TY - JOUR AU - Becker, S. A. AU - Palsson, B. O. PY - 2005 DA - 2005// TI - Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation JO - BMC Microbiology VL - 5 UR - https://doi.org/10.1186/1471-2180-5-8 DO - 10.1186/1471-2180-5-8 ID - Becker2005 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. AU - Kawashima, S. AU - Okuno, Y. AU - Hattori, M. PY - 2004 DA - 2004// TI - The KEGG resource for deciphering the genome JO - Nucl Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh063 DO - 10.1093/nar/gkh063 ID - Kanehisa2004 ER - TY - JOUR AU - Fitz-Gibbon, S. T. AU - House, C. H. PY - 1999 DA - 1999// TI - Whole genome-based phylogenetic analysis of free-living microorganisms JO - Nucleic Acids Res VL - 27 UR - https://doi.org/10.1093/nar/27.21.4218 DO - 10.1093/nar/27.21.4218 ID - Fitz-Gibbon1999 ER - TY - JOUR AU - Ma, H. W. AU - Zeng, A. P. PY - 2004 DA - 2004// TI - Phylogenetic comparison of metabolic capacities of organisms at genome level JO - Mol Phylogenet Evol VL - 31 UR - https://doi.org/10.1016/j.ympev.2003.08.011 DO - 10.1016/j.ympev.2003.08.011 ID - Ma2004 ER - TY - JOUR AU - Snel, B. AU - Bork, P. AU - Huynen, M. A. PY - 1999 DA - 1999// TI - Genome phylogeny based on gene content JO - Nat Genet VL - 21 UR - https://doi.org/10.1038/5052 DO - 10.1038/5052 ID - Snel1999 ER - TY - JOUR AU - Snel, B. AU - Bork, P. AU - Huynen, M. A. PY - 2002 DA - 2002// TI - Genomes in flux: the evolution of archaeal and proteobacterial gene content JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.176501 DO - 10.1101/gr.176501 ID - Snel2002 ER - TY - JOUR AU - Wolf, Y. I. AU - Rogozin, I. B. AU - Grishin, N. V. AU - Tatusov, R. L. AU - Koonin, E. V. PY - 2001 DA - 2001// TI - Genome trees constructed using five different approaches suggest new major bacterial clades JO - BMC Evol Biol VL - 1 UR - https://doi.org/10.1186/1471-2148-1-8 DO - 10.1186/1471-2148-1-8 ID - Wolf2001 ER - TY - JOUR AU - Yang, S. AU - Doolittle, R. F. AU - Bourne, P. E. PY - 2005 DA - 2005// TI - Phylogeny determined by protein domain content JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0408810102 DO - 10.1073/pnas.0408810102 ID - Yang2005 ER - TY - JOUR AU - Hong, S. H. AU - Kim, T. Y. AU - Lee, S. Y. PY - 2004 DA - 2004// TI - Phylogenetic analysis based on genome-scale metabolic pathway reaction content JO - Appl Microbiol Biotechnol VL - 65 ID - Hong2004 ER - TY - JOUR AU - Tatusov, R. L. AU - Koonin, E. V. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - A Genomic Perspective on Protein Families JO - Science VL - 278 UR - https://doi.org/10.1126/science.278.5338.631 DO - 10.1126/science.278.5338.631 ID - Tatusov1997 ER - TY - JOUR AU - Dandekar, T. AU - Schuster, S. AU - Snel, B. AU - Huynen, M. A. AU - Bork, P. PY - 1999 DA - 1999// TI - Pathway Alignment: application to the comparative analysis of glycolytic enzymes JO - Biochem J VL - 343 UR - https://doi.org/10.1042/bj3430115 DO - 10.1042/bj3430115 ID - Dandekar1999 ER - TY - JOUR AU - Forst, C. V. AU - Schulten, K. PY - 1999 DA - 1999// TI - Evolution of Metabolism: A New Method for the Comparison of Metabolic Pathways Using Genomic Information JO - J Comp Biol VL - 6 UR - https://doi.org/10.1089/106652799318319 DO - 10.1089/106652799318319 ID - Forst1999 ER - TY - JOUR AU - Forst, C. V. AU - Schulten, K. PY - 2001 DA - 2001// TI - Phylogenetic analysis of metabolic pathways JO - J Mol Evol VL - 52 UR - https://doi.org/10.1007/s002390010178 DO - 10.1007/s002390010178 ID - Forst2001 ER - TY - JOUR AU - Heymans, M. AU - Singh, A. K. PY - 2003 DA - 2003// TI - Deriving phylogenetic trees from the similarity analysis of metabolic pathways JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg1018 DO - 10.1093/bioinformatics/btg1018 ID - Heymans2003 ER - TY - JOUR AU - Schilling, C. H. AU - Palsson, B. ∅. PY - 1998 DA - 1998// TI - The underlying pathway structure of biochemical reaction networks JO - Proc Natl Acad Sci USA VL - 95 UR - https://doi.org/10.1073/pnas.95.8.4193 DO - 10.1073/pnas.95.8.4193 ID - Schilling1998 ER - TY - JOUR AU - Schilling, C. H. AU - Letscher, D. AU - Palsson, B. ∅. PY - 2000 DA - 2000// TI - Theory for the systematic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective JO - J Theor Biol VL - 203 UR - https://doi.org/10.1006/jtbi.2000.1073 DO - 10.1006/jtbi.2000.1073 ID - Schilling2000 