Agalinis skinneriana; Cercospora zeina; Cercospora kikuchii; Cercospora sorghi; Mycosphaerella graminicola; Setosphaeria turcica; Magnaporthe oryzae; Cotesia flavipes; Cotesia marginiventris; Grindelia Xpaludosa; Grindelia chiloensis; Grindelia fastigiata; Grindelia lanceolata; Grindelia squarrosa; Leucadendron coniferum; Leucadendron salicifolium; Leucadendron tinctum; Leucadendron meridianum; Laodelphax striatellus; Sogatella furcifera; Phoxinus eos; Phoxinus rigidus; Phoxinus brevispinosus; Phoxinus bicolor; Tetranychus urticae; Tetranychus turkestani; Tetranychus ludeni; Tetranychus neocaledonicus; Tetranychus amicus; Amphitetranychus viennensis; Eotetranychus rubiphilus; Eotetranychus tiliarium; Oligonychus perseae; Panonychus citri; Bryobia rubrioculus; Schizonobia bundi; Petrobia harti; Xerus princeps; Spermophilus tridecemlineatus and Sciurus carolinensis. 相似文献
992.
Pukall R Lapidus A Nolan M Copeland A Glavina Del Rio T Lucas S Chen F Tice H Cheng JF Chertkov O Bruce D Goodwin L Kuske C Brettin T Detter JC Han C Pitluck S Pati A Mavrommatis K Ivanova N Ovchinnikova G Chen A Palaniappan K Schneider S Rohde M Chain P D'haeseleer P Göker M Bristow J Eisen JA Markowitz V Kyrpides NC Klenk HP Hugenholtz P 《Standards in genomic sciences》2009,1(3):234-241
Stackebrandtia nassauensis Labeda and Kroppenstedt (2005) is the type species of the genus Stackebrandtia, and a member of the actinobacterial family Glycomycetaceae. Stackebrandtia currently contains two species, which are differentiated from Glycomyces spp. by cellular fatty acid and menaquinone composition. Strain LLR-40K-21(T) is Gram-positive, aerobic, and nonmotile, with a branched substrate mycelium and on some media an aerial mycelium. The strain was originally isolated from a soil sample collected from a road side in Nassau, Bahamas. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of the actinobacterial suborder Glycomycineae. The 6,841,557 bp long single replicon genome with its 6487 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
993.
Anderson I Tindall BJ Pomrenke H Göker M Lapidus A Nolan M Copeland A Glavina Del Rio T Chen F Tice H Cheng JF Lucas S Chertkov O Bruce D Brettin T Detter JC Han C Goodwin L Land M Hauser L Chang YJ Jeffries CD Pitluck S Pati A Mavromatis K Ivanova N Ovchinnikova G Chen A Palaniappan K Chain P Rohde M Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP 《Standards in genomic sciences》2009,1(3):218-225
Halorhabdus utahensis Wainø et al. 2000 is the type species of the genus, which is of phylogenetic interest because of its location on one of the deepest branches within the very extensive euryarchaeal family Halobacteriaceae. H. utahensis is a free-living, motile, rod shaped to pleomorphic, Gram-negative archaeon, which was originally isolated from a sediment sample collected from the southern arm of Great Salt Lake, Utah, USA. When grown on appropriate media, H. utahensis can form polyhydroxybutyrate (PHB). Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the a member of halobacterial genus Halorhabdus, and the 3,116,795 bp long single replicon genome with its 3027 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
994.
Saunders E Pukall R Abt B Lapidus A Glavina Del Rio T Copeland A Tice H Cheng JF Lucas S Chen F Nolan M Bruce D Goodwin L Pitluck S Ivanova N Mavromatis K Ovchinnikova G Pati A Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Chain P Meincke L Sims D Brettin T Detter JC Göker M Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Han C 《Standards in genomic sciences》2009,1(2):174-182
Eggerthella lenta (Eggerth 1935) Wade et al. 1999, emended Würdemann et al. 2009 is the type species of the genus Eggerthella, which belongs to the actinobacterial family Coriobacteriaceae. E. lenta is a Gram-positive, non-motile, non-sporulating pathogenic bacterium that can cause severe bacteremia. The strain described in this study has been isolated from a rectal tumor in 1935. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Eggerthella, and the 3,632,260 bp long single replicon genome with its 3123 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
995.
