Faeder, James R.: search on Z-Library

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1

Translational Systems Approaches to the Biology of Inflammation and Healing

Vodovotz, Yoram, Constantine, Gregory, Faeder, James, Mi, Qi, Rubin, Jonathan, Bartels, John, Sarkar, Joydeep, Squires, Robert H., Okonkwo, David O., Gerlach, Jörg, Zamora, Ruben, Luckhart, Shirley, E

Journal:

Immunopharmacology and Immunotoxicology

Year:

2010

Language:

english

File:

PDF, 909 KB

english, 2010

2

[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) - Adaptive coarse-graining for transient and quasi-equilibrium analyses of stochastic gene regulation

Tapia, Jose Juan, Faeder, James R., Munsky, Brian

Year:

2012

Language:

english

File:

PDF, 726 KB

english, 2012

3

236

Sheehan, Robert P., Garg, Abhishek, Gaffen, Sarah L., Faeder, James R.

Journal:

Year:

2013

Language:

english

File:

PDF, 42 KB

english, 2013

4

Modeling the T cell immune response: a fascinating challenge

Morel, Penelope A., Faeder, James R., Hawse, William F., Miskov-Zivanov, Natasa

Journal:

Journal of Pharmacokinetics and Pharmacodynamics

Year:

2014

Language:

english

File:

PDF, 467 KB

english, 2014

5

Memory of Germinant Stimuli in Bacterial Spores

Wang, Shiwei, Faeder, James R., Setlow, Peter, Li, Yong-qing

Journal:

Year:

2015

Language:

english

File:

PDF, 1.95 MB

english, 2015

6

Mathematical and computational models of immune-receptor signalling

Goldstein, Byron, Faeder, James R., Hlavacek, William S.

Journal:

Nature Reviews Immunology

Year:

2004

Language:

english

File:

PDF, 307 KB

english, 2004

7

RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry

Smith, Adam M, Xu, Wen, Sun, Yao, Faeder, James R, Marai, G Elisabeta

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 2.04 MB

english, 2012

8

The Seventh q-bio Conference: meeting report and preface

Nemenman, Ilya, Faeder, James R, Gnanakaran, S, Hlavacek, William S, Munsky, Brian, Wall, Michael E, Jiang, Yi

Journal:

Physical Biology

Year:

2014

Language:

english

File:

PDF, 921 KB

english, 2014

9

A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine Kinases

Barua, Dipak, Faeder, James R., Haugh, Jason M., Kannan, Natarajan

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 658 KB

english, 2009

10

A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity

Michael L. Blinov, James R. Faeder, Byron Goldstein, William S. Hlavacek

Journal:

Year:

2006

Language:

english

File:

PDF, 593 KB

english, 2006

11

Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems

Hogg, Justin S., Harris, Leonard A., Stover, Lori J., Nair, Niketh S., Faeder, James R., Stelling, Jorg

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.64 MB

english, 2014

12

BioNetGen 2.2: Advances in Rule-Based Modeling

Harris, Leonard A., Hogg, Justin S., Tapia, José-Juan, Sekar, John A. P., Gupta, Sanjana, Korsunsky, Ilya, Arora, Arshi, Barua, Dipak, Sheehan, Robert P., Faeder, James R.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.14 MB

english, 2016

13

The interplay of double phosphorylation and scaffolding in MAPK pathways

PaweŁ Kocieniewski, James R. Faeder, Tomasz Lipniacki

Journal:

Journal of Theoretical Biology

Year:

2012

Language:

english

File:

PDF, 663 KB

english, 2012

14

Modeling the early signaling events mediated by FcεRI

Byron Goldstein, James R. Faeder, William S. Hlavacek, Michael L. Blinov, Antonio Redondo, Carla Wofsy

Journal:

Molecular Immunology

Year:

2002

Language:

english

File:

PDF, 239 KB

english, 2002

15

Aggregation of Membrane Proteins by Cytosolic Cross-Linkers: Theory and Simulation of the LAT-Grb2-SOS1 System

Nag, Ambarish, Monine, Michael I., Faeder, James R., Goldstein, Byron

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 1.17 MB

english, 2009

16

Structure-Based Kinetic Models of Modular Signaling Protein Function: Focus on Shp2

Barua, Dipak, Faeder, James R., Haugh, Jason M.

