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Semantic ScholarNucleic Acids Research, Volume 27
Volume 27, Number 1, January 1999
- Claude Discala, Marion Ninnin, Frédéric Achard, Emmanuel Barillot, Guy Vaysseix:
DBcat: a catalog of biological databases. 10-11 - Dennis A. Benson, Mark S. Boguski, David J. Lipman, James Ostell, B. F. Francis Ouellette, Barbara A. Rapp, David L. Wheeler:
GenBank. 12-17 - Guenter Stoesser, Mary Ann Tuli, Rodrigo Lopez, Peter Sterk:
The EMBL Nucleotide Sequence Database. 18-24 - Hideaki Sugawara, Satoru Miyazaki, Takashi Gojobori, Yoshio Tateno:
DNA Data Bank of Japan dealing with large-scale data submission. 25-28 - Hiroyuki Ogata, Susumu Goto, Kazushige Sato, Wataru Fujibuchi, Hidemasa Bono, Minoru Kanehisa:
KEGG: Kyoto Encyclopedia of Genes and Genomes. 29-34 - M. P. Skupski, M. Booker, Andrew D. Farmer, M. Harpold, Wen Huang, Jeff T. Inman, Donald Kiphart, C. Kodira, S. Root, Faye D. Schilkey, Jolene Schwertfeger, Adam C. Siepel, D. Stamper, Nina Thayer, R. Thompson, Jennifer R. Wortman, J. J. Zhuang, Carol Harger:
The Genome Sequence DataBase: towards an integrated functional genomics resource. 35-38 - Winona C. Barker, John S. Garavelli, Peter B. McGarvey, Christopher R. Marzec, Bruce C. Orcutt, Geetha Y. Srinivasarao, Lai-Su L. Yeh, Robert S. Ledley, Hans-Werner Mewes, Friedhelm Pfeiffer, Akira Tsugita, Cathy H. Wu:
The PIR-International Protein Sequence Database. 39-43 - Hans-Werner Mewes, Klaus Heumann, Andreas Kaps, Klaus F. X. Mayer, Friedhelm Pfeiffer, S. Stocker, Dmitrij Frishman:
MIPS: a database for genomes and protein sequences. 44-48 - Amos Bairoch, Rolf Apweiler:
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. 49-54 - Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-Toole, Markus Krummenacker:
Eco Cyc: encyclopedia of Escherichia coli genes and metabolism. 55-58 - Heladia Salgado, Alberto Santos-Zavaleta, Ulises Garza-Ramos, Jacques van Helden, Edgar Díaz-Peredo, Julio Collado-Vides:
RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. 59-60 - M. Choudhary, C. Mackenzie, N. J. Mouncey, S. Kaplan:
RsGDB, the Rhodobacter sphaeroides Genome Database. 61-62 - Yasukazu Nakamura, Takakazu Kaneko, Nobuyuki Miyajima, Satoshi Tabata:
Extension of CyanoBase. CyanoMutants: repository of mutant information on Synechocystis sp. strain PCC6803. 66-68 - Peter E. Hodges, Andrew H. Z. McKee, Brian P. Davis, William E. Payne, James I. Garrels:
The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data. 69-73 - Stephen A. Chervitz, Erich T. Hester, Catherine A. Ball, Kara Dolinski, Selina S. Dwight, Midori A. Harris, Gail Juvik, Alice Malekian, Shannon Roberts, TaiYun Roe, Charles R. Scafe, Mark Schroeder, Gavin Sherlock, Shuai Weng, Yan Zhu, J. Michael Cherry, David Botstein:
Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. 74-78 - Seung Yon Rhee, Shuai Weng, Deverie K. Bongard-Pierce, Margarita Garcia-Hernandez, Alice Malekian, David J. Flanders, J. Michael Cherry:
Unified display of Arabidopsis thaliana physical maps from AtDB, the A.thaliana database. 79-84 - Catherine Sanchez, Corinne Lachaize, Florence Janody, Bernard Bellon, Laurence Röder, Jérôme Euzenat, François Rechenmann, Bernard Jacq:
