Publications by authors named "Boris N Kholodenko"

100Publications

Mapping connections in signaling networks with ambiguous modularity.

NPJ Syst Biol Appl 2019 23;5:19. Epub 2019 May 23.

2Systems Biology Ireland, University College Dublin, Dublin, Ireland.

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http://dx.doi.org/10.1038/s41540-019-0096-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6533310PMC
April 2020

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor.

PLoS Comput Biol 2019 01 17;15(1):e1006706. Epub 2019 Jan 17.

Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6353226PMC
January 2019

Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling.

Cell Syst 2018 08 11;7(2):161-179.e14. Epub 2018 Jul 11.

Systems Biology Ireland, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland; School of Medicine and Medical Science, University College Dublin, Dublin, Ireland; Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.06.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6149545PMC
August 2018

New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signaling.

Semin Cancer Biol 2019 02 5;54:162-173. Epub 2018 Mar 5.

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Ireland; School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland. Electronic address:

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http://dx.doi.org/10.1016/j.semcancer.2018.02.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6123307PMC
February 2019

Performance of objective functions and optimisation procedures for parameter estimation in system biology models.

NPJ Syst Biol Appl 2017 8;3:20. Epub 2017 Aug 8.

Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.

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http://dx.doi.org/10.1038/s41540-017-0023-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5548920PMC
August 2017

Modeling of Receptor Tyrosine Kinase Signaling: Computational and Experimental Protocols.

Methods Mol Biol 2017 ;1636:417-453

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.

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http://dx.doi.org/10.1007/978-1-4939-7154-1_27DOI Listing
April 2018

Integrating network reconstruction with mechanistic modeling to predict cancer therapies.

Sci Signal 2016 11 22;9(455):ra114. Epub 2016 Nov 22.

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.

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http://stke.sciencemag.org/cgi/doi/10.1126/scisignal.aae0535
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http://dx.doi.org/10.1126/scisignal.aae0535DOI Listing
November 2016

Probing the Heterogeneity of Protein Kinase Activation in Cells by Super-resolution Microscopy.

ACS Nano 2017 01 3;11(1):249-257. Epub 2016 Nov 3.

R. Dimbleby Department of Cancer Research, Randall Division of Cell and Molecular Biophysics, Division of Cancer Studies, King's College London , Guy's Campus New Hunt's House, London SE1 1UL, U.K.

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http://dx.doi.org/10.1021/acsnano.6b05356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5269639PMC
January 2017

SARAH Domain-Mediated MST2-RASSF Dimeric Interactions.

PLoS Comput Biol 2016 Oct 7;12(10):e1005051. Epub 2016 Oct 7.

School of Physics & Institute for Discovery, University College Dublin, Belfield, Dublin, Ireland.

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http://dx.doi.org/10.1371/journal.pcbi.1005051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5055338PMC
October 2016

Rac1 and RhoA: Networks, loops and bistability.

Small GTPases 2018 07 10;9(4):316-321. Epub 2016 Sep 10.

e Edinburgh Cancer Research Center , IGMM, University of Edinburgh , Edinburgh , UK.

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http://dx.doi.org/10.1080/21541248.2016.1224399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5997137PMC
July 2018

MAPK kinase signalling dynamics regulate cell fate decisions and drug resistance.

Curr Opin Struct Biol 2016 12 10;41:151-158. Epub 2016 Aug 10.

Systems Biology Ireland, University College Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Ireland; School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2016.07.019DOI Listing
December 2016

The complexities and versatility of the RAS-to-ERK signalling system in normal and cancer cells.

Semin Cell Dev Biol 2016 10 24;58:96-107. Epub 2016 Jun 24.

Systems Biology Ireland, UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland. Electronic address:

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http://dx.doi.org/10.1016/j.semcdb.2016.06.011DOI Listing
October 2016

Bistability in the Rac1, PAK, and RhoA Signaling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches.

