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Pearson, W.R.1
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Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
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Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. of special interest Nucleic Acids Res. 25:1997;3389-3402 The latest version of the National Center for Biotechnology linformation's basic local alignment search tool programs for sequence comparison includes new ideas based on wide-spread experience with previous versions: the construction of gapped alignments and the ability to generate and apply profiles from significant hits in an iterative fashion. Not identical to WU-BLAST2 by Warren Gish, which also does gapped alignments.
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Lipman, D.7
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Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks
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Applying motif and profile searches
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Bork P, Gibson T. Applying motif and profile searches. Methods Enzymol. 266:1996;162-184.
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Methods Enzymol
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Identification of functional residues and secondary structure from protein multiple sequence alignment
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Livingstone C, Barton G. Identification of functional residues and secondary structure from protein multiple sequence alignment. Methods Enzymol. 266:1996;497-512.
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Methods Enzymol
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Livingstone, C.1
Barton, G.2
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7
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0029785147
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Mapping the protein universe
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of special interest. An all-on-all comparison of 3D protein structures using the Dali method leads to a classification scheme for folds, an overview of the space of all known protein structures and provides tools leading to the unification of apparently unrelated protein families.
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Holm L, Sander C. Mapping the protein universe. of special interest Science. 273:1996;595-603 An all-on-all comparison of 3D protein structures using the Dali method leads to a classification scheme for folds, an overview of the space of all known protein structures and provides tools leading to the unification of apparently unrelated protein families.
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Science
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Holm, L.1
Sander, C.2
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8
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0030957151
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Aerolysin and pertussis toxin share a common receptor-binding domain
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of special interest. An example of an unexpected discovery of structural similarity leading to the unification of functionally but remotely related protein families and interesting hypotheses about functional apsects.
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Rossjohn J, Buckley J, Hazes B, Murzin A, Read R, Parker M. Aerolysin and pertussis toxin share a common receptor-binding domain. of special interest EMBO J. 16:1997;3426-3434 An example of an unexpected discovery of structural similarity leading to the unification of functionally but remotely related protein families and interesting hypotheses about functional apsects.
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EMBO J
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Rossjohn, J.1
Buckley, J.2
Hazes, B.3
Murzin, A.4
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0029587166
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A method to predict functional residues in proteins
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Casari G, Sander C, Valencia A. A method to predict functional residues in proteins. Nat Struct Biol. 2:1995;171-178.
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Casari, G.1
Sander, C.2
Valencia, A.3
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10
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0031157904
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Classification of protein families and detection of the determinant residues with an improved self-organizing map
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of special interest. An algorithm using protein vectors in abstract sequence space. The vectors are classified by a neural network which derives the tree-determinant (subfamily-specific) residues.
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Andrade M, Casari G, Sander C, Valencia A. Classification of protein families and detection of the determinant residues with an improved self-organizing map. of special interest Biol Cybern. 76:1997;441-450 An algorithm using protein vectors in abstract sequence space. The vectors are classified by a neural network which derives the tree-determinant (subfamily-specific) residues.
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Biol Cybern
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Andrade, M.1
Casari, G.2
Sander, C.3
Valencia, A.4
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0029967362
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SRS: Information retrieval system for molecular biology data banks
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Etzold T, Ulyanov A, Argos P. SRS: information retrieval system for molecular biology data banks. Methods Enzymol. 266:1996;114-128.
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Methods Enzymol
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Etzold, T.1
Ulyanov, A.2
Argos, P.3
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13
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0029653518
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Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
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Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tom J-F, Dougherty BA, Merrick JM, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269:1995;496-512.
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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
Tom J-F8
Dougherty, B.A.9
Merrick, J.M.10
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14
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0030585734
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Evaluation of gene structure prediction programs
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Burset M, Guigó R. Evaluation of gene structure prediction programs. Genomics. 34:1996;353-367.
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Genomics
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Burset, M.1
Guigó, R.2
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0030253209
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Computational analysis of transcriptional regulatory elements: A field in flux
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of special interest. Summary of an international workshop containing references for the latest advances in the field. Identification of transcriptional elements is very important for the detection of genes in genome sequences.
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Bucher P, Fickett J, Hatzigeorgiou A. Computational analysis of transcriptional regulatory elements: a field in flux. of special interest Comput Appl Biosci. 12:1996;361-362 Summary of an international workshop containing references for the latest advances in the field. Identification of transcriptional elements is very important for the detection of genes in genome sequences.
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Comput Appl Biosci
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Bucher, P.1
Fickett, J.2
Hatzigeorgiou, A.3
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16
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0030927867
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Searching for regulatory elements in human noncoding sequences
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of special interest. Description of the latest developments in the detection of regulatory element in human DNA and model vertebrates.
