Publications of OCSANA tool

OCSANA+: Optimal Control and Simulation of Signaling Networks from Network Analysis
Lauren Marazzi, Andrew Gainer-Dewar, Paola Vera-Licona. Bioinformatics, Volume 36, Issue 19, 1 October 2020, Pages 4960–4962, https://doi.org/10.1093/bioinformatics/btaa625

preprint found at biorxiv: https://doi.org/10.1101/806315

OCSANA: optimal combinations of interventions from network analysis
Paola Vera-Licona, Eric Bonnet, Emmanuel Barillot, Andrei Zinovyev. Bioinformatics, Volume 29, Issue 12, 15 June 2013, Pages 1571–1573, https://doi.org/10.1093/bioinformatics/btt195

Publications using or citing OCSANA tool

Control of Intracellular Molecular Networks Using Algebraic Methods
Luis Sordo Vieira, Reinhard C. Laubenbacher, David Murrugarra bioRxiv 682989; doi: https://doi.org/10.1101/682989

Quantifying Side Effects in Multistate Discrete Networks David Murrugarra and Elena Dimitrova.arxiv,2019. https://arxiv.org/abs/1906.09465

The Phosphatase PRL-3 Is Involved in Key Steps of Cancer Metastasis
Laura Duciel, Luis Cristobal Monraz Gomez et al. Journal of molecular biology, 431, 17, 8 2019. https://www.sciencedirect.com/science/article/pii/S0022283619303705?via%3Dihub

Understanding the Effectiveness of Data Reduction in Public Transportation Networks
Bläsius, Thomas and Fischbeck, Philipp and Friedrich, Tobias and Schirneck, Martin. Algorithms and Models for the Web Graph,2019 http://dx.doi.org/10.1007/978-3-030-25070-6_7

A Boolean network control algorithm guided by forward dynamic programming
Moradi M, Goliaei S, Foroughmand-Araabi M-H (2019) . PLoS ONE 14(5): e0215449. https://doi.org/10.1371/journal.pone.0215449

Computing Signal Transduction in Signaling Networks modeled as Boolean Networks, Petri Nets, and Hypergraphs Luis Sordo Vieira, Paola Vera-Licona bioRxiv 272344; doi: https://doi.org/10.1101/272344

Macrophage mediated recognition and clearance of Borrelia burgdorferinelicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation
Sarah J. Benjamin, Kelly L. Hawley, Paola Vera-Licona, Carson J. La Vake, Jorge L. Cervantes, Rachel Burns, Oscar Luo, Yijun Ruan, Melissa J. Caimano, Justin D. Radolf, Juan C. Salazar. bioRxiv 593566; https://doi.org/10.1101/593566

In-Silico Methodologies for Cancer Multidrug Optimization
Hasan, D. M., Eldin, A. S., Khedr, A. E., & Fahmy, H. (2018). INTERNATIONAL JOURNAL OF COMPUTERS & TECHNOLOGY, 17(2), 7186-7205. https://doi.org/10.24297/ijct.v17i2.7168

Conceptual and computational framework for logical modelling of biological networks deregulated in diseases
Arnau Montagud, Pauline Traynard, Loredana Martignetti,Eric Bonnet,Emmanuel Barillot,Andrei Zinovyev, Laurence Calzone. Briefings in Bioinformatics, Volume 20, Issue 4, 1 January 2019, https://doi.org/10.1093/bib/bbx163

Community-driven roadmap for integrated disease maps
Marek Ostaszewski,Stephan Gebel,Inna Kuperstein,Alexander Mazein,Andrei Zinovyev,Ugur Dogrusoz,Jan Hasenauer,Ronan M T Fleming,Nicolas Le Novère,Piotr Gawron,Thomas Ligon,Anna Niarakis,David Nickerson,Daniel Weindl,Rudi Balling,Emmanuel Barillot,Charles Auffray,Reinhard Schneider. Briefings in Bioinformatics, Volume 20, Issue 2, 1 January 2019, https://doi.org/10.1093/bib/bby024

Application of Atlas of Cancer Signalling Network in preclinical studies
L Cristobal Monraz Gomez,Maria Kondratova,Jean-Marie Ravel,Emmanuel Barillot,Andrei Zinovyev,Inna Kuperstein. Briefings in Bioinformatics, Volume 20, Issue 2, 1 January 2019, https://doi.org/10.1093/bib/bby031

The Phosphatase PRL-3 Is Involved in Key Steps of Cancer Metastasis
Laura Duciel,Luis Cristobal Monraz Gomez,Maria Kondratova,Inna Kuperstein,Simon Saule Journal of Molecular Biology, Volume 431, Issue 17, 1 January 2019, https://doi.org/10.1016/j.jmb.2019.06.008

A Boolean network control algorithm guided by forward dynamic programming
Mohammad Moradi,Sama Goliaei,Mohammad-Hadi Foroughmand-Araabi,Gareth J. Baxter.PLOS ONE, Volume 14, Issue 5, 1 January 2019, https://doi.org/10.1371/journal.pone.0215449