Cell Syst 2016 01 27;2(1):38-48. Epub 2016 Jan 27.

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland; School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland; Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia.

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http://dx.doi.org/10.1016/j.cels.2016.01.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4802415PMC
January 2016

Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients.

Sci Signal 2015 Dec 22;8(408):ra130. Epub 2015 Dec 22.

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland. The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia. St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales 2052, Australia.

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http://dx.doi.org/10.1126/scisignal.aab0990DOI Listing
December 2015

Frequency modulation of ERK activation dynamics rewires cell fate.

Mol Syst Biol 2015 Nov 27;11(11):838. Epub 2015 Nov 27.

Department of Biomedicine, University of Basel, Basel, Switzerland

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670727PMC
http://dx.doi.org/10.15252/msb.20156458DOI Listing
November 2015

Feedback regulation in cell signalling: Lessons for cancer therapeutics.

Semin Cell Dev Biol 2016 Feb 19;50:85-94. Epub 2015 Oct 19.

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland; School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland. Electronic address:

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http://dx.doi.org/10.1016/j.semcdb.2015.09.024DOI Listing
February 2016

Drug Resistance Resulting from Kinase Dimerization Is Rationalized by Thermodynamic Factors Describing Allosteric Inhibitor Effects.

Cell Rep 2015 Sep 3;12(11):1939-49. Epub 2015 Sep 3.

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland; School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.08.014DOI Listing
September 2015

The dynamic control of signal transduction networks in cancer cells.

Nat Rev Cancer 2015 Sep 20;15(9):515-27. Epub 2015 Aug 20.

Systems Biology Ireland, University College Dublin.

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http://dx.doi.org/10.1038/nrc3983DOI Listing
September 2015

Protein-protein interactions generate hidden feedback and feed-forward loops to trigger bistable switches, oscillations and biphasic dose-responses.

Mol Biosyst 2015 Oct;11(10):2750-62

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.

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http://xlink.rsc.org/?DOI=C5MB00385G
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http://dx.doi.org/10.1039/c5mb00385gDOI Listing
October 2015

DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks.

Sci Rep 2015 Jul 29;5:12569. Epub 2015 Jul 29.

1] Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland [2] Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland [3] School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland.

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http://dx.doi.org/10.1038/srep12569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4518224PMC
July 2015

Silence on the relevant literature and errors in implementation.

Nat Biotechnol 2015 Apr;33(4):336-9

1] Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland. [2] Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland. [3] School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland.

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http://dx.doi.org/10.1038/nbt.3185DOI Listing
April 2015

Network-based identification of feedback modules that control RhoA activity and cell migration.

J Mol Cell Biol 2015 Jun 16;7(3):242-52. Epub 2015 Mar 16.

Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea

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http://dx.doi.org/10.1093/jmcb/mjv017DOI Listing
June 2015

Species differential regulation of COX2 can be described by an NFκB-dependent logic AND gate.

Cell Mol Life Sci 2015 Jun 20;72(12):2431-43. Epub 2015 Feb 20.

Systems Biology Ireland, University College Dublin, Dublin 4, Ireland.

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http://dx.doi.org/10.1007/s00018-015-1850-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4439527PMC
June 2015

Feedforward regulation of mRNA stability by prolonged extracellular signal-regulated kinase activity.

FEBS J 2015 Feb 8;282(4):613-29. Epub 2015 Jan 8.

Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences (IMS), Tsurumi-ku, Yokohama, Kanagawa, Japan.

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http://dx.doi.org/10.1111/febs.13172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4334673PMC
February 2015

Ubiquitin chain specific auto-ubiquitination triggers sustained oscillation, bistable switches and excitable firing.

IET Syst Biol 2014 Dec;8(6):282-92

School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland.

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http://dx.doi.org/10.1049/iet-syb.2014.0024DOI Listing
December 2014

The ErbB4 CYT2 variant protects EGFR from ligand-induced degradation to enhance cancer cell motility.

