-
1
-
-
0029653518
-
Wholegenome random sequencing and assembly of Haemophilus influenzae Rd
-
Fleischmann RD, Adams MD, White O, et al. Wholegenome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995;269:496-512.
-
(1995)
Science
, vol.269
, pp. 496-512
-
-
Fleischmann, R.D.1
Adams, M.D.2
White, O.3
-
2
-
-
0028829125
-
The minimal gene complement of Mycoplasma genitalium
-
Fraser CM, Gocayne JD, White O, et al. The minimal gene complement of Mycoplasma genitalium. Science 1995;270: 397-403.
-
(1995)
Science
, vol.270
, pp. 397-403
-
-
Fraser, C.M.1
Gocayne, J.D.2
White, O.3
-
3
-
-
0032508046
-
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
-
Cole ST, Brosch R, Parkhill J, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998;393:537-44.
-
(1998)
Nature
, vol.393
, pp. 537-544
-
-
Cole, S.T.1
Brosch, R.2
Parkhill, J.3
-
4
-
-
10244239321
-
Life with 6000 genes
-
Goffeau A, Barrell BG, Bussey H, et al. Life with 6000 genes. Science 1996;274:546,563-547.
-
(1996)
Science
, vol.274
, Issue.546
, pp. 563-547
-
-
Goffeau, A.1
Barrell, B.G.2
Bussey, H.3
-
5
-
-
0032509302
-
The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: A platform for investigating biology
-
The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 1998;282:2012-8.
-
(1998)
Science
, vol.282
, pp. 2012-2018
-
-
-
6
-
-
0034708758
-
A whole-genome assembly of Drosophila
-
Myers EW, Sutton GG, Delcher AL, et al. A whole-genome assembly of Drosophila. Science 2000;287:2196-204.
-
(2000)
Science
, vol.287
, pp. 2196-2204
-
-
Myers, E.W.1
Sutton, G.G.2
Delcher, A.L.3
-
7
-
-
0034649566
-
The Arabidopsis Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
-
The Arabidopsis Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000;408 796-815.
-
(2000)
Nature
, vol.408
, pp. 796-815
-
-
-
8
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Waterston RH, Lindblad-Toh K, Birney E, et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002;420 520-62.
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Waterston, R.H.1
Lindblad-Toh, K.2
Birney, E.3
-
9
-
-
1842684068
-
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
-
Gibbs RA, Weinstock GM, Metzker ML, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004;428:493-521.
-
(2004)
Nature
, vol.428
, pp. 493-521
-
-
Gibbs, R.A.1
Weinstock, G.M.2
Metzker, M.L.3
-
10
-
-
33750995860
-
The genome of the sea urchin Strongylocentrotus purpuratus
-
Sodergren E, Weinstock GM, Davidson EH, et al. The genome of the sea urchin Strongylocentrotus purpuratus. Science 2006;314 941-52.
-
(2006)
Science
, vol.314
, pp. 941-952
-
-
Sodergren, E.1
Weinstock, G.M.2
Davidson, E.H.3
-
11
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature 2001;409:860-921.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
Linton, L.M.2
Birren, B.3
-
12
-
-
0035895505
-
The sequence of the human genome
-
Venter JC, Adams MD, Myers EW, et al. The sequence of the human genome. Science 2001;291:1304-51.
-
(2001)
Science
, vol.291
, pp. 1304-1351
-
-
Venter, J.C.1
Adams, M.D.2
Myers, E.W.3
-
13
-
-
7244245762
-
Finishing the euchromatic sequence of the human genome
-
International Human Genome Sequencing Consortium
-
International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 2004;431 931-45.
-
(2004)
Nature
, vol.431
, pp. 931-945
-
-
-
14
-
-
33748322018
-
Analysis of the Salmonella typhimurium proteome through environmental response toward infectious conditions
-
Adkins JN, Mottaz HM, Norbeck AD, et al. Analysis of the Salmonella typhimurium proteome through environmental response toward infectious conditions. Mol Cell Proteomics 2006;5:1450-61.
