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1

Towards Unifying Systems Biology - Using Pathway Data in Biopax Format for SBML Simulators

Ruebenacker, Oliver, Moraru, Ion I., Blinov, Michael L.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 34 KB

english, 2009

2

Using 3D-modeling Technologies to Increase Road Safety

Eliseev, Michael, Tomchinskaya, Tatyana, Lipenkov, Alexandr, Blinov, Alexandr

Journal:

Transportation Research Procedia

Year:

2017

Language:

english

File:

PDF, 555 KB

english, 2017

3

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0

Rougny, Adrien, Touré, Vasundra, Moodie, Stuart, Balaur, Irina, Czauderna, Tobias, Borlinghaus, Hanna, Dogrusoz, Ugur, Mazein, Alexander, Dräger, Andreas, Blinov, Michael L., Villéger, Alice, Haw, Rob

Journal:

Journal of Integrative Bioinformatics

Language:

english

File:

PDF, 2.31 MB

english

4

LibSBGN: Electronic Processing of SBGN maps

Demir, Emek, Dogrusoz, Ugur, Le Novère, Nicolas, Matsuoka, Yukiko, Sorokin, Anatoly, Funahashi, Akira, Mi, Huaiyu, Kitano, Hiroaki, Aladjem, Mirit, van Iersel, Martijn, Blinov, Michael, Boyd, Sarah, V

Journal:

Bioentrepreneur

Year:

2010

File:

PDF, 1.38 MB

2010

5

Two MYB Proteins in a Self-Organizing Activator-Inhibitor System Produce Spotted Pigmentation Patterns

Ding, Baoqing, Patterson, Erin L., Holalu, Srinidhi V., Li, Jingjian, Johnson, Grace A., Stanley, Lauren E., Greenlee, Anna B., Peng, Foen, Bradshaw, H.D., Blinov, Michael L., Blackman, Benjamin K., Y

Journal:

Current Biology

Year:

2020

Language:

english

File:

PDF, 4.77 MB

english, 2020

6

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

7

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

8

Automated structure elucidation of two unexpected products in a reaction of an α,β-unsaturated pyruvate

Gary J. Sharman, Ian C. Jones, Mark P. Parnell, Michael C. Willis, Mary F. Mahon, Dean V. Carlson, Antony Williams, Mikhail Elyashberg, Kirill Blinov, Sergey G. Molodtsov

Journal:

Magnetic Resonance in Chemistry

Year:

2004

Language:

english

File:

PDF, 115 KB

english, 2004

9

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

10

Molecular machines or pleiomorphic ensembles: signaling complexes revisited

Bruce J Mayer, Michael L Blinov, Leslie M Loew

Journal:

Journal of Biology

Year:

2009

Language:

english

File:

PDF, 1023 KB

english, 2009

11

Center and composition conditions for Abel differential equation, and rational curves

Michael Blinov, Yosef Yomdin

Journal:

Qualitative Theory of Dynamical Systems

Year:

2001

Language:

english

File:

PDF, 211 KB

english, 2001

12

Using views of Systems Biology Cloud: application for model building

Oliver Ruebenacker, Michael Blinov

Journal:

Theory in Biosciences

Year:

2011

Language:

english

File:

PDF, 275 KB

english, 2011

13

Depicting signaling cascades

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

Journal:

Nature Biotechnology

Year:

2006

Language:

english

File:

PDF, 103 KB

english, 2006

14

'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

15

Under-representation of the −455A β-fibrinogen allele in survivors of pulmonary embolism

Sergey I Kapustin, Michael N Blinov, Ludmila P Papayan, Eugeny N Imyanitov, Mike J Mitchell, Geoffrey F Savidge

Journal:

Thrombosis Research

Year:

2002

Language:

english

File:

PDF, 54 KB

english, 2002

16

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

17

A mathematical Model of Signaling in Podocyte Foot Processes

Falkenberg, Cibele V., Blinov, Michael L., Loew, Leslie M.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 37 KB

english, 2011

18

Multi-Network Modeling of Cancer Cell States

Blinov, Michael L., Udyavar, Akshata, Yarbrough, Wendell, Wang, JiaLiang, Estrada, Lourdes, Quaranta, Vito

