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1

Multiscale Computational Models of Complex Biological Systems

Walpole, Joseph, Papin, Jason A., Peirce, Shayn M.

Journal:

Annual Review of Biomedical Engineering

Year:

2013

Language:

english

File:

PDF, 703 KB

english, 2013

2

Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks

Eytan Ruppin, Jason A Papin, Luis F de Figueiredo, Stefan Schuster

Journal:

Current Opinion in Biotechnology

Year:

2010

Language:

english

File:

PDF, 471 KB

english, 2010

3

Ten simple rules for biologists learning to program

Carey, Maureen A., Papin, Jason A., Markel, Scott

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.16 MB

english, 2018

4

Perspective: Dimensions of the scientific method

Voit, Eberhard O., Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2019

Language:

english

File:

PDF, 1.46 MB

english, 2019

5

Systems analyses characterize integrated functions of biochemical networks

Erwin P. Gianchandani, David L. Brautigan, Jason A. Papin

Journal:

Trends in Biochemical Sciences

Year:

2006

Language:

english

File:

PDF, 616 KB

english, 2006

6

A metabolic network approach for the identification and prioritization of antimicrobial drug targets

Arvind K. Chavali, Kevin M. D’Auria, Erik L. Hewlett, Richard D. Pearson, Jason A. Papin

Journal:

Trends in Microbiology

Year:

2012

Language:

english

File:

PDF, 608 KB

english, 2012

7

Integrating Cellular Metabolism into a Multiscale Whole-Body Model

Krauss, Markus, Schaller, Stephan, Borchers, Steffen, Findeisen, Rolf, Lippert, Jörg, Kuepfer, Lars, Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.11 MB

english, 2012

8

Chemical Basis of Metabolic Network Organization

Zhu, Qiang, Qin, Tao, Jiang, Ying-Ying, Ji, Cong, Kong, De-Xin, Ma, Bin-Guang, Zhang, Hong-Yu, Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 237 KB

english, 2011

9

Quantifying the Contribution of the Liver to Glucose Homeostasis: A Detailed Kinetic Model of Human Hepatic Glucose Metabolism

König, Matthias, Bulik, Sascha, Holzhütter, Hermann-Georg, Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.99 MB

english, 2012

10

Anatomically accurate model of EMG during index finger flexion and abduction derived from diffusion tensor imaging

Pereira Botelho, Diego, Curran, Kathleen, Lowery, Madeleine M., Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2019

Language:

english

File:

PDF, 3.51 MB

english, 2019

11

Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma

Hannig, Jennifer, SchÃ¤fer, Hendrik, Ackermann, JÃ¶rg, Hebel, Marie, SchÃ¤fer, Tim, DÃ¶ring, Claudia, Hartmann, Sylvia, Hansmann, Martin-Leo, Koch, Ina, Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2020

Language:

english

File:

PDF, 14.47 MB

english, 2020

12

Phthalimide neovascular factor 1 (PNF1) modulates MT1-MMP activity in human microvascular endothelial cells

Kristen A. Wieghaus, Erwin P. Gianchandani, Rebekah A. Neal, Mikell A. Paige, Milton L. Brown, Jason A. Papin, Edward A. Botchwey

Journal:

Biotechnology and Bioengineering

Year:

2009

Language:

english

File:

PDF, 705 KB

english, 2009

13

The Genome-Scale Metabolic Extreme Pathway Structure in Haemophilus influenzae Shows Significant Network Redundancy

JASON A. PAPIN, NATHAN D. PRICE, JEREMY S. EDWARDS, BERNHARD Ø. PALSSON

Journal:

Journal of Theoretical Biology

Year:

2002

Language:

english

File:

PDF, 778 KB

english, 2002

14

Bioinformatics and cellular signaling

Jason Papin, Shankar Subramaniam

Journal:

Current Opinion in Biotechnology

Year:

2004

Language:

english

File:

PDF, 94 KB

english, 2004

15

Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk

Jason A Papin, Bernhard O Palsson

Journal:

Journal of Theoretical Biology

Year:

2004

Language:

english

File:

PDF, 959 KB

english, 2004

16

Site-specific fracture plane determination using the FIB/TEM

Robert E. Hackenberg, Robert D. Field, Pallas A. Papin, Jason C. Cooley, David F. Teter

Journal:

Ultramicroscopy

Year:

2007

Language:

english

File:

PDF, 581 KB

english, 2007

17

Network-based analysis of metabolic regulation in the human red blood cell

Nathan D. Price, Jennifer L. Reed, Jason A. Papin, Sharon J. Wiback, Bernhard O. Palsson

Journal:

Journal of Theoretical Biology

Year:

2003

Language:

english

File:

PDF, 407 KB

english, 2003

18

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

Paul A Jensen, Kyla A Lutz, Jason A Papin

Journal:

BMC Systems Biology

Year:

2011

Language:

english

File:

PDF, 468 KB

english, 2011

19

Systems analysis of the transcriptional response of human ileocecal epithelial cells toClostridium difficiletoxins and effects on cell cycle control