-
(2006)
Mol Cell Proteomics
, vol.5
, pp. 1450-1461
-
-
Adkins, J.N.1
Mottaz, H.M.2
Norbeck, A.D.3
-
15
-
-
0037435030
-
Mass spectrometry-based proteomics
-
Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 2003;422:198-207.
-
(2003)
Nature
, vol.422
, pp. 198-207
-
-
Aebersold, R.1
Mann, M.2
-
16
-
-
0035106351
-
-
Washburn MP, Wolters D, Yates JR, 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001;19:242-7.
-
Washburn MP, Wolters D, Yates JR, 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001;19:242-7.
-
-
-
-
17
-
-
34548452940
-
Whole proteome analysis of post-translational modifications: Applications of massspectrometry for proteogenomic annotation
-
Gupta N, Tanner S, Jaitly N, et al. Whole proteome analysis of post-translational modifications: Applications of massspectrometry for proteogenomic annotation. Genome Res 2007;17:1362-77.
-
(2007)
Genome Res
, vol.17
, pp. 1362-1377
-
-
Gupta, N.1
Tanner, S.2
Jaitly, N.3
-
19
-
-
0037561991
-
GenDB - an open source genome annotation system for prokaryote genomes
-
Meyer F, Goesmann A, McHardy AC, et al. GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 2003;31:2187-95.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 2187-2195
-
-
Meyer, F.1
Goesmann, A.2
McHardy, A.C.3
-
21
-
-
0033485517
-
Improved microbial gene identification with GLIMMER
-
Delcher AL, Harmon D, Kasif S, et al. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999;27 4636-41.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 4636-4641
-
-
Delcher, A.L.1
Harmon, D.2
Kasif, S.3
-
22
-
-
0032518163
-
Microbial gene identification using interpolated Markov models
-
Salzberg SL, Delcher AL, Kasif S, et al. Microbial gene identification using interpolated Markov models. Nucleic Acids Res 1998;26:544-8.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 544-548
-
-
Salzberg, S.L.1
Delcher, A.L.2
Kasif, S.3
-
23
-
-
0032900737
-
CRITICA: Coding region identification tool invoking comparative analysis
-
Badger JH, Olsen GJ. CRITICA: Coding region identification tool invoking comparative analysis. Mol Biol Evol 1999; 16:512-24.
-
(1999)
Mol Biol Evol
, vol.16
, pp. 512-524
-
-
Badger, J.H.1
Olsen, G.J.2
-
24
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol 1990;215:403-10.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
-
25
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
-
26
-
-
0027399530
-
-
Gish W, States DJ. Identification of protein coding regions by database similarity search. Nat Genet 1993;3:266-72.
-
Gish W, States DJ. Identification of protein coding regions by database similarity search. Nat Genet 1993;3:266-72.
-
-
-
-
27
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997;278:631-7.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
28
-
-
0035175673
-
TIGRFAMs: A protein family resource for the functional identification of proteins
-
Haft DH, Loftus BJ, Richardson DL, et al. TIGRFAMs: A protein family resource for the functional identification of proteins. Nucleic Acids Res 2001;29:41-3.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 41-43
-
-
Haft, D.H.1
Loftus, B.J.2
Richardson, D.L.3
-
31
-
-
0032972509
-
PSORT: A program for detecting sorting signals in proteins and predicting their subcellular localization
-
Nakai K, Horton P. PSORT: A program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 1999;24:34-6.
-
(1999)
Trends Biochem Sci
, vol.24
, pp. 34-36
-
-
Nakai, K.1
Horton, P.2
-
32
-
-
0030614959
-
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
-
Nielsen H, Engelbrecht J, Brunak S, et al. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 1997;10:1-6.
-
(1997)
Protein Eng
, vol.10
, pp. 1-6
-
-
Nielsen, H.1
Engelbrecht, J.2
Brunak, S.3
-
38
-
-
0037268583
-
Comparative gene prediction in human and mouse
-
Parra G, Agarwal P, Abril JF, et al. Comparative gene prediction in human and mouse. Genome Res 2003;13:108-17.
