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CMSB (cmsb)
Editions
Publications
Viewing Publication 1 - 100 from 656
2023
Computational Methods in Systems Biology - 21st International Conference, CMSB 2023, Luxembourg City, Luxembourg, September 13-15, 2023, Proceedings
Jun Pang 0001
,
Joachim Niehren
, editors,
Volume 14137 of
Lecture Notes in Computer Science
, Springer,
2023.
[doi]
A Formal Approach for Tuning Stochastic Oscillators
Paolo Ballarini
,
Mahmoud Bentriou
,
Paul-Henry Cournède
.
cmsb 2023
:
1-17
[doi]
Phenotype Control of Partially Specified Boolean Networks
Nikola Benes
,
Lubos Brim
,
Samuel Pastva
,
David Safránek
,
Eva Smijáková
.
cmsb 2023
:
18-35
[doi]
A More Expressive Spline Representation for SBML Models Improves Code Generation Performance in AMICI
Lorenzo Contento
,
Paul Stapor
,
Daniel Weindl
,
Jan Hasenauer
.
cmsb 2023
:
36-43
[doi]
Cell-Level Pathway Scoring Comparison with a Biologically Constrained Variational Autoencoder
Pelin Gundogdu
,
Miriam Payá-Milans
,
Inmaculada Alamo-Alvarez
,
Isabel A. Nepomuceno-Chamorro
,
Joaquín Dopazo
,
Carlos Loucera
.
cmsb 2023
:
62-77
[doi]
On Estimating Derivatives of Input Signals in Biochemistry
Mathieu Hemery
,
François Fages
.
cmsb 2023
:
78-96
[doi]
Harissa: Stochastic Simulation and Inference of Gene Regulatory Networks Based on Transcriptional Bursting
Ulysse Herbach
.
cmsb 2023
:
97-105
[doi]
Approximate Constrained Lumping of Polynomial Differential Equations
Alexander Leguizamon-Robayo
,
Antonio Jiménez-Pastor
,
Mirco Tribastone
,
Max Tschaikowski
,
Andrea Vandin
.
cmsb 2023
:
106-123
[doi]
Intuitive Modelling and Formal Analysis of Collective Behaviour in Foraging Ants
Rocco De Nicola
,
Luca Di Stefano 0001
,
Omar Inverso
,
Serenella Valiani
.
cmsb 2023
:
44-61
[doi]
Core SBML and Its Formal Semantics
Joachim Niehren
,
Cédric Lhoussaine
,
Athénaïs Vaginay
.
cmsb 2023
:
124-143
[doi]
Average Sensitivity of Nested Canalizing Multivalued Functions
Elisabeth Remy
,
Paul Ruet
.
cmsb 2023
:
144-156
[doi]
Tackling Universal Properties of Minimal Trap Spaces of Boolean Networks
Sara Riva
,
Jean-Marie Lagniez
,
Gustavo Magaña López
,
Loïc Paulevé
.
cmsb 2023
:
157-174
[doi]
SAF: SAT-Based Attractor Finder in Asynchronous Automata Networks
Takehide Soh
,
Morgan Magnin
,
Daniel Le Berre
,
Mutsunori Banbara
,
Naoyuki Tamura
.
cmsb 2023
:
175-183
[doi]
Condition for Periodic Attractor in 4-Dimensional Repressilators
Honglu Sun
,
Maxime Folschette
,
Morgan Magnin
.
cmsb 2023
:
184-201
[doi]
Attractor Identification in Asynchronous Boolean Dynamics with Network Reduction
Elisa Tonello
,
Loïc Paulevé
.
cmsb 2023
:
202-219
[doi]
3D Hybrid Cellular Automata for Cardiac Electrophysiology: A Concept Study
Lilly Maria Treml
.
cmsb 2023
:
220-235
[doi]
Fridge Compiler: Optimal Circuits from Molecular Inventories
Lancelot Wathieu
,
Gus Henry Smith
,
Luis Ceze
,
Chris Thachuk
.
cmsb 2023
:
236-252
[doi]
Joint Distribution of Protein Concentration and Cell Volume Coupled by Feedback in Dilution
Iryna Zabaikina
,
Pavol Bokes
,
Abhyudai Singh
.