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 35 KB

english, 2012

19

Pathway Commons at Virtual Cell: Use of Pathway Data For Mathematical Modeling

Blinov, Michael L., Ruebenacker, Oliver, Schaff, James C., Loew, Leslie M., Moraru, Ion I.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 36 KB

english, 2012

20

Logic modeling and the ridiculome under the rug

Michael L Blinov, Ion I Moraru

Journal:

Year:

2012

Language:

english

File:

PDF, 302 KB

english, 2012

21

Modeling Cluster Formation by Multivalent Interacting Proteins: Nephrin-Nck-NWasp Signaling in the Foot Process of Kidney Podocytes

Falkenberg, Cibele V., Blinov, Michael L., Loew, Leslie M.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 35 KB

english, 2013

22

System Biology Pathway Exchange - Bridging Pathway Data And Quantitative Models

Ruebenacker, Oliver, Blinov, Michael L., Moraru, Ion I.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 37 KB

english, 2010

23

A Mathematical Model for Nephrin Localization in Podocyte Foot Processes

Falkenberg, Cibele V., Blinov, Michael L., Azeloglu, Evren U., Neves, Susana R., Iyengar, Ravi, Loew, Leslie M.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 48 KB

english, 2012

24

Analysis of Size and Compositional Distributions of Pleomorphic Ensembles Arising from Clustering of Multivalent Biological Molecules

Falkenberg, Cibele V., Blinov, Michael L., Loew, Leslie M.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 42 KB

english, 2014

25

A predictive mathematical model of the DNA damage G2 checkpoint

Kesseler, Kevin J., Blinov, Michael L., Elston, Timothy C., Kaufmann, William K., Simpson, Dennis A.

Journal:

Journal of Theoretical Biology

Year:

2013

Language:

english

File:

PDF, 918 KB

english, 2013

26

Pleomorphic Ensembles: Formation of Large Clusters Composed of Weakly Interacting Multivalent Molecules

Falkenberg, Cibele V., Blinov, Michael L., Loew, Leslie M.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 1.01 MB

english, 2013

27

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

28

Proliferating dynamic modeling in systems biology studies

Blinov, Michael L.

Journal:

Molecular BioSystems

Year:

2011

Language:

english

File:

PDF, 1000 KB

english, 2011

29

[IEEE 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering - Boston, MA, USA (2007.10.14-2007.10.17)] 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering - XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes

Blinov, Michael L., Moraru, Ion I.

Year:

2007

Language:

english

File:

PDF, 1.91 MB

english, 2007

30

[IEEE 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007) - Fremont, CA, USA (2007.11.2-2007.11.4)] 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007) - Kinetic Modeling Using BioPAX Ontology

Ruebenacker, Oliver, Moraru, Ion I., Schaff, James C., Blinov, Michael L.

Year:

2007

Language:

english

File:

PDF, 443 KB

english, 2007

31

SPIE Proceedings [SPIE SPIE Sensing Technology + Applications - Baltimore, Maryland, United States (Monday 20 April 2015)] Quantum Information and Computation XIII - Scalable quantum computing architecture with mixed species ion chains

Donkor, Eric, Pirich, Andrew R., Hayduk, Michael, Wright, John, Auchter, Carolyn, Chou, Chen-Kuan, Graham, Richard D., Noel, Thomas W., Sakrejda, Tomasz, Zhou, Zichao, Blinov, Boris B.

Year:

2015

Language:

english

File:

PDF, 959 KB

english, 2015

32

[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

33

Rule-Based Modeling with Virtual Cell: Effect of UBE3A on Dendritic Spine Morphogenesis

Bloom, Judy E., Blinov, Michael L., Loew, Leslie M.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 38 KB

english, 2016

34

Using Rules & Pathway Databases to Create Quantitative Mechanistic Models in Virtual Cell

Blinov, Michael L., Vasilescu, Dan, Schaff, James C., Moraru, Ion I., Loew, Leslie M.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 39 KB

english, 2015

35

Rule-Based Modeling and Simulation for Beginners: Intuitive Graphical Interface within Virtual Cell

Blinov, Michael L., Vasilescu, Dan, Moraru, Ion I., Loew, Leslie M., Schaff, James C.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 36 KB

english, 2016

36

Rule-based Modeling with Virtual Cell

Schaff, James C., Vasilescu, Dan, Moraru, Ion I., Loew, Leslie M., Blinov, Michael L.

