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Volume 39; Issue Database
Main
Nucleic Acids Research
Volume 39; Issue Database
Nucleic Acids Research
Volume 39; Issue Database
1
The Gypsy Database (GyDB) of mobile genetic elements: release 2.0
Llorens, C.
,
Futami, R.
,
Covelli, L.
,
Dominguez-Escriba, L.
,
Viu, J. M.
,
Tamarit, D.
,
Aguilar-Rodriguez, J.
,
Vicente-Ripolles, M.
,
Fuster, G.
,
Bernet, G. P.
,
Maumus, F.
,
Munoz-Pomer, A.
,
Sempere, J. M
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 3.35 MB
Your tags:
english, 2011
2
Protegen: a web-based protective antigen database and analysis system
Yang, B.
,
Sayers, S.
,
Xiang, Z.
,
He, Y.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 2.14 MB
Your tags:
english, 2011
3
ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures
Herzig, V.
,
Wood, D. L. A.
,
Newell, F.
,
Chaumeil, P.-A.
,
Kaas, Q.
,
Binford, G. J.
,
Nicholson, G. M.
,
Gorse, D.
,
King, G. F.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 4.38 MB
Your tags:
english, 2011
4
MatrixDB, the extracellular matrix interaction database
Chautard, E.
,
Fatoux-Ardore, M.
,
Ballut, L.
,
Thierry-Mieg, N.
,
Ricard-Blum, S.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 3.00 MB
Your tags:
english, 2011
5
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans
Lee, T.-Y.
,
Bo-Kai Hsu, J.
,
Chang, W.-C.
,
Huang, H.-D.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 7.88 MB
Your tags:
english, 2011
6
Reactome: a database of reactions, pathways and biological processes
Croft, D.
,
O'Kelly, G.
,
Wu, G.
,
Haw, R.
,
Gillespie, M.
,
Matthews, L.
,
Caudy, M.
,
Garapati, P.
,
Gopinath, G.
,
Jassal, B.
,
Jupe, S.
,
Kalatskaya, I.
,
Mahajan, S.
,
May, B.
,
Ndegwa, N.
,
Schmidt, E.
,
Shamov
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 10.73 MB
Your tags:
english, 2011
7
CDD: a Conserved Domain Database for the functional annotation of proteins
Marchler-Bauer, A.
,
Lu, S.
,
Anderson, J. B.
,
Chitsaz, F.
,
Derbyshire, M. K.
,
DeWeese-Scott, C.
,
Fong, J. H.
,
Geer, L. Y.
,
Geer, R. C.
,
Gonzales, N. R.
,
Gwadz, M.
,
Hurwitz, D. I.
,
Jackson, J. D.
,
Ke, Z
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 6.80 MB
Your tags:
english, 2011
8
AREsite: a database for the comprehensive investigation of AU-rich elements
Gruber, A. R.
,
Fallmann, J.
,
Kratochvill, F.
,
Kovarik, P.
,
Hofacker, I. L.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 959 KB
Your tags:
english, 2011
9
DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs
Knox, C.
,
Law, V.
,
Jewison, T.
,
Liu, P.
,
Ly, S.
,
Frolkis, A.
,
Pon, A.
,
Banco, K.
,
Mak, C.
,
Neveu, V.
,
Djoumbou, Y.
,
Eisner, R.
,
Guo, A. C.
,
Wishart, D. S.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 1.31 MB
Your tags:
english, 2011
10
starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data
Yang, J.-H.
,
Li, J.-H.
,
Shao, P.
,
Zhou, H.
,
Chen, Y.-Q.
,
Qu, L.-H.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 3.84 MB
Your tags:
english, 2011
11
lncRNAdb: a reference database for long noncoding RNAs
Amaral, P. P.
,
Clark, M. B.
,
Gascoigne, D. K.
,
Dinger, M. E.
,
Mattick, J. S.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 3.02 MB
Your tags:
english, 2011
12
PREX: PeroxiRedoxin classification indEX, a database of subfamily assignments across the diverse peroxiredoxin family
Soito, L.
,
Williamson, C.
,
Knutson, S. T.
,
Fetrow, J. S.
,
Poole, L. B.
,
Nelson, K. J.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 2.81 MB
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english, 2011
13
REPAIRtoire--a database of DNA repair pathways
Milanowska, K.
,
Krwawicz, J.
,
Papaj, G.
,
Kosinski, J.
,
Poleszak, K.
,
Lesiak, J.
,
Osinska, E.
,
Rother, K.
,
Bujnicki, J. M.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 3.02 MB
Your tags:
english, 2011
14
The Comparative Toxicogenomics Database: update 2011
Davis, A. P.
,
King, B. L.
,
Mockus, S.
,
Murphy, C. G.
,
Saraceni-Richards, C.
,
Rosenstein, M.
,
Wiegers, T.
,
Mattingly, C. J.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 5.64 MB
Your tags:
english, 2011
15
IEDB-3D: structural data within the immune epitope database
Ponomarenko, J.
,
Papangelopoulos, N.
,
Zajonc, D. M.
,
Peters, B.
,
Sette, A.
,
Bourne, P. E.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 13.09 MB
Your tags:
english, 2011
16
Database resources of the National Center for Biotechnology Information
Sayers, E. W.
,
Barrett, T.
,
Benson, D. A.
,
Bolton, E.
,
Bryant, S. H.
,
Canese, K.
,
Chetvernin, V.
,
Church, D. M.
,
DiCuccio, M.
,
Federhen, S.
,
Feolo, M.
,
Fingerman, I. M.
,
Geer, L. Y.
,
Helmberg, W.
,
Kap
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 146 KB
Your tags:
english, 2011
17
miRBase: integrating microRNA annotation and deep-sequencing data
Kozomara, A.
,
Griffiths-Jones, S.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 5.11 MB
Your tags:
english, 2011
18
3did: identification and classification of domain-based interactions of known three-dimensional structure
Stein, A.
,
Ceol, A.
,
Aloy, P.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 4.55 MB
Your tags:
english, 2011
19
The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms
Xu, Q.
,
Dunbrack, R. L.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 15.84 MB
Your tags:
english, 2011
20
Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes
Cer, R. Z.
,
Bruce, K. H.
,
Mudunuri, U. S.
,
Yi, M.
,
Volfovsky, N.
,
Luke, B. T.
,
Bacolla, A.
,
Collins, J. R.
,
Stephens, R. M.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 10.31 MB
Your tags:
english, 2011
21
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
Szklarczyk, D.
,
Franceschini, A.
,
Kuhn, M.
,
Simonovic, M.
,
Roth, A.
,
Minguez, P.
,
Doerks, T.
,
Stark, M.
,
Muller, J.
,
Bork, P.
,
Jensen, L. J.
,
Mering, C. v.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 8.47 MB
Your tags:
english, 2011
22
The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl
Bombarely, A.
