Volume 35,
Number Database-Issue,
January 2007
All articles in this issue are published under an open access model:
Articles:
- Michael Y. Galperin:
The Molecular Biology Database Collection: 2007 update.
3-4
Electronic Edition (link) BibTeX
- 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, Yuri Kapustin, Oleg Khovayko, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Vadim Miller, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko:
Database resources of the National Center for Biotechnology Information.
5-12
Electronic Edition (link) BibTeX
- Hideaki Sugawara, Takashi Abe, Takashi Gojobori, Yoshio Tateno:
DDBJ working on evaluation and classification of bacterial genes in INSDC.
13-15
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- Tamara Kulikova, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Lawrence Bower, Paul Browne, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, Gemma Hoad, Carola Kanz, Charles Lee, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Maria Pilar Garcia Pastor, Sheila Plaister, Siamak Sobhany, Peter Stoehr, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler:
EMBL Nucleotide Sequence Database in 2006.
16-20
Electronic Edition (link) BibTeX
- Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
GenBank.
21-25
Electronic Edition (link) BibTeX
- Donna R. Maglott, James Ostell, Kim D. Pruitt, Tatiana A. Tatusova:
Entrez Gene: gene-centered information at NCBI.
26-31
Electronic Edition (link) BibTeX
- Christoph Dieterich, M. W. Franz, Martin Vingron:
Developments in CORG: a gene-centric comparative genomics resource.
32-35
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- Sunil Archak, Eshwar Meduri, P. Sravana Kumar, Javaregowda Nagaraju:
InSatDb: a microsatellite database of fully sequenced insect genomes.
36-39
Electronic Edition (link) BibTeX
- Conrad A. Nieduszynski, Shin-ichiro Hiraga, Prashanth Ak, Craig J. Benham, Anne D. Donaldson:
OriDB: a DNA replication origin database.
40-46
Electronic Edition (link) BibTeX
- Byungwook Lee, Taehyung Kim, Seon-Kyu Kim, Kwang Hyung Lee, Doheon Lee:
Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications.
47-50
Electronic Edition (link) BibTeX
- Lei Bao, Mi Zhou, Ligang Wu, Lu Lu, Dan Goldowitz, Robert W. Williams, Yan Cui:
PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits.
51-54
Electronic Edition (link) BibTeX
- John E. Karro, Yangpan Yan, Deyou Zheng, Zhaolei Zhang, Nicholas Carriero, Philip Cayting, Paul M. Harrison, Mark Gerstein:
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.
55-60
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- Kim D. Pruitt, Tatiana A. Tatusova, Donna R. Maglott:
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
61-65
Electronic Edition (link) BibTeX
- Cristian Chaparro, Romain Guyot, Andrea Zuccolo, Benoît Piégu, Olivier Panaud:
RetrOryza: a database of the rice LTR-retrotransposons.
66-70
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- I. Agrafioti, Michael P. H. Stumpf:
SNPSTR: a database of compound microsatellite-SNP markers.
71-75
Electronic Edition (link) BibTeX
- Gang Wu, Yuanpu Zheng, Imran Qureshi, Htar Thant Zin, Tyler Beck, Blazej Bulka, Stephen J. Freeland:
SGDB: a database of synthetic genes re-designed for optimizing protein over-expression.
76-79
Electronic Edition (link) BibTeX
- Yevgeniy Gelfand, Alfredo Rodriguez, Gary Benson:
TRDB - The Tandem Repeats Database.
80-87
Electronic Edition (link) BibTeX
- Axel Visel, Simon Minovitsky, Inna Dubchak, Len A. Pennacchio:
VISTA Enhancer Browser - a database of tissue-specific human enhancers.
88-92
Electronic Edition (link) BibTeX
- Namshin Kim, Alexander V. Alekseyenko, Meenakshi Roy, Christopher Lee:
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.
93-98
Electronic Edition (link) BibTeX
- Yeunsook Lee, Younghee Lee, Bumjin Kim, Youngah Shin, Seungyoon Nam, Pora Kim, Namshin Kim, Won-Hyong Chung, Jaesang Kim, Sanghyuk Lee:
ECgene: an alternative splicing database update.
99-103
Electronic Edition (link) BibTeX
- Jun-ichi Takeda, Yutaka Suzuki, Mitsuteru Nakao, Tsuyoshi Kuroda, Sumio Sugano, Takashi Gojobori, Tadashi Imanishi:
H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational.
104-109
Electronic Edition (link) BibTeX
- Tyler S. Alioto:
U12DB: a database of orthologous U12-type spliceosomal introns.
110-115
Electronic Edition (link) BibTeX
- Anil G. Jegga, Jing Chen, Sivakumar Gowrisankar, Mrunal A. Deshmukh, Ranga Chandra Gudivada, Sue Kong, Vivek Kaimal, Bruce J. Aronow:
GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.
116-121
Electronic Edition (link) BibTeX
- Vincent Ferretti, Christian Poitras, Dominique Bergeron, Benoit Coulombe, François Robert, Mathieu Blanchette:
PReMod: a database of genome-wide mammalian cis-regulatory module predictions.
122-126
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- Mikhail Pachkov, Ionas Erb, Nacho Molina, Erik van Nimwegen:
SwissRegulon: a database of genome-wide annotations of regulatory sites.
127-131
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- Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza R. Vasconcelos, Julio Collado-Vides:
Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes.
132-136
Electronic Edition (link) BibTeX
- C. Jiang, Z. Xuan, F. Zhao, M. Q. Zhang:
TRED: a transcriptional regulatory element database, new entries and other development.
137-140
Electronic Edition (link) BibTeX
- Tao He, Pufeng Du, Yanda Li:
dbRES: a web-oriented database for annotated RNA editing sites.
141-144
Electronic Edition (link) BibTeX
- Taishin Kin, Kouichirou Yamada, Goro Terai, Hiroaki Okida, Yasuhiko Yoshinari, Yukiteru Ono, Aya Kojima, Yuki Kimura, Takashi Komori, Kiyoshi Asai:
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences.
145-148
Electronic Edition (link) BibTeX
- Molly Megraw, Praveen Sethupathy, Benoit Corda, Artemis G. Hatzigeorgiou:
miRGen: a database for the study of animal microRNA genomic organization and function.
149-155
Electronic Edition (link) BibTeX
- Yong Zhang, Jiongtang Li, Lei Kong, Ge Gao, Qing-Rong Liu, Liping Wei:
NATsDB: Natural Antisense Transcripts DataBase.
156-161
Electronic Edition (link) BibTeX
- Maciej Szymanski, Volker A. Erdmann, Jan Barciszewski:
Noncoding RNAs database (ncRNAdb).
162-164
Electronic Edition (link) BibTeX
- Ju Youn Lee, Ijen Yeh, Ji Yeon Park, Bin Tian:
PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.
165-168
Electronic Edition (link) BibTeX
- James R. Cole, B. Chai, Ryan J. Farris, Q. Wang, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, A. M. Bandela, E. Cardenas, George M. Garrity, James M. Tiedje:
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data.
169-172
Electronic Edition (link) BibTeX
- Ernesto Picardi, Teresa Maria Rosaria Regina, Axel Brennicke, Carla Quagliariello:
REDIdb: the RNA editing database.
173-177
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- Ken C. Pang, Stuart Stephen, Marcel E. Dinger, Pär G. Engström, Boris Lenhard, John S. Mattick:
RNAdb 2.0 - an expanded database of mammalian non-coding RNAs.
178-182
Electronic Edition (link) BibTeX
- Jun Xie, Ming Zhang, Tao Zhou, Xia Hua, LiSha Tang, Weilin Wu:
Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs.
183-187
Electronic Edition (link) BibTeX
- Michael Hiller, Swetlana Nikolajewa, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schuster, Rolf Backofen, Matthias Platzer:
TassDB: a database of alternative tandem splice sites.
188-192
Electronic Edition (link) BibTeX
- The Universal Protein Resource (UniProt).
193-197
Electronic Edition (link) BibTeX
- Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N. Jorissen, Michael K. Gilson:
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities.
198-201
Electronic Edition (link) BibTeX
- Di Wu, Feng Cui, Robert L. Jernigan, Zhijun Wu:
PIDD: database for Protein Inter-atomic Distance Distributions.
202-207
Electronic Edition (link) BibTeX
- Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
eSLDB: eukaryotic subcellular localization database.
208-212
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- Joshua L. Heazlewood, Robert E. Verboom, Julian Tonti-Filippini, Ian Small, A. Harvey Millar:
SUBA: the Arabidopsis Subcellular Database.
213-218
Electronic Edition (link) BibTeX
- Gonzalo López, Alfonso Valencia, Michael L. Tress:
FireDB - a database of functionally important residues from proteins of known structure.
219-223
Electronic Edition (link) BibTeX
- Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Virginie Buillard, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Louise Daugherty, Mark Dibley, Robert D. Finn, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicolas Hulo, Sarah Hunter, Daniel Kahn, Alexander Kanapin, Anish Kejariwal, Alberto Labarga, Petra S. Langendijk-Genevaux, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Christine A. Orengo, Robert Petryszak, Jeremy D. Selengut, Christian J. A. Sigrist, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, Corin Yeats:
New developments in the InterPro database.
224-228
Electronic Edition (link) BibTeX
- Andreas Zanzoni, Gabriele Ausiello, Allegra Via, Pier Federico Gherardini, Manuela Helmer-Citterich:
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites.
