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1

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

Saez-Rodriguez, Julio, Alexopoulos, Leonidas G, Epperlein, Jonathan, Samaga, Regina, Lauffenburger, Douglas A, Klamt, Steffen, Sorger, Peter K

Journal:

Molecular Systems Biology

Year:

2009

Language:

english

File:

PDF, 1.83 MB

english, 2009

2

Determination of the Poisson's ratio of the cell: recovery properties of chondrocytes after release from complete micropipette aspiration

Wendy R. Trickey, Frank P.T. Baaijens, Tod A. Laursen, Leonidas G. Alexopoulos, Farshid Guilak

Journal:

Journal of Biomechanics

Year:

2006

Language:

english

File:

PDF, 415 KB

english, 2006

3

Verification of systems biology research in the age of collaborative competition

Meyer, Pablo, Alexopoulos, Leonidas G, Bonk, Thomas, Califano, Andrea, Cho, Carolyn R, de la Fuente, Alberto, de Graaf, David, Hartemink, Alexander J, Hoeng, Julia, Ivanov, Nikolai V, Koeppl, Heinz, L

Journal:

Nature Biotechnology

Year:

2011

Language:

english

File:

PDF, 492 KB

english, 2011

4

Zonal Uniformity in Mechanical Properties of the Chondrocyte Pericellular Matrix: Micropipette Aspiration of Canine Chondrons Isolated by Cartilage Homogenization

Farshid Guilak, Leonidas G. Alexopoulos, Mansoor A. Haider, H. Ping Ting-Beall, Lori A. Setton

Journal:

Annals of Biomedical Engineering

Year:

2005

Language:

english

File:

PDF, 203 KB

english, 2005

5

Mechanism-based biomarker discovery

Antoranz, Asier, Sakellaropoulos, Theodore, Saez-Rodriguez, Julio, G. Alexopoulos, Leonidas

Journal:

Drug Discovery Today

Year:

2017

Language:

english

File:

PDF, 807 KB

english, 2017

6

Flexible Neuro-Fuzzy Systems: Structures, Learning and Performance Evaluation—L. Rutkowski (Boston, MA: Kluwer Academic Publishers, 2004, ISBN: 1-402-08042-5) Reviewed by A. E. Gaweda

Melas, Ioannis N., Samaga, Regina, Alexopoulos, Leonidas G., Klamt, Steffen, Bonneau, Richard

Journal:

IEEE Transactions on Neural Networks

Year:

2006

Language:

english

File:

PDF, 29 KB

english, 2006

7

Dynamics and heterogeneity of brain damage in multiple sclerosis

Kotelnikova, Ekaterina, Kiani, Narsis A., Abad, Elena, Martinez-Lapiscina, Elena H., Andorra, Magi, Zubizarreta, Irati, Pulido-Valdeolivas, Irene, Pertsovskaya, Inna, Alexopoulos, Leonidas G., Olsson,

Journal:

PLoS Computational Biology

Year:

2017

Language:

english

File:

PDF, 11.95 MB

english, 2017

8

Alterations in the Mechanical Properties of the Human Chondrocyte Pericellular Matrix With Osteoarthritis

Alexopoulos, Leonidas G., Haider, Mansoor A., Vail, Thomas P., Guilak, Farshid

Journal:

Journal of Biomechanical Engineering

Year:

2003

Language:

english

File:

PDF, 319 KB

english, 2003

9

A facile consensus ranking approach enhances virtual screening robustness and identifies a cell-active DYRK1α inhibitor

Mavrogeni, Maria E, Pronios, Filippos, Zareifi, Danae, Vasilakaki, Sofia, Lozach, Olivier, Alexopoulos, Leonidas, Meijer, Laurent, Myrianthopoulos, Vassilios, Mikros, Emmanuel

Journal:

Future Medicinal Chemistry

Year:

2018

Language:

english

File:

PDF, 3.21 MB

english, 2018

10

Affinity crystallography reveals binding of pomegranate juice anthocyanins at the inhibitor site of glycogen phosphorylase: the contribution of sugar moiety to potency and its implications to binding mode.

