PLoS Comput Biol Volume 1(7); December 2005

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Volume 1(7); December 2005

Message from ISCB

The Eighth Annual Bio-Ontologies Meeting

Phillip Lord, Robert Stevens, James A Butler, and Robin McEntire

PLoS Comput Biol. 2005 December; 1(7): e77. Published online 2005 December 30. doi: 10.1371/journal.pcbi.0010077.

PMCID: PMC1323465

| Full Text | PDF–205K |

Perspectives

Time to Organize the Bioinformatics Resourceome

Nicola Cannata, Emanuela Merelli, and Russ B Altman

PLoS Comput Biol. 2005 December; 1(7): e76. Published online 2005 December 30. doi: 10.1371/journal.pcbi.0010076.

PMCID: PMC1323464

| Full Text | PDF–93K | Correction |

Research Articles

PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny

Rahul Siddharthan, Eric D Siggia, and Erik van Nimwegen

PLoS Comput Biol. 2005 December; 1(7): e67. Prepublished online 2005 October 27. Published online 2005 December 9. doi: 10.1371/journal.pcbi.0010067.

PMCID: PMC1309704

The Activity Reaction Core and Plasticity of Metabolic Networks

Eivind Almaas, Zoltán N Oltvai, and Albert-László Barabási

PLoS Comput Biol. 2005 December; 1(7): e68. Prepublished online 2005 November 2. Published online 2005 December 16. doi: 10.1371/journal.pcbi.0010068.

PMCID: PMC1314881

Revealing Posttranscriptional Regulatory Elements Through Network-Level Conservation

Chang S Chan, Olivier Elemento, and Saeed Tavazoie

PLoS Comput Biol. 2005 December; 1(7): e69. Prepublished online 2005 November 2. Published online 2005 December 9. doi: 10.1371/journal.pcbi.0010069.

PMCID: PMC1309705

Comparing the Dictyostelium and Entamoeba Genomes Reveals an Ancient Split in the Conosa Lineage

Jie Song, Qikai Xu, Rolf Olsen, William F Loomis, Gad Shaulsky, Adam Kuspa, and Richard Sucgang

PLoS Comput Biol. 2005 December; 1(7): e71. Prepublished online 2005 November 7. Published online 2005 December 16. doi: 10.1371/journal.pcbi.0010071.

PMCID: PMC1314882

| Abstract | Full Text | PDF–126K |

Folding Free Energies of 5′-UTRs Impact Post-Transcriptional Regulation on a Genomic Scale in Yeast

Markus Ringnér and Morten Krogh

PLoS Comput Biol. 2005 December; 1(7): e72. Prepublished online 2005 November 9. Published online 2005 December 9. doi: 10.1371/journal.pcbi.0010072.

PMCID: PMC1309706

Selective Constraint on Noncoding Regions of Hominid Genomes

Eliot C Bush and Bruce T Lahn

PLoS Comput Biol. 2005 December; 1(7): e73. Prepublished online 2005 November 11. Published online 2005 December 16. doi: 10.1371/journal.pcbi.0010073.

PMCID: PMC1314883

Functional Alignment of Regulatory Networks: A Study of Temperate Phages

Ala Trusina, Kim Sneppen, Ian B Dodd, Keith E Shearwin, and J. Barry Egan

PLoS Comput Biol. 2005 December; 1(7): e74. Published online 2005 December 23. doi: 10.1371/journal.pcbi.0010074.

PMCID: PMC1317652

| Abstract | Full Text | PDF–523K |

Genome Trees from Conservation Profiles

Fredj Tekaia and Edouard Yeramian

PLoS Comput Biol. 2005 December; 1(7): e75. Published online 2005 December 16. doi: 10.1371/journal.pcbi.0010075.

PMCID: PMC1314884

Segregation of the Brain into Gray and White Matter: A Design Minimizing Conduction Delays

Quan Wen and Dmitri B Chklovskii

PLoS Comput Biol. 2005 December; 1(7): e78. Published online 2005 December 30. doi: 10.1371/journal.pcbi.0010078.

PMCID: PMC1323466

| Abstract | Full Text | PDF–314K |

New Maximum Likelihood Estimators for Eukaryotic Intron Evolution

Hung D Nguyen, Maki Yoshihama, and Naoya Kenmochi

PLoS Comput Biol. 2005 December; 1(7): e79. Published online 2005 December 30. doi: 10.1371/journal.pcbi.0010079.