,
Menda, N.
,
Tecle, I. Y.
,
Buels, R. M.
,
Strickler, S.
,
Fischer-York, T.
,
Pujar, A.
,
Leto, J.
,
Gosselin, J.
,
Mueller, L. A.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 2.96 MB
Your tags:
english, 2011
23
Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics
Fei, Z.
,
Joung, J.-G.
,
Tang, X.
,
Zheng, Y.
,
Huang, M.
,
Lee, J. M.
,
McQuinn, R.
,
Tieman, D. M.
,
Alba, R.
,
Klee, H. J.
,
Giovannoni, J. J.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 8.50 MB
Your tags:
english, 2011
24
ASD: a comprehensive database of allosteric proteins and modulators
Huang, Z.
,
Zhu, L.
,
Cao, Y.
,
Wu, G.
,
Liu, X.
,
Chen, Y.
,
Wang, Q.
,
Shi, T.
,
Zhao, Y.
,
Wang, Y.
,
Li, W.
,
Li, Y.
,
Chen, H.
,
Chen, G.
,
Zhang, J.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 3.33 MB
Your tags:
english, 2011
25
The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics
Blake, J. A.
,
Bult, C. J.
,
Kadin, J. A.
,
Richardson, J. E.
,
Eppig, J. T.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 7.10 MB
Your tags:
english, 2011
26
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources
Gremse, M.
,
Chang, A.
,
Schomburg, I.
,
Grote, A.
,
Scheer, M.
,
Ebeling, C.
,
Schomburg, D.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 12.48 MB
Your tags:
english, 2011
27
NCBI GEO: archive for functional genomics data sets--10 years on
Barrett, T.
,
Troup, D. B.
,
Wilhite, S. E.
,
Ledoux, P.
,
Evangelista, C.
,
Kim, I. F.
,
Tomashevsky, M.
,
Marshall, K. A.
,
Phillippy, K. H.
,
Sherman, P. M.
,
Muertter, R. N.
,
Holko, M.
,
Ayanbule, O.
,
Yefano
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 2.06 MB
Your tags:
english, 2011
28
BRENDA, the enzyme information system in 2011
Scheer, M.
,
Grote, A.
,
Chang, A.
,
Schomburg, I.
,
Munaretto, C.
,
Rother, M.
,
Sohngen, C.
,
Stelzer, M.
,
Thiele, J.
,
Schomburg, D.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 7.11 MB
Your tags:
english, 2011
29
Extending CATH: increasing coverage of the protein structure universe and linking structure with function
Cuff, A. L.
,
Sillitoe, I.
,
Lewis, T.
,
Clegg, A. B.
,
Rentzsch, R.
,
Furnham, N.
,
Pellegrini-Calace, M.
,
Jones, D.
,
Thornton, J.
,
Orengo, C. A.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 9.84 MB
Your tags:
english, 2011
30
CADgene: a comprehensive database for coronary artery disease genes
Liu, H.
,
Liu, W.
,
Liao, Y.
,
Cheng, L.
,
Liu, Q.
,
Ren, X.
,
Shi, L.
,
Tu, X.
,
Wang, Q. K.
,
Guo, A.-Y.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 5.01 MB
Your tags:
english, 2011
31
HitPredict: a database of quality assessed protein-protein interactions in nine species
Patil, A.
,
Nakai, K.
,
Nakamura, H.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 539 KB
Your tags:
english, 2011
32
KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions
Chen, X.-w.
,
Jeong, J. C.
,
Dermyer, P.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 172 KB
Your tags:
english, 2011
33
RBPDB: a database of RNA-binding specificities
Cook, K. B.
,
Kazan, H.
,
Zuberi, K.
,
Morris, Q.
,
Hughes, T. R.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 11.86 MB
Your tags:
english, 2011
34
UKPMC: a full text article resource for the life sciences
McEntyre, J. R.
,
Ananiadou, S.
,
Andrews, S.
,
Black, W. J.
,
Boulderstone, R.
,
Buttery, P.
,
Chaplin, D.
,
Chevuru, S.
,
Cobley, N.
,
Coleman, L.-A.
,
Davey, P.
,
Gupta, B.
,
Haji-Gholam, L.
,
Hawkins, C.
,
Horn
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 7.34 MB
Your tags:
english, 2011
35
PCDDB: the protein circular dichroism data bank, a repository for circular dichroism spectral and metadata
Whitmore, L.
,
Woollett, B.
,
Miles, A. J.
,
Klose, D. P.
,
Janes, R. W.
,
Wallace, B. A.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 1.88 MB
Your tags:
english, 2011
36
PDBe: Protein Data Bank in Europe
Velankar, S.
,
Alhroub, Y.
,
Alili, A.
,
Best, C.
,
Boutselakis, H. C.
,
Caboche, S.
,
Conroy, M. J.
,
Dana, J. M.
,
van Ginkel, G.
,
Golovin, A.
,
Gore, S. P.
,
Gutmanas, A.
,
Haslam, P.
,
Hirshberg, M.
,
John, M.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 10.44 MB
Your tags:
english, 2011
37
TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea
Shao, Y.
,
Harrison, E. M.
,
Bi, D.
,
Tai, C.
,
He, X.
,
Ou, H.-Y.
,
Rajakumar, K.
,
Deng, Z.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 4.30 MB
Your tags:
english, 2011
38
NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data
Hackenberg, M.
,
Barturen, G.
,
Oliver, J. L.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 3.20 MB
Your tags:
english, 2011
39
COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer
Forbes, S. A.
,
Bindal, N.
,
Bamford, S.
,
Cole, C.
,
Kok, C. Y.
,
Beare, D.
,
Jia, M.
,
Shepherd, R.
,
Leung, K.
,
Menzies, A.
,
Teague, J. W.
,
Campbell, P. J.
,
Stratton, M. R.
,
Futreal, P. A.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 5.41 MB
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english, 2011
40
Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites
Zanzoni, A.
,
Carbajo, D.
,
Diella, F.
,
Gherardini, P. F.
,
Tramontano, A.
,
Helmer-Citterich, M.
,
Via, A.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 2.49 MB
Your tags:
english, 2011
41
The UCSC Genome Browser database: update 2011
Fujita, P. A.
,
Rhead, B.
,
Zweig, A. S.
,
Hinrichs, A. S.
,
Karolchik, D.
,
Cline, M. S.
,
Goldman, M.
,
Barber, G. P.
,
Clawson, H.
,
Coelho, A.
,
Diekhans, M.
,
Dreszer, T. R.
,
Giardine, B. M.
,
Harte, R. A.
,
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 1.92 MB
Your tags:
english, 2011
42
RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions
Sato, Y.
,
Antonio, B. A.
,
Namiki, N.
,
Takehisa, H.
,
Minami, H.
,
Kamatsuki, K.