Drakou, Christina, Gardeli, Chryssavgi, Tsialtas, Ioannis, Alexopoulos, Serafeim, Mallouchos, A, Koulas, Symeon, Tsagkarakou, Anastasia, Asimakopoulos, Demetres, Leonidas, Demetres D., Psarra, Anna Ma

Journal:

Journal of Agricultural and Food Chemistry

Year:

2020

File:

PDF, 972 KB

2020

11

PROTEOMICS DISCOVERY OF BIOMARKERS FOR ATRIAL FIBRILLATION IN PATIENTS WITH CARDIOVASCULAR DISEASE

Tzani, Aspasia, Doulamis, Ilias P., Antoranz, Asier, Samanidis, George, Pliaka, Vicky, Gkogkos, Anastasios, Konstantopoulos, Panagiotis, Sakellaropoulos, Theodore, Alexopoulos, Leonidas, Perreas, Kons

Journal:

Journal of the American College of Cardiology

Year:

2017

Language:

english

File:

PDF, 353 KB

english, 2017

12

The species translation challenge—A systems biology perspective on human and rat bronchial epithelial cells

Poussin, Carine, Mathis, Carole, Alexopoulos, Leonidas G, Messinis, Dimitris E, Dulize, Rémi H J, Belcastro, Vincenzo, Melas, Ioannis N, Sakellaropoulos, Theodore, Rhrissorrakrai, Kahn, Bilal, Erhan,

Journal:

Scientific Data

Year:

2014

Language:

english

File:

PDF, 1.61 MB

english, 2014

13

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

Neidlin, Michael, Korcari, Antonion, Macheras, Giorgos, Alexopoulos, Leonidas G.

Journal:

Annals of Biomedical Engineering

Year:

2017

Language:

english

File:

PDF, 1003 KB

english, 2017

14

Proteomic profile of patients with atrial fibrillation undergoing cardiac surgery†

Doulamis, Ilias P, Samanidis, George, Tzani, Aspasia, Antoranz, Asier, Gkogkos, Anastasios, Konstantopoulos, Panagiotis, Pliaka, Vaia, Minia, Angeliki, Alexopoulos, Leonidas G, Perrea, Despina N, Perr

Journal:

Interactive Cardiovascular and Thoracic Surgery

Year:

2018

Language:

english

File:

PDF, 719 KB

english, 2018

15

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

Benjamin D. Cosgrove, Bracken M. King, Maya A. Hasan, Leonidas G. Alexopoulos, Paraskevi A. Farazi, Bart S. Hendriks, Linda G. Griffith, Peter K. Sorger, Bruce Tidor, Jinghai J. Xu, Douglas A. Lauffen

Journal:

Toxicology and Applied Pharmacology

Year:

2009

Language:

english

File:

PDF, 2.11 MB

english, 2009

16

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

Messinis, Dimitris E., Melas, Ioannis N., Hur, Junguk, Varshney, Navya, Alexopoulos, Leonidas G., Bai, Jane P.F.

Journal:

CPT: Pharmacometrics & Systems Pharmacology

Year:

2018

Language:

english

File:

PDF, 346 KB

english, 2018

17

Can ReGeneraTing Agents Improve Functional Recovery of Transected Peripheral Nerve through a Nerve Gap Bridged with an Artery Graft?

