Genomes and Genes
Summary: The sum of chemical changes that occur within the tissues of an organism consisting of anabolism (biosysthesis) and catabolism; the buildup and breakdown of molecules for utilization by the body.
Publications245 found, 100 shown here
- Role of insulin, adipocyte hormones, and nutrient-sensing pathways in regulating fuel metabolism and energy homeostasis: a nutritional perspective of diabetes, obesity, and cancerStephen Marshall
Hexos Inc, 18304 NE 153rd Street, Woodinville, WA 98072, USA
Sci STKE 2006:re7. 2006..Glucose and amino acids trigger signaling cascades that regulate various aspects of fuel and energy metabolism and control the growth, proliferation, and survival of cells...
- The systems biology markup language (SBML): a medium for representation and exchange of biochemical network modelsM Hucka
Control and Dynamical Systems, MC 107 81, California Institute of Technology, Pasadena, CA 91125, USA
Bioinformatics 19:524-31. 2003..Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively...
- Circadian integration of metabolism and energeticsJoseph Bass
Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
Science 330:1349-54. 2010..Here, we review advances in understanding the interrelationship among circadian disruption, sleep deprivation, obesity, and diabetes and implications for rational therapeutics for these conditions...
- Autophagy and metabolismJoshua D Rabinowitz
Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, 241 Carl Icahn Laboratory, Washington Road, Princeton University, Princeton, NJ 08544, USA
Science 330:1344-8. 2010..The resulting breakdown products are inputs to cellular metabolism, through which they are used to generate energy and to build new proteins and membranes...
- CD36, a scavenger receptor involved in immunity, metabolism, angiogenesis, and behaviorRoy L Silverstein
Department of Cell Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
Sci Signal 2:re3. 2009..Identification of the precise CD36 signaling pathways in specific cells elicited in response to specific ligands may yield novel targets for drug development...
- A general model for the origin of allometric scaling laws in biologyG B West
Theoretical Division, T 8, Mail Stop B285, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
Science 276:122-6. 1997..More generally, the model predicts structural and functional properties of vertebrate cardiovascular and respiratory systems, plant vascular systems, insect tracheal tubes, and other distribution networks...
- Metabolite profiling for plant functional genomicsO Fiehn
Max Planck Institute of Molecular Plant Physiology, 14424 Potsdam, Germany
Nat Biotechnol 18:1157-61. 2000..These results demonstrate the use of metabolite profiling as a tool to significantly extend and enhance the power of existing functional genomics approaches...
- NMR-based metabolic profiling and metabonomic approaches to problems in molecular toxicologyMuireann Coen
Department of Biomolecular Medicine, Surgery, Oncology, Reproductive Biology and Anesthetics Division, Faculty of Medicine, Imperial College London, London, UK
Chem Res Toxicol 21:9-27. 2008..The use of biological fluids as a source of whole organism metabolic information enhances the use of this approach in minimally invasive longitudinal studies...
- Network biology: understanding the cell's functional organizationAlbert Laszlo Barabasi
Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
Nat Rev Genet 5:101-13. 2004
- Expansion of the BioCyc collection of pathway/genome databases to 160 genomesPeter D Karp
Bioinformatics Research Group, SRI International EK207, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
Nucleic Acids Res 33:6083-9. 2005..Only by harnessing the expertise of many scientists we can hope to produce biological databases, which accurately reflect the depth and breadth of knowledge that the biomedical research community is producing...
- FGFs and metabolismAlexei Kharitonenkov
Eli Lilly and Company, Lilly Research Laboratories, Biotechnology Discovery Research, Lilly Corporate Center, Indianapolis, IN 46285, USA
Curr Opin Pharmacol 9:805-10. 2009..morphogenesis, angiogenesis, hematopoiesis, and survival, this decade provided clues on FGF roles in metabolism. In particular, 'hormone-like' FGF19, FGF21, and FGF23, were shown to be involved in glucose, lipid, bile acid, ..
- A salvage pathway for phytol metabolism in ArabidopsisTill Ischebeck
Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, , 14476 Golm, Germany
J Biol Chem 281:2470-7. 2006..Thus, Arabidopsis contains a distinct enzymatic machinery for redirecting free phytol released from chlorophyll degradation into chloroplast lipid metabolism.
- Exercise training and protein metabolism: influences of contraction, protein intake, and sex-based differencesNicholas A Burd
Exercise Metabolism Research Group, Dept of Kinesiology, McMaster Univ, 1280 Main St, West Hamilton, ON, Canada L8S 4K1
J Appl Physiol 106:1692-701. 2009..Furthermore, we examine the underlying anabolic signaling pathways and molecules that regulate these processes...
- Adenine nucleotide metabolism in human blood--important roles for leukocytes and erythrocytesS Heptinstall
Centre for Integrated Systems Biology and Medicine, Institute of Clinical Research, University of Nottingham, UK
J Thromb Haemost 3:2331-9. 2005..Rapid metabolism of ADP and ATP by endothelial cells is important in protecting platelets from their effects...
- A metabolome study of the steady-state relation between central metabolism, amino acid biosynthesis and penicillin production in Penicillium chrysogenumUly Nasution
Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
Metab Eng 10:10-23. 2008The relation between central metabolism and the penicillin biosynthesis pathway in Penicillium chrysogenum was studied by manipulating the steady-state flux in both pathways...