Grasping at molecular interactions and genetic networks in Drosophila melanogaster using FlyNets, an Internet database. 89-94 - Judith A. Blake, Joel E. Richardson, Muriel T. Davisson, Janan T. Eppig:
The Mouse Genome Database (MGD): genetic and genomic information about the laboratory mouse. The Mouse Genome Database Group. 95-98 - Carol J. Bult, Debra M. Krupke, Janan T. Eppig:
Electronic access to mouse tumor data: the Mouse Tumor Biology Database (MTB) project. 99-105 - Martin Ringwald, Mary E. Mangan, Janan T. Eppig, James A. Kadin, Joel E. Richardson:
GXD: a gene expression database for the laboratory mouse. The Gene Expression Database Group. 106-112 - Frédéric Achard, Guy Vaysseix, Philippe Dessen, Emmanuel Barillot:
Virgil database for rich links (1999 update). 113-114 - Emmanuel Barillot, Stuart Pook, Frédéric Guyon, Christophe Cussat-Blanc, Eric Viara, Guy Vaysseix:
The HuGeMap Database: interconnection and visualization of human genome maps. 119-122 - Ulf Leser, Hugues Roest Crollius, Hans Lehrach, Ralf Sudbrak:
IXDB, an X chromosome integrated database (update). 123-127 - Marcella Attimonelli, N. Altamura, R. Benne, C. Boyen, A. Brennicke, A. Carone, J. M. Cooper, Domenica D'Elia, A. de Montalvo, B. de Pinto, Mariateresa De Robertis, P. Golik, J. M. Grienenberger, V. Knoop, Cecilia Lanave, Jaga Lazowska, A. Lemagnen, B. S. Malladi, F. Memeo, M. Monnerot, Sandrine Pilbout, A. H. V. Schapira, P. Sloof, Piotr P. Slonimski, K. Stevens, Cecilia Saccone:
MitBASE: a comprehensive and integrated mitochondrial DNA database. 128-133 - Cecilia Lanave, Marcella Attimonelli, Mariateresa De Robertis, Flavio Licciulli, Sabino Liuni, Elisabetta Sbisà, Cecilia Saccone:
Update of AMmtDB: a database of multi-aligned metazoa mitochondrial DNA sequences. 134-137 - Florian Burckhardt, Arndt von Haeseler, Sonja Meyer:
HvrBase: compilation of mtDNA control region sequences from primates. 138-142 - Marcella Attimonelli, J. M. Cooper, Domenica D'Elia, A. de Montalvo, Mariateresa De Robertis, Heikki Lehväslaiho, S. B. Malladi, F. Memeo, K. Stevens, A. H. V. Schapira, Cecilia Saccone:
Update of the Human MitBASE database. 143-146 - B. de Pinto, S. B. Malladi, N. Altamura:
MitBASE pilot: a database on nuclear genes involved in mitochondrial biogenesis and its regulation in Saccharomyces cerevisiae. 147-149 - A. Carone, S. B. Malladi, Marcella Attimonelli, Cecilia Saccone:
Vertebrate MitBASE: a specialised database on vertebrate mitochondrial DNA sequences. 150-152 - Curt Scharfe, Paolo Zaccaria, K. Hörtnagel, M. Jaksch, Thomas Klopstock, R. Lill, Holger Prokisch, K. D. Gerbitz, Hans-Werner Mewes, Thomas Meitinger:
MITOP: database for mitochondria-related proteins, genes and diseases. 153-155 - Luigi R. Ceci, Mariateresa Volpicella, Sabino Liuni, Vito Volpetti, Flavio Licciulli, Raffaele Gallerani:
PLMItRNA, a database for higher plant mitochondrial tRNAs and tRNA genes. 156-157 - Maciej Szymanski, Miroslawa Z. Barciszewska, Jan Barciszewski, Volker A. Erdmann:
5S Ribosomal RNA Data Bank. 158-160 - Dmitry A. Samarsky, Maurille J. Fournier:
A comprehensive database for the small nucleolar RNAs from Saccharomyces cerevisiae. 161-164 - Bonnie L. Maidak, James R. Cole, Charles T. Parker Jr., George M. Garrity, Niels Larsen, Bing Li, Timothy G. Lilburn, Michael J. McCaughey, Gary J. Olsen, Ross A. Overbeek, Sakti Pramanik, Thomas M. Schmidt, James M. Tiedje, Carl R. Woese:
A new version of the RDP (Ribosomal Database Project). 171-173 - Peter De Rijk, Elmar Robbrecht, Sybren de Hoog, An Caers, Yves Van de Peer, Rupert De Wachter:
Database on the structure of large subunit ribosomal RNA. 174-178 - Yves Van de Peer, Elmar Robbrecht, Sybren de Hoog, An Caers, Peter De Rijk, Rupert De Wachter:
Database on the structure of small subunit ribosomal RNA. 179-183 - Pavel V. Baranov, Andrew V. Kubarenko, Olga L. Gurvich, Tatyana A. Shamolina, Richard Brimacombe:
The Database of Ribosomal Cross-links: an update. 184-185 - Daniel A. Lafontaine, Patrick Deschênes, Frédéric Bussière, Véronique Poisson, Jean-Pierre Perreault:
The viroid and viroid-like RNA database. 186-187 - Graziano Pesole, Sabino Liuni, Giorgio Grillo, Matilde Ippedico, Alessandra Larizza, Wojciech Makalowski, Cecilia Saccone:
UTRdb: a specialized database of 5' and 3' untranslated regions of eukaryotic mRNAs. 188-191 - Volker A. Erdmann, Maciej Szymanski, Abraham Hochberg, Nathan de Groot, Jan Barciszewski:
Collection of mRNA-like non-coding RNAs. 192-195 - Jef Rozenski, Pamela F. Crain, James A. McCloskey:
The RNA Modification Database: 1999 update. 196-197 - Christian J. Stoeckert Jr., Fidel Salas, Brian P. Brunk, G. Christian Overton:
EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis. 200-203 - Victoria Hawkins, David Doll, Roger Eugene Bumgarner, Todd Smith, Chris Abajian, Leroy E. Hood, Peter S. Nelson:
PEDB: the Prostate Expression Database. 204-208 - Marie-Paule Lefranc, Véronique Giudicelli, Chantal Ginestoux, Julia G. Bodmer, Werner Müller, Ronald Bontrop, Marc Lemaitre, Ansar Malik, Valérie Barbié, Denys Chaume:
IMGT, the international ImMunoGeneTics database. 209-212 - Kay Hofmann, Philipp Bucher, Laurent Falquet, Amos Bairoch:
The PROSITE database, its status in 1999. 215-219 - Terri K. Attwood, Darren R. Flower, A. P. Lewis, J. E. Mabey, S. R. Morgan, Philip Scordis, J. N. Selley, W. Wright:
PRINTS prepares for the new millennium. 220-225 - Jorja G. Henikoff, Steven Henikoff, Shmuel Pietrokovski:
New features of the Blocks Database servers. 226-228 - Chris P. Ponting, Jörg Schultz, Frank Milpetz, Peer Bork:
SMART: identification and annotation of domains from signalling and extracellular protein sequences. 229-232 - Kirill Degtyarenko, A. C. North, John B. C. Findlay:
PROMISE: a database of bioinorganic motifs. 233-236 - Andres Kreegipuu, Nikolaj Blom, Søren Brunak:
PhosphoBase, a database of phosphorylation sites: release 2.0. 237-239 - Aron Marchler-Bauer, Kenneth J. Addess, Colombe Chappey, Lewis Y. Geer, Thomas Madej, Yo Matsuo, Yanli Wang, Stephen H. Bryant:
MMDB: Entrez's 3D structure database. 240-243 - Victor V. Solovyev, Asaf A. Salamov:
INFOGENE: a database of known gene structures and predicted genes and proteins in sequences of genome sequencing projects. 248-250 - Steven E. Brenner, Derren Barken, Michael Levitt:
The PRESAGE database for structural genomics. 251-253 - Tim J. P. Hubbard, Bart Ailey, Steven E. Brenner, Alexey G. Murzin, Cyrus Chothia:
SCOP: a Structural Classification of Proteins database. 254-256 - János Murvai, Kristian Vlahovicek, Endre Barta, Csaba Szepesvári, Cristina Acatrinei, Sándor Pongor:
The SBASE protein domain library, release 6.0: a collection of annotated protein sequence segments. 257-259 - Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Robert D. Finn, Erik L. L. Sonnhammer:
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. 260-262 - Florence Corpet, Jérôme Gouzy, Daniel Kahn:
Recent improvements of the ProDom database of protein domain families. 263-267 - Christine A. Orengo, Frances M. G. Pearl, James E. Bray, Annabel E. Todd, A. C. Martin, Loredana Lo Conte, Janet M. Thornton:
The CATH Database provides insights into protein structure/function relationships. 275-279 - José María Carazo, Ernst H. K. Stelzer, A. Engel, I. Fita, C. Henn, J. Machtynger, P. McNeil, David M. Shotton, Monica Chagoyen, Pedro A. de Alarcón, R. Fritsch, J. B. Heymann, Susana G. Kalko, J. J. Pittet, Patricia Rodriguez-Tomé, Thomas Boudier:
Organising multi-dimensional biological image information: the BioImage Database. 280-283 - Geetha Y. Srinivasarao, Lai-Su L. Yeh, Christopher R. Marzec, Bruce C. Orcutt, Winona C. Barker, Friedhelm Pfeiffer:
Database of protein sequence alignments: PIR-ALN. 284-285 - M. Michael Gromiha, Jianghong An, Hidetoshi Kono, Motohisa Oobatake, Hatsuho Uedaira, Akinori Sarai:
ProTherm: Thermodynamic Database for Proteins and Mutants. 286-288 - Christine Hoogland, Jean-Charles Sanchez, Luisa Tonella, Amos Bairoch, Denis F. Hochstrasser, Ron D. Appel:
The SWISS-2DPAGE database: what has changed during the last year. 289-291 - Yasukazu Nakamura, Takashi Gojobori, Toshimichi Ikemura:
Codon usage tabulated from the international DNA sequence databases; its status 1999. 292 - Mark E. Dalphin, Peter A. Stockwell, Warren Tate, Chris M. Brown:
TransTerm, the translational signal database, extended to include full coding sequences and untranslated regions. 293-294 - Stephane Rombauts, Patrice Déhais, Marc Van Montagu, Pierre Rouzé:
PlantCARE, a plant cis-acting regulatory element database. 295-296 - Kenichi Higo, Yoshihiro Ugawa, Masao Iwamoto, Tomoko Korenaga:
Plant cis-acting regulatory DNA elements (PLACE) database: 1999. 297-300 - Mikhail S. Gelfand, Inna Dubchak, I. Dralyuk, Manfred Zorn:
ASDB: database of alternatively spliced genes. 301-302 - Nikolay A. Kolchanov, Elena A. Ananko, Olga A. Podkolodnaya, Elena V. Ignatieva, Irina L. Stepanenko, Olga V. Kel-Margoulis, Alexander E. Kel, Tatyana I. Merkulova, T. N. Goryachkovskaya, T. V. Busygina, F. A. Kolpakov, Nikolay L. Podkolodny, Andrey N. Naumochkin, Aida G. Romashchenko:
Transcription Regulatory Regions Database (TRRD): its status in 1999. 303-306 - Rouaïda Périer, Thomas Junier, Claude Bonnard, Philipp Bucher:
The Eukaryotic Promoter Database (EPD): recent developments. 307-309 - T. Heinemeyer, Xin Chen, Holger Karas, Alexander E. Kel, Olga V. Kel-Margoulis, Ines Liebich, T. Meinhardt, Ingmar Reuter, Frank Schacherer, Edgar Wingender:
Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. 318-322 - Izabela Makalowska, Erik S. Ferlanti, Andreas D. Baxevanis, David Landsman:
Histone Sequence Database: sequences, structures, post-translational modifications and genetic loci. 323-324 - Sharmila Banerjee-Basu, Erik S. Ferlanti, Joseph F. Ryan, Andreas D. Baxevanis:
The Homeodomain Resource: sequences, structures and genomic information. 336-337 - Mikita Suyama, Takahiro Nagase, Osamu Ohara:
HUGE: a database for human large proteins identified by Kazusa cDNA sequencing project. 338-339 - Emmanouil Skoufos, Matthew D. Healy, Michael S. Singer, Prakash M. Nadkarni, Perry L. Miller, Gordon M. Shepherd:
Olfactory Receptor Database: a database of the largest eukaryotic gene family. 343-345 - Robert W. Shafer, Derek Stevenson, Bryan Chan:
Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database. 348-352 - Frank Dorkeld, Alain Bernheim, Philippe Dessen, Jean-Loup Huret:
A database on cytogenetics in haematology and oncology. 353-354 - Shinsei Minoshima, Susumu Mitsuyama, Saho Ohno, Takashi Kawamura, Nobuyoshi Shimizu:
Keio Mutation Database for eye disease genes (KMeyeDB). 358-361 - Kaj A. E. Stenberg, Pentti Riikonen, Mauno Vihinen:
KinMutBase, a database of human disease-causing protein kinase mutations. 362-364 - Flavio Licciulli, Domenico Catalano, Domenica D'Elia, V. Lorusso, Marcella Attimonelli:
KEYnet: a keywords database for biosequences functional organization. 365-367 - Ramneek Gupta, Hanne Birch, Kristoffer Rapacki, Søren Brunak, Jan E. Hansen:
O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins. 370-372 - Lynda B. M. Ellis, C. Douglas Hershberger, Lawrence P. Wackett:
The University of Minnesota Biocatalysis/Biodegradation Database: specialized metabolism for functional genomics. 373-376 - Susumu Goto, Takaaki Nishioka, Minoru Kanehisa:
LIGAND database for enzymes, compounds and reactions. 377-379
Volume 27, Number 13, July 1999
- Tom J. Parry, Cynthia Cushman, Anna M. Gallegos, Arun B. Agrawal, Michele Richardson, Lori E. Andrews, Lara Maloney, Victor R. Mokler, Francine E. Wincott, Pamela A. Pavco:
Bioactivity of anti-angiogenic ribozymes targeting Flt-1 and KDR mRNA. 2569-2577 - Alberto di Silvio, Carol Imbriano, Roberto Mantovani:
Dissection of the NF-Y transcriptional activation potential. 2578-2584 - Peter G. Zaphiropoulos:
RNA molecules containing exons originating from different members of the cytochrome P450 2C gene subfamily (CYP2C) in human epidermis and liver. 2585-2590 - Hideto Yonekura, Hideyuki Migita, Shigeru Sakurai, Hua Wang, Shin-ichi Harada, Md. Joynal Abedin, Sho-ichi Yamagishi, Hiroshi Yamamoto:
Antisense display - a method for functional gene screening: evaluation in a cell-free system and isolation of angiogenesis-related genes. 2591-2600 - Tatyana Shamma, Ian S. Haworth:
Spermine inhibition of the 2, 5-diaziridinyl-1, 4-benzoquinone (DZQ) crosslinking reaction with DNA duplexes containing poly(purine). poly(pyrimidine) tracts. 2601-2609 - Richard T. Blaszak, Vladimir Potaman, Richard R. Sinden, John J. Bissler:
DNA structural transitions within the PKD1 gene. 2610-2617 - Martin Lützelberger, Thomas Groß, Norbert F. Käufer:
Srp2, an SR protein family member of fission yeast: in vivo characterization of its modular domains. 2618-2626 - Thangavel Alphonse Thanaraj:
A clean data set of EST-confirmed splice sites from Homo sapiens and standards for clean-up procedures. 2627-2637 - Pavel Janscak, Ursula Sandmeier, Thomas A. Bickle:
Single amino acid substitutions in the HsdR subunit of the type IB restriction enzyme EcoAI uncouple the DNA translocation and DNA cleavage activities of the enzyme. 2638-2643 - D. Steponaviciene, Z. Maneliene, M. Petrusyte, A. Janulaitis:
BseSI, a restriction endonuclease from Bacillus stearothermophilus Jo 10-553, which recognizes the novel hexanucleotide sequence 5'- G(G/T)GC(A/C)C-3'. 2644-2645 - Olga I. Ornatsky, David M. Cox, Padma Tangirala, John J. Andreucci, Zoë A. Quinn, Jeffrey L. Wrana, Ron Prywes, Yie-Teh Yu, John C. McDermott:
Post-translational control of the MEF2A transcriptional regulatory protein. 2646-2654 - Stuart Wilson, Nicholas Warr, Deborah L. Taylor, Felicity Z. Watts:
The role of Schizosaccharomyces pombe Rad32, the Mre11 homologue, and other DNA damage response proteins in non-homologous end joining and telomere length maintenance. 2655-2661 - T. Fujino, N. Navaratnam, A. Jarmuz, Arndt von Haeseler, J. Scott:
C-->U editing of apolipoprotein B mRNA in marsupials: identification and characterisation of APOBEC-1 from the American opossum Monodelphus domestica. 2662-2671 - Colin B. Reese, Quanlai Song:
A new approach to the synthesis of branched and branched cyclic oligoribonucleotides. 2672-2681 - Julie Dawn Thompson, Frédéric Plewniak, Olivier Poch:
A comprehensive comparison of multiple sequence alignment programs. 2682-2690 - Juan Aymami, Christine M. Nunn, Stephen Neidle:
DNA minor groove recognition of a non-self-complementary AT-rich sequence by a tris-benzimidazole ligand. 2691-2698 - A. Debin, Cyril Laboulais, Mohammed Ouali, C. Malvy, Marc Le Bret, F. Svinarchuk:
Stability of G, A triple helices. 2699-2707 - Lela Johnson, Paul D. Gershon:
RNA binding characteristics and overall topology of the vaccinia poly(A) polymerase-processivity factor-primer complex. 2708-2721 - Sébastien Gingras, Jacques Simard, Bernd Groner, Edith Pfitzner:
p300/CBP is required for transcriptional induction by interleukin-4 and interacts with Stat6. 2722-2729 - L. Meunier, R. Mayer, M. Monsigny, A. C. Roche:
The nuclear export signal-dependent localization of oligonucleopeptides enhances the inhibition of the protein expression from a gene transcribed in cytosol. 2730-2736 - Claudio D. Giannini, W. Kurt Roth, Albrecht Piiper, Stefan Zeuzem:
Enzymatic and antisense effects of a specific anti-Ki-ras ribozyme in vitro and in cell culture. 2737-2744 - Sonia Broccoli, Jean-François Marquis, Barbara Papadopoulou, Martin Olivier, Marc Drolet:
Characterization of a Leishmania donovani gene encoding a protein that closely resembles a type IB topoisomerase. 2745-2752 - Jae-Young Oh, Jinmi Kim:
ATP hydrolysis activity of the DEAD box protein Rok1p is required for in vivo ROK1 function. 2753-2759 - Neeman Mohibullah, Amy Donner, Joseph A. Ippolito, Trevor Williams:
SELEX and missing phosphate contact analyses reveal flexibility within the AP-2[alpha] protein: DNA binding complex. 2760-2769 - Masayuki Nashimoto, Duane R. Wesemann, Susanna Geary, Masato Tamura, Roger L. Kaspar:
Long 5' leaders inhibit removal of a 3' trailer from a precursor tRNA by mammalian tRNA 3' processing endoribonuclease. 2770-2776 - Saija Haapa, Suvi Taira, Eini Heikkinen, Harri Savilahti:
An efficient and accurate integration of mini-Mu transposons in vitro: a general methodology for functional genetic analysis and molecular biology applications. 2777-2784 - Marta Palmieri, Maria Paola Sasso, Rossana Monese, Marcello Merola, Laura Faggioli, Michael Tovey, Adriana Furia:
Interaction of the nuclear protein CBF1 with the kappaB site of the IL- 6 gene promoter. 2785-2791