-
1
-
-
0029653518
-
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
-
1. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb J-F, Dougherty BA, Merrick JM et al.: Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995, 269:496-512. The first complete genome of a cellular life form to be sequenced. Includes a detailed description of the sequencing and sequence assembly methods and an initial functional classification of the encoded proteins.
-
(1995)
Science
, vol.269
, pp. 496-512
-
-
Fleischmann, R.D.1
Adams, M.D.2
White, O.3
Clayton, R.A.4
Kirkness, E.F.5
Kerlavage, A.R.6
Bult, C.J.7
Tomb, J.-F.8
Dougherty, B.A.9
Merrick, J.M.10
-
2
-
-
0028829125
-
The minimal gene complement of Mycoplasme genitalium
-
2. Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM et al.: The minimal gene complement of Mycoplasme genitalium. Science 1995, 270:397-403. The second bacterial genome sequence reported, providing, for the first time, the opportunity for comparison of complete genomes of two phylogenetically distant cellular life forms.
-
(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
Fleischmann, R.D.6
Bult, C.J.7
Kerlavage, A.R.8
Sutton, G.9
Kelley, J.M.10
-
3
-
-
0029894792
-
The yeast genome project: What did we learn?
-
3. Dujon B: The yeast genome project: what did we learn? Trends Genet 1996, 12:263-270. The best available overview of the yeast genome project results. Issues such as gene identification, protein function prediction, duplications, and impact of genome sequencing on experimental studies are briefly discussed. Clearly, the actual analysis of the sequence belongs to the future and will require many iterations.
-
(1996)
Trends Genet
, vol.12
, pp. 263-270
-
-
Dujon, B.1
-
4
-
-
16044367245
-
Complete genome sequence of the methanogenic Archaeon, Methanococcus jannaschii
-
4. Bult CJ, White O, Olsen GJ, Zhon L, Fleishmann RD, Sutton GG1 Blake JA, Fitzgerald LM, Clayton RA, Gocayne JD et al.: Complete genome sequence of the methanogenic Archaeon, Methanococcus jannaschii. Science 1996, 273:1058-1073. The first complete archaeal genome sequence. Assignment to functional categories was possible only for 38% of the putative M. jannaschii proteins, and significant sequence similarity was reported for 44%. The majority of proteins predicted to be involved in translation, transcription, and replication are most closely related to eukaryotic homologs, in accord with the rRNA-based phylogeny [23]. By contrast, many metabolic enzymes as well as transport systems and polysaccharide biosynthesis enzymes show similarity exclusively or primarily to bacterial proteins. Evidently, further analysis of the M. jannaschii genome sequence - both computational and experimental -presents a major challenge to comparative genomics.
-
(1996)
Science
, vol.273
, pp. 1058-1073
-
-
Bult, C.J.1
White, O.2
Olsen, G.J.3
Zhon, L.4
Fleishmann, R.D.5
Sutton, G.G.6
Blake, J.A.7
Fitzgerald, L.M.8
Clayton, R.A.9
Gocayne, J.D.10
-
5
-
-
0030113436
-
Sequencing and analysis of bacterial genomes
-
5. Koonin EV, Mushegian AR, Rudd KE: Sequencing and analysis of bacterial genomes. Curr Biol 1996, 6:404-416. An overview of the current bacterial and archaeal genome sequencing projects. A preliminary comparison of the H. influenzae and M. genitalium genomes is also presented, with an emphasis on the peculiarities of the small genome of M. genitalium, such as the virtual absence of regulatory systems common in other bacteria.
-
(1996)
Curr Biol
, vol.6
, pp. 404-416
-
-
Koonin, E.V.1
Mushegian, A.R.2
Rudd, K.E.3
-
6
-
-
0027057935
-
Comprehensive computer analysis of the 182 predicted open reading frames of yeast chromosome III
-
6. Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E: Comprehensive computer analysis of the 182 predicted open reading frames of yeast chromosome III. Prot Sci 1992, 1:1677-1690.
