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Author Index Vol. 347 (2005)
Gene 347 (2005) 303 – 304 www.elsevier.com/locate/gene
Author Index Vol. 347 (2005) Alvarez, M., Shah, R., Rhodes, S.J. and Bidwell, J.P. Two promoters control the mouse Nmp4/CIZ transcription factor gene (347) 43 Amoutzias, G.D., Weiner, J. and Bornberg-Bauer, E. Phylogenetic profiling of protein interaction networks in eukaryotic transcription factors reveals focal proteins being ancestral to hubs (347) 247 Aniello, F., see Pulcrano, G. (347) 99 Auffray, C., see Bortoli, S. (347) 65 Baccam, S.L., see Jackson, S.M. (347) 35 Balaban, N.Q., see Lipshtat, A. (347) 265 Bastolla, U., Porto, M., Roman, H.E. and Vendruscolo, M. Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles (review) (347) 219 Bastolla, U., see Briones, C. (347) 237 Bidwell, J.P., see Alvarez, M. (347) 43 Biham, O., see Lipshtat, A. (347) 265 Blohm, D., see Kochzius, M. (347) 295 Bongini, L. and Rampioni, A. Topological properties of the energy landscape of small peptides (347) 231 Bornberg-Bauer, E., see Amoutzias, G.D. (347) 247 Bortoli, S., Renault, V., Mariage-Samson, R., Eveno, E., Auffray, C., Butler-Browne, G. and Pie´tu, G. Modifications in the myogenic program induced by in vivo and in vitro aging (347) 65 Branno, M., see Pulcrano, G. (347) 99 Briones, C. and Bastolla, U. Protein evolution in viral quasispecies under selective pressure: A thermodynamic and phylogenetic analysis (347) 237 Bryant, D., see Rodrigue, N. (347) 207 Butler-Browne, G., see Bortoli, S. (347) 65 Chen, B., Kayukawa, T., Jiang, H., Monteiro, A., Hoshizaki, S. and Ishikawa, Y. DaTrypsin, a novel clip-domain serine proteinase gene up-regulated during winter and summer diapauses of the onion maggot, Delia antiqua (347) 115 Coelho, M.M., see Pala, I. (347) 283 Conklin, K.F., see Simmons, H.M. (347) 137 Dokholyan, N.V. The architecture of the protein domain universe (347) 199 Domingo, E., see Manrubia, S.C. (347) 273 Du, D., see Sun, Q. (347) 55 Eipper, B.A., see McPherson, C.E. (347) 125 Escarmı´s, C., see Manrubia, S.C. (347) 273 Eveno, E., see Bortoli, S. (347) 65
doi:10.1016/S0378-1119(05)00096-X
Fisher, D.E., see Hershey, C.L. (347) 73 Fucci, L., see Pulcrano, G. (347) 99 Garcia, A.J., see Hutmacher, D.W. (347) 1 Gelfand, M.S., see Kotelnikova, E.A. (347) 255 Greene, J.C., see Jackson, S.M. (347) 35 Han, H., see Sun, Q. (347) 55 Hao, L. and Nei, M. Rapid expansion of killer cell immunoglobulin-like receptor genes in primates and their coevolution with MHC Class I genes (347) 149 Hershey, C.L. and Fisher, D.E. Genomic analysis of the Microphthalmia locus and identification of the MITF-J/Mitf-J isoform (347) 73 Hoshizaki, S., see Chen, B. (347) 115 Huang, H., see Sun, Q. (347) 55 Huang, X., see Sun, Q. (347) 55 Hudacek, A.W., see Simmons, H.M. (347) 137 Hutmacher, D.W. and Garcia, A.J. Scaffold-based bone engineering by using genetically modified cells (347) 1 Ishii, N., see Ohashi, Y. (347) 11 Ishikawa, Y., see Chen, B. (347) 115 Itaya, M., see