- Bioavailability and metabolism of fucoxanthin in rats: structural characterization of metabolites by LC-MS (APCI)Ravi Kumar Sangeetha
Department of Biochemistry and Nutrition, Central Food Technological Research Institute, CSIR, Mysore, 570 020, India
Mol Cell Biochem 333:299-310. 2010This study reports bioavailability and metabolism of fucoxanthin (FUCO) from brown algae Padina tetrastromatica in rats. Rats were divided into two groups (n = 25/group)...
- The circadian clock and metabolismOren Froy
Institute of Biochemistry, Food Science and Nutrition, Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
Clin Sci (Lond) 120:65-72. 2011..and physiological functions in addition to the expression and/or activity of enzymes and hormones involved in metabolism. In turn, key metabolic enzymes and transcription activators interact with and affect the core clock mechanism...
- Chemometrics in metabonomicsJohan Trygg
Research Group for Chemometrics, Institute of Chemistry, Umea University, Sweden
J Proteome Res 6:469-79. 2007..This is illustrated by examples from the literature...
- Genome-scale microbial in silico models: the constraints-based approachNathan D Price
Department of Bioengineering, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 2093-0412, USA
Trends Biotechnol 21:162-9. 2003..These results are useful as a basis for iterative model building and for several practical applications...
- Organizational invariance and metabolic closure: analysis in terms of (M,R) systemsJuan Carlos Letelier
Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
J Theor Biol 238:949-61. 2006..formulation of (M,R) systems in terms of mappings and sets of mappings, which is grounded in the metaphor of metabolism as a mathematical mapping...
- Transplantation of adipose tissue and stem cells: role in metabolism and diseaseThien T Tran
Joslin Diabetes Center and Harvard Medical School, Boston, MA 02215, USA
Nat Rev Endocrinol 6:195-213. 2010..metabolic effects, subcutaneous white adipose tissue and brown adipose tissue have the potential to benefit metabolism by improving glucose homeostasis and increasing energy consumption...
- Metabolism and bioavailability of flavonoids in chemoprevention: current analytical strategies and future prospectusJeevan K Prasain
Department of Pharmacology and Toxicology, Purdue UAB Botanicals Center for Age Related Disease, UAB Center for Nutrient Gene Interaction in Cancer Prevention, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
Mol Pharm 4:846-64. 2007..behavior of these compounds following oral ingestion is needed as well as their absorption, distribution, metabolism, and excretion (ADME)...
- Depression of cell metabolism and proliferation by membrane-permeable and -impermeable modulators: role for AMP-to-ATP ratioMichael A Menze
Division of Cellular, Developmental and Integrative Biology, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Am J Physiol Regul Integr Comp Physiol 288:R501-10. 2005..a nonhydrolyzable analog of 5'-AMP and potent activator of AMP-activated protein kinase, significantly depresses metabolism and proliferation of macrophages...
- The modulation of androgen metabolism by estradiol, minocycline, and indomethacin in a cell culture modelA Tilakaratne
Department of Periodontology, Faculty of Dental Sciences, University of Peradeniya, Sri Lanka
J Periodontol 73:585-90. 2002..to clarify the proanabolic effects of minocycline and indomethacin by studying their effects on androgen metabolism and mediation by estradiol...
- Hydroxycitrate has long-term effects on feeding behavior, body weight regain and metabolism after body weight loss in male ratsMonika Leonhardt
Institute of Animal Sciences, Swiss Federal Institute of Technology, CH 8603 Schwerzenbach, Switzerland
J Nutr 132:1977-82. 2002..The fact that HCA did not change plasma BHB concentration does not support a role for increased hepatic fatty acid oxidation in the anorectic effect of HCA...
- Effects of dietary fatty acids and exercise on body-weight regulation and metabolism in ratsMichael Pellizzon
Department of Nutrition and Food Science, Wayne State University, Detroit, MI 48202, USA
Obes Res 10:947-55. 2002..diets (HF) made with different dietary fatty acids and exercise on body-weight regulation, adiposity, and metabolism. RESEARCH METHODS AND PROCEDURES: Male Wistar rats born to dams fed HF diets (40% w/w) made with either fish oil ..
- Metabolism in the era of molecular biologyRichard W Hanson
Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106-4935, USA
J Biol Chem 280:1705-15. 2005
- In vitro fertilization improves childhood growth and metabolismHarriet L Miles
The National Research Centre for Growth and Development and Liggins Institute, University of Auckland, Auckland 1010, New Zealand
J Clin Endocrinol Metab 92:3441-5. 2007..There is limited information regarding the long-term outcome of children born after in vitro fertilization (IVF), although an increase in rare imprinted gene disorders such as Beckwith-Wiedemann syndrome has been reported...
- Improving glucose and glutamine metabolism of human HEK 293 and Trichoplusia ni insect cells engineered to express a cytosolic pyruvate carboxylase enzymeCynthia B Elias
Animal Cell Technology Dept, Biotechnology Research Institute, , , Canada H4P 2R2, and Cell Culture Technology Dept, German Research Centre for Biotechnology mbH, Braunschweig, Germany
Biotechnol Prog 19:90-7. 2003..Differences in the amino acid utilization pattern were also observed, indicating changes in the basic metabolism of the cells...
