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Items: 1 to 50 of 59

1.

A device for high-throughput monitoring of degradation in soft tissue samples.

Tzeranis DS, Panagiotopoulos I, Gkouma S, Kanakaris G, Georgiou N, Vaindirlis N, Vasileiou G, Neidlin M, Gkousioudi A, Spitas V, Macheras GA, Alexopoulos LG.

J Biomech. 2018 Jun 6;74:180-186. doi: 10.1016/j.jbiomech.2018.04.040. Epub 2018 May 3.

PMID:
29773424
2.

Selective cytotoxicity of the herbal substance acteoside against tumor cells and its mechanistic insights.

Cheimonidi C, Samara P, Polychronopoulos P, Tsakiri EN, Nikou T, Myrianthopoulos V, Sakellaropoulos T, Zoumpourlis V, Mikros E, Papassideri I, Argyropoulou A, Halabalaki M, Alexopoulos LG, Skaltsounis AL, Tsitsilonis OE, Aligiannis NN, Trougakos IP.

Redox Biol. 2018 Jun;16:169-178. doi: 10.1016/j.redox.2018.02.015. Epub 2018 Mar 1.

3.

Translational systems pharmacology-based predictive assessment of drug-induced cardiomyopathy.

Messinis DE, Melas IN, Hur J, Varshney N, Alexopoulos LG, Bai JPF.

CPT Pharmacometrics Syst Pharmacol. 2018 Mar;7(3):166-174. doi: 10.1002/psp4.12272. Epub 2018 Jan 17.

4.

Network-based technologies for early drug discovery.

Fotis C, Antoranz A, Hatziavramidis D, Sakellaropoulos T, Alexopoulos LG.

Drug Discov Today. 2018 Mar;23(3):626-635. doi: 10.1016/j.drudis.2017.12.001. Epub 2017 Dec 30. Review.

PMID:
29294361
5.

Cue-Signal-Response Analysis in 3D Chondrocyte Scaffolds with Anabolic Stimuli.

Neidlin M, Korcari A, Macheras G, Alexopoulos LG.

Ann Biomed Eng. 2018 Feb;46(2):345-353. doi: 10.1007/s10439-017-1964-8. Epub 2017 Nov 16.

PMID:
29147820
6.

Dynamics and heterogeneity of brain damage in multiple sclerosis.

Kotelnikova E, Kiani NA, Abad E, Martinez-Lapiscina EH, Andorra M, Zubizarreta I, Pulido-Valdeolivas I, Pertsovskaya I, Alexopoulos LG, Olsson T, Martin R, Paul F, Tegnér J, Garcia-Ojalvo J, Villoslada P.

PLoS Comput Biol. 2017 Oct 26;13(10):e1005757. doi: 10.1371/journal.pcbi.1005757. eCollection 2017 Oct.

7.

Combined Virtual and Experimental Screening for CK1 Inhibitors Identifies a Modulator of p53 and Reveals Important Aspects of in Silico Screening Performance.

Myrianthopoulos V, Lozach O, Zareifi D, Alexopoulos L, Meijer L, Gorgoulis VG, Mikros E.

Int J Mol Sci. 2017 Oct 6;18(10). pii: E2102. doi: 10.3390/ijms18102102.

8.

Novel approaches to develop community-built biological network models for potential drug discovery.

Talikka M, Bukharov N, Hayes WS, Hofmann-Apitius M, Alexopoulos L, Peitsch MC, Hoeng J.

Expert Opin Drug Discov. 2017 Aug;12(8):849-857. doi: 10.1080/17460441.2017.1335302. Epub 2017 Jun 6. Review.

PMID:
28585481
9.

Quantifying Cartilage Biomechanical Properties Using a Linearized Frequency-Domain Method.

Gkousioudi A, Tzeranis DS, Kanakaris GP, Saloufas M, Alexopoulos LG.

Ann Biomed Eng. 2017 Sep;45(9):2061-2074. doi: 10.1007/s10439-017-1861-1. Epub 2017 Jun 1.

PMID:
28573419
10.

Mechanism-based biomarker discovery.

Antoranz A, Sakellaropoulos T, Saez-Rodriguez J, Alexopoulos LG.

