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1
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85031636166
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Genomes online database (GOLD) The best maintained and most comprehensive internet database of genome projects and related information
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Genomes online database (GOLD) http://geta.life.uiuc.edu/~nikos/genomes.html The best maintained and most comprehensive internet database of genome projects and related information.
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Genomes and proteomes: Towards a multidimensional view of biology
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Williams K.L. Genomes and proteomes: towards a multidimensional view of biology. Electrophoresis. 20:1999;678-688.
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Electrophoresis
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Williams, K.L.1
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Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima
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Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A.et al. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature. 399:1999;323-329.
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4
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0033552961
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Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori
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Landmark publication of the first duplicate genome sequence from a single (pathogenic) species. Heralds the beginning of the true age of comparative genomics. Analysis of the complete genome sequence of two strains from different continents revealed 206 unshared coding regions, or about 7% coding-region divergence. Almost half of these genes are clustered in a single hypervariable region termed a 'strain-specific plasticity zone'. Overall genome organisation differs by 10 inverted or transposed regions. This study has successfully detected a wide range of strain-specific sequences and has led to a better understanding of the gene pool of the species.
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Alm R.A., Ling L.S., Moir D.T., King B.L., Brown E.D., Doig P.C., Smith D.R., Noonan B., Guild B.C., deJonge B.L.et al. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature. 397:1999;176-180. Landmark publication of the first duplicate genome sequence from a single (pathogenic) species. Heralds the beginning of the true age of comparative genomics. Analysis of the complete genome sequence of two strains from different continents revealed 206 unshared coding regions, or about 7% coding-region divergence. Almost half of these genes are clustered in a single hypervariable region termed a 'strain-specific plasticity zone'. Overall genome organisation differs by 10 inverted or transposed regions. This study has successfully detected a wide range of strain-specific sequences and has led to a better understanding of the gene pool of the species.
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Nature
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Alm, R.A.1
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Smith, D.R.7
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Alignment of whole genomes
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Delcher A.L., Kasif S., Fleischmann R.D., Peterson J., White O., Salzberg S.L. Alignment of whole genomes. Nucleic Acids Res. 27:1999;2369-2376.
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Saunders N.J., Moxon E.R. Implications of sequencing bacterial genomes for pathogenesis and vaccine development. Curr Opin Biotechnol. 9:1998;618-623.
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Saunders, N.J.1
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0032561496
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Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis
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Stephens R.S., Kalman S., Lammel C., Fan J., Marathe R., Aravind L., Mitchell W., Olinger L., Tatusov R.L., Zhao Q.et al. Genome sequence of an obligate intracellular pathogen of humans: chlamydia trachomatis. Science. 282:1998;754-759.
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Stephens, R.S.1
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0032540874
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Complete genome sequence of Treponema pallidum, the syphilis spirochete [see comments]
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Fraser C.M., Norris S.J., Weinstock G.M., White O., Sutton G.G., Dodson R., Gwinn M., Hickey E.K., Clayton R., Ketchum K.A.et al. Complete genome sequence of Treponema pallidum, the syphilis spirochete [see comments]. Science. 281:1998;375-388.
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Fraser, C.M.1
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9
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0032491377
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Predicting function: From genes to genomes and back
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Detailed review of how function can be ascribed to novel sequences through homology. The computational process of ascribing putative function to protein sequences is benefiting immensely from the sequencing of microbial genomes. This extensive review offers perhaps the first summary of how our knowledge of 'function' has improved since the first microbial genome sequence. This paper emphasises the need to begin examining protein function in light of higher order processes, such as regulation of gene expression, metabolic pathways and signalling cascades.
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Bork P., Dandekar T., Diaz-Lazcoz Y., Eisenhaber F., Huynen M., Yuan Y. Predicting function: from genes to genomes and back. J Mol Biol. 283:1998;707-725. Detailed review of how function can be ascribed to novel sequences through homology. The computational process of ascribing putative function to protein sequences is benefiting immensely from the sequencing of microbial genomes. This extensive review offers perhaps the first summary of how our knowledge of 'function' has improved since the first microbial genome sequence. This paper emphasises the need to begin examining protein function in light of higher order processes, such as regulation of gene expression, metabolic pathways and signalling cascades.