229-231
Electronic Edition (link) BibTeX
- Paolo Sonego, Mircea Pacurar, Somdutta Dhir, Attila Kertész-Farkas, András Kocsor, Zoltán Gáspári, Jack A. M. Leunissen, Sándor Pongor:
A Protein Classification Benchmark collection for machine learning.
232-236
Electronic Edition (link) BibTeX
- Aron Marchler-Bauer, John B. Anderson, Myra K. Derbyshire, Carol DeWeese-Scott, Noreen R. Gonzales, Marc Gwadz, Luning Hao, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Dmitri M. Krylov, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Shennan Lu, Gabriele H. Marchler, Mikhail Mullokandov, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Jodie J. Yin, Dachuan Zhang, Stephen H. Bryant:
CDD: a conserved domain database for interactive domain family analysis.
237-240
Electronic Edition (link) BibTeX
- Elon Portugaly, Nathan Linial, Michal Linial:
EVEREST: a collection of evolutionary conserved protein domains.
241-246
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- Huaiyu Mi, Nan Guo, Anish Kejariwal, Paul D. Thomas:
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways.
247-252
Electronic Edition (link) BibTeX
- Antonina Andreeva, Andreas Prlic, Tim J. P. Hubbard, Alexey G. Murzin:
SISYPHUS - structural alignments for proteins with non-trivial relationships.
253-259
Electronic Edition (link) BibTeX
- Jeremy D. Selengut, Daniel H. Haft, Tanja Davidsen, Anurhada Ganapathy, Michelle Gwinn-Giglio, William C. Nelson, Alexander R. Richter, Owen White:
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes.
260-264
Electronic Edition (link) BibTeX
- Shalin Seebah, Anita Suresh, Shaowei Zhuo, Yong How Choong, Hazel Chua, Danny Chuon, Roger Beuerman, Chandra Verma:
Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides.
265-268
Electronic Edition (link) BibTeX
- Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis:
REBASE - enzymes and genes for DNA restriction and modification.
269-270
Electronic Edition (link) BibTeX
- Mark D'Souza, Elizabeth M. Glass, Mustafa H. Syed, Yi Zhang, Alexis A. Rodriguez, Natalia Maltsev, Michael Y. Galperin:
Sentra: a database of signal transduction proteins for comparative genome analysis.
271-273
Electronic Edition (link) BibTeX
- Qinghu Ren, Kaixi Chen, Ian T. Paulsen:
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels.
274-279
Electronic Edition (link) BibTeX
- Philip Toukach, Hiren J. Joshi, René Ranzinger, Yuri Knirel, Claus-Wilhelm von der Lieth:
Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de.
280-286
Electronic Edition (link) BibTeX
- M. Frank, T. Lütteke, C.-W. von der Lieth:
GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages.
287-290
Electronic Edition (link) BibTeX
- Lesley H. Greene, Tony E. Lewis, Sarah Addou, Alison Cuff, Timothy Dallman, Mark Dibley, Oliver Redfern, Frances M. G. Pearl, Rekha Nambudiry, Adam Reid, Ian Sillitoe, Corin Yeats, Janet M. Thornton, Christine A. Orengo:
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.
291-297
Electronic Edition (link) BibTeX
- Yanli Wang, Kenneth J. Addess, Jie Chen, Lewis Y. Geer, Jane He, Siqian He, Shennan Lu, Thomas Madej, Aron Marchler-Bauer, Paul A. Thiessen, Naigong Zhang, Stephen H. Bryant:
MMDB: annotating protein sequences with Entrez's 3D-structure database.
298-300
Electronic Edition (link) BibTeX
- Helen M. Berman, Kim Henrick, Haruki Nakamura, John L. Markley:
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.
301-303
Electronic Edition (link) BibTeX
- Kate F. Fulton, Mark A. Bate, Noel G. Faux, Khalid Mahmood, Chris Betts, Ashley M. Buckle:
Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium.
304-307
Electronic Edition (link) BibTeX
- Derek Wilson, Martin Madera, Christine Vogel, Cyrus Chothia, Julian Gough:
The SUPERFAMILY database in 2007: families and functions.
308-313
Electronic Edition (link) BibTeX
- M. Michael Gromiha, Yukimitsu Yabuki, Srinesh Kundu, Sivasundaram Suharnan, Makiko Suwa:
TMBETA-GENOME: database for annotated ß-barrel membrane proteins in genomic sequences.
314-316
Electronic Edition (link) BibTeX
- Chesley M. Leslin, Alexej Abyzov, Valentin A. Ilyin:
TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method.
317-321
Electronic Edition (link) BibTeX
- Gil Alterovitz, Michael Xiang, Mamta Mohan, Marco Ramoni:
GO PaD: the Gene Ontology Partition Database.
322-327
Electronic Edition (link) BibTeX
- Yuying Tian, Allan W. Dickerman:
GeneTrees: a phylogenomics resource for prokaryotes.
328-331
Electronic Edition (link) BibTeX
- T. Ryan Gregory, James A. Nicol, Heidi Tamm, Bellis Kullman, Kaur Kullman, Ilia J. Leitch, Brian G. Murray, Donald F. Kapraun, Johann Greilhuber, Michael D. Bennett:
Eukaryotic genome size databases.
332-338
Electronic Edition (link) BibTeX
- Masaki Hirahata, Takashi Abe, Naoto Tanaka, Yoshikazu Kuwana, Yasumasa Shigemoto, Satoru Miyazaki, Yoshiyuki Suzuki, Hideaki Sugawara:
Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes.
339-342
Electronic Edition (link) BibTeX
- Ikuo Uchiyama:
MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups.
343-346
Electronic Edition (link) BibTeX
- Leslie Klis McNeil, Claudia Reich, Ramy K. Aziz, Daniela Bartels, Matthew Cohoon, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Kaitlyn Hwang, Michael Kubal, Gohar Rem Margaryan, Folker Meyer, William Mihalo, Gary J. Olsen, Robert Olson, Andrei Osterman, Daniel Paarmann, Tobias Paczian, Bruce D. Parrello, Gordon D. Pusch, Dmitry A. Rodionov, Xinghua Shi, Olga Vassieva, Veronika Vonstein, Olga Zagnitko, Fangfang Xia, Jenifer Zinner, Ross A. Overbeek, Rick Stevens:
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.
347-353
Electronic Edition (link) BibTeX
- M. Louise Riley, Thorsten Schmidt, Irena I. Artamonova, Christian Wagner, Andreas Volz, Klaus Heumann, Hans-Werner Mewes, Dmitrij Frishman:
PEDANT genome database: 10 years online.
354-357
Electronic Edition (link) BibTeX
- Christian von Mering, Lars Juhl Jensen, Michael Kuhn, Samuel Chaffron, Tobias Doerks, Beate Krüger, Berend Snel, Peer Bork:
STRING 7 - recent developments in the integration and prediction of protein interactions.
358-362
Electronic Edition (link) BibTeX
- Christophe Combet, Nicolas Garnier, Céline Charavay, Delphine Grando, Daniel Crisan, Julien Lopez, Alexandre Dehne-Garcia, Christophe Geourjon, Emmanuel Bettler, Chantal Hulo, Philippe Le Mercier, Ralf Bartenschlager, Helmut Diepolder, Darius Moradpour, Jean-Michel Pawlotsky, Charles M. Rice, Christian Trépo, François Penin, Gilbert Deléage:
euHCVdb: the European hepatitis C virus database.
363-366
Electronic Edition (link) BibTeX
- Saravanamuttu Gnaneshan, Samreen Ijaz, Joanne Moran, Mary Ramsay, Jonathan Green:
HepSEQ: International Public Health Repository for Hepatitis B.
367-370
Electronic Edition (link) BibTeX
- Calvin Pan, Joseph Kim, Lamei Chen, Qi Wang, Christopher Lee:
The HIV positive selection mutation database.
371-375
Electronic Edition (link) BibTeX
- Suhua Chang, Jiajie Zhang, Xiaoyun Liao, Xinxing Zhu, Dahai Wang, Jiang Zhu, Tao Feng, Baoli Zhu, George F. Gao, Jian Wang, Huanming Yang, Jun Yu, Jing Wang:
Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research.
376-380
Electronic Edition (link) BibTeX
- Paul Wei-Che Hsu, Li-Zen Lin, Sheng-Da Hsu, Justin Bo-Kai Hsu, Hsien-Da Huang:
ViTa: prediction of host microRNAs targets on viruses.
381-385
Electronic Edition (link) BibTeX
- Luke E. Ulrich, Igor B. Zhulin:
MiST: a microbial signal transduction database.
386-390
Electronic Edition (link) BibTeX
- Carol Ecale Zhou, Jason Smith, Marisa Lam, Adam Zemla, M. D. Dyer, Tom Slezak:
MvirDB - a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications.
391-394
Electronic Edition (link) BibTeX
- Sung Ho Yoon, Young-Kyu Park, Soohyun Lee, Doil Choi, Tae Kwang Oh, Cheol-Goo Hur, Jihyun F. Kim:
Towards pathogenomics: a web-based resource for pathogenicity islands.