Sci Signal 2014 Aug 19;7(339):ra78. Epub 2014 Aug 19.

Richard Dimbleby Department of Cancer Research, Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Medical School Campus, London SE1 1UL, UK. Division of Cancer Studies, King's College London, London SE1 1UL, UK. Breakthrough Breast Cancer Research Unit, Research Oncology, King's College London, Guy's Hospital, London SE1 9RT, UK. UCL Cancer Institute, Paul O'Gorman Building, University College London, London WC1E 6BT, UK.

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http://dx.doi.org/10.1126/scisignal.2005157DOI Listing
August 2014

Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses.

J R Soc Interface 2014 Sep;11(98):20140383

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland

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http://dx.doi.org/10.1098/rsif.2014.0383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233687PMC
September 2014

Protein interaction switches coordinate Raf-1 and MST2/Hippo signalling.

Nat Cell Biol 2014 Jul 15;16(7):673-84. Epub 2014 Jun 15.

1] Systems Biology Ireland, University College Dublin, Dublin 4, Ireland [2] Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland [3] School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Ireland [4].

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http://dx.doi.org/10.1038/ncb2986DOI Listing
July 2014

The APC network regulates the removal of mutated cells from colonic crypts.

Cell Rep 2014 Apr 27;7(1):94-103. Epub 2014 Mar 27.

Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.02.043DOI Listing
April 2014

Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration.

PLoS Comput Biol 2014 Feb 13;10(2):e1003385. Epub 2014 Feb 13.

Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland ; Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland ; School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland.

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http://dx.doi.org/10.1371/journal.pcbi.1003385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3923657PMC
February 2014

Polyubiquitin chain assembly and organization determine the dynamics of protein activation and degradation.

Front Physiol 2014 24;5. Epub 2014 Jan 24.

Systems Biology Ireland, University College Dublin Dublin, Ireland ; Conway Institute, University College Dublin Dublin, Ireland ; School of Medicine and Medical Science, University College Dublin Dublin, Ireland.

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http://dx.doi.org/10.3389/fphys.2014.00004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901042PMC
January 2014

Evaluating strategies to normalise biological replicates of Western blot data.

PLoS One 2014 27;9(1):e87293. Epub 2014 Jan 27.

Systems Biology Ireland, University College Dublin, Dublin, Republic of Ireland ; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Republic of Ireland ; School of Medicine and Medical Science, University College Dublin, Dublin, Republic of Ireland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087293PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3903630PMC
September 2014

Systems biology-embedded target validation: improving efficacy in drug discovery.

Wiley Interdiscip Rev Syst Biol Med 2014 Jan-Feb;6(1):1-11. Epub 2013 Nov 8.

Systems Biology Ireland, University College Dublin, Dublin, Ireland.

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http://doi.wiley.com/10.1002/wsbm.1253
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http://dx.doi.org/10.1002/wsbm.1253DOI Listing
October 2014

Systems medicine: opportunities and challenges for systems biology approaches.

FEBS J 2013 Dec 30;280(23):5937. Epub 2013 Oct 30.

Systems Biology Ireland, Conway Institute of Biomolecular and Biomedical Research and School of Medicine and Medical Science, University College Dublin, Ireland.

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http://dx.doi.org/10.1111/febs.12560DOI Listing
December 2013

Complexity of receptor tyrosine kinase signal processing.

Cold Spring Harb Perspect Biol 2013 Aug 1;5(8):a009043. Epub 2013 Aug 1.

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.

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http://dx.doi.org/10.1101/cshperspect.a009043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3721286PMC
August 2013

When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling.

Cell Commun Signal 2013 Jul 31;11:52. Epub 2013 Jul 31.

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.

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http://dx.doi.org/10.1186/1478-811X-11-52DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734146PMC
July 2013

Control of the G-protein cascade dynamics by GDP dissociation inhibitors.