-
(2003)
Genome Res
, vol.13
, pp. 108-117
-
-
Parra, G.1
Agarwal, P.2
Abril, J.F.3
-
39
-
-
17444437765
-
Integrating genomic homology into gene structure prediction
-
Korf I, Flicek P, Duan D, et al. Integrating genomic homology into gene structure prediction. Bioinformatics 2001;17(Suppl. 1):S140-8.
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL. 1
-
-
Korf, I.1
Flicek, P.2
Duan, D.3
-
40
-
-
0031586003
-
Prediction of complete gene structures in human genomic DNA
-
Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997;268:78-94.
-
(1997)
J Mol Biol
, vol.268
, pp. 78-94
-
-
Burge, C.1
Karlin, S.2
-
42
-
-
33748641351
-
EGASP: The human ENCODE Genome Annotation Assessment Project
-
Guigo R, Flicek P, Abril JF, et al. EGASP: The human ENCODE Genome Annotation Assessment Project. Genome Biol 2006;7(Suppl 1):S21-31.
-
(2006)
Genome Biol
, vol.7
, Issue.SUPPL. 1
-
-
Guigo, R.1
Flicek, P.2
Abril, J.F.3
-
43
-
-
0346505461
-
Computational gene prediction using multiple sources of evidence
-
Allen JE, Pertea M, Salzberg SL. Computational gene prediction using multiple sources of evidence. Genome Res 2004;14:142-8.
-
(2004)
Genome Res
, vol.14
, pp. 142-148
-
-
Allen, J.E.1
Pertea, M.2
Salzberg, S.L.3
-
44
-
-
28944435815
-
Large-scale prokaryotic gene prediction and comparison to genome annotation
-
Nielsen P, Krogh A. Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics 2005;21 4322-9.
-
(2005)
Bioinformatics
, vol.21
, pp. 4322-4329
-
-
Nielsen, P.1
Krogh, A.2
-
45
-
-
1842768392
-
Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing
-
Wu JQ, Shteynberg D, Arumugam M, et al. Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing. Genome Res 2004;14:665-71.
-
(2004)
Genome Res
, vol.14
, pp. 665-671
-
-
Wu, J.Q.1
Shteynberg, D.2
Arumugam, M.3
-
46
-
-
0034674334
-
Computational and experimental analysis identifies many novel human genes
-
Miyajima N, Burge CB, Saito T. Computational and experimental analysis identifies many novel human genes. Biochem Biophys Res Commun 2000;272:801-7.
-
(2000)
Biochem Biophys Res Commun
, vol.272
, pp. 801-807
-
-
Miyajima, N.1
Burge, C.B.2
Saito, T.3
-
47
-
-
0035417329
-
Assessment of the total number of human transcription units
-
Das M, Burge CB, Park E, et al. Assessment of the total number of human transcription units. Genomics 2001;77: 71-8.
-
(2001)
Genomics
, vol.77
, pp. 71-78
-
-
Das, M.1
Burge, C.B.2
Park, E.3
-
48
-
-
0037417884
-
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes
-
Guigo R, Dermitzakis ET, Agarwal P, et al. Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc Natl Acad Sci USA 2003;100 1140-5.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 1140-1145
-
-
Guigo, R.1
Dermitzakis, E.T.2
Agarwal, P.3
-
49
-
-
3142702204
-
TANDEM: Matching proteins with tandem mass spectra
-
Craig R, Beavis RC. TANDEM: Matching proteins with tandem mass spectra. Bioinformatics 2004;20:1466-7.
-
(2004)
Bioinformatics
, vol.20
, pp. 1466-1467
-
-
Craig, R.1
Beavis, R.C.2
-
50
-
-
0000857494
-
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng JK, McCormack AL, Yates JR. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 1994;5:976-89.
-
(1994)
J Am Soc Mass Spectrom
, vol.5
, pp. 976-989
-
-
Eng, J.K.1
McCormack, A.L.2
Yates, J.R.3
-
51
-
-
0033434080
-
Probability-based protein identification by searching sequence databases using mass spectrometry data
-
Perkins DN, Pappin DJ, Creasy DM, et al. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999;20: 3551-67.
