Publications, 1997-2016

PubMed Summary

2016

Johnson HE, Haugh JM (2016).
Are filopodia privileged signaling structures in migrating cells?
Biophysical Journal, 111: 1827-1830. (doi:10.1016/j.bpj.2016.09.022)
Liu X, Asokan SB, Bear JE, Haugh JM (2016).
Quantitative analysis of B-lymphocyte migration directed by CXCL13.
Integrative Biology, 8: 894-903. (doi:10.1039/c6ib00128a)
King SJ, Asokan SB, Haynes EM, Zimmerman SP, Rotty JD, Alb JG Jr, Tagliatela A, Blake DR, Lebedeva IP, Marston D, Johnson HE, Parsons M, Sharpless NE,
Kuhlman B, Haugh JM, Bear JE (2016).
Lamellipodia are crucial for haptotactic sensing and response.
Journal of Cell Science, 129: 2329-2342. (doi:10.1242/jcs.184507)
Lauffenburger DA, Haugh JM, Byrne HM, Linding R (2016).
Systems cell biology: an overview.
in Encyclopedia of Cell Biology, RA Bradshaw and PD Stahl, Editors-in-Chief.
Volume 4, pp. 1-3. Academic Press, Waltham, MA. (doi:10.1016/B978-0-12-394447-4.40044-1)

2015

Haynes EM, Asokan SB, King SJ, Johnson HE, Haugh JM, Bear JE (2015).
GMFβ controls branched actin content and lamellipodial retraction in fibroblasts.
Journal of Cell Biology, 209: 803-812. (doi:10.1083/jcb.201501094)
Liu X, Welf ES, Haugh JM (2015).
Linking morphodynamics and directional persistence of T lymphocyte migration.
Journal of the Royal Society Interface, 12: pii:20141412. (doi:10.1098/rsif.2014.1412)
Herring LE, Grant KG, Blackburn K, Haugh JM, Goshe MB (2015).
Development of a tandem affinity phosphoproteomic method with motif
selectivity and its application in analysis of signal transduction networks.
Journal of Chromatography B, 988: 166-174. (doi:10.1016/j.jchromb.2015.02.017)
Johnson HE, King SJ, Asokan SB, Rotty JD, Bear JE, Haugh JM (2015).
F-actin bundles direct the initiation and orientation of lamellipodia
through adhesion-based signaling.
Journal of Cell Biology, 208: 443-455. (doi:10.1083/jcb.201406102)
Featured in the biosights podcast series and JCB journal club
Rotty JD, Wu C, Haynes EM, Winkelman JD, Suarez C, Johnson HE, Haugh JM,
Kovar DR, Bear JE (2015).
Profilin-1 serves as a gatekeeper for actin assembly by Arp2/3-dependent
and -independent pathways.
Developmental Cell, 32: 54-67. (doi:10.1016/j.devcel.2014.10.026)

2014

Asokan SB, Johnson HE, Rahman A, King SJ, Rotty JD, Lebedeva I, Haugh JM,
Bear JE (2014).
Mesenchymal chemotaxis requires selective inactivation of Myosin II
at the leading edge via a non-canonical PLCγ/PKCα pathway.
Developmental Cell, 31: 747-760. (doi:10.1016/j.devcel.2014.10.024)
Rahman A, Haugh JM (2014).
Deactivation of a negative regulator: a distinct signal transduction mechanism,
pronounced in Akt signaling.
Biophysical Journal, 107: L29-L32. (doi:10.1016/j.bpj.2014.10.003)
Vernekar VN, Wallace CS, Wu M, Chao JT, O'Connor S, Raleigh A, Liu X,
Haugh JM, Reichert WM (2014).
Bi-ligand surfaces with oriented and patterned protein for real-time tracking
of cell migration.
Colloids and Surfaces B: Biointerfaces, 123: 225-235. (doi:10.1016/j.colsurfb.2014.09.020)
Bear JE, Haugh JM (2014).
Directed migration of mesenchymal cells: where signaling and
the cytoskeleton meet.
Current Opinion in Cell Biology, 30C: 74-82. (doi:10.1016/j.ceb.2014.06.005)
Ahmed S, Grant KG, Edwards LE, Rahman A, Cirit M, Goshe MB, Haugh JM (2014).
Data-driven modeling reconciles kinetics of ERK phosphorylation, localization, and activity states.
Molecular Systems Biology, 10: 718 (14 pages). (doi:10.1002/msb.134708)

