pypi: BooleanNet | Projects | Ecosyste.ms: Papers

10.3389/fphys.2018.00680

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
Cited 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: about 6 years ago

10.1016/j.ebiom.2021.103390

AI-guided discovery of the invariant host response to viral pandemics
Cited 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 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: almost 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 tools
Cited 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: over 11 years ago

10.12688/f1000research.13254.2

Simulation and visualization of multiple KEGG pathways using BioNSi
Cited 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 modelling
Cited by: 14
Author(s): Max Flöttmann, Falko Krause, Edda Klipp, Marcus Krantz
Software Mentions: 4
Published: over 11 years ago

10.15252/embj.2018100003

A common molecular logic determines embryonic stem cell self‐renewal and reprogramming
Cited 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 Networks
Cited by: 10
Author(s): Leshi Chen, Don Kulasiri, Sandhya Samarasinghe
Software Mentions: 4
Published: almost 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 analysis
Cited 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 analysis
Cited 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 Treatment
Cited 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: 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: about 10 years ago

10.1186/s12918-015-0193-8

Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks
Cited by: 19
Author(s): Takahide Mori, Max Flöttmann, Marcus Krantz, Tatsuya Akutsu, Edda Klipp
Software Mentions: 3
Published: about 9 years ago

10.18632/oncotarget.23973

Boolean analysis identifies CD38 as a biomarker of aggressive localized prostate cancer
Cited 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: over 6 years ago

10.1186/1471-2105-16-S13-S3

Dynamical modeling of uncertain interaction-based genomic networks
Cited 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 data
Cited by: 1
Author(s): Daniella T. Vo, Shayal Charisma Singh, Sara Safa, Debashis Sahoo
Software Mentions: 2
Published: over 3 years ago

10.1186/1752-0509-6-96

The Cell Collective: Toward an open and collaborative approach to systems biology
Cited 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: over 12 years ago

10.1371/journal.pcbi.1004338

Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome
Cited by: 100
Author(s): Steven N. Steinway, Matthew B. Biggs, Thomas P. Loughran, Jason A. Papin, Réka Albert
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0130033

A Semiquantitative Framework for Gene Regulatory Networks: Increasing the Time and Quantitative Resolution of Boolean Networks
Cited 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 Models
Cited 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: almost 12 years ago

10.1186/1478-811X-11-43

Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks
Cited by: 99
Author(s): Regina Samaga, Steffen Klamt
Software Mentions: 2
Published: over 11 years ago

10.3389/fphys.2020.00275

Computational Approach to Identifying Universal Macrophage Biomarkers
Cited 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 networks
Cited by: 30
Author(s): Stefan Karl, Thomas Dandekar
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pcbi.1007429

Model-driven discovery of calcium-related protein-phosphatase inhibition in plant guard cell signaling
Cited by: 16
Author(s): Parul Maheshwari, Hao Du, Jen Sheen, Sarah M. Assmann, Réka Albert
Software Mentions: 1
Published: almost 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 Leukemia
Cited by: 162
Author(s): Assieh Saadatpour, Rui-Sheng Wang, Aijun Liao, Xin Liu, Thomas P. Loughran, István Albert, Réka Albert
Software Mentions: 1
Published: almost 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 PI3K
Cited 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 approach
Cited 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 strategies
Cited 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 loops
Cited 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: almost 7 years ago

10.1038/s41416-019-0450-5

Low tumour PPM1H indicates poor prognosis in colorectal cancer via activation of cancer-associated fibroblasts
Cited 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 scientists
Cited by: 252
Author(s): István Albert, Juilee Thakar, Song Li, Ranran Zhang, Réka Albert
Software Mentions: 1
Published: almost 16 years ago

10.3389/fphys.2020.00927

A Guard Cell Abscisic Acid (ABA) Network Model That Captures the Stomatal Resting State
Cited by: 12
Author(s): Parul Maheshwari, Sarah M. Assmann, Réka Albert
Software Mentions: 1
Published: about 4 years ago

10.3389/fphys.2018.01046

CANA: A Python Package for Quantifying Control and Canalization in Boolean Networks
Cited by: 18
Author(s): Rion Brattig Correia, Alexander J. Gates, Xuan Wang, Luís M. Rocha
Software Mentions: 1
Published: about 6 years ago

10.3389/fphys.2018.00774

Global Stabilization of Boolean Networks to Control the Heterogeneity of Cellular Responses
Cited by: 7
Author(s): Jung‐Min Yang, Chun-Kyung Lee, Kwang-Hyun Cho
Software Mentions: 1
Published: about 6 years ago

10.1186/1752-0509-8-53

Stabilization of perturbed Boolean network attractors through compensatory interactions
Cited by: 48
Author(s): Colin Campbell, Réka Albert
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0009101

A Boolean Model of the Pseudomonas syringae hrp Regulon Predicts a Tightly Regulated System
Cited by: 20
Author(s): Dan MacLean, David J. Studholme
Software Mentions: 1
Published: over 14 years ago

10.1186/gb-2008-9-10-r157

Boolean implication networks derived from large scale, whole genome microarray datasets
Cited by: 101
Author(s): Debashis Sahoo, David L. Dill, Andrew J. Gentles, Robert Tibshirani, Sylvia K. Plevritis
Software Mentions: 1
Published: over 16 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 Cancer
Cited 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 checkpoint
Cited by: 19
Author(s): Dávid Deritei, Jordan C. Rozum, Erzsébet Ravasz Regan, Réka Albert
Software Mentions: 1
Published: almost 5 years ago

Projects: pypi: BooleanNet

Papers Mentioning BooleanNet 41