-
1
-
-
3042641339
-
Correction of sequence-based artifacts in serial analysis of gene expression
-
Akmaev,V.R. and Wang,C.J. (2004) Correction of sequence-based artifacts in serial analysis of gene expression. Bioinformatics, 20, 1254-1263.
-
(2004)
Bioinformatics
, vol.20
, pp. 1254-1263
-
-
Akmaev, V.R.1
Wang, C.J.2
-
2
-
-
0037350957
-
SLAM: Cross-species gene finding and alignment with a generalized pair hidden Markov model
-
Alexandersson,M., Cawley,S. and Pachter,L. (2003) SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res., 13, 496-502.
-
(2003)
Genome Res.
, vol.13
, pp. 496-502
-
-
Alexandersson, M.1
Cawley, S.2
Pachter, L.3
-
3
-
-
0025183708
-
Basic local alignment search tool
-
Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
4
-
-
0034834248
-
Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data
-
Beaudoing,E. and Gautheret,D. (2001) Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data. Genome Res., 11, 1520-1526.
-
(2001)
Genome Res.
, vol.11
, pp. 1520-1526
-
-
Beaudoing, E.1
Gautheret, D.2
-
5
-
-
2442706422
-
An overview of Ensembl
-
Birney,E., Andrews,T.D., Bevan,P., Caccamo,M., Chen,Y., Clarke,L., Coates,G., Cuff,J., Curwen,V., Cutts,T. et al. (2004a) An overview of Ensembl. Genome Res., 14, 925-928.
-
(2004)
Genome Res.
, vol.14
, pp. 925-928
-
-
Birney, E.1
Andrews, T.D.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
-
6
-
-
2442713832
-
GeneWise and genomewise
-
Birney,E., Clamp,M. and Durbin,R. (2004b) 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
-
7
-
-
0036338127
-
Alternative splicing and genome complexity
-
Brett,D., Pospisil,H., Valcarcel,J., Reich,J. and Bork,P. (2002) Alternative splicing and genome complexity. Nat. Genet., 30, 29-30.
-
(2002)
Nat. Genet.
, vol.30
, pp. 29-30
-
-
Brett, D.1
Pospisil, H.2
Valcarcel, J.3
Reich, J.4
Bork, P.5
-
8
-
-
9144234728
-
The Mouse Genome Database (MGD): Integrating biology with the genome
-
(Database issue)
-
Bult,C.J., Blake,J.A., Richardson,J.E., Kadin,J.A., Eppig,J.T., Baldarelli,R.M., Barsanti,K., Baya,M., Beal,J.S., Boddy,W.J. et al. (2004) The Mouse Genome Database (MGD): integrating biology with the genome. Nucleic Acids Res., 32, (Database issue), D476-D481.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Bult, C.J.1
Blake, J.A.2
Richardson, J.E.3
Kadin, J.A.4
Eppig, J.T.5
Baldarelli, R.M.6
Barsanti, K.7
Baya, M.8
Beal, J.S.9
Boddy, W.J.10
-
9
-
-
0031586003
-
Prediction of complete gene structures in human genomic DNA
-
Burge,C. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
-
(1997)
J. Mol. Biol.
, vol.268
, pp. 78-94
-
-
Burge, C.1
Karlin, S.2
-
10
-
-
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
-
11
-
-
0031955518
-
Base-calling of automated sequencer traces using phred. I. Accuracy assessment
-
Ewing,B., Hillier,L., Wendl,M.C. and Green,P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res., 8, 175-185.
-
(1998)
Genome Res.
, vol.8
, pp. 175-185
-
-
Ewing, B.1
Hillier, L.2
Wendl, M.C.3
Green, P.4
-
12
-
-
4344623260
-
Integrative annotation of 21,037 human genes validated by full-length cDNA clones
-
Imanishi,T., Itoh,T., Suzuki,Y., O'Donovan,C., Fukuchi,S., Koyanagi,K.O., Barrero,R.A., Tamura,T., Yamaguchi-Kabata,Y., Tanino,M. et al. (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol., 2, E162.
-
(2004)
PLoS Biol.
, vol.2
-
-
Imanishi, T.1
Itoh, T.2
Suzuki, Y.3
O'Donovan, C.4
Fukuchi, S.5
Koyanagi, K.O.6
Barrero, R.A.7
Tamura, T.8
Yamaguchi-Kabata, Y.9
Tanino, M.10
-
13
-
-
0037370478
-
Bioinformatics in the post-sequence era
-
Kanehisa,M. and Bork,P. (2003) Bioinformatics in the post-sequence era. Nat. Genet., 33(suppl.), 305-310.
-
(2003)
Nat. Genet.
, vol.33
, Issue.SUPPL.
, pp. 305-310
-
-
Kanehisa, M.1
Bork, P.2
-
14
-
-
0037079054
-
Computational systems biology
-
Kitano,H. (2002) Computational systems biology. Nature, 420, 206-210.
