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FUNDAMENTALS OF SYSTEMS BIOLOGY

FROM SYNTHETIC CIRCUITS TO WHOLE-CELL MODELS

9781420084108 ::  FUNDAMENTALS OF SYSTEMS BIOLOGY
ISBN:

9781420084108

EditorialTAYLOR & FRANCIS GROUP
Edicion:
Páginas:367
Idioma:INGLES
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PLAZO DE ENTREGA 20 DIAS

FOR DECADES BIOLOGY HAS FOCUSED ON DECODING CELLULAR PROCESSES ONE GENE AT A TIME, BUT MANY OF THE MOST PRESSING BIOLOGICAL QUESTIONS, AS WELL AS DISEASES SUCH AS CANCER AND HEART DISEASE, ARE RELATED TO COMPLEX SYSTEMS INVOLVING THE INTERACTION OF HUNDREDS, OR EVEN THOUSANDS, OF GENE PRODUCTS AND OTHER FACTORS. HOW DO WE BEGIN TO UNDERSTAND THIS COMPLEXITY? FUNDAMENTALS OF SYSTEMS BIOLOGY: FROM SYNTHETIC CIRCUITS TO WHOLE-CELL MODELS INTRODUCES STUDENTS TO METHODS THEY CAN USE TO TACKLE COMPLEX SYSTEMS HEAD-ON, CAREFULLY WALKING THEM THROUGH STUDIES THAT COMPRISE THE FOUNDATION AND FRONTIER OF SYSTEMS BIOLOGY. THE FIRST SECTION OF THE BOOK FOCUSES ON BRINGING STUDENTS QUICKLY UP TO SPEED WITH A VARIETY OF MODELING METHODS IN THE CONTEXT OF A SYNTHETIC BIOLOGICAL CIRCUIT. THIS INNOVATIVE APPROACH BUILDS INTUITION ABOUT THE STRENGTHS AND WEAKNESSES OF EACH METHOD AND BECOMES CRITICAL IN THE BOOK’S SECOND HALF, WHERE MUCH MORE COMPLICATED NETWORK MODELS ARE ADDRESSED—INCLUDING TRANSCRIPTIONAL, SIGNALING, METABOLIC, AND EVEN INTEGRATED MULTI-NETWORK MODELS.THE APPROACH MAKES THE WORK MUCH MORE ACCESSIBLE TO NOVICES (UNDERGRADUATES, MEDICAL STUDENTS, AND BIOLOGISTS NEW TO MATHEMATICAL MODELING) WHILE STILL HAVING MUCH TO OFFER EXPERIENCED MODELERS--WHETHER THEIR INTERESTS ARE MICROBES, ORGANS, WHOLE ORGANISMS, DISEASES, SYNTHETIC BIOLOGY, OR JUST ABOUT ANY FIELD THAT INVESTIGATES LIVING SYSTEMS.