,
Sugimoto, K.
,
Shimizu, Y.
,
Hirochika, H.
,
Nagamura, Y.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 13.69 MB
Your tags:
english, 2011
43
dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa
Gaudet, P.
,
Fey, P.
,
Basu, S.
,
Bushmanova, Y. A.
,
Dodson, R.
,
Sheppard, K. A.
,
Just, E. M.
,
Kibbe, W. A.
,
Chisholm, R. L.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 4.52 MB
Your tags:
english, 2011
44
LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana
Rastogi, S.
,
Rost, B.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 2.28 MB
Your tags:
english, 2011
45
Towards BioDBcore: a community-defined information specification for biological databases
Gaudet, P.
,
Bairoch, A.
,
Field, D.
,
Sansone, S.-A.
,
Taylor, C.
,
Attwood, T. K.
,
Bateman, A.
,
Blake, J. A.
,
Bult, C. J.
,
Cherry, J. M.
,
Chisholm, R. L.
,
Cochrane, G.
,
Cook, C. E.
,
Eppig, J. T.
,
Galperi
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 1.37 MB
Your tags:
english, 2011
46
T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research
Burren, O. S.
,
Adlem, E. C.
,
Achuthan, P.
,
Christensen, M.
,
Coulson, R. M. R.
,
Todd, J. A.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 1.70 MB
Your tags:
english, 2011
47
PhEVER: a database for the global exploration of virus-host evolutionary relationships
Palmeira, L.
,
Penel, S.
,
Lotteau, V.
,
Rabourdin-Combe, C.
,
Gautier, C.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 6.93 MB
Your tags:
english, 2011
48
The BioGRID Interaction Database: 2011 update
Stark, C.
,
Breitkreutz, B.-J.
,
Chatr-aryamontri, A.
,
Boucher, L.
,
Oughtred, R.
,
Livstone, M. S.
,
Nixon, J.
,
Van Auken, K.
,
Wang, X.
,
Shi, X.
,
Reguly, T.
,
Rust, J. M.
,
Winter, A.
,
Dolinski, K.
,
Tyers,
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 4.45 MB
Your tags:
english, 2011
49
PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database
Zhang, H.
,
Jin, J.
,
Tang, L.
,
Zhao, Y.
,
Gu, X.
,
Gao, G.
,
Luo, J.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
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50
miRTarBase: a database curates experimentally validated microRNA-target interactions
Hsu, S.-D.
,
Lin, F.-M.
,
Wu, W.-Y.
,
Liang, C.
,
Huang, W.-C.
,
Chan, W.-L.
,
Tsai, W.-T.
,
Chen, G.-Z.
,
Lee, C.-J.
,
Chiu, C.-M.
,
Chien, C.-H.
,
Wu, M.-C.
,
Huang, C.-Y.
,
Tsou, A.-P.
,
Huang, H.-D.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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51
EMDataBank.org: unified data resource for CryoEM
Lawson, C. L.
,
Baker, M. L.
,
Best, C.
,
Bi, C.
,
Dougherty, M.
,
Feng, P.
,
van Ginkel, G.
,
Devkota, B.
,
Lagerstedt, I.
,
Ludtke, S. J.
,
Newman, R. H.
,
Oldfield, T. J.
,
Rees, I.
,
Sahni, G.
,
Sala, R.
,
Velan
Journal:
Nucleic Acids Research
Year:
2011
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english
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52
SAHG, a comprehensive database of predicted structures of all human proteins
Motono, C.
,
Nakata, J.
,
Koike, R.
,
Shimizu, K.
,
Shirota, M.
,
Amemiya, T.
,
Tomii, K.
,
Nagano, N.
,
Sakaya, N.
,
Misoo, K.
,
Sato, M.
,
Kidera, A.
,
Hiroaki, H.
,
Shirai, T.
,
Kinoshita, K.
,
Noguchi, T.
,
Ota,
Journal:
Nucleic Acids Research
Year:
2011
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english
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53
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila
Gallo, S. M.
,
Gerrard, D. T.
,
Miner, D.
,
Simich, M.
,
Des Soye, B.
,
Bergman, C. M.
,
Halfon, M. S.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
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54
GPCRDB: information system for G protein-coupled receptors
Vroling, B.
,
Sanders, M.
,
Baakman, C.
,
Borrmann, A.
,
Verhoeven, S.
,
Klomp, J.
,
Oliveira, L.
,
de Vlieg, J.
,
Vriend, G.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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55
EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities
Hsin, K.-Y.
,
Morgan, H. P.
,
Shave, S. R.
,
Hinton, A. C.
,
Taylor, P.
,
Walkinshaw, M. D.
Journal:
Nucleic Acids Research
Year:
2011
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english
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56
IsoBase: a database of functionally related proteins across PPI networks
Park, D.
,
Singh, R.
,
Baym, M.
,
Liao, C.-S.
,
Berger, B.
Journal:
Nucleic Acids Research
Year:
2011
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english
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57
DAnCER: Disease-Annotated Chromatin Epigenetics Resource
Turinsky, A. L.
,
Turner, B.
,
Borja, R. C.
,
Gleeson, J. A.
,
Heath, M.
,
Pu, S.
,
Switzer, T.
,
Dong, D.
,
Gong, Y.
,
On, T.
,
Xiong, X.
,
Emili, A.
,
Greenblatt, J.
,
Parkinson, J.
,
Zhang, Z.
,
Wodak, S. J.
Journal:
Nucleic Acids Research
Year:
2011
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english
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58
The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection
Galperin, M. Y.
,
Cochrane, G. R.
Journal:
Nucleic Acids Research
Year:
2011
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english
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59
PRIDB: a protein-RNA interface database
Lewis, B. A.
,
Walia, R. R.
,
Terribilini, M.
,
Ferguson, J.
,
Zheng, C.
,
Honavar, V.
,
Dobbs, D.
Journal:
Nucleic Acids Research
Year:
2011
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english
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60
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011
Waterhouse, R. M.
,
Zdobnov, E. M.
,
Tegenfeldt, F.
,
Li, J.
,
Kriventseva, E. V.
Journal:
Nucleic Acids Research
Year:
2011
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english
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61
PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes
Kumar, P.
,
Chaitanya, P. S.
,
Nagarajaram, H. A.
Journal:
Nucleic Acids Research
Year:
2011
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english
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62
PROMISCUOUS: a database for network-based drug-repositioning
von Eichborn, J.
,
Murgueitio, M. S.
,
Dunkel, M.
,
Koerner, S.
,
Bourne, P. E.
,
Preissner, R.
Journal:
Nucleic Acids Research
Year:
2011
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english
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63
Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations
Gonzalez-Galarza, F. F.
,
Christmas, S.
,
Middleton, D.
,
Jones, A. R.
Journal:
Nucleic Acids Research
Year:
2011
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english
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64
mESAdb: microRNA Expression and Sequence Analysis Database
Kaya, K. D.