395-400
Electronic Edition (link) BibTeX
- E. E. Snyder, N. Kampanya, J. Lu, Eric K. Nordberg, H. R. Karur, M. Shukla, Jeetendra Soneja, Y. Tian, Tian Xue, H. Yoo, F. Zhang, C. Dharmanolla, N. V. Dongre, J. J. Gillespie, J. Hamelius, M. Hance, K. I. Huntington, D. Jukneliene, J. Koziski, L. Mackasmiel, S. P. Mane, V. Nguyen, A. Purkayastha, J. Shallom, G. Yu, Y. Guo, J. Gabbard, D. Hix, A. F. Azad, S. C. Baker, S. M. Boyle, Y. Khudyakov, X. J. Meng, C. Rupprecht, J. Vinje, Oswald Crasta, M. J. Czar, Allan Dickerman, J. Dana Eckart, Ron Kenyon, Rebecca Will, J. C. Setubal, Bruno W. S. Sobral:
PATRIC: The VBI PathoSystems Resource Integration Center.
401-406
Electronic Edition (link) BibTeX
- Alexei E. Kazakov, Michael J. Cipriano, Pavel S. Novichkov, Simon Minovitsky, Dmitry V. Vinogradov, Adam Arkin, Andrey A. Mironov, Mikhail S. Gelfand, Inna Dubchak:
RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes.
407-412
Electronic Edition (link) BibTeX
- Kim Brügger:
The Sulfolobus database.
413-415
Electronic Edition (link) BibTeX
- Chia-Hung Chang, Yu-Chung Chang, Anthony Underwood, Chien-Shun Chiou, Cheng-Yan Kao:
VNTRDB: a bacterial variable number tandem repeat locus database.
416-421
Electronic Edition (link) BibTeX
- Bradley I. Arshinoff, Garret Suen, Eric M. Just, Sohel M. Merchant, Warren A. Kibbe, Rex L. Chisholm, Roy D. Welch:
Xanthusbase: adapting wikipedia principles to a model organism database.
422-426
Electronic Edition (link) BibTeX
- Cristina Aurrecoechea, Mark Heiges, Haiming Wang, Zhiming Wang, Steve Fischer, Philippa Rhodes, John A. Miller, Eileen Kraemer, Christian J. Stoeckert Jr., David S. Roos, Jessica C. Kissinger:
ApiDB: integrated resources for the apicomplexan bioinformatics resource center.
427-430
Electronic Edition (link) BibTeX
- Junichi Watanabe, Hiroyuki Wakaguri, Masahide Sasaki, Yutaka Suzuki, Sumio Sugano:
Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs.
431-438
Electronic Edition (link) BibTeX
- Olivier Arnaiz, Scott Cain, Jean Cohen, Linda Sperling:
ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data.
439-444
Electronic Edition (link) BibTeX
- Emmet A. O'Brien, Liisa B. Koski, Yue Zhang, LiuSong Yang, Eric Wang, Michael W. Gray, Gertraud Burger, B. Franz Lang:
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs).
445-451
Electronic Edition (link) BibTeX
- Martha B. Arnaud, Maria C. Costanzo, Marek S. Skrzypek, Prachi Shah, Gail Binkley, Christopher Lane, Stuart R. Miyasato, Gavin Sherlock:
Sequence resources at the Candida Genome Database.
452-456
Electronic Edition (link) BibTeX
- Alexandre Gattiker, Christa Niederhauser-Wiederkehr, James Moore, Leandro Hermida, Michael Primig:
The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction.
457-462
Electronic Edition (link) BibTeX
- Luciano Fernandez-Ricaud, Jonas Warringer, Elke Ericson, Kerstin Glaab, Pär Davidsson, Fabian Nilsson, Graham J. L. Kemp, Olle Nerman, Anders Blomberg:
PROPHECY - a yeast phenome database, update 2006.
463-467
Electronic Edition (link) BibTeX
- Robert S. Nash, Shuai Weng, Benjamin C. Hitz, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Michael S. Livstone, Rose Oughtred, Julie Park, Marek S. Skrzypek, Chandra L. Theesfeld, Gail Binkley, Qing Dong, Christopher Lane, Stuart R. Miyasato, Anand Sethuraman, Mark Schroeder, Kara Dolinski, David Botstein, J. Michael Cherry:
Expanded protein information at SGD: new pages and proteome browser.
468-471
Electronic Edition (link) BibTeX
- Lisa R. Girard, Tristan J. Fiedler, Todd W. Harris, Felicia Carvalho, Igor Antoshechkin, Michael Han, Paul W. Sternberg, Lincoln D. Stein, Martin Chalfie:
WormBook: the online review of Caenorhabditis elegans biology.
472-475
Electronic Edition (link) BibTeX
- Liangjiang Wang, Suzhi Wang, Yonghua Li, Martin S. R. Paradesi, Susan J. Brown:
BeetleBase: the model organism database for Tribolium castaneum.
476-479
Electronic Edition (link) BibTeX
- Donald G. Gilbert:
DroSpeGe: rapid access database for new Drosophila species genomes.
480-485
Electronic Edition (link) BibTeX
- Madeline A. Crosby, Joshua L. Goodman, Victor B. Strelets, Peili Zhang, William M. Gelbart:
FlyBase: genomes by the dozen.
486-491
Electronic Edition (link) BibTeX
- Thomas Horn, Zeynep Arziman, Juerg Berger, Michael Boutros:
GenomeRNAi: a database for cell-based RNAi phenotypes.
492-497
Electronic Edition (link) BibTeX
- Christoph Dieterich, Waltraud Roeseler, Patrick Sobetzko, Ralf J. Sommer:
Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus.
498-502
Electronic Edition (link) BibTeX
- Daniel Lawson, Peter Arensburger, Peter Atkinson, Nora J. Besansky, Robert V. Bruggner, Ryan Butler, Kathryn S. Campbell, George K. Christophides, Scott Christley, Emmanuel Dialynas, David Emmert, Martin Hammond, Catherine A. Hill, Ryan C. Kennedy, Neil F. Lobo, M. Robert MacCallum, Gregory R. Madey, Karine Megy, Seth Redmond, Susan Russo, David W. Severson, Eric O. Stinson, Pantelis Topalis, Evgeni M. Zdobnov, Ewan Birney, William M. Gelbart, Fotis C. Kafatos, Christos Louis, Frank H. Collins:
VectorBase: a home for invertebrate vectors of human pathogens.
503-505
Electronic Edition (link) BibTeX
- Tamberlyn Bieri, Darin Blasiar, Philip Ozersky, Igor Antoshechkin, Carol Bastiani, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J. Chen, Paul Davis, Tristan J. Fiedler, Lisa R. Girard, Michael Han, Todd W. Harris, Ranjana Kishore, Raymond Lee, Sheldon McKay, Hans-Michael Müller, Cecilia Nakamura, Andrei Petcherski, Arun Rangarajan, Anthony Rogers, Gary Schindelman, Erich M. Schwarz, William Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Richard Durbin, Lincoln D. Stein, Paul W. Sternberg, John Spieth:
WormBase: new content and better access.
506-510
Electronic Edition (link) BibTeX
- Jens Barthelmes, Christian Ebeling, Antje Chang, Ida Schomburg, Dietmar Schomburg:
BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.
511-514
Electronic Edition (link) BibTeX
- Gemma L. Holliday, Daniel E. Almonacid, Gail J. Bartlett, Noel M. O'Boyle, James W. Torrance, Peter Murray-Rust, John B. O. Mitchell, Janet M. Thornton:
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.
515-520
Electronic Edition (link) BibTeX
- David S. Wishart, Dan Tzur, Craig Knox, Roman Eisner, Anchi Guo, Nelson Young, Dean Cheng, Kevin Jewell, David Arndt, Summit Sawhney, Chris Fung, Lisa Nikolai, Mike Lewis, Marie-Aude Coutouly, Ian J. Forsythe, Peter Tang, Savita Shrivastava, Kevin Jeroncic, Paul Stothard, Godwin Amegbey, David Block, David. D. Hau, James Wagner, Jessica Miniaci, Melisa Clements, Mulu Gebremedhin, Natalie Guo, Ying Zhang, Gavin E. Duggan, Glen D. MacInnis, Alim M. Weljie, Reza Dowlatabadi, Fiona Bamforth, Derrick Clive, Russell Greiner, Liang Li, Tom Marrie, Brian D. Sykes, Hans J. Vogel, Lori Querengesser:
HMDB: the Human Metabolome Database.
521-526
Electronic Edition (link) BibTeX
- Manish Sud, Eoin Fahy, Dawn Cotter, Alex Brown, Edward A. Dennis, Christopher K. Glass, Alfred H. Merrill Jr., Robert C. Murphy, Christian R. H. Raetz, David W. Russell, Shankar Subramaniam:
LMSD: LIPID MAPS structure database.
527-532
Electronic Edition (link) BibTeX
- Claudia Choi, Richard Münch, Stefan Leupold, Johannes Klein, Inga Siegel, Bernhard Thielen, Beatrice Benkert, Martin Kucklick, Max Schobert, Jens Barthelmes, Christian Ebeling, Isam Haddad, Maurice Scheer, Andreas Grote, Karsten Hiller, Boyke Bunk, Kerstin Schreiber, Ida Retter, Dietmar Schomburg, Dieter Jahn:
SYSTOMONAS - an integrated database for systems biology analysis of Pseudomonas.
533-537
Electronic Edition (link) BibTeX
- H. Craig Mak, Mike Daly, Bianca Gruebel, Trey Ideker:
CellCircuits: a database of protein network models.
538-545
Electronic Edition (link) BibTeX
- Yoshinobu Igarashi, Alexey M. Eroshkin, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Jeffrey W. Smith, Andrei Osterman, Adam Godzik:
CutDB: a proteolytic event database.
546-549
Electronic Edition (link) BibTeX
- Fedor Kolpakov, Vladimir Poroikov, Ruslan N. Sharipov, Yury Kondrakhin, Alexey Zakharov, Alexey Lagunin, Luciano Milanesi, Alexander E. Kel:
CYCLONET - an integrated database on cell cycle regulation and carcinogenesis.
