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Nucleic Acids Research, Volume 28
Volume 28, Number 1, January 2000
- Andreas D. Baxevanis:
The Molecular Biology Database Collection: an online compilation of relevant database resources. 1-7 - Claude Discala, Xavier Benigni, Emmanuel Barillot, Guy Vaysseix:
DBcat: a catalog of 500 biological databases. 8-9 - David L. Wheeler, Colombe Chappey, Alex E. Lash, Detlef D. Leipe, Thomas L. Madden, Gregory D. Schuler, Tatiana A. Tatusova, Barbara A. Rapp:
Database resources of the National Center for Biotechnology Information. 10-14 - Dennis A. Benson, Ilene Karsch-Mizrachi
, David J. Lipman, James Ostell, Barbara A. Rapp, David L. Wheeler:
GenBank. 15-18 - Wendy Baker, Alexandra van den Broek, Evelyn Camon, Pascal Hingamp
The EMBL Nucleotide Sequence Database. 19-23 - Yoshio Tateno, Satoru Miyazaki, Motonori Ota, Hideaki Sugawara, Takashi Gojobori:
DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams. 24-26 - Minoru Kanehisa, Susumu Goto:
KEGG: Kyoto Encyclopedia of Genes and Genomes. 27-30 - Carol Harger, Guanghong Chen, Andrew D. Farmer, Wen Huang, Jeff T. Inman, Donald Kiphart, Faye D. Schilkey, M. P. Skupski, Jennifer W. Weller:
The Genome Sequence DataBase. 31-32 - Roman L. Tatusov, Michael Y. Galperin
The COG database: a tool for genome-scale analysis of protein functions and evolution. 33-36 - Hans-Werner Mewes, Dmitrij Frishman, Christian Gruber, Birgitta Geier, Dirk Haase, Andreas Kaps, Kai Lemcke, Gertrud Mannhaupt, Friedhelm Pfeiffer
MIPS: a database for genomes and protein sequences. 37-40 - Winona C. Barker, John S. Garavelli
The Protein Information Resource (PIR). 41-44 - Amos Bairoch
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. 45-48 - Golan Yona, Nathan Linial, Michal Linial
ProtoMap: automatic classification of protein sequences and hierarchy of protein families. 49-55 - Peter D. Karp
The EcoCyc and MetaCyc databases. 56-59 - Kenneth E. Rudd:
EcoGene: a genome sequence database for Escherichia coli K-12. 60-64 - Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Dulce Millán-Zárate, Frederick R. Blattner, Julio Collado-Vides:
RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12. 65-67 - Guy Perrière, Philippe Bessières, Bernard Labedan:
EMGLib: the Enhanced Microbial Genomes Library (update 2000). 68-71 - Yasukazu Nakamura, Takakazu Kaneko, Satoshi Tabata:
CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000. 72 - Maria C. Costanzo, Jennifer D. Hogan, Michael E. Cusick, Brian P. Davis, Ann M. Fancher, Peter E. Hodges, Pinar Kondu
The Yeast Proteome Database (YPD) and Caenorhabditis elegans Proteome Database (WormPD): comprehensive resources for the organization and comparison of model organism protein information. 73-76 - Catherine A. Ball, Kara Dolinski
Integrating functional genomic information into the Saccharomyces Genome Database. 77-80 - Anuj Kumar, Kei-Hoi Cheung, Petra Ross-MacDonald, Paulo S. R. Coelho, Perry L. Miller, Michael Snyder:
TRIPLES: a database of gene function in Saccharomyces cerevisiae. 81-84 - Pascal J. Lopez
YIDB: the Yeast Intron DataBase. 85-86 - Mark E. Waugh, Peter T. Hraber, Jennifer W. Weller, Yihe Wu, Guanghong Chen, Jeff T. Inman, Donald Kiphart, Bruno W. S. Sobral