cmsb 2023
:
253-268
[doi]
2022
An Extension of ERODE to Reduce Boolean Networks By Backward Boolean Equivalence
Georgios Argyris
,
Alberto Lluch-Lafuente
,
Mirco Tribastone
,
Max Tschaikowski
,
Andrea Vandin
.
cmsb 2022
:
294-301
[doi]
Bayesian Learning of Effective Chemical Master Equations in Crowded Intracellular Conditions
Svitlana Braichenko
,
Ramon Grima
,
Guido Sanguinetti
.
cmsb 2022
:
239-258
[doi]
MobsPy: A Meta-species Language for Chemical Reaction Networks
Fabricio Cravo
,
Matthias Függer
,
Thomas Nowak
,
Gayathri Prakash
.
cmsb 2022
:
277-285
[doi]
Qualitative Dynamics of Chemical Reaction Networks: An Investigation Using Partial Tropical Equilibrations
Aurélien Desoeuvres
,
Peter Szmolyan
,
Ovidiu Radulescu
.
cmsb 2022
:
61-85
[doi]
Stability Versus Meta-stability in a Skin Microbiome Model
Eléa Thibault Greugny
,
Georgios N. Stamatas
,
François Fages
.
cmsb 2022
:
179-197
[doi]
Abstraction-Based Segmental Simulation of Chemical Reaction Networks
Martin Helfrich
,
Milan Ceska 0002
,
Jan Kretínský
,
Stefan Marticek
.
cmsb 2022
:
41-60
[doi]
Algebraic Biochemistry: A Framework for Analog Online Computation in Cells
Mathieu Hemery
,
François Fages
.
cmsb 2022
:
3-20
[doi]
Exact Linear Reduction for Rational Dynamical Systems
Antonio Jiménez-Pastor
,
Joshua Paul Jacob
,
Gleb Pogudin
.
cmsb 2022
:
198-216
[doi]
Probabilistic Multivariate Early Warning Signals
Ville Laitinen
,
Leo Lahti
.
cmsb 2022
:
259-274
[doi]
Abstract Simulation of Reaction Networks via Boolean Networks
Joachim Niehren
,
Athénaïs Vaginay
,
Cristian Versari
.
cmsb 2022
:
21-40
[doi]
Variable Stabilisation in Boolean Monotonic Model Pools
Samuel Pastva
.
cmsb 2022
:
122-137
[doi]
Computational Methods in Systems Biology - 20th International Conference, CMSB 2022, Bucharest, Romania, September 14-16, 2022, Proceedings
Ion Petre
,
Andrei Paun
, editors,
Volume 13447 of
Lecture Notes in Computer Science
, Springer,
2022.
[doi]
Variable-Depth Simulation of Most Permissive Boolean Networks
Théo Roncalli
,
Loïc Paulevé
.
cmsb 2022
:
138-157
[doi]
Prioritization of Candidate Genes Through Boolean Networks
Clémence Réda
,
Andrée Delahaye-Duriez
.
cmsb 2022
:
89-121
[doi]
Limit Cycle Analysis of a Class of Hybrid Gene Regulatory Networks
Honglu Sun
,
Maxime Folschette
,
Morgan Magnin
.
cmsb 2022
:
217-236
[doi]
Minimal Trap Spaces of Logical Models are Maximal Siphons of Their Petri Net Encoding
Van-Giang Trinh
,
Belaid Benhamou
,
Kunihiko Hiraishi
,
Sylvain Soliman
.
cmsb 2022
:
158-176
[doi]
eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems
Matej Troják
,
David Safránek
,
Branislav Brozmann
,
Lubos Brim
.
cmsb 2022
:
302-309
[doi]
Automated Generation of Conditional Moment Equations for Stochastic Reaction Networks
Hanna Josephine Wiederanders
,
Anne-Lena Moor
,
Christoph Zechner
.
cmsb 2022
:
286-293
[doi]
2021
Reducing Boolean Networks with Backward Boolean Equivalence
Georgios Argyris
,
Alberto Lluch-Lafuente
,
Mirco Tribastone
,
Max Tschaikowski
,
Andrea Vandin
.
