A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes Export

@article{doak2009, abstract = {Author Summary Even though there is only a single large biological network within any cell and all pathways are to some extent connected, the partition of the entire cellular network into smaller units (e.g., KEGG pathways) is extremely important for understanding biological processes. Biological pathway reconstruction, therefore, is essential for understanding the biological functions that a newly sequenced genome encodes and recently for studying the functionality of a natural environment via metagenomics. The common practice of pathway reconstruction in metagenomics first identifies functions encoded by the metagenomic sequences and then reconstructs pathways from the annotated functions by mapping the functions to reference pathways. To address the issues of both incomplete data (e.g., metagenomes, unlike individual genomes, are most likely incomplete) and pathway redundancy (e.g., the same function is involved in multiple pathway units), we formulate a parsimony version of the pathway reconstruction/inference problem, called MinPath (Minimal set of Pathways): given a set of reference pathways and a set of functions that can be mapped to one or more pathways, MinPath aims at finding a minimum number of pathways that can explain all functions. MinPath achieves a more conservative, yet more faithful, estimation of the biological pathways encoded by genomes and metagenomes.}, author = {Ye, Yuzhen and Doak, Thomas G.}, citeulike-article-id = {5439686}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000465}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19680427}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19680427}, day = {14}, doi = {10.1371/journal.pcbi.1000465}, issn = {1553-7358}, journal = {PLoS Comput Biol}, keywords = {genome-annotation, genome-sequencing, metabolism}, month = {August}, number = {8}, pages = {e1000465+}, posted-at = {2009-08-15 18:53:55}, priority = {0}, publisher = {Public Library of Science}, title = {A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes}, url = {http://dx.doi.org/10.1371/journal.pcbi.1000465}, volume = {5}, year = {2009} }

TY - JOUR ID - doak2009 L3 - citeulike-article-id:5439686 N2 - Author Summary Even though there is only a single large biological network within any cell and all pathways are to some extent connected, the partition of the entire cellular network into smaller units (e.g., KEGG pathways) is extremely important for understanding biological processes. Biological pathway reconstruction, therefore, is essential for understanding the biological functions that a newly sequenced genome encodes and recently for studying the functionality of a natural environment via metagenomics. The common practice of pathway reconstruction in metagenomics first identifies functions encoded by the metagenomic sequences and then reconstructs pathways from the annotated functions by mapping the functions to reference pathways. To address the issues of both incomplete data (e.g., metagenomes, unlike individual genomes, are most likely incomplete) and pathway redundancy (e.g., the same function is involved in multiple pathway units), we formulate a parsimony version of the pathway reconstruction/inference problem, called MinPath (Minimal set of Pathways): given a set of reference pathways and a set of functions that can be mapped to one or more pathways, MinPath aims at finding a minimum number of pathways that can explain all functions. MinPath achieves a more conservative, yet more faithful, estimation of the biological pathways encoded by genomes and metagenomes. IS - 8 JF - PLoS Comput Biol SN - 1553-7358 TI - A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes PB - Public Library of Science VL - 5 SP - e1000465 KW - genome-annotation KW - genome-sequencing KW - metabolism AU - Ye, Yuzhen AU - Doak, Thomas PY - 2009/08/14/ UR - http://dx.doi.org/10.1371/journal.pcbi.1000465 ER -