{"title":"Metabolic Pathways","authors":"Steffen Schmidt, T. Dandekar","doi":"10.7551/mitpress/3215.003.0014","DOIUrl":"https://doi.org/10.7551/mitpress/3215.003.0014","url":null,"abstract":"This is the first of two volumes of the Second Edition of a well known treatise, formerly titled Chemical Pathways of Metabolism. Fourteen outstanding authorities have prepared the 12 chapters in this first volume. The Editor was well qualified to select the best persons for each topic and to review their contributions critically. It is a basic treatise for the advanced student and investigator in the field of biochemistry as applied to elucidation of metabolic processes.","PeriodicalId":111388,"journal":{"name":"Gene Regulations and Metabolism","volume":"120 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1961-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128780420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Toward Computer Simulation of the Whole Cell","authors":"M. Tomita","doi":"10.7551/mitpress/3215.003.0015","DOIUrl":"https://doi.org/10.7551/mitpress/3215.003.0015","url":null,"abstract":"","PeriodicalId":111388,"journal":{"name":"Gene Regulations and Metabolism","volume":"83 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115763501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Specificity of Protein-DNA Interactions","authors":"G. Stormo","doi":"10.7551/mitpress/3215.003.0007","DOIUrl":"https://doi.org/10.7551/mitpress/3215.003.0007","url":null,"abstract":"","PeriodicalId":111388,"journal":{"name":"Gene Regulations and Metabolism","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127339049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
R. Apweiler, M. Biswas, W. Fleischmann, E. Kriventseva, N. Mulder
{"title":"Automation of Protein Sequence Characterization and Its Application in Whole Proteome Analysis","authors":"R. Apweiler, M. Biswas, W. Fleischmann, E. Kriventseva, N. Mulder","doi":"10.7551/mitpress/3215.003.0004","DOIUrl":"https://doi.org/10.7551/mitpress/3215.003.0004","url":null,"abstract":"","PeriodicalId":111388,"journal":{"name":"Gene Regulations and Metabolism","volume":"59 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131441947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Freier, R. Hofestädt, Matthias Lange, U. Scholz
{"title":"Information Fusion and Metabolic Network Control","authors":"A. Freier, R. Hofestädt, Matthias Lange, U. Scholz","doi":"10.7551/mitpress/3215.003.0005","DOIUrl":"https://doi.org/10.7551/mitpress/3215.003.0005","url":null,"abstract":"","PeriodicalId":111388,"journal":{"name":"Gene Regulations and Metabolism","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127704200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
N. Kolchanov, E. A. Ananko, V. A. Likhoshvai, O. Podkolodnaya, E. Ignatieva, A. Ratushny, Y. Matushkin
{"title":"Gene Networks Description and Modeling in the GeneNet System","authors":"N. Kolchanov, E. A. Ananko, V. A. Likhoshvai, O. Podkolodnaya, E. Ignatieva, A. Ratushny, Y. Matushkin","doi":"10.7551/mitpress/3215.003.0010","DOIUrl":"https://doi.org/10.7551/mitpress/3215.003.0010","url":null,"abstract":"","PeriodicalId":111388,"journal":{"name":"Gene Regulations and Metabolism","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122253565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Regulation of Cellular States in Mammalian Cells from a Genomewide View","authors":"Sui Huang","doi":"10.7551/mitpress/3215.003.0011","DOIUrl":"https://doi.org/10.7551/mitpress/3215.003.0011","url":null,"abstract":"","PeriodicalId":111388,"journal":{"name":"Gene Regulations and Metabolism","volume":"39 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127418718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Predicting Protein Function and Nworks on a Genomewide Scale","authors":"E. Marcotte","doi":"10.7551/mitpress/3215.003.0013","DOIUrl":"https://doi.org/10.7551/mitpress/3215.003.0013","url":null,"abstract":"Perhaps the most significant finding from the more than 80 genomes that have been sequenced as of 2002 has been the extent of our ignorance about the constituents of cells. In virtually every genome sequenced, the majority of genes have never been studied directly. In spite of this, for about half of the genes at least one near or distant relative has been studied, so we glean our knowledge from the activities of these relatives. Until recently such methods for extending information to proteins with similar sequences or structures (homology-based methods) have been the only form of inference about protein function. Homology-based annotation, with algorithms such as BLAST (Alt-schul et al., 1997; http://www.ncbi.nlm.nih.gov/BLAST), has been wildly successful in extending knowledge from the small set of experimentally characterized proteins to the tens of thousands of proteins found in genome sequencing projects. However, these methods perform as one might expect: they provide information only for proteins with very closely related functions. They reveal little about proteins that work together but typically have unrelated sequences or structures. Thus, the homology-based methods cannot be used to reconstruct metabolic or signaling pathways or other protein interaction networks. That such a bias exists shows that there are different aspects to protein function; methods that reveal one aspect do not necessarily reveal others. The two most important aspects of protein function, defined in figure 9.1, will be referred to as the molecular function and the cellular function of proteins. The homology-based methods tend to find only the molec","PeriodicalId":111388,"journal":{"name":"Gene Regulations and Metabolism","volume":"76 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123219783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Discovery of DNA Regulatory Motifs","authors":"A. McGuire, G. Church","doi":"10.7551/mitpress/3215.003.0009","DOIUrl":"https://doi.org/10.7551/mitpress/3215.003.0009","url":null,"abstract":"","PeriodicalId":111388,"journal":{"name":"Gene Regulations and Metabolism","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127970056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Are the Eyes Homologous?","authors":"J. Ahouse","doi":"10.7551/mitpress/3215.003.0002","DOIUrl":"https://doi.org/10.7551/mitpress/3215.003.0002","url":null,"abstract":"","PeriodicalId":111388,"journal":{"name":"Gene Regulations and Metabolism","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130299861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}