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Nucleic Acids Research, Volume 29
Volume 29, Number 1, January 2001
- Andreas D. Baxevanis:
The Molecular Biology Database Collection: an updated compilation of biological database resources. 1-10 - David L. Wheeler, Deanna M. Church, Alex E. Lash, Detlef D. Leipe, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Tatiana A. Tatusova, Lukas Wagner, Barbara A. Rapp:
Database resources of the National Center for Biotechnology Information. 11-16 - Guenter Stoesser, Wendy Baker, Alexandra van den Broek, Evelyn Camon, Maria Garcia-Pastor, Carola Kanz, Tamara Kulikova, Vincent Lombard, Rodrigo Lopez
, Helen E. Parkinson
The EMBL nucleotide sequence database. 17-21 - Roman L. Tatusov, Darren A. Natale
The COG database: new developments in phylogenetic classification of proteins from complete genomes. 22-28 - Winona C. Barker, John S. Garavelli
Protein Information Resource: a community resource for expert annotation of protein data. 29-32 - Evgenia V. Kriventseva, Wolfgang Fleischmann, Evgeni M. Zdobnov
CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins. 33-36 - Rolf Apweiler
The InterPro database, an integrated documentation resource for protein families, domains and functional sites. 37-40 - Daniel H. Haft, Brendan J. Loftus
TIGRFAMs: a protein family resource for the functional identification of proteins. 41-43 - Rolf Apweiler
Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes. 44-48 - Kevin A. T. Silverstein, Elizabeth Shoop, James E. Johnson, Alan Kilian, John L. Freeman, Timothy M. Kunau, Ihab A. Awad, Margaret Mayer, Ernest F. Retzel:
The MetaFam Server: a comprehensive protein family resource. 49-51 - Cathy H. Wu
iProClass: an integrated, comprehensive and annotated protein classification database. 52-54 - Sabine Dietmann
A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. 55-57 - János Murvai, Kristian Vlahovicek
The SBASE protein domain library, release 8.0: a collection of annotated protein sequence segments. 58-60 - S. Balaji, S. Sujatha, S. Sai Chetan Kumar, Narayanaswamy Srinivasan:
PALI - a database of Phylogeny and ALIgnment of homologous protein structures. 61-65 - Junichi Watanabe, Masahide Sasaki, Yutaka Suzuki, Sumio Sugano:
FULL-malaria: a database for a full-length enriched cDNA library from human malaria parasite, Plasmodium falciparum. 70-71 - Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Dulce Millán-Zárate, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Ernesto Pérez-Rueda
RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. 72-74 - Maria C. Costanzo, Matthew E. Crawford, Jodi E. Hirschman, Janice E. Kranz
YPDTM, PombePDTM and WormPDTM: model organism volumes of the BioKnowledgeTM Library, an integrated resource for protein information. 75-79 - Catherine A. Ball, Heng Jin, Gavin Sherlock
Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. 80-81 - Lincoln Stein, Paul W. Sternberg, Richard Durbin
WormBase: network access to the genome and biology of Caenorhabditis elegans. 82-86 - Judy Sprague, Eckehard Doerry, Sarah A. Douglas, Monte Westerfield:
The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research. 87-90 - Judith A. Blake
The Mouse Genome Database (MGD): integration nexus for the laboratory mouse. 91-94 - Carol J. Bult, Debra M. Krupke
Web-based access to mouse models of human cancers: the Mouse Tumor Biology (MTB) Database. 95-97 - Martin Ringwald, Janan T. Eppig, Dale A. Begley, John P. Corradi, Ingeborg J. McCright, Terry F. Hayamizu, David P. Hill, James A. Kadin, Joel E. Richardson:
The Mouse Gene Expression Database (GXD). 98-101 - Eva Huala
The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. 102-105 - Jian Hu, Chris Mungall, Andy Law, Richard Papworth, J. Paul Nelson, Alison Brown, Irene Simpson, Shirley Leckie, David W. Burt
The ARKdb: genome databases for farmed and other animals. 106-110 - Michael Gribskov
PlantsP: a functional genomics database for plant phosphorylation. 111-113 - Callum J. Bell, Richard A. Dixon, Andrew D. Farmer, H. Raul Flores, Jeff T. Inman, Robert A. Gonzales, Maria J. Harrison, Nancy L. Paiva, Angela D. Scott, Jennifer W. Weller, Gregory D. May:
The Medicago Genome Initiative: a model legume database. 114-117 - Carl A. Price, Ellen M. Reardon:
Mendel, a database of nomenclature for sequenced plant genes. 118-119 - David Lonsdale, Mark L. Crowe
Mendel-GFDb and Mendel-ESTS: databases of plant gene families and ESTs annotated with gene family numbers and gene family names. 120-122 - Jeremy D. Peterson, Lowell A. Umayam, Tanja Dickinson, Erin K. Hickey, Owen White:
The Comprehensive Microbial Resource. 123-125 - Axel Bernal, Uy Ear, Nikos Kyrpides
Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. 126-127 - Nelli Shimko, Lin Liu, B. Franz Lang, Gertraud Burger:
GOBASE: the organelle genome database. 128-132 - M. Mar Albà
VIDA: a virus database system for the organization of animal virus genome open reading frames. 133-136 - Kim D. Pruitt
RefSeq and LocusLink: NCBI gene-centered resources. 137-140 - Shaying Zhao:
A comprehensive BAC resource. 141-143 - Michael Morley
GenMapDB: a database of mapped human BAC clones. 144-147 - Marco Pagni
trEST, trGEN and Hits: access to databases of predicted protein sequences. 148-151 - Gavin Sherlock
The Stanford Microarray Database. 152-155 - Jun Sese, Hitoshi Nikaidou, Shoko Kawamoto, Yuichi Minesaki, Shinichi Morishita
BodyMap incorporated PCR-based expression profiling data and a gene ranking system. 156-158 - John Quackenbush
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. 159-164 - Patricia Rodriguez-Tomé, Philip Lijnzaad:
RHdb: the Radiation Hybrid database. 165-166 - Fabrizio Damiano
PLMItRNA, a database for mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes. 167-168 - Jan Gorodkin
SRPDB (Signal Recognition Particle Database). 169-170 - Bjarne Knudsen, Jacek Wower, Christian Zwieb, Jan Gorodkin
tmRDB (tmRNA database). 171-172 - Bonnie L. Maidak, James R. Cole, Timothy G. Lilburn, Charles T. Parker Jr.
The RDP-II (Ribosomal Database Project). 173-174 - Jan Wuyts, Peter De Rijk, Yves Van de Peer
The European Large Subunit Ribosomal RNA Database. 175-177 - Jesús García-Martínez
RISSC: a novel database for ribosomal 16S'23S RNA genes spacer regions. 178-180 - Joel A. Klappenbach, Paul Saxman, James R. Cole, Thomas M. Schmidt:
rrndb: the Ribosomal RNA Operon Copy Number Database. 181-184 - Henrik T. Yudate, Makiko Suwa
HUNT: launch of a full-length cDNA database from the Helix Research Institute. 185-188 - Volker A. Erdmann, Miroslawa Z. Barciszewska, Maciej Szymanski
The non-coding RNAs as riboregulators. 189-193 - F. H. D. van Batenburg, Alexander P. Gultyaev, C. W. A. Pleij:
PseudoBase: structural information on RNA pseudoknots. 194-195 - Stefan Gräf, Dirk Strothmann, Stefan Kurtz, Gerhard Steger:
HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns. 196-198 - John S. Garavelli
The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database. 199-201 - Jimmy Y. Huang, Douglas L. Brutlag:
The EMOTIF database. 202-204 - George Johnson, Tai Te Wu:
Kabat Database and its applications: future directions. 205-206 - Marie-Paule Lefranc
IMGT, the international ImMunoGeneTics database. 207-209 - James Robinson
IMGT/HLA Database - a sequence database for the human major histocompatibility complex. 210-213 - T. N. Bhat, Philip E. Bourne, Zukang Feng, Gary Gilliland, Shri Jain, Veerasamy Ravichandran, Bohdan Schneider
The PDB data uniformity project. 214-218 - Tamotsu Noguchi, Hideo Matsuda, Yutaka Akiyama
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB). 219-220 - Roman A. Laskowski
PDBsum: summaries and analyses of PDB structures. 221-222 - Frances M. G. Pearl
A rapid classification protocol for the CATH Domain Database to support structural genomics. 223-227 - Ilya N. Shindyalov, Philip E. Bourne:
A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm. 228-229 - Wing Lok Abe Kurtz Chiu, Chun Ngai Sze, Lai Nang Ip, Sze Ki Chan, Steve Chik Fun Au-Yeung:
NTDB: Thermodynamic Database for Nucleic Acids. 230-233 - Alan Christoffels, Antoine van Gelder, Gary Greyling, Robert Miller, Tania Hide, Winston A. Hide
STACK: Sequence Tag Alignment and Consensus Knowledgebase. 234-238 - Ioannis Xenarios, Esteban Fernandez
DIP: The Database of Interacting Proteins: 2001 update. 239-241 - Gary D. Bader, Ian M. Donaldson, Cheryl Wolting, B. F. Francis Ouellette
BIND - The Biomolecular Interaction Network Database. 242-245 - Tala Bakheet, Mathias Frevel, Bryan R. G. Williams
ARED: human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins. 246-254 - M. Burset
SpliceDB: database of canonical and non-canonical mammalian splice sites. 255-259 - Hongkai Ji, Qing Zhou, Fang Wen, Huiyu Xia, Xin Lu, Yanda Li:
AsMamDB: an alternative splice database of mammals. 260-263 - Pavel V. Baranov
RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression. 264-267 - Richard J. Roberts
REBASE - restriction enzymes and methylases. 268-269 - Christoph Grunau
MethDB - a public database for DNA methylation data. 270-274 - Ian M. Morison
The imprinted gene and parent-of-origin effect database. 275-276 - Ruti Hershberg, Gill Bejerano, Alberto Santos-Zavaleta, Hanah Margalit
PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites. 277-0 - Takahiro Ishii, Ken-ichi Yoshida
DBTBS: a database of Bacillus subtilis promoters and transcription factors. 278-280 - Edgar Wingender
The TRANSFAC system on gene expression regulation. 281-283 - Julia V. Ponomarenko
ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another. 284-287 - Maciej Szymanski
Aminoacyl-tRNA synthetases database. 288-290 - Sharmila Banerjee-Basu, Daniel W. Sink, Andreas D. Baxevanis:
The Homeodomain Resource: sequences, structures, DNA binding sites and genomic information. 291-293 - Nicolas Le Novère, Jean-Pierre Changeux:
LGICdb: the ligand-gated ion channel database. 294-295 - Rami Kantor, Rhoderick Machekano, Matthew J. Gonzales, Kathryn Dupnik, Jonathan M. Schapiro, Robert W. Shafer:
Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs. 296-299 - Alan E. Levine, David L. Steffen:
OrCGDB: a database of genes involved in oral cancer. 300-302 - Jean-Loup Huret, Philippe Dessen, Alain Bernheim:
Atlas of Genetics and Cytogenetics in Oncology and Haematology, updated. 303-304 - Olivier Cohen, Marie-Ange Mermet, Jacques Demongeot:
HC Forum®: a web site based on an international human cytogenetic database. 305-307 - Stephen T. Sherry
dbSNP: the NCBI database of genetic variation. 308-311 - Julia V. Ponomarenko
rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations. 312-316 - Michael V. Osier, Kei-Hoi Cheung, Judith R. Kidd, Andrew J. Pakstis, Perry L. Miller, Kenneth K. Kidd:
ALFRED: an allele frequency database for diverse populations and DNA polymorphisms - an update. 317-319 - Christian M. Ruitberg, Dennis J. Reeder, John M. Butler:
STRBase: a short tandem repeat DNA database for the human identity testing community. 320-322 - Anne Bahr, Julie Dawn Thompson, Jean-Claude Thierry, Olivier Poch:
BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. 323-326 - Shinsei Minoshima, Susumu Mitsuyama, Masafumi Ohtsubo, Takashi Kawamura
The KMDB/MutationView: a mutation database for human disease genes. 327-328 - Wilfred W. Li, Boojala V. B. Reddy, Ilya N. Shindyalov, Philip E. Bourne:
CKAAPs DB: a conserved key amino acid positions database. 329-331 - Catherine A. Cooper, Mathew J. Harrison, Marc R. Wilkins, Nicolle H. Packer
GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources. 332-335 - Eduardo Gonzalez-Couto, Brian Hayes, Anne Danckaert:
The life sciences Global Image Database (GID). 336-339 - Lynda B. M. Ellis, C. Douglas Hershberger, Edward M. Bryan, Lawrence P. Wackett:
The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes. 340-343 - Kanako Watanabe, James Nelson, Shigeaki Harayama
ICB database: the gyrB database for identification and classification of bacteria. 344-345 - Florence Horn, Gerrit Vriend, Fred E. Cohen:
Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems. 346-349
Volume 29, Number 13, July 2001
- Lisa Hooker, Rebecca Strong, Ralph Adams, Balraj Handa, John H. Merrett, Joseph A. Martin, Klaus Klumpp:
A sensitive, single-tube assay to measure the enzymatic activities of influenza RNA polymerase and other poly(A) polymerases: application to kinetic and inhibitor analysis. 2691-2698 - Brian P. Chadwick
Histone variant macroH2A contains two distinct macrochromatin domains capable of directing macroH2A to the inactive X chromosome. 2699-2705 - Ulrike Fiedler, H. Th. Marc Timmers:
Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation. 2706-2714 - Virgen Rodriguez-Wells, Stephen J. Plotch, Jeffrey J. DeStefano
Primer-dependent synthesis by poliovirus RNA-dependent RNA polymerase (3Dpol). 2715-2724 - Nathalie Berthet
Translesional synthesis on DNA templates containing the 2'-deoxyribonolactone lesion. 2725-2732 - Anthony Henras, Christophe Dez
Accumulation of H/ACA snoRNPs depends on the integrity of the conserved central domain of the RNA-binding protein Nhp2p. 2733-2746 - Frédérique Barloy-Hubler
Ribosomal protein gene cluster analysis in eubacterium genomics: homology between Sinorhizobium meliloti strain 1021 and Bacillus subtilis. 2747-2756 - Frédéric Freund, Florence Boulmé, Simon Litvak, Laura Tarrago-Litvak:
Initiation of HIV-2 reverse transcription: a secondary structure model of the RNA?tRNALys3 duplex. 2757-2765 - Majid Fardaei
In vivo co-localisation of MBNL protein with DMPK expanded-repeat transcripts. 2766-2771 - Scott J. Garforth, Dipak Patel, Min Feng, Jon R. Sayers:
Unusually wide co-factor tolerance in a metalloenzyme; divalent metal ions modulate endo?exonuclease activity in T5 exonuclease. 2772-2779 - Tomoko Kuwabara
Significantly higher activity of a cytoplasmic hammerhead ribozyme than a corresponding nuclear counterpart: engineered tRNAs with an extended 3' end can be exported efficiently and specifically to the cytoplasm in mammalian cells. 2780-2788 - David L. Crowe, Dan C. Nguyen, Kenneth J. Tsang, Satoru Kyo:
E2F-1 represses transcription of the human telomerase reverse transcriptase gene. 2789-2794 - Besik I. Kankia, Vitaly Buckin, Victor A. Bloomfield:
Hexamminecobalt(III)-induced condensation of calf thymus DNA: circular dichroism and hydration measurements. 2795-2801 - Istvan Boldogh, Daun Milligan, Myung Soog Lee, Heather Bassett, R. Stephen Lloyd
hMYH cell cycle-dependent expression, subcellular localization and association with replication foci: evidence suggesting replication-coupled repair of adenine: 8-oxoguanine mispairs. 2802-2809 - Deqi Huang, Maarit Jokela, Jussi Tuusa, Sven Skog, Kari Poikonen, Juhani E. Syväoja:
E2F mediates induction of the Sp1-controlled promoter of the human DNA polymerase B-subunit gene POLE2. 2810-2821 - Ellen L. Shen, Daniel F. Bogenhagen:
Developmentally-regulated packaging of mitochondrial DNA by the HMG-box protein mtTFA during Xenopus oogenesis. 2822-2828 - Bindu Nanduri, Robert L. Eoff, Alan J. Tackett, Kevin D. Raney:
Measurement of steady-state kinetic parameters for DNA unwinding by the bacteriophage T4 Dda helicase: use of peptide nucleic acids to trap single-stranded DNA products of helicase reactions. 2829-2835 - So-Jung Choi, So-Youn Park, Tae-Hee Han:
14-3-3 associates with and activates the MEF2D transcription factor during muscle cell differentiation. 2836-2842 - Payam Mohaghegh, Julia K. Karow, Robert M. Brosh Jr., Vilhelm A. Bohr, Ian D. Hickson
The Bloom's and Werner's syndrome proteins are DNA structure-specific helicases. 2843-2849 - Barmak Modrek, Alissa M. Resch, Catherine S. Grasso, Christopher J. Lee:
Genome-wide detection of alternative splicing in expressed sequences of human genes. 2850-2859 - Nicholas M. Luscombe, Roman A. Laskowski, Janet M. Thornton
Amino acid?base interactions: a three-dimensional analysis of protein?DNA interactions at an atomic level. 2860-2874 - Dongyu Guo, Xiaohua Wu, Deepak K. Rajpal, John-Stephen Taylor, Zhigang Wang:
Translesion synthesis by yeast DNA polymerase from templates containing lesions of ultraviolet radiation and acetylaminofluorene. 2875-2883 - Paul Bertone
SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. 2884-2898 - Lucymara F. Agnez-Lima
DNA repair and sequence context affect 1O2-induced mutagenesis in bacteria. 2899-2903
- Fadi Abdi, E. Morton Bradbury, Norman Doggett, Xian Chen:
Rapid characterization of DNA oligomers and genotyping of single nucleotide polymorphism using nucleotide-specific mass tags. 61 - Serena Bernacchi
Exciton interaction in molecular beacons: a sensitive sensor for short range modifications of the nucleic acid structure. 62 - Philippe Marc
yMGV: a database for visualization and data mining of published genome-wide yeast expression data. 63 - Yumin Teng, Shirong Yu, Raymond Waters:
The mapping of nucleosomes and regulatory protein binding sites at the Saccharomyces cerevisiae MFA2 gene: a high resolution approach. 64 - Christoph Grunau
Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. 65 - Yuzhi Zhang, Brendan D. Price, Sotirios Tetradis, Subrata Chakrabarti, Gautam Maulik, G. Mike Makrigiorgos:
Reproducible and inexpensive probe preparation for oligonucleotide arrays. 66 - Sonia Trigueros
Novel display of knotted DNA molecules by two-dimensional gel electrophoresis. 67 - Ina I. Vandenbroucke, Jo Vandesompele, Anne De Paepe, Ludwine Messiaen:
Quantification of splice variants using real-time PCR. 68 - Katarina Lindroos, Ulrika Liljedahl, Mirja Raitio, Ann-Christine Syvänen:
Minisequencing on oligonucleotide microarrays: comparison of immobilisation chemistries. 69
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