Drug Discov Today. 2017 Aug;22(8):1209-1215. doi: 10.1016/j.drudis.2017.04.013. Epub 2017 Apr 27. Review.

PMID:
28458042
11.

Examining the In Vitro Efficacy of the IAP Antagonist Birinapant as a Single Agent or in Combination With Dacarbazine to Induce Melanoma Cell Death.

Vetma V, Rožanc J, Charles EM, Hellwig CT, Alexopoulos LG, Rehm M.

Oncol Res. 2017 Nov 2;25(9):1489-1494. doi: 10.3727/096504017X14897145996933. Epub 2017 Mar 23.

PMID:
28337955
12.

A Biologically-Based Computational Approach to Drug Repurposing for Anthrax Infection.

Bai JP, Sakellaropoulos T, Alexopoulos LG.

Toxins (Basel). 2017 Mar 10;9(3). pii: E99. doi: 10.3390/toxins9030099.

13.

Computed Biological Relations among Five Select Treatment-Related Organ/Tissue Toxicities.

Sakellaropoulos T, Herod TJ, Alexopoulos LG, Bai JP.

Chem Res Toxicol. 2016 May 16;29(5):914-23. doi: 10.1021/acs.chemrestox.6b00060. Epub 2016 Apr 21.

PMID:
27063352
14.

Computational Approaches to Accelerating Novel Medicine and Better Patient Care from Bedside to Benchtop.

Sakellaropoulos T, Hur J, Melas IN, Guo EY, Alexopoulos L, Bohlooly M, Bai JP.

Adv Protein Chem Struct Biol. 2016;102:147-79. doi: 10.1016/bs.apcsb.2015.09.005. Epub 2015 Oct 29. Review.

PMID:
26827605
15.

Designing Experiments to Discriminate Families of Logic Models.

Videla S, Konokotina I, Alexopoulos LG, Saez-Rodriguez J, Schaub T, Siegel A, Guziolowski C.

Front Bioeng Biotechnol. 2015 Sep 4;3:131. doi: 10.3389/fbioe.2015.00131. eCollection 2015.

16.

Network-Based Analysis of Nutraceuticals in Human Hepatocellular Carcinomas Reveals Mechanisms of Chemopreventive Action.

Michailidou M, Melas IN, Messinis DE, Klamt S, Alexopoulos LG, Kolisis FN, Loutrari H.

CPT Pharmacometrics Syst Pharmacol. 2015 Jun;4(6):350-61. doi: 10.1002/psp4.40. Epub 2015 Jun 1.

17.

Network reconstruction based on proteomic data and prior knowledge of protein connectivity using graph theory.

Stavrakas V, Melas IN, Sakellaropoulos T, Alexopoulos LG.

PLoS One. 2015 May 28;10(5):e0128411. doi: 10.1371/journal.pone.0128411. eCollection 2015.

18.

Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury.

Melas IN, Sakellaropoulos T, Iorio F, Alexopoulos LG, Loh WY, Lauffenburger DA, Saez-Rodriguez J, Bai JP.

Integr Biol (Camb). 2015 Aug;7(8):904-20. doi: 10.1039/c4ib00294f.

PMID:
25932872
19.

A crowd-sourcing approach for the construction of species-specific cell signaling networks.

Bilal E, Sakellaropoulos T, Melas IN, Messinis DE, Belcastro V, Rhrissorrakrai K, Meyer P, Norel R, Iskandar A, Blaese E, Rice JJ, Peitsch MC, Hoeng J, Stolovitzky G, Alexopoulos LG, Poussin C; Challenge Participants.

Bioinformatics. 2015 Feb 15;31(4):484-91. doi: 10.1093/bioinformatics/btu659. Epub 2014 Oct 7.

20.

Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge.

Rhrissorrakrai K, Belcastro V, Bilal E, Norel R, Poussin C, Mathis C, Dulize RH, Ivanov NV, Alexopoulos L, Rice JJ, Peitsch MC, Stolovitzky G, Meyer P, Hoeng J.

Bioinformatics. 2015 Feb 15;31(4):471-83. doi: 10.1093/bioinformatics/btu611. Epub 2014 Sep 17.

21.

Signaling networks in MS: a systems-based approach to developing new pharmacological therapies.

