Recent Publications

For a list of all publications, click here.

For a list of publications in PubMed, click here.

2012

Differential risk of tuberculosis reactivation among anti-TNF therapies is due to drug binding kinetics and permeability.
Fallahi-Sichani M, Flynn JL, Linderman JJ, Kirschner DE. Journal of Immunology. 188(7) : 3169-3178, 2012.

2011

Ruffles limit diffusion in the plasma membrane during macropinosome formation.
Welliver TP, Chang SL, Linderman JJ and Swanson JA. Journal of Cell Science. 124 : 4106-4114, 2011.

Systems biology approaches for understanding cellular mechanisms of immunity in lymph nodes during infection.
Mirsky HP, Miller MJ, Linderman JJ, Kirschner DE. Journal of Theoretical Biology. 287 : 160-170, 2011.

Hi-Fi transmission of periodic signals amid cell-to-cell variability.
Jovic A, Wade SM, Miyawaki A, Neubig RR, Linderman JJ, Takayama S. Molecular Biosystems. 7 : 2238-2244, 2011.

Multiscale computational modeling reveals a critical role for TNFR1 dynamics in tuberculosis granuloma formation.
Fallahi-Sichani M, El-Kebir M, Marino S, Kirschner DE, Linderman JJ. The Journal of Immunology. 186(6) : 3472-3483, 2011.

Integrin organization: Linking adhesion ligand nanopatterns with altered cell responses.
Comisar WA, Mooney DJ, Linderman JJ. Journal of Theoretical Biology. 274(1) : 120-130, 2011.

2010

Phase-locked signals elucidate circuit architecture of an oscillatory pathway.
Jovic A, Howell B, Cote M, Wade SM, Mehta K, Miyawaki A, Neubig RR, Linderman JJ, Takayama S. PLoS Computational Biology. 6(12) : e1001040, 2010.

A multifaceted approach to modeling the immune response in tuberculosis.
Marino S, Linderman JJ, Kirschner DE. Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 3(4) : 479-489, 2010.

Identification of key processes that control tumor necrosis factor availability in a tuberculosis granuloma.
Fallahi-Sichani M, Schaller MA, Kirschner DE, Kunkel SL, Linderman JJ. PLoS Computational Biology. 6(5) : e1000778, 2010.

Characterizing the dynamics of CD4+ T cell priming within a lymph node.
Linderman JJ, Riggs T, Pande M, Miller M, Marino S, Kirschner DE. The Journal of Immunology. 184(6) : 2873-2885, 2010.

2009

A computational approach to inferring cellular protein-binding affinities from quantitative fluorescence resonance energy transfer imaging.
Mehta K, Hoppe AD, Kainkaryam R, Woolf PJ, Linderman JJ. Proteomics. 9(23) : 5371-5383, 2009.

Quantitative inference of cellular parameters from microfluidic cell culture systems.
Mehta K, Mehta G, Takayama S, Linderman JJ. Biotechnology and Bioengineering. 103(5) : 996-974, 2009.

Lipid raft-mediated regulation of G-protein coupled receptor signaling by ligands which influence receptor dimerization: A computational study.
Fallahi-Sichani M, Linderman JJ. PLoS ONE. 4(8) : e6604, 2009.

Hard top soft bottom microfluidic devices for cell culture and chemical analysis.
Mehta G, Lee J, Cha W, et al. Analytical Chemistry. 81(10) : 3714-3722, 2009.

Mathematical and computational approaches can complement experimental studies of host-pathogen interactions.
Kirschner DE, Linderman JJ. Cellular Microbiology. 11(4) : 531-539, 2009.

Modeling of G-protein-coupled receptor signaling pathways.
Linderman JJ. The Journal of Biological Chemistry. 284 : 5427-5431, 2009.

2008

Collision coupling, crosstalk, and compartmentalization in G-protein coupled receptor systems: can a single model explain disparate results?
Brinkerhoff CJ, Traynor JR, Linderman JJ. Journal of Theoretical Biology. 255(3) : 278-286, 2008.