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Duret L, Bucher P. Searching for regulatory elements in human noncoding sequences. of special interest Curr Opin Struct Biol. 7:1997;399-406 Description of the latest developments in the detection of regulatory element in human DNA and model vertebrates.
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Curr Opin Struct Biol
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Duret, L.1
Bucher, P.2
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17
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0029830044
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Gene recognition via spliced sequence alignment
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of special interest. Formalization of a commonly used method for gene detection in nucleotide sequences based on finding matching expressed sequence tags (cDNA fragments) and/or proteins using dynamic programming.
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Gelfand M, Mironov A, Pevzner P. Gene recognition via spliced sequence alignment. of special interest Proc Natl Acad Sci USA. 93:1996;9061-9066 Formalization of a commonly used method for gene detection in nucleotide sequences based on finding matching expressed sequence tags (cDNA fragments) and/or proteins using dynamic programming.
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Proc Natl Acad Sci USA
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Gelfand, M.1
Mironov, A.2
Pevzner, P.3
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18
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0031021210
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Biology's new Rosetta stone
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of special interest. The authors express their concerns about the quality of results from the yeast genome project. They point out problems with some of the annotations derived by sequence similarity rather than experimentation and with putative short open reading frames that may not be expressed.
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Das S, Yu L, Gaitatzes C, Rogers R, Freeman J, Bienkowska J, Adams R, Smith T, Lindelien J. Biology's new Rosetta stone. of special interest Nature. 385:1997;29-30 The authors express their concerns about the quality of results from the yeast genome project. They point out problems with some of the annotations derived by sequence similarity rather than experimentation and with putative short open reading frames that may not be expressed.
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Nature
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Das, S.1
Yu, L.2
Gaitatzes, C.3
Rogers, R.4
Freeman, J.5
Bienkowska, J.6
Adams, R.7
Smith, T.8
Lindelien, J.9
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19
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0003067660
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Toward pathway engineering: A new database of genetic and molecular pathways
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of special interest. Development of one of the best and most compehensive collections of information on gene function and metabolic pathways.
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Kanehisa M. Toward pathway engineering: a new database of genetic and molecular pathways. of special interest Sci Technol Japan. 59:1996;34-38 Development of one of the best and most compehensive collections of information on gene function and metabolic pathways.
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Sci Technol Japan
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Kanehisa, M.1
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20
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0030847958
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EcoCyc: Enyclopedia of Escherichia coli genes and metabolism
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Karp P, Riley M, Paley S, Pellegrini-Toole A, Krummenacker M. EcoCyc: enyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 25:1997;43-51.
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Karp, P.1
Riley, M.2
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Krummenacker, M.5
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21
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0030111235
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Metabolism and evolution of Haemophilus influenzae deduced from a whole-genone comparison with Escherichia coli
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of special interest. Comparison of these two bacteria resulted in assignment of many genes to metabolic pathways.
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Tatusov RL, Mushegian AR, Bork P, Brown NP, Hayes WS, Borodovsky M, Rudd KE, Koonin EV. Metabolism and evolution of Haemophilus influenzae deduced from a whole-genone comparison with Escherichia coli. of special interest Curr Biol. 6:1996;279-291 Comparison of these two bacteria resulted in assignment of many genes to metabolic pathways.
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Curr Biol
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Tatusov, R.L.1
Mushegian, A.R.2
Bork, P.3
Brown, N.P.4
Hayes, W.S.5
Borodovsky, M.6
Rudd, K.E.7
Koonin, E.V.8
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22
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0030219788
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Computational comparisons of model genomes
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of special interest. Genome comparison needs new methodologies to cope with the aggregate data from multiple sequences. Here, relative gene position is used for functional classification and gene functional class is derived by an automated procedure based on keywords associated to homologs.
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Ouzounis C, Casari G, Sander C, Tamames J, Valencia A. Computational comparisons of model genomes. of special interest Trends Biotechnol. 14:1996;280-285 Genome comparison needs new methodologies to cope with the aggregate data from multiple sequences. Here, relative gene position is used for functional classification and gene functional class is derived by an automated procedure based on keywords associated to homologs.
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(1996)
Trends Biotechnol
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Ouzounis, C.1
Casari, G.2
Sander, C.3
Tamames, J.4
Valencia, A.5
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23
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0030811859
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Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium
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Himmelreich R, Plagens H, Hilbert H, Reiner B, Hermann R. Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium. Nucleic Acids Res. 25:1997;701-712.
