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  • 1
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    Enzymology. A moving story (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-02-23
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907122/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907122/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Falke, Joseph J -- R01 GM040731/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Feb 22;295(5559):1480-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biophysics Program and the Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA. falke@colorado.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11859184" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/chemistry ; Binding Sites ; Catalysis ; Cyclophilin A/*chemistry/*metabolism ; Hydrogen Bonding ; Models, Molecular ; Nitrogen/chemistry ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Cancer. BRCA2 enters the fray (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-09-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, John H -- Elledge, Stephen J -- New York, N.Y. -- Science. 2002 Sep 13;297(5588):1822-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12228708" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; BRCA1 Protein/metabolism ; BRCA2 Protein/*chemistry/*metabolism ; Binding Sites ; Breast Neoplasms/genetics ; Crystallography, X-Ray ; DNA/*metabolism ; DNA Damage ; *DNA Repair ; DNA, Single-Stranded/metabolism ; DNA-Binding Proteins/metabolism ; Female ; Genes, BRCA1 ; Genes, BRCA2 ; Genetic Predisposition to Disease ; Humans ; Mice ; Ovarian Neoplasms/genetics ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rad51 Recombinase ; Rats ; Recombination, Genetic ; Replication Protein A
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Visualization and functional analysis of RNA-dependent RNA polymerase lattices (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-06-22
    Description: Positive-strand RNA viruses such as poliovirus replicate their genomes on intracellular membranes of their eukaryotic hosts. Electron microscopy has revealed that purified poliovirus RNA-dependent RNA polymerase forms planar and tubular oligomeric arrays. The structural integrity of these arrays correlates with cooperative RNA binding and RNA elongation and is sensitive to mutations that disrupt intermolecular contacts predicted by the polymerase structure. Membranous vesicles isolated from poliovirus-infected cells contain structures consistent with the presence of two-dimensional polymerase arrays on their surfaces during infection. Therefore, host cytoplasmic membranes may function as physical foundations for two-dimensional polymerase arrays, conferring the advantages of surface catalysis to viral RNA replication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lyle, John M -- Bullitt, Esther -- Bienz, Kurt -- Kirkegaard, Karla -- AI-42119/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2002 Jun 21;296(5576):2218-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12077417" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; HeLa Cells ; Humans ; Hydrogen-Ion Concentration ; Inclusion Bodies, Viral/metabolism/ultrastructure ; Microscopy, Electron ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Poliovirus/*enzymology/physiology ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; RNA Replicase/*chemistry/isolation & purification/*metabolism/ultrastructure ; RNA, Viral/biosynthesis/*metabolism ; Viral Core Proteins/metabolism ; Virus Replication
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1 (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-02-09
    Description: Double-stranded RNA-mediated gene interference (RNAi) in Caenorhabditis elegans systemically inhibits gene expression throughout the organism. To investigate how gene-specific silencing information is transmitted between cells, we constructed a strain that permits visualization of systemic RNAi. We used this strain to identify systemic RNA interference-deficient (sid) loci required to spread gene-silencing information between tissues but not to initiate or maintain an RNAi response. One of these loci, sid-1, encodes a conserved protein with predicted transmembrane domains. SID-1 is expressed in cells sensitive to RNAi, is localized to the cell periphery, and is required cell-autonomously for systemic RNAi.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Winston, William M -- Molodowitch, Christina -- Hunter, Craig P -- New York, N.Y. -- Science. 2002 Mar 29;295(5564):2456-9. Epub 2002 Feb 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11834782" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Caenorhabditis elegans/embryology/*genetics/metabolism ; Caenorhabditis elegans Proteins/chemistry/*genetics/*physiology ; Calmodulin-Binding Proteins/genetics ; Cytoplasm/metabolism ; Embryo, Nonmammalian/physiology ; *Gene Silencing ; Genes, Helminth ; Germ Cells/metabolism ; Green Fluorescent Proteins ; Intestines/metabolism ; Luminescent Proteins/genetics ; Membrane Proteins/chemistry/*genetics/*physiology ; Molecular Sequence Data ; Mosaicism ; Muscle Proteins/genetics ; Muscles/metabolism ; Mutation ; Protein Structure, Tertiary ; RNA, Double-Stranded/*genetics/metabolism ; RNA, Helminth/*genetics/metabolism ; Recombinant Fusion Proteins/metabolism ; Transgenes
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Crystal structure of the GpIbalpha-thrombin complex essential for platelet aggregation (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-12
