Kousaku Okubo,
Hideaki Sugawara, Takashi Gojobori, and Yoshio Tateno
DDBJ in preparation for overview of research activities
behind data submissions Nucl. Acids Res. 2006 34: D6-D9;
doi:10.1093/nar/gkj111 [Abstract][FREE
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Guy Cochrane,
Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Wendy Baker,
Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Paul Browne,
Alexandra van den Broek, Matias Castro, Karyn Duggan, Ruth Eberhardt,
Nadeem Faruque, John Gamble, Carola Kanz, Tamara Kulikova, Charles Lee,
Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Michelle
McHale, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Maria
Pilar Garcia Pastor, Siamak Sobhany, Peter Stoehr, Katerina Tzouvara,
Robert Vaughan, Dan Wu, Weimin Zhu, and Rolf Apweiler
Rivka L. Glaser,
Joshua P. Ramsay, and Ian M. Morison
The imprinted gene and parent-of-origin effect database now
includes parental origin of de novo mutations Nucl.
Acids Res. 2006 34: D29-D31; doi:10.1093/nar/gkj101 [Abstract][FREE
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P. Siguier, J.
Perochon, L. Lestrade, J. Mahillon, and M. Chandler
Grant H. Jacobs,
Peter A. Stockwell, Warren P. Tate, and Chris M. Brown
Transterm—extended search facilities and improved
integration with other databases Nucl. Acids Res. 2006 34:
D37-D40; doi:10.1093/nar/gkj159 [Abstract][FREE
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Jeremy D.
Glasner, Michael Rusch, Paul Liss, Guy Plunkett, III, Eric L. Cabot,
Aaron Darling, Bradley D. Anderson, Paul Infield-Harm, Michael C.
Gilson, and Nicole T. Perna
ASAP: a resource for annotating, curating, comparing, and
disseminating genomic data Nucl. Acids Res. 2006 34:
D41-D45; doi:10.1093/nar/gkj164 [Abstract][FREE
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Stefan Stamm,
Jean-Jack Riethoven, Vincent Le Texier, Chellappa Gopalakrishnan,
Vasudev Kumanduri, Yesheng Tang, Nuno L. Barbosa-Morais, and Thangavel
Alphonse Thanaraj
Dirk Holste,
George Huo, Vivian Tung, and Christopher B. Burge
HOLLYWOOD: a comparative relational database
of alternative splicing Nucl. Acids Res. 2006 34: D56-D62;
doi:10.1093/nar/gkj048 [Abstract][FREE
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Enrique Blanco,
Domènec Farré, M. Mar Albà, Xavier Messeguer, and Roderic Guigó
ABS: a database of Annotated regulatory Binding Sites from
orthologous promoters Nucl. Acids Res. 2006 34: D63-D67;
doi:10.1093/nar/gkj116 [Abstract][FREE
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G. Robertson, M.
Bilenky, K. Lin, A. He, W. Yuen, M. Dagpinar, R. Varhol, K. Teague, O.
L. Griffith, X. Zhang, Y. Pan, M. Hassel, M. C. Sleumer, W. Pan, E. D.
Pleasance, M. Chuang, H. Hao, Y. Y. Li, N. Robertson, C. Fjell, B. Li,
S. B. Montgomery, T. Astakhova, J. Zhou, J. Sander, A. S. Siddiqui, and
S. J. M. Jones
cisRED: a database system for genome-scale computational
discovery of regulatory elements Nucl. Acids Res. 2006 34:
D68-D73; doi:10.1093/nar/gkj075 [Abstract][FREE
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Christoph D.
Schmid, Rouaïda Perier, Viviane Praz, and Philipp Bucher
EPD in its twentieth year: towards complete promoter
coverage of selected model organisms Nucl. Acids Res. 2006
34: D82-D85; doi:10.1093/nar/gkj146 [Abstract][FREE
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Riu Yamashita,
Yutaka Suzuki, Hiroyuki Wakaguri, Katsuki Tsuritani, Kenta Nakai, and
Sumio Sugano
DBTSS: DataBase of Human Transcription Start Sites, progress
report 2006 Nucl. Acids Res. 2006 34: D86-D89;
doi:10.1093/nar/gkj129 [Abstract][FREE
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Vidhya
Jagannathan, Emmanuelle Roulet, Mauro Delorenzi, and Philipp Bucher
HTPSELEX—a database of high-throughput SELEX libraries for
transcription factor binding sites Nucl. Acids Res. 2006
34: D90-D94; doi:10.1093/nar/gkj049 [Abstract][FREE
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Dominique
Vlieghe, Albin Sandelin, Pieter J. De Bleser, Kris Vleminckx, Wyeth W.
Wasserman, Frans van Roy, and Boris Lenhard
V. Matys, O. V.
Kel-Margoulis, E. Fricke, I. Liebich, S. Land, A. Barre-Dirrie, I.
