TY - JOUR AU - Liolios, K. AU - Mavromatis, K. AU - Tavernarakis, N. AU - Kyrpides, N. C. PY - 2008 DA - 2008// TI - The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata JO - Nucleic Acids Research VL - 36, database issue ID - Liolios2008 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. AU - Hattori, M. PY - 2006 DA - 2006// TI - From genomics to chemical genomics: new developments in KEGG JO - Nucleic Acids Research VL - 34, database issue UR - https://doi.org/10.1093/nar/gkj102 DO - 10.1093/nar/gkj102 ID - Kanehisa2006 ER - TY - JOUR AU - Krieger, C. J. AU - Zhang, P. AU - Mueller, L. A. PY - 2004 DA - 2004// TI - MetaCyc: a multiorganism database of metabolic pathways and enzymes JO - Nucleic Acids Research VL - 32, database issue UR - https://doi.org/10.1093/nar/gkh100 DO - 10.1093/nar/gkh100 ID - Krieger2004 ER - TY - JOUR AU - Reed, J. L. AU - Vo, T. D. AU - Schilling, C. H. AU - Palsson, B. O. PY - 2003 DA - 2003// TI - An expanded genome-scale of Escherichia coli k-12 (i JR904 GSM/GPR) JO - Genome Biology VL - 4 UR - https://doi.org/10.1186/gb-2003-4-9-r54 DO - 10.1186/gb-2003-4-9-r54 ID - Reed2003 ER - TY - JOUR AU - Fong, S. S. AU - Palsson, B. Ø. PY - 2004 DA - 2004// TI - Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes JO - Nature Genetics VL - 36 UR - https://doi.org/10.1038/ng1432 DO - 10.1038/ng1432 ID - Fong2004 ER - TY - JOUR AU - Handorf, T. AU - Ebenhöh, O. AU - Heinrich, R. PY - 2005 DA - 2005// TI - Expanding metabolic networks: scopes of compounds, robustness, and evolution JO - Journal of Molecular Evolution VL - 61 UR - https://doi.org/10.1007/s00239-005-0027-1 DO - 10.1007/s00239-005-0027-1 ID - Handorf2005 ER - TY - JOUR AU - Ebenhöh, O. AU - Handorf, T. AU - Heinrich, R. PY - 2005 DA - 2005// TI - A cross species comparison of metabolic network functions JO - Genome Informatics VL - 16 ID - Ebenhöh2005 ER - TY - JOUR AU - Handorf, T. AU - Christian, N. AU - Ebenhöh, O. AU - Kahn, D. PY - 2008 DA - 2008// TI - An environmental perspective on metabolism JO - Journal of Theoretical Biology VL - 252 UR - https://doi.org/10.1016/j.jtbi.2007.10.036 DO - 10.1016/j.jtbi.2007.10.036 ID - Handorf2008 ER - TY - JOUR AU - Aguilar, D. AU - Aviles, F. X. AU - Querol, E. AU - Sternberg, M. J. E. PY - 2004 DA - 2004// TI - Analysis of phenetic trees based on metabolic capabilites across the three domains of life JO - The Journal of Molecular Biology VL - 340 UR - https://doi.org/10.1016/j.jmb.2004.04.059 DO - 10.1016/j.jmb.2004.04.059 ID - Aguilar2004 ER - TY - JOUR AU - Matthäus, F. AU - Salazar, C. AU - Ebenhöh, O. PY - 2008 DA - 2008// TI - Biosynthetic potentials of metabolites and their hierarchical organization JO - PLoS Computational Biology VL - 4 UR - https://doi.org/10.1371/journal.pcbi.1000049 DO - 10.1371/journal.pcbi.1000049 ID - Matthäus2008 ER - TY - JOUR AU - McLeod, M. P. AU - Warren, R. L. AU - Hsiao, W. W. L. PY - 2006 DA - 2006// TI - The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse JO - Proceedings of the National Academy of Sciences of the United States of America VL - 103 UR - https://doi.org/10.1073/pnas.0607048103 DO - 10.1073/pnas.0607048103 ID - McLeod2006 ER - TY - JOUR AU - Matsuzaki, M. AU - Misumi, O. AU - Shin-I, T. PY - 2004 DA - 2004// TI - Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D JO - Nature VL - 428 UR - https://doi.org/10.1038/nature02398 DO - 10.1038/nature02398 ID - Matsuzaki2004 ER - TY - JOUR AU - Visick, K. L. AU - Ruby, E. G. PY - 2006 DA - 2006// TI - Vibrio fischeri and its host: it takes two to tango JO - Current Opinion in Microbiology VL - 9 UR - https://doi.org/10.1016/j.mib.2006.10.001 DO - 10.1016/j.mib.2006.10.001 ID - Visick2006 ER - TY - JOUR AU - Johnson, T. J. AU - Kariyawasam, S. AU - Wannemuehler, Y. PY - 2007 DA - 2007// TI - The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes JO - Journal of Bacteriology VL - 189 UR - https://doi.org/10.1128/JB.01726-06 DO - 10.1128/JB.01726-06 ID - Johnson2007 ER - TY - JOUR AU - Shigenobu, S. AU - Watanabe, H. AU - Hattori, M. AU - Sakaki, Y. AU - Ishikawa, H. PY - 2000 DA - 2000// TI - Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS JO - Nature VL - 407 UR - https://doi.org/10.1038/35024074 DO - 10.1038/35024074 ID - Shigenobu2000 ER - TY - JOUR AU - Gil, R. AU - Silva, F. J. AU - Zientz, E. PY - 2003 DA - 2003// TI - The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes JO - Proceedings of the National Academy of Sciences of the United States of America VL - 100 UR - https://doi.org/10.1073/pnas.1533499100 DO - 10.1073/pnas.1533499100 ID - Gil2003 ER - TY - JOUR AU - Degnan, P. H. AU - Lazarus, A. B. AU - Wernegreen, J. J. PY - 2005 DA - 2005// TI - Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects JO - Genome Research VL - 15 UR - https://doi.org/10.1101/gr.3771305 DO - 10.1101/gr.3771305 ID - Degnan2005 ER - TY - BOOK AU - Cox, T. F. AU - Cox, M. A. A. PY - 1994 DA - 1994// TI - Multidimensional Scaling PB - Hall CY - Boca Raton, Fla, USA ID - Cox1994 ER - TY - JOUR AU - Wheeler, D. L. AU - Barrett, T. AU - Benson, D. A. PY - 2008 DA - 2008// TI - Database resources of the National Center for Biotechnology Information JO - Nucleic Acids Research VL - 36, database issue ID - Wheeler2008 ER - TY - JOUR AU - Retief, J. D. PY - 2000 DA - 2000// TI - Phylogenetic analysis using PHYLIP JO - Methods in Molecular Biology VL - 132 ID - Retief2000 ER - TY - JOUR AU - Robinson, D. F. AU - Foulds, L. R. PY - 1981 DA - 1981// TI - Comparison of phylogenetic trees JO - Mathematical Biosciences VL - 53 UR - https://doi.org/10.1016/0025-5564(81)90043-2 DO - 10.1016/0025-5564(81)90043-2 ID - Robinson1981 ER - TY - JOUR AU - Ebenhöh, O. AU - Handorf, T. AU - Kahn, D. PY - 2006 DA - 2006// TI - Evolutionary changes of metabolic networks and their biosynthetic capacities JO - IEE Proceedings: Systems Biology VL - 153 ID - Ebenhöh2006 ER - TY - JOUR AU - Handorf, T. AU - Ebenhöh, O. PY - 2007 DA - 2007// TI - MetaPath Online: a web server implementation of the network expansion algorithm JO - Nucleic Acids Research VL - 35 UR - https://doi.org/10.1093/nar/gkm287 DO - 10.1093/nar/gkm287 ID - Handorf2007 ER - TY - JOUR AU - Kruse, K. AU - Ebenhöh, O. PY - 2008 DA - 2008// TI - Comparing flux balance analysis to network expansion: producibility, sustainability and the scope of compounds JO - Genome Informatics VL - 20 ID - Kruse2008 ER - TY - BOOK AU - Hartigan, J. A. PY - 1975 DA - 1975// TI - Clustering Algorithms PB - Sons CY - New York, NY, USA ID - Hartigan1975 ER -