550-556
Electronic Edition (link) BibTeX
- Arnaud Ceol, Andrew Chatr-aryamontri, Elena Santonico, Roberto Sacco, Luisa Castagnoli, Gianni Cesareni:
DOMINO: a database of domain-peptide interactions.
557-560
Electronic Edition (link) BibTeX
- Samuel Kerrien, Y. Alam-Faruque, B. Aranda, I. Bancarz, A. Bridge, C. Derow, Emily Dimmer, M. Feuermann, A. Friedrichsen, R. Huntley, C. Kohler, J. Khadake, C. Leroy, A. Liban, C. Lieftink, Luisa Montecchi-Palazzi, Sandra E. Orchard, J. Risse, K. Robbe, Bernd Roechert, David Thorneycroft, Y. Zhang, Rolf Apweiler, Henning Hermjakob:
IntAct - open source resource for molecular interaction data.
561-565
Electronic Edition (link) BibTeX
- Magesh Jayapandian, Adriane Chapman, V. Glenn Tarcea, Cong Yu, Aaron Elkiss, Angela Ianni, Bin Liu, Arnab Nandi, Carlos Santos, Philip Andrews, Brian Athey, David J. States, H. V. Jagadish:
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together.
566-571
Electronic Edition (link) BibTeX
- Andrew Chatr-aryamontri, Arnaud Ceol, Luisa Montecchi-Palazzi, Giuliano Nardelli, Maria Victoria Schneider, Luisa Castagnoli, Gianni Cesareni:
MINT: the Molecular INTeraction database.
572-574
Electronic Edition (link) BibTeX
- Petras J. Kundrotas, Emil Alexov:
PROTCOM: searchable database of protein complexes enhanced with domain-domain structures.
575-579
Electronic Edition (link) BibTeX
- Emily R. Jefferson, Thomas P. Walsh, Timothy J. Roberts, Geoffrey J. Barton:
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions.
580-589
Electronic Edition (link) BibTeX
- Gautam Chaurasia, Yasir Iqbal, Christian Hänig, Hanspeter Herzel, Erich E. Wanker, Matthias E. Futschik:
UniHI: an entry gate to the human protein interactome.
590-594
Electronic Edition (link) BibTeX
- Kieran Hervold, Andrew Martin, Roger A. Kirkpatrick, Paul F. Mc Kenna, F. A. Ramirez-Weber:
Hedgehog Signaling Pathway Database: a repository of current annotation efforts and resources for the Hh research community.
595-598
Electronic Edition (link) BibTeX
- Fiona M. McCarthy, Susan M. Bridges, Nan Wang, G. Bryce Magee, W. Paul Williams, Dawn S. Luthe, Shane C. Burgess:
AgBase: a unified resource for functional analysis in agriculture.
599-603
Electronic Edition (link) BibTeX
- Zhi-Liang Hu, Eric Ryan Fritz, James M. Reecy:
AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond.
604-609
Electronic Edition (link) BibTeX
- Tim J. P. Hubbard, B. L. Aken, K. Beal, B. Ballester, Mario Cáccamo, Yuan Chen, Laura Clarke, G. Coates, Fiona Cunningham, Tim Cutts, Thomas Down, S. C. Dyer, S. Fitzgerald, J. Fernandez-Banet, Stefan Gräf, S. Haider, Martin Hammond, J. Herrero, Richard C. G. Holland, Kevin L. Howe, K. Howe, N. Johnson, Andreas Kähäri, Damian Keefe, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, I. Longden, Craig Melsopp, Karine Megy, Patrick Meidl, B. Ouverdin, A. Parker, Andreas Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, J. Severin, Guy Slater, Damian Smedley, G. Spudich, S. Trevanion, Albert J. Vilella, J. Vogel, S. White, M. Wood, Tony Cox, Val Curwen, Richard Durbin, X. M. Fernandez-Suarez, Paul Flicek, Arek Kasprzyk, Glenn Proctor, Stephen M. J. Searle, James Smith, Abel Ureta-Vidal, Ewan Birney:
Ensembl 2007.
610-617
Electronic Edition (link) BibTeX
- Constance M. Smith, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Martin Ringwald:
The mouse Gene Expression Database (GXD): 2007 update.
618-623
Electronic Edition (link) BibTeX
- Raquel Egea, Sònia Casillas, Enol Fernández, Miquel Àngel Senar, Antonio Barbadilla:
MamPol: a database of nucleotide polymorphism in the Mammalia class.
624-629
Electronic Edition (link) BibTeX
- Janan T. Eppig, Judith A. Blake, Carol J. Bult, James A. Kadin, Joel E. Richardson:
The mouse genome database (MGD): new features facilitating a model system.
630-637
Electronic Edition (link) BibTeX
- Dale A. Begley, Debra M. Krupke, Matthew J. Vincent, John P. Sundberg, Carol J. Bult, Janan T. Eppig:
Mouse Tumor Biology Database (MTB): status update and future directions.
638-642
Electronic Edition (link) BibTeX
- Molly A. Bogue, Stephen C. Grubb, Terry P. Maddatu, Carol J. Bult:
Mouse Phenome Database (MPD).
643-649
Electronic Edition (link) BibTeX
- Hirohide Uenishi, Tomoko Eguchi-Ogawa, Hiroki Shinkai, Naohiko Okumura, Kohei Suzuki, Daisuke Toki, Noriyuki Hamasima, Takashi Awata:
PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences.
650-653
Electronic Edition (link) BibTeX
- Jue Ruan, Yiran Guo, Heng Li, Yafeng Hu, Fei Song, Xin Huang, Karsten Kristiansen, Lars Bolund, Jun Wang:
PigGIS: Pig Genomic Informatics System.
654-657
Electronic Edition (link) BibTeX
- Simon N. Twigger, Mary Shimoyama, Susan Bromberg, Anne E. Kwitek, Howard J. Jacob:
The Rat Genome Database, update 2007 - Easing the path from disease to data and back again.
658-662
Electronic Edition (link) BibTeX
- Daryl J. Thomas, Kate R. Rosenbloom, Hiram Clawson, Angie S. Hinrichs, Heather Trumbower, Brian J. Raney, Donna Karolchik, Galt P. Barber, Rachel A. Harte, Jennifer Hillman-Jackson, Robert M. Kuhn, Brooke L. Rhead, Kayla E. Smith, Archana Thakkapallayil, Ann S. Zweig, David Haussler, W. James Kent:
The ENCODE Project at UC Santa Cruz.
663-667
Electronic Edition (link) BibTeX
- Robert M. Kuhn, Donna Karolchik, Ann S. Zweig, Heather Trumbower, Daryl J. Thomas, Archana Thakkapallayil, Charles W. Sugnet, Mario Stanke, Kayla E. Smith, Adam C. Siepel, Kate R. Rosenbloom, Brooke L. Rhead, Brian J. Raney, Andy Pohl, J. S. Pedersen, Fan Hsu, Angela S. Hinrichs, Rachel A. Harte, Mark Diekhans, Hiram Clawson, Gill Bejerano, Galt P. Barber, Robert Baertsch, David Haussler, W. James Kent:
The UCSC genome browser database: update 2007.
668-673
Electronic Edition (link) BibTeX
- Alecksandr Kutchma, Nayeem Quayum, Jan Jensen:
GeneSpeed: protein domain organization of the transcriptome.
674-679
Electronic Edition (link) BibTeX
- Dongmei Zuo, Stephanie E. Mohr, Yanhui Hu, Elena Taycher, Andreas Rolfs, Jason Kramer, Janice Williamson, Joshua LaBaer:
PlasmID: a centralized repository for plasmid clone information and distribution.
680-684
Electronic Edition (link) BibTeX
- Koichiro Higasa, Katsuyuki Miyatake, Yoji Kukita, Tomoko Tahira, Kenshi Hayashi:
D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples.
685-689
Electronic Edition (link) BibTeX
- Sjozef van Baal, Polynikis Kaimakis, Manyphong Phommarinh, Daphne Koumbi, Harry Cuppens, Francesca Riccardino, Milan Macek Jr., Charles R. Scriver, George P. Patrinos:
FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide.
690-695
Electronic Edition (link) BibTeX
- Philip Groth, Nadia Pavlova, Ivan Kalev, Spas Tonov, Georgi Georgiev, Hans-Dieter Pohlenz, Bertram Weiss:
PhenomicDB: a new cross-species genotype/phenotype resource.
696-699
Electronic Edition (link) BibTeX
- Anil G. Jegga, Sivakumar Gowrisankar, Jing Chen, Bruce J. Aronow:
PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease.
700-706
Electronic Edition (link) BibTeX
- Shengting Li, Lijia Ma, Heng Li, Søren Vang, Yafeng Hu, Lars Bolund, Jun Wang:
Snap: an integrated SNP annotation platform.
707-710
Electronic Edition (link) BibTeX
- Jungsun Park, Sohyun Hwang, Yong Seok Lee, Sang-Cheol Kim, Doheon Lee:
SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms.
711-715
Electronic Edition (link) BibTeX
- Daryl J. Thomas, Heather Trumbower, Andrew D. Kern, Brooke L. Rhead, Robert M. Kuhn, David Haussler, W. James Kent:
Variation resources at UC Santa Cruz.
716-720
Electronic Edition (link) BibTeX
- Maureen E. Higgins, Martine Claremont, John E. Major, Chris Sander, Alex E. Lash:
CancerGenes: a gene selection resource for cancer genome projects.
