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51

A Hidden Feedback in Signaling Cascades Is Revealed

Ventura, Alejandra C., Sepulchre, Jacques-A., Merajver, Sofía D., Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 587 KB

english, 2008

52

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species

Freilich, Shiri, Kreimer, Anat, Borenstein, Elhanan, Gophna, Uri, Sharan, Roded, Ruppin, Eytan, Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 630 KB

english, 2010

53

Rule-Based Cell Systems Model of Aging using Feedback Loop Motifs Mediated by Stress Responses

Kriete, Andres, Bosl, William J., Booker, Glenn, Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.21 MB

english, 2010

54

Predicting the Distribution of Spiral Waves from Cell Properties in a Developmental-Path Model of Dictyostelium Pattern Formation

Geberth, Daniel, Hütt, Marc-Thorsten, Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 744 KB

english, 2009

55

Memory Switches in Chemical Reaction Space

Ramakrishnan, Naren, Bhalla, Upinder S., Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 496 KB

english, 2008

56

Evolution under Fluctuating Environments Explains Observed Robustness in Metabolic Networks

Soyer, Orkun S., Pfeiffer, Thomas, Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 452 KB

english, 2010

57

A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast

Kundaje, Anshul, Xin, Xiantong, Lan, Changgui, Lianoglou, Steve, Zhou, Mei, Zhang, Li, Leslie, Christina, Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 1.54 MB

english, 2008

58

Positional Information Generated by Spatially Distributed Signaling Cascades

Muñoz-García, Javier, Neufeld, Zoltan, Kholodenko, Boris N., Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.02 MB

english, 2009

59

Detailed Simulations of Cell Biology with Smoldyn 2.1

Andrews, Steven S., Addy, Nathan J., Brent, Roger, Arkin, Adam P., Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.30 MB

english, 2010

60

A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189

Suthers, Patrick F., Dasika, Madhukar S., Kumar, Vinay Satish, Denisov, Gennady, Glass, John I., Maranas, Costas D., Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 875 KB

english, 2009

61

Transcriptional Dynamics of the Embryonic Stem Cell Switch

Chickarmane, Vijay, Troein, Carl, Nuber, Ulrike A., Sauro, Herbert M., Peterson, Carsten

Journal:

PLoS Computational Biology

Year:

2006

Language:

english

File:

PDF, 1014 KB

english, 2006

62

Noise Management by Molecular Networks

Bruggeman, Frank J., Blüthgen, Nils, Westerhoff, Hans V., Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 328 KB

english, 2009

63

Spontaneous Reaction Silencing in Metabolic Optimization

Nishikawa, Takashi, Gulbahce, Natali, Motter, Adilson E., Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 510 KB

english, 2008

64

A Stochastic Model for Microtubule Motors Describes the In Vivo Cytoplasmic Transport of Human Adenovirus

Gazzola, Mattia, Burckhardt, Christoph J., Bayati, Basil, Engelke, Martin, Greber, Urs F., Koumoutsakos, Petros, Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 290 KB

english, 2009

65

A Reappraisal of How to Build Modular, Reusable Models of Biological Systems

Neal, Maxwell L., Cooling, Michael T., Smith, Lucian P., Thompson, Christopher T., Sauro, Herbert M., Carlson, Brian E., Cook, Daniel L., Gennari, John H., Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 438 KB

english, 2014

66

Minimum Criteria for DNA Damage-Induced Phase Advances in Circadian Rhythms

Hong, Christian I., Zámborszky, Judit, Csikász-Nagy, Attila, Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 277 KB

english, 2009

67

Computational Complementation: A Modelling Approach to Study Signalling Mechanisms during Legume Autoregulation of Nodulation

Han, Liqi, Hanan, Jim, Gresshoff, Peter M., Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 631 KB

english, 2010

68

Automatic Assignment of EC Numbers

Egelhofer, Volker, Schomburg, Ida, Schomburg, Dietmar, Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 588 KB

english, 2010

69

Spatial Simulations of Myxobacterial Development

Holmes, Antony B., Kalvala, Sara, Whitworth, David E., Sauro, Herbert M.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.15 MB

english, 2010

70

Systems Biomedicine || Software Tools for Systems Biology

Sauro, Herbert M.