Journal:

Biophysical Journal

Year:

2007

Language:

english

File:

PDF, 720 KB

english, 2007

17

In vivo, in vitro, and in silico studies suggest a conserved immune module that regulates malaria parasite transmission from mammals to mosquitoes

Price, Ian, Ermentrout, Bard, Zamora, Ruben, Wang, Bo, Azhar, Nabil, Mi, Qi, Constantine, Gregory, Faeder, James R., Luckhart, Shirley, Vodovotz, Yoram

Journal:

Journal of Theoretical Biology

Year:

2013

Language:

english

File:

PDF, 1.63 MB

english, 2013

18

[IEEE 2009 Winter Simulation Conference - (WSC 2009) - Austin, TX, USA (2009.12.13-2009.12.16)] Proceedings of the 2009 Winter Simulation Conference (WSC) - Compartmental rule-based modeling of biochemical systems

Harris, Leonard A, Hogg, Justin S., Faeder, James R.

Year:

2009

Language:

english

File:

PDF, 618 KB

english, 2009

19

[ACM Press the 2nd ACM Conference - Chicago, Illinois (2011.08.01-2011.08.03)] Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '11 - Emulation of biological networks in reconfigurable hardware

Miskov-Zivanov, Natasa, Bresticker, Andrew, Krishnaswamy, Deepa, Venkatakrishnan, Sreesan, Marculescu, Diana, Faeder, James R.

Year:

2011

Language:

english

File:

PDF, 1.05 MB

english, 2011

20

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems

Chylek, Lily A., Harris, Leonard A., Tung, Chang-Shung, Faeder, James R., Lopez, Carlos F., Hlavacek, William S.

Journal:

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Year:

2014

Language:

english

File:

PDF, 1.21 MB

english, 2014

21

[IEEE 2011 IEEE Symposium on Biological Data Visualization (BioVis) - Providence, RI, USA (2011.10.23-2011.10.24)] 2011 IEEE Symposium on Biological Data Visualization (BioVis). - RuleBender: Integrated visualization for biochemical rule-based modeling

Smith, Adam M., Xu, Wen, Sun, Yao, Faeder, James R., Marai, G. Elisabeta

Year:

2011

Language:

english

File:

PDF, 527 KB

english, 2011

22

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

Donovan, Rory M., Tapia, Jose-Juan, Sullivan, Devin P., Faeder, James R., Murphy, Robert F., Dittrich, Markus, Zuckerman, Daniel M., Meier-Schellersheim, Martin

Journal:

PLoS Computational Biology

Year:

2016

Language:

english

File:

PDF, 2.97 MB

english, 2016

23

Parallel Tempering with Lasso for model reduction in systems biology

Gupta, Sanjana, Lee, Robin E. C., Faeder, James R., Finley, Stacey

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 4.30 MB

2020

24

[IEEE 2016 IEEE International High Level Design Validation and Test Workshop (HLDVT) - Santa Cruz, CA, USA (2016.10.7-2016.10.8)] 2016 IEEE International High Level Design Validation and Test Workshop (HLDVT) - High-level modeling and verification of cellular signaling

Miskov-Zivanov, Natasa, Zuliani, Paolo, Wang, Qinsi, Clarke, Edmund M., Faeder, James R.

Year:

2016

Language:

english

File:

PDF, 1.32 MB

english, 2016

25

Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories

Donovan, Rory M., Sedgewick, Andrew J., Faeder, James R., Zuckerman, Daniel M.