Mol Biosyst 2013 Oct;9(10):2454-62

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.

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http://dx.doi.org/10.1039/c3mb70152bDOI Listing
October 2013

Pseudophosphatase STYX modulates cell-fate decisions and cell migration by spatiotemporal regulation of ERK1/2.

Proc Natl Acad Sci U S A 2013 Jul 11;110(31):E2934-43. Epub 2013 Jul 11.

Biotechnology Institute Thurgau, University of Konstanz, Kreuzlingen, Switzerland.

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http://dx.doi.org/10.1073/pnas.1301985110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3732994PMC
July 2013

Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology.

BMC Syst Biol 2013 Jul 6;7:57. Epub 2013 Jul 6.

Systems Biology Ireland, Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.

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http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
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http://dx.doi.org/10.1186/1752-0509-7-57DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726398PMC
July 2013

A dynamic model of the hypoxia-inducible factor 1α (HIF-1α) network.

J Cell Sci 2013 Mar 6;126(Pt 6):1454-63. Epub 2013 Feb 6.

Systems Biology Ireland, University College Dublin, Dublin 4, Ireland.

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http://dx.doi.org/10.1242/jcs.119974DOI Listing
March 2013

It takes two to tango--signalling by dimeric Raf kinases.

Mol Biosyst 2013 Apr;9(4):551-8

Systems Biology Ireland, University College Dublin, Dublin 4, Ireland.

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http://xlink.rsc.org/?DOI=C2MB25393C
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http://dx.doi.org/10.1039/c2mb25393cDOI Listing
April 2013

Crosstalk and signaling switches in mitogen-activated protein kinase cascades.

Front Physiol 2012 18;3:355. Epub 2012 Sep 18.

Systems Biology Ireland, University College Dublin Dublin, Ireland.

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http://journal.frontiersin.org/article/10.3389/fphys.2012.00
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http://dx.doi.org/10.3389/fphys.2012.00355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3449335PMC
October 2012

Mammalian protein expression noise: scaling principles and the implications for knockdown experiments.

Mol Biosyst 2012 Nov;8(11):3068-76

Mount Sinai School of Medicine, Dept. of Pharmacology and Systems Therapeutics, New York, NY 10029, USA.

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http://xlink.rsc.org/?DOI=c2mb25168j
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http://dx.doi.org/10.1039/c2mb25168jDOI Listing
November 2012

Catching transcriptional regulation by thermostatistical modeling.

Phys Biol 2012 Aug 7;9(4):045007. Epub 2012 Aug 7.

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.

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http://dx.doi.org/10.1088/1478-3975/9/4/045007DOI Listing
August 2012

Signalling by protein phosphatases and drug development: a systems-centred view.

FEBS J 2013 Jan 14;280(2):751-65. Epub 2012 Mar 14.

Systems Biology Ireland, University College Dublin, Belfield, Ireland.

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http://dx.doi.org/10.1111/j.1742-4658.2012.08522.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368988PMC
January 2013

Cross-talk between mitogenic Ras/MAPK and survival PI3K/Akt pathways: a fine balance.

Biochem Soc Trans 2012 Feb;40(1):139-46

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.

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http://www.biochemsoctrans.org/content/ppbiost/40/1/139.full
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http://researchrepository.ucd.ie/bitstream/handle/10197/5019
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http://biochemsoctrans.org/lookup/doi/10.1042/BST20110609
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http://dx.doi.org/10.1042/BST20110609DOI Listing
February 2012

The topology design principles that determine the spatiotemporal dynamics of G-protein cascades.

Mol Biosyst 2012 Mar 4;8(3):730-43. Epub 2012 Jan 4.

Institute of Theoretical and Experimental Biophysics, Pushchino, Moscow Region, Russia.

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http://dx.doi.org/10.1039/c2mb05375fDOI Listing
March 2012

Switches, excitable responses and oscillations in the Ring1B/Bmi1 ubiquitination system.