-
(1999)
Electrophoresis
, vol.20
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, D.J.2
Creasy, D.M.3
-
52
-
-
0029645432
-
Mining genomes: Correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases
-
Yates JR, 3rd, Eng JK, McCormack AL. Mining genomes: Correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal Chem 1995;67:3202-10.
-
(1995)
Anal Chem
, vol.67
, pp. 3202-3210
-
-
Yates 3rd, J.R.1
Eng, J.K.2
McCormack, A.L.3
-
53
-
-
0030751012
-
Identifying the major proteome components of Haemophilus influenzae type-strain NCTC 8143
-
Link AJ, Hays LG, Carmack EB, et al. Identifying the major proteome components of Haemophilus influenzae type-strain NCTC 8143. Electrophoresis 1997;18:1314-34.
-
(1997)
Electrophoresis
, vol.18
, pp. 1314-1334
-
-
Link, A.J.1
Hays, L.G.2
Carmack, E.B.3
-
54
-
-
0035350894
-
Mass spectrometry allows direct identification of proteins in large genomes
-
Kuster B, Mortensen P, Andersen JS, et al. Mass spectrometry allows direct identification of proteins in large genomes. Proteomics 2001;1:641-50.
-
(2001)
Proteomics
, vol.1
, pp. 641-650
-
-
Kuster, B.1
Mortensen, P.2
Andersen, J.S.3
-
55
-
-
0035346719
-
Interrogating the human genome using uninterpreted mass spectrometry data
-
Choudhary JS, Blackstock WP, Creasy DM, et al. Interrogating the human genome using uninterpreted mass spectrometry data. Proteomics 2001;1:651-67.
-
(2001)
Proteomics
, vol.1
, pp. 651-667
-
-
Choudhary, J.S.1
Blackstock, W.P.2
Creasy, D.M.3
-
56
-
-
0942287072
-
Proteogenomic mapping as a complementary method to perform genome annotation
-
Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 2004;4:59-77.
-
(2004)
Proteomics
, vol.4
, pp. 59-77
-
-
Jaffe, J.D.1
Berg, H.C.2
Church, G.M.3
-
57
-
-
4444350869
-
The complete genome and proteome of Mycoplasma mobile
-
Jaffe JD, Stange-Thomann N, Smith C, et al. The complete genome and proteome of Mycoplasma mobile. Genome Res 2004;14 1447-61.
-
(2004)
Genome Res
, vol.14
, pp. 1447-1461
-
-
Jaffe, J.D.1
Stange-Thomann, N.2
Smith, C.3
-
58
-
-
23744515352
-
Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias
-
Wang R, Prince JT, Marcotte EM. Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias. Genome Res 2005;15:1118-26.
-
(2005)
Genome Res
, vol.15
, pp. 1118-1126
-
-
Wang, R.1
Prince, J.T.2
Marcotte, E.M.3
-
59
-
-
0034868629
-
Proteomics reveals open reading frames in Mycobacterium tuberculosis H37Rv not predicted by genomics
-
Jungblut PR, Muller EC, Mattow J, et al. Proteomics reveals open reading frames in Mycobacterium tuberculosis H37Rv not predicted by genomics. Infect Immun 2001;69: 5905-7.
-
(2001)
Infect Immun
, vol.69
, pp. 5905-5907
-
-
Jungblut, P.R.1
Muller, E.C.2
Mattow, J.3
-
60
-
-
25444475024
-
Genome annotation of Anopheles gambiae using mass spectrometry-derived data
-
Kalume DE, Peri S, Reddy R, et al. Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics 2005; 6:128.
-
(2005)
BMC Genomics
, vol.6
, pp. 128
-
-
Kalume, D.E.1
Peri, S.2
Reddy, R.3
-
61
-
-
20144381803
-
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry
-
Desiere F, Deutsch EW, Nesvizhskii AI, et al. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol 2005;6:R9.