Kevin M D’Auria, Gina M Donato, Mary C Gray, Glynis L Kolling, Cirle A Warren, Lauren M Cave, Michael D Solga, Joanne A Lannigan, Jason A Papin, Erik L Hewlett

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 321 KB

english, 2012

20

The application of flux balance analysis in systems biology

Erwin P. Gianchandani, Arvind K. Chavali, Jason A. Papin

Journal:

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Year:

2010

Language:

english

File:

PDF, 455 KB

english, 2010

21

Systems Analysis of Small Signaling Modules Relevant to Eight Human Diseases

Kelly F. Benedict, Feilim Mac Gabhann, Robert K. Amanfu, Arvind K. Chavali, Erwin P. Gianchandani, Lydia S. Glaw, Matthew A. Oberhardt, Bryan C. Thorne, Jason H. Yang, Jason A. Papin, Shayn M. Peirce,

Journal:

Annals of Biomedical Engineering

Year:

2011

Language:

english

File:

PDF, 1.13 MB

english, 2011

22

Reconstruction of cellular signalling networks and analysis of their properties

Papin, Jason A., Hunter, Tony, Palsson, Bernhard O., Subramaniam, Shankar

Journal:

Nature Reviews Molecular Cell Biology

Year:

2005

Language:

english

File:

PDF, 223 KB

english, 2005

23

Genome-wide functional annotation and structural verification of metabolic ORFeome ofChlamydomonas reinhardtii

Lila Ghamsari, Santhanam Balaji, Yun Shen, Xinping Yang, Dawit Balcha, Changyu Fan, Tong Hao, Haiyuan Yu, Jason A Papin, Kourosh Salehi-Ashtiani

Journal:

Year:

2011

Language:

english

File:

PDF, 800 KB

english, 2011

24

Metabolic systems analysis to advance algal biotechnology

Brian J. Schmidt, Xiefan Lin-Schmidt, Austin Chamberlin, Kourosh Salehi-Ashtiani, Jason A. Papin

Journal:

Biotechnology Journal

Year:

2010

Language:

english

File:

PDF, 506 KB

english, 2010

25

Hierarchical thinking in network biology: the unbiased modularization of biochemical networks

Jason A. Papin, Jennifer L. Reed, Bernhard O. Palsson

Journal:

Trends in Biochemical Sciences

Year:

2004

Language:

english

File:

PDF, 208 KB

english, 2004

26

Comparison of network-based pathway analysis methods

Jason A. Papin, Joerg Stelling, Nathan D. Price, Steffen Klamt, Stefan Schuster, Bernhard O. Palsson

Journal:

Trends in Biotechnology

Year:

2004

Language:

english

File:

PDF, 498 KB

english, 2004

27

Development of network-based pathway definitions: the need to analyze real metabolic networks

Bernhard O. Palsson, Nathan D. Price, Jason A. Papin

Journal:

Trends in Biotechnology

Year:

2003

Language:

english

File:

PDF, 796 KB

english, 2003

28

Genome-scale microbial in silico models: the constraints-based approach

Nathan D Price, Jason A Papin, Christophe H Schilling, Bernhard O Palsson

Journal:

Trends in Biotechnology

Year:

2003

Language:

english

File:

PDF, 598 KB

english, 2003

29

Metabolic pathways in the post-genome era

Jason A. Papin, Nathan D. Price, Sharon J. Wiback, David A. Fell, Bernhard O. Palsson

Journal:

Trends in Biochemical Sciences

Year:

2003

Language:

english

File:

PDF, 1.39 MB

english, 2003

30

Predicting biological system objectives de novo from internal state measurements

Erwin P Gianchandani, Matthew A Oberhardt, Anthony P Burgard, Costas D Maranas, Jason A Papin

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 623 KB

english, 2008

31

Multiscale computational analysis ofXenopus laevismorphogenesis reveals key insights of systems-level behavior

Scott H Robertson, Chris K Smith, Anna L Langhans, Sara E McLinden, Matthew A Oberhardt, Karoly R Jakab, Bette Dzamba, Douglas W DeSimone, Jason A Papin, Shayn M Peirce

Journal:

BMC Systems Biology

Year:

2007

Language:

english

File:

PDF, 2.53 MB

english, 2007

32

Proteomic and network analysis characterize stage-specific metabolism inTrypanosoma cruzi

Seth B Roberts, Jennifer L Robichaux, Arvind K Chavali, Patricio A Manque, Vladimir Lee, Ana M Lara, Jason A Papin, Gregory A Buck

Journal:

BMC Systems Biology

Year:

2009

Language:

english

File:

PDF, 1.17 MB

english, 2009

33

Deterministic Mechanical Model of T-Killer Cell Polarization Reproduces the Wandering of Aim between Simultaneously Engaged Targets

Kim, Mun Ju, Maly, Ivan V., Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 514 KB

english, 2009

34

Characterizing emergent properties of immunological systems with multi-cellular rule-based computational modeling

Arvind K. Chavali, Erwin P. Gianchandani, Kenneth S. Tung, Michael B. Lawrence, Shayn M. Peirce, Jason A. Papin

Journal:

Trends in Immunology

Year:

2008

Language:

english

File:

PDF, 833 KB

english, 2008

35

Mechanistic systems modeling to guide drug discovery and development

Schmidt, Brian J., Papin, Jason A., Musante, Cynthia J.