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J Mol Biol
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Bork, P.1
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Yuan, Y.6
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10
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Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli
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Tatusov R.L., Mushegian A.R., Bork P., Brown N.P., Hayes W.S., Borodovsky M., Rudd K.E., Koonin E.V. Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr Biol. 6:1996;279-291.
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Tatusov, R.L.1
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Borodovsky, M.6
Rudd, K.E.7
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Differential genome analysis applied to the species-specific features of Helicobacter pylori
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Huynen M., Dandekar T., Bork P. Differential genome analysis applied to the species-specific features of Helicobacter pylori. FEBS Lett. 426:1998;1-5.
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FEBS Lett
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Huynen, M.1
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0032509179
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Comparison of the complete protein sets of worm and yeast: Orthology and divergence
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Outstanding example of the ability of in silico methods to help find genes responsible for certain phenotypes using the 'species-filter' approach. This comprehensive comparison of the first two eukaryotic genomes sequenced, S. cerevisiae and the latter, identified genes unique to the latter that may prove to be restricted to metazoans and play a role in multicellularity.
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Chervitz S.A., Aravind L., Sherlock G., Ball C.A., Koonin E.V., Dwight S.S., Harris M.A., Dolinski K., Mohr S., Smith T.et al. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science. 282:1998;2022-2028. Outstanding example of the ability of in silico methods to help find genes responsible for certain phenotypes using the 'species-filter' approach. This comprehensive comparison of the first two eukaryotic genomes sequenced, S. cerevisiae and the latter, identified genes unique to the latter that may prove to be restricted to metazoans and play a role in multicellularity.
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Science
, vol.282
, pp. 2022-2028
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Chervitz, S.A.1
Aravind, L.2
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Ball, C.A.4
Koonin, E.V.5
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Smith, T.10
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14
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0032189860
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Concordance analysis of microbial genomes
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A rare example showing the importance of combining in silico and experimental approaches to hypothesis testing. Using the 'species-filter' approach in combination with experimental approaches the authors search for drug targets - essential genes restricted to pathogenic prokaryotes. Useful software for comparing shared and unshared genes between complete genomes available on the internet is described.
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Bruccoleri R.E., Dougherty T.J., Davison D.B. Concordance analysis of microbial genomes. Nucleic Acids Res. 26:1998;4482-4486. A rare example showing the importance of combining in silico and experimental approaches to hypothesis testing. Using the 'species-filter' approach in combination with experimental approaches the authors search for drug targets - essential genes restricted to pathogenic prokaryotes. Useful software for comparing shared and unshared genes between complete genomes available on the internet is described.
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(1998)
Nucleic Acids Res
, vol.26
, pp. 4482-4486
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Bruccoleri, R.E.1
Dougherty, T.J.2
Davison, D.B.3
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New antibiotic discovery, novel screens, novel targets and impact of microbial genomics
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Allsop A.E. New antibiotic discovery, novel screens, novel targets and impact of microbial genomics. Curr Opin Microbiol. 1:1998;530-534.
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Curr Opin Microbiol
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Allsop, A.E.1
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Bacterial genome sequencing and drug discovery
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Allsop A.E. Bacterial genome sequencing and drug discovery. Curr Opin Biotechnol. 9:1998;637-642.
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Curr Opin Biotechnol
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Allsop, A.E.1
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0343322243
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Use of the complete genome sequence information of Haemophilus influenzae strain Rd to investigate lipopolysaccharide biosynthesis
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Hood D.W., Deadman M.E., Allen T., Masoud H., Martin A., Brisson J.R., Fleischmann R., Venter J.C., Richards J.C., Moxon E.R. Use of the complete genome sequence information of Haemophilus influenzae strain Rd to investigate lipopolysaccharide biosynthesis. Mol Microbiol. 22:1996;951-965.