Alexopoulos, George, Pavlidis, Leonidas, Tsagarakis, Myron, Delimpaltas, Alexandros, Tsimponis, Antonios, Papalois, Apostolos, Batistatou, Anna, Papoudou-Bai, Alexandra, Barritault, Denis, Demiri, Eft

Journal:

Journal of Reconstructive Microsurgery Open

Year:

2019

Language:

english

File:

PDF, 453 KB

english, 2019

18

Proteomics discovery of biomarkers in statin-treated patients with advanced coronary artery disease

Tzani, Aspasia, Doulamis, Ilias, Konstantopoulos, Panagiotis, Antoranz, Asier, Pliaka, Vaia, Minia, Aggeliki, Gkogkos, Anastasios, Samanidis, George, Sakellaropoulos, Theodore, Alexopoulos, Leonidas,

Journal:

Atherosclerosis

Year:

2017

Language:

english

File:

PDF, 155 KB

english, 2017

19

Targeted proteomics identification of biomarkers for diabetes mellitus in patients with cardiovascular disease

Doulamis, Ilias, Tzani, Aspasia, Konstantopoulos, Panagiotis, Antoranz, Asier, Plakia, Vaia, Minia, Aggeliki, Gkogkos, Anastasios, Samanidis, George, Alexopoulos, Leonidas, Perreas, Konstantinos, Perr

Journal:

Atherosclerosis

Year:

2017

Language:

english

File:

PDF, 51 KB

english, 2017

20

Non Linear Programming (NLP) Formulation for Quantitative Modeling of Protein Signal Transduction Pathways

Mitsos, Alexander, Melas, Ioannis N., Morris, Melody K., Saez-Rodriguez, Julio, Lauffenburger, Douglas A., Alexopoulos, Leonidas G., Rao, Christopher V.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.27 MB

english, 2012

21

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

Rukhlenko, Oleksii S., Khorsand, Fahimeh, Krstic, Aleksandar, Rozanc, Jan, Alexopoulos, Leonidas G., Rauch, Nora, Erickson, Keesha E., Hlavacek, William S., Posner, Richard G., Gómez-Coca, Silvia, Ros

Journal:

Year:

2018

Language:

english

File:

PDF, 7.09 MB

english, 2018

22

A Novel Spatiotemporal Analysis of Peri-Ictal Spiking to Probe the Relation of Spikes and Seizures in Epilepsy

Krishnan, Balu, Vlachos, Ioannis, Faith, Aaron, Mullane, Steven, Williams, Korwyn, Alexopoulos, Andreas, Iasemidis, Leonidas

Journal:

Annals of Biomedical Engineering

Year:

2014

Language:

english

File:

PDF, 1.49 MB

english, 2014

23

A Novel Multiplex Based Platform for Osteoarthritis Drug Candidate Evaluation

Neidlin, Michael, Chantzi, Efthymia, Macheras, George, Gustafsson, Mats G., Alexopoulos, Leonidas G.

Journal:

Annals of Biomedical Engineering

Year:

2020

File:

PDF, 726 KB

2020

24

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, Vesna, Rožanc, Jan, Charles, Emilie M., Hellwig, Christian T., Alexopoulos, Leonidas G., Rehm, Markus

Journal:

Oncology Research Featuring Preclinical and Clinical Cancer Therapeutics

Year:

2017

Language:

english

File:

PDF, 895 KB

english, 2017

25

An ex vivo tissue model of cartilage degradation suggests that cartilage state can be determined from secreted key protein patterns

Neidlin, Michael, Chantzi, Efthymia, Macheras, George, Gustafsson, Mats G., Alexopoulos, Leonidas G., Sampen, Hee-Jeong Im

Journal:

Year:

2019

File:

PDF, 1.42 MB

2019

26

Hyper-osmotic stress induces volume change and calcium transients in chondrocytes by transmembrane, phospholipid, and G-protein pathways

Geoffrey R Erickson, Leonidas G Alexopoulos, Farshid Guilak

Journal:

Journal of Biomechanics

Year:

2001

Language:

english

File:

PDF, 231 KB

english, 2001

27

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

Cosgrove, Benjamin D., Alexopoulos, Leonidas G., Hang, Ta-chun, Hendriks, Bart S., Sorger, Peter K., Griffith, Linda G., Lauffenburger, Douglas A.