Journal:

Drug Discovery Today

Year:

2013

Language:

english

File:

PDF, 572 KB

english, 2013

36

Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks

Brochado, Ana Rita, Andrejev, Sergej, Maranas, Costas D., Patil, Kiran R., Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 787 KB

english, 2012

37

Analysis of Metabolic Capabilities Using Singular Value Decomposition of Extreme Pathway Matrices

Price, Nathan D., Reed, Jennifer L., Papin, Jason A., Famili, Iman, Palsson, Bernhard O.

Journal:

Biophysical Journal

Year:

2003

Language:

english

File:

PDF, 406 KB

english, 2003

38

Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease

Arvind K Chavali, Anna S Blazier, Jose L Tlaxca, Paul A Jensen, Richard D Pearson, Jason A Papin

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 964 KB

english, 2012

39

The JAK-STAT Signaling Network in the Human B-Cell: An Extreme Signaling Pathway Analysis

Papin, Jason A., Palsson, Bernhard O.

Journal:

Biophysical Journal

Year:

2004

Language:

english

File:

PDF, 259 KB

english, 2004

40

Matrix Rigidity Regulates Cancer Cell Growth by Modulating Cellular Metabolism and Protein Synthesis

Tilghman, Robert W., Blais, Edik M., Cowan, Catharine R., Sherman, Nicholas E., Grigera, Pablo R., Jeffery, Erin D., Fox, Jay W., Blackman, Brett R., Tschumperlin, Daniel J., Papin, Jason A., Parsons,

Journal:

Year:

2012

Language:

english

File:

PDF, 1.81 MB

english, 2012

41

Environments that Induce Synthetic Microbial Ecosystems

Klitgord, Niels, Segrè, Daniel, Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 939 KB

english, 2010

42

Computational Models of Algae Metabolism for Industrial Applications

Koskimaki, Jacob E., Blazier, Anna S., Clarens, Andres F., Papin, Jason A.

Journal:

Industrial Biotechnology

Year:

2013

Language:

english

File:

PDF, 604 KB

english, 2013

43

MicroRNAs induced in melanoma treated with combination targeted therapy of Temsirolimus and Bevacizumab

Wagenseller, Aubrey G, Shada, Amber, D’Auria, Kevin M, Murphy, Cheryl, Sun, Dandan, Molhoek, Kerrington R, Papin, Jason A, Dutta, Anindya, Slingluff Jr, Craig L

Journal:

Journal of Translational Medicine

Year:

2013

Language:

english

File:

PDF, 807 KB

english, 2013

44

Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major

Chavali, Arvind K, Whittemore, Jeffrey D, Eddy, James A, Williams, Kyle T, Papin, Jason A

Journal:

Molecular Systems Biology

Year:

2008

Language:

english

File:

PDF, 1.34 MB

english, 2008

45

Applications of genome-scale metabolic reconstructions

Oberhardt, Matthew A, Palsson, Bernhard Ø, Papin, Jason A

Journal:

Molecular Systems Biology

Year:

2009

Language:

english

File:

PDF, 717 KB

english, 2009

46

Selectin Mechanokinetics and Two-Dimensional Bond Formation Determine and are Reported by Nano-Motion Dynamic Patterns

Schmidt, Brian J., Papin, Jason A., Lawrence, Michael B.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 35 KB

english, 2010

47

Robust Design: A Repertoire of Biological, Ecological, and Engineering Case Studies.Santa Fe Institute Studies in the Sciences of Complexity. Edited by Erica Jen

Journal:

Quarterly Review of Biology

Year:

2006

Language:

english

File:

PDF, 91 KB

english, 2006

48

X-ray Imaging and Controlled Solidification of Al-Cu Alloys Toward Microstructures by Design

Clarke, Amy J., Tourret, Damien, Imhoff, Seth D., Gibbs, Paul J., Fezzaa, Kamel, Cooley, Jason C., Lee, Wah-Keat, Deriy, Alex, Patterson, Brian M., Papin, Pallas A., Clarke, Kester D., Field, Robert D

Journal:

Advanced Engineering Materials

Year:

2015

Language:

english

File:

PDF, 1.54 MB

english, 2015

49

Integration of expression data in genome-scale metabolic network reconstructions

Blazier, Anna S., Papin, Jason A.

Journal:

Frontiers in Physiology

Year:

2012

Language:

english

File:

PDF, 669 KB

english, 2012

50

Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems

Gianchandani, Erwin P., Papin, Jason A., Price, Nathan D., Joyce, Andrew R., Palsson, Bernhard O.

Journal:

PLoS Computational Biology

Year:

2006

Language:

english

File:

PDF, 1.36 MB

english, 2006