Mavrommatis K Pukall R Rohde C Chen F Sims D Brettin T Kuske C Detter JC Han C Lapidus A Copeland A Glavina Del Rio T Nolan M Lucas S Tice H Cheng JF Bruce D Goodwin L Pitluck S Ovchinnikova G Pati A Ivanova N Chen A Palaniappan K Chain P D'haeseleer P Göker M Bristow J Eisen JA Markowitz V Hugenholtz P Rohde M Klenk HP Kyrpides NC 《Standards in genomic sciences》2009,1(2):93-100
Cryptobacterium curtum Nakazawa etal. 1999 is the type species of the genus, and is of phylogenetic interest because of its very distant and isolated position within the family Coriobacteriaceae. C. curtum is an asaccharolytic, opportunistic pathogen with a typical occurrence in the oral cavity, involved in dental and oral infections like periodontitis, inflammations and abscesses. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the actinobacterial family Coriobacteriaceae, and this 1,617,804 bp long single replicon genome with its 1364 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
996.
Mavrommatis K Gronow S Saunders E Land M Lapidus A Copeland A Glavina Del Rio T Nolan M Lucas S Chen F Tice H Cheng JF Bruce D Goodwin L Pitluck S Pati A Ivanova N Chen A Palaniappan K Chain P Hauser L Chang YJ Jeffries CD Brettin T Detter JC Han C Bristow J Göker M Rohde M Eisen JA Markowitz V Kyrpides NC Klenk HP Hugenholtz P 《Standards in genomic sciences》2009,1(2):101-109
Capnocytophaga ochracea (Prévot et al. 1956) Leadbetter et al. 1982 is the type species of the genus Capnocytophaga. It is of interest because of its location in the Flavobacteriaceae, a genomically not yet charted family within the order Flavobacteriales. The species grows as fusiform to rod shaped cells which tend to form clumps and are able to move by gliding. C. ochracea is known as a capnophilic (CO(2)-requiring) organism with the ability to grow under anaerobic as well as aerobic conditions (oxygen concentration larger than 15%), here only in the presence of 5% CO(2). Strain VPI 2845(T), the type strain of the species, is portrayed in this report as a gliding, Gram-negative bacterium, originally isolated from a human oral cavity. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the flavobacterial genus Capnocytophaga, and the 2,612,925 bp long single replicon genome with its 2193 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
997.
Land M Lapidus A Mayilraj S Chen F Copeland A Del Rio TG Nolan M Lucas S Tice H Cheng JF Chertkov O Bruce D Goodwin L Pitluck S Rohde M Göker M Pati A Ivanova N Mavromatis K Chen A Palaniappan K Hauser L Chang YJ Jeffries CC Brettin T Detter JC Han C Chain P Tindall BJ Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP 《Standards in genomic sciences》2009,1(1):46-53
Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO(2) atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome with its 7100 protein-coding and 77 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
998.
Lapidus A Pukall R Labuttii K Copeland A Del Rio TG Nolan M Chen F Lucas S Tice H Cheng JF Bruce D Goodwin L Pitluck S Rohde M Göker M Pati A Ivanova N Mavrommatis K Chen A Palaniappan K D'haeseleer P Chain P Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP 《Standards in genomic sciences》2009,1(1):3-11
Brachybacterium faecium Collins et al. 1988 is the type species of the genus, and is of phylogenetic interest because of its location in the Dermabacteraceae, a rather isolated family within the actinobacterial suborder Micrococcineae. B. faecium is known for its rod-coccus growth cycle and the ability to degrade uric acid. It grows aerobically or weakly anaerobically. The strain described in this report is a free-living, nonmotile, Gram-positive bacterium, originally isolated from poultry deep litter. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the actinobacterial family Dermabacteraceae, and the 3,614,992 bp long single replicon genome with its 3129 protein-coding and 69 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
999.
Expressed sequence tags (ESTs) from fungal-infected plant tissues are composed of a mixture of plant and fungal sequences. Using freely available software and tools, a novel procedure is described for distinguishing plant and fungal DNA sequences. Although the GenBank non-redundant (NR) database is larger and therefore one would presume that BLASTX analysis of it would be more accurate, superior resolution of 700 randomly selected fungal ESTs was found with Standalone TBLASTX analyses with a local matching database composed of a plant and a fungal genome. Standalone TBLASTX analyses of 3,983 ESTs from nine different fungal-infected plant EST libraries also proved to be superior in identifying the origin of sequences as either plant or fungal compared to GenBank BLASTX analysis. Standalone TBLASTX with a matching database comprised of a single plant and a single fungal genome appears to be a faster and more accurate method than BLASTX searches of the GenBank non-redundant database to distinguish fungal and plant sequences in mixed EST collections. 相似文献
1000.