-
1
-
-
33644874573
-
The UCSC Genome Browser Database: Update 2006
-
Hinrichs,A.S., Karolchik,D., Baertsch,R., Barber,G.P., Bejerano,G., Clawson,H., Diekhans,M., Furey,T.S., Harte,R.A., Hsu,F. et al. (2006) The UCSC Genome Browser Database: Update 2006. Nucleic Acids Res., 34, D590-D598.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Hinrichs, A.S.1
Karolchik, D.2
Baertsch, R.3
Barber, G.P.4
Bejerano, G.5
Clawson, H.6
Diekhans, M.7
Furey, T.S.8
Harte, R.A.9
Hsu, F.10
-
2
-
-
33644876253
-
Database resources of the National Center for Biotechnology Information
-
Wheeler,D.L., Barrett,T., Benson,D.A., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., DiCuccio,M., Edgar,R., Federhen,S. et al. (2006) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 34, D173-D180.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Wheeler, D.L.1
Barrett, T.2
Benson, D.A.3
Bryant, S.H.4
Canese, K.5
Chetvernin, V.6
Church, D.M.7
DiCuccio, M.8
Edgar, R.9
Federhen, S.10
-
3
-
-
13444304332
-
The Vertebrate Genome Annotation (Vega) database
-
Ashurst,J.L., Chen,C.K., Gilbert,J.G., Jekosch,K., Keenan,S., Meidl,P., Searle,S.M., Stalker,J., Storey,R., Trevanion,S. et al. (2005) The Vertebrate Genome Annotation (Vega) database. Nucleic Acids Res., 33, D459-D465.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Ashurst, J.L.1
Chen, C.K.2
Gilbert, J.G.3
Jekosch, K.4
Keenan, S.5
Meidl, P.6
Searle, S.M.7
Stalker, J.8
Storey, R.9
Trevanion, S.10
-
4
-
-
33644873213
-
The Universal Protein Resource (UniProt): An expanding universe of protein information
-
Wu,C.H., Apweiler,R., Bairoch,A., Natale,D.A., Barker,W.C., Boeckmann,B., Ferro,S., Gasteiger,E., Huang,H., Lopez,R. et al. (2006) The Universal Protein Resource (UniProt): An expanding universe of protein information. Nucleic Acids Res., 34, D187-D191.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Wu, C.H.1
Apweiler, R.2
Bairoch, A.3
Natale, D.A.4
Barker, W.C.5
Boeckmann, B.6
Ferro, S.7
Gasteiger, E.8
Huang, H.9
Lopez, R.10
-
5
-
-
33750460281
-
Insights into social insects from the genome of the honeybee Apis mellifera
-
The Honeybee Genome Sequencing Consortium
-
The Honeybee Genome Sequencing Consortium (2006) Insights into social insects from the genome of the honeybee Apis mellifera. Nature, 443, 931-949.
-
(2006)
Nature
, vol.443
, pp. 931-949
-
-
-
6
-
-
33644863282
-
WormBase: Better software, richer content
-
Schwarz,E.M., Antoshechkin,I., Bastiani,C., Bieri,T., Blasiar,D., Canaran,P., Chan,J., Chen,N., Chen,W.J., Davis,P. et al. (2006) WormBase: Better software, richer content. Nucleic Acids Res., 34, D475-D478.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Schwarz, E.M.1
Antoshechkin, I.2
Bastiani, C.3
Bieri, T.4
Blasiar, D.5
Canaran, P.6
Chan, J.7
Chen, N.8
Chen, W.J.9
Davis, P.10
-
7
-
-
9144269670
-
EnsMart: A generic system for fast and flexible access to biological data
-
Kasprzyk,A., Keefe,D., Smedley,D., London,D., Spooner,W., Melsopp,C., Hammond,M., Rocca-Serra,P., Cox,T. and Birney,E. (2004) EnsMart: A generic system for fast and flexible access to biological data. Genome Res., 14, 160-169.
-
(2004)
Genome Res.