-
(2002)
Nature
, vol.420
, pp. 206-210
-
-
Kitano, H.1
-
15
-
-
0042968976
-
The power of the 3′ UTR: Translational control and development
-
Kuersten,S. and Goodwin,E.B. (2003) The power of the 3′ UTR: translational control and development. Nat. Rev. Genet., 4 626-637.
-
(2003)
Nat. Rev. Genet.
, vol.4
, pp. 626-637
-
-
Kuersten, S.1
Goodwin, E.B.2
-
16
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander,E.S., Linton,L.M., Birren,B., Nusbaum,C., Zody,M.C., Baldwin,J., Devon,K., Dewar,K., Doyle,M., FitzHugh,W. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409 860-921.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
Linton, L.M.2
Birren, B.3
Nusbaum, C.4
Zody, M.C.5
Baldwin, J.6
Devon, K.7
Dewar, K.8
Doyle, M.9
FitzHugh, W.10
-
17
-
-
0033853089
-
SAGEmap: A public gene expression resource
-
Lash,A.E., Tolstoshev,C.M., Wagner,L., Schuler,G.D., Strausberg,R.L., Riggins,G.J. and Altschul,S.F. (2000) SAGEmap: a public gene expression resource. Genome Res., 10, 1051-1060.
-
(2000)
Genome Res.
, vol.10
, pp. 1051-1060
-
-
Lash, A.E.1
Tolstoshev, C.M.2
Wagner, L.3
Schuler, G.D.4
Strausberg, R.L.5
Riggins, G.J.6
Altschul, S.F.7
-
18
-
-
0034761768
-
A comparative molecular analysis of developing mouse forelimbs and hindlimbs using serial analysis of gene expression (SAGE)
-
Margulies,E.H., Kardia,S.L. and Innis,J.W. (2001) A comparative molecular analysis of developing mouse forelimbs and hindlimbs using serial analysis of gene expression (SAGE). Genome Res. 11, 1686-1698.
-
(2001)
Genome Res.
, vol.11
, pp. 1686-1698
-
-
Margulies, E.H.1
Kardia, S.L.2
Innis, J.W.3
-
19
-
-
9144270582
-
Gene expression analysis of plant host-pathogen interactions by SuperSAGE
-
Matsumura,H., Reich,S., Ito,A., Saitoh,H., Kamoun,S., Winter,P., Kahl,G., Reuter,M., Kruger,D.H. and Terauchi,R. (2003) Gene expression analysis of plant host-pathogen interactions by SuperSAGE. Proc. Natl Acad. Sci. USA, 100, 15718-15723.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 15718-15723
-
-
Matsumura, H.1
Reich, S.2
Ito, A.3
Saitoh, H.4
Kamoun, S.5
Winter, P.6
Kahl, G.7
Reuter, M.8
Kruger, D.H.9
Terauchi, R.10
-
20
-
-
0142104045
-
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
-
Okazaki,Y., Furuno,M., Kasukawa,T., Adachi,J., Bono,H., Kondo,S., Nikaido,I., Osato,N., Saito,R., Suzuki,H. et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420, 563-573.
-
(2002)
Nature
, vol.420
, pp. 563-573
-
-
Okazaki, Y.1
Furuno, M.2
Kasukawa, T.3
Adachi, J.4
Bono, H.5
Kondo, S.6
Nikaido, I.7
Osato, N.8
Saito, R.9
Suzuki, H.10
-
21
-
-
0141789672
-
RNA binding protein sex-lethal (Sxl) and control of Drosophila sex determination and dosage compensation
-
Penalva,L.O. and Sanchez,L. (2003) RNA binding protein sex-lethal (Sxl) and control of Drosophila sex determination and dosage compensation. Microbiol. Mol. Biol. Rev., 67, 343-359.
-
(2003)
Microbiol. Mol. Biol. Rev.
, vol.67
, pp. 343-359
-
-
Penalva, L.O.1
Sanchez, L.2
-
22
-
-
0037803473
-
Assessment of SAGE in transcript identification
-
Pleasance,E.D., Marra,M.A. and Jones,S.J. (2003) Assessment of SAGE in transcript identification. Genome Res., 13, 1203-1215.
-
(2003)
Genome Res.
, vol.13
, pp. 1203-1215
-
-
Pleasance, E.D.1
Marra, M.A.2
Jones, S.J.3
-
23
-
-
0035002807
-
Evaluation of gene-finding programs on mammalian sequences
-
Rogic,S., Mackworth,A.K. and Ouellette,F.B. (2001) Evaluation of gene-finding programs on mammalian sequences. Genome Res., 11 817-832.
-
(2001)
Genome Res.
, vol.11
, pp. 817-832
-
-
Rogic, S.1
Mackworth, A.K.2
Ouellette, F.B.3
-
24
-
-
0036246030
-
Using the transcriptome to annotate the genome
-
Saha,S., Sparks,A.B., Rago,C., Akmaev,V., Wang,C.J., Vogelstein,B., Kinzler,K.W. and Velculescu,V.E. (2002) Using the transcriptome to annotate the genome. Nat. Biotechnol., 20, 508-512.
