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Transterm—extended search facilities and improved integration with other databases.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d37, doi. 10.1093/nar/gkj159
By:
- Jacobs, Grant H.;
- Stockwell, Peter A.;
- Tate, Warren P.;
- Brown, Chris M.
Publication type:
Article
E-MSD: improving data deposition and structure quality.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d287, doi. 10.1093/nar/gkj163
By:
- Tagari, M.;
- Tate, J.;
- Swaminathan, G. J.;
- Newman, R.;
- Naim, A.;
- Vranken, W.;
- Kapopoulou, A.;
- Hussain, A.;
- Fillon, J.;
- Henrick, K.;
- Velankar, S.
Publication type:
Article
The Molecular Biology Database Collection: 2006 update.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d3, doi. 10.1093/nar/gkj162
By:
- Galperin, Michael Y.
Publication type:
Article
The Universal Protein Resource (UniProt): an expanding universe of protein information.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d187
By:
- Wu, Cathy H.;
- Apweiler, Rolf;
- Bairoch, Amos;
- Natale, Darren A.;
- Barker, Winona C.;
- Boeckmann, Brigitte;
- Ferro, Serenella;
- Gasteiger, Elisabeth;
- Huang, Hongzhan;
- Lopez, Rodrigo;
- Magrane, Michele;
- Martin, Maria J.;
- Mazumder, Raja;
- O'Donovan, Claire;
- Redaschi, Nicole;
- Suzek, Baris
Publication type:
Article
Génolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d432, doi. 10.1093/nar/gkj160
By:
- Sherman, David;
- Durrens, Pascal;
- Iragne, Florian;
- Beyne, Emmanuelle;
- Nikolski, Macha;
- Souciet, Jean-Luc
Publication type:
Article
ASAP: a resource for annotating, curating, comparing, and disseminating genomic data.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d41, doi. 10.1093/nar/gkj164
By:
- Glasner, Jeremy D.;
- Rusch, Michael;
- Liss, Paul;
- Plunkett, Guy;
- Cabot, Eric L.;
- Darling, Aaron;
- Anderson, Bradley D.;
- Infield-Harm, Paul;
- Gilson, Michael C.;
- Perna, Nicole T.
Publication type:
Article
Database resources of the National Center for Biotechnology Information.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d173, doi. 10.1093/nar/gkj158
By:
- Wheeler, David L.;
- Barrett, Tanya;
- Benson, Dennis A.;
- Bryant, Stephen H.;
- Canese, Kathi;
- Chetvernin, Vyacheslav;
- Church, Deanna M.;
- DiCuccio, Michael;
- Edgar, Ron;
- Federhen, Scott;
- Geer, Lewis Y.;
- Helmberg, Wolfgang;
- Kapustin, Yuri;
- Kenton, David L.;
- Khovayko, Oleg;
- Lipman, David J.;
- Madden, Thomas L.;
- Maglott, Donna R.;
- Ostell, James;
- Pruitt, Kim D.
Publication type:
Article
GenBank.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d16, doi. 10.1093/nar/gkj157
By:
- Benson, Dennis A.;
- Karsch-Mizrachi, Ilene;
- Lipman, David J.;
- Ostell, James;
- Wheeler, David L.