721-726
Electronic Edition (link) BibTeX
- Wen-Hui Su, Chuan-Chuan Chao, Shiou-Hwei Yeh, Ding-Shinn Chen, Pei-Jer Chen, Yuh-Shan Jou:
OncoDB.HCC: an integrated oncogenomic database of hepatocellular carcinoma revealed aberrant cancer target genes and loci.
727-731
Electronic Edition (link) BibTeX
- Suisheng Tang, Zhuo Zhang, Sin Lam Tan, Man-Hung Eric Tang, Arun Prashanth Kumar, Suresh Kumar Ramadoss, Vladimir B. Bajic:
KBERG: KnowledgeBase for Estrogen Responsive Genes.
732-736
Electronic Edition (link) BibTeX
- Wuxue Zhang, Yong Zhang, Hui Zheng, Chen Zhang, Wei Xiong, John G. Olyarchuk, Michael Walker, Weifeng Xu, Min Zhao, Shuqi Zhao, Zhuan Zhou, Liping Wei:
SynDB: a Synapse protein DataBase based on synapse ontology.
737-741
Electronic Edition (link) BibTeX
- Erin M. Hulbert, Luc J. Smink, Ellen C. Adlem, James E. Allen, David B. Burdick, Oliver S. Burren, Christopher C. Cavnor, Geoffrey E. Dolman, Daisy Flamez, Karen F. Friery, Barry C. Healy, Sarah A. Killcoyne, Burak Kutlu, Helen Schuilenburg, Neil M. Walker, Josyf Mychaleckyj, Decio L. Eizirik, Linda S. Wicker, John A. Todd, Nathan Goodman:
T1DBase: integration and presentation of complex data for type 1 diabetes research.
742-746
Electronic Edition (link) BibTeX
- Helen E. Parkinson, Misha Kapushesky, Mohammadreza Shojatalab, Niran Abeygunawardena, R. Coulson, Anna Farne, Ele Holloway, N. Kolesnykov, P. Lilja, M. Lukk, R. Mani, Tim Rayner, Anjan Sharma, E. William, Ugis Sarkans, Alvis Brazma:
ArrayExpress - a public database of microarray experiments and gene expression profiles.
747-750
Electronic Edition (link) BibTeX
- Joan M. Mazzarelli, John Brestelli, Regina K. Gorski, Junmin Liu, Elisabetta Manduchi, Deborah F. Pinney, Jonathan Schug, Peter White, Klaus H. Kaestner, Christian J. Stoeckert Jr.:
EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes.
751-755
Electronic Edition (link) BibTeX
- Fei Pan, Chi-Hsien Chiu, Sudip Pulapura, Michael R. Mehan, Juan Nunez-Iglesias, Kangyu Zhang, Kiran Kamath, Michael S. Waterman, Caleb E. Finch, Xianghong Jasmine Zhou:
Gene Aging Nexus: a web database and data mining platform for microarray data on aging.
756-759
Electronic Edition (link) BibTeX
- Tanya Barrett, Dennis B. Troup, Stephen E. Wilhite, Pierre Ledoux, Dmitry Rudnev, Carlos Evangelista, Irene F. Kim, Alexandra Soboleva, Maxim Tomashevsky, Ron Edgar:
NCBI GEO: mining tens of millions of expression profiles - database and tools update.
760-765
Electronic Edition (link) BibTeX
- Janos Demeter, Catherine Beauheim, Jeremy Gollub, Tina Hernandez-Boussard, Heng Jin, Donald Maier, John C. Matese, Michael Nitzberg, Farrell Wymore, Zachariah K. Zachariah, Patrick O. Brown, Gavin Sherlock, Catherine A. Ball:
The Stanford Microarray Database: implementation of new analysis tools and open source release of software.
766-770
Electronic Edition (link) BibTeX
- Yanling Zhang, Yong Zhang, Jun Adachi, Jesper V. Olsen, Rong Shi, Gustavo de Souza, Erica Pasini, Leonard J. Foster, Boris Macek, Alexandre Zougman, Chanchal Kumar, Jacek R. Wisniewski, Jan Wang, Matthias Mann:
MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes.
771-779
Electronic Edition (link) BibTeX
- Yi-Bu Chen, Ansuman Chattopadhyay, Phillip Bergen, Cynthia Gadd, Nancy Tannery:
The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System - a one-stop gateway to online bioinformatics databases and software tools.
780-785
Electronic Edition (link) BibTeX
- Megan Sickmeier, Justin A. Hamilton, Tanguy LeGall, Vladimir Vacic, Marc S. Cortese, Agnes Tantos, Beata Szabo, Peter Tompa, Jake Chen, Vladimir N. Uversky, Zoran Obradovic, A. Keith Dunker:
DisProt: the Database of Disordered Proteins.
786-793
Electronic Edition (link) BibTeX
- C. J. Zheng, L. Y. Han, B. Xie, C. Y. Liew, S. Ong, J. Cui, H. L. Zhang, Z. Q. Tang, S. H. Gan, L. Jiang, Yu Zong Chen:
PharmGED: Pharmacogenetic Effect Database.
794-799
Electronic Edition (link) BibTeX
- Alexander Loy, Frank Maixner, Michael Wagner, Matthias Horn:
probeBase - an online resource for rRNA-targeted oligonucleotide probes: new features 2007.
800-804
Electronic Edition (link) BibTeX
- Wenwu Cui, Dennis D. Taub, Kevin Gardner:
qPrimerDepot: a primer database for quantitative real time PCR.
805-809
Electronic Edition (link) BibTeX
- Nuwee Wiwatwattana, Christopher M. Landau, G. Jamie Cope, Gabriel A. Harp, Anuj Kumar:
Organelle DB: an updated resource of eukaryotic protein localization and function.
810-814
Electronic Edition (link) BibTeX
- Agatha Schlüter, Stéphane Fourcade, Enric Domènech-Estévez, Toni Gabaldón, Jaime Huerta-Cepas, Guillaume Berthommier, Raymond Ripp, Ronald J. A. Wanders, Olivier Poch, Aurora Pujol:
PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.
815-822
Electronic Edition (link) BibTeX
- Eduardo Ruiz-Pesini, Marie T. Lott, Vincent Procaccio, Jason C. Poole, Marty C. Brandon, Dan Mishmar, Christina Yi, James Kreuziger, Pierre Baldi, Douglas C. Wallace:
An enhanced MITOMAP with a global mtDNA mutational phylogeny.
823-828
Electronic Edition (link) BibTeX
- Cameron Johnson, Lewis Bowman, Alex T. Adai, Vicki Vance, Venkatesan Sundaresan:
CSRDB: a small RNA integrated database and browser resource for cereals.
829-833
Electronic Edition (link) BibTeX
- Manuel Spannagl, Octave Noubibou, Dirk Haase, Li Yang, Heidrun Gundlach, Tobias Hindemitt, Kathrin Klee, Georg Haberer, Heiko Schoof, Klaus F. X. Mayer:
MIPSPlantsDB - plant database resource for integrative and comparative plant genome research.
834-840
Electronic Edition (link) BibTeX
- Lorenz Bülow, Martin Schindler, Reinhard Hehl:
PathoPlant®: a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses.
841-845
Electronic Edition (link) BibTeX
- Kevin L. Childs, John P. Hamilton, Wei Zhu, Eugene Ly, Foo Cheung, Hank Wu, Pablo D. Rabinowicz, Chris D. Town, C. Robin Buell, Agnes P. Chan:
The TIGR Plant Transcript Assemblies database.
846-851
Electronic Edition (link) BibTeX
- Nigel S. Walker, Nicholas Stiffler, Alice Barkan:
POGs/PlantRBP: a resource for comparative genomics in plants.
852-856
Electronic Edition (link) BibTeX
- Claudia Galuschka, Martin Schindler, Lorenz Bülow, Reinhard Hehl:
AthaMap web tools for the analysis and identification of co-regulated genes.
857-862
Electronic Edition (link) BibTeX
- Takeshi Obayashi, Kengo Kinoshita, Kenta Nakai, Masayuki Shibaoka, Shinpei Hayashi, Motoshi Saeki, Daisuke Shibata, Kazuki Saito, Hiroyuki Ohta:
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis.
863-869
Electronic Edition (link) BibTeX
- Timothy A. Erwin, Erica G. Jewell, Christopher G. Love, Geraldine A. C. Lim, Xi Li, Ross Chapman, Jacqueline Batley, Jason E. Stajich, Emmanuel Mongin, Elia Stupka, Bruce Ross, German C. Spangenberg, David Edwards:
BASC: an integrated bioinformatics system for Brassica research.
870-873
Electronic Edition (link) BibTeX
- Yong Li, Mario G. Rosso, Prisca Viehoever, Bernd Weisshaar:
GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions.
874-878
Electronic Edition (link) BibTeX
- Huazong Zeng, Lijun Luo, Weixiong Zhang, Jie Zhou, Zuofeng Li, Hongyan Liu, Tiansheng Zhu, Xiangqian Feng, Yang Zhong:
PlantQTL-GE: a database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information.
879-882
Electronic Edition (link) BibTeX
- Shu Ouyang, Wei Zhu, John A. Hamilton Jr., Haining Lin, Matthew Campbell, Kevin L. Childs, Françoise Thibaud-Nissen, Renae L. Malek, Yuandan Lee, Li Zheng, Joshua Orvis, Brian Haas, Jennifer Wortman, C. Robin Buell:
The TIGR Rice Genome Annotation Resource: improvements and new features.