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Hood, D.W.1
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Moxon, E.R.10
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18
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0032953228
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Comparative genomes of Chlamydia pneumoniae and C-trachomatis
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Kalman S., Mitchell W., Marathe R., Lammel C., Fan L.L., Hyman R.W., Olinger L., Grimwood L., Davis R.W., Stephens R.S. Comparative genomes of Chlamydia pneumoniae and C-trachomatis. Nat Genet. 21:1999;385-389.
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Nat Genet
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Kalman, S.1
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Fan, L.L.5
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Olinger, L.7
Grimwood, L.8
Davis, R.W.9
Stephens, R.S.10
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0032512051
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The genome sequence of Rickettsia prowazekii and the origin of mitochondria
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Andersson S.G., Zomorodipour A., Andersson J.O., Sicheritz-Ponten T., Alsmark U.C., Podowski R.M., Naslund A.K., Eriksson A.S., Winkler H.H., Kurland C.G. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature. 396:1998;133-140.
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Nature
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Andersson, S.G.1
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Alsmark, U.C.5
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The Mycobacterium tuberculosis genomic sequence: Anatomy of a master adaptor
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Bishai W. The Mycobacterium tuberculosis genomic sequence: anatomy of a master adaptor. Trends Microbiol. 6:1998;464-465.
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Trends Microbiol
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Bishai, W.1
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Databases in genomic research
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Gelbart W.M. Databases in genomic research. Science. 282:1998;659-661.
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Science
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Gelbart, W.M.1
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What is there (WIT)? Interactive metabolic reconstruction on the web
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What is there (WIT)? Interactive metabolic reconstruction on the web. http://wit.mcs.anl.gov/WIT2/.
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24
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0033515250
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Building working cells 'in silico'
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The concept of 'in silico' cells is at present an underdeveloped yet exciting possibility that holds the promise of allowing researchers to combine all aspects of cell biology into a single system that 'lives' within a computer. From genes, to metabolic pathways, to information on stochiometric ratios of protein products within a cell - once sufficient information has been collected and entered into these model cells, this will be a technology to watch in the future (see [25]).
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Normile D. Building working cells 'in silico'. Science. 284:1999;80-81. The concept of 'in silico' cells is at present an underdeveloped yet exciting possibility that holds the promise of allowing researchers to combine all aspects of cell biology into a single system that 'lives' within a computer. From genes, to metabolic pathways, to information on stochiometric ratios of protein products within a cell - once sufficient information has been collected and entered into these model cells, this will be a technology to watch in the future (see [25]).
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Science
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Normile, D.1
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A general computational framework for modeling cellular structure and function
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Schaff J., Fink C.C., Slepchenko B., Carson J.H., Loew L.M. A general computational framework for modeling cellular structure and function. Biophys J. 73:1997;1135-1146.
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Schaff, J.1
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26
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84984932472
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Exploring the new world of the genome with DNA microarrays
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Review of the subject in a special issue devoted to advances in microarray technology.
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Brown P.O., Botstein D. Exploring the new world of the genome with DNA microarrays. Nat Genet. 21:1999;33-37. Review of the subject in a special issue devoted to advances in microarray technology.
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Nat Genet
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Brown, P.O.1
Botstein, D.2
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0033048778
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Genomic profiling of drug sensitivities via induced haploinsufficiency
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Giaever G., Shoemaker D.D., Jones T.W., Liang H., Winzeler E.A., Astromoff A., Davis R.W. Genomic profiling of drug sensitivities via induced haploinsufficiency. Nat Genet. 21:1999;278-283.
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Nat Genet
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Giaever, G.1
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Winzeler, E.A.5
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Davis, R.W.7
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28
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0032555671
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Direct allelic variation scanning of the yeast genome [see comments]
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Winzeler E.A., Richards D.R., Conway A.R., Goldstein A.L., Kalman S., McCullough M.J., McCusker J.H., Stevens D.A., Wodicka L., Lockhart D.J., Davis R.W. Direct allelic variation scanning of the yeast genome [see comments]. Science. 281:1998;1194-1197.