-
(1992)
Prot Sci
, vol.1
, pp. 1677-1690
-
-
Bork, P.1
Ouzounis, C.2
Sander, C.3
Scharf, M.4
Schneider, R.5
Sonnhammer, E.6
-
7
-
-
0028105794
-
Yeast chromosome III: New gene functions
-
7. Koonin EV, Bork P, Sander C: Yeast chromosome III: new gene functions. EMBO J 1994, 13:493-503.
-
(1994)
EMBO J
, vol.13
, pp. 493-503
-
-
Koonin, E.V.1
Bork, P.2
Sander, C.3
-
8
-
-
0028291320
-
Large scale bacterial gene discovery by similarity search
-
8. Robison K, Gilbert W, Church GM: Large scale bacterial gene discovery by similarity search. Nat Genet 1994, 7:205-214.
-
(1994)
Nat Genet
, vol.7
, pp. 205-214
-
-
Robison, K.1
Gilbert, W.2
Church, G.M.3
-
9
-
-
0029133912
-
Exploring the Mycoplasma capricolum genome: A minimal cell reveals its physiology
-
9. Bork P, Ouzounis C, Casari G, Schneider R, Sander C, Dolan M, Gilbert W, Gillevet PM: Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology. Mol Microbiol 1995, 16:955-967.
-
(1995)
Mol Microbiol
, vol.16
, pp. 955-967
-
-
Bork, P.1
Ouzounis, C.2
Casari, G.3
Schneider, R.4
Sander, C.5
Dolan, M.6
Gilbert, W.7
Gillevet, P.M.8
-
10
-
-
0029559311
-
Sequence similarity analysis of Escherichia coli proteins: Functional and evolutionary implications
-
10. Koonin EV, Tatusov RL, Rudd KE: Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications. Proc Natl Acad Sci USA 1995, 92:11921-11925.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 11921-11925
-
-
Koonin, E.V.1
Tatusov, R.L.2
Rudd, K.E.3
-
13
-
-
0029144085
-
Challenging times for bioinformatics
-
13. Casari G, Andrade MA, Bork P, Boyle J, Daruvar A, Ouzounis CA, Schneider R, Tamames J, Valencia A, Sander C: Challenging times for bioinformatics. Nature 1995, 376:647-648.
-
(1995)
Nature
, vol.376
, pp. 647-648
-
-
Casari, G.1
Andrade, M.A.2
Bork, P.3
Boyle, J.4
Daruvar, A.5
Ouzounis, C.A.6
Schneider, R.7
Tamames, J.8
Valencia, A.9
Sander, C.10
-
14
-
-
0029930365
-
More Haemophilus and Mycoplasma genes
-
14. Brosius J: More Haemophilus and Mycoplasma genes. Science 1996, 271:1302-1303.
-
(1996)
Science
, vol.271
, pp. 1302-1303
-
-
Brosius, J.1
-
15
-
-
0029930365
-
More Haemophilus and Mycoplasma genes
-
15. Robison K, Gilbert W, Church GM: More Haemophilus and Mycoplasma genes. Science 1996, 271:1302-1303.
-
(1996)
Science
, vol.271
, pp. 1302-1303
-
-
Robison, K.1
Gilbert, W.2
Church, G.M.3
-
16
-
-
0029930365
-
More Haemophilus and Mycoplasma genes
-
16. Venter JC: More Haemophilus and Mycoplasma genes. Science 1996, 271:1303-1304.
-
(1996)
Science
, vol.271
, pp. 1303-1304
-
-
Venter, J.C.1
-
17
-
-
0030111235
-
Metabolism and evolution of Haemophilus influenzae deduced from a whole genome comparison to Escherichia coli
-
17. Tatusov RL, Mushegian AR, Bork P, Brown NP, Borodovsky M, Hayes WS, Rudd KE, Koonin EV: Metabolism and evolution of Haemophilus influenzae deduced from a whole genome comparison to Escherichia coli. Curr Biol 1996, 6:279-291. A detailed re-analysis of the H. influenzae genome, including evaluation of the original set of predicted genes [1••], identification of new ones, prediction of a number of functions of putative gene products, and reconstruction of metabolic pathways. Using the comparison between H. influenzae and E. coli as a test case, an attempt was made to define the basic concepts important in genome comparison. (See also [33•].)