Publication type:
Article
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d394, doi. 10.1093/nar/gkj156
By:
- Salgado, Heladia;
- Gama-Castro, Socorro;
- Peralta-Gil, Martín;
- Díaz-Peredo, Edgar;
- Sánchez-Solano, Fabiola;
- Santos-Zavaleta, Alberto;
- Martínez-Flores, Irma;
- Jiménez-Jacinto, Verónica;
- Bonavides-Martínez, César;
- Segura-Salazar, Juan;
- Martínez-Antonio, Agustino;
- Collado-Vides, Julio
Publication type:
Article
RTPrimerDB: the real-time PCR primer and probe database, major update 2006.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d684, doi. 10.1093/nar/gkj155
By:
- Pattyn, Filip;
- Robbrecht, Piet;
- De Paepe, Anne;
- Speleman, Frank;
- Vandesompele, Jo
Publication type:
Article
Gramene: a bird's eye view of cereal genomes.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d717, doi. 10.1093/nar/gkj154
By:
- Jaiswal, Pankaj;
- Ni, Junjian;
- Yap, Immanuel;
- Ware, Doreen;
- Spooner, William;
- Youens-Clark, Ken;
- Ren, Liya;
- Liang, Chengzhi;
- Zhao, Wei;
- Ratnapu, Kiran;
- Faga, Benjamin;
- Canaran, Payan;
- Fogleman, Molly;
- Hebbard, Claire;
- Avraham, Shuly;
- Schmidt, Steven;
- Casstevens, Terry M.;
- Buckler, Edward S.;
- Stein, Lincoln;
- McCouch, Susan
Publication type:
Article
BIOZON: a hub of heterogeneous biological data.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d235, doi. 10.1093/nar/gkj153
By:
- Birkland, Aaron;
- Yona, Golan
Publication type:
Article
OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d599, doi. 10.1093/nar/gkj152
By:
- Lenffer, Johann;
- Nicholas, Frank W.;
- Castle, Kao;
- Rao, Arjun;
- Gregory, Stefan;
- Poidinger, Michael;
- Mailman, Matthew D.;
- Ranganathan, Shoba
Publication type:
Article
SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d617, doi. 10.1093/nar/gkj151
By:
- Packer, Bernice R.;
- Yeager, Meredith;
- Burdett, Laura;
- Welch, Robert;
- Beerman, Michael;
- Qi, Liqun;
- Sicotte, Hugues;
- Staats, Brian;
- Acharya, Mekhala;
- Crenshaw, Andrew;
- Eckert, Andrew;
- Puri, Vinita;
- Gerhard, Daniela S.;
- Chanock, Stephen J.
Publication type:
Article
EDITORIAL.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d1, doi. 10.1093/nar/gkj150
By:
- Bateman, Alex
Publication type:
Article
Pfam: clans, web tools and services.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d247, doi. 10.1093/nar/gkj149
By:
- Finn, Robert D.;
- Mistry, Jaina;
- Schuster-Böckler, Benjamin;
- Griffiths-Jones, Sam;
- Hollich, Volker;
- Lassmann, Timo;
- Moxon, Simon;
- Marshall, Mhairi;
- Khanna, Ajay;
- Durbin, Richard;
- Eddy, Sean R.;
- Sonnhammer, Erik L. L.;
- Bateman, Alex
Publication type:
Article
MIPS: analysis and annotation of proteins from whole genomes in 2005.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d169, doi. 10.1093/nar/gkj148
By:
- Mewes, H. W.;
- Frishman, D.;
- Mayer, K. F. X.;
- Münsterkötter, M.;
- Noubibou, O.;
- Pagel, P.;
- Rattei, T.;
- Oesterheld, M.;
- Ruepp, A.;
- Stümpflen, V.
Publication type:
Article
The HUGO Gene Nomenclature Database, 2006 updates.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d319, doi. 10.1093/nar/gkj147
By:
- Eyre, Tina A.;
- Ducluzeau, Fabrice;
- Sneddon, Tam P.;
- Povey, Sue;
- Bruford, Elspeth A.;
- Lush, Michael J.
Publication type:
Article
EPD in its twentieth year: towards complete promoter coverage of selected model organisms.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d82, doi. 10.1093/nar/gkj146
By:
- Schmid, Christoph D.;
- Perier, Rouaïda;
- Praz, Viviane;
- Bucher, Philipp
Publication type:
Article
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d332, doi. 10.1093/nar/gkj145
By:
- Liolios, Konstantinos;
- Tavernarakis, Nektarios;
- Hugenholtz, Philip;
- Kyrpides, Nikos C.