Reuter, D. Chekmenev, M. Krull, K. Hornischer, N. Voss, P. Stegmaier, B.
Lewicki-Potapov, H. Saxel, A. E. Kel, and E. Wingender
TRANSFAC® and its module TRANSCompel®:
transcriptional gene regulation in eukaryotes Nucl. Acids
Res. 2006 34: D108-D110; doi:10.1093/nar/gkj143 [Abstract][FREE
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Tala Bakheet,
Bryan R. G. Williams, and Khalid S. A. Khabar
Priyanka Shahi,
Serguei Loukianiouk, Andreas Bohne-Lang, Marc Kenzelmann, Stefan Küffer,
Sabine Maertens, Roland Eils, Herrmann-Josef Gröne, Norbert Gretz, and
Benedikt Brors
Martin Mokrejs,
Václav Vopálensky, Ondrej Kolenaty, Tomás Masek, Zuzana Feketová, Petra
Sekyrová, Barbora Skaloudová, Vítezslav Kríz, and Martin Pospísek
A. Olson, N.
Sheth, J. S. Lee, G. Hannon, and R. Sachidanandam
RNAi Codex: a portal/database for short-hairpin RNA (shRNA)
gene-silencing constructs Nucl. Acids Res. 2006 34:
D153-D157; doi:10.1093/nar/gkj051 [Abstract][FREE
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Laurent
Lestrade and Michel J. Weber
snoRNA-LBME-db, a comprehensive database of human H/ACA and
C/D box snoRNAs Nucl. Acids Res. 2006 34: D158-D162;
doi:10.1093/nar/gkj002 [Abstract][FREE
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Ebbe Sloth
Andersen, Magnus Alm Rosenblad, Niels Larsen, Jesper Cairo Westergaard,
Jody Burks, Iwona K. Wower, Jacek Wower, Jan Gorodkin, Tore Samuelsson,
and Christian Zwieb
H. W. Mewes, D.
Frishman, K. F. X. Mayer, M. Münsterkötter, O. Noubibou, P. Pagel, T.
Rattei, M. Oesterheld, A. Ruepp, and V. Stümpflen
MIPS: analysis and annotation of proteins from whole genomes
in 2005 Nucl. Acids Res. 2006 34: D169-D172;
doi:10.1093/nar/gkj148 [Abstract][FREE
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David L.
Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi
Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron
Edgar, Scott Federhen, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin,
David L. Kenton, Oleg Khovayko, David J. Lipman, Thomas L. Madden, Donna
R. Maglott, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Lynn M.
Schriml, Edwin Sequeira, Stephen T. Sherry, Karl Sirotkin, Alexandre
Souvorov, Grigory Starchenko, Tugba O. Suzek, Roman Tatusov, Tatiana A.
Tatusova, Lukas Wagner, and Eugene Yaschenko
Database resources of the National Center for Biotechnology
Information Nucl. Acids Res. 2006 34: D173-D180;
doi:10.1093/nar/gkj158 [Abstract][FREE
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Milton H.
Saier, Jr, Can V. Tran, and Ravi D. Barabote
TCDB: the Transporter Classification Database for membrane
transport protein analyses and information Nucl. Acids Res.
2006 34: D181-D186; doi:10.1093/nar/gkj001 [Abstract][FREE
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Cathy H. Wu,
Rolf Apweiler, Amos Bairoch, Darren A. Natale, Winona C. Barker,
Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan
Huang, Rodrigo Lopez, Michele Magrane, Maria J. Martin, Raja Mazumder,
Claire O'Donovan, Nicole Redaschi, and Baris Suzek
The Universal Protein Resource (UniProt): an expanding
universe of protein information Nucl. Acids Res. 2006 34:
D187-D191; doi:10.1093/nar/gkj161 [Abstract][FREE
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Christopher P.
Toseland, Helen McSparron, Matthew N. Davies, and Darren R. Flower
PPD v1.0—an integrated, web-accessible database of
experimentally determined protein pKa values Nucl. Acids Res. 2006 34: D199-D203; doi:10.1093/nar/gkj035 [Abstract][FREE
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M. D. Shaji
Kumar, K. Abdulla Bava, M. Michael Gromiha, Ponraj Prabakaran, Koji
Kitajima, Hatsuho Uedaira, and Akinori Sarai
ProTherm and ProNIT: thermodynamic databases for proteins
and protein–nucleic acid interactions Nucl. Acids Res. 2006
34: D204-D206; doi:10.1093/nar/gkj103 [Abstract][FREE
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Michelle K. M.