,
Karakulah, G.
,
Yakicier, C. M.
,
Acar, A. C.
,
Konu, O.
Journal:
Nucleic Acids Research
Year:
2011
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english
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65
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila
Murali, T.
,
Pacifico, S.
,
Yu, J.
,
Guest, S.
,
Roberts, G. G.
,
Finley, R. L.
Journal:
Nucleic Acids Research
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2011
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english
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66
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes
Roberts, R. J.
,
Chang, Y.-C.
,
Hu, Z.
,
Rachlin, J. N.
,
Anton, B. P.
,
Pokrzywa, R. M.
,
Choi, H.-P.
,
Faller, L. L.
,
Guleria, J.
,
Housman, G.
,
Klitgord, N.
,
Mazumdar, V.
,
McGettrick, M. G.
,
Osmani, L.
,
Sw
Journal:
Nucleic Acids Research
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2011
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67
The RNA modification database, RNAMDB: 2011 update
Cantara, W. A.
,
Crain, P. F.
,
Rozenski, J.
,
McCloskey, J. A.
,
Harris, K. A.
,
Zhang, X.
,
Vendeix, F. A. P.
,
Fabris, D.
,
Agris, P. F.
Journal:
Nucleic Acids Research
Year:
2011
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english
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68
FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum
Wong, P.
,
Walter, M.
,
Lee, W.
,
Mannhaupt, G.
,
Munsterkotter, M.
,
Mewes, H.-W.
,
Adam, G.
,
Guldener, U.
Journal:
Nucleic Acids Research
Year:
2011
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english
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69
genenames.org: the HGNC resources in 2011
Seal, R. L.
,
Gordon, S. M.
,
Lush, M. J.
,
Wright, M. W.
,
Bruford, E. A.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 2.15 MB
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70
TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology
Hong, D.
,
Park, S.-S.
,
Ju, Y. S.
,
Kim, S.
,
Shin, J.-Y.
,
Kim, S.
,
Yu, S.-B.
,
Lee, W.-C.
,
Lee, S.
,
Park, H.
,
Kim, J.-I.
,
Seo, J.-S.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
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71
The RCSB Protein Data Bank: redesigned web site and web services
Rose, P. W.
,
Beran, B.
,
Bi, C.
,
Bluhm, W. F.
,
Dimitropoulos, D.
,
Goodsell, D. S.
,
Prlic, A.
,
Quesada, M.
,
Quinn, G. B.
,
Westbrook, J. D.
,
Young, J.
,
Yukich, B.
,
Zardecki, C.
,
Berman, H. M.
,
Bourne, P.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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72
ChemProt: a disease chemical biology database
Taboureau, O.
,
Nielsen, S. K.
,
Audouze, K.
,
Weinhold, N.
,
Edsgard, D.
,
Roque, F. S.
,
Kouskoumvekaki, I.
,
Bora, A.
,
Curpan, R.
,
Jensen, T. S.
,
Brunak, S.
,
Oprea, T. I.
Journal:
Nucleic Acids Research
Year:
2011
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english
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73
MIPS: curated databases and comprehensive secondary data resources in 2010
Mewes, H. W.
,
Ruepp, A.
,
Theis, F.
,
Rattei, T.
,
Walter, M.
,
Frishman, D.
,
Suhre, K.
,
Spannagl, M.
,
Mayer, K. F. X.
,
Stumpflen, V.
,
Antonov, A.
Journal:
Nucleic Acids Research
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2011
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74
Subscriptions
Journal:
Nucleic Acids Research
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2011
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english
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75
GenBank
Benson, D. A.
,
Karsch-Mizrachi, I.
,
Lipman, D. J.
,
Ostell, J.
,
Sayers, E. W.
Journal:
Nucleic Acids Research
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2011
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english
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76
TOPSAN: a dynamic web database for structural genomics
Ellrott, K.
,
Zmasek, C. M.
,
Weekes, D.
,
Sri Krishna, S.
,
Bakolitsa, C.
,
Godzik, A.
,
Wooley, J.
Journal:
Nucleic Acids Research
Year:
2011
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english
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77
IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data
Sharman, J. L.
,
Mpamhanga, C. P.
,
Spedding, M.
,
Germain, P.
,
Staels, B.
,
Dacquet, C.
,
Laudet, V.
,
Harmar, A. J.
Journal:
Nucleic Acids Research
Year:
2011
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english
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78
PCDB: a database of protein conformational diversity
Juritz, E. I.
,
Alberti, S. F.
,
Parisi, G. D.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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79
The IMGT/HLA database
Robinson, J.
,
Mistry, K.
,
McWilliam, H.
,
Lopez, R.
,
Parham, P.
,
Marsh, S. G. E.
Journal:
Nucleic Acids Research
Year:
2011
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english
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80
The Pancreatic Expression database: 2011 update
Cutts, R. J.
,
Gadaleta, E.
,
Hahn, S. A.
,
Crnogorac-Jurcevic, T.
,
Lemoine, N. R.
,
Chelala, C.
Journal:
Nucleic Acids Research
Year:
2011
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english
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81
AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis
Li, P.
,
Zang, W.
,
Li, Y.
,
Xu, F.
,
Wang, J.
,
Shi, T.
Journal:
Nucleic Acids Research
Year:
2011
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english
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82
GlycomeDB--a unified database for carbohydrate structures
Ranzinger, R.
,
Herget, S.
,
von der Lieth, C.-W.
,
Frank, M.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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83
TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins
Schaefer, U.
,
Schmeier, S.
,
Bajic, V. B.
Journal:
Nucleic Acids Research
Year:
2011
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english
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84
SCLD: a stem cell lineage database for the annotation of cell types and developmental lineages
Hemphill, E. E.
,
Dharia, A. P.
,
Lee, C.
,
Jakuba, C. M.
,
Gibson, J. D.
,
Kolling, F. W.
,
Nelson, C. E.
Journal:
Nucleic Acids Research
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2011
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english
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85
Ongoing and future developments at the Universal Protein Resource
Journal:
Nucleic Acids Research
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2011
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english
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86
P2CS: a database of prokaryotic two-component systems
Barakat, M.
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Ortet, P.
,
Whitworth, D. E.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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87
SuperSweet--a resource on natural and artificial sweetening agents
Ahmed, J.
,
Preissner, S.
,
Dunkel, M.
,
Worth, C. L.
,
Eckert, A.
,
Preissner, R.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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88
CPLA 1.0: an integrated database of protein lysine acetylation
Liu, Z.
,
Cao, J.
,
Gao, X.
,
Zhou, Y.
,
Wen, L.
,
Yang, X.
,
Yao, X.
,
Ren, J.
,
Xue, Y.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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89
ViralZone: a knowledge resource to understand virus diversity
Hulo, C.