Publication type:
Article
The UCSC Genome Browser Database: update 2006.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d590, doi. 10.1093/nar/gkj144
By:
- Hinrichs, A. S.;
- Karolchik, D.;
- Baertsch, R.;
- Barber, G. P.;
- Bejerano, G.;
- Clawson, H.;
- Diekhans, M.;
- Furey, T. S.;
- Harte, R. A.;
- Hsu, F.;
- Hillman-Jackson, J.;
- Kuhn, R. M.;
- Pedersen, J. S.;
- Pohl, A.;
- Raney, B. J.;
- Rosenbloom, K. R.;
- Siepel, A.;
- Smith, K. E.;
- Sugnet, C. W.;
- Sultan-Qurraie, A.
Publication type:
Article
TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d108, doi. 10.1093/nar/gkj143
By:
- Matys, V.;
- Kel-Margoulis, O. V.;
- Fricke, E.;
- Liebich, I.;
- Land, S.;
- Barre-Dirrie, A.;
- Reuter, I.;
- Chekmenev, D.;
- Krull, M.;
- Hornischer, K.;
- Voss, N.;
- Stegmaier, P.;
- Lewicki-Potapov, B.;
- Saxel, H.;
- Kel, A. E.;
- Wingender, E.
Publication type:
Article
The tmRDB and SRPDB resources.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d163, doi. 10.1093/nar/gkj142
By:
- Andersen, Ebbe Sloth;
- Rosenblad, Magnus Alm;
- Larsen, Niels;
- Westergaard, Jesper Cairo;
- Burks, Jody;
- Wower, Iwona K.;
- Wower, Jacek;
- Gorodkin, Jan;
- Samuelsson, Tore;
- Zwieb, Christian
Publication type:
Article
DRASTIC—INSIGHTS: querying information in a plant gene expression database.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d712, doi. 10.1093/nar/gkj136
By:
- Button, Davina K.;
- Gartland, Kevan M. A.;
- Ball, Leslie D.;
- Natanson, Louis;
- Gartland, Jill S.;
- Lyon, Gary D.
Publication type:
Article
xBASE, a collection of online databases for bacterial comparative genomics.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d335, doi. 10.1093/nar/gkj140
By:
- Chaudhuri, Roy R.;
- Pallen, Mark J.
Publication type:
Article
The LIFEdb database in 2006.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d415, doi. 10.1093/nar/gkj139
By:
- Mehrle, Alexander;
- Rosenfelder, Heiko;
- Schupp, Ingo;
- del Val, Coral;
- Arlt, Dorit;
- Hahne, Florian;
- Bechtel, Stephanie;
- Simpson, Jeremy;
- Hofmann, Oliver;
- Hide, Winston;
- Glatting, Karl-Heinz;
- Huber, Wolfgang;
- Pepperkok, Rainer;
- Poustka, Annemarie;
- Wiemann, Stefan
Publication type:
Article
PRIDE: a public repository of protein and peptide identifications for the proteomics community.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d659, doi. 10.1093/nar/gkj138
By:
- Jones, Philip;
- Côté, Richard G.;
- Martens, Lennart;
- Quinn, Antony F.;
- Taylor, Chris F.;
- Derache, William;
- Hermjakob, Henning;
- Apweiler, Rolf
Publication type:
Article
BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d628, doi. 10.1093/nar/gkj137
By:
- Ogasawara, Osamu;
- Otsuji, Makiko;
- Watanabe, Kouji;
- Iizuka, Takayasu;
- Tamura, Takuro;
- Hishiki, Teruyoshi;
- Kawamoto, Shoko;
- Okubo, Kousaku
Publication type:
Article
Human protein reference database—2006 update.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d411, doi. 10.1093/nar/gkj141
By:
- Mishra, Gopa R.;
- Suresh, M.;
- Kumaran, K.;
- Kannabiran, N.;
- Suresh, Shubha;
- Bala, P.;
- Shivakumar, K.;
- Anuradha, N.;
- Reddy, Raghunath;
- Raghavan, T. Madhan;
- Menon, Shalini;
- Hanumanthu, G.;
- Gupta, Malvika;
- Upendran, Sapna;
- Gupta, Shweta;
- Mahesh, M.;
- Jacob, Bincy;
- Mathew, Pinky;
- Chatterjee, Pritam;
- Arun, K. S.