2013

Johnson HE, Haugh JM (2013).
Quantitative analysis of phosphoinositide 3-kinase (PI3K) signaling using live-cell
total internal reflection fluorescence (TIRF) microscopy.
Current Protocols in Cell Biology, 61: 14.14.1-24 (Methods Article). (doi:10.1002/0471143030.cb1414s61)
Welf ES, Johnson HE, Haugh JM (2013).
Bidirectional coupling between integrin-mediated signaling and actomyosin mechanics explains matrix-dependent intermittency of leading-edge motility.
Molecular Biology of the Cell, 24: 3945-3955. (doi:10.1091/mbc.E13-06-0311)
Ott LE, Sung EJ, Melvin AT, Sheats MK, Haugh JM, Adler KB, Jones SL (2013).
Fibroblast migration is regulated by Myristoylated Alanine-Rich C-Kinase Substrate
(MARCKS) protein.
PLOS ONE, 8: e66512. (doi:10.1371/journal.pone.0066512)

2012

Cirit M, Grant KG, Haugh JM (2012).
Systemic perturbation of the ERK signaling pathway by the
proteasome inhibitor, MG132.
PLOS ONE, 7: e50975. (doi:10.1371/journal.pone.0050975)
Haugh JM (2012).
Cell regulation: a time to signal, a time to respond.
BioEssays, 34: 528-529 (Comment). (doi:10.1002/bies.201200077)
Haugh JM (2012).
Live-cell fluorescence microscopy with molecular biosensors:
What are we really measuring?
Biophysical Journal, 102: 2003-2011 (featured article). (doi:10.1016/j.bpj.2012.03.055)
Featured in the Biophysical Journal best of 2012 issue
Welf ES, Ahmed S, Johnson, HE, Melvin AT, Haugh JM (2012).
Migrating fibroblasts reorient directionality by a metastable,
PI3K-dependent mechanism.
Journal of Cell Biology, 197: 105-114. (doi:10.1083/jcb.201108152)
Featured in the biosights podcast series and JCB journal club
Featured in the Cell Migration Gateway
Welf ES, Haugh JM (2012).
Stochastic models of cell protrusion arising from spatiotemporal signaling
and adhesion dynamics.
Methods in Cell Biology, 110: 223-241 (Methods Article). (doi:10.1016/B978-0-12-388403-9.00009-6)
Cirit M, Haugh JM (2012).
Data-driven modelling of receptor tyrosine kinase signalling networks quantifies receptor-specific potencies of PI3K- and Ras-dependent ERK activation.
Biochemical Journal, 441: 77-85. (doi:10.1042/BJ20110833)

