Herbert M Sauro: search on Z-Library

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1

A Model for p53 Dynamics Triggered by DNA Damage

Chickarmane, Vijay, Ray, Animesh, Sauro, Herbert M., Nadim, Ali

Journal:

SIAM Journal on Applied Dynamical Systems

Year:

2007

Language:

english

File:

PDF, 434 KB

english, 2007

2

Introduction to the Special Issue on Computational Synthetic Biology

Myers, Chris J., Sauro, Herbert, Wipat, Anil

Journal:

ACM Journal on Emerging Technologies in Computing Systems

Year:

2014

Language:

english

File:

PDF, 60 KB

english, 2014

3

Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars

Cai, Yizhi, Lux, Matthew W., Adam, Laura, Peccoud, Jean, Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 592 KB

english, 2009

4

Preliminary Studies on the In Silico Evolution of Biochemical Networks

Anastasia Deckard, Herbert M Sauro

Journal:

Year:

2004

Language:

english

File:

PDF, 289 KB

english, 2004

5

Moiety-conserved cycles and metabolic control analysis: problems in sequestration and metabolic channelling

Herbert M. Sauro

Journal:

Year:

1994

Language:

english

File:

PDF, 1.14 MB

english, 1994

6

SCAMP: A metabolic simulator and control analysis program

Herbert M. Sauro, David A. Fell

Journal:

Mathematical and Computer Modelling

Year:

1991

Language:

english

File:

PDF, 1.13 MB

english, 1991

7

Conservation analysis in biochemical networks: computational issues for software writers

Herbert M. Sauro, Brian Ingalls

Journal:

Biophysical Chemistry

Year:

2004

Language:

english

File:

PDF, 396 KB

english, 2004

8

Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation

Vijay Chickarmane, Boris N. Kholodenko, Herbert M. Sauro

Journal:

Journal of Theoretical Biology

Year:

2007

Language:

english

File:

PDF, 312 KB

english, 2007

9

Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories

Brian P. Ingalls, Herbert M. Sauro

Journal:

Journal of Theoretical Biology

Year:

2003

Language:

english

File:

PDF, 255 KB

english, 2003

10

Control analysis of time-dependent metabolic systems

Luis Acerenza, Herbert M. Sauro, Henrik Kacser

Journal:

Journal of Theoretical Biology

Year:

1989

Language:

english

File:

PDF, 1.08 MB

english, 1989

11

In vitrocontrol analysis of an enzyme system: Experimental and analytical developments

Herbert M. Sauro, John Barrett

Journal:

Molecular and Cellular Biochemistry

Year:

1995

Language:

english

File:

PDF, 849 KB

english, 1995

12

Design and implementation of three incoherent feed-forward motif based biological concentration sensors

Robert Entus, Brian Aufderheide, Herbert M. Sauro

Journal:

Systems and Synthetic Biology

Year:

2007

Language:

english

File:

PDF, 549 KB

english, 2007

13

Book reviews

Dave Edwards, Lisa C. Ranford-Cartwright, Elizabeth A. Shephard, Herbert Sauro

Journal:

Molecular Biotechnology

Year:

2001

Language:

english

File:

PDF, 77 KB

english, 2001

14

Essential information for synthetic DNA sequences

Peccoud, Jean, Anderson, J Christopher, Chandran, Deepak, Densmore, Douglas, Galdzicki, Michal, Lux, Matthew W, Rodriguez, Cesar A, Stan, Guy-Bart, Sauro, Herbert M

Journal:

Nature Biotechnology

Year:

2011

Language:

english

File:

PDF, 171 KB

english, 2011

15

Quantitative analysis of signaling networks

Herbert M. Sauro, Boris N. Kholodenko

Journal:

Progress in Biophysics and Molecular Biology

Year:

2004

Language:

english

File:

PDF, 1.11 MB

english, 2004

16

Computational tools for metabolic engineering

Wilbert B. Copeland, Bryan A. Bartley, Deepak Chandran, Michal Galdzicki, Kyung H. Kim, Sean C. Sleight, Costas D. Maranas, Herbert M. Sauro

Journal:

Metabolic Engineering

Year:

2012

Language:

english

File:

PDF, 332 KB

english, 2012

17

Metabolic control and its analysis : Additional relationships between elasticities and control coefficients

David A. FELL, Herbert M. SAURO

Journal:

Year:

1985

Language:

english

File:

PDF, 740 KB

english, 1985

18

Metabolic control and its analysis : Extensions to the theory and matrix method

Herbert M. SAURO, J. Rankin SMALL, David A. FELL

Journal:

Year:

1987

Language:

english

File:

PDF, 800 KB

english, 1987

19

Enzyme-enzyme interactions and control analysis : 2. The case of non-independence: heterologous associations

Herbert M. SAURO, Henrik KACSER

Journal:

Year:

1990

Language:

english

File:

PDF, 797 KB

english, 1990

20

Enzyme-enzyme interactions and control analysis : 1. The case of non-additivity: monomer-oligomer associations

Henrik KACSER, Herbert M SAURO, Luis ACERENZA

Journal:

Year:

1990

Language:

english

File:

PDF, 1.13 MB

english, 1990

21

Metabolic control analysis : The effects of high enzyme concentrations

David A. FELL, Herbert M. SAURO

Journal:

Year:

1990

Language:

english

File:

PDF, 549 KB

english, 1990

22

Control by Enzymes, Coenzymes and Conserved Moieties : A Generalisation of the Connectivity Theorem of Metabolic Control Analysis

Boris N. Kholodenko, Herbert M. Sauro, Hans V. Westerhoff

Journal:

Year:

1994

Language:

english

File:

PDF, 836 KB

english, 1994

23

Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration

Sauro, Herbert M., Hucka, Michael, Finney, Andrew, Wellock, Cameron, Bolouri, Hamid, Doyle, John, Kitano, Hiroaki

Journal:

Omics A Journal of Integrative Biology

Year:

2003

Language:

english

File:

PDF, 523 KB

english, 2003

24

Sensitivity summation theorems for stochastic biochemical reaction systems

Kyung Hyuk Kim, Herbert M. Sauro

Journal:

Mathematical Biosciences

Year:

2010

Language:

english

File:

PDF, 617 KB

english, 2010

25

Measuring Retroactivity from Noise in Gene Regulatory Networks

Kim, Kyung Hyuk, Sauro, Herbert M.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 705 KB

english, 2011

26

Synthetic biology: It's an analog world

Sauro, Herbert M., Kim, Kyung

Journal:

Year:

2013

Language:

english

File:

PDF, 246 KB

english, 2013

27

Flow-Based Cytometric Analysis of Cell Cycle via Simulated Cell Populations

Brown, M. Rowan, Summers, Huw D., Rees, Paul, Smith, Paul J., Chappell, Sally C., Errington, Rachel J., Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 3.54 MB

english, 2010

28

Randomized BioBrick Assembly: A Novel DNA Assembly Method for Randomizing and Optimizing Genetic Circuits and Metabolic Pathways

Sleight, Sean C., Sauro, Herbert M.

Journal:

ACS Synthetic Biology

Year:

2013

Language:

english

File:

PDF, 1.61 MB

english, 2013

29

TinkerCell: modular CAD tool for synthetic biology

Deepak Chandran, Frank T Bergmann, Herbert M Sauro

Journal:

Journal of Biological Engineering

Year:

2009

Language:

english

File:

PDF, 2.68 MB

english, 2009

30

Fan-out in gene regulatory networks

Kyung H Kim, Herbert M Sauro

Journal:

Journal of Biological Engineering

Year:

2010

Language:

english

File:

PDF, 2.18 MB

english, 2010

31

Computational Systems Biology || Standards, Platforms, and Applications

Sauro, Herbert M.

Year:

2006

Language:

english

File:

PDF, 395 KB

english, 2006

32

Visualization of Evolutionary Stability Dynamics and Competitive Fitness of Escherichia coli Engineered with Randomized Multigene Circuits

Sleight, Sean C., Sauro, Herbert M.

Journal:

ACS Synthetic Biology

Year:

2013

Language:

english

File:

PDF, 3.09 MB

english, 2013

33

Proposed Data Model for the Next Version of the Synthetic Biology Open Language

Roehner, Nicholas, Oberortner, Ernst, Pocock, Matthew, Beal, Jacob, Clancy, Kevin, Madsen, Curtis, Misirli, Goksel, Wipat, Anil, Sauro, Herbert, Myers, Chris J.

Journal:

ACS Synthetic Biology

Year:

2015

Language:

english

File:

PDF, 727 KB

english, 2015

34

Hierarchical Modeling for Synthetic Biology

Chandran, Deepak, Sauro, Herbert M.