Publication type:
Article
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d135, doi. 10.1093/nar/gkj135
By:
- Hsu, Paul W.C.;
- Huang, Hsien-Da;
- Hsu, Sheng-Da;
- Lin, Li-Zen;
- Tsou, Ann-Ping;
- Tseng, Ching-Ping;
- Stadler, Peter F.;
- Washietl, Stefan;
- Hofacker, Ivo L.
Publication type:
Article
The UCSC Archaeal Genome Browser.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d407, doi. 10.1093/nar/gkj134
By:
- Schneider, Kevin L.;
- Pollard, Katherine S.;
- Baertsch, Robert;
- Pohl, Andy;
- Lowe, Todd M.
Publication type:
Article
Ensembl 2006.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d556, doi. 10.1093/nar/gkj133
By:
- Birney, E.;
- Andrews, D.;
- Caccamo, M.;
- Chen, Y.;
- Clarke, L.;
- Coates, G.;
- Cox, T.;
- Cunningham, F.;
- Curwen, V.;
- Cutts, T.;
- Down, T.;
- Durbin, R.;
- Fernandez-Suarez, X. M.;
- Flicek, P.;
- Gräf, S.;
- Hammond, M.;
- Herrero, J.;
- Howe, K.;
- Iyer, V.;
- Jekosch, K.
Publication type:
Article
SuperNatural: a searchable database of available natural compounds.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d678, doi. 10.1093/nar/gkj132
By:
- Dunkel, Mathias;
- Fullbeck, Melanie;
- Neumann, Stefanie;
- Preissner, Robert
Publication type:
Article
DBD: a transcription factor prediction database.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d74, doi. 10.1093/nar/gkj131
By:
- Kummerfeld, Sarah K.;
- Teichmann, Sarah A.
Publication type:
Article
EMBL Nucleotide Sequence Database: developments in 2005.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d10, doi. 10.1093/nar/gkj130
By:
- Cochrane, Guy;
- Aldebert, Philippe;
- Althorpe, Nicola;
- Andersson, Mikael;
- Baker, Wendy;
- Baldwin, Alastair;
- Bates, Kirsty;
- Bhattacharyya, Sumit;
- Browne, Paul;
- van den Broek, Alexandra;
- Castro, Matias;
- Duggan, Karyn;
- Eberhardt, Ruth;
- Faruque, Nadeem;
- Gamble, John;
- Kanz, Carola;
- Kulikova, Tamara;
- Lee, Charles;
- Leinonen, Rasko;
- Lin, Quan
Publication type:
Article
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d86, doi. 10.1093/nar/gkj129
By:
- Yamashita, Riu;
- Suzuki, Yutaka;
- Wakaguri, Hiroyuki;
- Tsuritani, Katsuki;
- Nakai, Kenta;
- Sugano, Sumio
Publication type:
Article
LMPD: LIPID MAPS proteome database.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d507, doi. 10.1093/nar/gkj122
By:
- Cotter, Dawn;
- Maer, Andreia;
- Guda, Chittibabu;
- Saunders, Brian;
- Subramaniam, Shankar
Publication type:
Article
MetaCyc: a multiorganism database of metabolic pathways and enzymes.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d511, doi. 10.1093/nar/gkj128
By:
- Caspi, Ron;
- Foerster, Hartmut;
- Fulcher, Carol A.;
- Hopkinson, Rebecca;
- Ingraham, John;
- Kaipa, Pallavi;
- Krummenacker, Markus;
- Paley, Suzanne;
- Pick, John;
- Rhee, Seung Y.;
- Tissier, Christophe;
- Zhang, Peifen;
- Karp, Peter D.