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Nucleic Acids Res
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Himmelreich, R.1
Plagens, H.2
Hilbert, H.3
Reiner, B.4
Hermann, R.5
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24
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0030993173
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Dynamic bacterial genome organization
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of special interest. Comparison of the first full bacterial genomes shows an extraordinary complexity and variability of gene order.
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Kolstø A. Dynamic bacterial genome organization. of special interest Mol Microbiol. 24:1997;241-248 Comparison of the first full bacterial genomes shows an extraordinary complexity and variability of gene order.
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Mol Microbiol
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Kolstø, A.1
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0031024670
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Conserved clusters of functionality related genes in two bacterial genomes
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Tamames J, Casari G, Ouzounis C, Valencia A. Conserved clusters of functionality related genes in two bacterial genomes. J Mol Evol. 44:1997;66-73.
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J Mol Evol
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Tamames, J.1
Casari, G.2
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Valencia, A.4
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27
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0031588599
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Comparison between the Escherichia coli and Bacillus subtilis genomes suggests that a major function of polynucleotide phosphorylase is to synthesize CDP
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Danchin A. Comparison between the Escherichia coli and Bacillus subtilis genomes suggests that a major function of polynucleotide phosphorylase is to synthesize CDP. DNA Res. 4:1997;9-18.
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DNA Res
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Danchin, A.1
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0030340124
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HinCyc: A knowledge base of the complete genome and metabolic pathways of H. influenzae
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Karp P, Ouzounis C, Paley S. HinCyc: a knowledge base of the complete genome and metabolic pathways of H. influenzae. Ismb. 4:1996;116-124.
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Ismb
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Karp, P.1
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0030953242
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Microbial pathogenesis: Genomics and beyond
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of special interest. Review on the use of genomic bacterial information for elucidation of bacterial biochemistry with stress on pathogenicity.
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Strauss E, Falkow S. Microbial pathogenesis: genomics and beyond. of special interest Science. 276:1997;707-712 Review on the use of genomic bacterial information for elucidation of bacterial biochemistry with stress on pathogenicity.
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Science
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Strauss, E.1
Falkow, S.2
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30
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0030597980
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The emergence of major cellular processes in evolution
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of special interest. Analysis of the species distribution of set of protein families leads to a hypothesis about the evolutionary split between the three kingdoms.
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Ouzounis C, Kyrpides N. The emergence of major cellular processes in evolution. of special interest FEBS Lett. 390:1996;119-123 Analysis of the species distribution of set of protein families leads to a hypothesis about the evolutionary split between the three kingdoms.
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Ouzounis, C.1
Kyrpides, N.2
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31
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0029789824
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A minimal gene set for cellular life derived by comparison of complete bacterial genomes
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of special interest. An analysis of the conserved proteins between the H. influenzae and the M. genitalium bacterial genomes. A set of conserved proteins is proposed as representing a minimal cell.
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Mushegian A, Koonin E. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. of special interest Proc Natl Acad Sci USA. 93:1996;10268-10273 An analysis of the conserved proteins between the H. influenzae and the M. genitalium bacterial genomes. A set of conserved proteins is proposed as representing a minimal cell.
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Proc Natl Acad Sci USA
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Mushegian, A.1
Koonin, E.2
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32
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0030868589
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Comparison of archaeal and bacterial genomes: Computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea
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of special interest. Through the comparison of the first complete genomes and the kingdom expansion of their proteins the authors conclude that M. jannaschii has a very heterogeneous behaviour by protein functional class.
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Koonin E, Mushegian A, Galperin M, Walker D. Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. of special interest Mol Microbiol. 25:1997;619-637 Through the comparison of the first complete genomes and the kingdom expansion of their proteins the authors conclude that M. jannaschii has a very heterogeneous behaviour by protein functional class.
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Mol Microbiol
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Koonin, E.1
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Galperin, M.3
Walker, D.4
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Positionally cloned human disease genes: Patterns of evolutionary conservation and functional motifs
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Bork, P.4
Koonin, E.5
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36
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0031547964
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Complete transcriptional map of yeast chromosome XI in different life conditions
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of special interest. Transcriptional maps of full genomes provide experimental evidence for gene function. Such techniques are expected to grow in importance. Here is one of the first large scale examples.
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Richard G, Fairhead C, Dujon B. Complete transcriptional map of yeast chromosome XI in different life conditions. of special interest J Mol Biol. 268:1997;303-321 Transcriptional maps of full genomes provide experimental evidence for gene function. Such techniques are expected to grow in importance. Here is one of the first large scale examples.
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J Mol Biol
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Richard, G.1
Fairhead, C.2
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0030041205
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Developments in matrix-assisted laser desorption/ionization peptide mass spectrometry
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The use of position specific rotamers in model building by homology
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