- 14-3-3-affinity purification of over 200 human phosphoproteins reveals new links to regulation of cellular metabolism, proliferation and traffickingMercedes Pozuelo Rubio
MRC Protein Phosphorylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
Biochem J 379:395-408. 2004..cell growth, regulators of cell proliferation, including enzymes of DNA replication, proteins of anti-oxidative metabolism, regulators of actin dynamics and cellular trafficking, and proteins whose deregulation has been implicated in ..
- Metabolism and calcium antagonism of sodium alginate oligosaccharidesTakamitsu Chaki
Central Research Institute, Maruha Group Inc, Tsukuba, Ibaraki, Japan
Biosci Biotechnol Biochem 71:1819-25. 2007..Our results suggest that NaAOs are substantially excreted into the feces, although some of them may be absorbed internally, exerting antagonist activity towards the calcium channels, especially voltage-operated calcium channels...
- The effect of oral glucose loads on tissue metabolism during angiotensin II receptor and beta-receptor blockade in obese hypertensive subjectsM Boschmann
Franz-Volhard Clinical Research Center, , Berlin, Berlin, Germany
Horm Metab Res 38:323-9. 2006..The phenomenon could be related to a direct angiotensin II effect on tissue metabolism. To address the issue, we recruited eighteen obese hypertensive patients...
- Influence of temperature on metabolism and breathing during mammalian ontogenesisJacopo P Mortola
Department of Physiology, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, Que, Canada H3G 1Y6
Respir Physiol Neurobiol 149:155-64. 2005..Presumably, this indicates that respiratory regulation develops independently from the individual's metabolic history...
- From prebiotic chemistry to cellular metabolism--the chemical evolution of metabolism before Darwinian natural selectionEnrique Meléndez-Hevia
Instituto del Metabolismo Celular, Calle Manuel de Falla no 15, La Laguna, 38208 Tenerife, Canary Islands, Spain
J Theor Biol 252:505-19. 2008It is generally assumed that the complex map of metabolism is a result of natural selection working at the molecular level...
- The trade-off between rate and yield in the design of microbial metabolismS A Frank
Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
J Evol Biol 23:609-13. 2010....
- A network perspective on metabolism and agingQuinlyn A Soltow
Department of Medicine, Emory University, Atlanta, GA 30322, USA
Integr Comp Biol 50:844-54. 2010..Here, we advocate the use of metabolic networks to expand the work from genomics and proteomics. As metabolism is the final fingerprint of functionality and has been implicated in multiple theories of aging, metabolomic ..
- PPARdelta/beta: the lobbyist switching macrophage allegiance in favor of metabolismBeatrice Desvergne
Center of Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH 1015 Lausanne, Switzerland
Cell Metab 7:467-9. 2008..In two studies by Kang et al. (2008) and Odegaard et al. (2008) in this issue of Cell Metabolism, we learn that alternative activation (M2a) of resident macrophages in liver and adipose tissue depends highly ..
- Metabolism strikes back: metabolic flux regulates cell signalingChristian M Metallo
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Genes Dev 24:2717-22. 2010..This mechanism ensures that cells do not engage in anabolic metabolism when nutrients are limiting, and highlights how substrate availability for protein modifications can modulate ..
- Sleep and metabolism: shared circuits, new connectionsAntoine Adamantidis
Department of Psychiatry, Stanford University School of Medicine, Palo Alto, CA 94304 5742, USA
Trends Endocrinol Metab 19:362-70. 2008..New optical tools that remotely control neuronal circuit activity provide an effective means to understand the cooperativity of shared circuits in regulating hypothalamic functions such as sleep and metabolism.
- A minimal model of metabolism-based chemotaxisMatthew D Egbert
Centre for Computational Neuroscience and Robotics, University of Sussex, Brighton, United Kingdom
PLoS Comput Biol 6:e1001004. 2010Since the pioneering work by Julius Adler in the 1960's, bacterial chemotaxis has been predominantly studied as metabolism-independent. All available simulation models of bacterial chemotaxis endorse this assumption...
- Bone and metabolism: a complex crosstalkLiesbet Lieben
Laboratory for Experimental Medicine and Endocrinology, Department of Experimental Medicine, Katholieke Universiteit Leuven, Leuven, Belgium
Horm Res 71:134-8. 2009Until recently, communication from metabolism to bone was considered purely unidirectional, involving complex interactions among an adipocyte-derived factor (leptin), the sympathetic nervous system and neuropeptides...
- The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesisCharles E Massie
CRUK Cambridge Research Institute, Cambridge, UK
EMBO J 30:2719-33. 2011..cancer and regulates cancer cell growth via its unexpected role as a hormone-dependent modulator of anabolic metabolism. In conclusion, it is possible to progress from transcriptional studies to a promising therapeutic target by ..
- H2S induced hypometabolism in mice is missing in sedated sheepPhilippe Haouzi
Penn State Heart and Vascular Institute, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, United States
Respir Physiol Neurobiol 160:109-15. 2008..We measured metabolism in conscious mice (24 g) exposed to H(2)S (60 ppm) at an ambient temperature of 23-24 degrees C...
- Coral larvae under ocean acidification: survival, metabolism, and metamorphosisMasako Nakamura
Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
PLoS ONE 6:e14521. 2011..These results imply that acidified seawater impacts larval physiology, suggesting that suppressed metabolism and metamorphosis may alter the dispersal potential of larvae and subsequently reduce the resilience of coral ..