The Phytophthora Genome Initiative Database: informatics and analysis for distributed pathogenomic research. 87-90 - W. James Kent, Alan M. Zahler
The Intronerator: exploring introns and alternative splicing in Caenorhabditis elegans. 91-93 - Xiaowu Gai
Gene discovery using the maize genome database ZmDB. 94-96 - Katsumi Sakata, Baltazar A. Antonio, Yoshiyuki Mukai, Hideki Nagasaki, Yasumichi Sakai, Kazuyoshi Makino, Takuji Sasaki:
INE: a rice genome database with an integrated map view. 97-101 - Curtis J. Palm, Nancy A. Federspiel, Ronald W. Davis:
DAtA: Database of Arabidopsis thaliana Annotation. 102-103 - Jo L. Dicks, Mary Anderson, Linda Cardle, Sam Cartinhour, Matthew Couchman, Guy Davenport
UK CropNet: a collection of databases and bioinformatics resources for crop plant genomics. 104-107 - Judith A. Blake
The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse. 108-111 - Carol J. Bult, Debra M. Krupke
Mouse Tumor Biology Database (MTB): enhancements and current status. 112-114 - Martin Ringwald, Janan T. Eppig, James A. Kadin, Joel E. Richardson:
GXD: a Gene Expression Database for the laboratory mouse: current status and recent enhancements. 115-119 - R. Ploger, J. Zhang, Douglas E. Bassett
XREFdb: cross-referencing the genetics and genes of mammals and model organisms. 120-122 - Ross A. Overbeek, Niels Larsen, Gordon D. Pusch, Mark D'Souza, Evgeni Selkov Jr., Nikos Kyrpides
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. 123-125 - Donna R. Maglott, Kenneth S. Katz, Hugues Sicotte, Kim D. Pruitt
NCBI's LocusLink and RefSeq. 126-128 - Shaying Zhao:
Human BAC Ends. 129-132 - Takeshi Kawashima, Shuichi Kawashima
MAGEST: MAboya Gene Expression patterns and Sequence Tags. 133-135 - Teruyoshi Hishiki, Shoko Kawamoto, Shinichi Morishita
BodyMap: a human and mouse gene expression database. 136-138 - Nicolas Pollet
Axeldb: a Xenopus laevis database focusing on gene expression. 139-140 - John Quackenbush
The TIGR Gene Indices: reconstruction and representation of expressed gene sequences. 141-145 - Patricia Rodriguez-Tomé, Philip Lijnzaad:
RHdb: the Radiation Hybrid database. 146-147 - Marcella Attimonelli, N. Altamura, R. Benne, A. Brennicke, J. M. Cooper, Domenica D'Elia
MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status. 148-152 - Cecilia Lanave, Sabino Liuni, Flavio Licciulli
Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences. 153-154 - Curt Scharfe, Paolo Zaccaria, K. Hörtnagel, M. Jaksch, Thomas Klopstock, M. Dembowski, R. Lill
MITOP, the mitochondrial proteome database: 2000 update. 155-158 - Vito Volpetti, Raffaele Gallerani, Caterina De Benedetto, Sabino Liuni, Flavio Licciulli
PLMItRNA, a database for tRNAs and tRNA genes in plant mitochondria: enlargement and updating. 159-162 - Graziano Pesole, Carmela Gissi, Domenico Catalano
MitoNuc and MitoAln: two related databases of nuclear genes coding for mitochondrial proteins. 163-165 - Maciej Szymanski
5S ribosomal RNA database Y2K. 166-167 - Kelly P. Williams:
The tmRNA Website. 168-1 - Christian Zwieb, Jacek Wower:
tmRDB (tmRNA database). 169-170 - Christian Zwieb, Tore Samuelsson:
SRPDB (Signal Recognition Particle Database). 171-172 - Bonnie L. Maidak, James R. Cole, Timothy G. Lilburn, Charles T. Parker Jr.