, vol.14
, pp. 160-169
-
-
Kasprzyk, A.1
Keefe, D.2
Smedley, D.3
London, D.4
Spooner, W.5
Melsopp, C.6
Hammond, M.7
Rocca-Serra, P.8
Cox, T.9
Birney, E.10
-
8
-
-
2442706422
-
An overview of Ensembl
-
Birney,E., Andrews,D.T., Bevan,P., Caccamo,M., Chen,Y., Clarke,L., Coates,G., Cuff,J., Curwen,V., Cutts,T. et al. (2004) An overview of Ensembl. Genome Res., 14, 925-928.
-
(2004)
Genome Res.
, vol.14
, pp. 925-928
-
-
Birney, E.1
Andrews, D.T.2
Bevan, P.3
Caccamo, M.4
Chen, Y.5
Clarke, L.6
Coates, G.7
Cuff, J.8
Curwen, V.9
Cutts, T.10
-
9
-
-
2442713832
-
GeneWise and genomewise
-
Birney,E., Clamp,M. and Durbin,R. (2004) GeneWise and genomewise. Genome Res., 14, 988-995.
-
(2004)
Genome Res.
, vol.14
, pp. 988-995
-
-
Birney, E.1
Clamp, M.2
Durbin, R.3
-
10
-
-
2442712567
-
The Ensembl computing architecture
-
Cuff,J.A., Coates,G.M., Cutts,T.J. and Rae,M. (2004) The Ensembl computing architecture. Genome Res., 14, 971-975.
-
(2004)
Genome Res.
, vol.14
, pp. 971-975
-
-
Cuff, J.A.1
Coates, G.M.2
Cutts, T.J.3
Rae, M.4
-
11
-
-
2442707676
-
The Ensembl automatic gene annotation system
-
Curwen,V., Eyras,E., Andrews,T.D., Clarke,L., Mongin,E., Searle,S.M. and Clamp,M. (2004) The Ensembl automatic gene annotation system. Genome Res., 14, 942-950.
-
(2004)
Genome Res.
, vol.14
, pp. 942-950
-
-
Curwen, V.1
Eyras, E.2
Andrews, T.D.3
Clarke, L.4
Mongin, E.5
Searle, S.M.6
Clamp, M.7
-
12
-
-
2442700175
-
ESTGenes: Alternative splicing from ESTs in Ensembl
-
Eyras,E., Caccamo,M., Curwen,V. and Clamp,M. (2004) ESTGenes: alternative splicing from ESTs in Ensembl. Genome Res., 14, 976-987.
-
(2004)
Genome Res.
, vol.14
, pp. 976-987
-
-
Eyras, E.1
Caccamo, M.2
Curwen, V.3
Clamp, M.4
-
13
-
-
2442689013
-
The Ensembl analysis pipeline
-
Potter,S.C., Clarke,L., Curwen,V., Keenan,S., Mongin,E., Searle,S.M., Stabenau,A., Storey,R. and Clamp,M. (2004) The Ensembl analysis pipeline. Genome Res., 14, 934-941.
-
(2004)
Genome Res.
, vol.14
, pp. 934-941
-
-
Potter, S.C.1
Clarke, L.2
Curwen, V.3
Keenan, S.4
Mongin, E.5
Searle, S.M.6
Stabenau, A.7
Storey, R.8
Clamp, M.9
-
14
-
-
2442665184
-
The otter annotation system
-
Searle,S.M., Gilbert,J., Iyer,V. and Clamp,M. (2004) The otter annotation system. Genome Res., 14, 963-970.
-
(2004)
Genome Res.
, vol.14
, pp. 963-970
-
-
Searle, S.M.1
Gilbert, J.2
Iyer, V.3
Clamp, M.4
-
15
-
-
2442666425
-
The Ensembl core software libraries
-
Stabenau,A., McVicker,G., Melsopp,C., Proctor,G., Clamp,M. and Birney,E. (2004) The Ensembl core software libraries. Genome Res., 14, 929-933.
-
(2004)
Genome Res.