Ohashi, Y. (347) 11 Jackson, S.M., Whitworth, A.J., Greene, J.C., Libby, R.T., Baccam, S.L., Pallanck, L.J. and La Spada, A.R. A SCA7 CAG/CTG repeat expansion is stable in Drosophila melanogaster despite modulation of genomic context and gene dosage (347) 35 Jiang, H., see Chen, B. (347) 115 Kapoor, M., see Simmons, H.M. (347) 137 Kaufmann, K., Melzer, R. and Theigen, G. MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants (review) (347) 183 Kayukawa, T., see Chen, B. (347) 115 Kern, R., see Widerak, M. (347) 109 Kikuchi, H., Takami, Y. and Nakayama, T. GCN5: a supervisor in all-inclusive control of vertebrate cell cycle progression through transcription regulation of various cell cyclerelated genes (347) 83 Kochzius, M. and Blohm, D. Genetic population structure of the lionfish Pterois miles (Scorpaenidae, Pteroinae) in the Gulf of Aqaba and northern Red Sea (347) 295 Kordisˇ, D. A genomic perspective on the chromodomain-containing retrotransposons: Chromoviruses (review) (347) 161 Kotelnikova, E.A., Makeev, V.J. and Gelfand, M.S. Evolution of transcription factor DNA binding sites (347) 255
304
Author Index
La Spada, A.R., see Jackson, S.M. (347) 35 Lartillot, N., see Rodrigue, N. (347) 207 La´zaro, E., see Manrubia, S.C. (347) 273 Leonardo, R., see Pulcrano, G. (347) 99 Li, J., see Sun, Q. (347) 55 Liang, Y., see Sun, Q. (347) 55 Libby, R.T., see Jackson, S.M. (347) 35 Lipshtat, A., Perets, H.B., Balaban, N.Q. and Biham, O. Modeling of negative autoregulated genetic networks in single cells (347) 265 Lobry, J.R., see Zagordi, O. (347) 175 Mains, R.E., see McPherson, C.E. (347) 125 Makeev, V.J., see Kotelnikova, E.A. (347) 255 Malki, A., see Widerak, M. (347) 109 Mancini, P., see Pulcrano, G. (347) 99 Manrubia, S.C., Escarmı´s, C., Domingo, E. and La´zaro, E. High mutation rates, bottlenecks, and robustness of RNA viral quasispecies (347) 273 Mariage-Samson, R., see Bortoli, S. (347) 65 McPherson, C.E., Eipper, B.A. and Mains, R.E. Multiple novel isoforms of Trio are expressed in the developing rat brain (347) 125 Melzer, R., see Kaufmann, K. (347) 183 Michishita, T., see Ohashi, Y. (347) 11 Monteiro, A., see Chen, B. (347) 115 Nakayama, T., see Kikuchi, H. (347) 83 Nei, M., see Hao, L. (347) 149 Ohashi, Y., Yamashiro, A., Washio, T., Ishii, N., Ohshima, H., Michishita, T., Tomita, M. and Itaya, M. In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations (347) 11 Ohshima, H., see Ohashi, Y. (347) 11 Pai, J.-t. and Ruoslahti, E. Identification of endothelial genes up-regulated in vivo (347) 21 Pala, I. and Coelho, M.M. Contrasting views over a hybrid complex: Between speciation and evolutionary bdead-endQ (347) 283 Pallanck, L.J., see Jackson, S.M. (347) 35 Perets, H.B., see Lipshtat, A. (347) 265 Philippe, H., see Rodrigue, N. (347) 207 Pie´tu, G., see Bortoli, S. (347) 65 Piscopo, M., see Pulcrano, G. (347) 99