cmsb 2021
:
1-18
[doi]
Aeon 2021: Bifurcation Decision Trees in Boolean Networks
Nikola Benes
,
Lubos Brim
,
Samuel Pastva
,
David Safránek
.
cmsb 2021
:
230-237
[doi]
Automated Inference of Production Rules for Glycans
Ansuman Biswas
,
Ashutosh Gupta
,
Meghana Missula
,
Mukund Thattai
.
cmsb 2021
:
57-73
[doi]
LNetReduce: Tool for Reducing Linear Dynamic Networks with Separated Timescales
Marion Buffard
,
Aurélien Desoeuvres
,
Aurélien Naldi
,
Clément Requilé
,
Andrei Yu. Zinovyev
,
Ovidiu Radulescu
.
cmsb 2021
:
238-244
[doi]
Abstraction of Markov Population Dynamics via Generative Adversarial Nets
Francesca Cairoli
,
Ginevra Carbone
,
Luca Bortolussi
.
cmsb 2021
:
19-35
[doi]
Computational Methods in Systems Biology - 19th International Conference, CMSB 2021, Bordeaux, France, September 22-24, 2021, Proceedings
Eugenio Cinquemani
,
Loïc Paulevé
, editors,
Volume 12881 of
Lecture Notes in Computer Science
, Springer,
2021.
[doi]
Ppsim: A Software Package for Efficiently Simulating and Visualizing Population Protocols
David Doty
,
Eric E. Severson
.
cmsb 2021
:
245-253
[doi]
Greening R. Thomas' Framework with Environment Variables: A Divide and Conquer Approach
Laetitia Gibart
,
Hélène Collavizza
,
Jean-Paul Comet
.
cmsb 2021
:
36-56
[doi]
Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs
Mathieu Hemery
,
François Fages
,
Sylvain Soliman
.
cmsb 2021
:
74-90
[doi]
Web-Based Structural Identifiability Analyzer
Ilia Ilmer
,
Alexey Ovchinnikov
,
Gleb Pogudin
.
cmsb 2021
:
254-265
[doi]
Interpretable Exact Linear Reductions via Positivity
Gleb Pogudin
,
Xingjian Zhang
.
cmsb 2021
:
91-107
[doi]
Explainable Artificial Neural Network for Recurrent Venous Thromboembolism Based on Plasma Proteomics
Misbah Razzaq
,
Louisa Goumidi
,
Maria-Jesus Iglesias
,
Gaëlle Munsch
,
Maria Bruzelius
,
Manal Ibrahim-Kosta
,
Lynn Butler
,
Jacob Odeberg
,
Pierre-Emmanuel Morange
,
David Alexandre Tregouet
.
cmsb 2021
:
108-121
[doi]
Neural Networks to Predict Survival from RNA-seq Data in Oncology
Mathilde Sautreuil
,
Sarah Lemler
,
Paul-Henry Cournède
.
cmsb 2021
:
122-140
[doi]
BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems
Gaurav Saxena
,
Miguel Ponce de Leon
,
Arnau Montagud
,
David Vicente Dorca
,
Alfonso Valencia
.
cmsb 2021
:
266-279
[doi]
Microbial Community Decision Making Models in Batch and Chemostat Cultures
Axel Theorell
,
Jörg Stelling
.
cmsb 2021
:
141-158
[doi]
Learning Boolean Controls in Regulated Metabolic Networks: A Case-Study
Kerian Thuillier
,
Caroline Baroukh
,
Alexander Bockmayr
,
Ludovic Cottret
,
Loïc Paulevé
,
Anne Siegel
.
cmsb 2021
:
159-180
[doi]
Population Design for Synthetic Gene Circuits
Baptiste Turpin
,
Eline Y. Bijman
,
Hans-Michael Kaltenbach
,
Jörg Stelling
.
cmsb 2021
:
181-197
[doi]
Nonlinear Pattern Matching in Rule-Based Modeling Languages
Tom Warnke
,
Adelinde M. Uhrmacher
.
cmsb 2021
:
198-214
[doi]
Protein Noise and Distribution in a Two-Stage Gene-Expression Model Extended by an mRNA Inactivation Loop
Candan Çelik
,
Pavol Bokes
,
Abhyudai Singh
.
cmsb 2021
:
215-229
[doi]
2020
Computational Methods in Systems Biology - 18th International Conference, CMSB 2020, Konstanz, Germany, September 23-25, 2020, Proceedings
Alessandro Abate
,
Tatjana Petrov
,
Verena Wolf
, editors,
Volume 12314 of
Lecture Notes in Computer Science
, Springer,
2020.