883-887
Electronic Edition (link) BibTeX
- Nathalie Pavy, James J. Johnson, John A. Crow, Charles Paule, Timothy M. Kunau, John MacKay, Ernest F. Retzel:
ForestTreeDB: a database dedicated to the mining of tree transcriptomes.
888-894
Electronic Edition (link) BibTeX
- Carolyn J. Lawrence, Mary L. Schaeffer, Trent E. Seigfried, Darwin A. Campbell, Lisa C. Harper:
MaizeGDB's new data types, resources and activities.
895-900
Electronic Edition (link) BibTeX
- Nunzio D'Agostino, Mario Aversano, Luigi Frusciante, Maria Luisa Chiusano:
TomatEST database: in silico exploitation of EST data to explore expression patterns in tomato species.
901-905
Electronic Edition (link) BibTeX
- Stefan Günther, Dorothea Hempel, Mathias Dunkel, Kristian Rother, Robert Preissner:
SuperHapten: a comprehensive database for small immunogenic compounds.
906-910
Electronic Edition (link) BibTeX
Volume 35,
Number Web-Server-Issue,
July 2007
Editorials
Articles
- Joanne A. Fox, Scott McMillan, B. F. Francis Ouellette:
Conducting Research on the Web: 2007 Update for the Bioinformatics Links Directory.
3-5
Electronic Edition (link) BibTeX
- Alberto Labarga, Franck Valentin, Mikael Andersson, Rodrigo Lopez:
Web Services at the European Bioinformatics Institute.
6-11
Electronic Edition (link) BibTeX
- Mounir Errami, Jonathan D. Wren, Justin M. Hicks, Harold R. Garner:
eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications.
12-15
Electronic Edition (link) BibTeX
- Ildefonso Cases, David G. Pisano, Eduardo Andres, Angel Carro, José María Fernández, Gonzalo Gómez-López, Jose M. Rodriguez, Jaime F. Vera, Alfonso Valencia, Ana María Rojas:
CARGO: a web portal to integrate customized biological information.
16-20
Electronic Edition (link) BibTeX
- José M. Fernández, Robert Hoffmann, Alfonso Valencia:
iHOP web services.
21-26
Electronic Edition (link) BibTeX
- Jake Gunn Glanville, Dan Kirshner, Nandini Krishnamurthy, Kimmen Sjölander:
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis.
27-32
Electronic Edition (link) BibTeX
- Thomas M. Keane, Thomas J. Naughton, James O. McInerney:
MultiPhyl: a high-throughput phylogenomics webserver using distributed computing.
33-37
Electronic Edition (link) BibTeX
- Joaquín Tárraga, Ignacio Medina, Leonardo Arbiza, Jaime Huerta-Cepas, Toni Gabaldón, Joaquín Dopazo, Hernán Dopazo:
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.
38-42
Electronic Edition (link) BibTeX
- Warren A. Kibbe:
OligoCalc: an online oligonucleotide properties calculator.
43-46
Electronic Edition (link) BibTeX
- Peng Jiang, Haonan Wu, Jiawei Wei, Fei Sang, Xiao Sun, Zuhong Lu:
RF-DYMHC: detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features.
47-51
Electronic Edition (link) BibTeX
- Ibtissem Grissa, Gilles Vergnaud, Christine Pourcel:
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.
52-57
Electronic Edition (link) BibTeX
- Roy Eric Collins, Gabrielle Rocap:
REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis.
58-62
Electronic Edition (link) BibTeX
- Ming-Fang Tsai, Yi-Jung Lin, Yu-Chang Cheng, Kuo-Hsi Lee, Cheng-Chih Huang, Yuan-Tsong Chen, Adam Yao:
PrimerZ: streamlined primer design for promoters, exons and human SNPs.
63-65
Electronic Edition (link) BibTeX
- Yung-fu Chen, Rung Ching Chen, Lin Yu Tseng, Elong Lin, Yung-Kuan Chan, Ren-Hao Pan:
NTMG (N-terminal Truncated Mutants Generator for cDNA): an automatic multiplex PCR assays design for generating various N-terminal truncated cDNA mutants.
66-70
Electronic Edition (link) BibTeX
- Andreas Untergasser, Harm Nijveen, Xiangyu Rao, Ton Bisseling, René Geurts, Jack A. M. Leunissen:
Primer3Plus, an enhanced web interface to Primer3.
71-74
Electronic Edition (link) BibTeX
- Ramón Díaz-Uriarte, Andreu Alibés, Edward R. Morrissey, Andrés Cañada, Oscar M. Rueda, Mariana L. Neves:
Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite.
75-80
Electronic Edition (link) BibTeX
- Lucía Conde, David Montaner, Jordi Burguet-Castell, Joaquín Tárraga, Ignacio Medina, Fátima Al-Shahrour, Joaquín Dopazo:
ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling.
81-85
Electronic Edition (link) BibTeX
- Hubert Rehrauer, Stefan Zoller, Ralph Schlapbach:
MAGMA: analysis of two-channel microarrays made easy.
86-90
Electronic Edition (link) BibTeX
- Fátima Al-Shahrour, Pablo Minguez, Joaquín Tárraga, Ignacio Medina, Eva Alloza, David Montaner, Joaquín Dopazo:
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.
91-96
Electronic Edition (link) BibTeX
- Hong-Yu Ou, Xinyi He, Ewan M. Harrison, Bridget R. Kulasekara, Ali Bin Thani, Aras Kadioglu, Stephen Lory, Jay C. D. Hinton, Michael R. Barer, Zixin Deng, Kumar Rajakumar:
MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands.
97-104
Electronic Edition (link) BibTeX
- Yue Lu, Xin He, Sheng Zhong:
Cross-species microarray analysis with the OSCAR system suggests an INSR->Pax6->NQO1 neuro-protective pathway in aging and Alzheimer's disease.
105-114
Electronic Edition (link) BibTeX
- Deepak Grover, Alonzo S. Woodfield, Ranjana Verma, Peter P. Zandi, Douglas F. Levinson, James B. Potash:
QuickSNP: an automated web server for selection of tagSNPs.
115-120
Electronic Edition (link) BibTeX
- Hongkun Zheng, Junjie Shi, Xiaodong Fang, Yuan Li, Søren Vang, Wei Fan, Junyi Wang, Zhang Zhang, Wen Wang, Karsten Kristiansen, Jun Wang:
FGF: A web tool for Fishing Gene Family in a whole genome database.
121-125
Electronic Edition (link) BibTeX
- Pere Puigbò, Eduard Guzmán, Antoni Romeu, Santiago Garcia-Vallvé:
OPTIMIZER: a web server for optimizing the codon usage of DNA sequences.
126-131
Electronic Edition (link) BibTeX
- Michael C. Angellotti, Shafquat B. Bhuiyan, Guorong Chen, Xiu-Feng Wan:
CodonO: codon usage bias analysis within and across genomes.
132-136
Electronic Edition (link) BibTeX
- Chun Liang, Gang Wang, Lin Liu, Guoli Ji, Yuansheng Liu, Jinqiao Chen, Jason S. Webb, Greg Reese, Jeffrey F. D. Dean:
WebTraceMiner: a web service for processing and mining EST sequence trace files.
137-142
Electronic Edition (link) BibTeX
- Shivashankar H. Nagaraj, Nandan Deshpande, Robin B. Gasser, Shoba Ranganathan:
ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform.
143-147
Electronic Edition (link) BibTeX
- Rowan A. C. Mitchell, Nathalie Castells-Brooke, Jan Taubert, Paul Verrier, David J. Leader, Christopher J. Rawlings:
Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence.
148-151
Electronic Edition (link) BibTeX
- Yan Zhang, Shiuh-Ming Luoh, Lawrence S. Hon, Robert Baertsch, William I. Wood, Zemin Zhang:
GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database.
152-158
Electronic Edition (link) BibTeX
- Byungwook Lee, Taehui Hong, Sang Jin Byun, Taeha Woo, Yoon Jeong Choi:
ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences.
159-162
Electronic Edition (link) BibTeX
- Tomás Norambuena, Rodrigo Malig, Francisco Melo:
SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation.
163-168
Electronic Edition (link) BibTeX
- Da Wei Huang, Brad T. Sherman, Qina Tan, Joseph Kir, David Liu, David Bryant, Yongjian Guo, Robert M. Stephens, Michael W. Baseler, H. Clifford Lane, Richard A. Lempicki:
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists.
169-175
Electronic Edition (link) BibTeX
- Nicolas Goffard, Georg Weiller:
PathExpress: a web-based tool to identify relevant pathways in gene expression data.
176-181
Electronic Edition (link) BibTeX
- Yuki Moriya, Masumi Itoh, Shujiro Okuda, Akiyasu C. Yoshizawa, Minoru Kanehisa:
KAAS: an automatic genome annotation and pathway reconstruction server.
182-185
Electronic Edition (link) BibTeX
- Christina Backes, Andreas Keller, Jan Küntzer, Benny Kneissl, Nicole Comtesse, Yasser A. Elnakady, Rolf Müller, Eckart Meese, Hans-Peter Lenhof:
GeneTrail - advanced gene set enrichment analysis.
186-192
Electronic Edition (link) BibTeX
- Jüri Reimand, Meelis Kull, Hedi Peterson, Jaanus Hansen, Jaak Vilo:
g: Profiler - a web-based toolset for functional profiling of gene lists from large-scale experiments.