, vol.14
, pp. 929-933
-
-
Stabenau, A.1
McVicker, G.2
Melsopp, C.3
Proctor, G.4
Clamp, M.5
Birney, E.6
-
16
-
-
2442718832
-
The Ensembl website: Mechanics of a genome browser
-
Stalker,J., Gibbins,B., Meidl,P., Smith,J., Spooner,W., Hotz,H.R. and Cox,A.V. (2004) The Ensembl website: Mechanics of a genome browser. Genome Res., 14, 951-955.
-
(2004)
Genome Res.
, vol.14
, pp. 951-955
-
-
Stalker, J.1
Gibbins, B.2
Meidl, P.3
Smith, J.4
Spooner, W.5
Hotz, H.R.6
Cox, A.V.7
-
17
-
-
33644876924
-
Ensembl 2006
-
Birney,E., Andrews,D., Caccamo,M., Chen,Y., Clarke,L., Coates,G., Cox,T., Cunningham,F., Curwen,V., Cutts,T. et al. (2006) Ensembl 2006. Nucleic Acids Res., 34, D556-D561.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Birney, E.1
Andrews, D.2
Caccamo, M.3
Chen, Y.4
Clarke, L.5
Coates, G.6
Cox, T.7
Cunningham, F.8
Curwen, V.9
Cutts, T.10
-
18
-
-
0037267806
-
Human-mouse alignments with BLASTZ
-
Schwartz,S., Kent,W.J., Smit,A., Zhang,Z., Baertsch,R., Hardison,R.C., Haussler,D. and Miller,W. (2003) Human-mouse alignments with BLASTZ. Genome Res., 13, 103-107.
-
(2003)
Genome Res.
, vol.13
, pp. 103-107
-
-
Schwartz, S.1
Kent, W.J.2
Smit, A.3
Zhang, Z.4
Baertsch, R.5
Hardison, R.C.6
Haussler, D.7
Miller, W.8
-
19
-
-
0141815478
-
Evolution's cauldron: Duplication, deletion and rearrangement in the mouse and human genomes
-
Kent,W.J., Baertsch,R., Hinrichs,A., Miller,W. and Haussler,D. (2003) Evolution's cauldron: Duplication, deletion and rearrangement in the mouse and human genomes. Proc. Natl Acad. Sci. USA, 100, 11484-11489.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 11484-11489
-
-
Kent, W.J.1
Baertsch, R.2
Hinrichs, A.3
Miller, W.4
Haussler, D.5
-
20
-
-
0023988195
-
Genomic mapping by fingerprinting random clones: A mathematical analysis
-
Lander,E.S. and Waterman,M.S. (1988) Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics, 2, 231-239.
-
(1988)
Genomics
, vol.2
, pp. 231-239
-
-
Lander, E.S.1
Waterman, M.S.2
-
21
-
-
7444260846
-
The ENCODE (ENCyclopedia Of DNA Elements) Project
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306, 636-640.
-
(2004)
Science
, vol.306
, pp. 636-640
-
-
-
22
-
-
33748641351
-
EGASP: The human ENCODE Genome Annotation Assessment Project
-
Guigó,R., Flicek,P., Abril,J.F., Reymond,A., Lagarde,J., Denoeud,F., Antonarakis,S., Ashburner,M., Bajic,V.B., Birney,B. et al. (2006) EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol., 7, S2.
-
(2006)
Genome Biol.
, vol.7
-
-
Guigó, R.1
Flicek, P.2
Abril, J.F.3
Reymond, A.4
Lagarde, J.5
Denoeud, F.6
Antonarakis, S.7
Ashburner, M.8
Bajic, V.B.9
Birney, B.10
-
23
-
-
33748645500
-
GENCODE: Producing a reference annotation for ENCODE
-
Harrow,J., Denoeud,F., Frankish,A., Reymond,A., Chen,C.K., Chrast,J., Lagarde,J., Gilbert,J.G., Storey,R., Swarbreck,D. et al. (2006) GENCODE: producing a reference annotation for ENCODE. Genome Biol., 7 (Suppl. 1), S4.1-S4.9.
-
(2006)
Genome Biol.
