-
1
-
-
0037264654
-
Leveraging the mouse genome for gene prediction in human: From whole-genome shotgun reads to a global synteny map
-
Flicek P. Keibler E, Hu P, Korf I, Brent MR: Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome Res 2003, 13:46-54.
-
(2003)
Genome Res
, vol.13
, pp. 46-54
-
-
Flicek, P.1
Keibler, E.2
Hu, P.3
Korf, I.4
Brent, M.R.5
-
2
-
-
1842818736
-
Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat
-
Dewey C, Wu JQ, Cawley S, Alexandersson M, Gibbs R, Pachter L: Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Res 2004, 14:661-664.
-
(2004)
Genome Res
, vol.14
, pp. 661-664
-
-
Dewey, C.1
Wu, J.Q.2
Cawley, S.3
Alexandersson, M.4
Gibbs, R.5
Pachter, L.6
-
3
-
-
1542537849
-
Combining phylogenetic and hidden Markov models in biosequence analysis
-
Siepel A, Haussler D: Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol 2004, 11:413-428.
-
(2004)
J Comput Biol
, vol.11
, pp. 413-428
-
-
Siepel, A.1
Haussler, D.2
-
4
-
-
0037417884
-
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes
-
Guigo R, Dermitzakis ET, Agarwal P, Ponting CP, Parra G, Reymond A, Abril JF, Keibler E, Lyle R, Ucla C, 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, 100:1140-1145.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 1140-1145
-
-
Guigo, R.1
Dermitzakis, E.T.2
Agarwal, P.3
Ponting, C.P.4
Parra, G.5
Reymond, A.6
Abril, J.F.7
Keibler, E.8
Lyle, R.9
Ucla, C.10
-
5
-
-
12944266836
-
Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags
-
de Souza SJ, Camargo AA, Briones MR, Costa FF, Nagai MA, Verjovski-Almeida S, Zago MA, Andrade LE, Carrer H, El-Dorry HF, et al.: Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags. Proc Natl Acad Sci USA 2000, 97:12690-12693.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 12690-12693
-
-
de Souza, S.J.1
Camargo, A.A.2
Briones, M.R.3
Costa, F.F.4
Nagai, M.A.5
Verjovski-Almeida, S.6
Zago, M.A.7
Andrade, L.E.8
Carrer, H.9
El-Dorry, H.F.10
-
6
-
-
2942521197
-
Recent advances in gene structure prediction
-
Brent MR, Guigo R: Recent advances in gene structure prediction. Curr Opin Struct Biol 2004, 14:264-272.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 264-272
-
-
Brent, M.R.1
Guigo, R.2
-
7
-
-
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, 67:3202-3210.
-
(1995)
Anal Chem
, vol.67
, pp. 3202-3210
-
-
Yates III, J.R.1
Eng, J.K.2
McCormack, A.L.3
-
8
-
-
20144381803
-
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry
-
Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Donohoe S, 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
Mallick, P.4
King, N.L.5
Eng, J.K.6
Aderem, A.7
Boyle, R.8
Brunner, E.9
Donohoe, S.10
-
9
-
-
0035350894
-
Mass spectrometry allows direct identification of proteins in large genomes
-
Kuster B, Mortensen P, Andersen JS, Mann M: Mass spectrometry allows direct identification of proteins in large genomes. Proteomics 2001, 1:641-650.
-
(2001)
Proteomics
, vol.1
, pp. 641-650
-
-
Kuster, B.1
Mortensen, P.2
Andersen, J.S.3
Mann, M.4
-
10
-
-
0035346719
-
Interrogating the human genome using uninterpreted mass spectrometry data
-
Choudhary JS, Blackstock WP, Creasy DM, Cottrell JS: Interrogating the human genome using uninterpreted mass spectrometry data. Proteomics 2001, 1:651-667.