-
(2005)
Genome Biol
, vol.6
-
-
Desiere, F.1
Deutsch, E.W.2
Nesvizhskii, A.I.3
-
62
-
-
33745054329
-
Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics
-
Fermin D, Allen BB, Blackwell TW, et al. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol 2006;7:R35.
-
(2006)
Genome Biol
, vol.7
-
-
Fermin, D.1
Allen, B.B.2
Blackwell, T.W.3
-
63
-
-
33846884410
-
Improving gene annotation using peptide mass spectrometry
-
Tanner S, Shen Z, Ng J, et al. Improving gene annotation using peptide mass spectrometry. Genome Res 2007;17: 231-9.
-
(2007)
Genome Res
, vol.17
, pp. 231-239
-
-
Tanner, S.1
Shen, Z.2
Ng, J.3
-
64
-
-
0037224550
-
Parallel identification of new genes in Saccharomyces cerevisiae
-
Oshiro G, Wodicka LM, Washburn MP, et al. Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res 2002;12 1210-20.
-
(2002)
Genome Res
, vol.12
, pp. 1210-1220
-
-
Oshiro, G.1
Wodicka, L.M.2
Washburn, M.P.3
-
65
-
-
34249717879
-
A high-quality catalog of the Drosophila melanogaster proteome
-
Brunner E, Ahrens CH, Mohanty S, et al. A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol 2007; 25:576-83.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 576-583
-
-
Brunner, E.1
Ahrens, C.H.2
Mohanty, S.3
-
66
-
-
0037143692
-
Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags
-
Lipton MS, Pasa-Tolic L, Anderson GA, et al. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc Natl Acad Sci USA 2002;99: 11049-54.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 11049-11054
-
-
Lipton, M.S.1
Pasa-Tolic, L.2
Anderson, G.A.3
-
67
-
-
2342526611
-
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
-
Kolker E, Makarova KS, Shabalina S, et al. Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucleic Acids Res 2004;32: 2353-61.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 2353-2361
-
-
Kolker, E.1
Makarova, K.S.2
Shabalina, S.3
-
68
-
-
39749194466
-
Proteomics analysis of the causative agent of typhoid fever
-
Ansong C, Yoon H, Norbeck AD, et al. Proteomics analysis of the causative agent of typhoid fever. J Proteome Res 2008; 7 546-57.
-
(2008)
J Proteome Res
, vol.7
, pp. 546-557
-
-
Ansong, C.1
Yoon, H.2
Norbeck, A.D.3
-
69
-
-
33750967325
-
Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics
-
Hixson KK, Adkins JN, Baker SE, et al. Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics. J Proteome Res 2006;5: 3008-17.
-
(2006)
J Proteome Res
, vol.5
, pp. 3008-3017
-
-
Hixson, K.K.1
Adkins, J.N.2
Baker, S.E.3
-
70
-
-
23844468451
-
Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics
-
Elias DA, Monroe ME, Marshall MJ, et al. Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics. Proteomics 2005;5:3120-30.
-
(2005)
Proteomics
, vol.5
, pp. 3120-3130
-
-
Elias, D.A.1
Monroe, M.E.2
Marshall, M.J.3
-
71
-
-
13844316454
-
Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations
-
Kolker E, Picone AF, Galperin MY, et al. Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci USA 2005; 102:2099-104.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 2099-2104
-
-
Kolker, E.1
Picone, A.F.2
Galperin, M.Y.3
-
72
-
-
33847208190
-
Experimental determination of translational starts using peptide mass mapping and tandem mass spectrometry within the proteome of Mycobacterium tuberculosis
-
Rison SC, Mattow J, Jungblut PR, et al. Experimental determination of translational starts using peptide mass mapping and tandem mass spectrometry within the proteome of Mycobacterium tuberculosis. Microbiology 2007; 153:521-8.
-
(2007)
Microbiology
, vol.153
, pp. 521-528
-
-
Rison, S.C.1
Mattow, J.2
Jungblut, P.R.3
-
73
-
-
34250886391
-
Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis
-
Aivaliotis M, Gevaert K, Falb M, et al. Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis. J Proteome Res 2007;6 2195-204.
