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: pypi: BooleanNet
https://packages.ecosyste.ms/registries/pypi.org/packages/BooleanNet
Boolean Network Simulation Toolbox
1 version
Latest release: over 10 years ago
29 downloads last month
Papers Mentioning BooleanNet 41
10.3389/fphys.2018.00680
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological NetworksCited by: 59
Author(s): Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loı̈c Paulevé
Software Mentions: 9
Published: over 6 years ago
10.1016/j.ebiom.2021.103390
AI-guided discovery of the invariant host response to viral pandemicsCited by: 31
Author(s): Debashis Sahoo, Gajanan D. Katkar, Soni Khandelwal, Mahdi Behroozikhah, Amanraj Claire, Vanessa Castillo, Courtney Tindle, MacKenzie Fuller, Sahar Taheri, Thomas F. Rogers, Nathan Beutler, Sydney I. Ramirez, Stephen A. Rawlings, Victor Pretorius, Davey M Smith, Dennis R. Burton, Laura E. Crotty Alexander, Jason Duran, Shane Crotty, Jennifer M. Dan, Soumita Das, Pradipta Ghosh
Software Mentions: 7
Published: over 3 years ago
10.1186/1752-0509-6-133
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalismsCited 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
10.1186/1752-0509-7-135
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and toolsCited by: 134
Author(s): Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolás Rodríguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalvès, Julien Dorier, Michel Le Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xénarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Sáez-Rodríguez, Tomáš Helikar
Software Mentions: 4
Published: almost 12 years ago
10.12688/f1000research.13254.2
Simulation and visualization of multiple KEGG pathways using BioNSiCited by: 2
Author(s): Adva Yeheskel, Adam Reiter, Metsada Pasmanik‐Chor, Amir Rubinstein
Software Mentions: 4
Published: over 6 years ago
10.1186/1752-0509-7-58
Reaction-contingency based bipartite Boolean modellingCited by: 14
Author(s): Max Flöttmann, Falko Krause, Edda Klipp, Marcus Krantz
Software Mentions: 4
Published: almost 12 years ago
10.15252/embj.2018100003
A common molecular logic determines embryonic stem cell self‐renewal and reprogrammingCited by: 31
Author(s): Sara‐Jane Dunn, Meng Amy Li, Elena Carbognin, Austin Smith, Graziano Martello
Software Mentions: 4
Published: almost 6 years ago
10.3389/fphys.2018.01328
A Novel Data-Driven Boolean Model for Genetic Regulatory NetworksCited by: 10
Author(s): Leshi Chen, Don Kulasiri, Sandhya Samarasinghe
Software Mentions: 4
Published: about 6 years ago
10.1186/s12918-018-0534-5
Regulation of dual specificity phosphatases in breast cancer during initial treatment with Herceptin: a Boolean model analysisCited by: 7
Author(s): Petronela Buiga, Ari Elson, Lydia Tabernero, Jean-Marc Schwartz
Software Mentions: 4
Published: over 6 years ago
10.1002/pld3.123
Identification of gene expression logical invariants in <i>Arabidopsis</i>Cited by: 8
Author(s): Sonalisa Pandey, Debashis Sahoo
Software Mentions: 3
Published: over 5 years ago
10.1186/1471-2105-12-490
"Antelope": a hybrid-logic model checker for branching-time Boolean GRN analysisCited by: 34
Author(s): Gustavo Arellano, Julián Argil, Eugenio Azpeitia, Mariana Benítez, Miguel Carrillo, Pedro Arturo Góngora, David A. Rosenblueth, Elena Álvarez-Buylla
Software Mentions: 3
Published: almost 13 years ago
10.3389/fphar.2020.00187
Repositioning of Hypoglycemic Drug Linagliptin for Cancer TreatmentCited by: 8
Author(s): Yong Li, Yiqun Li, Dengke Li, Kaiming Li, Quan Zhengyang, Ziyi Wang, Zhenxiao Sun
Software Mentions: 3
Published: over 4 years ago
10.1016/j.csbj.2020.03.001
Concepts in Boolean network modeling: What do they all mean?Cited by: 96
Author(s): Julian Schwab, Silke D. Kühlwein, Nensi Ikonomi, Michael Kühl, Hans A. Kestler
Software Mentions: 3