Chow, Abdullah A. Amin, Kate F. Fulton, Thushan Fernando, Lawrence
Kamau, Chris Batty, Michael Louca, Storm Ho, James C. Whisstock, Stephen
P. Bottomley, and Ashley M. Buckle
The REFOLD database: a tool for the optimization of protein
expression and refolding Nucl. Acids Res. 2006 34:
D207-D212; doi:10.1093/nar/gkj080 [Abstract][FREE
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J. Lynn Fink,
Rajith N. Aturaliya, Melissa J. Davis, Fasheng Zhang, Kelly Hanson,
Melvena S. Teasdale, Chikatoshi Kai, Jun Kawai, Piero Carninci,
Yoshihide Hayashizaki, and Rohan D. Teasdale
Nicolas Hulo,
Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Edouard De Castro,
Petra S. Langendijk-Genevaux, Marco Pagni, and Christian J. A. Sigrist
SitesBase: a database for structure-based protein–ligand
binding site comparisons Nucl. Acids Res. 2006 34:
D231-D234; doi:10.1093/nar/gkj062 [Abstract][FREE
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V. S. Gowri, O.
Krishnadev, C. S. Swamy, and N. Srinivasan
MulPSSM: a database of multiple position-specific scoring
matrices of protein domain families Nucl. Acids Res. 2006
34: D243-D246; doi:10.1093/nar/gkj043 [Abstract][FREE
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Robert D. Finn,
Jaina Mistry, Benjamin Schuster-Böckler, Sam Griffiths-Jones, Volker
Hollich, Timo Lassmann, Simon Moxon, Mhairi Marshall, Ajay Khanna,
Richard Durbin, Sean R. Eddy, Erik L. L. Sonnhammer, and Alex Bateman
Flexible Structural Neighborhood—a database of protein
structural similarities and alignments Nucl. Acids Res.
2006 34: D277-D280; doi:10.1093/nar/gkj124 [Abstract][FREE
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Corin Yeats,
Michael Maibaum, Russell Marsden, Mark Dibley, David Lee, Sarah Addou,
and Christine A. Orengo
Ursula Pieper,
Narayanan Eswar, Fred P. Davis, Hannes Braberg, M. S. Madhusudhan,
Andrea Rossi, Marc Marti-Renom, Rachel Karchin, Ben M. Webb, David
Eramian, Min-Yi Shen, Libusha Kelly, Francisco Melo, and Andrej Sali
MODBASE: a database of annotated comparative protein
structure models and associated resources Nucl. Acids Res.
2006 34: D291-D295; doi:10.1093/nar/gkj059 [Abstract][FREE
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Samuel Flores,
Nathaniel Echols, Duncan Milburn, Brandon Hespenheide, Kevin Keating,
Jason Lu, Stephen Wells, Eric Z. Yu, Michael Thorpe, and Mark Gerstein
The Database of Macromolecular Motions: new features added
at the decade mark Nucl. Acids Res. 2006 34: D296-D301;
doi:10.1093/nar/gkj046 [Abstract][FREE
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Andrei
Kouranov, Lei Xie, Joanna de la Cruz, Li Chen, John Westbrook, Philip E.
Bourne, and Helen M. Berman
Simon Whelan,
Paul I. W. de Bakker, Emmanuel Quevillon, Nicolas Rodriguez, and Nick
Goldman
PANDIT: an evolution-centric database of protein and
associated nucleotide domains with inferred trees Nucl.
Acids Res. 2006 34: D327-D331; doi:10.1093/nar/gkj087 [Abstract][FREE
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Konstantinos
Liolios, Nektarios Tavernarakis, Philip Hugenholtz, and Nikos C.
Kyrpides
The Genomes On Line Database (GOLD) v.2: a monitor of genome
projects worldwide Nucl. Acids Res. 2006 34: D332-D334;
doi:10.1093/nar/gkj145 [Abstract][FREE
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Roy R.
Chaudhuri and Mark J. Pallen
xBASE, a collection of online databases for bacterial
comparative genomics Nucl. Acids Res. 2006 34: D335-D337;
doi:10.1093/nar/gkj140 [Abstract][FREE
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Emmanuel
Perrodou, Caroline Deshayes, Jean Muller, Christine Schaeffer, Alain Van
Dorsselaer, Raymond Ripp, Olivier Poch, Jean-Marc Reyrat, and Odile
Lecompte
Victor M.
Markowitz, Frank Korzeniewski, Krishna Palaniappan, Ernest Szeto, Greg
Werner, Anu Padki, Xueling Zhao, Inna Dubchak, Philip Hugenholtz, Iain
Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Natalia Ivanova,
and Nikos C. Kyrpides
Feng Chen,
Aaron J. Mackey, Christian J. Stoeckert, Jr, and David S. Roos
OrthoMCL-DB: querying a comprehensive multi-species
collection of ortholog groups Nucl. Acids Res. 2006 34:
D363-D368; doi:10.1093/nar/gkj123 [Abstract][FREE
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Natalia
Maltsev, Elizabeth Glass, Dinanath Sulakhe, Alexis Rodriguez, Mustafa H.