2011

Haugh JM (2011).
Cells see the light to bring signaling under control.
Nature Methods, 8: 808-809 (News & Views). (doi:10.1038/nmeth.1708)
Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS (2011).
Guidelines for visualizing and annotating rule-based models.
Molecular BioSystems, 7: 2779-2795. (doi:10.1039/C1MB05077J)
Cirit M, Haugh JM (2011).
Quantitative models of signal transduction networks: How detailed should they be?
Communicative & Integrative Biology, 4: 353-356 (Addendum Article). (doi:10.4161/cib.4.3.15149)
Melvin AT, Welf ES, Wang Y, Irvine DJ, Haugh JM (2011).
In chemotaxing fibroblasts, both high-fidelity and weakly biased cell movements
track the localization of PI3K signaling.
Biophysical Journal, 100: 1893-1901 (featured article). (doi:10.1016/j.bpj.2011.02.047)
Ahmed S, Yang H, Ozcam AE, Efimenko K, Weiger MC, Genzer J, Haugh JM (2011).
Poly(vinylmethylsiloxane) elastomer networks as functional materials for
cell adhesion and migration studies.
Biomacromolecules, 12: 1265-1271. (doi:10.1021/bm101549y)
Welf ES, Haugh JM (2011).
Signaling pathways that control cell migration: models and analysis.
Wiley Interdisciplinary Reviews Systems Biology & Medicine, 3: 231-240
(Focused Review). (doi:10.1002/wsbm.110)
Buhrman G, Kumar VSS, Cirit M, Haugh JM, Mattos C (2011).
Allosteric modulation of Ras-GTP is linked to signal transduction
through Raf kinase.
Journal of Biological Chemistry, 286: 3323-3331. (doi:10.1074/jbc.M110.193854)

2010

Cirit M, Wang C-C, Haugh JM (2010).
Systematic quantification of negative feedback mechanisms in the
extracellular signal-regulated kinase (ERK) signaling network.
Journal of Biological Chemistry, 285: 36736-36744. (doi:10.1074/jbc.M110.148759)
Cirit M, Krajcovic M, Choi CK, Welf ES, Horwitz AF, Haugh JM (2010).
Stochastic model of integrin-mediated signaling and adhesion dynamics
at the leading edges of migrating cells.
PLOS Computational Biology, 6: e1000688. (doi:10.1371/journal.pcbi.1000688)
Featured in the Cell Migration Gateway
Welf ES, Haugh JM (2010).
Stochastic dynamics of membrane protrusion mediated by the DOCK180/Rac pathway in migrating cells.
Cellular and Molecular Bioengineering, 3: 30-39. (doi:10.1007/s12195-010-0100-8)
Featured in the Cell Migration Gateway
Weiger MC, Ahmed S, Welf ES, Haugh JM (2010).
Directional persistence of cell migration coincides with stability of
asymmetric intracellular signaling.
Biophysical Journal, 98: 67-75 (featured article). (doi:10.1016/j.bpj.2009.09.051)
Featured by Faculty of 1000 and in the Cell Migration Gateway

2009

Haugh JM (2009).
Analysis of reaction-diffusion systems with anomalous subdiffusion.
Biophysical Journal, 97: 435-442. (doi:10.1016/j.bpj.2009.05.014)
Haugh JM, Elston TC, Cirit M, Wang C-C, Hao N, Yildirim N (2009).
Data-driven, mechanistic modeling of biochemical reaction networks.
In Methods in Bioengineering: Systems Analysis of Biological Networks.
A. Jayaraman and J. Hahn, eds., Artech House, pp. 57-74. (Review)
(ISBN 978-1-59693-406-1)
Barua D, Faeder JR, Haugh JM (2009).
A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases.
PLOS Computational Biology, 5: e1000364 (9 pages). (doi:10.1371/journal.pcbi.1000364)
Wang C-C, Cirit M, Haugh JM (2009).
PI3K-dependent crosstalk interactions converge with Ras as quantifiable inputs integrated by Erk.
Molecular Systems Biology, 5: 246 (11 pages). (doi:10.1038/msb.2009.4)
Weiger MC, Wang C-C, Krajcovic M, Melvin AT, Rhoden JJ, Haugh JM (2009).
Spontaneous phosphoinositide 3-kinase signaling dynamics drive spreading
and random migration of fibroblasts.
Journal of Cell Science, 122: 313-323. (doi:10.1242/jcs.037564)