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 975 KB

english, 2013

26

The eighth q-bio conference: meeting report and special issue preface

Hlavacek, William S, Gnanakaran, S, Munsky, Brian, Wall, Michael E, Faeder, James R, Jiang, Yi, Nemenman, Ilya, Resnekov, Orna

Journal:

Physical Biology

Year:

2015

Language:

english

File:

PDF, 244 KB

english, 2015

27

Rule-based modeling of biochemical networks

James R. Faeder, Michael L. Blinov, Byron Goldstein, William S. Hlavacek

Journal:

Year:

2005

Language:

english

File:

PDF, 242 KB

english, 2005

28

[ACM Press the 2005 ACM symposium - Santa Fe, New Mexico (2005.03.13-2005.03.17)] Proceedings of the 2005 ACM symposium on Applied computing - SAC '05 - Graphical rule-based representation of signal-transduction networks

Faeder, James R., Blinov, Michael L., Hlavacek, William S.

Year:

2005

Language:

english

File:

PDF, 274 KB

english, 2005

29

[ACM Press the International Conference - Wshington DC, USA (2013.09.22-2013.09.25)] Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics - BCB'13 - Studies of biological networks with statistical model checking

Miskov-Zivanov, Natasa, Zuliani, Paolo, Clarke, Edmund M., Faeder, James R.

Year:

2007

Language:

english

File:

PDF, 188 KB

english, 2007

30

Effect of magnitude and variability of energy of activation in multisite ultrasensitive biochemical processes

Lagunes, Leonila, Bardwell, Lee, Enciso, German A., Faeder, James R.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 5.10 MB

2020

31

Stochastic effects and bistability in T cell receptor signaling

Tomasz Lipniacki, Beata Hat, James R. Faeder, William S. Hlavacek

Journal:

Journal of Theoretical Biology

Year:

2008

Language:

english

File:

PDF, 2.05 MB

english, 2008

32

[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

33

[ACM Press the 25th edition - Pittsburgh, Pennsylvania, USA (2015.05.20-2015.05.22)] Proceedings of the 25th edition on Great Lakes Symposium on VLSI - GLSVLSI '15 - Design Automation for Biological Models

Sullivan, Devin P., Arepally, Rohan, Murphy, Robert F., Tapia, Jose-Juan, Faeder, James R., Dittrich, Markus, Czech, Jacob

Year:

2015

Language:

english

File:

PDF, 1.14 MB

english, 2015

34

The role of intracellular interactions in the collective polarization of tissues and its interplay with cellular geometry

Shadkhoo, Shahriar, Mani, Madhav, Faeder, James R.

Journal:

PLoS Computational Biology

Year:

2019

Language:

english

File:

PDF, 6.39 MB

english, 2019

35

'On-the-fly' or 'generate-first' modeling?

Blinov, Michael L., Faeder, James R., Yang, Jin, Goldstein, Byron, Hlavacek, William S.

Journal:

Nature Biotechnology

Year:

2005

Language:

english

File:

PDF, 97 KB

english, 2005

36

A compartmental model reveals a mechanism for misregulation of neutrophil trafficking in sepsis

Justin S. Hogg, James R. Faeder, Robert S. Parker, Gilles Clermont

Journal:

Journal of Critical Care

Year:

2009

Language:

english

File:

PDF, 187 KB

english, 2009

37

Analysis and verification of the HMGB1 signaling pathway

Haijun Gong, Paolo Zuliani, Anvesh Komuravelli, James R Faeder, Edmund M Clarke

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 763 KB

english, 2010

38

q-bio 2007: a watershed moment in modern biology

Edwards, Jeremy S, Faeder, James R, Hlavacek, William S, Jiang, Yi, Nemenman, Ilya, Wall, Michael E

Journal:

Molecular Systems Biology

Year:

2007

Language:

english

File:

PDF, 71 KB

english, 2007

39

Perturbation biology links temporal protein changes to drug responses in a melanoma cell line