193-200
Electronic Edition (link) BibTeX
- Christoph D. Schmid, Thierry Sengstag, Philipp Bucher, Mauro Delorenzi:
MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data.
201-205
Electronic Edition (link) BibTeX
- Purvesh Khatri, Calin Voichita, Khalid Kattan, Nadeem Ansari, Avani Khatri, Constantin Georgescu, Adi L. Tarca, Sorin Draghici:
Onto-Tools: new additions and improvements in 2006.
206-211
Electronic Edition (link) BibTeX
- Carolina Perez-Iratxeta, Peer Bork, Miguel A. Andrade-Navarro:
Update of the G2D tool for prioritization of gene candidates to inherited diseases.
212-216
Electronic Edition (link) BibTeX
- Katherine A. Romer, Guy-Richard Kayombya, Ernest Fraenkel:
WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches.
217-220
Electronic Edition (link) BibTeX
- Huai-Kuang Tsai, Meng-Yuan Chou, Ching Hua Shih, Grace Tzu-Wei Huang, Tien-Hsien Chang, Wen-Hsiung Li:
MYBS: a comprehensive web server for mining transcription factor binding sites in yeast.
221-226
Electronic Edition (link) BibTeX
- Toshiyuki Okumura, Hiroki Makiguchi, Yuko Makita, Riu Yamashita, Kenta Nakai:
Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions.
227-231
Electronic Edition (link) BibTeX
- William A. Thompson, Lee Aaron Newberg, Sean Conlan, Lee Ann McCue, Charles E. Lawrence:
The Gibbs Centroid Sampler.
232-237
Electronic Edition (link) BibTeX
- Li-Wei Chang, Burr R. Fontaine, Gary D. Stormo, Rakesh Nagarajan:
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis.
238-244
Electronic Edition (link) BibTeX
- Shannan J. Ho Sui, Debra L. Fulton, David J. Arenillas, Andrew T. Kwon, Wyeth W. Wasserman:
oPOSSUM: integrated tools for analysis of regulatory motif over-representation.
245-252
Electronic Edition (link) BibTeX
- Shaun Mahony, Panayiotis V. Benos:
STAMP: a web tool for exploring DNA-binding motif similarities.
253-258
Electronic Edition (link) BibTeX
- Jonathan M. Carlson, Arijit Chakravarty, Charles E. DeZiel, Robert H. Gross:
SCOPE: a web server for practical de novo motif discovery.
259-264
Electronic Edition (link) BibTeX
- Zhao Xu, Hao Wang:
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons.
265-268
Electronic Edition (link) BibTeX
- Jean-François Lucier, Jonathan Perreault, Jean-François Noël, Gilles Boire, Jean-Pierre Perreault:
RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures.
269-274
Electronic Edition (link) BibTeX
- Guoqing Lu, Thaine W. Rowley, Rebecca Garten, Ruben O. Donis:
FluGenome: a web tool for genotyping influenza A virus.
275-279
Electronic Edition (link) BibTeX
- Yiming Bao, Pavel Bolotov, Dmitry Dernovoy, Boris Kiryutin, Tatiana A. Tatusova:
FLAN: a web server for influenza virus genome annotation.
280-284
Electronic Edition (link) BibTeX
- Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, Stephen M. Mount:
SplicePort - An interactive splice-site analysis tool.
285-291
Electronic Edition (link) BibTeX
- Zoé Lacroix, Christophe Legendre, Louiqa Raschid, Ben Snyder:
BIPASS: BioInformatics Pipeline Alternative Splicing Services.
292-296
Electronic Edition (link) BibTeX
- Sylvain Foissac, Michael Sammeth:
ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets.
297-299
Electronic Edition (link) BibTeX
- Mugdha Khaladkar, Vivian Bellofatto, Jason Tsong-Li Wang, Bin Tian, Bruce A. Shapiro:
RADAR: a web server for RNA data analysis and research.
300-304
Electronic Edition (link) BibTeX
- Eva Freyhult, Vincent Moulton, Peter Clote:
RNAbor: a web server for RNA structural neighbors.
305-309
Electronic Edition (link) BibTeX
- Anke Busch, Rolf Backofen:
INFO-RNA - a server for fast inverse RNA folding satisfying sequence constraints.
310-313
Electronic Edition (link) BibTeX
- Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang:
RSRE: RNA structural robustness evaluator.
314-319
Electronic Edition (link) BibTeX
- Jens Reeder, Peter Steffen, Robert Giegerich:
pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows.
320-324
Electronic Edition (link) BibTeX
- Cagri Aksay, Raheleh Salari, Emre Karakoç, Can Alkan, Süleyman Cenk Sahinalp:
taveRNA: a web suite for RNA algorithms and applications.
325-329
Electronic Edition (link) BibTeX
- Alexander Kaiser, Jan Krüger, Dirk Evers:
RNA Movies 2: sequential animation of RNA secondary structures.
330-334
Electronic Edition (link) BibTeX
- Andreas R. Gruber, Richard Neuböck, Ivo L. Hofacker, Stefan Washietl:
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures.
335-338
Electronic Edition (link) BibTeX
- Peng Jiang, Haonan Wu, Wenkai Wang, Wei Ma, Xiao Sun, Zuhong Lu:
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.
339-344
Electronic Edition (link) BibTeX
- Lei Kong, Yong Zhang, Zhi-Qiang Ye, Xiao-Qiao Liu, Shuqi Zhao, Liping Wei, Ge Gao:
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.
345-349
Electronic Edition (link) BibTeX
- Helena Tåquist, Yuanyuan Cui, David H. Ardell:
TFAM 1.0: an online tRNA function classifier.
350-353
Electronic Edition (link) BibTeX
- Jianlin Cheng:
DOMAC: an accurate, hybrid protein domain prediction server.
354-356
Electronic Edition (link) BibTeX
- Harianto Tjong, Sanbo Qin, Huan-Xiang Zhou:
PI2PE: protein interface/interior prediction engine.
357-362
Electronic Edition (link) BibTeX
- Narcis Fernandez-Fuentes, Carlos J. Madrid-Aliste, Brajesh Kumar Rai, J. Eduardo Fajardo, András Fiser:
M4T: a comparative protein structure modeling server.
363-368
Electronic Edition (link) BibTeX
- Björn Wallner, Per Larsson, Arne Elofsson:
Pcons.net: protein structure prediction meta server.
369-374
Electronic Edition (link) BibTeX
- Ian W. Davis, Andrew Leaver-Fay, Vincent B. Chen, Jeremy N. Block, Gary J. Kapral, Xueyi Wang, Laura Weston Murray, W. Bryan Arendall III, Jack Snoeyink, Jane S. Richardson, David C. Richardson:
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.
375-383
Electronic Edition (link) BibTeX
- Alper Uzun, Chesley M. Leslin, Alexej Abyzov, Valentin A. Ilyin:
Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways.
384-392
Electronic Edition (link) BibTeX
- Marc A. Martí-Renom, Ursula Pieper, Mallur S. Madhusudhan, Andrea Rossi, Narayanan Eswar, Fred P. Davis, Fátima Al-Shahrour, Joaquín Dopazo, Andrej Sali:
DBAli tools: mining the protein structure space.
393-397
Electronic Edition (link) BibTeX
- Kengo Kinoshita, Yoichi Murakami, Haruki Nakamura:
eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.
398-402
Electronic Edition (link) BibTeX
- Christian X. Weichenberger, Manfred J. Sippl:
NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures.
403-406
Electronic Edition (link) BibTeX
- Markus Wiederstein, Manfred J. Sippl:
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins.
407-410
Electronic Edition (link) BibTeX
- Stefan J. Suhrer, Markus Gruber, Manfred J. Sippl:
QSCOP-BLAST - fast retrieval of quantified structural information for protein sequences of unknown structure.
411-415
Electronic Edition (link) BibTeX
- Allegra Via, Daniele Peluso, Pier Federico Gherardini, Emanuele de Rinaldis, Teresa Colombo, Gabriele Ausiello, Manuela Helmer-Citterich:
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures.
416-419
Electronic Edition (link) BibTeX
- Yan-Long Lai, Shih-Chung Yen, Sung-Huan Yu, Jenn-Kang Hwang:
pKNOT: the protein KNOT web server.
420-424
Electronic Edition (link) BibTeX
- Grigory Kolesov, Peter Virnau, Mehran Kardar, Leonid A. Mirny:
Protein knot server: detection of knots in protein structures.
425-428
Electronic Edition (link) BibTeX
- Lukas Käll, Anders Krogh, Erik L. L. Sonnhammer:
Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server.
429-432
Electronic Edition (link) BibTeX
- Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, Jörg Hau, Olivier Martin, Dmitri Kuznetsov, Laurent Falquet:
MyHits: improvements to an interactive resource for analyzing protein sequences.
433-437
Electronic Edition (link) BibTeX
- Chi-Hua Tung, Jinn-Moon Yang:
fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies.
438-443
Electronic Edition (link) BibTeX
- Coral del Val, Peter Ernst, Mechthild Falkenhahn, C. Fladerer, Karl-Heinz Glatting, Sándor Suhai, Agnes Hotz-Wagenblatt:
ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ.
444-450
Electronic Edition (link) BibTeX
- Enrico Ferraro, Daniele Peluso, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich:
SH3-Hunter: discovery of SH3 domain interaction sites in proteins.
451-454
Electronic Edition (link) BibTeX
- Norman E. Davey, Richard J. Edwards, Denis C. Shields:
The SLiMDisc server: short, linear motif discovery in proteins.