[doi]
Comparing Probabilistic and Logic Programming Approaches to Predict the Effects of Enzymes in a Neurodegenerative Disease Model
Sophie Le Bars
,
Jérémie Bourdon
,
Carito Guziolowski
.
cmsb 2020
:
141-156
[doi]
Accelerating Reactions at the DNA Can Slow Down Transient Gene Expression
Pavol Bokes
,
Julia Klein
,
Tatjana Petrov
.
cmsb 2020
:
44-60
[doi]
What is a Cell Cycle Checkpoint? The TotemBioNet Answer
Déborah Boyenval
,
Gilles Bernot
,
Hélène Collavizza
,
Jean-Paul Comet
.
cmsb 2020
:
362-372
[doi]
Kaemika App: Integrating Protocols and Chemical Simulation - Integrating Protocols and Chemical Simulation
Luca Cardelli
.
cmsb 2020
:
373-379
[doi]
Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision
Stéphanie Chevalier
,
Vincent Noël
,
Laurence Calzone
,
Andrei Yu. Zinovyev
,
Loïc Paulevé
.
cmsb 2020
:
193-209
[doi]
Rate Equations for Graphs
Vincent Danos
,
Tobias Heindel
,
Ricardo Honorato-Zimmer
,
Sandro Stucki
.
cmsb 2020
:
3-26
[doi]
Graphical Conditions for Rate Independence in Chemical Reaction Networks
Elisabeth Degrand
,
François Fages
,
Sylvain Soliman
.
cmsb 2020
:
61-78
[doi]
Interval Constraint Satisfaction and Optimization for Biological Homeostasis and Multistationarity
Aurélien Desoeuvres
,
Gilles Trombettoni
,
Ovidiu Radulescu
.
cmsb 2020
:
79-101
[doi]
Qualitative Analysis of Mammalian Circadian Oscillations: Cycle Dynamics and Robustness
Ousmane Diop
,
Madalena Chaves
,
Laurent Tournier
.
cmsb 2020
:
176-192
[doi]
Control Strategy Identification via Trap Spaces in Boolean Networks
Laura Cifuentes Fontanals
,
Elisa Tonello
,
Heike Siebert
.
cmsb 2020
:
159-175
[doi]
ModRev - Model Revision Tool for Boolean Logical Models of Biological Regulatory Networks
Filipe Gouveia
,
Inês Lynce
,
Pedro T. Monteiro
.
cmsb 2020
:
339-348
[doi]
Drawing the Line: Basin Boundaries in Safe Petri Nets
Stefan Haar
,
Loïc Paulevé
,
Stefan Schwoon
.
cmsb 2020
:
321-336
[doi]
On the Complexity of Quadratization for Polynomial Differential Equations
Mathieu Hemery
,
François Fages
,
Sylvain Soliman
.
cmsb 2020
:
120-140
[doi]
fnyzer: A Python Package for the Analysis of Flexible Nets
Jorge Júlvez
,
Stephen G. Oliver
.
cmsb 2020
:
349-355
[doi]
2: Simultaneous Inference and Model Checking of Chemical Reaction Networks
Gareth W. Molyneux
,
Alessandro Abate
.
cmsb 2020
:
255-279
[doi]
Growth Dependent Computation of Chokepoints in Metabolic Networks
Alexandru Oarga
,
Bridget Bannerman
,
Jorge Júlvez
.
cmsb 2020
:
102-119
[doi]
Core Models of Receptor Reactions to Evaluate Basic Pathway Designs Enabling Heterogeneous Commitments to Apoptosis
Marielle Péré
,
Madalena Chaves
,
Jérémie Roux
.