-
(2007)
J Proteome Res
, vol.6
, pp. 2195-2204
-
-
Aivaliotis, M.1
Gevaert, K.2
Falb, M.3
-
74
-
-
0038333588
-
Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides
-
Gevaert K, Goethals M, Martens L, et al. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat Biotechnol 2003;21:566-9.
-
(2003)
Nat Biotechnol
, vol.21
, pp. 566-569
-
-
Gevaert, K.1
Goethals, M.2
Martens, L.3
-
75
-
-
0029894345
-
Knowing when not to stop: Selenocysteine incorporation in eukaryotes
-
Low SC, Berry MJ. Knowing when not to stop: Selenocysteine incorporation in eukaryotes. Trends Biochem Sci 1996;21:203-8.
-
(1996)
Trends Biochem Sci
, vol.21
, pp. 203-208
-
-
Low, S.C.1
Berry, M.J.2
-
76
-
-
0037121962
-
The function of SECIS RNA in translational control of gene expression in Escherichia coli
-
Thanbichler M, Bock A. The function of SECIS RNA in translational control of gene expression in Escherichia coli. EMBO J 2002;21 6925-34.
-
(2002)
EMBO J
, vol.21
, pp. 6925-6934
-
-
Thanbichler, M.1
Bock, A.2
-
77
-
-
0025743489
-
Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3′ untranslated region
-
Berry MJ, Banu L, Chen YY, et al. Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3′ untranslated region. Nature 1991;353: 273-6.
-
(1991)
Nature
, vol.353
, pp. 273-276
-
-
Berry, M.J.1
Banu, L.2
Chen, Y.Y.3
-
78
-
-
0031557397
-
Selenoprotein synthesis in archaea: Identification of an mRNA element of Methanococcus jannaschii probably directing selenocysteine insertion
-
Wilting R, Schorling S, Persson BC, et al. Selenoprotein synthesis in archaea: Identification of an mRNA element of Methanococcus jannaschii probably directing selenocysteine insertion. J Mol Biol 1997;266:637-41.
-
(1997)
J Mol Biol
, vol.266
, pp. 637-641
-
-
Wilting, R.1
Schorling, S.2
Persson, B.C.3
-
79
-
-
0032519347
-
The nature of the minimal 'selenocysteine insertion sequence' (SECIS) in Escherichia coli
-
Liu Z, Reches M, Groisman I, et al. The nature of the minimal 'selenocysteine insertion sequence' (SECIS) in Escherichia coli. Nucleic Acids Res 1998;26:896-902.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 896-902
-
-
Liu, Z.1
Reches, M.2
Groisman, I.3
-
80
-
-
0025341614
-
Features of the formate dehydrogenase mRNA necessary for decoding of the UGA codon as selenocysteine
-
Zinoni F, Heider J, Bock A. Features of the formate dehydrogenase mRNA necessary for decoding of the UGA codon as selenocysteine. Proc Natl Acad Sci USA 1990;87: 4660-4.
-
(1990)
Proc Natl Acad Sci USA
, vol.87
, pp. 4660-4664
-
-
Zinoni, F.1
Heider, J.2
Bock, A.3
-
81
-
-
0034872728
-
In silico identification of novel selenoproteins in the Drosophila melanogaster genome
-
Castellano S, Morozova N, Morey M, et al. In silico identification of novel selenoproteins in the Drosophila melanogaster genome. EMBO Rep 2001;2:697-702.
-
(2001)
EMBO Rep
, vol.2
, pp. 697-702
-
-
Castellano, S.1
Morozova, N.2
Morey, M.3
-
82
-
-
1242321034
-
Reconsidering the evolution of eukaryotic selenoproteins: A novel nonmammalian family with scattered phylogenetic distribution
-
Castellano S, Novoselov SV, Kryukov GV, et al. Reconsidering the evolution of eukaryotic selenoproteins: A novel nonmammalian family with scattered phylogenetic distribution. EMBO Rep 2004;5:71-7.