The RDP (Ribosomal Database Project) continues. 173-174 - Yves Van de Peer
The European Small Subunit Ribosomal RNA database. 175-176 - Peter De Rijk
The European Large Subunit Ribosomal RNA database. 177-178 - Martin Pelchat, Patrick Deschênes, Jean-Pierre Perreault:
The database of the smallest known auto-replicable RNA species: viroids and viroid-like RNAs. 179-180 - Nicholas J. Schisler, Jeffrey D. Palmer:
The IDB and IEDB: intron sequence and evolution databases. 181-184 - Serge Saxonov, Iraj Daizadeh, Alexei Fedorov, Walter Gilbert:
EID: the Exon?Intron Database?an exhaustive database of protein-coding intron-containing genes. 185-190 - Meena K. Sakharkar, Manyuan Long, Tin Wee Tan, Sandro J. de Souza:
ExInt: an Exon/Intron database. 191-192 - Graziano Pesole, Sabino Liuni, Giorgio Grillo, Flavio Licciulli
UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. 193-196 - Volker A. Erdmann, Maciej Szymanski
Non-coding, mRNA-like RNAs database Y2K. 197-200 - F. H. D. van Batenburg, Alexander P. Gultyaev, C. W. A. Pleij, J. Ng, J. Oliehoek:
PseudoBase: a database with RNA pseudoknots. 201-204 - Julia V. Ponomarenko
SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation. 205-208 - John S. Garavelli
The RESID Database of protein structure modifications: 2000 update. 209-211 - Peter S. Nelson, Nigel Clegg, Burak Eroglu, Victoria Hawkins, Roger Eugene Bumgarner, Todd Smith, Leroy E. Hood:
The Prostate Expression Database (PEDB): status and enhancements in 2000. 212-213 - George Johnson, Tai Te Wu:
Kabat Database and its applications: 30 years after the first variability plot. 214-218 - Manuel Ruiz, Véronique Giudicelli
IMGT, the international ImMunoGeneTics database. 219-221 - Christian Schönbach
FIMM, a database of functional molecular immunology. 222-224 - Terri K. Attwood
PRINTS-S: the database formerly known as PRINTS. 225-227 - Jorja G. Henikoff, Elizabeth A. Greene, Shmuel Pietrokovski
Increased coverage of protein families with the Blocks Database servers. 228-230 - Jörg Schultz, Richard R. Copley, Tobias Doerks, Chris P. Ponting
SMART: a web-based tool for the study of genetically mobile domains. 231-234 - Helen M. Berman
The Protein Data Bank. 235-242 - Yanli Wang, Kenneth J. Addess, Lewis Y. Geer, Thomas Madej, Aron Marchler-Bauer, Diane Zimmerman, Stephen H. Bryant:
MMDB: 3D structure data in Entrez. 243-245 - Jan Reichert, Andreas Jabs, Peter Slickers, Jürgen Sühnel:
The IMB Jena Image Library of Biological Macromolecules. 246-249 - Roberto Sánchez, Ursula Pieper
MODBASE, a database of annotated comparative protein structure models. 250-253 - Steven E. Brenner, Patrice Koehl
The ASTRAL compendium for protein structure and sequence analysis. 254-256 - Loredana Lo Conte, Bart Ailey, Tim J. P. Hubbard, Steven E. Brenner, Alexey G. Murzin, Cyrus Chothia:
SCOP: a Structural Classification of Proteins database. 257-259 - János Murvai, Kristian Vlahovicek
The SBASE protein domain library, release 7.0: a collection of annotated protein sequence segments. 260-262 - Alex Bateman, Ewan Birney
The Pfam Protein Families Database. 263-266 - Florence Corpet, Florence Servant
ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. 267-269 - Antje Krause, Jens Stoye
The SYSTERS protein sequence cluster set. 270-272 - Hongzhan Huang, Chunlin Xiao, Cathy H. Wu
ProClass protein family database. 273-276 - Frances M. G. Pearl
Assigning genomic sequences to CATH. 277-282 - M. Michael Gromiha, Jianghong An, Hidetoshi Kono, Motohisa Oobatake, Hatsuho Uedaira, Ponraj Prabakaran
ProTherm, version 2.0: thermodynamic database for proteins and mutants. 283-285 - Christine Hoogland
The 1999 SWISS-2DPAGE database update. 286-288 - Ioannis Xenarios, Danny W. Rice
DIP: the Database of Interacting Proteins. 289-291 - Yasukazu Nakamura, Takashi Gojobori, Toshimichi Ikemura:
Codon usage tabulated from international DNA sequence databases: status for the year 2000. 292 - Grant H. Jacobs, Peter A. Stockwell, Mark J. Schreiber, Warren Tate, Chris M. Brown:
Transterm: a database of messenger RNA components and signals. 293-295 - I. Dralyuk, Michael Brudno, Mikhail S. Gelfand, Manfred Zorn, Inna Dubchak:
ASDB: database of alternatively spliced genes. 296-297 - Nikolay A. Kolchanov, Olga A. Podkolodnaya, Elena A. Ananko, Elena V. Ignatieva, Irina L. Stepanenko, Olga V. Kel-Margoulis, Alexander E. Kel, Tatyana I. Merkulova, T. N. Goryachkovskaya, T. V. Busygina, Fedor A. Kolpakov
Transcription Regulatory Regions Database (TRRD): its status in 2000. 298-301 - Rouaïda Cavin Périer, Viviane Praz, Thomas Junier, Claude Bonnard, Philipp Bucher:
The Eukaryotic Promoter Database (EPD). 302-303 - Amos Bairoch
The ENZYME database in 2000. 304-305 - Richard J. Roberts
REBASE ? restriction enzymes and methylases. 306-307 - David Ghosh:
Object-oriented Transcription Factors Database (ooTFD). 308-310 - Olga V. Kel-Margoulis, Aida G. Romashchenko, Nikolay A. Kolchanov, Edgar Wingender
COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation. 311-315 - Edgar Wingender
TRANSFAC: an integrated system for gene expression regulation. 316-319 - Steven A. Sullivan, L. Aravind, Izabela Makalowska
The Histone Database: a comprehensive WWW resource for histones and histone fold-containing proteins. 320-322 - Neil D. Rawlings
MEROPS: the peptidase database. 323-325 - Maciej Szymanski
Aminoacyl-tRNA synthetases database Y2K. 326-328 - Sharmila Banerjee-Basu, Joseph F. Ryan, Andreas D. Baxevanis:
The Homeodomain Resource: a prototype database for a large protein family. 329-330 - Reiko Kikuno, Takahiro Nagase, Mikita Suyama
HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project. 331-332 - Eckhard Jankowsky
The DExH/D protein family database. 333-334 - Mark D'Souza, Margaret F. Romine
SENTRA, a database of signal transduction proteins. 335-336 - Alexander V. Spirov, Timothy Bowler, John Reinitz:
HOX Pro: a specialized database for clusters and networks of homeobox genes. 337-340 - Emmanouil Skoufos, Luis N. Marenco, Prakash M. Nadkarni, Perry L. Miller, Gordon M. Shepherd:
Olfactory Receptor Database: a sensory chemoreceptor resource. 341-343 - Francine B. Perler:
InBase, the Intein Database. 344-345 - Robert W. Shafer, Duane R. Jung, Bradley J. Betts
Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database. 346-348 - Jean-Loup Huret, Sylvaine Le Minor, Frank Dorkeld, Philippe Dessen, Alain Bernheim:
Atlas of Genetics and Cytogenetics in Oncology and Haematology, an Interactive Database. 349-351 - Elizabeth M. Smigielski, Karl Sirotkin, Minghong Ward, Stephen T. Sherry
dbSNP: a database of single nucleotide polymorphisms. 352-355 - Anthony J. Brookes, Heikki Lehväslaiho, Marianne Siegfried, Jana G. Boehm, Yan P. Yuan, Chandra M. Sarkar, Peer Bork
HGBASE: a database of SNPs and other variations in and around human genes. 356-360 - Kei-Hoi Cheung, Michael V. Osier, Judith R. Kidd, Andrew J. Pakstis, Perry L. Miller, Kenneth K. Kidd:
ALFRED: an allele frequency database for diverse populations and DNA polymorphisms. 361-363 - Shinsei Minoshima, Susumu Mitsuyama, Saho Ohno, Takashi Kawamura
Keio Mutation Database (KMDB) for human disease gene mutations. 364-368 - Kaj A. E. Stenberg, Pentti Riikonen, Mauno Vihinen:
KinMutBase, a database of human disease-causing protein kinase mutations. 369-371 - Domenico Catalano
Update of KEYnet: a gene and protein names database for biosequences functional organisation. 372-373 - Shuichi Kawashima
AAindex: Amino Acid index database. 374 - Uma Nagaswamy, Neil Voss
Database of non-canonical base pairs found in known RNA structures. 375-376 - Lynda B. M. Ellis, C. Douglas Hershberger, Lawrence P. Wackett:
The University of Minnesota Biocatalysis/Biodegradation Database: microorganisms, genomics and prediction. 377-379 - Susumu Goto, Takaaki Nishioka, Minoru Kanehisa:
LIGAND: chemical database of enzyme reactions. 380-382