- Peroxisome proliferator-activated receptor-gamma coactivator-1alpha in muscle links metabolism to inflammationChristoph Handschin
Biozentrum, University of Basel, Basel and Institute of Physiology and Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
Clin Exp Pharmacol Physiol 36:1139-43. 20091. In higher eukaryotes, metabolism and immunity are tightly coupled...
- The clinical significance of betaine, an osmolyte with a key role in methyl group metabolismMichael Lever
Biochemistry Unit, Canterbury Health Laboratories, Christchurch, New Zealand
Clin Biochem 43:732-44. 2010..Its metabolism methylates homocysteine to methionine, also producing N,N-dimethylglycine...
- Myocardial substrate metabolism in the normal and failing heartWilliam C Stanley
Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio 44106 4970, USA
Physiol Rev 85:1093-129. 2005The alterations in myocardial energy substrate metabolism that occur in heart failure, and the causes and consequences of these abnormalities, are poorly understood...
- METATOOL: for studying metabolic networksT Pfeiffer
Humboldt University Berlin, Institute of Biology, Invalidenstrasse 42, D 10115 Berlin, Germany
Bioinformatics 15:251-7. 1999..In addition, we define 'enzyme subsets' to be groups of enzymes that operate together in fixed flux proportions in all steady states of the system...
- Metabonomics in toxicology: a reviewDonald G Robertson
Metabonomics Evaluation Group, Department of World Wide Safety Sciences, Pfizer Global Research and Development, Ann Arbor, Michigan 48105, USA
Toxicol Sci 85:809-22. 2005..The jargon, logistics, and applications of the technology are covered in some detail with emphasis on recent work in the field...
- Systematic identification of conserved metabolites in GC/MS data for metabolomics and biomarker discoveryMark P Styczynski
Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56 469c, Cambridge, Massachusetts 02139, USA
Anal Chem 79:966-73. 2007..By systematically cataloguing conserved metabolite peaks prior to data analysis methods, our approach broadens the scope of metabolomics and facilitates biomarker discovery...
- Sir2 links chromatin silencing, metabolism, and agingL Guarente
Department of Biology, Massachusetts Institute of Technology (MIT, Cambridge, Massachusetts 02139 USA
Genes Dev 14:1021-6. 2000
- Theodor Bücher Lecture. Metabolomics, modelling and machine learning in systems biology - towards an understanding of the languages of cells. Delivered on 3 July 2005 at the 30th FEBS Congress and the 9th IUBMB conference in BudapestDouglas B Kell
School of Chemistry, Faraday Building, The University of Manchester, UK
FEBS J 273:873-94. 2006..These include fields such as chemical genomics, synthetic biology, distributed computational environments for biological data and modelling, single cell diagnostics/bionanotechnology, and computational linguistics/text mining...
- The evolution of connectivity in metabolic networksThomas Pfeiffer
Computational Laboratory, ETH Zurich, Zurich, Switzerland
PLoS Biol 3:e228. 2005..Specifically, our simulations indicate that group transfer reactions are essential for the emergence of hubs...
- The Pathway Tools cellular overview diagram and Omics ViewerSuzanne M Paley
Bioinformatics Research Group, SRI International EK207, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
Nucleic Acids Res 34:3771-8. 2006....
- From measurements of metabolites to metabolomics: an 'on the fly' perspective illustrated by recent studies of carbon-nitrogen interactionsMark Stitt
Departments of Metabolic Networks and Molecular Physiology, Max Planck Institut fur Molekulare Pflanzenphysiologie, Am Muhlenberg 1, 14476, Golm, Germany
Curr Opin Biotechnol 14:136-44. 2003..A major future challenge concerns the integration of the information gained from metabolite profiling into an accessible body of knowledge...
- Energy balance for analysis of complex metabolic networksDaniel A Beard
Department of Bioengineering, University of Washington, Seattle, Washington 98915, USA
Biophys J 83:79-86. 2002..We show that EBA eliminates thermodynamically infeasible results associated with FBA...
- Human metabolic phenotypes link directly to specific dietary preferences in healthy individualsSerge Rezzi
BioAnalytical Science, Metabonomics and Biomarkers, Nestle Research Center, P O Box 44, CH 1000 Lausanne 26, Switzerland
J Proteome Res 6:4469-77. 2007..measured using 1H NMR spectroscopy, including the postprandial lipoprotein profile and gut microbial co-metabolism. These data suggest that specific dietary preferences can influence basal metabolic state and gut microbiome ..
- Stochastic approaches for modelling in vivo reactionsT E Turner
Oxford Centre for Industrial and Applied Mathematics, Mathematical Institute, 24 29 St Giles, Oxford OX1 3LB, UK
Comput Biol Chem 28:165-78. 2004..We then describe recent efforts to include the fluctuation effects caused by the structural organisation of the cytoplasm and the limited diffusion of molecules due to macromolecular crowding...
- Metabolic pathways in the post-genome eraJason A Papin
Department of Bioengineering, University of California, San Diego, La Jolla 92093-0412, USA
Trends Biochem Sci 28:250-8. 2003..Recently, these properties have also been studied in genome-scale networks. Thus, network-based pathways are emerging as an important paradigm for analysis of biological systems...
- Dynamic modeling of genetic networks using genetic algorithm and S-systemShinichi Kikuchi
Computational Biology Research Center CBRC, National Institute of Advanced Industrial Science and Technology AIST, 2 41 6 Aomi, Koto ku, Tokyo, 135 0064, Japan
Bioinformatics 19:643-50. 2003....
