Pub Date : 1961-10-01DOI: 10.7551/mitpress/3215.003.0014
Steffen Schmidt, T. Dandekar
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.
{"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}
Pub Date : 1900-01-01DOI: 10.7551/mitpress/3215.003.0015
M. Tomita
{"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}
Pub Date : 1900-01-01DOI: 10.7551/mitpress/3215.003.0007
G. Stormo
{"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}
Pub Date : 1900-01-01DOI: 10.7551/mitpress/3215.003.0004
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}
Pub Date : 1900-01-01DOI: 10.7551/mitpress/3215.003.0005
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}
Pub Date : 1900-01-01DOI: 10.7551/mitpress/3215.003.0010
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}
Pub Date : 1900-01-01DOI: 10.7551/mitpress/3215.003.0011
Sui Huang
{"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}
Pub Date : 1900-01-01DOI: 10.7551/mitpress/3215.003.0013
E. Marcotte
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
也许从2002年的80多个基因组测序中最重要的发现是我们对细胞成分的无知程度。实际上，在每一个基因组测序中，大多数基因从未被直接研究过。尽管如此，对于大约一半的基因，至少有一个近亲或远亲被研究过，所以我们从这些近亲的活动中收集我们的知识。直到最近，这种将信息扩展到具有相似序列或结构的蛋白质的方法(基于同源的方法)一直是推断蛋白质功能的唯一形式。基于同源的注释，使用BLAST等算法(Alt-schul et al.， 1997;http://www.ncbi.nlm.nih.gov/BLAST)，在将知识从一小组实验表征的蛋白质扩展到基因组测序项目中发现的数万种蛋白质方面取得了巨大的成功。然而，这些方法的作用正如人们所期望的那样:它们只提供功能非常密切相关的蛋白质的信息。它们很少揭示协同工作的蛋白质，但通常具有不相关的序列或结构。因此，基于同源性的方法不能用于重建代谢或信号通路或其他蛋白质相互作用网络。这种偏见的存在表明蛋白质的功能有不同的方面;揭示一个方面的方法不一定揭示其他方面。图9.1中定义的蛋白质功能的两个最重要的方面将被称为蛋白质的分子功能和细胞功能。基于同源性的方法往往只找到分子
{"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}
Pub Date : 1900-01-01DOI: 10.7551/mitpress/3215.003.0009
A. McGuire, G. Church
{"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}
Pub Date : 1900-01-01DOI: 10.7551/mitpress/3215.003.0002
J. Ahouse
{"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}
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