, vol.7
, Issue.SUPPL. 1
-
-
Harrow, J.1
Denoeud, F.2
Frankish, A.3
Reymond, A.4
Chen, C.K.5
Chrast, J.6
Lagarde, J.7
Gilbert, J.G.8
Storey, R.9
Swarbreck, D.10
-
24
-
-
0034764307
-
SSAHA: A fast search method for large DNA databases
-
Ning,Z., Cox,A.J. and Mullikin,J.C. (2001) SSAHA: A fast search method for large DNA databases. Genome Res., 11, 1725-1729.
-
(2001)
Genome Res.
, vol.11
, pp. 1725-1729
-
-
Ning, Z.1
Cox, A.J.2
Mullikin, J.C.3
-
25
-
-
33746540479
-
TranscriptSNPView: A genome-wide catalog of mouse coding variation
-
Cunningham,F., Rios,D., Griffiths,M., Smith,J., Ning,Z., Cox,T., Flicek,P., Marin-Garcin,P., Herrero,J., Rogers,J. et al. (2006) TranscriptSNPView: A genome-wide catalog of mouse coding variation. Nature Genet., 38, 853.
-
(2006)
Nature Genet.
, vol.38
, pp. 853
-
-
Cunningham, F.1
Rios, D.2
Griffiths, M.3
Smith, J.4
Ning, Z.5
Cox, T.6
Flicek, P.7
Marin-Garcin, P.8
Herrero, J.9
Rogers, J.10
-
26
-
-
28644447707
-
Genome sequence, comparative analysis and haplotype structure of the domestic dog
-
Lindblad-Toh,K., Wade,C.M., Mikkelsen,T.S., Karlsson,E.K., Jaffe,D.B., Kamal,M., Clamp,M., Chang,J.L., Kulbokas,E.J., III, Zody,M.C. et al. (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature, 438, 803-819.
-
(2005)
Nature
, vol.438
, pp. 803-819
-
-
Lindblad-Toh, K.1
Wade, C.M.2
Mikkelsen, T.S.3
Karlsson, E.K.4
Jaffe, D.B.5
Kamal, M.6
Clamp, M.7
Chang, J.L.8
Kulbokas III, E.J.9
Zody, M.C.10
-
27
-
-
0242578620
-
A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon,S. and Gascuel,O. (2003) A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol., 52, 696-704.
-
(2003)
Syst. Biol.
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
28
-
-
13244255415
-
MUSCLE: A multiple sequence alignment method with reduced time and space complexity
-
Edgar,R.C. (2004) MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
29
-
-
20744436518
-
Tree pattern matching in phylogenetic trees: Automatic search for orthologs or paralogs in homologous gene sequence databases
-
Dufayard,J.F., Duret,L., Penel,S., Gouy,M., Rechenmann,F. and Perriere,G. (2005) Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics, 21, 2596-2603.
-
(2005)
Bioinformatics
, vol.21
, pp. 2596-2603
-
-
Dufayard, J.F.1
Duret, L.2
Penel, S.3
Gouy, M.4
Rechenmann, F.5
Perriere, G.6
-
30
-
-
33644876458
-
TreeFam: A curated database of phylogenetic trees of animal gene families
-
Li,H., Coghlan,A., Ruan,J., Coin,L.J., Heriche,J.K., Osmotherly,L., Li,R., Liu,T., Zhang,Z., Bolund,L. et al. (2006) TreeFam: A curated database of phylogenetic trees of animal gene families. Nucleic Acids Res., 34, D572-D580.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Li, H.1
Coghlan, A.2
Ruan, J.3
Coin, L.J.4
Heriche, J.K.5
Osmotherly, L.6
Li, R.7
Liu, T.8
Zhang, Z.9
Bolund, L.10
-
31
-
-
33747884344
-
Data storage and analysis in ArrayExpress
-
Brazma,A., Kapushesky,M., Parkinson,H., Sarkans,U. and Shojatalab,M. (2006) Data storage and analysis in ArrayExpress. Meth. Enzymol., 411, 370-386.
-
(2006)
Meth. Enzymol.
, vol.411
, pp. 370-386
-
-
Brazma, A.1
Kapushesky, M.2
Parkinson, H.3
Sarkans, U.4
Shojatalab, M.5
|