Publication type:
Article
Pathguide: a Pathway Resource List.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d504, doi. 10.1093/nar/gkj126
By:
- Bader, Gary D.;
- Cary, Michael P.;
- Sander, Chris
Publication type:
Article
iMOTdb—a comprehensive collection of spatially interacting motifs in proteins.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d285, doi. 10.1093/nar/gkj125
By:
- Pugalenthi, Ganesan;
- Bhaduri, Anirban;
- Sowdhamini, R.
Publication type:
Article
Flexible Structural Neighborhood—a database of protein structural similarities and alignments.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d277
By:
- Li, Zhanwen;
- Ye, Yuzhen;
- Godzik, Adam
Publication type:
Article
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d363, doi. 10.1093/nar/gkj123
By:
- Chen, Feng;
- Mackey, Aaron J.;
- Stoeckert, Christian J.;
- Roos, David S.
Publication type:
Article
MitoP2: the mitochondrial proteome database—now including mouse data.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d705, doi. 10.1093/nar/gkj127
By:
- Prokisch, H.;
- Andreoli, C.;
- Ahting, U.;
- Heiss, K.;
- Ruepp, A.;
- Scharfe, C.;
- Meitinger, T.
Publication type:
Article
EndoNet: an information resource about endocrine networks.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d540, doi. 10.1093/nar/gkj121
By:
- Potapov, Anatolij;
- Liebich, Ines;
- Dönitz, Jürgen;
- Schwarzer, Knut;
- Sasse, Nicole;
- Schoeps, Torsten;
- Crass, Torsten;
- Wingender, Edgar
Publication type:
Article
The RCSB PDB information portal for structural genomics.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d302, doi. 10.1093/nar/gkj120
By:
- Kouranov, Andrei;
- Xie, Lei;
- de la Cruz, Joanna;
- Chen, Li;
- Westbrook, John;
- Bourne, Philip E.;
- Berman, Helen M.
Publication type:
Article
Phytophthora functional genomics database (PFGD): functional genomics of phytophthora–plant interactions.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d465, doi. 10.1093/nar/gkj119
By:
- Gajendran, Kamal;
- Gonzales, Michael D.;
- Farmer, Andrew;
- Archuleta, Eric;
- Win, Joe;
- Waugh, Mark E.;
- Kamoun, Sophien
Publication type:
Article
DDBJ in preparation for overview of research activities behind data submissions.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d6, doi. 10.1093/nar/gkj111
By:
- Okubo, Kousaku;
- Sugawara, Hideaki;
- Gojobori, Takashi;
- Tateno, Yoshio
Publication type:
Article
TreeFam: a curated database of phylogenetic trees of animal gene families.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d572
By:
- Li, Heng;
- Coghlan, Avril;
- Ruan, Jue;
- Coin, Lachlan James;
- Hériché, Jean-Karim;
- Osmotherly, Lara;
- Li, Ruiqiang;
- Liu, Tao;
- Zhang, Zhang;
- Bolund, Lars;
- Wong, Gane Ka-Shu;
- Zheng, Weimou;
- Dehal, Paramvir;
- Wang, Jun;
- Durbin, Richard
Publication type:
Article
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d63, doi. 10.1093/nar/gkj116
By:
- Blanco, Enrique;
- Farré, Domènec;
- Albà, M. Mar;
- Messeguer, Xavier;
- Guigó, Roderic
Publication type:
Article
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d95, doi. 10.1093/nar/gkj115
By:
- Vlieghe, Dominique;
- Sandelin, Albin;
- De Bleser, Pieter J.;
- Vleminckx, Kris;
- Wasserman, Wyeth W.;
- van Roy, Frans;
- Lenhard, Boris
Publication type:
Article

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