2008

Monine MI, Haugh JM (2008).
Cell population-based model of dermal wound invasion with heterogeneous
intracellular signaling properties.
Cell Adhesion & Migration, 2: 137-145. (link)
(Simulation codes and instructions)
Haugh JM (2008).
Cells get in shape for a crawl.
Nature, 453: 461-462. (News & Views)
(doi:10.1038/453461a)
Monine MI, Haugh JM (2008).
Signal transduction at point-blank range: analysis of a spatial coupling mechanism for pathway crosstalk.
Biophysical Journal, 95: 2172-2182. (doi:10.1529/biophysj.108.128892)
Featured in the Cell Migration Gateway and the Signaling Gateway
(Simulation codes and instructions)
Comfort KK, Haugh JM (2008).
Combinatorial signal transduction responses mediated by interleukin-2 and -4 receptors in a helper TH2 cell line.
Cellular and Molecular Bioengineering, 1: 163-172. (doi:10.1007/s12195-008-0015-9)
Barua D, Faeder JR, Haugh JM (2008).
Computational models of tandem Src homology 2 domain interactions and application to phosphoinositide 3-kinase.
Journal of Biological Chemistry, 283: 7338-7345. (doi:10.1074/jbc.M708359200)
DeLisa M, Haugh J (2008).
First International Conference on Biomolecular Engineering (ICBE).
Biotechnology Progress, 24: 1. (Editorial)
(doi:10.1021/bp0704889)
See the special issue on the 1st ICBE
Haugh JM (2008).
Mathematical modeling of biological signaling networks.
In Wiley Encyclopedia of Chemical Biology.  John Wiley & Sons. (Review) (doi:10.1002/9780470048672.wecb646)

2007

Haugh JM (2007).
Membrane-binding/modification model of signaling protein activation and
analysis of its control by cell morphology.
Biophysical Journal, 92: L93-L95. (doi:10.1529/biophysj.107.105213)
Haugh JM, Kelly RM (2007).
Biochemical Engineering.
In Encyclopedia of Science & Technology, 10th Ed.  McGraw-Hill.
Barua D, Faeder JR, Haugh JM (2007).
Structure-based kinetic models of modular signaling protein function:
Focus on Shp2.
Biophysical Journal, 92: 2290-2300. (doi:10.1529/biophysj.106.093484)
Haugh JM, Weiger MC (2007).
Modeling intracellular signal transduction processes.
In Chemical Biology: From Small Molecules to Systems Biology and Drug Design,
S. Schreiber, T. Kapoor, & G. Wess, eds.  Wiley-VCH, Vol. 3, pp. 1061-1081. (Review)
ISBN-10: 3-527-31150-5

2006

Schneider IC, Haugh JM (2006).
Mechanisms of gradient sensing and chemotaxis:
Conserved pathways, diverse regulation.
Cell Cycle, 5: 1130-1134. (Extra View)
(link)
Haugh JM, Schneider IC (2006).
Effectiveness factor for spatial gradient sensing in living cells.
Chemical Engineering Science, 61: 5603-5611. (doi:10.1016/j.ces.2006.04.041)
Haugh JM (2006).
Deterministic model of dermal wound invasion incorporating receptor-mediated signal transduction and spatial gradient sensing.
Biophysical Journal, 90: 2297-2308. (doi:10.1529/biophysj.105.077610)
Kaur H*, Park CS*, Lewis JM, Haugh JM (2006).  (*co-first authors).
Quantitative model of Ras/phosphoinositide 3-kinase signalling cross-talk
based on co-operative molecular assembly.
Biochemical Journal, 393: 235-243. (doi:10.1042/BJ20051022)

2005

Schneider IC, Haugh JM (2005).
Quantitative elucidation of a distinct spatial gradient-sensing mechanism
in fibroblasts.
Journal of Cell Biology, 171: 883-892. (doi:10.1083/jcb.200509028)
Featured in JCB      Featured in the Cell Migration Gateway
Monine MI, Haugh JM (2005).
Reactions on cell membranes: Comparison of continuum theory and
Brownian dynamics simulations.
Journal of Chemical Physics, 123: 074908 (6 pages). (doi:10.1063/1.2000236)
(Simulation codes and instructions)
Schneider IC, Parrish EM, Haugh JM (2005).
Spatial analysis of 3' phosphoinositide signaling in living fibroblasts,
III: Influence of cell morphology and morphological polarity.
Biophysical Journal, 89: 1420-1430. (doi:10.1529/biophysj.105.061218)