Published: almost 5 years ago
10.1186/1752-0509-8-75
Boolean ErbB network reconstructions and perturbation simulations reveal individual drug response in different breast cancer cell linesCited 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
10.1186/s12918-015-0193-8
Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networksCited by: 19
Author(s): Takahide Mori, Max Flöttmann, Marcus Krantz, Tatsuya Akutsu, Edda Klipp
Software Mentions: 3
Published: over 9 years ago
10.18632/oncotarget.23973
Boolean analysis identifies CD38 as a biomarker of aggressive localized prostate cancerCited by: 15
Author(s): Debashis Sahoo, Wei Wei, Heidi Auman, Antonio Hurtado-Coll, Peter R. Carroll, Ladan Fazli, Martin Gleave, Daniel W. Lin, Peter S. Nelson, Jeff Simko, Ian M. Thompson, Robin J. Leach, Dean A. Troyer, Lawrence D. True, Jesse K. McKenney, Ziding Feng, James D. Brooks
Software Mentions: 2
Published: almost 7 years ago
10.1186/1471-2105-16-S13-S3
Dynamical modeling of uncertain interaction-based genomic networksCited by: 8
Author(s): Daniel N. Mohsenizadeh, Hua Jiang, Michael Bittner, Edward R. Dougherty
Software Mentions: 2
Published: almost 9 years ago
10.1186/s12859-020-03941-4
Boolean implication analysis unveils candidate universal relationships in microbiome dataCited by: 1
Author(s): Daniella T. Vo, Shayal Charisma Singh, Sara Safa, Debashis Sahoo
Software Mentions: 2
Published: almost 4 years ago
10.1186/1752-0509-6-96
The Cell Collective: Toward an open and collaborative approach to systems biologyCited by: 179
Author(s): Tomáš Helikar, Bryan Kowal, Sean McClenathan, Mitchell A. Bruckner, Thaine W. Rowley, Alex Madrahimov, Benjamin Wicks, Manish Shrestha, Kahani Limbu, Jim Rogers
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pcbi.1004338
Inference of Network Dynamics and Metabolic Interactions in the Gut MicrobiomeCited by: 100
Author(s): Steven N. Steinway, Matthew B. Biggs, Thomas P. Loughran, Jason A. Papin, Réka Albert
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0130033
A Semiquantitative Framework for Gene Regulatory Networks: Increasing the Time and Quantitative Resolution of Boolean NetworksCited by: 12
Author(s): Johan Kerkhofs, Liesbet Geris
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0046417
Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative ModelsCited by: 15
Author(s): Tomáš Helikar, Bryan Kowal, Alex Madrahimov, Manish Shrestha, Jay Pedersen, Kahani Limbu, Ishwor Thapa, Thaine W. Rowley, Rahul Satalkar, Naomi Kochi, John Konvalina, Jim Rogers
Software Mentions: 2
Published: about 12 years ago
10.1186/1478-811X-11-43
Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networksCited by: 99
Author(s): Regina Samaga, Steffen Klamt
Software Mentions: 2
Published: almost 12 years ago
10.3389/fphys.2020.00275
Computational Approach to Identifying Universal Macrophage BiomarkersCited by: 22
Author(s): Dharanidhar Dang, Sahar Taheri, Soumita Das, Pradipta Ghosh, Lawrence S. Prince, Debashis Sahoo
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2105-14-306
Jimena: efficient computing and system state identification for genetic regulatory networksCited by: 30
Author(s): Stefan Karl, Thomas Dandekar
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pcbi.1007429
Model-driven discovery of calcium-related protein-phosphatase inhibition in plant guard cell signalingCited by: 16
Author(s): Parul Maheshwari, Hao Du, Jen Sheen, Sarah M. Assmann, Réka Albert
Software Mentions: 1
Published: about 5 years ago
10.1371/journal.pcbi.1002267
Dynamical and Structural Analysis of a T Cell Survival Network Identifies Novel Candidate Therapeutic Targets for Large Granular Lymphocyte LeukemiaCited by: 162
Author(s): Assieh Saadatpour, Rui-Sheng Wang, Aijun Liao, Xin Liu, Thomas P. Loughran, István Albert, Réka Albert
Software Mentions: 1
