-
1
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: protein phylogenetic profiles
-
Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO, (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A 96: 4285-4288.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
2
-
-
0030597980
-
The emergence of major cellular processes in evolution
-
Ouzounis C, Kyrpides N, (1996) The emergence of major cellular processes in evolution. FEBS Lett 390: 119-123.
-
(1996)
FEBS Lett
, vol.390
, pp. 119-123
-
-
Ouzounis, C.1
Kyrpides, N.2
-
3
-
-
0031024670
-
Conserved clusters of functionally related genes in two bacterial genomes
-
Tamames J, Casari G, Ouzounis C, Valencia A, (1997) Conserved clusters of functionally related genes in two bacterial genomes. J Mol Evol 44: 66-73.
-
(1997)
J Mol Evol
, vol.44
, pp. 66-73
-
-
Tamames, J.1
Casari, G.2
Ouzounis, C.3
Valencia, A.4
-
4
-
-
0033055062
-
The use of gene clusters to infer functional coupling
-
Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N, (1999) The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A 96: 2896-2901.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 2896-2901
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
5
-
-
0033523989
-
Protein interaction maps for complete genomes based on gene fusion events
-
Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA, (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86-90.
-
(1999)
Nature
, vol.402
, pp. 86-90
-
-
Enright, A.J.1
Iliopoulos, I.2
Kyrpides, N.C.3
Ouzounis, C.A.4
-
6
-
-
0033523854
-
A combined algorithm for genome-wide prediction of protein function
-
Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D, (1999) A combined algorithm for genome-wide prediction of protein function. Nature 402: 83-86.
-
(1999)
Nature
, vol.402
, pp. 83-86
-
-
Marcotte, E.M.1
Pellegrini, M.2
Thompson, M.J.3
Yeates, T.O.4
Eisenberg, D.5
-
7
-
-
55449085523
-
Genome trees from conservation profiles
-
Tekaia F, Yeramian E, (2005) Genome trees from conservation profiles. PLoS Comput Biol 1: e75.
-
(2005)
PLoS Comput Biol
, vol.1
-
-
Tekaia, F.1
Yeramian, E.2
-
8
-
-
0037350415
-
The phylogenetic extent of metabolic enzymes and pathways
-
Peregrin-Alvarez JM, Tsoka S, Ouzounis CA, (2003) The phylogenetic extent of metabolic enzymes and pathways. Genome Res 13: 422-427.
-
(2003)
Genome Res
, vol.13
, pp. 422-427
-
-
Peregrin-Alvarez, J.M.1
Tsoka, S.2
Ouzounis, C.A.3
-
9
-
-
0042889111
-
Identification of functional links between genes using phylogenetic profiles
-
Wu J, Kasif S, DeLisi C, (2003) Identification of functional links between genes using phylogenetic profiles. Bioinformatics 19: 1524-1530.
-
(2003)
Bioinformatics
, vol.19
, pp. 1524-1530
-
-
Wu, J.1
Kasif, S.2
DeLisi, C.3
-
10
-
-
0038141205
-
Classification schemes for protein structure and function
-
Ouzounis CA, Coulson RM, Enright AJ, Kunin V, Pereira-Leal JB, (2003) Classification schemes for protein structure and function. Nat Rev Genet 4: 508-519.
-
(2003)
Nat Rev Genet
, vol.4
, pp. 508-519
-
-
Ouzounis, C.A.1
Coulson, R.M.2
Enright, A.J.3
Kunin, V.4
Pereira-Leal, J.B.5
-
11
-
-
14644418424
-
Improving genome annotations using phylogenetic profile anomaly detection
-
Mikkelsen TS, Galagan JE, Mesirov JP, (2005) Improving genome annotations using phylogenetic profile anomaly detection. Bioinformatics 21: 464-470.