Effect of multiple genetic polymorphisms on antigen presentation and susceptibility to Mycobacterium tuberculosis infection.
Chang ST, Linderman JJ, Kirschner DE. Infection and Immunity. 76(7) : 3221-3232, 2008.

Diffusion-limited reactions in G-protein activation: unexpected consequences of antagonist and agonist competition.
Brinkerhoff CJ, Choi JS, Linderman JJ. Journal of Theoretical Biology. 251(4) : 561-569, 2008.

Endogenous regulators of G protein signaling differentially modulate full and partial mu-opioid agonists at adenylyl cyclase as predicted by a collision coupling model.
Clark MJ, Linderman JJ, Traynor JR. Molecular Pharmacology. 73(5) : 1538-1548, 2008.

A comparison of random vs. chemotaxis-driven contacts of T cells with dendritic cells during repertoire scanning.
Riggs T, Walts A, Perry N, et al. Journal of Theoretical Biology. 250(4) : 732-751, 2008.

2007

Engineering RGD nanopatterned hydrogels to control preosteoblast behavior: a combined computational and experimental approach.
Comisar WA, Kazmers NH, Mooney DJ, Linderman JJ. Biomaterials. 28(30) : 4409-4417, 2007.

Both ligand- and cell-specific parameters control ligand agonism in a kinetic model of g protein-coupled receptor signaling.
Kinzer-Ursem TL and Linderman JJ. PLoS Computational Biology. 3(1) : e6, 2007.

Toward a multiscale model of antigen presentation in immunity.
Kirschner DE, Chang ST, Riggs TW, Perry N, Linderman JJ. Immunological Reviews. 216(1) : 93-118, 2007.

Polyelectrolyte-Clay-Protein Layer Films on Microfluidic PDMS Bioreactor Surfaces for Primary Murine Bone Marrow Culture.
Mehta G, Keil MJ, Lee JW, Kotov N, Linderman JJ, Takayama S. Advanced Functional Materials. 17(15) : 2701-2709, 2007.

Quantitative measurement and control of oxygen levels in microfluidic poly(dimethylsiloxane) bioreactors during cell culture.
Mehta G, Mehta K, Sud D, et al. Biomedical Microdevices. 9(2) : 123-134, 2007.

Simple transporter trafficking model for amphetamine-induced dopamine efflux.
Thwar PK, Guptaroy B, Zhang M, Gnegy ME, Burns MA, Linderman JJ. Synapse. 61(7) : 500-514, 2007.

Electrodeless direct current dielectrophoresis using reconfigurable field-shaping oil barriers.
Thwar PK, Linderman JJ, Burns MA. Electrophoresis. 28(24) : 4572-4581, 2007.

2006

Peptide length-based prediction of peptide-MHC class II binding.
Chang ST, Ghosh D, Kirschner DE, Linderman JJ. Bioinformatics. 22(22) : 2761-2767, 2006.

Optical imaging in microfluidic bioreactors enables oxygen monitoring for continuous cell culture.
Sud D, Mehta G, Mehta K, Linderman JJ, Takayama S, Mycek M. Journal of Biomedical Optics. 11 : 050504-1 - 050504-3, 2006.

Multi-scale modeling to predict ligand presentation within RGD nanopatterned hydrogels.
Comisar WA, Hsiong SX, Kong HJ, Mooney DJ, Linderman JJ. Biomaterials. 27(10) : 2322-2329, 2006.

Multiple receptor states are required to describe both kinetic binding and activation of neutrophils via N-formyl peptide receptor ligands.
Kinzer-Ursem TL, Sutton KL, Waller A, Omann GM, Linderman JJ. Cellular Signalling. 18(10) : 1732-1747, 2006.

Model-based analysis and design of a microchannel reactor for tissue engineering.
Mehta K and Linderman JJ. Biotechnol Bioeng. 94(3) : 596-609, 2006.