Porto, M., see Bastolla, U. (347) 219 Pulcrano, G., Leonardo, R., Aniello, F., Mancini, P., Piscopo, M., Branno, M. and Fucci, L. PLAUF is a novel P. lividus sea urchin RNA-binding protein (347) 99 Rampioni, A., see Bongini, L. (347) 231 Renault, V., see Bortoli, S. (347) 65 Rhodes, S.J., see Alvarez, M. (347) 43 Richarme, G., see Widerak, M. (347) 109 Rodrigue, N., Lartillot, N., Bryant, D. and Philippe, H. Site interdependence attributed to tertiary structure in amino acid sequence evolution (347) 207 Roman, H.E., see Bastolla, U. (347) 219 Ruis, B.L., see Simmons, H.M. (347) 137 Ruoslahti, E., see Pai, J.-t. (347) 21 Shah, R., see Alvarez, M. (347) 43 Simmons, H.M., Ruis, B.L., Kapoor, M., Hudacek, A.W. and Conklin, K.F. Identification of NOM1, a nucleolar, eIF4A binding protein encoded within the chromosome 7q36 breakpoint region targeted in cases of pediatric acute myeloid leukemia (347) 137 Sun, Q., Li, J., Wang, C., Huang, X., Huang, H., Du, D., Liang, Y. and Han, H. Overexpression of mouse GlcNAc-1-phosphotransferase-g subunit in cells induced an I-cell-like phenotype of mucolipidosis (347) 55 Takami, Y., see Kikuchi, H. (347) 83 Theigen, G., see Kaufmann, K. (347) 183 Tomita, M., see Ohashi, Y. (347) 11 Vendruscolo, M., see Bastolla, U. (347) 219 Wang, C., see Sun, Q. (347) 55 Washio, T., see Ohashi, Y. (347) 11 Weiner, J., see Amoutzias, G.D. (347) 247 Whitworth, A.J., see Jackson, S.M. (347) 35 Widerak, M., Kern, R., Malki, A. and Richarme, G. U2552 methylation at the ribosomal A-site is a negative modulator of translational accuracy (347) 109 Yamashiro, A., see Ohashi, Y. (347) 11 Zagordi, O. and Lobry, J.R. Forcing reversibility in the no-strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons (347) 175
Author Index Vol. 347 (2005) Alvarez, M., Shah, R., Rhodes, S.J. and Bidwell, J.P. Two promoters control the mouse Nmp4/CIZ transcription factor gene (347) 43 Amoutzias, G.D., Weiner, J. and Bornberg-Bauer, E. Phylogenetic profiling of protein interaction networks in eukaryotic transcription factors reveals focal proteins being ancestral to hubs (347) 247 Aniello, F., see Pulcrano, G. (347) 99 Auffray, C., see Bortoli, S. (347) 65 Baccam, S.L., see Jackson, S.M. (347) 35 Balaban, N.Q., see Lipshtat, A. (347) 265 Bastolla, U., Porto, M., Roman, H.E. and Vendruscolo, M. Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles (review) (347) 219 Bastolla, U., see Briones, C. (347) 237 Bidwell, J.P., see Alvarez, M. (347) 43 Biham, O., see Lipshtat, A. (347) 265 Blohm, D., see Kochzius, M. (347) 295 Bongini, L. and Rampioni, A. Topological properties of the energy landscape of small peptides (347) 231 Bornberg-Bauer, E., see Amoutzias, G.D. (347) 247 Bortoli, S., Renault, V., Mariage-Samson, R., Eveno, E., Auffray, C., Butler-Browne, G. and Pie´tu, G. Modifications in the myogenic program induced by in vivo and in vitro aging (347) 65 Branno, M., see Pulcrano, G. (347) 99 Briones, C. and Bastolla, U. Protein evolution in viral quasispecies under selective pressure: A thermodynamic and phylogenetic analysis (347) 237 Bryant, D., see Rodrigue, N. (347) 207 Butler-Browne, G., see Bortoli, S. (347) 65 