Year:

2010

Language:

english

File:

PDF, 932 KB

english, 2010

71

[ACM Press the International Conference - San Jose, California (2012.11.05-2012.11.08)] Proceedings of the International Conference on Computer-Aided Design - ICCAD '12 - Modeling and design automation of biological circuits and systems

Miskov-Zivanov, Natasa, Faeder, James R., Myers, Chris J., Sauro, Herbert M.

Year:

2012

Language:

english

File:

PDF, 345 KB

english, 2012

72

Controlling E. coli Gene Expression Noise

Kim, Kyung Hyuk, Choi, Kiri, Bartley, Bryan, Sauro, Herbert M.

Journal:

IEEE Transactions on Biomedical Circuits and Systems

Year:

2015

Language:

english

File:

PDF, 1.65 MB

english, 2015

73

[IEEE 2006 International Conference of the IEEE Engineering in Medicine and Biology Society - New York, NY, USA (2006.08.30-2006.09.3)] 2006 International Conference of the IEEE Engineering in Medicine and Biology Society - Simulation of biochemical networks - Cellular networks as dynamic control systems

Sauro, Herbert M.

Year:

2006

Language:

english

File:

PDF, 202 KB

english, 2006

74

Data Integration and Mining for Synthetic Biology Design

Misirli, Goksel, Hallinan, Jennifer, Pocock, Matthew, Lord, Phillip, McLaughlin, James Alastair, Sauro, Herbert, Wipat, Anil

Journal:

ACS Synthetic Biology

Year:

2016

Language:

english

File:

PDF, 1002 KB

english, 2016

75

The Computational Versatility of Proteomic Signaling Networks

Journal:

Current Proteomics

Year:

2004

Language:

english

File:

PDF, 302 KB

english, 2004

76

Non-equilibrium/equilibrium reactions: which controls?

FELL, DAVID A., SAURO, HERBERT M.

Journal:

Biochemical Society Transactions

Year:

1986

Language:

english

File:

PDF, 200 KB

english, 1986

77

Substrate cycles: do they really cause amplification?

FELL, DAVID A., SAURO, HERBERT M.

Journal:

Biochemical Society Transactions

Year:

1985

Language:

english

File:

PDF, 191 KB

english, 1985

78

The role of co-operativity in metabolism

SAURO, HERBERT M., FELL, DAVID A.

Journal:

Biochemical Society Transactions

Year:

1987

Language:

english

File:

PDF, 242 KB

english, 1987

79

phraSED-ML: A paraphrased, human-readable adaptation of SED-ML

Choi, Kiri, Smith, Lucian P., Medley, J. Kyle, Sauro, Herbert M.

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2016

Language:

english

File:

PDF, 732 KB

english, 2016

80

Synthetic biology: How best to build a cell.

Collins, James J, Maxon, Mary, Ellington, Andy, Fussenegger, Martin, Weiss, Ron, Sauro, Herbert

Journal:

Year:

2014

Language:

english

File:

PDF, 2.66 MB

english, 2014

81

A Visual Language for Protein Design

Cox, Robert Sidney, McLaughlin, James Alastair, Grünberg, Raik, Beal, Jacob, Wipat, Anil, Sauro, Herbert M.

Journal:

ACS Synthetic Biology

Year:

2017

Language:

english

File:

PDF, 392 KB

english, 2017

82

Control and regulation of pathways via negative feedback

Sauro, Herbert M.

Journal:

Journal of The Royal Society Interface

Year:

2017

Language:

english

File:

PDF, 665 KB

english, 2017

83

Synthetic biology: Enter the living machine

Journal:

Year:

2017

Language:

english

File:

PDF, 320 KB

english, 2017

84

Synthetic Biology: Engineering Living Systems from Biophysical Principles

Bartley, Bryan A., Kim, Kyung, Medley, J. Kyle, Sauro, Herbert M.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 1.92 MB

english, 2017

85

Modularity defined

Sauro, Herbert M

Journal:

Molecular Systems Biology

Year:

2008

Language:

english

File:

PDF, 83 KB

english, 2008

86

Putting the “Control” in Metabolic Control Analysis

Rao, Christopher V., Sauro, Herbert M., Arkin, Adam P.