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Science
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Winzeler, E.A.1
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Bacterial population genetics, evolution and epidemiology
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Spratt B.G., Maiden M.C. Bacterial population genetics, evolution and epidemiology. Philos Trans R Soc Lond Biol. 354:1999;701-710.
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Philos Trans R Soc Lond Biol
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Spratt, B.G.1
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0033612136
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Comparative genomics of BCG vaccines by whole-genome DNA microarray
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A premier example of how microarray technology can be used to survey for heritable genetic variation that may provide the genetic basis for important phenotypes. In this case, genetic variation in tuberculosis vaccine strains that may explain observed temporal and geographic differences in vaccine effectiveness.
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Behr M.A., Wilson M.A., Gill W.P., Salamon H., Schoolnik G.K., Rane S., Small P.M. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science. 284:1999;1520-1523. A premier example of how microarray technology can be used to survey for heritable genetic variation that may provide the genetic basis for important phenotypes. In this case, genetic variation in tuberculosis vaccine strains that may explain observed temporal and geographic differences in vaccine effectiveness.
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Science
, vol.284
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Behr, M.A.1
Wilson, M.A.2
Gill, W.P.3
Salamon, H.4
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Small, P.M.7
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Pathoadaptive mutations: Gene loss and variation in bacterial pathogens
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Sokurenko E.V., Hasty D.L., Dykhuizen D.E. Pathoadaptive mutations: gene loss and variation in bacterial pathogens. Trends Microbiol. 7:1999;191-195.
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Trends Microbiol
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Gordon S.V., Heym B., Parkhill J., Barrell B., Cole S.T. New insertion sequences and a novel repeated sequence in the genome of Mycobacterium tuberculosis H37Rv. Microbiology. 145:1999;881-892.
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Microbiology
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Gordon, S.V.1
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Isaksson A., Landegren U. Accessing genomic information: alternatives to PCR. Curr Opin Biotechnol. 10:1999;11-15.
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Isaksson, A.1
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Is it time to uproot the tree of life?
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See papers [36-41]. Excellent synopsis of the current debate over how much horizontal gene transfer contributes to the evolution of bacterial genomes.
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Pennisi E. Is it time to uproot the tree of life? Science. 284:1999;1305-1307. See papers [36-41]. Excellent synopsis of the current debate over how much horizontal gene transfer contributes to the evolution of bacterial genomes.
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Science
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Pennisi, E.1
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Genome phylogeny based on gene content
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Snel B., Bork P., Huynen M.A. Genome phylogeny based on gene content. Nat Genet. 21:1999;108-110.
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Nat Genet
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Is there a phylogenetic signal in prokaryote proteins?
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Teichmann S.A., Mitchison G. Is there a phylogenetic signal in prokaryote proteins? J Mol Evol. 49:1999;98-107.
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J Mol Evol
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Lake J.A., Jain R., Rivera M.C. Mix and match in the tree of life. Science. 283:1999;2027-2028.
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Science
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Baumler A.J. The record of horizontal gene transfer in Salmonella. Trends Microbiol. 5:1997;318-322.
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Jain R., Rivera M.C., Lake J.A. Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA. 96:1999;3801-3806.
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NIH urged to fund centers to merge computing and biology
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Evidence that future funding will place emphasis on the establishment of 'centers of excellence' dedicated to projects that merge computational and empirical approaches. As so many genome projects now focus on pathogenic species, this initiative will hopefully have an important impact on the study of pathogenesis.
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Malakoff D. NIH urged to fund centers to merge computing and biology. Science. 284:1999;1742. Evidence that future funding will place emphasis on the establishment of 'centers of excellence' dedicated to projects that merge computational and empirical approaches. As so many genome projects now focus on pathogenic species, this initiative will hopefully have an important impact on the study of pathogenesis.
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Science
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Malakoff, D.1
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Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum
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Gardner M.J., Tettelin H., Carucci D.J., Cummings L.M., Aravind L., Koonin E.V., Shallom S., Mason T., Yu K., Fujii C.et al. Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science. 282:1998;1126-1132.
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Gardner, M.J.1
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