,
de Castro, E.
,
Masson, P.
,
Bougueleret, L.
,
Bairoch, A.
,
Xenarios, I.
,
Le Mercier, P.
Journal:
Nucleic Acids Research
Year:
2011
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english
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90
UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions
Robasky, K.
,
Bulyk, M. L.
Journal:
Nucleic Acids Research
Year:
2011
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english
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91
HIT: linking herbal active ingredients to targets
Ye, H.
,
Ye, L.
,
Kang, H.
,
Zhang, D.
,
Tao, L.
,
Tang, K.
,
Liu, X.
,
Zhu, R.
,
Liu, Q.
,
Chen, Y. Z.
,
Li, Y.
,
Cao, Z.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 5.51 MB
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92
GreenPhylDB v2.0: comparative and functional genomics in plants
Rouard, M.
,
Guignon, V.
,
Aluome, C.
,
Laporte, M.-A.
,
Droc, G.
,
Walde, C.
,
Zmasek, C. M.
,
Perin, C.
,
Conte, M. G.
Journal:
Nucleic Acids Research
Year:
2011
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english
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93
Rfam: Wikipedia, clans and the "decimal" release
Gardner, P. P.
,
Daub, J.
,
Tate, J.
,
Moore, B. L.
,
Osuch, I. H.
,
Griffiths-Jones, S.
,
Finn, R. D.
,
Nawrocki, E. P.
,
Kolbe, D. L.
,
Eddy, S. R.
,
Bateman, A.
Journal:
Nucleic Acids Research
Year:
2011
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english
File:
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94
The European Nucleotide Archive
Leinonen, R.
,
Akhtar, R.
,
Birney, E.
,
Bower, L.
,
Cerdeno-Tarraga, A.
,
Cheng, Y.
,
Cleland, I.
,
Faruque, N.
,
Goodgame, N.
,
Gibson, R.
,
Hoad, G.
,
Jang, M.
,
Pakseresht, N.
,
Plaister, S.
,
Radhakrishnan, R.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
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95
PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea
Yu, N. Y.
,
Laird, M. R.
,
Spencer, C.
,
Brinkman, F. S. L.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 80 KB
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96
MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis
Gelly, J.-C.
,
Orgeur, M.
,
Jacq, C.
,
Lelandais, G.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
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97
The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes
McCall, M. N.
,
Uppal, K.
,
Jaffee, H. A.
,
Zilliox, M. J.
,
Irizarry, R. A.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
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98
BSDB: the biomolecule stretching database
Sikora, M.
,
Sulkowska, J. I.
,
Witkowski, B. S.
,
Cieplak, M.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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99
DIMA 3.0: Domain Interaction Map
Luo, Q.
,
Pagel, P.
,
Vilne, B.
,
Frishman, D.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 1.18 MB
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100
KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data
Sakurai, N.
,
Ara, T.
,
Ogata, Y.
,
Sano, R.
,
Ohno, T.
,
Sugiyama, K.
,
Hiruta, A.
,
Yamazaki, K.
,
Yano, K.
,
Aoki, K.
,
Aharoni, A.
,
Hamada, K.
,
Yokoyama, K.
,
Kawamura, S.
,
Otsuka, H.
,
Tokimatsu, T.
,
Kanehis
Journal:
Nucleic Acids Research
Year:
2011
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english
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101
Laminin database: a tool to retrieve high-throughput and curated data for studies on laminins
Golbert, D. C. F.
,
Linhares-Lacerda, L.
,
Almeida, L. G.
,
Correa-de-Santana, E.
,
de Oliveira, A. R.
,
Mundstein, A. S.
,
Savino, W.
,
de Vasconcelos, A. T. R.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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PDF, 79 KB
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102
Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies
Kim, D.-N.
,
Altschuler, J.
,
Strong, C.
,
McGill, G.
,
Bathe, M.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 2.43 MB
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103
Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing
Park, B.
,
Park, J.
,
Cheong, K.-C.
,
Choi, J.
,
Jung, K.
,
Kim, D.
,
Lee, Y.-H.
,
Ward, T. J.
,
O'Donnell, K.
,
Geiser, D. M.
,
Kang, S.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 3.86 MB
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104
IGRhCellID: integrated genomic resources of human cell lines for identification
Shiau, C.-K.
,
Gu, D.-L.
,
Chen, C.-F.
,
Lin, C.-H.
,
Jou, Y.-S.
Journal:
Nucleic Acids Research
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2011
Language:
english
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105
Entrez Gene: gene-centered information at NCBI
Maglott, D.
,
Ostell, J.
,
Pruitt, K. D.
,
Tatusova, T.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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PDF, 5.13 MB
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106
dbDNV: a resource of duplicated gene nucleotide variants in human genome
Ho, M.-R.
,
Tsai, K.-W.
,
Chen, C.-h.
,
Lin, W.-c.
Journal:
Nucleic Acids Research
Year:
2011
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english
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107
Ensembl 2011
Flicek, P.
,
Amode, M. R.
,
Barrell, D.
,
Beal, K.
,
Brent, S.
,
Chen, Y.
,
Clapham, P.
,
Coates, G.
,
Fairley, S.
,
Fitzgerald, S.
,
Gordon, L.
,
Hendrix, M.
,
Hourlier, T.
,
Johnson, N.
,
Kahari, A.
,
Keefe, D.
,
K
Journal:
Nucleic Acids Research
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2011
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108
DDPC: Dragon Database of Genes associated with Prostate Cancer
Maqungo, M.
,
Kaur, M.
,
Kwofie, S. K.
,
Radovanovic, A.
,
Schaefer, U.
,
Schmeier, S.
,
Oppon, E.
,
Christoffels, A.
,
Bajic, V. B.
Journal:
Nucleic Acids Research
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2011
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english
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109
SPIKE: a database of highly curated human signaling pathways
Paz, A.
,
Brownstein, Z.
,
Ber, Y.
,
Bialik, S.
,
David, E.
,
Sagir, D.
,
Ulitsky, I.
,
Elkon, R.
,
Kimchi, A.
,
Avraham, K. B.
,
Shiloh, Y.
,
Shamir, R.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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110
The Sequence Read Archive
Leinonen, R.
,
Sugawara, H.
,
Shumway, M.
Journal:
Nucleic Acids Research
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2011
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english
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111
The mouse Gene Expression Database (GXD): 2011 update
Finger, J. H.
,
Smith, C. M.
,
Hayamizu, T. F.
,
McCright, I. J.
,
Eppig, J. T.
,
Kadin, J. A.
,
Richardson, J. E.
,
Ringwald, M.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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112
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes
Winsor, G. L.
,
Lam, D. K. W.
,
Fleming, L.
,
Lo, R.
,
Whiteside, M. D.
,
Yu, N. Y.
,
Hancock, R. E. W.
