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Selected Publications

Modeling of signaling pathways in chondrocytes based on phosphoproteomic and cytokine release data. Melas IN, Chairakaki AD, Chatzopoulou EI, Messinis DE, Katopodi T, Pliaka V, Samara S, Mitsos A, Dailiana Z, Kollia P, Alexopoulos LG. Osteoarthritis Cartilage. 2014 Mar;22(3):509-18. doi: 10.1016/j.joca.2014.01.001.

Phosphoproteomics in drug discovery. Morris MK, Chi A, Melas IN, Alexopoulos LG. Drug Discov Today. 2014 Apr;19(4):425-32. doi: 10.1016/j.drudis.2013.10.010.

Detecting and removing inconsistencies between experimental data and signaling network topologies using integer linear programming on interaction graphs. Melas IN, Samaga R, Alexopoulos LG, Klamt S. PLoS Comput Biol. 2013;9(9):e1003204. doi: 10.1371/journal.pcbi.1003204.

Leveraging systems biology approaches in clinical pharmacology. Melas IN, Kretsos K, Alexopoulos LG. Biopharm Drug Dispos. 2013 Dec;34(9):477-88. doi: 10.1002/bdd.1859.

Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data IN Melas , A Mitsos , DE Messinis , TS Weiss , J Saez-Rodriguez and LG Alexopoulos 2012 Mol. BioSyst., DOI: 10.1039/C2MB05482E

Verification of systems biology research in the age of collaborative competition. P Meyer, LG Alexopoulos, C Cho, A Fuente, D Graaf, AJ Hartemink, J Hoeng, NV Ivanov, H Koepp, R Linding, D Marbach, R Norel1, MC Peitsch, JJ Rice, A Royyuru, F Schacherer, J Sprengel1, D Vitkup, G Stolovitzky, Sept 2011 Nat Biotech 29: 9

Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge. RJ Prill, J Saez-Rodriguez, LG Alexopoulos, PK Sorger, G Stolovitzky. Sept 2011 Science Signal.

Combined logical and data-driven models for linking signalling pathways to cellular response. IN Melas, A Mitsos, DE Messinis , TS Weiss, LG Alexopoulos. Jul 2011 BMC Syst Biol. 5;5:107 [‘Highly accessed’ paper]

Setting the Standards for Signal Transduction Research. J Saez-Rodriguez*, LG Alexopoulos*, and G Stolovitzky (*Equal contributors) 2011 Sci. Signal., Vol. 4, Issue 160, p. pe10. doi: 10.1126/scisignal.20018441.

Networks inferred from biochemical data reveal profound differences in TLR and inflammatory signaling between normal and transformed hepatocytes. LG Alexopoulos*, J Saez-Rodriguez*, BD Cosgrove, DA Lauffenburger, PK Sorger . (*Equal contributors) 2010 Molecular & Cellular Proteomics doi: 10.1074/mcp.M110.000406

Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data. A Mitsos, I Melas, P Siminelakis, A Chairakaki, J Saez-Rodriguez, and LG Alexopoulos. 2009 PloS Comp Biol. 5(12): e1000591. doi:10.1371/journal.pcbi.1000591 *BIO-IT Best Practice Award*

The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Klamt S. 2009. PLoS Comput Biol. 5(8):e1000438.

Developmental and osteoarthritic changes in Col6a1-knockout mice: Biomechanics of type VI collagen in the cartilage pericellular matrix. Alexopoulos LG, Youn I, Bonaldo P, Guilak F. Arthritis Rheum. 2009 Mar;60(3):771-9.

The pericellular matrix as a transducer of biomechanical and biochemical signals in articular cartilage. Guilak F, Alexopoulos LG, Upton ML, Youn I, Choi JB, Cao L, Setton LA, Haider MA. Ann N Y Acad Sci. 2006 Apr;1068:498-512. Review.

The biomechanical role of the chondrocyte pericellular matrix in articular cartilage. Alexopoulos LG, Setton LA, Guilak F. Acta Biomater. 2005 May;1(3):317-25. Epub 2005 Mar 4.

Determination of the Poisson's ratio of the cell: recovery properties of chondrocytes after release from complete micropipette aspiration. Trickey WR, Baaijens FP, Laursen TA, Alexopoulos LG, Guilak F. J Biomech. 2006;39(1):78-87. Epub 2005 Jan 13.

Osteoarthritic changes in the biphasic mechanical properties of the chondrocyte pericellular matrix in articular cartilage. Alexopoulos LG, Williams GM, Upton ML, Setton LA, Guilak F. J Biomech. 2005 Mar;38(3):509-17.

Alterations in the mechanical properties of the human chondrocyte pericellular matrix with osteoarthritis. Alexopoulos LG, Haider MA, Vail TP, Guilak F. J Biomech Eng. 2003 Jun;125(3):323-33. *Richard Skalak Best Paper Award, ASME*