Chen, B., Kayukawa, T., Jiang, H., Monteiro, A., Hoshizaki, S. and Ishikawa, Y. DaTrypsin, a novel clip-domain serine proteinase gene up-regulated during winter and summer diapauses of the onion maggot, Delia antiqua (347) 115 Coelho, M.M., see Pala, I. (347) 283 Conklin, K.F., see Simmons, H.M. (347) 137 Dokholyan, N.V. The architecture of the protein domain universe (347) 199 Domingo, E., see Manrubia, S.C. (347) 273 Du, D., see Sun, Q. (347) 55 Eipper, B.A., see McPherson, C.E. (347) 125 Escarmı´s, C., see Manrubia, S.C. (347) 273 Eveno, E., see Bortoli, S. (347) 65
doi:10.1016/S0378-1119(05)00096-X
Fisher, D.E., see Hershey, C.L. (347) 73 Fucci, L., see Pulcrano, G. (347) 99 Garcia, A.J., see Hutmacher, D.W. (347) 1 Gelfand, M.S., see Kotelnikova, E.A. (347) 255 Greene, J.C., see Jackson, S.M. (347) 35 Han, H., see Sun, Q. (347) 55 Hao, L. and Nei, M. Rapid expansion of killer cell immunoglobulin-like receptor genes in primates and their coevolution with MHC Class I genes (347) 149 Hershey, C.L. and Fisher, D.E. Genomic analysis of the Microphthalmia locus and identification of the MITF-J/Mitf-J isoform (347) 73 Hoshizaki, S., see Chen, B. (347) 115 Huang, H., see Sun, Q. (347) 55 Huang, X., see Sun, Q. (347) 55 Hudacek, A.W., see Simmons, H.M. (347) 137 Hutmacher, D.W. and Garcia, A.J. Scaffold-based bone engineering by using genetically modified cells (347) 1 Ishii, N., see Ohashi, Y. (347) 11 Ishikawa, Y., see Chen, B. (347) 115 Itaya, M., see Ohashi, Y. (347) 11 Jackson, S.M., Whitworth, A.J., Greene, J.C., Libby, R.T., Baccam, S.L., Pallanck, L.J. and La Spada, A.R. A SCA7 CAG/CTG repeat expansion is stable in Drosophila melanogaster despite modulation of genomic context and gene dosage (347) 35 Jiang, H., see Chen, B. (347) 115 Kapoor, M., see Simmons, H.M. (347) 137 Kaufmann, K., Melzer, R. and Theigen, G. MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants (review) (347) 183 Kayukawa, T., see Chen, B. (347) 115 Kern, R., see Widerak, M. (347) 109 Kikuchi, H., Takami, Y. and Nakayama, T. GCN5: a supervisor in all-inclusive control of vertebrate cell cycle progression through transcription regulation of various cell cyclerelated genes (347) 83 Kochzius, M. and Blohm, D. Genetic population structure of the lionfish Pterois miles (Scorpaenidae, Pteroinae) in the Gulf of Aqaba and northern Red Sea (347) 295 Kordisˇ, D. A genomic perspective on the chromodomain-containing retrotransposons: Chromoviruses (review) (347) 161 Kotelnikova, E.A., Makeev, V.J. and Gelfand, M.S. Evolution of transcription factor DNA binding sites (347) 255
304
Author Index
La Spada, A.R., see Jackson, S.M. (347) 35 Lartillot, N., see Rodrigue, N. (347) 207 La´zaro, E., see Manrubia, S.C. (347) 273 Leonardo, R., see Pulcrano, G. (347) 99 Li, J., see Sun, Q. (347) 55 Liang, Y., see Sun, Q. (347) 55 Libby, R.T., see Jackson, S.M. (347) 35 Lipshtat, A., Perets, H.B., Balaban, N.Q. and Biham, O. Modeling of negative autoregulated genetic networks in single cells (347) 265 Lobry, J.R., see Zagordi, O. (347) 175 Mains, R.E., see