- Minimal cut sets in biochemical reaction networksSteffen Klamt
Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr 1, D 39106 Magdeburg, Germany
Bioinformatics 20:226-34. 2004..Such studies will help to identify crucial parts in the network structure and to find suitable targets for repressing undesired metabolic functions...
- Catabolic responses of chondrocyte-seeded peptide hydrogel to dynamic compressionJohn D Kisiday
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
Ann Biomed Eng 37:1368-75. 2009..These data suggest that partially mature cartilage tissue engineering constructs may be susceptible to catabolic degradation...
- In silico simulation of biological network dynamicsLukasz Salwinski
UCLA-DOE Institute for Genomics and Proteomics, Howard Hughes Medical Institute, Molecular Biology Institute, Los Angeles, CA 90095-1570, USA
Nat Biotechnol 22:1017-9. 2004..The parallel architecture of FPGAs, which can simulate the basic reaction steps of biological networks, attains simulation rates at least an order of magnitude greater than currently available microprocessors...
- A multi-scaled approach for simulating chemical reaction systemsKevin Burrage
Department of Mathematics, Advanced Computational Modelling Centre, University of Queensland, Brisbane QLD4072, Australia
Prog Biophys Mol Biol 85:217-34. 2004..We then apply this approach to a biologically inspired problem involving the expression and activity of LacZ and LacY proteins in E. coli, and conclude with a discussion on the significance of this work...
- The need for speed in stochastic simulationLarry Lok
Nat Biotechnol 22:964-5. 2004
- An algorithm for linear metabolic pathway alignmentMing Chen
Group of Bioinformatics, College of Life Science, Zhejiang University, Hangzhou, China
In Silico Biol 5:111-28. 2005Metabolic pathway alignment represents one of the most powerful tools for comparative analysis of metabolism. It involves recognition of metabolites common to a set of functionally-related metabolic pathways, interpretation of biological ..
- Simulating complex intracellular processes using object-oriented computational modellingColin G Johnson
Computing Laboratory, University of Kent, Canterbury, CT2 7NF, UK
Prog Biophys Mol Biol 86:379-406. 2004..The paper also discusses the role of computer simulation in understanding complexity in biological systems, and the kinds of information which can be obtained about biology via simulation...
- Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructionsEvgeni V Nikolaev
Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Biophys J 88:37-49. 2005..The developed approaches thus provide novel and versatile tools for elucidating coupling relationships between metabolite concentrations with implications in biotechnological and medical applications...
- All systems go: launching cell simulation fueled by integrated experimental biology dataMasanori Arita
Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihoji, Tsuruoka, 997-0017 Yamagata, Japan
Curr Opin Biotechnol 16:344-9. 2005..The integration of parallel experimental datasets into dynamic simulation tools forms the remaining challenge for the systematic analysis and elucidation of biological networks and holds promise for biotechnological applications...
- Computation of elementary modes: a unifying framework and the new binary approachJulien Gagneur
Cellzome AG, Meyerhofstr 1, 69117 Heidelberg, Germany
BMC Bioinformatics 5:175. 2004..However, computing elementary modes is a hard computational task. In recent years we assisted in a multiplication of algorithms dedicated to it. We require a summarizing point of view and a continued improvement of the current methods...
- Automatic generation of cellular reaction networks with Moleculizer 1.0Larry Lok
The Molecular Sciences Institute, 2168 Shattuck Avenue, Berkeley, California 94704, USA
Nat Biotechnol 23:131-6. 2005..We apply this approach to the automatic generation of reaction systems for the study of signal transduction networks...
- Metabolomics, machine learning and modelling: towards an understanding of the language of cellsD B Kell
School of Chemistry, The University of Manchester, Faraday Building, Sackville Street, P O Box 88, Manchester M60 1QD, UK
Biochem Soc Trans 33:520-4. 2005..The language of cells is much richer than we had supposed, and we are now well placed to decode it...
- Properties of metabolic networks: structure versus functionR Mahadevan
Biophys J 88:L07-9. 2005
- The topological relationship between the large-scale attributes and local interaction patterns of complex networksA Vazquez
Department of Physics and Center for Complex Network Research, University of Notre Dame, Notre Dame, IN 46556, USA
Proc Natl Acad Sci U S A 101:17940-5. 2004..The identified topological framework may have important implications for our understanding of the origin and function of subgraphs in all complex networks...
- Integration of metabolic networks and gene expression in virtual realityYuting Yang
Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA
Bioinformatics 21:3645-50. 2005MOTIVATION: Metabolic networks combine metabolism and regulation. These complex networks are difficult to understand and visualize due to the amount and diverse types of information that need to be represented...
- Metabolic control analysis for large changes: extension to variable elasticity coefficientsL Acerenza
Systems Biology Laboratory, Faculty of Sciences, University of the Republic, Igvá 4225, Montevideo 11400, Uruguay
Syst Biol (Stevenage) 153:323-6. 2006..Our analysis shows that the pattern of control for large changes is quantitatively and qualitatively different from the one obtained applying the infinitesimal treatment...
- Detection of stoichiometric inconsistencies in biomolecular modelsAlbert Gevorgyan
Cell Systems Modelling Group, School of Life Sciences, Oxford Brookes University, Oxford OX30BP, UK
Bioinformatics 24:2245-51. 2008....