Kotelnikova E, Bernardo-Faura M, Silberberg G, Kiani NA, Messinis D, Melas IN, Artigas L, Schwartz E, Mazo I, Masso M, Alexopoulos LG, Mas JM, Olsson T, Tegner J, Martin R, Zamora A, Paul F, Saez-Rodriguez J, Villoslada P.

Mult Scler. 2015 Feb;21(2):138-46. doi: 10.1177/1352458514543339. Epub 2014 Aug 11. Review.

22.

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. Epub 2014 Jan 21.

23.

The species translation challenge-a systems biology perspective on human and rat bronchial epithelial cells.

Poussin C, Mathis C, Alexopoulos LG, Messinis DE, Dulize RH, Belcastro V, Melas IN, Sakellaropoulos T, Rhrissorrakrai K, Bilal E, Meyer P, Talikka M, Boué S, Norel R, Rice JJ, Stolovitzky G, Ivanov NV, Peitsch MC, Hoeng J.

Sci Data. 2014 Jun 10;1:140009. doi: 10.1038/sdata.2014.9. eCollection 2014.

24.

Identification of signaling pathways related to drug efficacy in hepatocellular carcinoma via integration of phosphoproteomic, genomic and clinical data.

Melas IN, Lauffenburger DA, Alexopoulos LG.

Proc IEEE Int Symp Bioinformatics Bioeng. 2013 Nov;2013. pii: 14026468.

25.

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. Epub 2013 Oct 18. Review.

PMID:
24141136
26.

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. Epub 2013 Sep 5.

27.

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. Epub 2013 Sep 17. Review.

28.

Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways.

Mitsos A, Melas IN, Morris MK, Saez-Rodriguez J, Lauffenburger DA, Alexopoulos LG.

PLoS One. 2012;7(11):e50085. doi: 10.1371/journal.pone.0050085. Epub 2012 Nov 30.

29.

Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data.

Melas IN, Mitsos A, Messinis DE, Weiss TS, Rodriguez JS, Alexopoulos LG.

Mol Biosyst. 2012 Apr;8(5):1571-84. doi: 10.1039/c2mb05482e. Epub 2012 Mar 23.

PMID:
22446821
30.

Modeling signaling pathways in articular cartilage.

Melas IN, Chairakaki AD, Mitsos A, Dailiana Z, Provatidis CG, Alexopoulos LG.

Conf Proc IEEE Eng Med Biol Soc. 2011;2011:3712-5. doi: 10.1109/IEMBS.2011.6090630.

PMID:
22255146
31.

Large-scale network models of IL-1 and IL-6 signalling and their hepatocellular specification.

Ryll A, Samaga R, Schaper F, Alexopoulos LG, Klamt S.

Mol Biosyst. 2011 Dec;7(12):3253-70. doi: 10.1039/c1mb05261f. Epub 2011 Oct 3.

PMID:
21968890
32.

Verification of systems biology research in the age of collaborative competition.

Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, Rice JJ, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D, Stolovitzky G.

Nat Biotechnol. 2011 Sep 8;29(9):811-5. doi: 10.1038/nbt.1968. No abstract available.

PMID:
21904331
33.

Crowdsourcing network inference: the DREAM predictive signaling network challenge.

Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G.

Sci Signal. 2011 Aug 30;4(189):mr7. doi: 10.1126/scisignal.2002212.

34.

Comparison of Goldmann and Pascal tonometry in relation to corneal hysteresis and central corneal thickness in nonglaucomatous eyes.

Mangouritsas G, Mourtzoukos S, Mantzounis A, Alexopoulos L.

Clin Ophthalmol. 2011;5:1071-7. doi: 10.2147/OPTH.S23086. Epub 2011 Aug 3.

35.

Comparing signaling networks between normal and transformed hepatocytes using discrete logical models.

Saez-Rodriguez J, Alexopoulos LG, Zhang M, Morris MK, Lauffenburger DA, Sorger PK.

Cancer Res. 2011 Aug 15;71(16):5400-11. doi: 10.1158/0008-5472.CAN-10-4453. Epub 2011 Jul 8.

36.

Combined logical and data-driven models for linking signalling pathways to cellular response.

Melas IN, Mitsos A, Messinis DE, Weiss TS, Alexopoulos LG.

BMC Syst Biol. 2011 Jul 5;5:107. doi: 10.1186/1752-0509-5-107.

