Advance online publication


The latest research papers, published online ahead of print. These online versions are definitive and may be cited using the digital object identifier (DOI).

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Research

Letters

Predicting PDZ domain–peptide interactions from primary sequences

Jiunn R Chen, Bryan H Chang, John E Allen, Michael A Stiffler & Gavin MacBeath

Published online: 17 August 2008; | doi:10.1038/nbt.1489

PDZ domains represent one of the largest families of interaction domains. Chen et al. develop a scoring matrix that enables prediction of peptide–PDZ domain interactions. Unlike previous methods, the model works to some extent for PDZ domains that were not part of the training set.


High-resolution metagenomics targets specific functional types in complex microbial communities

Marina G Kalyuzhnaya, Alla Lapidus, Natalia Ivanova, Alex C Copeland, Alice C McHardy, Ernest Szeto, Asaf Salamov, Igor V Grigoriev, Dominic Suciu, Samuel R Levine, Victor M Markowitz, Isidore Rigoutsos, Susannah G Tringe, David C Bruce, Paul M Richardson, Mary E Lidstrom & Ludmila Chistoserdova

Published online: 17 August 2008; | doi:10.1038/nbt.1488

Metagenomics, or shotgun sequencing of environmental DNA, is used to study complex microbial communities. Kalyuzhnaya et al. describe a method for targeting specific microbial subpopulations in environmental samples and use it to analyze microbes that metabolize C1 compounds.


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Computational Biology

Analysis

Network-based prediction of human tissue-specific metabolism

Tomer Shlomi, Moran N Cabili, Markus J Herrgård, Bernhard Ø Palsson & Eytan Ruppin

Published online: 17 August 2008; | doi:10.1038/nbt.1487

Metabolic network modeling in multicellular organisms is confounded by the existence of multiple tissues with distinct metabolic functions. By integrating a genome-scale metabolic network with tissue-specific gene- and protein-expression data, Shlomi et al. adapt constraint-based approaches used for microorganisms to predicting metabolism in ten human tissues. Their computational approach should facilitate interpretation of expression data in the context of metabolic disorders.


Until print versions of AOP papers are published, they should be cited in the style "Author(s) Nature Biotechnology advance online publication, day month year (doi:10.1038/nbtXXXXX)". Once the print version (identical to the AOP) is published, it should be cited as follows: "Author(s) Nature Biotechnology volume, page (year); advance online publication, (doi:10.1038/nbtXXXXX)".

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