McPherson, C.E. (347) 125 Makeev, V.J., see Kotelnikova, E.A. (347) 255 Malki, A., see Widerak, M. (347) 109 Mancini, P., see Pulcrano, G. (347) 99 Manrubia, S.C., Escarmı´s, C., Domingo, E. and La´zaro, E. High mutation rates, bottlenecks, and robustness of RNA viral quasispecies (347) 273 Mariage-Samson, R., see Bortoli, S. (347) 65 McPherson, C.E., Eipper, B.A. and Mains, R.E. Multiple novel isoforms of Trio are expressed in the developing rat brain (347) 125 Melzer, R., see Kaufmann, K. (347) 183 Michishita, T., see Ohashi, Y. (347) 11 Monteiro, A., see Chen, B. (347) 115 Nakayama, T., see Kikuchi, H. (347) 83 Nei, M., see Hao, L. (347) 149 Ohashi, Y., Yamashiro, A., Washio, T., Ishii, N., Ohshima, H., Michishita, T., Tomita, M. and Itaya, M. In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations (347) 11 Ohshima, H., see Ohashi, Y. (347) 11 Pai, J.-t. and Ruoslahti, E. Identification of endothelial genes up-regulated in vivo (347) 21 Pala, I. and Coelho, M.M. Contrasting views over a hybrid complex: Between speciation and evolutionary bdead-endQ (347) 283 Pallanck, L.J., see Jackson, S.M. (347) 35 Perets, H.B., see Lipshtat, A. (347) 265 Philippe, H., see Rodrigue, N. (347) 207 Pie´tu, G., see Bortoli, S. (347) 65 Piscopo, M., see Pulcrano, G. (347) 99
Porto, M., see Bastolla, U. (347) 219 Pulcrano, G., Leonardo, R., Aniello, F., Mancini, P., Piscopo, M., Branno, M. and Fucci, L. PLAUF is a novel P. lividus sea urchin RNA-binding protein (347) 99 Rampioni, A., see Bongini, L. (347) 231 Renault, V., see Bortoli, S. (347) 65 Rhodes, S.J., see Alvarez, M. (347) 43 Richarme, G., see Widerak, M. (347) 109 Rodrigue, N., Lartillot, N., Bryant, D. and Philippe, H. Site interdependence attributed to tertiary structure in amino acid sequence evolution (347) 207 Roman, H.E., see Bastolla, U. (347) 219 Ruis, B.L., see Simmons, H.M. (347) 137 Ruoslahti, E., see Pai, J.-t. (347) 21 Shah, R., see Alvarez, M. (347) 43 Simmons, H.M., Ruis, B.L., Kapoor, M., Hudacek, A.W. and Conklin, K.F. Identification of NOM1, a nucleolar, eIF4A binding protein encoded within the chromosome 7q36 breakpoint region targeted in cases of pediatric acute myeloid leukemia (347) 137 Sun, Q., Li, J., Wang, C., Huang, X., Huang, H., Du, D., Liang, Y. and Han, H. Overexpression of mouse GlcNAc-1-phosphotransferase-g subunit in cells induced an I-cell-like phenotype of mucolipidosis (347) 55 Takami, Y., see Kikuchi, H. (347) 83 Theigen, G., see Kaufmann, K. (347) 183 Tomita, M., see Ohashi, Y. (347) 11 Vendruscolo, M., see Bastolla, U. (347) 219 Wang, C., see Sun, Q. (347) 55 Washio, T., see Ohashi, Y. (347) 11 Weiner, J., see Amoutzias, G.D. (347) 247 Whitworth, A.J., see Jackson, S.M. (347) 35 Widerak, M., Kern, R., Malki, A. and Richarme, G. U2552 methylation at the ribosomal A-site is a negative modulator of translational accuracy (347) 109 Yamashiro, A., see Ohashi, Y. (347) 11 Zagordi, O. and Lobry, J.R. Forcing reversibility in the no-strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons (347) 175