-
(2004)
EMBO Rep
, vol.5
, pp. 71-77
-
-
Castellano, S.1
Novoselov, S.V.2
Kryukov, G.V.3
-
83
-
-
0038442808
-
Characterization of mammalian selenoproteomes
-
Kryukov GV, Castellano S, Novoselov SV, et al. Characterization of mammalian selenoproteomes. Science 2003; 300:1439-43.
-
(2003)
Science
, vol.300
, pp. 1439-1443
-
-
Kryukov, G.V.1
Castellano, S.2
Novoselov, S.V.3
-
84
-
-
0033607529
-
New mammalian selenocysteine-containing proteins identified with an algorithm that searches for selenocysteine insertion sequence elements
-
Kryukov GV, Kryukov VM, Gladyshev VN. New mammalian selenocysteine-containing proteins identified with an algorithm that searches for selenocysteine insertion sequence elements. J Biol Chem 1999;274:33888-97.
-
(1999)
J Biol Chem
, vol.274
, pp. 33888-33897
-
-
Kryukov, G.V.1
Kryukov, V.M.2
Gladyshev, V.N.3
-
85
-
-
1842859651
-
A survey of metazoan selenocysteine insertion sequences
-
Lambert A, Lescure A, Gautheret D. A survey of metazoan selenocysteine insertion sequences. Biochimie 2002;84:953-9.
-
(2002)
Biochimie
, vol.84
, pp. 953-959
-
-
Lambert, A.1
Lescure, A.2
Gautheret, D.3
-
86
-
-
0033621335
-
Novel selenoproteins identified in silico and in vivo by using a conserved RNA structural motif
-
Lescure A, Gautheret D, Carbon P, et al. Novel selenoproteins identified in silico and in vivo by using a conserved RNA structural motif. J Biol Chem 1999;274: 38147-54.
-
(1999)
J Biol Chem
, vol.274
, pp. 38147-38154
-
-
Lescure, A.1
Gautheret, D.2
Carbon, P.3
-
87
-
-
0035839432
-
Selenium metabolism in Drosophila: Selenoproteins, selenoprotein mRNA expression, fertility, and mortality
-
Martin-Romero FJ, Kryukov GV, Lobanov AV, et al. Selenium metabolism in Drosophila: Selenoproteins, selenoprotein mRNA expression, fertility, and mortality. J Biol Chem 2001;276:29798-804.
-
(2001)
J Biol Chem
, vol.276
, pp. 29798-29804
-
-
Martin-Romero, F.J.1
Kryukov, G.V.2
Lobanov, A.V.3
-
88
-
-
3142740663
-
Comparative genomics
-
Hardison RC. Comparative genomics. PLoS Biol 2003;1: E58.
-
(2003)
PLoS Biol
, vol.1
-
-
Hardison, R.C.1
-
90
-
-
44249086202
-
Comparative bacterial proteomics: Analysis of the core genome concept
-
Callister SJ, McCue LA, Turse JE, et al. Comparative bacterial proteomics: Analysis of the core genome concept. PLoS ONE 2008; 3:e1542.
-
(2008)
PLoS ONE
, vol.3
-
-
Callister, S.J.1
McCue, L.A.2
Turse, J.E.3
-
91
-
-
20644462362
-
Micros for microbes: Non-coding regulatory RNAs in bacteria
-
Gottesman S. Micros for microbes: Non-coding regulatory RNAs in bacteria. Trends Genet 2005;21:399-404.
-
(2005)
Trends Genet
, vol.21
, pp. 399-404
-
-
Gottesman, S.1
-
92
-
-
26444496661
-
The silencing of pseudogenes
-
Mira A, Pushker R. The silencing of pseudogenes. Mol Biol Evol 2005;22:2135-8.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 2135-2138
-
-
Mira, A.1
Pushker, R.2
-
93
-
-
12344250822
-
Function of alternative splicing
-
Stamm S, Ben-Ari S, Rafalska I, et al. Function of alternative splicing. Gene 2005;344:1-20.