-
(1996)
Curr Biol
, vol.6
, pp. 279-291
-
-
Tatusov, R.L.1
Mushegian, A.R.2
Bork, P.3
Brown, N.P.4
Borodovsky, M.5
Hayes, W.S.6
Rudd, K.E.7
Koonin, E.V.8
-
18
-
-
0014800108
-
Distinguishing homologous from analogous proteins
-
18. Fitch WM: Distinguishing homologous from analogous proteins. Systematic Zool 1970, 19:99-106.
-
(1970)
Systematic Zool
, vol.19
, pp. 99-106
-
-
Fitch, W.M.1
-
19
-
-
0030210340
-
Gene order is not conserved in bacterial evolution
-
19. Mushegian AR, Koonin EV: Gene order is not conserved in bacterial evolution. Trends Gene: 1996, 12:289-290.
-
(1996)
Trends Gene
, vol.12
, pp. 289-290
-
-
Mushegian, A.R.1
Koonin, E.V.2
-
20
-
-
0030249023
-
Non-orthologous gene displacement
-
in press
-
20. Koonin EV, Mushegian AR, Bork P: Non-orthologous gene displacement. Trends Genet 1996, in press. In this report, non-orthologous gene displacement is defined as a major evolutionary phenomenon. The 11 unequivocal cases of non-orthologous displacement between H. influenzae and M. genitalium and possible evolutionary mechanisms leading to displacement are discussed.
-
(1996)
Trends Genet
-
-
Koonin, E.V.1
Mushegian, A.R.2
Bork, P.3
-
21
-
-
0027983037
-
Convergent evolution: The need to be explicit
-
21. Doolittle RF: Convergent evolution: the need to be explicit Trends Biochem Sci 1994, 19:15-18.
-
(1994)
Trends Biochem Sci
, vol.19
, pp. 15-18
-
-
Doolittle, R.F.1
-
22
-
-
0029789824
-
A minimal gene set for cellular life derived by comparison of complete bacterial genomes
-
in press
-
22. Mushegian AR, Koonin EV: A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci USA 1996, in press. Description of a theoretical minimal gene set derived by comparing the first two complete bacterial genomes and the logic behind its construction.
-
(1996)
Proc Natl Acad Sci USA
-
-
Mushegian, A.R.1
Koonin, E.V.2
-
23
-
-
0028055018
-
The winds of (evolutionary) change: Breathing new life into microbiology
-
23. Olsen GJ, Woese CR, Overbeek R: The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 1994, 176:1-6.
-
(1994)
J Bacteriol
, vol.176
, pp. 1-6
-
-
Olsen, G.J.1
Woese, C.R.2
Overbeek, R.3
-
24
-
-
0030023247
-
Determining divergence times of the major kingdoms of organisms with a protein clock
-
24. Doolittle RF, Feng DF, Tsang S, Cho G, Little E: Determining divergence times of the major kingdoms of organisms with a protein clock. Science 1996, 271:470-477.
-
(1996)
Science
, vol.271
, pp. 470-477
-
-
Doolittle, R.F.1
Feng, D.F.2
Tsang, S.3
Cho, G.4
Little, E.5
-
25
-
-
0028906201
-
An estimation of minimal genome size required for life
-
25. Itaya M: An estimation of minimal genome size required for life. FEBS Lett 1995, 362:257-260. An elegant experimental approach to the minimal genome problem. Bacillus subtilis genes were knocked out at random and the fraction of knockouts that rendered the bacteria unable to form colonies was determined. The results put the size of the minimal genome at -318 kbp.
-
(1995)
FEBS Lett
, vol.362
, pp. 257-260
-
-
Itaya, M.1
-
26
-
-
0028947022
-
Homologous nuclear-encoded mitochondrial and cytosolic isoproteins. A review of structure, biosynthesis and genes
-
26. Jaussi R: Homologous nuclear-encoded mitochondrial and cytosolic isoproteins. A review of structure, biosynthesis and genes. Eur J Biochem 1995, 228:551-561.