MCA: Boolean Networks Control Algorithm
Mohammad Moradi and Sama Goliaei, arxiv, https://arxiv.org/abs/1609.01604

Компьютерный поиск веществ, обладающих цитотоксичностью по отношению к клеточным линиям рака молочной железы Dubovskaya Varvara Igorevna. Dissertation http://ibmc.msk.ru/content/thesisDocs/DubovskajaVI_diss.pdf

Data Integration And Targeted Anticancer Drug Synergies Prediction
Gao, Xiaoting, (2016). Public Health Theses. 1098. https://elischolar.library.yale.edu/ysphtdl/1098

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms
Alexander Mazein,Marek Ostaszewski,Inna Kuperstein,Steven Watterson,Nicolas Le Novère,Diane Lefaudeux,Bertrand De Meulder,Johann Pellet,Irina Balaur,Mansoor Saqi,Maria Manuela Nogueira,Feng He,Andrew Parton,Nathanaël Lemonnier,Piotr Gawron,Stephan Gebel,Pierre Hainaut,Markus Ollert,Ugur Dogrusoz,Emmanuel Barillot,Andrei Zinovyev,Reinhard Schneider,Rudi Balling,Charles Auffray. npj Systems Biology and Applications, Volume 4, Issue 1, 1 January 2018, https://doi.org/10.1038/s41540-018-0059-y

A comparison of mechanistic signaling pathway activity analysis methods
Alicia Amadoz,Marta R Hidalgo,Cankut Çubuk,José Carbonell-Caballero,Joaquín Dopazo. Briefings in Bioinformatics, https://doi.org/10.1093/bib/bby040

Combinatorial optimization methods for solving the problems of group formation in classes
Lazović, Bojana. Dissertation, University of Belgrade, 2018. http://nardus.mpn.gov.rs/123456789/10267

The Minimal Hitting Set Generation Problem: Algorithms and Computation
Andrew Gainer-Dewar,Paola Vera-Licona. SIAM Journal on Discrete Mathematics, Volume 31, Issue 1, 1 January 2017, https://doi.org/10.1137/15M1055024

Identification of control targets in Boolean molecular network models via computational algebra
David Murrugarra,Alan Veliz-Cuba,Boris Aguilar,Reinhard Laubenbacher. BMC Systems Biology, Volume 10, Issue 1, 1 January 2016, https://doi.org/10.1186/s12918-016-0332-x

DrugTargetInspector: An assistance tool for patient treatment stratification
Lara Schneider,Daniel Stöckel,Tim Kehl,Andreas Gerasch,Nicole Ludwig,Petra Leidinger,Hanno Huwer,Stefan Tenzer,Oliver Kohlbacher,Andreas Hildebrandt,Michael Kaufmann,Manfred Gessler,Andreas Keller,Eckart Meese,Norbert Graf,Hans-Peter Lenhof. International Journal of Cancer, Volume 138, Issue 7, 1 January 2016, https://doi.org/10.1002/ijc.29897

The shortest path is not the one you know: application of biological network resources in precision oncology research
I. Kuperstein,L. Grieco,D. P., A. Cohen,D. Thieffry,A., Zinovyev,E. Barillot. Mutagenesis, Volume 30, Issue 2, 1 January 2015, https://doi.org/10.1093/mutage/geu078

Network-based approaches for drug response prediction and targeted therapy development in cancer
Mathurin Dorel,Emmanuel Barillot,Andrei Zinovyev,Inna Kuperstein.Biochemical and Biophysical Research Communications, Volume 464, Issue 2, 1 January 2015, https://doi.org/10.1016/j.bbrc.2015.06.094

Overcoming Complexity of Biological Systems: from Data Analysis to Mathematical Modeling
A. Zinovyev,D.C. Wunsch,G. Fridman,J. Levesley,I. Tyukin. Mathematical Modelling of Natural Phenomena, Volume 10, Issue 3, 1 January 2015, https://doi.org/10.1051/mmnp/201510314

Virtual screening of chemical compounds active against breast cancer cell lines based on cell cycle modelling, prediction of cytotoxicity and interaction with targets
V. Konova,A. Lagunin,P. Pogodin,E. Kolotova,A. Shtil,V. Poroikov.SAR and QSAR in Environmental Research, Volume 26, Issue 7-9, 1 January 2015, https://doi.org/10.1080/1062936X.2015.1076516

REGINA: REverse enGINeering Algorithm for gene regulatory networks
Dashko, P.M. Masters Thesis. Eindhoven University of Technology,2014, [https://pure.tue.nl/ws/portalfiles/portal/47009573/789178-1.pdf] (https://pure.tue.nl/ws/portalfiles/portal/47009573/789178-1.pdf)

Using Pairwise Ordering Preferences to Estimate Causal Effects in Gene Expression from a Mixture of Observational and Intervention Experiments, Quality Technology & Quantitative Management
G. Nuel, A. Rau & F. Jaffrézic (2014), 11:1, 23-37, DOI: 10.1080/16843703.2014.11673323 https://www.tandfonline.com/doi/abs/10.1080/16843703.2014.11673323