,
Brinkman, F. S. L.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
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113
NIASGBdb: NIAS Genebank databases for genetic resources and plant disease information
Takeya, M.
,
Yamasaki, F.
,
Uzuhashi, S.
,
Aoki, T.
,
Sawada, H.
,
Nagai, T.
,
Tomioka, K.
,
Tomooka, N.
,
Sato, T.
,
Kawase, M.
Journal:
Nucleic Acids Research
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2011
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english
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114
Nucleic Acids Research
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 51 KB
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115
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
Kawaji, H.
,
Severin, J.
,
Lizio, M.
,
Forrest, A. R. R.
,
van Nimwegen, E.
,
Rehli, M.
,
Schroder, K.
,
Irvine, K.
,
Suzuki, H.
,
Carninci, P.
,
Hayashizaki, Y.
,
Daub, C. O.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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116
PmiRKB: a plant microRNA knowledge base
Meng, Y.
,
Gou, L.
,
Chen, D.
,
Mao, C.
,
Jin, Y.
,
Wu, P.
,
Chen, M.
Journal:
Nucleic Acids Research
Year:
2011
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english
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117
PCRPi-DB: a database of computationally annotated hot spots in protein interfaces
Segura, J.
,
Fernandez-Fuentes, N.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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PDF, 4.62 MB
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118
CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data
Cao, Q.
,
Zhou, M.
,
Wang, X.
,
Meyer, C. A.
,
Zhang, Y.
,
Chen, Z.
,
Li, C.
,
Liu, X. S.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 5.56 MB
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119
ModBase, a database of annotated comparative protein structure models, and associated resources
Pieper, U.
,
Webb, B. M.
,
Barkan, D. T.
,
Schneidman-Duhovny, D.
,
Schlessinger, A.
,
Braberg, H.
,
Yang, Z.
,
Meng, E. C.
,
Pettersen, E. F.
,
Huang, C. C.
,
Datta, R. S.
,
Sampathkumar, P.
,
Madhusudhan, M. S.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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PDF, 6.17 MB
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120
Bovine Genome Database: integrated tools for genome annotation and discovery
Childers, C. P.
,
Reese, J. T.
,
Sundaram, J. P.
,
Vile, D. C.
,
Dickens, C. M.
,
Childs, K. L.
,
Salih, H.
,
Bennett, A. K.
,
Hagen, D. E.
,
Adelson, D. L.
,
Elsik, C. G.
Journal:
Nucleic Acids Research
Year:
2011
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english
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121
ZFIN: enhancements and updates to the zebrafish model organism database
Bradford, Y.
,
Conlin, T.
,
Dunn, N.
,
Fashena, D.
,
Frazer, K.
,
Howe, D. G.
,
Knight, J.
,
Mani, P.
,
Martin, R.
,
Moxon, S. A. T.
,
Paddock, H.
,
Pich, C.
,
Ramachandran, S.
,
Ruef, B. J.
,
Ruzicka, L.
,
Bauer Sc
Journal:
Nucleic Acids Research
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2011
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122
The RIKEN integrated database of mammals
Masuya, H.
,
Makita, Y.
,
Kobayashi, N.
,
Nishikata, K.
,
Yoshida, Y.
,
Mochizuki, Y.
,
Doi, K.
,
Takatsuki, T.
,
Waki, K.
,
Tanaka, N.
,
Ishii, M.
,
Matsushima, A.
,
Takahashi, S.
,
Hijikata, A.
,
Kozaki, K.
,
Furu
Journal:
Nucleic Acids Research
Year:
2011
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123
TMPad: an integrated structural database for helix-packing folds in transmembrane proteins
Lo, A.
,
Cheng, C.-W.
,
Chiu, Y.-Y.
,
Sung, T.-Y.
,
Hsu, W.-L.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 7.31 MB
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124
BISC: Binary SubComplexes in proteins database
Juettemann, T.
,
Gerloff, D. L.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 8.45 MB
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125
CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge
Ahmed, J.
,
Meinel, T.
,
Dunkel, M.
,
Murgueitio, M. S.
,
Adams, R.
,
Blasse, C.
,
Eckert, A.
,
Preissner, S.
,
Preissner, R.
Journal:
Nucleic Acids Research
Year:
2011
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english
File:
PDF, 4.63 MB
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126
COXPRESdb: a database to compare gene coexpression in seven model animals
Obayashi, T.
,
Kinoshita, K.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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PDF, 7.93 MB
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127
CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins
Khorshid, M.
,
Rodak, C.
,
Zavolan, M.
Journal:
Nucleic Acids Research
Year:
2011
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english
File:
PDF, 6.07 MB
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128
OMPdb: a database of -barrel outer membrane proteins from Gram-negative bacteria
Tsirigos, K. D.
,
Bagos, P. G.
,
Hamodrakas, S. J.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 2.30 MB
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129
SUPERFAMILY 1.75 including a domain-centric gene ontology method
de Lima Morais, D. A.
,
Fang, H.
,
Rackham, O. J. L.
,
Wilson, D.
,
Pethica, R.
,
Chothia, C.
,
Gough, J.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 3.75 MB
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130
AGRIS: the Arabidopsis Gene Regulatory Information Server, an update
Yilmaz, A.
,
Mejia-Guerra, M. K.
,
Kurz, K.
,
Liang, X.
,
Welch, L.
,
Grotewold, E.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 5.36 MB
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131
VnD: a structure-centric database of disease-related SNPs and drugs
Yang, J. O.
,
Oh, S.
,
Ko, G.
,
Park, S.-J.
,
Kim, W.-Y.
,
Lee, B.
,
Lee, S.
Journal:
Nucleic Acids Research
Year:
2011
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english
File:
PDF, 2.33 MB
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132
Pathway Commons, a web resource for biological pathway data
Cerami, E. G.
,
Gross, B. E.
,
Demir, E.
,
Rodchenkov, I.
,
Babur, O.
,
Anwar, N.
,
Schultz, N.
,
Bader, G. D.
,
Sander, C.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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PDF, 1.82 MB
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133
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing
Martelli, P. L.
,
D'Antonio, M.
,
Bonizzoni, P.
,
Castrignano, T.
,
D'Erchia, A. M.
,
D'Onorio De Meo, P.
,
Fariselli, P.
,
Finelli, M.
,
Licciulli, F.
,
Mangiulli, M.
,
Mignone, F.
,
Pavesi, G.
,
Picardi, E.
,
Ri
Journal:
Nucleic Acids Research
Year:
2011
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134
TRIP Database: a manually curated database of protein-protein interactions for mammalian TRP channels
Shin, Y.-C.
,
Shin, S.-Y.
,
So, I.
,
Kwon, D.
,
Jeon, J.-H.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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135
Effective--a database of predicted secreted bacterial proteins
Jehl, M.-A.
,
Arnold, R.