Journal:

Year:

2016

Language:

english

File:

PDF, 299 KB

english, 2016

37

Multivalent Molecules as Modulators of RNA Granule Size and Composition

Falkenberg, Cibele Vieira, Carson, John H., Blinov, Michael L.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 1.56 MB

english, 2017

38

Multivalent Signaling Clusters have Unique Sizes Determined by Membrane Localization and Excluded Volume: the Nephrin/Nck/N-WASP System

Youngstrom, Madeleine, Chattaraj, Aniruddha, Michalski, Paul J., Schaff, James C., Blinov, Michael L., Loew, Leslie M.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 44 KB

english, 2017

39

Modeling Analysis of RNA Granule Formation and Selectivity Mediated by Multivalent Interactions

Falkenberg, Cibele V., Carson, John H., Blinov, Michael L.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 44 KB

english, 2017

40

Extending Rule-Based Modeling to the Spatial Domain with Virtual Cell (VCELL)

Schaff, James C., Vasilescu, Dan, Moraru, Ion I., Loew, Leslie M., Blinov, Michael L.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 42 KB

english, 2017

41

Compartmental and Spatial Rule-Based Modeling with Virtual Cell

Blinov, Michael L., Schaff, James C., Vasilescu, Dan, Moraru, Ion I., Bloom, Judy E., Loew, Leslie M.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 1.66 MB

english, 2017

42

Report: NIA Workshop on Measures of Physiologic Resiliencies in Human Aging

Hadley, Evan C, Kuchel, George A, Newman, Anne B, Allore, Heather G, Bartley, Jenna M, Bergeman, Cindy S, Blinov, Michael L, Colon-Emeric, Cathleen S, Dabhar, Firdaus S, Dugan, Laura L, Dutta, Chhanda

Journal:

The Journals of Gerontology Series A Biological Sciences and Medical Sciences

Year:

2018

Language:

english

File:

PDF, 61 KB

english, 2018

43

Examining UBE3A's Possible Role in Dendritic Spine Morphogenesis

Bloom, Judy E., Sirois, Carissa, Blinov, Michael L., Chamberlain, Stormy J., Loew, Leslie M.

Journal:

Biophysical Journal

Year:

2018

File:

PDF, 45 KB

2018

44

LibSBGN: Electronic Processing of SBGN maps

Demir, Emek, Dogrusoz, Ugur, Le Novère, Nicolas, Matsuoka, Yukiko, Sorokin, Anatoly, Funahashi, Akira, Mi, Huaiyu, Kitano, Hiroaki, Aladjem, Mirit, van Iersel, Martijn, Blinov, Michael, Boyd, Sarah, V

Journal:

Bioentrepreneur

Year:

2010

Language:

english

File:

PDF, 1.38 MB

english, 2010

45

LibSBGN: Electronic Processing of SBGN maps

Demir, Emek, Dogrusoz, Ugur, Le Novère, Nicolas, Matsuoka, Yukiko, Sorokin, Anatoly, Funahashi, Akira, Mi, Huaiyu, Kitano, Hiroaki, Aladjem, Mirit, van Iersel, Martijn, Blinov, Michael, Boyd, Sarah, V

Journal:

Bioentrepreneur

Year:

2011

Language:

english

File:

PDF, 1.40 MB

english, 2011

46

LibSBGN: Electronic Processing of SBGN maps

Demir, Emek, Dogrusoz, Ugur, Le Novère, Nicolas, Matsuoka, Yukiko, Sorokin, Anatoly, Funahashi, Akira, Mi, Huaiyu, Kitano, Hiroaki, Aladjem, Mirit, van Iersel, Martijn, Blinov, Michael, Boyd, Sarah, V

Journal:

Bioentrepreneur

Year:

2011

File:

PDF, 1.40 MB

2011

47

ModelBricks—modules for reproducible modeling improving model annotation and provenance

Cowan, Ann E., Mendes, Pedro, Blinov, Michael L.

Journal:

npj Systems Biology and Applications

Year:

2019

Language:

english

File:

PDF, 1.31 MB

english, 2019

48

The Evaluation of Genetic Relationships within Acridid Grasshoppers (Orthoptera, Caelifera, Acrididae) on the Subfamily Level Using Molecular Markers

Sukhikh, Igor, Ustyantsev, Kirill, Bugrov, Alexander, Sergeev, Michael, Fet, Victor, Blinov, Alexander

Journal:

Folia Biologica

Year:

2019

File:

PDF, 225 KB

2019

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