IEEE/ACM Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) is a bimonthly journal that publishes archival research results related to the algorithmic, mathematical, statistical, and computational methods that are central in bioinformatics and computational biology. Read the full scope of TCBB

Expand your horizons with Colloquium, a monthly survey of abstracts from all CS transactions! Replaces OnlinePlus in January 2017.

From the March/April 2017 Issue

Genome-Wide Semi-Automated Annotation of Transporter Systems

By Oscar Dias, Daniel Gomes, Paulo Vilaca, Joao Cardoso, Miguel Rocha, Eugenio C. Ferreira, and Isabel Rocha

Featured article thumbnail imageUsually, transport reactions are added to genome-scale metabolic models (GSMMs) based on experimental data and literature. This approach does not allow associating specific genes with transport reactions, which impairs the ability of the model to predict effects of gene deletions. Novel methods for systematic genome-wide transporter functional annotation and their integration into GSMMs are therefore necessary. In this work, an automatic system to detect and classify all potential membrane transport proteins for a given genome and integrate the related reactions into GSMMs is proposed, based on the identification and classification of genes that encode transmembrane proteins. The Transport Reactions Annotation and Generation (TRIAGE) tool identifies the metabolites transported by each transmembrane protein and its transporter family. The localization of the carriers is also predicted and, consequently, their action is confined to a given membrane. The integration of the data provided by TRIAGE with highly curated models allowed the identification of new transport reactions. TRIAGE is included in the new release of merlin, a software tool previously developed by the authors, which expedites the GSMM reconstruction processes.

download PDF View the PDF of this article      csdl View this issue in the digital library

Editorials and Announcements


  • We are pleased to announce that Aidong Zhang, the SUNY Distinguished Professor in the Department of Computer Science and Engineering at the University at Buffalo, The State University of New York, has been named the new Editor-in-Chief of the IEEE/ACM Transactions on Computational Biology and Bioinformatics starting in 2017.

  • Get Your Journals as eBooks for Free


Guest Editorials

Reviewers List

Author Index

Access All Recently Published TCBB Articles

RSS Subscribe to the RSS feed of latest TCBB content added to the digital library

Mail Sign up for the Transactions Connection newsletter.

TCBB is a joint publication of the IEEE Computer Society, Association for Computing Machinery, IEEE Computational Intelligence Society, and the IEEE Engineering in Medicine and Biology Society.

IEEE Computer Society    ACM    Engineering in Medicine and Biology Society

Published in cooperation with: IEEE Control Systems Society

MEDLINE      PubMed

Indexed in MEDLINE®/PubMed® & ISI