455-459
Electronic Edition (link) BibTeX
- Takashi Ishida, Kengo Kinoshita:
PrDOS: prediction of disordered protein regions from amino acid sequence.
460-464
Electronic Edition (link) BibTeX
- Chung-Tsai Su, Chien-Yu Chen, Chen-Ming Hsu:
iPDA: integrated protein disorder analyzer.
465-472
Electronic Edition (link) BibTeX
- K. G. Tina, R. Bhadra, N. Srinivasan:
PIC: Protein Interactions Calculator.
473-476
Electronic Edition (link) BibTeX
- Joel Franklin, Patrice Koehl, Sebastian Doniach, Marc Delarue:
MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape.
477-482
Electronic Edition (link) BibTeX
- Ludovic Autin, Pierre Tufféry:
PMG: online generation of high-quality molecular pictures and storyboarded animations.
483-488
Electronic Edition (link) BibTeX
- C. Axel Innis:
siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins.
489-494
Electronic Edition (link) BibTeX
- K. Anton Feenstra, Walter Pirovano, Klaas Krab, Jaap Heringa:
Sequence harmony: detecting functional specificity from alignments.
495-498
Electronic Edition (link) BibTeX
- Harpreet Kaur Saini, Daniel Fischer:
FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments.
499-502
Electronic Edition (link) BibTeX
- Kshama Goyal, Debasisa Mohanty, Shekhar C. Mande:
PAR-3D: a server to predict protein active site residues.
503-505
Electronic Edition (link) BibTeX
- Adi Stern, Adi Doron-Faigenboim, Elana Erez, Eric Martz, Eran Bacharach, Tal Pupko:
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach.
506-511
Electronic Edition (link) BibTeX
- Clifford E. Felder, Jaime Prilusky, Israel Silman, Joel L. Sussman:
A server and database for dipole moments of proteins.
512-521
Electronic Edition (link) BibTeX
- Todd J. Dolinsky, Paul Czodrowski, Hui Li, Jens E. Nielsen, Jan H. Jensen, Gerhard Klebe, Nathan A. Baker:
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations.
522-525
Electronic Edition (link) BibTeX
- Shula Shazman, Gershon Celniker, Omer Haber, Fabian Glaser, Yael Mandel-Gutfreund:
Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces.
526-530
Electronic Edition (link) BibTeX
- Mark V. Berjanskii, David S. Wishart:
The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts.
531-537
Electronic Edition (link) BibTeX
- Jin-Rui Xu, Jing-Xian Zhang, Bu-Cong Han, Liang Liang, Zhi Liang Ji:
CytoSVM: an advanced server for identification of cytokine-receptor interactions.
538-542
Electronic Edition (link) BibTeX
- Hani Neuvirth, Uri Heinemann, David Birnbaum, Naftali Tishby, Gideon Schreiber:
ProMateus - an open research approach to protein-binding sites analysis.
543-548
Electronic Edition (link) BibTeX
- Narendra Kumar, Debasisa Mohanty:
MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes.
549-555
Electronic Edition (link) BibTeX
- P. Christoph Champ, Carlos J. Camacho:
FastContact: a free energy scoring tool for protein-protein complex structures.
556-560
Electronic Edition (link) BibTeX
- Yung-Chiang Chen, Yu-Shu Lo, Wen-Chang Hsu, Jinn-Moon Yang:
3D-partner: a web server to infer interacting partners and binding models.
561-567
Electronic Edition (link) BibTeX
- T. Bohme Leite, D. Gomes, Maria A. Miteva, Jacques Chomilier, Bruno O. Villoutreix, Pierre Tufféry:
Frog: a FRee Online druG 3D conformation generator.
568-572
Electronic Edition (link) BibTeX
- Gonzalo López, Alfonso Valencia, Michael L. Tress:
firestar - prediction of functionally important residues using structural templates and alignment reliability.
573-577
Electronic Edition (link) BibTeX
- Michael Terribilini, Jeffry D. Sander, Jae-Hyung Lee, Peter Zaback, Robert L. Jernigan, Vasant Honavar, Drena Dobbs:
RNABindR: a server for analyzing and predicting RNA-binding sites in proteins.
578-584
Electronic Edition (link) BibTeX
- Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C. J. Adams-Collier, Kenta Nakai:
WoLF PSORT: protein localization predictor.
585-587
Electronic Edition (link) BibTeX
- Yung-Hao Wong, Tzong-Yi Lee, Han-Kuen Liang, Chia-Mao Huang, Ting-Yuan Wang, Yi-Huan Yang, Chia-Huei Chu, Hsien-Da Huang, Ming-Tat Ko, Jenn-Kang Hwang:
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns.
588-594
Electronic Edition (link) BibTeX
- Joshua S. Kaminker, Yan Zhang, Colin K. Watanabe, Zemin Zhang:
CanPredict: a computational tool for predicting cancer-associated missense mutations.
595-598
Electronic Edition (link) BibTeX
- Jeffry D. Sander, Peter Zaback, J. Keith Joung, Daniel F. Voytas, Drena Dobbs:
Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool.
599-605
Electronic Edition (link) BibTeX
- Eoin Fahy, Manish Sud, Dawn Cotter, Shankar Subramaniam:
LIPID MAPS online tools for lipid research.
606-612
Electronic Edition (link) BibTeX
- Thomas Handorf, Oliver Ebenhöh:
MetaPath Online: a web server implementation of the network expansion algorithm.
613-618
Electronic Edition (link) BibTeX
- Jost Degenhardt, Martin Haubrock, Jürgen Dönitz, Edgar Wingender, Torsten Crass:
DEEP - A tool for differential expression effector prediction.
619-624
Electronic Edition (link) BibTeX
- Zhenjun Hu, David M. Ng, Takuji Yamada, Chunnuan Chen, Shuichi Kawashima, Joe Mellor, Bolan Linghu, Minoru Kanehisa, Joshua M. Stuart, Charles DeLisi:
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.
625-632
Electronic Edition (link) BibTeX
- Feng-Chi Chen, Chuang-Jong Chen, Trees-Juen Chuang:
INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events.
633-638
Electronic Edition (link) BibTeX
- Yun Sheng Chung, Wei-Hsun Lee, Chuan Yi Tang, Chin Lung Lu:
RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints.
639-644
Electronic Edition (link) BibTeX
- Sébastien Moretti, Fabrice Armougom, Iain M. Wallace, Desmond G. Higgins, C. Victor Jongeneel, Cédric Notredame:
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.
645-648
Electronic Edition (link) BibTeX
- Jimin Pei, Bong-Hyun Kim, Ming Tang, Nick V. Grishin:
PROMALS web server for accurate multiple protein sequence alignments.
649-652
Electronic Edition (link) BibTeX
- Ruslan Sadreyev, Ming Tang, Bong-Hyun Kim, Nick V. Grishin:
COMPASS server for remote homology inference.
653-658
Electronic Edition (link) BibTeX
- Fabrizio Ferrè, Yann Ponty, W. A. Lorenz, Peter Clote:
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities.
659-668
Electronic Edition (link) BibTeX
- Michael Brudno, Alexander Poliakov, Simon Minovitsky, Igor Ratnere, Inna Dubchak:
Multiple whole genome alignments and novel biomedical applications at the VISTA portal.
669-674
Electronic Edition (link) BibTeX
- Satish Chikkagoudar, Usman Roshan, Dennis R. Livesay:
eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities.
675-677
Electronic Edition (link) BibTeX
- Yi Zhou, Laura F. Landweber:
BLASTO: a tool for searching orthologous groups.
678-682
Electronic Edition (link) BibTeX
- Andreas Keller, Nicole Comtesse, Nicole Ludwig, Eckart Meese, Hans-Peter Lenhof:
SePaCS - a web-based application for classification of seroreactivity profiles.
683-687
Electronic Edition (link) BibTeX
- Swetlana Nikolajewa, Rainer Pudimat, Michael Hiller, Matthias Platzer, Rolf Backofen:
BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data.
688-693
Electronic Edition (link) BibTeX
- Alvaro Martinez Barrio, Daniel Soeria-Atmadja, Anders Nistér, Mats G. Gustafsson, Ulf Hammerling, Erik Bongcam-Rudloff:
EVALLER: a web server for in silico assessment of potential protein allergenicity.
694-700
Electronic Edition (link) BibTeX
- Leonid Zamdborg, Richard D. LeDuc, Kevin J. Glowacz, Yong-Bin Kim, Vinayak Viswanathan, Ian T. Spaulding, Bryan P. Early, Eric J. Bluhm, Shannee Babai, Neil L. Kelleher:
ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry.
701-706
Electronic Edition (link) BibTeX
- Chuan-Yih Yu, Yin-Hao Tsui, Yi-Hwa Yian, Ting-Yi Sung, Wen-Lian Hsu:
The Multi-Q web server for multiplexed protein quantitation.
707-712
Electronic Edition (link) BibTeX
- Sik Lok Lam:
DSHIFT: a web server for predicting DNA chemical shifts.
713-717
Electronic Edition (link) BibTeX
- Trias Thireou, Vassilis Atlamazoglou, Manolis Levakis, Elias Eliopoulos, Athanassios Hountas, George Tsoucaris, Kostas Bethanis:
CrystTwiV: a webserver for automated phase extension and refinement in X-ray crystallography.
718-722
Electronic Edition (link) BibTeX
Copyright © Sun May 17 00:14:47 2009
by Michael Ley (ley@uni-trier.de)