- Metabolic flux estimation--a self-adaptive evolutionary algorithm with singular value decompositionJing Yang
Department of Automatic Control and Systems Engineering, University of Sheffield, UK
IEEE/ACM Trans Comput Biol Bioinform 4:126-38. 2007..The proposed algorithm is also applied to the central metabolism of Corynebacterium glutamicum under lysine-producing conditions...
- MetaPath Online: a web server implementation of the network expansion algorithmThomas Handorf
Department of Theoretical Biophysics, Institute of Biology, Humboldt University Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
Nucleic Acids Res 35:W613-8. 2007..The web server is accessible through http://scopes.biologie.hu-berlin.de...
- Regularizing capacity of metabolic networksCarsten Marr
Bioinformatics Group, Department of Biology, Darmstadt University of Technology, D 64287 Darmstadt, Germany
Phys Rev E Stat Nonlin Soft Matter Phys 75:041917. 2007..This exceptionally pronounced regularization of dynamics encoded in the topology may explain why steady-state behavior is ubiquitous in metabolism.
- Piecewise multivariate modelling of sequential metabolic profiling dataMattias Rantalainen
Research Group for Chemometrics, Institute of Chemistry, Umea University, Umea, S 901 87, Sweden
BMC Bioinformatics 9:105. 2008..In metabolic profiling studies, the sampling rate and number of sampling points are often restricted due to experimental and biological constraints...
- PathExpress: a web-based tool to identify relevant pathways in gene expression dataNicolas Goffard
ARC Centre of Excellence for Integrative Legume Research and Bioinformatics Laboratory, Genomic Interactions Group, Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601 Australia
Nucleic Acids Res 35:W176-81. 2007..PathExpress is available at http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/...
- Using existing digital tools for efficient metabolic pathway simulationsLuca Macchiarulo
Fac of Electr Eng, Hawaii Univ, Honolulu, HI 96822, USA
Conf Proc IEEE Eng Med Biol Soc 1:4233-6. 2006....
- Applying genomics to organ transplantation medicine in both discovery and validation of biomarkersSunil Kurian
Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
Int Immunopharmacol 7:1948-60. 2007....
- The JigCell model builder: a spreadsheet interface for creating biochemical reaction network modelsMarc T Vass
Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 0106, USA
IEEE/ACM Trans Comput Biol Bioinform 3:155-64. 2006..All four paradigms had similar data entry times. The spreadsheet and scripting language approaches require significantly fewer screens to view the models than do the wizard or graphical layout approaches...
- Integration of metabolome data with metabolic networks reveals reporter reactionsTunahan Cakir
Department of Chemical Engineering, , Bebek, Istanbul, Turkey
Mol Syst Biol 2:50. 2006..Hereby, the reported approach represents an attempt to map different layers of regulation within metabolic networks through combination of metabolome and transcriptome data...
- Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysisVitaly A Selivanov
Departamento de Bioquimica i Biologia Molecular, University of Barcelona Barcelona 08028, Catalunya, Spain
Bioinformatics 22:2806-12. 2006..of isotopic isomer (isotopomer) accumulation in metabolites and reveal the underlying kinetic mechanisms of metabolism regulation...
- Functional stoichiometric analysis of metabolic networksR Urbanczik
Institute of Pharmacology, University of Bern, Switzerland
Bioinformatics 21:4176-80. 2005..Exhaustive descriptions of the metabolism can be obtained by computing the elementary vectors of this cone but, owing to a combinatorial explosion of the ..
- In silico techniques for the study and prediction of xenobiotic metabolism: a reviewS A Kulkarni
Safe Environments Programme, Health Canada, Ottawa, Ontario, Canada
Xenobiotica 35:955-73. 2005Knowledge about metabolism is very important to understand the health risks posed by chemicals...
- MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomicsIrena Spasic
School of Chemistry, Faraday Building, The University of Manchester, Manchester, M60 1QD, UK
BMC Bioinformatics 7:281. 2006..The metabolomic data produced need to be structured and annotated in a machine-usable form to facilitate the exploration of the hidden links between the genes and their functions...
- Review: on the analysis and interpretation of correlations in metabolomic dataRalf Steuer
University Potsdam, Insitute of Physics, Am Neuen Palais 10, Haus 19, 14469 Potsdam, Germany
Brief Bioinform 7:151-8. 2006A remarkable inherent feature of cellular metabolism is that the concentrations of a small but significant number of metabolites are strongly correlated when measurements of biological replicates are performed...
- Lipid mediator informatics-lipidomics: novel pathways in mapping resolutionCharles N Serhan
Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Thorn Building for Medical Research, 7th Floor, Brigham and Women s Hospital, Boston, MA 02115, USA
AAPS J 8:E284-97. 2006..Here, we review liquid chromatography tandem mass spectrometry-based lipidomic analyses to address bioactive lipid mediators in signaling pathways and the roles of lipid-derived mediators in resolution of inflammation...
- Computational tools for isotopically instationary 13C labeling experiments under metabolic steady state conditionsKatharina Nöh
Department of Simulation, Faculty 11 12, University of Siegen, D 57068 Siegen, Germany
Metab Eng 8:554-77. 2006..To explore the potential of the new approach all these tools are applied to the central metabolism of Escherichia coli...