BUILDING INTUITIONVARIATIONS ON A THEME OF CONTROLLEARNING OBJECTIVESVARIATIONSAUTOREGULATIONOUR THEME: A TYPICAL NEGATIVE AUTOREGULATORY CIRCUITSUMMARYRECOMMENDED READINGVARIATION: BOOLEAN REPRESENTATIONSLEARNING OBJECTIVESBOOLEAN LOGIC AND RULESSTATE MATRICESSTATE TRANSITIONSDYNAMICSTIMESCALESADVANTAGES AND DISADVANTAGES OF BOOLEAN ANALYSISSUMMARYRECOMMENDED READINGPROBLEMSVARIATION: ANALYTICAL SOLUTIONS OF ORDINARY DIFFERENTIAL EQUATIONSLEARNING OBJECTIVESSYNTHETIC BIOLOGICAL CIRCUITSFROM COMPARTMENT MODELS TO ODESSPECIFYING AND SIMPLIFYING ODES WITH ASSUMPTIONSTHE STEADY-STATE ASSUMPTIONSOLVING THE SYSTEM WITHOUT FEEDBACK: REMOVAL OF ACTIVATORKEY PROPERTIES OF THE SYSTEM DYNAMICSSOLVING THE SYSTEM WITHOUT FEEDBACK: ADDITION OF ACTIVATORCOMPARISON OF MODELING TO EXPERIMENTAL MEASUREMENTSADDITION OF AUTOREGULATORY FEEDBACKCOMPARISON OF THE REGULATED AND UNREGULATED SYSTEMSSUMMARYRECOMMENDED READINGPROBLEMSVARIATION: GRAPHICAL ANALYSISLEARNING OBJECTIVESREVISITING THE PROTEIN SYNTHESIS ODESPLOTTING X VERSUS DX/DTFIXED POINTS AND VECTOR FIELDSFROM VECTOR FIELDS TO TIME-COURSE PLOTSNONLINEARITYBIFURCATION ANALYSISADDING FEEDBACKTWO-EQUATION SYSTEMSSUMMARYRECOMMENDED READINGPROBLEMSVARIATION: NUMERICAL INTEGRATIONLEARNING OBJECTIVESTHE EULER METHODACCURACY AND ERRORTHE MIDPOINT METHODTHE RUNGE-KUTTA METHODSUMMARYRECOMMENDED READINGPROBLEMSVARIATION: STOCHASTIC SIMULATIONLEARNING OBJECTIVESSINGLE CELLS AND LOW MOLECULE NUMBERSSTOCHASTIC SIMULATIONSTHE PROBABILITY THAT TWO MOLECULES INTERACT AND REACT IN A GIVEN TIME INTERVALTHE PROBABILITY OF A GIVEN MOLECULAR REACTION OCCURRING OVER TIMETHE RELATIONSHIP BETWEEN KINETIC AND STOCHASTIC CONSTANTSGILLESPIE'S STOCHASTIC SIMULATION ALGORITHMSTOCHASTIC SIMULATION OF UNREGULATED GENE EXPRESSIONSTOCHASTIC SIMULATIONS VERSUS OTHER MODELING APPROACHESSUMMARYRECOMMENDED READINGPROBLEMSFROM CIRCUITS TO NETWORKSTRANSCRIPTIONAL REGULATIONLEARNING OBJECTIVESTRANSCRIPTIONAL REGULATION AND COMPLEXITYMORE COMPLEX TRANSCRIPTIONAL CIRCUITSTHE TRANSCRIPTIONAL REGULATORY FEED-FORWARD MOTIFBOOLEAN ANALYSIS OF THE MOST COMMON INTERNALLY CONSISTENT FEED-FORWARD MOTIF IDENTIFIED IN E. COLIAN ODE-BASED APPROACH TO ANALYZING THE COHERENT FEED-FORWARD LOOPROBUSTNESS OF THE COHERENT FEED-FORWARD LOOPEXPERIMENTAL INTERROGATION OF THE COHERENT FEED-FORWARD LOOPCHANGING THE INTERACTION FROM AN AND TO AN OR RELATIONSHIPTHE SINGLE-INPUT MODULEJUST-IN-TIME GENE EXPRESSIONGENERALIZATION OF THE FEED-FORWARD LOOPAN EXAMPLE OF A MULTIGENE FEED-FORWARD LOOP: FLAGELLAR BIOSYNTHESIS IN E. COLIOTHER REGULATORY MOTIFSSUMMARYRECOMMENDED READINGPROBLEMSSIGNAL TRANSDUCTIONLEARNING OBJECTIVESRECEPTOR-LIGAND BINDING TO FORM A COMPLEXAPPLICATION TO REAL RECEPTOR-LIGAND PAIRSFORMATION OF LARGER COMPLEXESPROTEIN LOCALIZATIONTHE NF-KB SIGNALING NETWORKA DETAILED MODEL OF NF-KB ACTIVITYALTERNATIVE REPRESENTATIONS FOR THE SAME PROCESSSPECIFYING PARAMETER VALUES FROM DATABOUNDING PARAMETER VALUESMODEL SENSITIVITY TO PARAMETER VALUESREDUCING COMPLEXITY BY ELIMINATING PARAMETERSPARAMETER INTERACTIONSSUMMARYRECOMMENDED READINGPROBLEMSMETABOLISMLEARNING OBJECTIVESCELLULAR METABOLISMMETABOLIC REACTIONSCOMPARTMENT MODELS OF METABOLITE CONCENTRATIONTHE MICHAELIS-MENTEN EQUATION FOR ENZYME KINETICSDETERMINING KINETIC PARAMETERS FOR THE MICHAELIS-MENTEN SYSTEMINCORPORATING ENZYME INHIBITORY EFFECTSFLUX BALANCE ANALYSISSTEADY-STATE ASSUMPTIONAND EXCHANGE FLUXESSOLUTION SPACESTHE OBJECTIVE FUNCTIONDEFINING THE OPTIMIZATION PROBLEMSOLVING FBA PROBLEMS USING MATLABAPPLICATIONS OF FBA TO LARGE-SCALE METABOLIC MODELSUSING FBA FOR METABOLIC ENGINEERINGSUMMARYRECOMMENDED READINGPROBLEMSINTEGRATED MODELSLEARNING OBJECTIVESDYNAMIC FBA: EXTERNAL VERSUS INTERNAL CONCENTRATIONSENVIRONMENTAL CONSTRAINTSINTEGRATION OF FBA SIMULATIONS OVER TIMECOMPARING DYNAMIC FBA TO EXPERIMENTAL DATAFBA AND TRANSCRIPTIONAL REGULATIONTRANSCRIPTIONAL REGULATORY CONSTRAINTSREGULATORY FBA: METHODREGULATORY FBA: APPLICATIONTOWARD WHOLE-CELL MODELINGSUMMARYRECOMMENDED READINGPROBLEMSGLOSSARY

BIOLOGIA
INGENIERIA ELECTRONICA
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