-
(1995)
Eur J Biochem
, vol.228
, pp. 551-561
-
-
Jaussi, R.1
-
27
-
-
0028941917
-
Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplication
-
27. Brown JR, Doolittle WF: Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplication. Proc Natl Acad Sci USA 1995, 92:2441-2445.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 2441-2445
-
-
Brown, J.R.1
Doolittle, W.F.2
-
29
-
-
0023184331
-
Bacterial evolution
-
29. Woese CR: Bacterial evolution. Microbiol Rev 1987, 51:221-271.
-
(1987)
Microbiol Rev
, vol.51
, pp. 221-271
-
-
Woese, C.R.1
-
30
-
-
0026282909
-
Early evolution and the origin of eukaryotes
-
30. Sogin ML: Early evolution and the origin of eukaryotes. Curr Opin Genet Dev 1991, 1:457-463.
-
(1991)
Curr Opin Genet Dev
, vol.1
, pp. 457-463
-
-
Sogin, M.L.1
-
32
-
-
0029654109
-
The origins and evolution of eukaryotic proteins
-
32. Doolittle RF: The origins and evolution of eukaryotic proteins. Philos Trans R Soc Lond Biol 1995, 349:235-240. A provocative discussion of alternative explanations for the evolution of eukaryotes and difficulties encountered by each of them. A paradoxical situation is noticed whereby certain highly conserved eukaryotic proteins (e.g. actin and tubulin) show only very limited similarity to bacterial proteins. It is speculated that at early stages of evolution, perhaps within a cell with an RNA genome, the rate of sequence change could have been much greater than in modern-type cells.
-
(1995)
Philos Trans R Soc Lond Biol
, vol.349
, pp. 235-240
-
-
Doolittle, R.F.1
-
33
-
-
85030290427
-
-
National Center for Biotechnology Information: Complete Genomes on World Wide Web URL
-
33. National Center for Biotechnology Information: Complete Genomes on World Wide Web URL: http://www.ncbi.nlm.nih.gov/ Complete-Genomes/ A detailed presentation of the results of comparative analyses of complete genomes performed by our group [5•,10,1 2,17•,19,20•,22•]. Separate World Wide Web pages are available for E. coli, H. influenzae, M. genitalium and the theoretically derived minimal gene set, detailing the observed sequence similarities, functional predictions and families of paralogs.
-
-
-
-
34
-
-
85030281747
-
-
The Institute for Genome Research TIGR Microbial Database on World Wide Web URL
-
34. The Institute for Genome Research TIGR Microbial Database on World Wide Web URL: http://www.tigr.org/tdb/mdb/ The TIGR Microbial Database contains comprehensive information on bacterial and archaeal genome sequencing (1••,2••,4••) performed at The Institute for Genome Research in Rockville, Maryland.
-
-
-
-
35
-
-
85030289925
-
-
European Molecular Biology Laboratory GeneQuiz on World Wide Web URL
-
35. European Molecular Biology Laboratory GeneQuiz on World Wide Web URL: http://www.embl-heidelberg.de/-genequiz
-
-
-
-
36
-
-
85030280778
-
-
Computational Biology in the Mathematics and Computer Science Division at Argonne National Laboratory: Phylogeny Metabolism Alignments (PUMA) on World Wide Web URL
-
36. Computational Biology in the Mathematics and Computer Science Division at Argonne National Laboratory: Phylogeny Metabolism Alignments (PUMA) on World Wide Web URL: http://www.mcs.anl.gov/home/compbio/PUMA/
-
-
-
-
37
-
-
85030280650
-
-
GenomeNet Japan (Kyoto University) on World Wide Web URL
-
37. GenomeNet Japan (Kyoto University) on World Wide Web URL: http://www.genome.ad.jp
-
-
-
-
38
-
-
85030289090
-
-
Institute for Marine Biosciences Sulfolobus solfataricus Genome Project on World Wide Web URL
-
38. Institute for Marine Biosciences Sulfolobus solfataricus Genome Project on World Wide Web URL: http://www.imb.nrc.ca/imb/sulfolob/
-
-
-
-
39
-
-
85030290197
-
-
Saccharomyces Genome Database (Department of Genetics, Stanford University School of Medicine) on World Wide Web URL
-
39. Saccharomyces Genome Database (Department of Genetics, Stanford University School of Medicine) on World Wide Web URL: http://genome-www.stanford.edu/Saccharomyces
-
-
-
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