-
(2005)
Gene
, vol.344
, pp. 1-20
-
-
Stamm, S.1
Ben-Ari, S.2
Rafalska, I.3
-
94
-
-
21244439380
-
Regulation of apoptosis by alternative pre-mRNA splicing
-
Schwerk C, Schulze-Osthoff K. Regulation of apoptosis by alternative pre-mRNA splicing. Mol Cell 2005;19:1-13.
-
(2005)
Mol Cell
, vol.19
, pp. 1-13
-
-
Schwerk, C.1
Schulze-Osthoff, K.2
-
95
-
-
0036338127
-
Alternative splicing and genome complexity
-
Brett D, Pospisil H, Valcarcel J, et al. Alternative splicing and genome complexity. Nat Genet 2002;30:29-30.
-
(2002)
Nat Genet
, vol.30
, pp. 29-30
-
-
Brett, D.1
Pospisil, H.2
Valcarcel, J.3
-
96
-
-
0345316714
-
Increase of functional diversity by alternative splicing
-
Kriventseva EV, Koch I, Apweiler R, et al. Increase of functional diversity by alternative splicing. Trends Genet 2003;19 124-8.
-
(2003)
Trends Genet
, vol.19
, pp. 124-128
-
-
Kriventseva, E.V.1
Koch, I.2
Apweiler, R.3
-
97
-
-
25444512373
-
Integrating alternative splicing detection into gene prediction
-
Foissac S, Schiex T. Integrating alternative splicing detection into gene prediction. BMC Bioinformatics 2005;6:25.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 25
-
-
Foissac, S.1
Schiex, T.2
-
98
-
-
0347623371
-
Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays
-
Johnson JM, Castle J, Garrett-Engele P, et al. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 2003;302:2141-4.
-
(2003)
Science
, vol.302
, pp. 2141-2144
-
-
Johnson, J.M.1
Castle, J.2
Garrett-Engele, P.3
-
99
-
-
0036337915
-
A genomic view of alternative splicing
-
Modrek B, Lee C. A genomic view of alternative splicing. Nat Genet 2002;30:13-19.
-
(2002)
Nat Genet
, vol.30
, pp. 13-19
-
-
Modrek, B.1
Lee, C.2
-
100
-
-
19044401068
-
Community genomics in microbial ecology and evolution
-
Allen EE, Banfield JF. Community genomics in microbial ecology and evolution. Nat Rev Microbiol 2005;3:489-98.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 489-498
-
-
Allen, E.E.1
Banfield, J.F.2
-
101
-
-
10344227692
-
Metagenomics: Application of genomics to uncultured microorganisms
-
Handelsman J. Metagenomics: Application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 2004; 68:669-85.
-
(2004)
Microbiol Mol Biol Rev
, vol.68
, pp. 669-685
-
-
Handelsman, J.1
-
102
-
-
21344465408
-
Community proteomics of a natural microbial biofilm
-
Ram RJ, Verberkmoes NC, Thelen MP, et al. Community proteomics of a natural microbial biofilm. Science 2005;308: 1915-20.
-
(2005)
Science
, vol.308
, pp. 1915-1920
-
-
Ram, R.J.1
Verberkmoes, N.C.2
Thelen, M.P.3
-
103
-
-
34047169728
-
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
-
Lo I, Denef VJ, Verberkmoes NC, et al. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 2007;446:537-41.
-
(2007)
Nature
, vol.446
, pp. 537-541
-
-
Lo, I.1
Denef, V.J.2
Verberkmoes, N.C.3
-
104
-
-
38649093306
-
Whole genome searching with shotgun proteomic data: Applications for genome annotation
-
Sevinsky JR, Cargile BJ, Bunger MK, et al. Whole genome searching with shotgun proteomic data: Applications for genome annotation. J Proteome Res 2008;7:80-8.
-
(2008)
J Proteome Res
, vol.7
, pp. 80-88
-
-
Sevinsky, J.R.1
Cargile, B.J.2
Bunger, M.K.3
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