Journal:

Molecular BioSystems

Year:

2010

Language:

english

File:

PDF, 2.30 MB

english, 2010

28

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

Sakellaropoulos, Theodore, Herod, Timothy J., Alexopoulos, Leonidas G, Bai, Jane P.F.

Journal:

Chemical Research in Toxicology

Year:

2016

Language:

english

File:

PDF, 1.53 MB

english, 2016

29

An ex vivo tissue model of cartilage degradation suggests that cartilage state can be determined from secreted key protein patterns

Neidlin, Michael, Chantzi, Efthymia, Macheras, George, Gustafsson, Mats G., Alexopoulos, Leonidas G., Sampen, Hee-Jeong Im

Journal:

Year:

2019

Language:

english

File:

PDF, 1.42 MB

english, 2019

30

Designing Experiments to Discriminate Families of Logic Models

Videla, Santiago, Konokotina, Irina, Alexopoulos, Leonidas G., Saez-Rodriguez, Julio, Schaub, Torsten, Siegel, Anne, Guziolowski, Carito

Journal:

Frontiers in Bioengineering and Biotechnology

Year:

2015

Language:

english

File:

PDF, 4.52 MB

english, 2015

31

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

Melas, Ioannis N., Mitsos, Alexander, Messinis, Dimitris E., Weiss, Thomas S., Rodriguez, Julio-Saez, Alexopoulos, Leonidas G.

Journal:

Molecular BioSystems

Year:

2012

Language:

english

File:

PDF, 4.51 MB

english, 2012

32

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

Myrianthopoulos, Vassilios, Lozach, Olivier, Zareifi, Danae, Alexopoulos, Leonidas, Meijer, Laurent, Gorgoulis, Vassilis, Mikros, Emmanuel

Journal:

International Journal of Molecular Sciences

Year:

2017

Language:

english

File:

PDF, 1.98 MB

english, 2017

33

Visceral white adipose tissue and serum proteomic alternations in metabolically healthy obese patients undergoing bariatric surgery

Doulamis, Ilias P., Konstantopoulos, Panagiotis, Tzani, Aspasia, Antoranz, Asier, Minia, Angeliki, Daskalopoulou, Afroditi, Charalampopoulos, Anestis, Alexopoulos, Leonidas, Perrea, Depsina N., Menena

Journal:

Year:

2018

Language:

english

File:

PDF, 1.14 MB

english, 2018

34

The biomechanical role of the chondrocyte pericellular matrix in articular cartilage

Leonidas G. Alexopoulos, Lori A. Setton, Farshid Guilak

Journal:

Acta Biomaterialia

Year:

2005

Language:

english

File:

PDF, 375 KB

english, 2005

35

Correction to: Cue-Signal-Response Analysis in 3D Chondrocyte Scaffolds with Anabolic Stimuli

Neidlin, Michael, Korcari, Antonion, Macheras, Giorgos, Alexopoulos, Leonidas G.

Journal:

Annals of Biomedical Engineering

Year:

2019

Language:

english

File:

PDF, 203 KB

english, 2019

36

COMBSecretomics: A pragmatic methodological framework for higher-order drug combination analysis using secretomics

Chantzi, Efthymia, Neidlin, Michael, Macheras, George A., Alexopoulos, Leonidas G., Gustafsson, Mats G., Zhang, Le

Journal:

Year:

2020

File:

PDF, 1.70 MB

2020

37

The Pericellular Matrix as a Transducer of Biomechanical and Biochemical Signals in Articular Cartilage

FARSHID GUILAK, LEONIDAS G. ALEXOPOULOS, MAUREEN L. UPTON, INCHAN YOUN, JAE BONG CHOI, LI CAO, LORI A. SETTON, MANSOOR A. HAIDER

Journal:

Annals of the New York Academy of Sciences

Year:

2006

Language:

english

File:

PDF, 285 KB

english, 2006

38

Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs

Melas, Ioannis N., Samaga, Regina, Alexopoulos, Leonidas G., Klamt, Steffen, Bonneau, Richard

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.18 MB

english, 2013

39

[IEEE 2008 8th IEEE International Conference on Bioinformatics and BioEngineering (BIBE) - Athens, Greece (2008.10.8-2008.10.10)] 2008 8th IEEE International Conference on BioInformatics and BioEngineering - Modeling pro-death signaling pathways in cancer hepatocytes using multi-combinatorial treatments of inhibitors and stimuli

Alexopoulos, Leonidas G., Lauffenburger, Douglas A., Sorger, Peter K.