-
(2001)
Proteomics
, vol.1
, pp. 651-667
-
-
Choudhary, J.S.1
Blackstock, W.P.2
Creasy, D.M.3
Cottrell, J.S.4
-
11
-
-
16544380346
-
HUPO (Human Proteome Organization) 3rd Annual World Congress Beijing, China, October 25-27, 2004
-
HUPO (Human Proteome Organization) 3rd Annual World Congress. Beijing, China, October 25-27, 2004. Mol Cell Proteomics 2004, 3(Suppl 10):S1-S352.
-
(2004)
Mol Cell Proteomics
, vol.3
, Issue.SUPPL. 10
-
-
-
12
-
-
3042818018
-
The International Protein Index: An integrated database for proteomics experiments
-
Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R: The International Protein Index: an integrated database for proteomics experiments. Proteomics 2004, 4:1985-1988.
-
(2004)
Proteomics
, vol.4
, pp. 1985-1988
-
-
Kersey, P.J.1
Duarte, J.2
Williams, A.3
Karavidopoulou, Y.4
Birney, E.5
Apweiler, R.6
-
13
-
-
33745011434
-
The Global Proteome Machine Organization: TANDEM project
-
The Global Proteome Machine Organization: TANDEM project [http://thegpm.org/TANDEM/index.html]
-
-
-
-
14
-
-
3142702204
-
TANDEM: Matching proteins with tandem mass spectra
-
Craig R, Beavis RC: TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20:1466-1467.
-
(2004)
Bioinformatics
, vol.20
, pp. 1466-1467
-
-
Craig, R.1
Beavis, R.C.2
-
15
-
-
0028841317
-
The SIR2 gene family, conserved from bacteria to humans, functions in silencing, cell cycle progression, and chromosome stability
-
Brachmann CB, Sherman JM, Devine SE, Cameron EE, Pillus L. Boeke JD: The SIR2 gene family, conserved from bacteria to humans, functions in silencing, cell cycle progression, and chromosome stability. Genes Dev 1995, 9:2888-2902.
-
(1995)
Genes Dev
, vol.9
, pp. 2888-2902
-
-
Brachmann, C.B.1
Sherman, J.M.2
Devine, S.E.3
Cameron, E.E.4
Pillus, L.5
Boeke, J.D.6
-
16
-
-
33745042055
-
Raw Data
-
Hupo PPP Raw Data [http://www.bioinformatics.med.umich.edu/app/hupo/raw/]
-
-
-
Hupo, P.P.P.1
-
17
-
-
33745024827
-
Six-Frame Translation of Human Genome (hg17)
-
Six-frame Translation of Human Genome (hg17) [http://www.stateslab.org/data/6frameorfs/index.htm]
-
-
-
-
18
-
-
23944493647
-
Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project
-
Adamski M, Blackwell T, Menon R. Martens L, Hermjakob H, Taylor C, Omenn GS, States DJ: Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project. Proteomics 2005, 5:3246-3261.
-
(2005)
Proteomics
, vol.5
, pp. 3246-3261
-
-
Adamski, M.1
Blackwell, T.2
Menon, R.3
Martens, L.4
Hermjakob, H.5
Taylor, C.6
Omenn, G.S.7
States, D.J.8
-
19
-
-
0027457620
-
Receiver-operating characteristic (ROC) plots: A fundamental evaluation tool in clinical medicine
-
Zweig MH, Campbell G: Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine. Clin Chem 1993, 39:561-577.
-
(1993)
Clin Chem
, vol.39
, pp. 561-577
-
-
Zweig, M.H.1
Campbell, G.2
-
20
-
-
3042735127
-
The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data
-
Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizhskii A: The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics 2004, 3:531-533.
-
(2004)
Mol Cell Proteomics
, vol.3
, pp. 531-533
-
-
Carr, S.1
Aebersold, R.2
Baldwin, M.3
Burlingame, A.4
Clauser, K.5
Nesvizhskii, A.6
-
21
-
-
7044272787
-
Potential for false positive identifications from large databases through tandem mass spectrometry
-
Cargile BJ, Bundy JL, Stephenson JL Jr: Potential for false positive identifications from large databases through tandem mass spectrometry. J Proteome Res 2004, 3:1082-1085.