-
(2005)
Bioinformatics
, vol.21
, pp. 464-470
-
-
Mikkelsen, T.S.1
Galagan, J.E.2
Mesirov, J.P.3
-
12
-
-
33644780644
-
Gene annotation and network inference by phylogenetic profiling
-
Wu J, Hu Z, DeLisi C, (2006) Gene annotation and network inference by phylogenetic profiling. BMC Bioinformatics 7: 80.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 80
-
-
Wu, J.1
Hu, Z.2
DeLisi, C.3
-
13
-
-
34447630272
-
An improved method for identifying functionally linked proteins using phylogenetic profiles
-
Cokus S, Mizutani S, Pellegrini M, (2007) An improved method for identifying functionally linked proteins using phylogenetic profiles. BMC Bioinformatics 8Suppl 4: S7.
-
(2007)
BMC Bioinformatics
, vol.8
-
-
Cokus, S.1
Mizutani, S.2
Pellegrini, M.3
-
14
-
-
0347364646
-
Genome evolution reveals biochemical networks and functional modules
-
von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, et al. (2003) Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci U S A 100: 15428-15433.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 15428-15433
-
-
von Mering, C.1
Zdobnov, E.M.2
Tsoka, S.3
Ciccarelli, F.D.4
Pereira-Leal, J.B.5
-
15
-
-
77957202889
-
A systematic study of genome context methods: calibration, normalization and combination
-
Ferrer L, Dale JM, Karp PD, (2010) A systematic study of genome context methods: calibration, normalization and combination. BMC Bioinformatics 11: 493.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 493
-
-
Ferrer, L.1
Dale, J.M.2
Karp, P.D.3
-
16
-
-
33745035630
-
Predicting genes for orphan metabolic activities using phylogenetic profiles
-
Chen L, Vitkup D, (2006) Predicting genes for orphan metabolic activities using phylogenetic profiles. Genome Biol 7: R17.
-
(2006)
Genome Biol
, vol.7
-
-
Chen, L.1
Vitkup, D.2
-
17
-
-
34347374679
-
Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment
-
Jothi R, Przytycka TM, Aravind L, (2007) Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics 8: 173.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 173
-
-
Jothi, R.1
Przytycka, T.M.2
Aravind, L.3
-
18
-
-
37848999335
-
Operons and the effect of genome redundancy in deciphering functional relationships using phylogenetic profiles
-
Moreno-Hagelsieb G, Janga SC, (2008) Operons and the effect of genome redundancy in deciphering functional relationships using phylogenetic profiles. Proteins 70: 344-352.
-
(2008)
Proteins
, vol.70
, pp. 344-352
-
-
Moreno-Hagelsieb, G.1
Janga, S.C.2
-
19
-
-
38349087234
-
Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling
-
Karimpour-Fard A, Hunter L, Gill RT, (2007) Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling. BMC Genomics 8: 393.
-
(2007)
BMC Genomics
, vol.8
, pp. 393
-
-
Karimpour-Fard, A.1
Hunter, L.2
Gill, R.T.3
-
20
-
-
33749608410
-
Comparative assessment of performance and genome dependence among phylogenetic profiling methods
-
Snitkin ES, Gustafson AM, Mellor J, Wu J, DeLisi C, (2006) Comparative assessment of performance and genome dependence among phylogenetic profiling methods. BMC Bioinformatics 7: 420.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 420
-
-
Snitkin, E.S.1
Gustafson, A.M.2
Mellor, J.3
Wu, J.4
DeLisi, C.5
-
21
-
-
33846157711
-
Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms?
-
Sun J, Li Y, Zhao Z, (2007) Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms? Biochem Biophys Res Commun 353: 985-991.
-
(2007)
Biochem Biophys Res Commun
, vol.353
, pp. 985-991
-
-
Sun, J.1
Li, Y.2
Zhao, Z.3
-
22
-
-
13844306368
-
Measuring genome conservation across taxa: divided strains and united kingdoms
-
Kunin V, Ahren D, Goldovsky L, Janssen P, Ouzounis CA, (2005) Measuring genome conservation across taxa: divided strains and united kingdoms. Nucleic Acids Res 33: 616-621.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 616-621
-
-
Kunin, V.1
Ahren, D.2
Goldovsky, L.3
Janssen, P.4
Ouzounis, C.A.5
-
23
-
-
0038486918
-
The balance of driving forces during genome evolution in prokaryotes
-
Kunin V, Ouzounis CA, (2003) The balance of driving forces during genome evolution in prokaryotes. Genome Res 13: 1589-1594.