37.

Strabismus in pediatric lens disorders.

Spanou N, Alexopoulos L, Manta G, Tsamadou D, Drakos H, Paikos P.

J Pediatr Ophthalmol Strabismus. 2011 May-Jun;48(3):163-6. doi: 10.3928/01913913-20100618-05. Epub 2010 Jun 23.

PMID:
21608524
38.

Setting the standards for signal transduction research.

Saez-Rodriguez J, Alexopoulos LG, Stolovitzky G.

Sci Signal. 2011 Feb 15;4(160):pe10. doi: 10.1126/scisignal.2001844.

PMID:
21325202
39.

Construction of signaling pathways and identification of drug effects on the liver cancer cell HepG2.

Alexopoulos LG, Melas IN, Chairakaki AD, Saez-Rodriguez J, Mitsos A.

Conf Proc IEEE Eng Med Biol Soc. 2010;2010:6717-20. doi: 10.1109/IEMBS.2010.5626246.

PMID:
21096084
40.

Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes.

Alexopoulos LG, Saez-Rodriguez J, Cosgrove BD, Lauffenburger DA, Sorger PK.

Mol Cell Proteomics. 2010 Sep;9(9):1849-65. doi: 10.1074/mcp.M110.000406. Epub 2010 May 10.

41.

Cytokine-associated drug toxicity in human hepatocytes is associated with signaling network dysregulation.

Cosgrove BD, Alexopoulos LG, Hang TC, Hendriks BS, Sorger PK, Griffith LG, Lauffenburger DA.

Mol Biosyst. 2010 Jul;6(7):1195-206. doi: 10.1039/b926287c. Epub 2010 Apr 1.

42.

Towards a rigorous assessment of systems biology models: the DREAM3 challenges.

Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, Stolovitzky G.

PLoS One. 2010 Feb 23;5(2):e9202. doi: 10.1371/journal.pone.0009202. Erratum in: PLoS One. 2010;5(3). doi: 10.1371/annotation/f633213a-dc4f-4bee-b6c5-72d50e7073b8.

43.

Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data.

Mitsos A, Melas IN, Siminelakis P, Chairakaki AD, Saez-Rodriguez J, Alexopoulos LG.

PLoS Comput Biol. 2009 Dec;5(12):e1000591. doi: 10.1371/journal.pcbi.1000591. Epub 2009 Dec 4.

44.

A multipathway phosphoproteomic signaling network model of idiosyncratic drug- and inflammatory cytokine-induced toxicity in human hepatocytes.

Cosgrove BD, Alexopoulos LG, Saez-Rodriguez J, Griffith LG, Lauffenburger DA.

Conf Proc IEEE Eng Med Biol Soc. 2009;2009:5452-5. doi: 10.1109/IEMBS.2009.5334019.

45.

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction.

Saez-Rodriguez J, Alexopoulos LG, Epperlein J, Samaga R, Lauffenburger DA, Klamt S, Sorger PK.

Mol Syst Biol. 2009;5:331. doi: 10.1038/msb.2009.87. Epub 2009 Dec 1.

46.

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.

PLoS Comput Biol. 2009 Aug;5(8):e1000438. doi: 10.1371/journal.pcbi.1000438. Epub 2009 Aug 7.

47.

Synergistic drug-cytokine induction of hepatocellular death as an in vitro approach for the study of inflammation-associated idiosyncratic drug hepatotoxicity.

Cosgrove BD, King BM, Hasan MA, Alexopoulos LG, Farazi PA, Hendriks BS, Griffith LG, Sorger PK, Tidor B, Xu JJ, Lauffenburger DA.

Toxicol Appl Pharmacol. 2009 Jun 15;237(3):317-30. doi: 10.1016/j.taap.2009.04.002. Epub 2009 Apr 9.

48.

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. doi: 10.1002/art.24293.

49.

Flexible informatics for linking experimental data to mathematical models via DataRail.

Saez-Rodriguez J, Goldsipe A, Muhlich J, Alexopoulos LG, Millard B, Lauffenburger DA, Sorger PK.

Bioinformatics. 2008 Mar 15;24(6):840-7. doi: 10.1093/bioinformatics/btn018. Epub 2008 Jan 24.

50.

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.

PMID:
16831947

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