Published: about 13 years ago
10.1371/journal.pcbi.1006402
Boolean model of growth signaling, cell cycle and apoptosis predicts the molecular mechanism of aberrant cell cycle progression driven by hyperactive PI3KCited by: 35
Author(s): Herbert Sizek, Andrew R Hamel, Dávid Deritei, Sarah Campbell, Erzsébet Ravasz Regan
Software Mentions: 1
Published: over 5 years ago
10.1186/s13637-015-0032-7
Identification of Th1/Th2 regulatory switch to promote healing response during leishmaniasis: a computational approachCited by: 8
Author(s): Piyali Ganguli, Saikat Chowdhury, Shomeek Chowdhury, Ram Rup Sarkar
Software Mentions: 1
Published: almost 9 years ago
10.1371/journal.pcbi.1008690
Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategiesCited by: 15
Author(s): David J. Wooten, Jorge Gómez Tejeda Zañudo, David Murrugarra, Austin M Perry, Anna Dongari-Bagtzoglou, Reinhard Laubenbacher, Clarissa J. Nobile, Réka Albert
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pbio.2003451
A new discrete dynamic model of ABA-induced stomatal closure predicts key feedback loopsCited by: 44
Author(s): Réka Albert, Bibhudendra Acharya, Byeong Wook Jeon, Jorge Gómez Tejeda Zañudo, Mengmeng Zhu, Karim Osman, Sarah M. Assmann
Software Mentions: 1
Published: about 7 years ago
10.1038/s41416-019-0450-5
Low tumour PPM1H indicates poor prognosis in colorectal cancer via activation of cancer-associated fibroblastsCited by: 7
Author(s): Xiaowen Xu, Li Zhu, Yun Yang, Ya-min Pan, Zhuo Feng, Ye Li, Wenjun Chang, Jinke Sui, Fuao Cao
Software Mentions: 1
Published: over 5 years ago
10.1186/1751-0473-3-16
Boolean network simulations for life scientistsCited by: 252
Author(s): István Albert, Juilee Thakar, Song Li, Ranran Zhang, Réka Albert
Software Mentions: 1
Published: about 16 years ago
10.3389/fphys.2020.00927
A Guard Cell Abscisic Acid (ABA) Network Model That Captures the Stomatal Resting StateCited by: 12
Author(s): Parul Maheshwari, Sarah M. Assmann, Réka Albert
Software Mentions: 1
Published: over 4 years ago
10.3389/fphys.2018.01046
CANA: A Python Package for Quantifying Control and Canalization in Boolean NetworksCited by: 18
Author(s): Rion Brattig Correia, Alexander J. Gates, Xuan Wang, Luís M. Rocha
Software Mentions: 1
Published: over 6 years ago
10.3389/fphys.2018.00774
Global Stabilization of Boolean Networks to Control the Heterogeneity of Cellular ResponsesCited by: 7
Author(s): Jung‐Min Yang, Chun-Kyung Lee, Kwang-Hyun Cho
Software Mentions: 1
Published: over 6 years ago
10.1186/1752-0509-8-53
Stabilization of perturbed Boolean network attractors through compensatory interactionsCited by: 48
Author(s): Colin Campbell, Réka Albert
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.pone.0009101
A Boolean Model of the Pseudomonas syringae hrp Regulon Predicts a Tightly Regulated SystemCited by: 20
Author(s): Dan MacLean, David J. Studholme
Software Mentions: 1
Published: almost 15 years ago
10.1186/gb-2008-9-10-r157
Boolean implication networks derived from large scale, whole genome microarray datasetsCited by: 101
Author(s): Debashis Sahoo, David L. Dill, Andrew J. Gentles, Robert Tibshirani, Sylvia K. Plevritis
Software Mentions: 1
Published: almost 17 years ago
10.1371/journal.pone.0162407
A Network-Based Data Integration Approach to Support Drug Repurposing and Multi-Target Therapies in Triple Negative Breast CancerCited by: 58
Author(s): Francesca Vitali, Laurie D. Cohen, Andrea Demartini, Antonella Amato, Vincenzo Eterno, Alberto Zambelli, Riccardo Bellazzi
Software Mentions: 1
Published: about 8 years ago
10.1038/s41598-019-52725-1
A feedback loop of conditionally stable circuits drives the cell cycle from checkpoint to checkpointCited by: 19
Author(s): Dávid Deritei, Jordan C. Rozum, Erzsébet Ravasz Regan, Réka Albert
Software Mentions: 1
Published: about 5 years ago