Syed, Tanuja Bompada, Yi Zhang, and Mark D'Souza
PUMA2—grid-based high-throughput analysis of genomes and
metabolic pathways Nucl. Acids Res. 2006 34: D369-D372;
doi:10.1093/nar/gkj095 [Abstract][FREE
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Huiquan Wang,
Miroslava Kaloper, and Craig J. Benham
SIDDBASE: a database containing the stress-induced DNA
duplex destabilization (SIDD) profiles of complete microbial
genomes Nucl. Acids Res. 2006 34: D373-D378;
doi:10.1093/nar/gkj007 [Abstract][FREE
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Sucheta
Tripathy, Varun N. Pandey, Bing Fang, Fidel Salas, and Brett M. Tyler
VMD: a community annotation database for oomycetes and
microbial genomes Nucl. Acids Res. 2006 34: D379-D381;
doi:10.1093/nar/gkj042 [Abstract][FREE
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Michael J.
Adams and John F. Antoniw
DPVweb: a comprehensive database of plant and fungal virus
genes and genomes Nucl. Acids Res. 2006 34: D382-D385;
doi:10.1093/nar/gkj023 [Abstract][FREE
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Craig M.
Shepherd, Ian A. Borelli, Gabriel Lander, Padmaja Natarajan, Vinay
Siddavanahalli, Chandrajit Bajaj, John E. Johnson, Charles L. Brooks,
III, and Vijay S. Reddy
Heladia
Salgado, Socorro Gama-Castro, Martín Peralta-Gil, Edgar Díaz-Peredo,
Fabiola Sánchez-Solano, Alberto Santos-Zavaleta, Irma Martínez-Flores,
Verónica Jiménez-Jacinto, César Bonavides-Martínez, Juan Segura-Salazar,
Agustino Martínez-Antonio, and Julio Collado-Vides
RegulonDB (version 5.0): Escherichia coli K-12
transcriptional regulatory network, operon organization, and growth
conditions Nucl. Acids Res. 2006 34: D394-D397;
doi:10.1093/nar/gkj156 [Abstract][FREE
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Jian Yang,
Lihong Chen, Jun Yu, Lilian Sun, and Qi Jin
Guido
Dieterich, Uwe Kärst, Elmar Fischer, Jürgen Wehland, and Lothar Jänsch
LEGER: knowledge database and visualization tool for
comparative genomics of pathogenic and non-pathogenic Listeria
species Nucl. Acids Res. 2006 34: D402-D406;
doi:10.1093/nar/gkj071 [Abstract][FREE
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Kevin L.
Schneider, Katherine S. Pollard, Robert Baertsch, Andy Pohl, and Todd M.
Lowe
Gopa R. Mishra,
M. Suresh, K. Kumaran, N. Kannabiran, Shubha Suresh, P. Bala, K.
Shivakumar, N. Anuradha, Raghunath Reddy, T. Madhan Raghavan, Shalini
Menon, G. Hanumanthu, Malvika Gupta, Sapna Upendran, Shweta Gupta, M.
Mahesh, Bincy Jacob, Pinky Mathew, Pritam Chatterjee, K. S. Arun, Salil
Sharma, K. N. Chandrika, Nandan Deshpande, Kshitish Palvankar, R.
Raghavnath, R. Krishnakanth, Hiren Karathia, B. Rekha, Rashmi Nayak, G.
Vishnupriya, H. G. Mohan Kumar, M. Nagini, G. S. Sameer Kumar, Rojan
Jose, P. Deepthi, S. Sujatha Mohan, T. K. B. Gandhi, H. C. Harsha,
Krishna S. Deshpande, Malabika Sarker, T. S. Keshava Prasad, and
Akhilesh Pandey
Alexander
Mehrle, Heiko Rosenfelder, Ingo Schupp, Coral del Val, Dorit Arlt,
Florian Hahne, Stephanie Bechtel, Jeremy Simpson, Oliver Hofmann,
Winston Hide, Karl-Heinz Glatting, Wolfgang Huber, Rainer Pepperkok,
Annemarie Poustka, and Stefan Wiemann
Mark Heiges,
Haiming Wang, Edward Robinson, Cristina Aurrecoechea, Xin Gao, Nivedita
Kaluskar, Philippa Rhodes, Sammy Wang, Cong-Zhou He, Yanqi Su, John
Miller, Eileen Kraemer, and Jessica C. Kissinger
Rex L.
Chisholm, Pascale Gaudet, Eric M. Just, Karen E. Pilcher, Petra Fey,
Sohel N. Merchant, and Warren A. Kibbe
dictyBase, the model organism database for Dictyostelium
discoideum Nucl. Acids Res. 2006 34: D423-D427;
doi:10.1093/nar/gkj090 [Abstract][FREE
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Fernán Agüero,
Wenlong Zheng, D. Brent Weatherly, Pablo Mendes, and Jessica C.