ER - TY - JOUR AU - Schuster, S. AU - Fell, D. A. AU - Dandekar, T. PY - 2000 DA - 2000// TI - A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks JO - Nature Biotechnol VL - 18 UR - https://doi.org/10.1038/73786 DO - 10.1038/73786 ID - Schuster2000 ER - TY - JOUR AU - Xiong, M. AU - Zhao, J. AU - Xiong, H. PY - 2004 DA - 2004// TI - Network-based regulatory pathways analysis JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth201 DO - 10.1093/bioinformatics/bth201 ID - Xiong2004 ER - TY - JOUR AU - Gagneur, J. AU - Klamt, S. PY - 2004 DA - 2004// TI - Computation of elementary modes: a unifying framework and the new binary approach JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-175 DO - 10.1186/1471-2105-5-175 ID - Gagneur2004 ER - TY - JOUR AU - Bunke, H. AU - Shearer, K. PY - 1997 DA - 1997// TI - On a relation between graph edit distance and maximum common subgraph JO - Pattern Rec Let VL - 18 UR - https://doi.org/10.1016/S0167-8655(97)00060-3 DO - 10.1016/S0167-8655(97)00060-3 ID - Bunke1997 ER - TY - CHAP AU - Zeigarnik, A. V. ED - Hansen, P. ED - Fowler, P. W. ED - Zheng, M. PY - 2000 DA - 2000// TI - On Hypercycles and Hypercircuits in Hypergraphs BT - Discrete Mathematical Chemistry, DIMACS series in discrete mathematics and theoretical computer science PB - American Mathematical Society CY - Providence, RI ID - Zeigarnik2000 ER - TY - JOUR AU - Zhu, D. AU - Qin, Z. S. PY - 2005 DA - 2005// TI - Structural comparison of metabolic networks in selected single cell organisms JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-8 DO - 10.1186/1471-2105-6-8 ID - Zhu2005 ER - TY - JOUR AU - Hucka, M. AU - Finney, A. AU - Bornstein, B. J. AU - Keating, S. M. AU - Shapiro, B. E. AU - Matthews, J. AU - Kovitz, B. L. AU - J, S. M. AU - Funahashi, A. AU - Doyle, J. C. AU - Kitano, H. PY - 2004 DA - 2004// TI - Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project JO - Syst Biol VL - 1 UR - https://doi.org/10.1049/sb:20045008 DO - 10.1049/sb:20045008 ID - Hucka2004 ER - TY - JOUR AU - Felsenstein, J. PY - 1996 DA - 1996// TI - Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods JO - Methods Enzymol VL - 266 UR - https://doi.org/10.1016/S0076-6879(96)66026-1 DO - 10.1016/S0076-6879(96)66026-1 ID - Felsenstein1996 ER - TY - JOUR AU - Fitch, W. AU - Margoliash, E. PY - 1967 DA - 1967// TI - Construction of phylogenetic trees JO - Science VL - 155 UR - https://doi.org/10.1126/science.155.3760.279 DO - 10.1126/science.155.3760.279 ID - Fitch1967 ER - TY - JOUR AU - Huson, D. H. PY - 1998 DA - 1998// TI - SplitsTree: analyzing and visualizing evolutionary data JO - Bioinformatics VL - 14 UR - https://doi.org/10.1093/bioinformatics/14.1.68 DO - 10.1093/bioinformatics/14.1.68 ID - Huson1998 ER - TY - JOUR AU - Brown, S. C. AU - Kruppa, G. AU - Dasseux, J. L. PY - 2005 DA - 2005// TI - Metabolomics applications of FT-ICR mass spectrometry JO - Mass Spectrom Rev VL - 24 UR - https://doi.org/10.1002/mas.20011 DO - 10.1002/mas.20011 ID - Brown2005 ER - TY - JOUR AU - Griffin, J. L. PY - 2004 DA - 2004// TI - Metabolic profiles to define the genome: can we hear the phenotypes? JO - Philos Trans R Soc Lond B Biol Sci VL - 359 UR - https://doi.org/10.1098/rstb.2003.1411 DO - 10.1098/rstb.2003.1411 ID - Griffin2004 ER - TY - JOUR AU - Sumner, L. W. AU - Mendes, P. AU - Dixon, R. A. PY - 2003 DA - 2003// TI - Plant metabolomics: large-scale phytochemistry in the functional genomics era JO - Phytochemistry VL - 62 UR - https://doi.org/10.1016/S0031-9422(02)00708-2 DO - 10.1016/S0031-9422(02)00708-2 ID - Sumner2003 ER - TY - JOUR AU - Berg, J. AU - Lässig, M. PY - 2004 DA - 2004// TI - Local graph alignment and motif search in biological networks JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0305199101 DO - 10.1073/pnas.0305199101 ID - Berg2004 ER - TY - JOUR AU - Huynen, M. A. AU - Dandekar, T. AU - Bork, P. PY - 1999 DA - 1999// TI - Variation and evolution of the citric-acid cycle: a genomic perspective JO - Trends Microbiol VL - 7 UR - https://doi.org/10.1016/S0966-842X(99)01539-5 DO - 10.1016/S0966-842X(99)01539-5 ID - Huynen1999 ER - TY - STD TI - [http://www.tbi.univie.ac.at/software/Vienna-RNL/] UR - http://www.tbi.univie.ac.at/software/Vienna-RNL/ ID - ref32 ER - TY - STD TI - [http://www.sbml.org/] UR - http://www.sbml.org/ ID - ref33 ER -