    Description: Direct interaction between platelet receptor glycoprotein Ibalpha (GpIbalpha) and thrombin is required for platelet aggregation and activation at sites of vascular injury. Abnormal GpIbalpha-thrombin binding is associated with many pathological conditions,including occlusive arterial thrombosis and bleeding disorders. The crystal structure of the GpIbalpha-thrombin complex at 2.6 angstrom resolution reveals simultaneous interactions of GpIbalpha with exosite I of one thrombin molecule,and with exosite II of a second thrombin molecule. In the crystal lattice,the periodic arrangement of GpIbalpha-thrombin complexes mirrors a scaffold that could serve as a driving force for tight platelet adhesion. The details of these interactions reconcile GpIbalpha-thrombin binding modes that are presently controversial,highlighting two distinct interfaces that are potential targets for development of novel antithrombotic drugs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dumas, John J -- Kumar, Ravindra -- Seehra, Jasbir -- Somers, William S -- Mosyak, Lidia -- New York, N.Y. -- Science. 2003 Jul 11;301(5630):222-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical and Screening Sciences, Wyeth, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12855811" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Blood Platelets/chemistry/physiology ; Crystallization ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Platelet Adhesiveness ; *Platelet Aggregation ; Platelet Glycoprotein GPIb-IX Complex/*chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thrombin/*chemistry/*metabolism
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  • 6
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    Structural biology. Complex II is complex too (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hederstedt, Lars -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):671-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Organism Biology, Lund University, SE-22362 Lund, Sweden. lars.hederstedt@cob.lu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560540" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Anaerobiosis ; Binding Sites ; Crystallography, X-Ray ; Electron Transport ; Electron Transport Complex II ; Escherichia coli/*enzymology ; Flavin-Adenine Dinucleotide/metabolism ; Heme/chemistry/metabolism ; Models, Molecular ; Multienzyme Complexes/antagonists & inhibitors/*chemistry/*metabolism ; Oxidation-Reduction ; Oxidoreductases/antagonists & inhibitors/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Reactive Oxygen Species/metabolism ; Succinate Dehydrogenase/antagonists & inhibitors/*chemistry/*metabolism ; Succinic Acid/metabolism ; Ubiquinone/chemistry/metabolism
    Print ISSN: 0036-8075
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  • 7
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    In-depth view of structure, activity, and evolution of rice chromosome 10 (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-07
    Description: Rice is the world's most important food crop and a model for cereal research. At 430 megabases in size, its genome is the most compact of the cereals. We report the sequence of chromosome 10, the smallest of the 12 rice chromosomes (22.4 megabases), which contains 3471 genes. Chromosome 10 contains considerable heterochromatin with an enrichment of repetitive elements on 10S and an enrichment of expressed genes on 10L. Multiple insertions from organellar genomes were detected. Collinearity was apparent between rice chromosome 10 and sorghum and maize. Comparison between the draft and finished sequence demonstrates the importance of finished sequence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rice Chromosome 10 Sequencing Consortium -- R01-LM06845/LM/NLM NIH HHS/ -- New York, N.Y. -- Science. 2003 Jun 6;300(5625):1566-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12791992" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosomes, Plant/*genetics ; Computational Biology ; DNA Transposable Elements ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Edible Grain/genetics ; *Evolution, Molecular ; Expressed Sequence Tags ; Genes, Plant ; *Genome, Plant ; Heterochromatin ; Oryza/*genetics/physiology ; Plant Diseases/genetics ; Plant Proteins/chemistry/*genetics/physiology ; Protein Structure, Tertiary ; Proteome ; Repetitive Sequences, Nucleic Acid ; Retroelements ; *Sequence Analysis, DNA ; Zea mays/genetics
    Print ISSN: 0036-8075
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  • 8
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    Comprehensive identification of human bZIP interactions with coiled-coil arrays (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-06-14
    Description: In eukaryotes, the combinatorial association of sequence-specific DNA binding proteins is essential for transcription. We have used protein arrays to test 492 pairings of a nearly complete set of coiled-coil strands from human basic-region leucine zipper (bZIP) transcription factors. We find considerable partnering selectivity despite the bZIPs' homologous sequences. The interaction data are of high quality, as assessed by their reproducibility, reciprocity, and agreement with previous observations. Biophysical studies in solution support the relative binding strengths observed with the arrays. New associations provide insights into the circadian clock and the unfolded protein response.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Newman, John R S -- Keating, Amy E -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2097-101. Epub 2003 Jun 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12805554" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Basic-Leucine Zipper Transcription Factors ; Chromatography, High Pressure Liquid ; Circadian Rhythm ; Circular Dichroism ; Cyclic AMP Response Element-Binding Protein/chemistry/metabolism ; DNA-Binding Proteins/chemistry/isolation & purification/*metabolism ; Dimerization ; G-Box Binding Factors ; Humans ; *Leucine Zippers ; Peptides/chemistry/isolation & purification/metabolism ; *Protein Array Analysis ; Protein Binding ; Protein Folding ; Protein Structure, Tertiary ; Signal Transduction ; Temperature ; Thermodynamics ; Transcription Factors/*chemistry/isolation & purification/*metabolism