-
(2003)
Genome Res
, vol.13
, pp. 1589-1594
-
-
Kunin, V.1
Ouzounis, C.A.2
-
24
-
-
32044440746
-
A minimal estimate for the gene content of the last universal common ancestor-exobiology from a terrestrial perspective
-
Ouzounis CA, Kunin V, Darzentas N, Goldovsky L, (2006) A minimal estimate for the gene content of the last universal common ancestor-exobiology from a terrestrial perspective. Res Microbiol 157: 57-68.
-
(2006)
Res Microbiol
, vol.157
, pp. 57-68
-
-
Ouzounis, C.A.1
Kunin, V.2
Darzentas, N.3
Goldovsky, L.4
-
25
-
-
43349107220
-
Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes
-
Gonzalez O, Zimmer R, (2008) Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes. Bioinformatics 24: 1257-1263.
-
(2008)
Bioinformatics
, vol.24
, pp. 1257-1263
-
-
Gonzalez, O.1
Zimmer, R.2
-
26
-
-
46249123102
-
Microbial genotype-phenotype mapping by class association rule mining
-
Tamura M, D'Haeseleer P, (2008) Microbial genotype-phenotype mapping by class association rule mining. Bioinformatics 24: 1523-1529.
-
(2008)
Bioinformatics
, vol.24
, pp. 1523-1529
-
-
Tamura, M.1
D'Haeseleer, P.2
-
27
-
-
76249105279
-
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network
-
Linghu B, Snitkin ES, Hu Z, Xia Y, Delisi C, (2009) Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biol 10: R91.
-
(2009)
Genome Biol
, vol.10
-
-
Linghu, B.1
Snitkin, E.S.2
Hu, Z.3
Xia, Y.4
Delisi, C.5
-
28
-
-
65249105934
-
Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes
-
Kastenmuller G, Schenk ME, Gasteiger J, Mewes HW, (2009) Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes. Genome Biol 10: R28.
-
(2009)
Genome Biol
, vol.10
-
-
Kastenmuller, G.1
Schenk, M.E.2
Gasteiger, J.3
Mewes, H.W.4
-
29
-
-
70749088913
-
Stratification of co-evolving genomic groups using ranked phylogenetic profiles
-
Freilich S, Goldovsky L, Gottlieb A, Blanc E, Tsoka S, et al. (2009) Stratification of co-evolving genomic groups using ranked phylogenetic profiles. BMC Bioinformatics 10: 355.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 355
-
-
Freilich, S.1
Goldovsky, L.2
Gottlieb, A.3
Blanc, E.4
Tsoka, S.5
-
30
-
-
0031215268
-
Fuzzy set theory in medicine
-
Steimann F, (1997) Fuzzy set theory in medicine. Artif Intell Med 11: 1-7.
-
(1997)
Artif Intell Med
, vol.11
, pp. 1-7
-
-
Steimann, F.1
-
31
-
-
0027976593
-
Deconvolutions based on singular value decomposition and the pseudoinverse: a guide for beginners
-
Hendler RW, Shrager RI, (1994) Deconvolutions based on singular value decomposition and the pseudoinverse: a guide for beginners. J Biochem Biophys Methods 28: 1-33.
-
(1994)
J Biochem Biophys Methods
, vol.28
, pp. 1-33
-
-
Hendler, R.W.1
Shrager, R.I.2
-
32
-
-
27544465780
-
CoGenT++: an extensive and extensible data environment for computational genomics
-
Goldovsky L, Janssen P, Ahren D, Audit B, Cases I, et al. (2005) CoGenT++: an extensive and extensible data environment for computational genomics. Bioinformatics 21: 3806-3810.
-
(2005)
Bioinformatics
, vol.21
, pp. 3806-3810
-
-
Goldovsky, L.1
Janssen, P.2
Ahren, D.3
Audit, B.4
Cases, I.5
-
33
-
-
0042594458
-
COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics
-
Janssen P, Enright AJ, Audit B, Cases I, Goldovsky L, et al. (2003) COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. Bioinformatics 19: 1451-1452.