PLoS Comput Biol 2011 Dec 15;7(12):e1002317. Epub 2011 Dec 15.

Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.

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http://dx.doi.org/10.1371/journal.pcbi.1002317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240587PMC
December 2011

Prolactin-stimulated activation of ERK1/2 mitogen-activated protein kinases is controlled by PI3-kinase/Rac/PAK signaling pathway in breast cancer cells.

Cell Signal 2011 Nov 25;23(11):1794-805. Epub 2011 Jun 25.

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust St., Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1016/j.cellsig.2011.06.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156300PMC
November 2011

Signalling over a distance: gradient patterns and phosphorylation waves within single cells.

Biochem Soc Trans 2010 Oct;38(5):1235-41

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.

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http://dx.doi.org/10.1042/BST0381235DOI Listing
October 2010

Formation of intracellular concentration landscapes by multisite protein modification.

Biophys J 2010 Jul;99(1):59-66

Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.

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http://dx.doi.org/10.1016/j.bpj.2010.04.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895390PMC
July 2010

Signalling ballet in space and time.

Nat Rev Mol Cell Biol 2010 Jun;11(6):414-26

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.

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http://www.nature.com/articles/nrm2901
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http://dx.doi.org/10.1038/nrm2901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2977972PMC
June 2010

Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics.

Cell 2010 May 20;141(5):884-96. Epub 2010 May 20.

Computational Systems Biology Research Group, Advanced Computational Sciences Department, RIKEN Advanced Science Institute, 1-7-22 Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1016/j.cell.2010.03.054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2888034PMC
May 2010

PI3K/Akt-sensitive MEK-independent compensatory circuit of ERK activation in ER-positive PI3K-mutant T47D breast cancer cells.

Cell Signal 2010 Sep 12;22(9):1369-78. Epub 2010 May 12.

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust St., Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1016/j.cellsig.2010.05.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2893265PMC
September 2010

Four-dimensional dynamics of MAPK information processing systems.

Wiley Interdiscip Rev Syst Biol Med 2009 Jul-Aug;1(1):28-44

Departement of Chemical Engineering, University of Delaware, Newark, DE 19716, USA.

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http://dx.doi.org/10.1002/wsbm.16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826817PMC
December 2010

Spatially distributed cell signalling.

FEBS Lett 2009 Dec;583(24):4006-12

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.

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http://dx.doi.org/10.1016/j.febslet.2009.09.045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795127PMC
December 2009

Toggle switches, pulses and oscillations are intrinsic properties of the Src activation/deactivation cycle.

FEBS J 2009 Aug;276(15):4102-18

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA.

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http://dx.doi.org/10.1111/j.1742-4658.2009.07117.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2924194PMC
August 2009

Endocytosis and signalling: a meeting with mathematics.

Mol Oncol 2009 Aug 16;3(4):308-20. Epub 2009 Jun 16.

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.

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http://dx.doi.org/10.1016/j.molonc.2009.05.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745732PMC
August 2009

Systems-level interactions between insulin-EGF networks amplify mitogenic signaling.

Mol Syst Biol 2009 7;5:256. Epub 2009 Apr 7.

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683723PMC
June 2009

Positional information generated by spatially distributed signaling cascades.

PLoS Comput Biol 2009 Mar 20;5(3):e1000330. Epub 2009 Mar 20.

School of Mathematical Sciences and Complex Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654021PMC
March 2009

Spatio-temporal dynamics of protein modification cascades.

SEB Exp Biol Ser 2008 ;61:141-59

Department of Pathology, Anatomy and Cell Biology, Jefferson Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.

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July 2011

Giving space to cell signaling.

Cell 2008 May;133(4):566-7

Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1016/j.cell.2008.04.033DOI Listing
May 2008

Signaling cascades as cellular devices for spatial computations.