,
Rattei, T.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 107 KB
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136
BriX: a database of protein building blocks for structural analysis, modeling and design
Vanhee, P.
,
Verschueren, E.
,
Baeten, L.
,
Stricher, F.
,
Serrano, L.
,
Rousseau, F.
,
Schymkowitz, J.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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PDF, 4.84 MB
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137
Phospho.ELM: a database of phosphorylation sites--update 2011
Dinkel, H.
,
Chica, C.
,
Via, A.
,
Gould, C. M.
,
Jensen, L. J.
,
Gibson, T. J.
,
Diella, F.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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PDF, 3.83 MB
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138
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
Huerta-Cepas, J.
,
Capella-Gutierrez, S.
,
Pryszcz, L. P.
,
Denisov, I.
,
Kormes, D.
,
Marcet-Houben, M.
,
Gabaldon, T.
Journal:
Nucleic Acids Research
Year:
2011
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english
File:
PDF, 4.35 MB
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139
PAIR: the predicted Arabidopsis interactome resource
Lin, M.
,
Shen, X.
,
Chen, X.
Journal:
Nucleic Acids Research
Year:
2011
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english
File:
PDF, 1.87 MB
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140
The RNA helicase database
Jankowsky, A.
,
Guenther, U.-P.
,
Jankowsky, E.
Journal:
Nucleic Acids Research
Year:
2011
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english
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PDF, 3.72 MB
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141
dbCRID: a database of chromosomal rearrangements in human diseases
Kong, F.
,
Zhu, J.
,
Wu, J.
,
Peng, J.
,
Wang, Y.
,
Wang, Q.
,
Fu, S.
,
Yuan, L.-L.
,
Li, T.
Journal:
Nucleic Acids Research
Year:
2011
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english
File:
PDF, 1019 KB
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142
A series of PDB related databases for everyday needs
Joosten, R. P.
,
te Beek, T. A. H.
,
Krieger, E.
,
Hekkelman, M. L.
,
Hooft, R. W. W.
,
Schneider, R.
,
Sander, C.
,
Vriend, G.
Journal:
Nucleic Acids Research
Year:
2011
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english
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PDF, 3.99 MB
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143
OMA 2011: orthology inference among 1000 complete genomes
Altenhoff, A. M.
,
Schneider, A.
,
Gonnet, G. H.
,
Dessimoz, C.
Journal:
Nucleic Acids Research
Year:
2011
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english
File:
PDF, 7.51 MB
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144
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system
Zhu, L. J.
,
Christensen, R. G.
,
Kazemian, M.
,
Hull, C. J.
,
Enuameh, M. S.
,
Basciotta, M. D.
,
Brasefield, J. A.
,
Zhu, C.
,
Asriyan, Y.
,
Lapointe, D. S.
,
Sinha, S.
,
Wolfe, S. A.
,
Brodsky, M. H.
Journal:
Nucleic Acids Research
Year:
2011
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File:
PDF, 5.17 MB
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145
YPA: an integrated repository of promoter features in Saccharomyces cerevisiae
Chang, D. T.-H.
,
Huang, C.-Y.
,
Wu, C.-Y.
,
Wu, W.-S.
Journal:
Nucleic Acids Research
Year:
2011
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english
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146
FINDbase: a worldwide database for genetic variation allele frequencies updated
Georgitsi, M.
,
Viennas, E.
,
Antoniou, D. I.
,
Gkantouna, V.
,
van Baal, S.
,
Petricoin, E. F.
,
Poulas, K.
,
Tzimas, G.
,
Patrinos, G. P.
Journal:
Nucleic Acids Research
Year:
2011
Language:
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PDF, 5.26 MB
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147
Nucleic Acids Research: VOLUME 39 DATABASE ISSUE JANUARY 1, 2011
Journal:
Nucleic Acids Research
Year:
2011
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148
The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium
Ringwald, M.
,
Iyer, V.
,
Mason, J. C.
,
Stone, K. R.
,
Tadepally, H. D.
,
Kadin, J. A.
,
Bult, C. J.
,
Eppig, J. T.
,
Oakley, D. J.
,
Briois, S.
,
Stupka, E.
,
Maselli, V.
,
Smedley, D.
,
Liu, S.
,
Hansen, J.
,
Bal
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 6.19 MB
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149
ThYme: a database for thioester-active enzymes
Cantu, D. C.
,
Chen, Y.
,
Lemons, M. L.
,
Reilly, P. J.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 2.20 MB
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150
ConsensusPathDB: toward a more complete picture of cell biology
Kamburov, A.
,
Pentchev, K.
,
Galicka, H.
,
Wierling, C.
,
Lehrach, H.
,
Herwig, R.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 3.99 MB
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151
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments
Parkinson, H.
,
Sarkans, U.
,
Kolesnikov, N.
,
Abeygunawardena, N.
,
Burdett, T.
,
Dylag, M.
,
Emam, I.
,
Farne, A.
,
Hastings, E.
,
Holloway, E.
,
Kurbatova, N.
,
Lukk, M.
,
Malone, J.
,
Mani, R.
,
Pilicheva, E.
,
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 66 KB
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152
WebGeSTer DB--a transcription terminator database
Mitra, A.
,
Kesarwani, A. K.
,
Pal, D.
,
Nagaraja, V.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 6.27 MB
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153
FragmentStore--a comprehensive database of fragments linking metabolites, toxic molecules and drugs
Ahmed, J.
,
Worth, C. L.
,
Thaben, P.
,
Matzig, C.
,
Blasse, C.
,
Dunkel, M.
,
Preissner, R.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 3.74 MB
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154
CCDB: a curated database of genes involved in cervix cancer
Agarwal, S. M.
,
Raghav, D.
,
Singh, H.
,
Raghava, G. P. S.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
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PDF, 2.62 MB
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155
DBASS3 and DBASS5: databases of aberrant 3'- and 5'-splice sites
Buratti, E.
,
Chivers, M.
,
Hwang, G.
,
Vorechovsky, I.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 2.72 MB
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156
AHD2.0: an update version of Arabidopsis Hormone Database for plant systematic studies
Jiang, Z.
,
Liu, X.
,
Peng, Z.
,
Wan, Y.
,
Ji, Y.
,
He, W.
,
Wan, W.
,
Luo, J.
,
Guo, H.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 10.17 MB
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157
miRGator v2.0 : an integrated system for functional investigation of microRNAs
Cho, S.
,
Jun, Y.
,
Lee, S.
,
Choi, H.-S.
,
Jung, S.
,
Jang, Y.
,
Park, C.
,
Kim, S.
,
Lee, S.
,
Kim, W.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 4.25 MB
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158
PHOSIDA 2011: the posttranslational modification database
Gnad, F.
,
Gunawardena, J.
,
Mann, M.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 9.83 MB
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159
The UCSC cancer genomics browser: update 2011
Sanborn, J. Z.
