Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: CellNOptR

https://packages.ecosyste.ms/registries/bioconductor.org/packages/CellNOptR

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
1 version
Latest release: about 1 year ago
6 dependent packages
34,087 downloads total

Papers Mentioning CellNOptR 25

10.12688/f1000research.2-192.v2

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages
Cited by: 3
Author(s): Emanuel Gonçalvès, Franz Mirlach, Julio Sáez-Rodríguez
Software Mentions: 8
Published: over 10 years ago

10.1186/1752-0509-6-133

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms
Cited by: 182
Author(s): Camille Terfve, Thomas Cokelaer, David Henriques, Aidan MacNamara, Emanuel Gonçalvès, Melody K. Morris, Martijn P. van Iersel, Douglas A. Lauffenburger, Julio Sáez-Rodríguez
Software Mentions: 7
Published: about 12 years ago

10.1093/bioinformatics/bts363

Integrating literature-constrained and data-driven inference of signalling networks
Cited by: 36
Author(s): Federica Eduati, Javier De Las Rivas, Barbara Di Camillo, Gianna Toffolo, Julio Sáez-Rodríguez
Software Mentions: 6
Published: over 12 years ago

10.15252/msb.20188664

Patient‐specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies
Cited by: 37
Author(s): Federica Eduati, Patricia Jaaks, Jessica Wappler, Thorsten Cramer, Christoph A. Merten, Mathew J. Garnett, Julio Sáez-Rodríguez
Software Mentions: 4
Published: almost 5 years ago

10.1093/bioinformatics/btaa561

Converting networks to predictive logic models from perturbation signalling data with CellNOpt
Cited by: 13
Author(s): Enio Gjerga, Panuwat Trairatphisan, Attila Gábor, Hermann Koch, Céline Chevalier, Franceco Ceccarelli, Aurélien Dugourd, Alexander Mitsos, Julio Sáez-Rodríguez
Software Mentions: 3
Published: over 4 years ago

10.1186/1752-0509-8-75

Boolean ErbB network reconstructions and perturbation simulations reveal individual drug response in different breast cancer cell lines
Cited by: 36
Author(s): Silvia von der Heyde, Christian Bender, Frauke Henjes, Johanna Sonntag, Ulrike Korf, Tim Beißbarth
Software Mentions: 3
Published: over 10 years ago

10.1098/rstb.2017.0073

Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing
Cited by: 12
Author(s): Clare Pacini, Magdalena J. Koziol
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-016-1402-1

Efficient randomization of biological networks while preserving functional characterization of individual nodes
Cited by: 32
Author(s): Francesco Iorio, Martí Bernardo-Faura, Andrea Gobbi, Thomas Cokelaer, Giuseppe Jurman, Julio Sáez-Rodríguez
Software Mentions: 3
Published: about 8 years ago

10.3389/fbioe.2019.00048

Bio-ModelChecker: Using Bounded Constraint Satisfaction to Seamlessly Integrate Observed Behavior With Prior Knowledge of Biological Networks
Cited by: 15
Author(s): Hooman Sedghamiz, Matthew M. Morris, Travis J. A. Craddock, Darrell Whitley, Gordon Broderick
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms22094897

In Silico Logical Modelling to Uncover Cooperative Interactions in Cancer
Cited by: 1
Author(s): Gianluca Selvaggio, Claudine Chaouiya, Florence Janody
Software Mentions: 2
Published: over 3 years ago

10.1093/bioinformatics/btab295

A novel constrained genetic algorithm-based Boolean network inference method from steady-state gene expression data
Cited by: 5
Author(s): Hung-Cuong Trinh, Yung-Keun Kwon
Software Mentions: 2
Published: over 3 years ago

10.1155/2014/362738

A Survey on Evolutionary Algorithm Based Hybrid Intelligence in Bioinformatics
Cited by: 17
Author(s): Shan Li, Liying Kang, Xing‐Ming Zhao
Software Mentions: 2
Published: almost 11 years ago

10.15252/msb.20145112

Phosphoproteomic analyses reveal novel cross‐modulation mechanisms between two signaling pathways in yeast
Cited by: 38
Author(s): Stefania Vaga, Martí Bernardo-Faura, Thomas Cokelaer, Alessio Maiolica, Christopher A. Barnes, Ludovic Gillet, Björn Hegemann, Frank van Drogen, Hoda Sharifian, Edda Klipp, Matthias Peter, Julio Sáez-Rodríguez, Ruedi Aebersold
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pbio.3000917

Unifying the mechanism of mitotic exit control in a spatiotemporal logical model
Cited by: 4
Author(s): Rowan Howell, Cinzia Klemm, Peter H. Thorpe, Attila Csikász‐Nagy
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pcbi.1004431

Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling
Cited by: 25
Author(s): Roland Keller, Marina B. Klein, Maria Thomas, Andreas Dräger, Ute Metzger, Markus F. Templin, Thomas Joos, Wolfgang E. Thasler, Andreas Zell, Ulrich M. Zanger
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pcbi.1005379

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
Cited by: 41
Author(s): David Henriques, Alejandro F. Villaverde, Miguel Rocha, Julio Sáez-Rodríguez, Julio R. Banga
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0182186

A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology
Cited by: 9
Author(s): David R. Penas, David Henriques, Patricia González, Ramón Doallo, Julio Sáez-Rodríguez, Julio R. Banga
Software Mentions: 2
Published: over 7 years ago

10.1186/1478-811X-11-46

Recent development and biomedical applications of probabilistic Boolean networks
Cited by: 80
Author(s): Panuwat Trairatphisan, Andrzej Mizera, Jun Pang, Alexandru Tantar, Jochen G. Schneider, Thomas Sauter
Software Mentions: 2
Published: almost 12 years ago

10.3389/fphys.2018.01335

Evaluating Uncertainty in Signaling Networks Using Logical Modeling
Cited by: 4
Author(s): Kirsten Thobe, Christina Kuznia, Christine Sers, Heike Siebert
Software Mentions: 2
Published: about 6 years ago

10.1038/cddis.2015.393

Prediction of disease–gene–drug relationships following a differential network analysis
Cited by: 55
Author(s): Sascha Zickenrott, Vladimir Espinosa Angarica, Bimal Babu Upadhyaya, Antonio del Sol
Software Mentions: 1
Published: almost 9 years ago

10.12688/f1000research.19592.1

Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz
Cited by: 19
Author(s): Aurora Blucher, Shannon K. McWeeney, Lincoln Stein, Guanming Wu
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0098001

optPBN: An Optimisation Toolbox for Probabilistic Boolean Networks
Cited by: 27
Author(s): Panuwat Trairatphisan, Andrzej Mizera, Jun Pang, Alexandru Tantar, Thomas Sauter
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0127216

Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET
Cited by: 20
Author(s): Ana R. Rodrı́guez, Isaac Crespo, Ganna Androsova, Antonio del Sol
Software Mentions: 1
Published: over 9 years ago

10.1093/bioinformatics/btv314

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach
Cited by: 20
Author(s): David Henriques, Miguel Rocha, Julio Sáez-Rodríguez, Julio R. Banga
Software Mentions: 1
Published: over 9 years ago

10.1186/1741-7007-10-92

Logic modeling and the ridiculome under the rug
Cited by: 5
Author(s): Michael L. Blinov, Ion I. Moraru
Software Mentions: 1
Published: about 12 years ago