Volume 28, Number 13, July 2000
- Michaela Scherr, John J. Rossi, Georg Sczakiel, Volker Patzel:
RNA accessibility prediction: a theoretical approach is consistent with experimental studies in cell extracts. 2455-2461 - Volker Patzel, Georg Sczakiel:
In vitro selection supports the view of a kinetic control of antisense RNA-mediated inhibition of gene expression in mammalian cells. 2462-2466 - Marie-Christine Chaboissier
Retrotransposition of the I factor, a non-long terminal repeat retrotransposon of Drosophila, generates tandem repeats at the 3' end. 2467-2472 - Ayumi Yamada
Complementation of defective translesion synthesis and UV light sensitivity in xeroderma pigmentosum variant cells by human and mouse DNA polymerase. 2473-2480 - Ceslovas Venclovas
Structure-based predictions of Rad1, Rad9, Hus1 and Rad17 participation in sliding clamp and clamp-loading complexes. 2481-2493 - Mireille Boyer, Nicolas Poujol, Emmanuel Margeat
Quantitative characterization of the interaction between purified human estrogen receptor and DNA using fluorescence anisotropy. 2494-2502 - Lucia Pellizzari, Angela D'Elia, Alessandra Rustighi, Guidalberto Manfioletti
Expression and function of the homeodomain-containing protein Hex in thyroid cells. 2503-2511 - Joby M. Chesnick, Megan Goff, James Graham, Christopher Ocampo, B. Franz Lang, Elias Seif, Gertraud Burger:
The mitochondrial genome of the stramenopile alga Chrysodidymus synuroideus. Complete sequence, gene content and genome organization. 2512-2518 - Catherine Elaine Koering, Genevieve Fourel, Emmanuelle Binet-Brasselet, Thierry Laroche, Franz Klein
Identification of high affinity Tbf1p-binding sites within the budding yeast genome. 2519-2526 - Maria C. Nagan
Importance of discriminator base stacking interactions: molecular dynamics analysis of A73 microhelixAla variants. 2527-2534 - Keith R. Fox, Sarah L. Allinson
Recognition of GT mismatches by Vsr mismatch endonuclease. 2535-2540 - Rajesh Bagga, Susan Michalowski, Rohit Sabnis, Jack D. Griffith, Beverly M. Emerson:
HMG I/Y regulates long-range enhancer-dependent transcription on DNA and chromatin by changes in DNA topology. 2541-2550 - Takehisa Nakahara, Qiu-Mei Zhang, Kazunari Hashiguchi, Shuji Yonei:
Identification of proteins of Escherichia coli and Saccharomyces cerevisiae that specifically bind to C/C mismatches in DNA. 2551-2556 - Kohtaro Fujimoto, Satoru Kyo, Masahiro Takakura, Taro Kanaya, Yasuhide Kitagawa, Hideaki Itoh, Morinobu Takahashi, Masaki Inoue:
Identification and characterization of negative regulatory elements of the human telomerase catalytic subunit (hTERT) gene promoter: possible role of MZF-2 in transcriptional repression of hTERT. 2557-2562 - Emma Southern, Mike Merrick:
The role of Region II in the RNA polymerase factor N (54). 2563-2570 - Tomohiko Kubo
The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNACys(GCA). 2571-2576 - Sabrina Ceccotti, Carmela Ciotta, Gilberto Fronza
Multiple mutations and frameshifts are the hallmark of defective hPMS2 in pZ189-transfected human tumor cells. 2577-2584 - Elke Feldmann, Viola Schmiemann, Wolfgang Goedecke, Susanne Reichenberger, Petra Pfeiffer:
DNA double-strand break repair in cell-free extracts from Ku80-deficient cells: implications for Ku serving as an alignment factor in non-homologous DNA end joining. 2585-2596 - Maik Jörg Lehmann, Volker Patzel, Georg Sczakiel:
Theoretical design of antisense genes with statistically increased efficacy. 2597-2604 - Qi-Xiang Li, Joan M. Robbins, Peter J. Welch, Flossie Wong-Staal, Jack R. Barber:
A novel functional genomics approach identifies mTERT as a suppressor of fibroblast transformation. 2605-2612 - Daniel Barsky
New insights into the structure of abasic DNA from molecular dynamics simulations. 2613-2626
- Martina Kovárová
New specificity and yield enhancer of polymerase chain reactions. 70
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