-
(2004)
J Proteome Res
, vol.3
, pp. 1082-1085
-
-
Cargile, B.J.1
Bundy, J.L.2
Stephenson Jr., J.L.3
-
22
-
-
0037108887
-
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
-
Keller A, Nesvizhskii AI, Kolker E, Aebersold R: Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 2002, 74:5383-5392.
-
(2002)
Anal Chem
, vol.74
, pp. 5383-5392
-
-
Keller, A.1
Nesvizhskii, A.I.2
Kolker, E.3
Aebersold, R.4
-
23
-
-
0043064042
-
A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases
-
Sadygov RG, Yates JR 3rd: A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases. Anal Chem 2003, 75:3792-3798.
-
(2003)
Anal Chem
, vol.75
, pp. 3792-3798
-
-
Sadygov, R.G.1
Yates III, J.R.2
-
24
-
-
27144497658
-
Characterization of the human blood plasma proteome
-
Shen Y, Kim J, Strittmatter EF, Jacobs JM, Camp DG 2nd, Fang R, Tolie N, Moore RJ, Smith RD: Characterization of the human blood plasma proteome. Proteomics 2005, 5:4034-4045.
-
(2005)
Proteomics
, vol.5
, pp. 4034-4045
-
-
Shen, Y.1
Kim, J.2
Strittmatter, E.F.3
Jacobs, J.M.4
Camp II, D.G.5
Fang, R.6
Tolie, N.7
Moore, R.J.8
Smith, R.D.9
-
25
-
-
0033434080
-
Probability-based protein identification by searching sequence databases using mass spectrometry data
-
Perkins DN, Pappin DJ, Creasy DM, Cottrell JS: Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567.
-
(1999)
Electrophoresis
, vol.20
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, D.J.2
Creasy, D.M.3
Cottrell, J.S.4
-
26
-
-
33644864034
-
Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study
-
States DJ, Omenn GS, Blackwell TW, Fermin D, Eng J, Speicher DW, Hanash SM: Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol 2006, 24:333-338.
-
(2006)
Nat Biotechnol
, vol.24
, pp. 333-338
-
-
States, D.J.1
Omenn, G.S.2
Blackwell, T.W.3
Fermin, D.4
Eng, J.5
Speicher, D.W.6
Hanash, S.M.7
-
27
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 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
-
28
-
-
13444251422
-
Ensembl 2005
-
Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, et al: Ensembl 2005. Nucleic Acids Res 2005:D447-453.
-
(2005)
Nucleic Acids Res
-
-
Hubbard, T.1
Andrews, D.2
Caccamo, M.3
Cameron, G.4
Chen, Y.5
Clamp, M.6
Clarke, L.7
Coates, G.8
Cox, T.9
Cunningham, F.10
-
29
-
-
13444273448
-
The Universal Protein Resource (UniProt)
-
Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, et al.: The Universal Protein Resource (UniProt). Nucleic Acids Res 2005:D154-159.
-
(2005)
Nucleic Acids Res
-
-
Bairoch, A.1
Apweiler, R.2
Wu, C.H.3
Barker, W.C.4
Boeckmann, B.5
Ferro, S.6
Gasteiger, E.7
Huang, H.8
Lopez, R.9
Magrane, M.10
-
30
-
-
0001290045
-
PROSITE: A documented database using patterns and profiles as motif descriptors
-
Sigrist CJ, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P: PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform 2002, 3:265-274.
-
(2002)
Brief Bioinform
, vol.3
, pp. 265-274
-
-
Sigrist, C.J.1
Cerutti, L.2
Hulo, N.3
Gattiker, A.4
Falquet, L.5
Pagni, M.6
Bairoch, A.7
Bucher, P.8
-
31
-
-
33745050944
-
-
University of Michigan Bioinformatics Program DAS Server
-
University of Michigan Bioinformatics Program DAS Server [http://www.bioinformatics.med.umich.edu/app/das]
-
-
-
|