    Print ISSN: 0036-8075
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  • 9
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    Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-10
    Description: Multidrug efflux pumps cause serious problems in cancer chemotherapy and treatment of bacterial infections. Yet high-resolution structures of ligand transporter complexes have previously been unavailable. We obtained x-ray crystallographic structures of the trimeric AcrB pump from Escherichia coli with four structurally diverse ligands. The structures show that three molecules of ligands bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilizing the binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Edward W -- McDermott, Gerry -- Zgurskaya, Helen I -- Nikaido, Hiroshi -- Koshland, Daniel E Jr -- AI 09644/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2003 May 9;300(5621):976-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12738864" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Infective Agents/chemistry/metabolism ; Anti-Infective Agents, Local/chemistry/metabolism ; Binding Sites ; Carrier Proteins/*chemistry/isolation & purification/*metabolism ; Cell Membrane/chemistry ; Chemistry, Physical ; Ciprofloxacin/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Dequalinium/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/isolation & purification/*metabolism ; Ethidium/chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Membrane Proteins/*chemistry/isolation & purification/*metabolism ; Models, Molecular ; Multidrug Resistance-Associated Proteins ; Physicochemical Phenomena ; Protein Binding ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rhodamines/chemistry/metabolism ; Static Electricity
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  • 10
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    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-19
    Description: We collected and completely sequenced 28,469 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. Nipponbare. Through homology searches of publicly available sequence data, we assigned tentative protein functions to 21,596 clones (75.86%). Mapping of the cDNA clones to genomic DNA revealed that there are 19,000 to 20,500 transcription units in the rice genome. Protein informatics analysis against the InterPro database revealed the existence of proteins presented in rice but not in Arabidopsis. Sixty-four percent of our cDNAs are homologous to Arabidopsis proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rice Full-Length cDNA Consortium -- National Institute of Agrobiological Sciences Rice Full-Length cDNA Project Team -- Kikuchi, Shoshi -- Satoh, Kouji -- Nagata, Toshifumi -- Kawagashira, Nobuyuki -- Doi, Koji -- Kishimoto, Naoki -- Yazaki, Junshi -- Ishikawa, Masahiro -- Yamada, Hitomi -- Ooka, Hisako -- Hotta, Isamu -- Kojima, Keiichi -- Namiki, Takahiro -- Ohneda, Eisuke -- Yahagi, Wataru -- Suzuki, Kohji -- Li, Chao Jie -- Ohtsuki, Kenji -- Shishiki, Toru -- Foundation of Advancement of International Science Genome Sequencing & Analysis Group -- Otomo, Yasuhiro -- Murakami, Kazuo -- Iida, Yoshiharu -- Sugano, Sumio -- Fujimura, Tatsuto -- Suzuki, Yutaka -- Tsunoda, Yuki -- Kurosaki, Takashi -- Kodama, Takeko -- Masuda, Hiromi -- Kobayashi, Michie -- Xie, Quihong -- Lu, Min -- Narikawa, Ryuya -- Sugiyama, Akio -- Mizuno, Kouichi -- Yokomizo, Satoko -- Niikura, Junko -- Ikeda, Rieko -- Ishibiki, Junya -- Kawamata, Midori -- Yoshimura, Akemi -- Miura, Junichirou -- Kusumegi, Takahiro -- Oka, Mitsuru -- Ryu, Risa -- Ueda, Mariko -- Matsubara, Kenichi -- RIKEN -- Kawai, Jun -- Carninci, Piero -- Adachi, Jun -- Aizawa, Katsunori -- Arakawa, Takahiro -- Fukuda, Shiro -- Hara, Ayako -- Hashizume, Wataru -- Hayatsu, Norihito -- Imotani, Koichi -- Ishii, Yoshiyuki -- Itoh, Masayoshi -- Kagawa, Ikuko -- Kondo, Shinji -- Konno, Hideaki -- Miyazaki, Ai -- Osato, Naoki -- Ota, Yoshimi -- Saito, Rintaro -- Sasaki, Daisuke -- Sato, Kenjiro -- Shibata, Kazuhiro -- Shinagawa, Akira -- Shiraki, Toshiyuki -- Yoshino, Masayasu -- Hayashizaki, Yoshihide -- Yasunishi, Ayako -- New York, N.Y. -- Science. 2003 Jul 18;301(5631):376-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, National Institute of Agrobiological Sciences, 2-1-2 Kannon-dai, Tsukuba, Ibaraki 305-8602, Japan. skikuchi@nias.affrc.go.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12869764" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Amino Acid Sequence ; Cloning, Molecular ; Computational Biology ; DNA, Complementary ; Databases, Nucleic Acid ; Databases, Protein ; Genes, Plant ; *Genome, Plant ; Molecular Sequence Data ; Open Reading Frames ; Oryza/*genetics ; Plant Proteins/chemistry/genetics/physiology ; Protein Structure, Tertiary ; RNA, Antisense/genetics ; *Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Transcription Factors/chemistry/genetics ; Transcription, Genetic
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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