,
Benz, S. C.
,
Craft, B.
,
Szeto, C.
,
Kober, K. M.
,
Meyer, L.
,
Vaske, C. J.
,
Goldman, M.
,
Smith, K. E.
,
Kuhn, R. M.
,
Karolchik, D.
,
Kent, W. J.
,
Stuart, J. M.
,
Haussler, D.
,
Zhu, J.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 6.73 MB
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english, 2011
160
AgBase: supporting functional modeling in agricultural organisms
McCarthy, F. M.
,
Gresham, C. R.
,
Buza, T. J.
,
Chouvarine, P.
,
Pillai, L. R.
,
Kumar, R.
,
Ozkan, S.
,
Wang, H.
,
Manda, P.
,
Arick, T.
,
Bridges, S. M.
,
Burgess, S. C.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 246 KB
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english, 2011
161
NCBI Epigenomics: a new public resource for exploring epigenomic data sets
Fingerman, I. M.
,
McDaniel, L.
,
Zhang, X.
,
Ratzat, W.
,
Hassan, T.
,
Jiang, Z.
,
Cohen, R. F.
,
Schuler, G. D.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 4.56 MB
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english, 2011
162
AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species
Aurrecoechea, C.
,
Barreto, A.
,
Brestelli, J.
,
Brunk, B. P.
,
Caler, E. V.
,
Fischer, S.
,
Gajria, B.
,
Gao, X.
,
Gingle, A.
,
Grant, G.
,
Harb, O. S.
,
Heiges, M.
,
Iodice, J.
,
Kissinger, J. C.
,
Kraemer, E. T.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 5.54 MB
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english, 2011
163
Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera
Munoz-Torres, M. C.
,
Reese, J. T.
,
Childers, C. P.
,
Bennett, A. K.
,
Sundaram, J. P.
,
Childs, K. L.
,
Anzola, J. M.
,
Milshina, N.
,
Elsik, C. G.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 92 KB
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english, 2011
164
DOMINE: a comprehensive collection of known and predicted domain-domain interactions
Yellaboina, S.
,
Tasneem, A.
,
Zaykin, D. V.
,
Raghavachari, B.
,
Jothi, R.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 4.22 MB
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english, 2011
165
Indian genetic disease database
Pradhan, S.
,
Sengupta, M.
,
Dutta, A.
,
Bhattacharyya, K.
,
Bag, S. K.
,
Dutta, C.
,
Ray, K.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 5.00 MB
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english, 2011
166
The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish
Lu, J.
,
Peatman, E.
,
Yang, Q.
,
Wang, S.
,
Hu, Z.
,
Reecy, J.
,
Kucuktas, H.
,
Liu, Z.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 7.93 MB
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english, 2011
167
Gramene database in 2010: updates and extensions
Youens-Clark, K.
,
Buckler, E.
,
Casstevens, T.
,
Chen, C.
,
DeClerck, G.
,
Derwent, P.
,
Dharmawardhana, P.
,
Jaiswal, P.
,
Kersey, P.
,
Karthikeyan, A. S.
,
Lu, J.
,
McCouch, S. R.
,
Ren, L.
,
Spooner, W.
,
Stein
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 14.76 MB
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english, 2011
168
ENCODE whole-genome data in the UCSC genome browser (2011 update)
Raney, B. J.
,
Cline, M. S.
,
Rosenbloom, K. R.
,
Dreszer, T. R.
,
Learned, K.
,
Barber, G. P.
,
Meyer, L. R.
,
Sloan, C. A.
,
Malladi, V. S.
,
Roskin, K. M.
,
Suh, B. B.
,
Hinrichs, A. S.
,
Clawson, H.
,
Zweig, A
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 1.87 MB
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english, 2011
169
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource
Sun, S.
,
Chen, J.
,
Li, W.
,
Altintas, I.
,
Lin, A.
,
Peltier, S.
,
Stocks, K.
,
Allen, E. E.
,
Ellisman, M.
,
Grethe, J.
,
Wooley, J.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 3.43 MB
Your tags:
english, 2011
170
VKCDB: voltage-gated K+ channel database updated and upgraded
Gallin, W. J.
,
Boutet, P. A.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 4.20 MB
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english, 2011
171
MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data
Gupta, R.
,
Bhattacharyya, A.
,
Agosto-Perez, F. J.
,
Wickramasinghe, P.
,
Davuluri, R. V.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 4.54 MB
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english, 2011
172
The Autophagy Database: an all-inclusive information resource on autophagy that provides nourishment for research
Homma, K.
,
Suzuki, K.
,
Sugawara, H.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 3.03 MB
Your tags:
english, 2011
173
CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality
Endo, T.
,
Ueno, K.
,
Yonezawa, K.
,
Mineta, K.
,
Hotta, K.
,
Satou, Y.
,
Yamada, L.
,
Ogasawara, M.
,
Takahashi, H.
,
Nakajima, A.
,
Nakachi, M.
,
Nomura, M.
,
Yaguchi, J.
,
Sasakura, Y.
,
Yamasaki, C.
,
Sera, M.
,
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 2.67 MB
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english, 2011
174
The International Nucleotide Sequence Database Collaboration
Cochrane, G.
,
Karsch-Mizrachi, I.
,
Nakamura, Y.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 1.32 MB
Your tags:
english, 2011
175
Full-parasites: database of full-length cDNAs of apicomplexa parasites, 2010 update
Tuda, J.
,
Mongan, A. E.
,
Tolba, M. E. M.
,
Imada, M.
,
Yamagishi, J.
,
Xuan, X.
,
Wakaguri, H.
,
Sugano, S.
,
Sugimoto, C.
,
Suzuki, Y.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 4.31 MB
Your tags:
english, 2011
176
New tools and methods for direct programmatic access to the dbSNP relational database
Saccone, S. F.
,
Quan, J.
,
Mehta, G.
,
Bolze, R.
,
Thomas, P.
,
Deelman, E.
,
Tischfield, J. A.
,
Rice, J. P.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 1.99 MB
Your tags:
english, 2011
177
YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface
Abdulrehman, D.
,
Monteiro, P. T.
,
Teixeira, M. C.
,
Mira, N. P.
,
Lourenco, A. B.
,
dos Santos, S. C.
,
Cabrito, T. R.
,
Francisco, A. P.
,
Madeira, S. C.
,
Aires, R. S.
,
Oliveira, A. L.
,
Sa-Correia, I.
,
Fre
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 1.48 MB
Your tags:
english, 2011
178
RepTar: a database of predicted cellular targets of host and viral miRNAs
Elefant, N.
,
Berger, A.
,
Shein, H.
,
Hofree, M.
,
Margalit, H.
,
Altuvia, Y.
Journal:
Nucleic Acids Research
Year:
2011
Language:
english
File:
PDF, 4.17 MB
Your tags:
english, 2011
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