- Hierarchy of metabolic compounds based on their synthesising capacityT Handorf
Department of Theoretical Biophysics, Institute of Biology, Humboldt University, Ivalidenstr 42, 10115 Berlin, Germany
Syst Biol (Stevenage) 153:359-63. 2006..In this way, it represents a new kind of map of metabolic networks, arranging the metabolic compounds according to their chemical capacity...
- Sizing up allometric scaling theoryVan M Savage
Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
PLoS Comput Biol 4:e1000171. 2008....
- The Edinburgh human metabolic network reconstruction and its functional analysisHongwu Ma
Computational Systems Biology, School of Informatics, The University of Edinburgh, Edinburgh, UK
Mol Syst Biol 3:135. 2007A better understanding of human metabolism and its relationship with diseases is an important task in human systems biology studies...
- Genomic Object Net: I. A platform for modelling and simulating biopathwaysMasao Nagasaki
Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
Appl Bioinformatics 2:181-4. 2003..Additionally, GON provides a tool to transform biopathway models in KEGG and BioCyc to the GON XML files for modelling and simulation. The tool avoids a lot of tedious work by users, enabling them to focus on the biological model...
- FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux mapsSteffen Klamt
Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, D 39106 Magdeburg, Germany
Bioinformatics 19:261-9. 2003..The need of a user-friendly platform for stoichiometric modeling of metabolic networks in silico is evident...
- Topological analysis of metabolic networks based on Petri net theoryIonela Zevedei-Oancea
Max Delbrueck Center for Molecular Medicine, Department of Bioinformatics Robert-Roessle-Str 10, 13092 Berlin-Buch, Germany
In Silico Biol 3:323-45. 2003..For example, the role of triose phosphate isomerase (TPI) in Trypanosoma brucei metabolism is evaluated by detecting siphons and traps...
- Stoichiometric design of metabolic networks: multifunctionality, clusters, optimization, weak and strong robustnessOliver Ebenhöh
Department of Theoretical Biophysics, Institute of Biology, Humboldt University, Invalidenstrasse 42, 10115 Berlin, Germany
Bull Math Biol 65:323-57. 2003..Under changing environmental conditions multifunctional networks prove to be optimal and will be selected...
- Dynamic simulation and metabolic re-design of a branched pathway using linlog kineticsDiana Visser
PURAC, P O Box 21, 4200 AA Gorinchem, The Netherlands
Metab Eng 5:164-76. 2003..Results show that the linlog approximation is able to describe the non-linear dynamics of this pathway very well for concentration changes up to a factor 20. Also the metabolic design equation was tested successfully...
- DRUG RESISTANCE AND PTERIDINE METABOLISM IN LEISHMANIAStephen Beverley; Fiscal Year: 2009..identified through the study of antifolate-resistant Leishmania parasites, which has lead us into studies of the metabolism of the unconjugated pteridine biopterin and the conjugated pteridine folate, and the development and application ..
- Vitamin B6 Effects on One-Carbon MetabolismJesse F Gregory; Fiscal Year: 2010..Thus, B6 nutrition is linked many vital cellular processes such as the synthesis of nucleotides and glutathione, metabolism of most amino acids, including sulfur amino acids, methylation processes, and gluconeogenesis...
- Pharmacogenetics of obesity and endocannabinergic modulation (POEM)Russell A Wilke; Fiscal Year: 2009..eCB/CB1 receptor signaling is involved in the regulation of food consumption and metabolism via multiple mechanisms: it regulates the rewarding properties of food via effects on central mesolimbic ..
- Pharmacogenetics of obesity and endocannabinergic modulation (POEM)Russell A Wilke; Fiscal Year: 2010..eCB/CB1 receptor signaling is involved in the regulation of food consumption and metabolism via multiple mechanisms: it regulates the rewarding properties of food via effects on central mesolimbic ..
- Dietary Methyl Score, Genomic DNA Methylation and Colorectal CancerEunyoung Cho; Fiscal Year: 2010One-carbon metabolism is a critical pathway in cancer epigenetics because it directs the methylation of DNA and RNA and is involved in DNA synthesis and repair. There is no good systemic marker of one-carbon metabolism status...
- Dietary Methyl Score, Genomic DNA Methylation and Colorectal CancerEunyoung Cho; Fiscal Year: 2009One-carbon metabolism is a critical pathway in cancer epigenetics because it directs the methylation of DNA and RNA and is involved in DNA synthesis and repair. There is no good systemic marker of one-carbon metabolism status...
- TOXICOLOGICAL SIGNIFICANCE OF ALKYLBENZENE METABOLISMWayne Backes; Fiscal Year: 2000..Benzene has been reported to be one of the most hazardous of the small aromatic hydrocarbons due to its metabolism by aromatic hydroxylation via reactive epoxide intermediates...
- Cellular Efflux and Metabolism of Protease InhibitorsAshim Mitra; Fiscal Year: 2004..of this study is to classify all anti-AIDS drugs, currently used clinically, under a new proposed Absorption-Metabolism Classification System (AMCS)...
- METABOLISM OF INTRAVENOUS LIPID EMULSIONSRichard Deckelbaum; Fiscal Year: 2007..is to characterize how specific types of triglycerides (TG) in intravenous (IV) lipid emulsions affect particle metabolism and impact upon the biological potentials of their component lipids...