Kissinger
TcruziDB: an integrated, post-genomics community resource
for Trypanosoma cruzi Nucl. Acids Res. 2006 34:
D428-D431; doi:10.1093/nar/gkj108 [Abstract][FREE
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David Sherman,
Pascal Durrens, Florian Iragne, Emmanuelle Beyne, Macha Nikolski, and
Jean-Luc Souciet
Jodi E.
Hirschman, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo,
Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Eurie L. Hong,
Michael S. Livstone, Robert Nash, Julie Park, Rose Oughtred, Marek
Skrzypek, Barry Starr, Chandra L. Theesfeld, Jennifer Williams, Rey
Andrada, Gail Binkley, Qing Dong, Christopher Lane, Stuart Miyasato,
Anand Sethuraman, Mark Schroeder, Mayank K. Thanawala, Shuai Weng, Kara
Dolinski, David Botstein, and J. Michael Cherry
Genome Snapshot: a new resource at the Saccharomyces
Genome Database (SGD) presenting an overview of the Saccharomyces
cerevisiae genome Nucl. Acids Res. 2006 34: D442-D445;
doi:10.1093/nar/gkj117 [Abstract][FREE
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Miguel C.
Teixeira, Pedro Monteiro, Pooja Jain, Sandra Tenreiro, Alexandra R.
Fernandes, Nuno P. Mira, Marta Alenquer, Ana T. Freitas, Arlindo L.
Oliveira, and Isabel Sá-Correia
The YEASTRACT database: a tool for the analysis of
transcription regulatory associations in Saccharomyces
cerevisiae Nucl. Acids Res. 2006 34: D446-D451;
doi:10.1093/nar/gkj013 [Abstract][FREE
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Kevin P. Byrne
and Kenneth H. Wolfe
Visualizing syntenic relationships among the hemiascomycetes
with the Yeast Gene Order Browser Nucl. Acids Res. 2006 34:
D452-D455; doi:10.1093/nar/gkj041 [Abstract][FREE
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Ulrich
Güldener, Gertrud Mannhaupt, Martin Münsterkötter, Dirk Haase, Matthias
Oesterheld, Volker Stümpflen, Hans-Werner Mewes, and Gerhard Adam
FGDB: a comprehensive fungal genome resource on the plant
pathogen Fusarium graminearum Nucl. Acids Res. 2006
34: D456-D458; doi:10.1093/nar/gkj026 [Abstract][FREE
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Rainer
Winnenburg, Thomas K. Baldwin, Martin Urban, Chris Rawlings, Jacob
Köhler, and Kim E. Hammond-Kosack
Kamal
Gajendran, Michael D. Gonzales, Andrew Farmer, Eric Archuleta, Joe Win,
Mark E. Waugh, and Sophien Kamoun
Phytophthora functional genomics database (PFGD): functional
genomics of phytophthora–plant interactions Nucl.
Acids Res. 2006 34: D465-D470; doi:10.1093/nar/gkj119 [Abstract][FREE
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David H.
Johnson, Jun Tsao, Ming Luo, and Mike Carson
SGCEdb: a flexible database and web interface integrating
experimental results and analysis for structural genomics focusing on
Caenorhabditis elegans Nucl. Acids Res. 2006 34:
D471-D474; doi:10.1093/nar/gkj036 [Abstract][FREE
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Material] OPEN ACCESS ARTICLE
Erich M.
Schwarz, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin
Blasiar, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J. Chen,
Paul Davis, Tristan J. Fiedler, Lisa Girard, Todd W. Harris, Eimear E.
Kenny, Ranjana Kishore, Dan Lawson, Raymond Lee, Hans-Michael Müller,
Cecilia Nakamura, Phil Ozersky, Andrei Petcherski, Anthony Rogers, Will
Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Richard Durbin,
John Spieth, Lincoln D. Stein, and Paul W. Sternberg
David Sims,
Borisas Bursteinas, Qiong Gao, Marketa Zvelebil, and Buzz Baum
FLIGHT: database and tools for the integration and
cross-correlation of large-scale RNAi phenotypic datasets Nucl. Acids Res. 2006 34: D479-D483; doi:10.1093/nar/gkj038 [Abstract][FREE
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Gary Grumbling,
Victor Strelets, and The FlyBase Consortium
Ian Flockhart,
Matthew Booker, Amy Kiger, Michael Boutros, Susan Armknecht, Nadire
Ramadan, Kris Richardson, Andrew Xu, Norbert Perrimon, and Bernard
Mathey-Prevot
Nicholas A.
Stover, Cynthia J. Krieger, Gail Binkley, Qing Dong, Dianna G. Fisk,
Robert Nash, Anand Sethuraman, Shuai Weng, and J. Michael Cherry
Tetrahymena Genome Database (TGD): a new genomic
resource for Tetrahymena thermophila research Nucl.
Acids Res. 2006 34: D500-D503; doi:10.1093/nar/gkj054 [Abstract][FREE
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Ron Caspi,
Hartmut Foerster, Carol A. Fulcher, Rebecca Hopkinson, John Ingraham,
Pallavi Kaipa, Markus Krummenacker, Suzanne Paley, John Pick, Seung Y.