Year:

2008

Language:

english

File:

PDF, 6.85 MB

english, 2008

40

Exploring risk management strategies for organic farmers: A Greek case study

Tzouramani, Irene, Alexopoulos, George, Kostianis, Giorgos, Kazakopoulos, Leonidas

Journal:

Renewable Agriculture and Food Systems

Year:

2014

Language:

english

File:

PDF, 131 KB

english, 2014

41

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

Melas, Ioannis N., Sakellaropoulos, Theodore, Iorio, Francesco, Alexopoulos, Leonidas G., Loh, Wei-Yin, Lauffenburger, Douglas A., Saez-Rodriguez, Julio, Bai, Jane P. F.

Journal:

Integrative Biology

Year:

2015

Language:

english

File:

PDF, 4.07 MB

english, 2015

42

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data

Samaga, Regina, Saez-Rodriguez, Julio, Alexopoulos, Leonidas G., Sorger, Peter K., Klamt, Steffen, Asthagiri, Anand R.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 2.19 MB

english, 2009

43

Pathway-based technologies for early drug discovery

Fotis, Chris, Antoranz, Asier, Hatziavramidis, Dimitris, Sakellaropoulos, Theodore, Alexopoulos, Leonidas G.

Journal:

Drug Discovery Today

Year:

2017

Language:

english

File:

PDF, 750 KB

english, 2017

44

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

Bai, Jane, Sakellaropoulos, Theodore, Alexopoulos, Leonidas

Journal:

Year:

2017

Language:

english

File:

PDF, 1.22 MB

english, 2017

45

Response to Dr. Schachar

Wendy R. Trickey, Frank P.T. Baaijens, Tod A. Laursen, Leonidas G. Alexopoulos, Farshid Guilak

Journal:

Journal of Biomechanics

Year:

2006

Language:

english

File:

PDF, 107 KB

english, 2006

46

Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data

Mitsos, Alexander, Melas, Ioannis N., Siminelakis, Paraskeuas, Chairakaki, Aikaterini D., Saez-Rodriguez, Julio, Alexopoulos, Leonidas G., Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.43 MB

english, 2009

47

Developmental and osteoarthritic changes in Col6a1-knockout mice: Biomechanics of type VI collagen in the cartilage pericellular matrix

Leonidas G. Alexopoulos, Inchan Youn, Paolo Bonaldo, Farshid Guilak

Journal:

Arthritis & Rheumatism

Year:

2009

Language:

english

File:

PDF, 317 KB

english, 2009

48

Phosphoproteomics in drug discovery

Morris, Melody K., Chi, An, Melas, Ioannis N., Alexopoulos, Leonidas G.

Journal:

Drug Discovery Today

Year:

2014

Language:

english

File:

PDF, 443 KB

english, 2014

49

Osteoarthritic changes in the biphasic mechanical properties of the chondrocyte pericellular matrix in articular cartilage

Leonidas G. Alexopoulos, Gregory M. Williams, Maureen L. Upton, Lori A. Setton, Farshid Guilak

Journal:

Journal of Biomechanics

Year:

2005

Language:

english

File:

PDF, 409 KB

english, 2005

50

Leveraging systems biology approaches in clinical pharmacology

Melas, Ioannis N., Kretsos, Kosmas, Alexopoulos, Leonidas G.

Journal:

Biopharmaceutics & Drug Disposition

Year:

2013

Language:

english

File:

PDF, 179 KB

english, 2013

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