- DRUG RESISTANCE AND PTERIDINE METABOLISM IN LEISHMANIAStephen M Beverley; Fiscal Year: 2010..identified through the study of antifolate-resistant Leishmania parasites, which has lead us into studies of the metabolism of the unconjugated pteridine biopterin and the conjugated pteridine folate, and the development and application ..
- Folate and S-adenosyimethionine in Methyl Group and One-carbon MetabolismConrad Wagner; Fiscal Year: 2009Regulation of methylation is intimately associated with folate metabolism. These two metabolic processes are connected by the enzyme, glycine N-methyltransferase, which is abundant in liver, exocrine pancreas and prostate as well as in ..
- Folate and S-adenosyimethionine in Methyl Group and One-carbon MetabolismConrad Wagner; Fiscal Year: 2010Regulation of methylation is intimately associated with folate metabolism. These two metabolic processes are connected by the enzyme, glycine N-methyltransferase, which is abundant in liver, exocrine pancreas and prostate as well as in ..
- REGULATION OF LIPID METABOLISM IN BACTERIACharles O Rock; Fiscal Year: 2011..The long term goal of the research program is to understand the biochemical and genetic regulation of lipid metabolism and membrane homeostasis in bacteria...
- Biomarkers for Arsenic Toxicity: Genetics, Epigenetics and FolateMARY VELESCA GAMBLE; Fiscal Year: 2011..As (InAs) is methylated to methylarsonic (MMA) and dimethylarsinic (DMA) acids via folate- dependent one-carbon metabolism. A reduced capacity to fully methylate As to DMA is associated with reduced urinary elimination of As...
- NEUROPEPTIDE Y--EFFECTS ON ENERGY METABOLISMCharles Billington; Fiscal Year: 1993This proposal focuses on the possibility that a central controller of energy metabolism might exist, a controller which influences not only food intake but provides complementary regulation of energy metabolism as well...
- Biomarkers for Arsenic Toxicity: Genetics, Epigenetics and FolateMARY VELESCA GAMBLE; Fiscal Year: 2010..As (InAs) is methylated to methylarsonic (MMA) and dimethylarsinic (DMA) acids via folate- dependent one-carbon metabolism. A reduced capacity to fully methylate As to DMA is associated with reduced urinary elimination of As...
- Homocysteine, Adiponectin, and Alcoholic Liver DiseaseZhenyuan Song; Fiscal Year: 2010..an adipokine predominantly secreted by adipose tissue, plays a central role in the regulation of energy metabolism, lipid and carbohydrate metabolism...
- Homocysteine, Adiponectin, and Alcoholic Liver DiseaseZhenyuan Song; Fiscal Year: 2009..an adipokine predominantly secreted by adipose tissue, plays a central role in the regulation of energy metabolism, lipid and carbohydrate metabolism...
- Perilipin and cellular triacylglycerol metabolismDawn L Brasaemle; Fiscal Year: 2010..Dysregulation of adipose TAG metabolism in obese individuals leads to release of excess fatty acids into circulation, which contributes to the ..
- Assessment of Nicotine Metabolism Among Underserved Pregnant Women from NE SCRIPTDonna Parker; Fiscal Year: 2007Assessment of Nicotine Metabolism Among Underserved Pregnant Women from NE SCRIPT Principal Investigator: Parker, Donna R...
- ATHEROSCLEROSIS AND PERIPHERAL APOPROTEIN E SYNTHESISDavid Williams; Fiscal Year: 1993..Apo E plays an important role in cholesterol metabolism by virtue of its interaction with cell surface receptors...
- A Prospective Study of Colorectal Cancer: One-Carbon Metabolism and InflammationCornelia Ulrich; Fiscal Year: 2009..of genetic variability and biomarkers in two specific pathways - inflammation and folate-mediated one-carbon metabolism - in colorectal cancer etiology within a large cohort of women...
- Diesel, Allergens and Gene Interaction and Child AtopyGrace LeMasters; Fiscal Year: 2009..This revision also serves to create new research objectives to explore the associations of nicotine metabolism and oxidative stress genetics outside of the scope of the parent grant, and will be completed in less than one ..
- PUBERTAL CHANGES IN BONE MINERAL METABOLISMSteven Abrams; Fiscal Year: 2000..accumulation is maximal during puberty, it is essential to understand the factors associated with mineral metabolism during this period of time...
- Nicotine Metabolism and the Development of Addiction in Adolescent Light SmokersMark Rubinstein; Fiscal Year: 2009..have shown that adult smokers with the presence of certain genetic markers associated with slower nicotine metabolism smoke fewer cigarettes and are more likely to quit...
- Quantitation of Tocopherol Metabolism in HumansAndrew Clifford; Fiscal Year: 2009..Still, more research on vitamin E is needed to fully understand its metabolism and function(s). The IOM/NAS has listed key research recommendations for vitamin E...
- The Use of 2-Deoxyglucose in Head and Neck Cancer TherapyDOUGLAS ROBERT SPITZ; Fiscal Year: 2011Cancer cells in general, relative to normal cells, demonstrate increased glucose metabolism but the mechanism for this is unknown...
- The Use of 2-Deoxyglucose in Head and Neck Cancer TherapyDOUGLAS ROBERT SPITZ; Fiscal Year: 2010Cancer cells in general, relative to normal cells, demonstrate increased glucose metabolism but the mechanism for this is unknown...