Rhee, Christophe Tissier, Peifen Zhang, and Peter D. Karp
MetaCyc: a multiorganism database of metabolic pathways and
enzymes Nucl. Acids Res. 2006 34: D511-D516;
doi:10.1093/nar/gkj128 [Abstract][FREE
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Lynda B. M.
Ellis, Dave Roe, and Lawrence P. Wackett
The University of Minnesota Biocatalysis/Biodegradation
Database: the first decade Nucl. Acids Res. 2006 34:
D517-D521; doi:10.1093/nar/gkj076 [Abstract][FREE
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Peter Block,
Christoph A. Sotriffer, Ingo Dramburg, and Gerhard Klebe
AffinDB: a freely accessible database of affinities for
protein–ligand complexes from the PDB Nucl. Acids Res. 2006
34: D522-D526; doi:10.1093/nar/gkj039 [Abstract][FREE
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pSTIING: a ‘systems’ approach towards integrating signalling
pathways, interaction and transcriptional regulatory networks in
inflammation and cancer Nucl. Acids Res. 2006 34:
D527-D534; doi:10.1093/nar/gkj044 [Abstract][FREE
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Chris Stark,
Bobby-Joe Breitkreutz, Teresa Reguly, Lorrie Boucher, Ashton
Breitkreutz, and Mike Tyers
Mathias Krull,
Susanne Pistor, Nico Voss, Alexander Kel, Ingmar Reuter, Deborah
Kronenberg, Holger Michael, Knut Schwarzer, Anatolij Potapov, Claudia
Choi, Olga Kel-Margoulis, and Edgar Wingender
TRANSPATH®: an information resource for storing
and visualizing signaling pathways and their pathological
aberrations Nucl. Acids Res. 2006 34: D546-D551;
doi:10.1093/nar/gkj107 [Abstract][FREE
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Nicolas Sierro,
Takehiro Kusakabe, Keun-Joon Park, Riu Yamashita, Kengo Kinoshita, and
Kenta Nakai
DBTGR: a database of tunicate promoters and their regulatory
elements Nucl. Acids Res. 2006 34: D552-D555;
doi:10.1093/nar/gkj064 [Abstract][FREE
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E. Birney, D.
Andrews, M. Caccamo, Y. Chen, L. Clarke, G. Coates, T. Cox, F.
Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M.
Fernandez-Suarez, P. Flicek, S. Gräf, M. Hammond, J. Herrero, K. Howe,
V. Iyer, K. Jekosch, A. Kähäri, A. Kasprzyk, D. Keefe, F. Kokocinski, E.
Kulesha, D. London, I. Longden, C. Melsopp, P. Meidl, B. Overduin, A.
Parker, G. Proctor, A. Prlic, M. Rae, D. Rios, S. Redmond, M. Schuster,
I. Sealy, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, A.
Stabenau, J. Stalker, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White,
C. Woodwark, and T. J. P. Hubbard
Andreas Ruepp,
Octave Noubibou Doudieu, Jos van den Oever, Barbara Brauner, Irmtraud
Dunger-Kaltenbach, Gisela Fobo, Goar Frishman, Corinna Montrone,
Christine Skornia, Steffi Wanka, Thomas Rattei, Philipp Pagel, Louise
Riley, Dmitrij Frishman, Dimitrij Surmeli, Igor V. Tetko, Matthias
Oesterheld, Volker Stümpflen, and H. Werner Mewes
The Mouse Functional Genome Database (MfunGD): functional
annotation of proteins in the light of their cellular context Nucl. Acids Res. 2006 34: D568-D571; doi:10.1093/nar/gkj074 [Abstract][FREE
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Heng Li, Avril
Coghlan, Jue Ruan, Lachlan James Coin, Jean-Karim Hériché, Lara
Osmotherly, Ruiqiang Li, Tao Liu, Zhang Zhang, Lars Bolund, Gane Ka-Shu
Wong, Weimou Zheng, Paramvir Dehal, Jun Wang, and Richard Durbin
Judy Sprague,
Leyla Bayraktaroglu, Dave Clements, Tom Conlin, David Fashena, Ken
Frazer, Melissa Haendel, Douglas G. Howe, Prita Mani, Sridhar
Ramachandran, Kevin Schaper, Erik Segerdell, Peiran Song, Brock
Sprunger, Sierra Taylor, Ceri E. Van Slyke, and Monte Westerfield
The Zebrafish Information Network: the zebrafish model
organism database Nucl. Acids Res. 2006 34: D581-D585;
doi:10.1093/nar/gkj086 [Abstract][FREE
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Kremena V.