-
(2003)
Bioinformatics
, vol.19
, pp. 1451-1452
-
-
Janssen, P.1
Enright, A.J.2
Audit, B.3
Cases, I.4
Goldovsky, L.5
-
34
-
-
24044478768
-
MagicMatch-cross-referencing sequence identifiers across databases
-
Smith M, Kunin V, Goldovsky L, Enright AJ, Ouzounis CA, (2005) MagicMatch-cross-referencing sequence identifiers across databases. Bioinformatics 21: 3429-3430.
-
(2005)
Bioinformatics
, vol.21
, pp. 3429-3430
-
-
Smith, M.1
Kunin, V.2
Goldovsky, L.3
Enright, A.J.4
Ouzounis, C.A.5
-
35
-
-
0028829125
-
The minimal gene complement of Mycoplasma genitalium
-
Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270: 397-403.
-
(1995)
Science
, vol.270
, pp. 397-403
-
-
Fraser, C.M.1
Gocayne, J.D.2
White, O.3
Adams, M.D.4
Clayton, R.A.5
-
36
-
-
0034641917
-
The complete sequence of the mucosal pathogen Ureaplasma urealyticum
-
Glass JI, Lefkowitz EJ, Glass JS, Heiner CR, Chen EY, et al. (2000) The complete sequence of the mucosal pathogen Ureaplasma urealyticum. Nature 407: 757-762.
-
(2000)
Nature
, vol.407
, pp. 757-762
-
-
Glass, J.I.1
Lefkowitz, E.J.2
Glass, J.S.3
Heiner, C.R.4
Chen, E.Y.5
-
37
-
-
0035836659
-
Complete genome sequence of an M1 strain of Streptococcus pyogenes
-
Ferretti JJ, McShan WM, Ajdic D, Savic DJ, Savic G, et al. (2001) Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc Natl Acad Sci U S A 98: 4658-4663.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 4658-4663
-
-
Ferretti, J.J.1
McShan, W.M.2
Ajdic, D.3
Savic, D.J.4
Savic, G.5
-
38
-
-
0034618559
-
Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS
-
Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H, (2000) Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407: 81-86.
-
(2000)
Nature
, vol.407
, pp. 81-86
-
-
Shigenobu, S.1
Watanabe, H.2
Hattori, M.3
Sakaki, Y.4
Ishikawa, H.5
-
39
-
-
0242300069
-
The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism
-
Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, et al. (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci U S A 100: 12984-12988.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 12984-12988
-
-
Waters, E.1
Hohn, M.J.2
Ahel, I.3
Graham, D.E.4
Adams, M.D.5
-
41
-
-
70350457960
-
The Mycoplasma genitalium MG_454 gene product resists killing by organic hydroperoxides
-
Saikolappan S, Sasindran SJ, Yu HD, Baseman JB, Dhandayuthapani S, (2009) The Mycoplasma genitalium MG_454 gene product resists killing by organic hydroperoxides. J Bacteriol 191: 6675-6682.
-
(2009)
J Bacteriol
, vol.191
, pp. 6675-6682
-
-
Saikolappan, S.1
Sasindran, S.J.2
Yu, H.D.3
Baseman, J.B.4
Dhandayuthapani, S.5
-
42
-
-
73449111594
-
Life on arginine for Mycoplasma hominis: clues from its minimal genome and comparison with other human urogenital mycoplasmas
-
Pereyre S, Sirand-Pugnet P, Beven L, Charron A, Renaudin H, et al. (2009) Life on arginine for Mycoplasma hominis: clues from its minimal genome and comparison with other human urogenital mycoplasmas. PLoS Genet 5: e1000677.
-
(2009)
PLoS Genet
, vol.5
-
-
Pereyre, S.1
Sirand-Pugnet, P.2
Beven, L.3
Charron, A.4
Renaudin, H.5
-
43
-
-
0033670249
-
Horizontal gene transfer in bacterial and archaeal complete genomes
-
Garcia-Vallve S, Romeu A, Palau J, (2000) Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res 10: 1719-1725.
-
(2000)
Genome Res
, vol.10
, pp. 1719-1725
-
-
Garcia-Vallve, S.1
Romeu, A.2
Palau, J.3
|