J Math Biol 2009 Jan 19;58(1-2):35-55. Epub 2008 Feb 19.

Institute of Computational Science and Swiss Institute of Bioinformatics, ETH Zurich, 8092, Zurich, Switzerland.

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http://dx.doi.org/10.1007/s00285-008-0162-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2574718PMC
January 2009

Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses.

Mol Syst Biol 2007 13;3:144. Epub 2007 Nov 13.

Department of Chemical Engineering, University of Delaware, Newark, DE, USA.

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http://dx.doi.org/10.1038/msb4100188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2132449PMC
December 2007

Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades.

Mol Syst Biol 2006 14;2:61. Epub 2006 Nov 14.

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Locust St, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1038/msb4100108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1682027PMC
January 2007

Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation.

J Theor Biol 2007 Jan 23;244(1):68-76. Epub 2006 May 23.

Keck Graduate Institute, 535 Watson Dr, Claremont, CA 91711, USA.

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http://dx.doi.org/10.1016/j.jtbi.2006.05.013DOI Listing
January 2007

Bistability from double phosphorylation in signal transduction. Kinetic and structural requirements.

FEBS J 2006 Sep;273(17):3915-26

Centre for Research in Theoretical Chemistry, Scientific Park of Barcelona, Spain.

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September 2006

Scaffolding protein Grb2-associated binder 1 sustains epidermal growth factor-induced mitogenic and survival signaling by multiple positive feedback loops.

J Biol Chem 2006 Jul 9;281(29):19925-38. Epub 2006 May 9.

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1074/jbc.M600482200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2312093PMC
July 2006

Cell-signalling dynamics in time and space.

Nat Rev Mol Cell Biol 2006 Mar;7(3):165-76

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1038/nrm1838DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1679905PMC
March 2006

Effects of sequestration on signal transduction cascades.

FEBS J 2006 Mar;273(5):895-906

Institute for Theoretical Biology, Humboldt University Berlin, Germany.

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March 2006

A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks.

BMC Bioinformatics 2006 Jan 23;7:34. Epub 2006 Jan 23.

Institute for System Dynamics and Control Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany.

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http://dx.doi.org/10.1186/1471-2105-7-34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1413560PMC
January 2006

Trading the micro-world of combinatorial complexity for the macro-world of protein interaction domains.

Biosystems 2006 Feb-Mar;83(2-3):152-66. Epub 2005 Oct 19.

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust St., Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1016/j.biosystems.2005.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1477537PMC
April 2006

Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity.

Biophys J 2005 Aug 27;89(2):951-66. Epub 2005 May 27.

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1529/biophysj.105.060533DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1366644PMC
August 2005

Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy.

J Theor Biol 2005 Feb;232(3):427-41

Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8087, USA.

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February 2005

Quantitative analysis of signaling networks.

Prog Biophys Mol Biol 2004 Sep;86(1):5-43

Computational Biology, Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.

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http://dx.doi.org/10.1016/j.pbiomolbio.2004.03.002DOI Listing
September 2004

Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data.

Bioinformatics 2004 Aug 22;20(12):1877-86. Epub 2004 Mar 22.

Department of Mathematics, Rutgers University, Piscataway, NJ 08854, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth173DOI Listing
August 2004

Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades.

J Cell Biol 2004 Feb 26;164(3):353-9. Epub 2004 Jan 26.

Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, 1020 Locust St., Philadelphia, PA 19107, USA.

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http://www.jcb.org/lookup/doi/10.1083/jcb.200308060
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2172246PMC
February 2004

Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law.

J Theor Biol 2003 Dec;225(4):477-87

Centrum voor Wiskunde en Informatica, Kruislaan 413, 1098 SJ Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/s0022-5193(03)00289-3DOI Listing
December 2003

Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors.

J Exp Biol 2003 Jun;206(Pt 12):2073-82

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1242/jeb.00298DOI Listing
June 2003