Star, Quingbin Song, Andy Zhu, and Erwin P. Böttinger
QTL MatchMaker: a multi-species quantitative trait loci
(QTL) database and query system for annotation of genes and QTL Nucl. Acids Res. 2006 34: D586-D589; doi:10.1093/nar/gkj027 [Abstract][FREE
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A. S. Hinrichs,
D. Karolchik, R. Baertsch, G. P. Barber, G. Bejerano, H. Clawson, M.
Diekhans, T. S. Furey, R. A. Harte, F. Hsu, J. Hillman-Jackson, R. M.
Kuhn, J. S. Pedersen, A. Pohl, B. J. Raney, K. R. Rosenbloom, A. Siepel,
K. E. Smith, C. W. Sugnet, A. Sultan-Qurraie, D. J. Thomas, H.
Trumbower, R. J. Weber, M. Weirauch, A. S. Zweig, D. Haussler, and W. J.
Kent
Johann Lenffer,
Frank W. Nicholas, Kao Castle, Arjun Rao, Stefan Gregory, Michael
Poidinger, Matthew D. Mailman, and Shoba Ranganathan
OMIA (Online Mendelian Inheritance in Animals): an enhanced
platform and integration into the Entrez search interface at
NCBI Nucl. Acids Res. 2006 34: D599-D601;
doi:10.1093/nar/gkj152 [Abstract][FREE
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Ghazi O.
Tadmouri, Mahmoud Taleb Al Ali, Sarah Al-Haj Ali, and Najib Al Khaja
Adil Elfilali,
Séverine Lair, Catia Verbeke, Philippe La Rosa, François Radvanyi, and
Emmanuel Barillot
ITTACA: a new database for integrated tumor transcriptome
array and clinical data analysis Nucl. Acids Res. 2006 34:
D613-D616; doi:10.1093/nar/gkj022 [Abstract][FREE
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Bernice R.
Packer, Meredith Yeager, Laura Burdett, Robert Welch, Michael Beerman,
Liqun Qi, Hugues Sicotte, Brian Staats, Mekhala Acharya, Andrew
Crenshaw, Andrew Eckert, Vinita Puri, Daniela S. Gerhard, and Stephen J.
Chanock
SNP500Cancer: a public resource for sequence validation,
assay development, and frequency analysis for genetic variation in
candidate genes Nucl. Acids Res. 2006 34: D617-D621;
doi:10.1093/nar/gkj151 [Abstract][FREE
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Tzong-Yi Lee,
Hsien-Da Huang, Jui-Hung Hung, Hsi-Yuan Huang, Yuh-Shyong Yang, and
Tzu-Hao Wang
Hideya Kawaji,
Takeya Kasukawa, Shiro Fukuda, Shintaro Katayama, Chikatoshi Kai, Jun
Kawai, Piero Carninci, and Yoshihide Hayashizaki
CAGE Basic/Analysis Databases: the CAGE resource for
comprehensive promoter analysis Nucl. Acids Res. 2006 34:
D632-D636; doi:10.1093/nar/gkj034 [Abstract][FREE
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Jeffrey H.
Christiansen, Yiya Yang, Shanmugasundaram Venkataraman, Lorna
Richardson, Peter Stevenson, Nicholas Burton, Richard A. Baldock, and
Duncan R. Davidson
Alex S. Nord,
Patricia J. Chang, Bruce R. Conklin, Antony V. Cox, Courtney A. Harper,
Geoffrey G. Hicks, Conrad C. Huang, Susan J. Johns, Michiko Kawamoto,
Songyan Liu, Elaine C. Meng, John H. Morris, Janet Rossant, Patricia
Ruiz, William C. Skarnes, Philippe Soriano, William L. Stanford, Doug
Stryke, Harald von Melchner, Wolfgang Wurst, Ken-ichi Yamamura, Stephen
G. Young, Patricia C. Babbitt, and Thomas E. Ferrin
The International Gene Trap Consortium Website: a portal to
all publicly available gene trap cell lines in mouse Nucl.
Acids Res. 2006 34: D642-D648; doi:10.1093/nar/gkj097 [Abstract][FREE
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Thomas
McLaughlin, Jennifer A. Siepen, Julian Selley, Jennifer A. Lynch, King
Wai Lau, Hujun Yin, Simon J. Gaskell, and Simon J. Hubbard
PepSeeker: a database of proteome peptide identifications
for investigating fragmentation patterns Nucl. Acids Res.
2006 34: D649-D654; doi:10.1093/nar/gkj066 [Abstract][FREE
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Frank Desiere,
Eric W. Deutsch, Nichole L. King, Alexey I. Nesvizhskii, Parag Mallick,
Jimmy Eng, Sharon Chen, James Eddes, Sandra N. Loevenich, and Ruedi
Aebersold
Philip Jones,
Richard G. Côté, Lennart Martens, Antony F. Quinn, Chris F. Taylor,
William Derache, Henning Hermjakob, and Rolf Apweiler
PRIDE: a public repository of protein and peptide
identifications for the proteomics community Nucl. Acids
Res. 2006 34: D659-D663; doi:10.1093/nar/gkj138 [Abstract][FREE
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Xiaochen Bo,
Shaoke Lou, Daochun Sun, Jing Yang, and Shengqi Wang
AOBase: a database for antisense oligonucleotides selection
and design Nucl. Acids Res. 2006 34: D664-D667;
doi:10.1093/nar/gkj065 [Abstract][FREE
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David S.