PMCID: PMC1323467

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		Other Issues: previous \| next \| latest \| archive Volume 1(7); December 2005 Message from ISCB The Eighth Annual Bio-Ontologies Meeting Phillip Lord, Robert Stevens, James A Butler, and Robin McEntire PLoS Comput Biol. 2005 December; 1(7): e77. Published online 2005 December 30. doi: 10.1371/journal.pcbi.0010077. PMCID: PMC1323465 \| Full Text \| PDF–205K \| Perspectives Time to Organize the Bioinformatics Resourceome Nicola Cannata, Emanuela Merelli, and Russ B Altman PLoS Comput Biol. 2005 December; 1(7): e76. Published online 2005 December 30. doi: 10.1371/journal.pcbi.0010076. PMCID: PMC1323464 \| Full Text \| PDF–93K \| Correction \| Research Articles PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny Rahul Siddharthan, Eric D Siggia, and Erik van Nimwegen PLoS Comput Biol. 2005 December; 1(7): e67. Prepublished online 2005 October 27. Published online 2005 December 9. doi: 10.1371/journal.pcbi.0010067. PMCID: PMC1309704 \| Abstract \| Full Text \| PDF–459K \| Supplementary Material \| The Activity Reaction Core and Plasticity of Metabolic Networks Eivind Almaas, Zoltán N Oltvai, and Albert-László Barabási PLoS Comput Biol. 2005 December; 1(7): e68. Prepublished online 2005 November 2. Published online 2005 December 16. doi: 10.1371/journal.pcbi.0010068. PMCID: PMC1314881 \| Abstract \| Full Text \| PDF–354K \| Supplementary Material \| Revealing Posttranscriptional Regulatory Elements Through Network-Level Conservation Chang S Chan, Olivier Elemento, and Saeed Tavazoie PLoS Comput Biol. 2005 December; 1(7): e69. Prepublished online 2005 November 2. Published online 2005 December 9. doi: 10.1371/journal.pcbi.0010069. PMCID: PMC1309705 \| Abstract \| Full Text \| PDF–400K \| Supplementary Material \| Comparing the Dictyostelium and Entamoeba Genomes Reveals an Ancient Split in the Conosa Lineage Jie Song, Qikai Xu, Rolf Olsen, William F Loomis, Gad Shaulsky, Adam Kuspa, and Richard Sucgang PLoS Comput Biol. 2005 December; 1(7): e71. Prepublished online 2005 November 7. Published online 2005 December 16. doi: 10.1371/journal.pcbi.0010071. PMCID: PMC1314882 \| Abstract \| Full Text \| PDF–126K \| Folding Free Energies of 5′-UTRs Impact Post-Transcriptional Regulation on a Genomic Scale in Yeast Markus Ringnér and Morten Krogh PLoS Comput Biol. 2005 December; 1(7): e72. Prepublished online 2005 November 9. Published online 2005 December 9. doi: 10.1371/journal.pcbi.0010072. PMCID: PMC1309706 \| Abstract \| Full Text \| PDF–192K \| Supplementary Material \| Selective Constraint on Noncoding Regions of Hominid Genomes Eliot C Bush and Bruce T Lahn PLoS Comput Biol. 2005 December; 1(7): e73. Prepublished online 2005 November 11. Published online 2005 December 16. doi: 10.1371/journal.pcbi.0010073. PMCID: PMC1314883 \| Abstract \| Full Text \| PDF–107K \| Supplementary Material \| Functional Alignment of Regulatory Networks: A Study of Temperate Phages Ala Trusina, Kim Sneppen, Ian B Dodd, Keith E Shearwin, and J. Barry Egan PLoS Comput Biol. 2005 December; 1(7): e74. Published online 2005 December 23. doi: 10.1371/journal.pcbi.0010074. PMCID: PMC1317652 \| Abstract \| Full Text \| PDF–523K \| Genome Trees from Conservation Profiles Fredj Tekaia and Edouard Yeramian PLoS Comput Biol. 2005 December; 1(7): e75. Published online 2005 December 16. doi: 10.1371/journal.pcbi.0010075. PMCID: PMC1314884 \| Abstract \| Full Text \| PDF–556K \| Supplementary Material \| Segregation of the Brain into Gray and White Matter: A Design Minimizing Conduction Delays Quan Wen and Dmitri B Chklovskii PLoS Comput Biol. 2005 December; 1(7): e78. Published online 2005 December 30. doi: 10.1371/journal.pcbi.0010078. PMCID: PMC1323466 \| Abstract \| Full Text \| PDF–314K \| New Maximum Likelihood Estimators for Eukaryotic Intron Evolution Hung D Nguyen, Maki Yoshihama, and Naoya Kenmochi PLoS Comput Biol. 2005 December; 1(7): e79. Published online 2005 December 30. doi: 10.1371/journal.pcbi.0010079. PMCID: PMC1323467 \| Abstract \| Full Text \| PDF–187K \| Supplementary Material \| Correction \|
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