Gene and context: integrative approaches to genome analysis.

[1]  D. Eisenberg,et al.  Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.

[2]  P. Bork,et al.  Variation and evolution of the citric-acid cycle: a genomic perspective. , 1999, Trends in microbiology.

[3]  B. Dujon,et al.  The genomic tree as revealed from whole proteome comparisons. , 1999, Genome research.

[4]  E. Kellogg,et al.  Phylogenetic relationships and evolution of the KNOTTED class of plant homeodomain proteins. , 1999, Molecular biology and evolution.

[5]  H. Mori,et al.  Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. , 1999, Molecular biology and evolution.

[6]  T. Gojobori,et al.  Identification of a ribonuclease H gene in both Mycoplasma genitalium and Mycoplasma pneumoniae by a new method for exhaustive identification of ORFs in the complete genome sequences , 1999, FEBS letters.

[7]  G. Mendz,et al.  The tricarboxylic acid cycle of Helicobacter pylori. , 1999, European journal of biochemistry.

[8]  A. Horswill,et al.  Studies of Regulation of Expression of the Propionate (prpBCDE) Operon Provide Insights into How Salmonella typhimurium LT2 Integrates Its 1,2-Propanediol and Propionate Catabolic Pathways , 1998, Journal of bacteriology.

[9]  Andrew Smith.  Genome sequence of the nematode C-elegans: A platform for investigating biology , 1998 .

[10]  J. Hackstein,et al.  A hydrogenosome with a genome , 1998, Nature.

[11]  Yan P. Yuan,et al.  Predicting function: from genes to genomes and back. , 1998, Journal of molecular biology.

[12]  J. Thompson,et al.  Multiple sequence alignment with Clustal X. , 1998, Trends in biochemical sciences.

[13]  B. Snel,et al.  Conservation of gene order: a fingerprint of proteins that physically interact. , 1998, Trends in biochemical sciences.

[14]  G. Rubin,et al.  A computer program for aligning a cDNA sequence with a genomic DNA sequence. , 1998, Genome research.

[15]  Michael Y. Galperin,et al.  Analogous enzymes: independent inventions in enzyme evolution. , 1998, Genome research.

[16]  T. Blumenthal.  Gene clusters and polycistronic transcription in eukaryotes , 1998, BioEssays : news and reviews in molecular, cellular and developmental biology.

[17]  M. Riley.  Systems for categorizing functions of gene products. , 1998, Current Opinion in Structural Biology.

[18]  M H Saier,et al.  Microbial genome analyses: global comparisons of transport capabilities based on phylogenies, bioenergetics and substrate specificities. , 1998, Journal of molecular biology.

[19]  R. Thauer,et al.  Thiol : fumarate reductase (Tfr) from Methanobacterium thermoautotrophicum , 1998 .

[20]  N J Russell,et al.  Citrate synthase and 2-methylcitrate synthase: structural, functional and evolutionary relationships. , 1998, Microbiology.

[21]  R. Huber,et al.  The complete genome of the hyperthermophilic bacterium Aquifex aeolicus , 1998, Nature.

[22]  C. Clayton,et al.  Helicobacter pylori porCDAB and oorDABCGenes Encode Distinct Pyruvate:Flavodoxin and 2-Oxoglutarate:Acceptor Oxidoreductases Which Mediate Electron Transport to NADP , 1998, Journal of bacteriology.

[23]  Volker F. Wendisch,et al.  Propionate oxidation in Escherichia coli: evidence for operation of a methylcitrate cycle in bacteria , 1997, Archives of Microbiology.

[24]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[25]  I. Steen,et al.  Biochemical and phylogenetic characterization of isocitrate dehydrogenase from a hyperthermophilic archaeon, Archaeoglobus fulgidus , 1997, Archives of Microbiology.

[26]  A. Blum,et al.  Cloning and Characterization of Helicobacter pyloriSuccinyl CoA:Acetoacetate CoA-transferase, a Novel Prokaryotic Member of the CoA-transferase Family* , 1997, The Journal of Biological Chemistry.

[27]  M. Huynen,et al.  Differential genome display. , 1997, Trends in genetics : TIG.

[28]  R. Overbeek,et al.  A reconstruction of the metabolism of Methanococcus jannaschii from sequence data. , 1997, Gene.

[29]  S. Anemüller,et al.  A succinate dehydrogenase with novel structure and properties from the hyperthermophilic archaeon Sulfolobus acidocaldarius: genetic and biophysical characterization , 1997, Journal of bacteriology.

[30]  J. Pollack,et al.  Malate/lactate dehydrogenase in mollicutes: evidence for a multienzyme protein. , 1997, Gene.

[31]  S. Oliver,et al.  Erratum: Overview of the yeast genome , 1997, Nature.

[32]  Michael Y. Galperin,et al.  Sequence analysis of an exceptionally conserved operon suggests enzymes for a new link between histidine and purine biosynthesis , 1997, Molecular microbiology.

[33]  A. Kolstø,et al.  Dynamic bacterial genome organization , 1997, Molecular microbiology.

[34]  H. Ochman,et al.  Amelioration of Bacterial Genomes: Rates of Change and Exchange , 1997, Journal of Molecular Evolution.

