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MACiE: exploring the diversity of biochemical reactions

by Gemma L. Holliday, Claudia Andreini, Julia D. Fischer, Syed Asad Rahman, Daniel E. Almonacid, Sophie T. Williams, William R. Pearson - Nucleic Acids Res , 2012
"... MACiE (which stands for Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and can be accessed from ..."
Abstract - Cited by 16 (4 self) - Add to MetaCart
MACiE (which stands for Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and can be accessed from

Exploring the diversity of complex metabolic networks

by Vassily Hatzimanikatis, Chunhui Li, Justin A. Ionita, Christopher S. Henry, Matthew D, Linda J. Broadbelt - Bioinformatics , 2005
"... * To whom correspondence should be addressed. Motivation: Metabolism, the network of chemical reactions that make life possible, is one of the most complex processes in nature. We describe here the development of a computational approach for the identification of every possible biochemical reaction ..."
Abstract - Cited by 33 (1 self) - Add to MetaCart
* To whom correspondence should be addressed. Motivation: Metabolism, the network of chemical reactions that make life possible, is one of the most complex processes in nature. We describe here the development of a computational approach for the identification of every possible biochemical reaction

Monetary Policy in a Data Rich Environment

by Ben S. Bernanke, Jean Boivin - Journal of Monetary Economics , 2002
"... Most empirical analyses of monetary policy have been confined to frameworks in which the Federal Reserve is implicitly assumed to exploit only a limited amount of information, despite the fact that the Fed actively monitors literally thousands of economic time series. This article explores the feasi ..."
Abstract - Cited by 149 (3 self) - Add to MetaCart
data-rich environment and provide a test of the hypothesis that Fed actions are explained solely by its forecasts of inflation and real activity. Finally, we explore the possibility of developing an “expert system ” that could aggregate diverse information and provide benchmark policy settings

Systems biology Exploring the diversity of complex metabolic networks

by Vassily Hatzimanikatis, Chunhui Li, Justin A. Ionita, Christopher S. Henry, Matthew D. Jankowski, Linda J. Broadbelt , 2005
"... Motivation: Metabolism, the network of chemical reactions that make life possible, is one of the most complex processes in nature. We describe here the development of a computational approach for the identification of every possible biochemical reaction from a given set of enzyme reaction rules that ..."
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Motivation: Metabolism, the network of chemical reactions that make life possible, is one of the most complex processes in nature. We describe here the development of a computational approach for the identification of every possible biochemical reaction from a given set of enzyme reaction rules

MULTIDIMENSIONAL EXPLORATION INTO BIOCHEMICAL PATHWAYS

by Johann Gasteiger, Martin Reitz, Oliver Sacher
"... The famous Biochemical Pathways wall chart has been converted into a reaction database. The web based retrieval system ..."
Abstract - Cited by 3 (0 self) - Add to MetaCart
The famous Biochemical Pathways wall chart has been converted into a reaction database. The web based retrieval system

Noise in gene expression: origins, consequences, and control

by Jonathan M. Raser, Erin K. O’shea - Science , 2005
"... Genetically identical cells and organisms exhibit remarkable diversity even when they have identical histories of environmental exposure. Noise, or variation, in the process of gene expression may contribute to this phenotypic variability. Recent studies suggest that this noise has multiple sources, ..."
Abstract - Cited by 111 (0 self) - Add to MetaCart
, including the stochastic or inherently random nature of the biochemical reactions of gene expression. In this review, we summarize noise terminology and comment on recent investigations into the sources, consequences, and control of noise in gene expression. A ny individual in a population of living

Stochasticity in Biochemical Reaction Networks

by unknown authors
"... Cellular processes are subject to vast amounts of random variation, which can cause isogenic cells to respond differently, despite identical environmental conditions. Recent experimental techniques make it possible to measure this variation in gene expression, protein abundance, and cellular behavio ..."
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biochemical circuits and nanoscale devices. The second workshop on Stochasticity in Biochemical Reaction Networks held at Banff International Research Station, 25-27, September 2009 served as an excellent venue to discuss the multifaceted progress in this field. The exciting research topic of stochasticity

Memory Switches in Chemical Reaction Space

by Naren Ramakrishnan, Upinder S. Bhalla - COMPUTATIONAL BIOLOGY , 2008
"... Just as complex electronic circuits are built from simple Boolean gates, diverse biological functions, including signal transduction, differentiation, and stress response, frequently use biochemical switches as a functional module. A relatively small number of such switches have been described in th ..."
Abstract - Cited by 14 (2 self) - Add to MetaCart
in the literature, and these exhibit considerable diversity in chemical topology. We asked if biochemical switches are indeed rare and if there are common chemical motifs and family relationships among such switches. We performed a systematic exploration of chemical reaction space by generating all possible

High Quality Visualization of Biochemical Pathways in BioPath

by Falk Schreiber , 2002
"... Biochemical reactions form large and complex networks. Comprehensible visual representations of these networks help biochemists understand the relationships between the chemical components. Typically pathway diagrams are manually produced drawings. Because of the steady progress of knowledge and t ..."
Abstract - Cited by 36 (18 self) - Add to MetaCart
the requirements for the visualization of biochemical pathways, presents a layout algorithm and shows how BioPath can be used to explore biochemical reaction networks.

Biochemical characterization of DNA damage checkpoint complexes: clamp loader and clamp complexes with specificity for 5’ recessed DNA

by Viola Ellison, Bruce Stillman - PLoS Biol , 2003
"... The cellular pathways involved in maintaining genome stability halt cell cycle progression in the presence of DNA damage or incomplete replication. Proteins required for this pathway include Rad17, Rad9, Hus1, Rad1, and Rfc-2, Rfc-3, Rfc-4, and Rfc-5. The heteropentamer replication factor C (RFC) lo ..."
Abstract - Cited by 60 (0 self) - Add to MetaCart
whereas RFC preferred 39 recessed end DNA substrates. Characterization of the biochemical loading reaction executed by the checkpoint clamp loader RSR suggests new insights into the mechanisms underlying recognition of damage-induced DNA structures and signaling to cell cycle controls. The observation
Results 1 - 10 of 570