Journal:

IFAC Proceedings Volumes

Year:

2004

Language:

english

File:

PDF, 6.72 MB

english, 2004

87

A portable structural analysis library for reaction networks

Bedaso, Yosef, Bergmann, Frank T., Choi, Kiri, Medley, Kyle, Sauro, Herbert M.

Journal:

Year:

2018

Language:

english

File:

PDF, 835 KB

english, 2018

88

Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation

Villaverde, Alejandro F., Banga, Julio R., Sauro, Herbert

Journal:

PLoS Computational Biology

Year:

2017

Language:

english

File:

PDF, 2.47 MB

english, 2017

89

Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology

Medley, J. Kyle, Choi, Kiri, König, Matthias, Smith, Lucian, Gu, Stanley, Hellerstein, Joseph, Sealfon, Stuart C., Sauro, Herbert M., Prlic, Andreas

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.85 MB

english, 2018

90

Tellurium: An extensible python-based modeling environment for systems and synthetic biology

Choi, Kiri, Medley, J. Kyle, König, Matthias, Stocking, Kaylene, Smith, Lucian, Gu, Stanley, Sauro, Herbert M.

Journal:

Year:

2018

Language:

english

File:

PDF, 1.19 MB

english, 2018

91

OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli

Hädicke, Oliver, von Kamp, Axel, Aydogan, Timur, Klamt, Steffen, Sauro, Herbert

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.47 MB

english, 2018

92

pySBOL: A Python Package for Genetic Design Automation and Standardization

Bartley, Bryan, Choi, Kiri, Samineni, Meher, Zundel, Zach, Nguyen, Tramy, Myers, Chris J., Sauro, Herbert

Journal:

ACS Synthetic Biology

Year:

2018

Language:

english

File:

PDF, 571 KB

english, 2018

93

Special Issue: Methods in Computational Biology

Carlson, Ross P., Sauro, Herbert M.

Journal:

Year:

2019

Language:

english

File:

PDF, 132 KB

english, 2019

94

Special Issue: Methods in Computational Biology

Carlson, Ross P., Sauro, Herbert M.

Journal:

Year:

2019

File:

PDF, 132 KB

2019

95

Application of Parameter Optimization to Search for Oscillatory Mass-Action Networks Using Python

Porubsky, Veronica, Sauro, Herbert

Journal:

Year:

2019

Language:

english

File:

PDF, 514 KB

english, 2019

96

SBML Reaction Finder: Retrieve and extract specific reactions from the BioModels database

Neal, Maxwell, Sauro, Herbert

Journal:

Bioentrepreneur

Year:

2012

Language:

english

File:

PDF, 197 KB

english, 2012

97

PyBioNetFit and the Biological Property Specification Language

Mitra, Eshan D., Suderman, Ryan, Colvin, Joshua, Ionkov, Alexander, Hu, Andrew, Sauro, Herbert M., Posner, Richard G., Hlavacek, William S.

Journal:

Year:

2019

Language:

english

File:

PDF, 4.86 MB

english, 2019

98

SBML Reaction Finder: Retrieve and extract specific reactions from the BioModels database

Neal, Maxwell, Sauro, Herbert

Journal:

Bioentrepreneur

Year:

2012

File:

PDF, 197 KB

2012

99

libsbmljsâEnabling webâbased SBML tools

Medley, J. Kyle, Hellerstein, Joseph, Sauro, Herbert M.

Journal:

Year:

2020

File:

PDF, 1.93 MB

2020

100

Improving reproducibility in computational biology research

Papin, Jason A., Mac Gabhann, Feilim, Sauro, Herbert M., Nickerson, David, Rampadarath, Anand

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 246 KB

2020