2005

Integrin dimerization and ligand organization: key components in integrin clustering for cell adhesion.
Brinkerhoff CJ and Linderman JJ. Tissue Engineering. 11(5-6) : 865-876, 2005.

G protein threshold behavior in the human neutrophil oxidant response: measurement of G proteins available for signaling in responding and nonresponding subpopulations.
Chang PS, Axelrod D, Omann GM, Linderman JJ. Cellular Signalling. 17(5) : 605-614, 2005.

Multiple mechanisms allow Mycobacterium tuberculosis to continuously inhibit MHC class II-mediated antigen presentation by macrophages.
Chang ST, Linderman JJ, Kirschner DE. Proceedings of the National Academy of Sciences of the USA. 102(12) : 4530-4535, 2005.

2004

Monte Carlo simulations of receptor dynamics: insights into cell signaling.
Brinkerhoff CJ, Woolf PJ, Linderman JJ. Journal of Molecular Histology. 35(7) : 667-677, 2004.

Magnetic bead isolation of neutrophil plasma membranes and quantification of membrane-associated guanine nucleotide binding proteins.
Chang PS, Absood A, Linderman JJ, Omann GM. Analytical Biochemistry. 325(2) : 175-184, 2004.

Receptor binding kinetics and cellular responses of six N-formyl peptide agonists in human neutrophils.
Waller A, Sutton KL, Kinzer-Ursem TL, et al. Biochemistry. 43(25) : 8204-8216, 2004.

Nanoscale Adhesion Ligand Organization Regulates Osteoblast Proliferation and Differentiation.
Lee KY, Alsberg E, Hsiong S, Comisar W, Linderman JJ, Ziff R, Mooney D. Nano Letters. 4 : 1501-1506, 2004.

An algebra of dimerization and its implications for G-protein coupled receptor signaling.
Woolf PJ and Linderman JJ. Journal of Theoretical Biology. 229(2) : 157-168, 2004.

2003

Priming-induced localization of G(ialpha2) in high density membrane microdomains.
Keil ML, Solomon NL, Lodhi IJ, et al. Biochemical and Biophysical Research Communications. 301(4) : 862-872, 2003.

Self organization of membrane proteins via dimerization.
Woolf PJ and Linderman JJ. Biophysical Chemistry. 104(1) : 217-227, 2003.

Untangling ligand induced activation and desensitization of G-protein-coupled receptors.
Woolf PJ and Linderman JJ. Biophysical Journal. 84(1) :3-13, 2003.

A spatial focusing model for G protein signals. Regulator of G protein signaling (RGS) protien-mediated kinetic scaffolding.
Zhong H, Wade SM, Woolf PJ, Linderman JJ, Traynor JR, Neubig RR. The Journal of Biological Chemistry. 278 : 7278-7284, 2003.

2002

Externally applied cyclic strain regulates localization of focal contact components in cultured smooth muscle cells.
Cunningham JJ, Linderman JJ, Mooney DJ. Annals of Biomedical Engineering. 30(7) : 927-935, 2002.

Quantification of fibronectin adsorption to silicone-rubber cell culture substrates.
Cunningham JJ, Nikolovski J, Linderman JJ, Mooney DJ. BioTechniques. 32(4) : 876, 878, 880, 2002.

2001

Validation of flow cytometric competitive binding protocols and characterization of fluorescently labeled ligands.
Waller A, Pipkorn D, Sutton KL, Linderman JJ, Omann GM. Cytometry. 45(2) : 102-114, 2001.

Uncovering biases in high throughput screens of G-protein coupled receptors.
Woolf PJ, Kenakin TP, Linderman JJ. Journal of Theoretical Biology. 208(4) : 403-418, 2001.

2000

Timing is everything the role of kinetics in G protein activation.
Shea LD, Neubig RR, Linderman JJ. Life Sciences. 68(6) : 647-658, 2000.

1999

Modeling activation and desensitization of G-protein coupled receptors provides insight into ligand efficacy.
Riccobene TA, Omann GM, Linderman JJ. Journal of Theoretical Biology. 200(2) : 207-222, 1999.