Journal:

ACS Synthetic Biology

Year:

2012

Language:

english

File:

PDF, 3.25 MB

english, 2012

35

[IEEE 2006 Winter Simulation Conference - Monterey, CA, USA (2006.12.3-2006.12.6)] Proceedings of the 2006 Winter Simulation Conference - Complexity Reduction of Biochemical Networks

Vallabhajosyula, Ravishankar, Sauro, Herbert

Year:

2006

Language:

english

File:

PDF, 167 KB

english, 2006

36

Nonlinear biochemical signal processing via noise propagation

Kim, Kyung Hyuk, Qian, Hong, Sauro, Herbert M.

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 771 KB

english, 2013

37

Computer-aided design of biological circuits using tinkercell

Chandran, Deepak, Bergmann, Frank T., Sauro, Herbert M.

Journal:

Bioengineered Bugs

Year:

2010

Language:

english

File:

PDF, 2.04 MB

english, 2010

38

[IEEE 2006 Winter Simulation Conference - Monterey, CA, USA (2006.12.3-2006.12.6)] Proceedings of the 2006 Winter Simulation Conference - Innovation in Software for Systems Biology. Is There Any?

Year:

2006

Language:

english

File:

PDF, 38 KB

english, 2006

39

[IEEE 2006 Winter Simulation Conference - Monterey, CA, USA (2006.12.3-2006.12.6)] Proceedings of the 2006 Winter Simulation Conference - SBW - A Modular Framework for Systems Biology

Bergmann, Frank, Sauro, Herbert

Year:

2006

Language:

english

File:

PDF, 1.15 MB

english, 2006

40

[IEEE 2006 Winter Simulation Conference - Monterey, CA, USA (2006.12.3-2006.12.6)] Proceedings of the 2006 Winter Simulation Conference - Challenges for Modeling and Simulation Methods in Systems Biology

Sauro, Herbert, Harel, David, Kwiatkowska, Marta, Shaffer, Clifford, Uhrmacher, Adelinde, Hucka, Michael, Mendes, Pedro, Stromback, Lena, Tyson, John

Year:

2006

Language:

english

File:

PDF, 164 KB

english, 2006

41

[IEEE 2012 IEEE 51st Annual Conference on Decision and Control (CDC) - Maui, HI, USA (2012.12.10-2012.12.13)] 2012 IEEE 51st IEEE Conference on Decision and Control (CDC) - Measuring the degree of modularity in gene regulatory networks from the relaxation of finite perturbations

Kim, Kyung Hyuk, Sauro, Herbert M.

Year:

2012

Language:

english

File:

PDF, 536 KB

english, 2012

42

Elasticities in Metabolic Control Analysis: algebraic derivation of simplified expressions

Woods, John H., Sauro, Herbert M.

Journal:

Year:

1997

Language:

english

File:

PDF, 598 KB

english, 1997

43

Computational Tools for Modeling Protein Networks

Bergmann, Frank, Vallabhajosyula, Ravishankar, Sauro, Herbert

Journal:

Current Proteomics

Year:

2006

Language:

english

File:

PDF, 729 KB

english, 2006

44

In search of noise-induced bimodality

Kim, Kyung, Sauro, Herbert M

Journal:

Year:

2012

Language:

english

File:

PDF, 299 KB

english, 2012

45

Context-Specific Metabolic Networks Are Consistent with Experiments

Becker, Scott A., Palsson, Bernhard O., Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 513 KB

english, 2008

46

Modeling the Effects of Cell Cycle M-phase Transcriptional Inhibition on Circadian Oscillation

Kang, Bin, Li, Yuan-Yuan, Chang, Xiao, Liu, Lei, Li, Yi-Xue, Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 508 KB

english, 2008

47

Global Entrainment of Transcriptional Systems to Periodic Inputs

Russo, Giovanni, di Bernardo, Mario, Sontag, Eduardo D., Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.64 MB

english, 2010

48

libRoadRunner: a high performance SBML simulation and analysis library: Table 1.

Somogyi, Endre T., Bouteiller, Jean-Marie, Glazier, James A., König, Matthias, Medley, J. Kyle, Swat, Maciej H., Sauro, Herbert M.

Journal:

Year:

2015

Language:

english

File:

PDF, 222 KB

english, 2015

49

Evolution of Evolvability in Gene Regulatory Networks

Crombach, Anton, Hogeweg, Paulien, Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 724 KB

english, 2008

50

Biosynthetic Potentials of Metabolites and Their Hierarchical Organization

Matthäus, Franziska, Salazar, Carlos, Ebenhöh, Oliver, Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 275 KB

english, 2008