Nyman, Elin, Stein, Richard R., Jing, Xiaohong, Wang, Weiqing, Marks, Benjamin, Zervantonakis, Ioannis K., Korkut, Anil, Gauthier, Nicholas P., Sander, Chris, Faeder, James R.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 16.38 MB

2020

40

The complexity of complexes in signal transduction

William S. Hlavacek, James R. Faeder, Michael L. Blinov, Alan S. Perelson, Byron Goldstein

Journal:

Biotechnology and Bioengineering

Year:

2003

Language:

english

File:

PDF, 339 KB

english, 2003

41

Selected papers from the Fourth Annual q-bio Conference on Cellular Information Processing

Nemenman, Ilya, Faeder, James R, Hlavacek, William S, Jiang, Yi, Wall, Michael E, Zilman, Anton

Journal:

Physical Biology

Year:

2011

Language:

english

File:

PDF, 716 KB

english, 2011

42

A bacterial size law revealed by a coarse-grained model of cell physiology

Bertaux, FranÃ§ois, von KÃ¼gelgen, Julius, Marguerat, Samuel, Shahrezaei, Vahid, Faeder, James R.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 1.85 MB

2020

43

[ACM Press the 50th Annual Design Automation Conference - Austin, Texas (2013.05.29-2013.06.07)] Proceedings of the 50th Annual Design Automation Conference on - DAC '13 - Dynamic behavior of cell signaling networks

Miskov-Zivanov, Natasa, Marculescu, Diana, Faeder, James R.

Year:

2013

Language:

english

File:

PDF, 881 KB

english, 2013

44

Guidelines for visualizing and annotating rule-based models

Chylek, Lily A., Hu, Bin, Blinov, Michael L., Emonet, Thierry, Faeder, James R., Goldstein, Byron, Gutenkunst, Ryan N., Haugh, Jason M., Lipniacki, Tomasz, Posner, Richard G., Yang, Jin, Hlavacek, Wil

Journal:

Molecular BioSystems

Year:

2011

Language:

english

File:

PDF, 1.43 MB

english, 2011

45

[ACM Press the International Conference - Wshington DC, USA (2013.09.22-2013.09.25)] Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics - BCB'13 - The Atomizer

Tapia, Jose-Juan, Faeder, James R.

Year:

2007

Language:

english

File:

PDF, 281 KB

english, 2007

46

[IEEE 2011 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society - Boston, MA (2011.08.30-2011.09.3)] 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society - Regulatory network analysis acceleration with reconfigurable hardware

Miskov-Zivanov, Natasa, Bresticker, Andrew, Krishnaswamy, Deepa, Venkatakrishnan, Sreesan, Kashinkunti, Prashant, Marculescu, Diana, Faeder, James R.

Year:

2011

Language:

english

File:

PDF, 847 KB

english, 2011

47

Kinetic Monte Carlo method for rule-based modeling of biochemical networks

Yang, Jin, Monine, Michael I., Faeder, James R., Hlavacek, William S.

Journal:

Physical Review E

Year:

2008

Language:

english

File:

PDF, 195 KB

english, 2008

48

Special section dedicated to The Sixth q-bio Conference: meeting report and preface

Nemenman, Ilya, Gnanakaran, S, Munsky, Brian, Wall, Michael E, Jiang, Yi, Hlavacek, William S, Faeder, James R

Journal:

Physical Biology

Year:

2013

Language:

english

File:

PDF, 184 KB

english, 2013

49

Multi-Scale Spatial Simulations Reveal the Effect of Dopamine Transporter Localization on Dopamine Neurotransmission

Kaya, Cihan, Block, Ethan R., Sorkin, Alexander, Faeder, James R., Bahar, Ivet

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 40 KB

english, 2016

50

Stochastic ordering of complexoform protein assembly by genetic circuits

Jensen, Mikkel Herholdt, Morris, Eliza J., Tran, Hai, Nash, Michael A., Tan, Cheemeng, Faeder, James R.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 3.64 MB

2020

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