Wishart, Craig Knox, An Chi Guo, Savita Shrivastava, Murtaza Hassanali,
Paul Stothard, Zhan Chang, and Jennifer Woolsey
DrugBank: a comprehensive resource for in silico drug
discovery and exploration Nucl. Acids Res. 2006 34:
D668-D672; doi:10.1093/nar/gkj067 [Abstract][FREE
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Nicolas Le
Novère, Benjamin Bornstein, Alexander Broicher, Mélanie Courtot, Marco
Donizelli, Harish Dharuri, Lu Li, Herbert Sauro, Maria Schilstra, Bruce
Shapiro, Jacky L. Snoep, and Michael Hucka
BioModels Database: a free, centralized database of curated,
published, quantitative kinetic models of biochemical and cellular
systems Nucl. Acids Res. 2006 34: D689-D691;
doi:10.1093/nar/gkj092 [Abstract][FREE
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Liying Cui,
Narayanan Veeraraghavan, Alexander Richter, Kerr Wall, Robert K. Jansen,
Jim Leebens-Mack, Izabela Makalowska, and Claude W. dePamphilis
Pankaj Jaiswal,
Junjian Ni, Immanuel Yap, Doreen Ware, William Spooner, Ken
Youens-Clark, Liya Ren, Chengzhi Liang, Wei Zhao, Kiran Ratnapu,
Benjamin Faga, Payan Canaran, Molly Fogleman, Claire Hebbard, Shuly
Avraham, Steven Schmidt, Terry M. Casstevens, Edward S. Buckler, Lincoln
Stein, and Susan McCouch
Mayumi Nakano,
Kan Nobuta, Kalyan Vemaraju, Shivakundan Singh Tej, Jeremy W. Skogen,
and Blake C. Meyers
Plant MPSS databases: signature-based transcriptional
resources for analyses of mRNA and small RNA Nucl. Acids
Res. 2006 34: D731-D735; doi:10.1093/nar/gkj077 [Abstract][FREE
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G. Droc, M.
Ruiz, P. Larmande, A. Pereira, P. Piffanelli, J. B. Morel, A. Dievart,
B. Courtois, E. Guiderdoni, and C. Périn
mtDB: Human Mitochondrial Genome Database, a resource for
population genetics and medical sciences Nucl. Acids Res.
2006 34: D749-D751; doi:10.1093/nar/gkj010 [Abstract][FREE
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Wei Zhao, Payan
Canaran, Rebecca Jurkuta, Theresa Fulton, Jeffrey Glaubitz, Edward
Buckler, John Doebley, Brandon Gaut, Major Goodman, Jim Holland, Stephen
Kresovich, Michael McMullen, Lincoln Stein, and Doreen Ware
Panzea: a database and resource for molecular and functional
diversity in the maize genome Nucl. Acids Res. 2006 34:
D752-D757; doi:10.1093/nar/gkj011 [Abstract][FREE
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Jeffry L.
Shultz, Deepak Kurunam, Kay Shopinski, M. Javed Iqbal, Samreen Kazi,
Kimberley Zobrist, Rabia Bashir, Satsuki Yaegashi, Nagajyothi Lavu,
Ahmed J. Afzal, Charles R. Yesudas, M. Abdelmajid Kassem, Chengcang Wu,
Hong Bin Zhang, Christopher D. Town, Khalid Meksem, and David A.
Lightfoot
The Soybean Genome Database (SoyGD): a browser for display
of duplicated, polyploid, regions and sequence tagged sites on the
integrated physical and genetic maps of Glycine max Nucl. Acids Res. 2006 34: D758-D765; doi:10.1093/nar/gkj050 [Abstract][FREE
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Zhangjun Fei,
Xuemei Tang, Rob Alba, and James Giovannoni
Tomato Expression Database (TED): a suite of data
presentation and analysis tools Nucl. Acids Res. 2006 34:
D766-D770; doi:10.1093/nar/gkj110 [Abstract][FREE
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Agnes P. Chan,
Geo Pertea, Foo Cheung, Dan Lee, Li Zheng, Cathy Whitelaw, Ana C.
Pontaroli, Phillip SanMiguel, Yinan Yuan, Jeffrey Bennetzen, William
Brad Barbazuk, John Quackenbush, and Pablo D. Rabinowicz
IMGT/LIGM-DB, the IMGT® comprehensive database of
immunoglobulin and T cell receptor nucleotide sequences Nucl. Acids Res. 2006 34: D781-D784; doi:10.1093/nar/gkj088 [Abstract][FREE
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