2004

Haugh JM (2004).
Mathematical model of human growth hormone (hGH)-stimulated cell proliferation explains the efficacy of hGH variants as receptor agonists or antagonists.
Biotechnology Progress, 20: 1337-1344. (doi:10.1021/bp0499101)
Haugh JM, Schneider IC, Lewis JM (2004).
On the cross-regulation of protein tyrosine phosphatases and receptor tyrosine kinases in intracellular signaling.
Journal of Theoretical Biology, 230: 119-132. (doi:10.1016/j.jtbi.2004.04.023)
Schneider IC, Haugh JM (2004).
Spatial analysis of 3' phosphoinositide signaling in living fibroblasts:
II. Parameter estimates for individual cells from experiments.
Biophysical Journal, 86: 599-608. (link)
Haugh JM, Schneider IC (2004).
Spatial analysis of 3' phosphoinositide signaling in living fibroblasts:
I. Uniform stimulation model and bounds on dimensionless groups.
Biophysical Journal, 86: 589-598. (link)

2003

Park CS, Schneider IC, Haugh JM (2003).
Kinetic analysis of platelet-derived growth factor receptor/phosphoinositide 3-kinase/Akt signaling in fibroblasts.
Journal of Biological Chemistry, 278: 37064-37072. (link)

2002

Haugh JM (2002).
Localization of receptor-mediated signal transduction pathways: The inside story.
Molecular Interventions, 2: 292-307. (Review)
(link)
Haugh JM (2002).
A unified model for signal transduction reactions in cellular membranes.
Biophysical Journal, 82: 591-604. (link)
Haugh JM, Meyer T (2002).
Active EGF receptors have limited access to PI(4,5)P2 in endosomes:
implications for phospholipase C and PI 3-kinase signaling.
Journal of Cell Science, 115: 303-310. (link)

1997-2000

Haugh JM, Codazzi F, Teruel M, Meyer T (2000).
Spatial sensing in fibroblasts mediated by 3' phosphoinositides.
Journal of Cell Biology, 151: 1269-1279. (doi:10.1083/jcb.151.6.1269)
Featured in JCB
Haugh JM, Wells A, Lauffenburger DA (2000).
Mathematical modeling of epidermal growth factor receptor signaling through the phospholipase C pathway: Mechanistic insights and predictions for molecular interventions.
Biotechnology & Bioengineering, 70: 225-238. (link)
Haugh JM, Huang AC, Wiley HS, Wells A, Lauffenburger DA (1999).
Internalized epidermal growth factor receptors participate in the activation of p21(ras) in fibroblasts.
Journal of Biological Chemistry, 274: 34350-34360. (link)
Haugh JM, Schooler K, Wells A, Wiley HS, Lauffenburger DA (1999).
Effect of epidermal growth factor receptor internalization on regulation of the phospholipase C-γ1 signaling pathway.
Journal of Biological Chemistry, 274: 8958-8965. (link)
Lauffenburger DA, Fallon EF, Haugh JM (1998).
Scratching the (cell) surface: Cytokine engineering for improved ligand/receptor trafficking dynamics.
Chemistry & Biology, 5: R257-R263. (Review)
(doi:10.1016/S1074-5521(98)90110-7)
Haugh JM, Lauffenburger DA (1998).
Analysis of receptor internalization as a mechanism for modulating signal transduction.
Journal of Theoretical Biology, 195: 187-218. (doi:10.1006/jtbi.1998.0791)
Haugh JM, Lauffenburger DA (1997).
Physical modulation of intracellular signaling processes by locational regulation.
Biophysical Journal, 72: 2014-2031. (link to PubMed Central)