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 508-512
-
-
Saha, S.1
Sparks, A.B.2
Rago, C.3
Akmaev, V.4
Wang, C.J.5
Vogelstein, B.6
Kinzler, K.W.7
Velculescu, V.E.8
-
25
-
-
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
-
26
-
-
18644368714
-
The Bioperl toolkit: Perl modules for the life sciences
-
Stajich,J.E., Block,D., Boulez,K., Brenner,S.E., Chervitz,S.A., Dagdigian,C., Fuellen,G., Gilbert,J.G., Korf,I., Lapp,H. et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res., 12, 1611-1618.
-
(2002)
Genome Res.
, vol.12
, pp. 1611-1618
-
-
Stajich, J.E.1
Block, D.2
Boulez, K.3
Brenner, S.E.4
Chervitz, S.A.5
Dagdigian, C.6
Fuellen, G.7
Gilbert, J.G.8
Korf, I.9
Lapp, H.10
-
27
-
-
0035408587
-
Genome annotation: From sequence to biology
-
Stein,L. (2001) Genome annotation: from sequence to biology. Nat. Rev. Genet., 2, 493-503.
-
(2001)
Nat. Rev. Genet.
, vol.2
, pp. 493-503
-
-
Stein, L.1
-
28
-
-
2442679088
-
SAGE is far more sensitive than EST for detecting low-abundance transcripts
-
Sun,M., Zhou,G., Lee,S., Chen,J., Shi,R.Z. and Wang,S.M. (2004) SAGE is far more sensitive than EST for detecting low-abundance transcripts. BMC Genomics, 5, 1.
-
(2004)
BMC Genomics
, vol.5
, pp. 1
-
-
Sun, M.1
Zhou, G.2
Lee, S.3
Chen, J.4
Shi, R.Z.5
Wang, S.M.6
-
29
-
-
0028789793
-
Serial analysis of gene expression
-
Velculescu,V.E., Zhang,L., Vogelstein,B. and Kinzler,K.W. (1995) Serial analysis of gene expression. Science, 270, 484-487.
-
(1995)
Science
, vol.270
, pp. 484-487
-
-
Velculescu, V.E.1
Zhang, L.2
Vogelstein, B.3
Kinzler, K.W.4
-
30
-
-
17444377577
-
LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome
-
Wahl,M., Heinzmann,U. and Imai,K. (2005) LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome. Bioinformatics, 21, 1391-1394.
-
(2005)
Bioinformatics
, vol.21
, pp. 1391-1394
-
-
Wahl, M.1
Heinzmann, U.2
Imai, K.3
-
31
-
-
0344688180
-
Transcriptome analysis of early chondrogenesis in ATDC5 cells induced by bone morphogenetic protein 4
-
Wahl,M., Shukunami,C., Heinzmann,U., Hamajima,K., Hiraki,Y. and Imai,K. (2004) Transcriptome analysis of early chondrogenesis in ATDC5 cells induced by bone morphogenetic protein 4. Genomics, 83, 45-58.
-
(2004)
Genomics
, vol.83
, pp. 45-58
-
-
Wahl, M.1
Shukunami, C.2
Heinzmann, U.3
Hamajima, K.4
Hiraki, Y.5
Imai, K.6
-
32
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Waterston,A.H., Lindblad-Toh,K., Birney,E., Rogers,J., Abril,J.F., Agarwal,P., Agarwala,R., Ainscough,R., Alexandersson,M., An,P. et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Waterston, A.H.1
Lindblad-Toh, K.2
Birney, E.3
Rogers, J.4
Abril, J.F.5
Agarwal, P.6
Agarwala, R.7
Ainscough, R.8
Alexandersson, M.9
An, P.10
-
33
-
-
9144233525
-
Database resources of the National Center for Biotechnology Information: Update
-
(Database issue)
-
Wheeler,D.L., Church,D.M., Edgar,R., Federhen,S., Helmberg,W., Madden,T.L., Pontius,J.U., Schuler,G.D., Schriml,L.M., Sequeira,E. et al. (2004) Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res., 32 Database issue), D35-D40.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Wheeler, D.L.1
Church, D.M.2
Edgar, R.3
Federhen, S.4
Helmberg, W.5
Madden, T.L.6
Pontius, J.U.7
Schuler, G.D.8
Schriml, L.M.9
Sequeira, E.10
-
34
-
-
0038349624
-
Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome
-
Zavolan,M., Kondo,S., Schonbach,C., Adachi,J., Hume,D.A., Hayashizaki,Y. and Gaasterland,T. (2003) Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res., 13 1290-1300.
-
(2003)
Genome Res.
, vol.13
, pp. 1290-1300
-
-
Zavolan, M.1
Kondo, S.2
Schonbach, C.3
Adachi, J.4
Hume, D.A.5
Hayashizaki, Y.6
Gaasterland, T.7
-
35
-
-
0036733640
-
Computational prediction of eukaryotic protein-coding genes
-
Zhang,M.Q. (2002) Computational prediction of eukaryotic protein-coding genes. Nat. Rev. Genet., 3, 698-709.
-
(2002)
Nat. Rev. Genet.
, vol.3
, pp. 698-709
-
-
Zhang, M.Q.1
|