[35]  J Hacker,et al.  Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution , 1997, Molecular microbiology.

[36]  R. Thauer,et al.  Structures and functions of four anabolic 2-oxoacid oxidoreductases in Methanobacterium thermoautotrophicum. , 1997, European journal of biochemistry.

[37]  A. Horswill,et al.  Propionate catabolism in Salmonella typhimurium LT2: two divergently transcribed units comprise the prp locus at 8.5 centisomes, prpR encodes a member of the sigma-54 family of activators, and the prpBCDE genes constitute an operon , 1997, Journal of bacteriology.

[38]  P. Bork,et al.  Non-orthologous gene displacement. , 1996, Trends in genetics : TIG.

[39]  J R Roth,et al.  Selfish operons: horizontal transfer may drive the evolution of gene clusters. , 1996, Genetics.

[40]  G. Ordal,et al.  CheC and CheD interact to regulate methylation of Bacillus subtilis methyl‐accepting chemotaxis proteins , 1996, Molecular microbiology.

[41]  E V Koonin,et al.  Gene order is not conserved in bacterial evolution. , 1996, Trends in genetics : TIG.

[42]  P. Bork,et al.  Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli , 1996, Current Biology.

[43]  G. Salmond,et al.  The bacterial ‘enigma’: cracking the code of cell–cell communication , 1995, Molecular microbiology.

[44]  M. Borodovsky,et al.  Intrinsic and extrinsic approaches for detecting genes in a bacterial genome. , 1994, Nucleic acids research.

[45]  R. Brodeur,et al.  Metabolic studies on Saccharomyces cerevisiae containing fused citrate synthase/malate dehydrogenase. , 1994, Biochemistry.

[46]  R. Overbeek,et al.  The winds of (evolutionary) change: breathing new life into microbiology , 1994 .

[47]  A. Danchin,et al.  Evidence for horizontal gene transfer in Escherichia coli speciation. , 1991, Journal of molecular biology.

[48]  D. Laporte,et al.  Regulation of the glyoxylate bypass operon: cloning and characterization of iclR , 1990, Journal of bacteriology.

[49]  T. Niermann,et al.  Properties and primary structure of the L-malate dehydrogenase from the extremely thermophilic archaebacterium Methanothermus fervidus. , 1990, European journal of biochemistry.

[50]  J. Piatigorsky,et al.  Enzyme/crystallins: Gene sharing as an evolutionary strategy , 1989, Cell.

[51]  T. Atkinson,et al.  From analysis to synthesis: new ligand binding sites on the lactate dehydrogenase framework. Part II. , 1989, Trends in biochemical sciences.

[52]  W B Whitman,et al.  Pathway of acetate assimilation in autotrophic and heterotrophic methanococci , 1987, Journal of bacteriology.

[53]  W. Cleland,et al.  pH profiles and isotope effects for aconitases from Saccharomycopsis lipolytica, beef heart, and beef liver. alpha-Methyl-cis-aconitate and threo-Ds-alpha-methylisocitrate as substrates. , 1984, Biochemistry.

[54]  R. W. Davis,et al.  The organization and transcription of the galactose gene cluster of Saccharomyces. , 1981, Journal of molecular biology.

[55]  G. Plaut,et al.  Identification of D-threo-alpha-methylisocitrate as stereochemically specific substrate for bovine heart aconitase and inhibitor of TPN-linked isocitrate dehydrogenase. , 1977, The Journal of biological chemistry.

[56]  G. Wilcox,et al.  Regulation of the L-arabinose operon BAD in vitro. , 1974, The Journal of biological chemistry.

[57]  W. Fitch.  Distinguishing homologous from analogous proteins. , 1970, Systematic zoology.

[58]  W. Fitch,et al.  Construction of phylogenetic trees. , 1967, Science.

[59]  B. Snel,et al.  Genome phylogeny based on gene content , 1999, Nature Genetics.

[60]  James R. Cole,et al.  A new version of the RDP (Ribosomal Database Project) , 1999, Nucleic Acids Res..

[61]  T. Gaasterland,et al.  Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. , 1998, Microbial & comparative genomics.

[62]  T Gaasterland,et al.  Constructing multigenome views of whole microbial genomes. , 1998, Microbial & comparative genomics.

[63]  Evgeni Selkov,et al.  MPW: the Metabolic Pathways Database , 1998, Nucleic Acids Res..

[64]  S. Chervitz,et al.  The two-component signaling pathway of bacterial chemotaxis: a molecular view of signal transduction by receptors, kinases, and adaptation enzymes. , 1997, Annual review of cell and developmental biology.

[65]  G. Paul,et al.  Molecular Diversity and Evolution of blaTEM Genes Encoding β-Lactamases Resistant to Clavulanic Acid in Clinical E. coli , 1997, Journal of Molecular Evolution.

[66]  A. Valencia,et al.  Conserved Clusters of Functionally Related Genes in Two Bacterial Genomes , 1997, Journal of Molecular Evolution.

[67]  M. Adams,et al.  Oxidoreductase-type enzymes and redox proteins involved in fermentative metabolisms of hyperthermophilic Archaea. , 1996, Advances in protein chemistry.