{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T08:05:53Z","timestamp":1778054753222,"version":"3.51.4"},"reference-count":47,"publisher":"Proceedings of the National Academy of Sciences","issue":"1","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2006,1,3]]},"abstract":"<jats:p>\n            Mapping biological pathways across microbial genomes is a highly important technique in functional studies of biological systems. Existing methods mainly rely on sequence-based orthologous gene mapping, which often leads to suboptimal mapping results because sequence-similarity information alone does not contain sufficient information for accurate identification of orthology relationship. Here we present an algorithm for pathway mapping across microbial genomes. The algorithm takes into account both sequence similarity and genomic structure information such as operons and regulons. One basic premise of our approach is that a microbial pathway could generally be decomposed into a few operons or regulons. We formulated the pathway-mapping problem to map genes across genomes to maximize their sequence similarity under the constraint that the mapped genes be grouped into a few operons, preferably coregulated in the target genome. We have developed an integer-programming algorithm for solving this constrained optimization problem and implemented the algorithm as a computer software program,\n            <jats:sc>p<\/jats:sc>\n            -\n            <jats:sc>map<\/jats:sc>\n            . We have tested\n            <jats:sc>p<\/jats:sc>\n            -\n            <jats:sc>map<\/jats:sc>\n            on a number of known homologous pathways. We conclude that using genomic structure information as constraints could greatly improve the pathway-mapping accuracy over methods that use sequence-similarity information alone.\n          <\/jats:p>","DOI":"10.1073\/pnas.0509737102","type":"journal-article","created":{"date-parts":[[2005,12,23]],"date-time":"2005-12-23T01:58:32Z","timestamp":1135303112000},"page":"129-134","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":26,"title":["Mapping of orthologous genes in the context of biological pathways: An application of integer programming"],"prefix":"10.1073","volume":"103","author":[{"given":"Fenglou","family":"Mao","sequence":"first","affiliation":[{"name":"Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831"}]},{"given":"Zhengchang","family":"Su","sequence":"additional","affiliation":[{"name":"Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831"}]},{"given":"Victor","family":"Olman","sequence":"additional","affiliation":[{"name":"Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831"}]},{"given":"Phuongan","family":"Dam","sequence":"additional","affiliation":[{"name":"Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831"}]},{"given":"Zhijie","family":"Liu","sequence":"additional","affiliation":[{"name":"Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831"}]},{"given":"Ying","family":"Xu","sequence":"additional","affiliation":[{"name":"Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831"}]}],"member":"341","published-online":{"date-parts":[[2005,12,22]]},"reference":[{"key":"e_1_3_2_1_2","first-page":"COMMENT1005","volume":"2","year":"2001","unstructured":"Koonin, E. V. (2001) Genome Biol. 2001;2(4): COMMENT1005.","journal-title":"Genome Biol. 2001"},{"key":"e_1_3_2_2_2","first-page":"COMMENT1002","volume":"2","year":"2001","unstructured":"Petsko, G. A. (2001) Genome Biol. 2001;2(2): COMMENT1002.","journal-title":"Genome Biol. 2001"},{"key":"e_1_3_2_3_2","first-page":"INTERACTIONS100","volume":"2","year":"2001","unstructured":"Jensen, R. A. (2001) Genome Biol. 2001;2(8): INTERACTIONS1002.","journal-title":"Genome Biol. 2001"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.93.19.10268"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg213"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.278.5338.631"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(61)80072-7"},{"key":"e_1_3_2_8_2","doi-asserted-by":"crossref","unstructured":"Stephanopoulos G. N. Aristidou A. A. & Nielsen J. (1998) Metabolic Engineering Principles and Methodologies (Academic San Diego).","DOI":"10.1016\/B978-012666260-3\/50002-9"},{"key":"e_1_3_2_9_2","first-page":"3","volume":"14","year":"2003","unstructured":"Su, Z., Dam, A., Chen, X., Olman, V., Jiang, T., Palenik, B. & Xu, Y. (2003) Genome Inform. 14, 3\u201313.","journal-title":"Genome Inform"},{"key":"e_1_3_2_10_2","first-page":"97","volume":"12","year":"2004","unstructured":"Dam, P., Su, Z., Olman, V. & Xu, Y. (2004) J Biol. Syst. 12, 97\u2013125.","journal-title":"J Biol. Syst"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0968-0004(98)01274-2"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.6.2896"},{"key":"e_1_3_2_13_2","first-page":"317","volume":"38","year":"1973","unstructured":"Eisenberg, M. A. (1973) Adv. Enzymol. Relat. Areas Mol. Biol. 38, 317\u2013372.4598072","journal-title":"Adv. Enzymol. Relat. Areas Mol. Biol"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00325702"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.182.16.4478-4490.2000"},{"key":"e_1_3_2_16_2","unstructured":"Wanner B. L. (1996) in Escherichia coli and Salmonella: Cellular and Molecular Biology eds. Neidhardt F. C. Curtiss R. I. III Gross C. A. Ingraham J. L. Lin E. C. C. Low K. B. Jr. Magasanik B. Reznikoff W. Schaechter M. Umbarger H. E. & Riley M. (Am. Soc. Microbiol. Washington DC) 2nd ed."},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.175.5.1316-1324.1993"},{"key":"e_1_3_2_18_2","first-page":"3","volume":"3","year":"2003","unstructured":"Kazakov, A. E., Vassieva, O., Gelfand, M. S., Osterman, A. & Overbeek, R. (2003) In Silico Biol. 3, 3\u201315.12762842","journal-title":"In Silico Biol"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gnf055"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.178.14.4122-4130.1996"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.178.3.854-861.1996"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi00658a007"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.174.15.5063-5071.1992"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1016\/0378-1119(95)00662-1"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-143-11-3431"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(86)90073-2"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(89)90131-9"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.180.5.1277-1286.1998"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.178.15.4344-4366.1996"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00696458"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.177.22.6411-6421.1995"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.184.15.4134-4140.2002"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M313358200"},{"key":"e_1_3_2_34_2","unstructured":"Palenik B. & Dyhrman S. T. (1998) Phosphorus in Plant Biology: Regulatory Roles in Molecular Cellular Organismic and Ecosystem Processes eds. Lynch J. P. & Deickman J. (American Society of Plant Physiologists Rockville MD)."},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.183.17.5008-5014.2001"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(92)91001-6"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1038\/35101614"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.1998.01122.x"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.1996.422952.x"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1142\/S0219720003000162"},{"key":"e_1_3_2_41_2","unstructured":"Liu X. Brutlag D. L. & Liu J. S. (2001) Pac. Symp. Biocomput. 127\u2013138.11262934"},{"key":"e_1_3_2_42_2","first-page":"211","volume":"15","year":"2004","unstructured":"Chen, X., Su, Z., Xu, Y. & Jiang, T. (2004) Genome Inform. 15 (2), 211\u2013222.","journal-title":"Genome Inform"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh510"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1147\/rd.471.0057"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0968-0004(00)01663-7"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/30.10.2212"}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.0509737102","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,12]],"date-time":"2022-04-12T14:09:51Z","timestamp":1649772591000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.0509737102"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,12,22]]},"references-count":47,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2006,1,3]]}},"alternative-id":["10.1073\/pnas.0509737102"],"URL":"https:\/\/doi.org\/10.1073\/pnas.0509737102","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,12,22]]},"assertion":[{"value":"2005-02-08","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2005-12-22","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}