cmsb 2020
:
298-320
[doi]
Classifier Construction in Boolean Networks Using Algebraic Methods
Robert Schwieger
,
Matías R. Bender
,
Heike Siebert
,
Christian Haase
.
cmsb 2020
:
210-233
[doi]
Parallel Parameter Synthesis for Multi-affine Hybrid Systems from Hybrid CTL Specifications
Eva Smijáková
,
Samuel Pastva
,
David Safránek
,
Lubos Brim
.
cmsb 2020
:
280-297
[doi]
Sequential Temporary and Permanent Control of Boolean Networks
Cui Su
,
Jun Pang 0001
.
cmsb 2020
:
234-251
[doi]
eBCSgen: A Software Tool for Biochemical Space Language
Matej Troják
,
David Safránek
,
Lukrécia Mertová
,
Lubos Brim
.
cmsb 2020
:
356-361
[doi]
Stationary Distributions and Metastable Behaviour for Self-regulating Proteins with General Lifetime Distributions
Candan Çelik
,
Pavol Bokes
,
Abhyudai Singh
.
cmsb 2020
:
27-43
[doi]
2019
Separators for Polynomial Dynamic Systems with Linear Complexity
Ines Abdeljaoued-Tej
,
Alia BenKahla
,
Ghassen Haddad
,
Annick Valibouze
.
cmsb 2019
:
373-378
[doi]
Computing Difference Abstractions of Metabolic Networks Under Kinetic Constraints
Emilie Allart
,
Joachim Niehren
,
Cristian Versari
.
cmsb 2019
:
266-285
[doi]
Biochemical Reaction Networks with Fuzzy Kinetic Parameters in Snoopy
George Assaf
,
Monika Heiner
,
Fei Liu 0006
.
cmsb 2019
:
302-307
[doi]
Control Variates for Stochastic Simulation of Chemical Reaction Networks
Michael Backenköhler
,
Luca Bortolussi
,
Verena Wolf
.
cmsb 2019
:
42-59
[doi]
Bounding First Passage Times in Chemical Reaction Networks - Poster Abstract
Michael Backenköhler
,
Luca Bortolussi
,
Verena Wolf
.
cmsb 2019
:
379-382
[doi]
Reachability Design Through Approximate Bayesian Computation
Mahmoud Bentriou
,
Paolo Ballarini
,
Paul-Henry Cournède
.
cmsb 2019
:
207-223
[doi]
Cell Volume Distributions in Exponentially Growing Populations
Pavol Bokes
,
Abhyudai Singh
.
cmsb 2019
:
140-154
[doi]
Computational Methods in Systems Biology - 17th International Conference, CMSB 2019, Trieste, Italy, September 18-20, 2019, Proceedings
Luca Bortolussi
,
Guido Sanguinetti
, editors,
Volume 11773 of
Lecture Notes in Computer Science
, Springer,
2019.
[doi]
The Kappa Simulator Made Interactive
Pierre Boutillier
.
cmsb 2019
:
296-301
[doi]
Spike - Reproducible Simulation Experiments with Configuration File Branching
Jacek Chodak
,
Monika Heiner
.
cmsb 2019
:
315-321
[doi]
BRE: IN - A Backend for Reasoning About Interaction Networks with Temporal Logic
Judah Goldfeder
,
Hillel Kugler
.
cmsb 2019
:
289-295
[doi]
Transient Memory in Gene Regulation
Calin C. Guet
,
Thomas A. Henzinger
,
Claudia Igler
,
Tatjana Petrov
,
Ali Sezgin
.
cmsb 2019
:
155-187
[doi]
Bayesian Parameter Estimation for Stochastic Reaction Networks from Steady-State Observations
Ankit Gupta
,
Mustafa Khammash
,
Guido Sanguinetti
.
cmsb 2019
:
342-346
[doi]
Data-Informed Parameter Synthesis for Population Markov Chains
Matej Hajnal
,
Morgane Nouvian
,
Tatjana Petrov
,
David Safránek
.
cmsb 2019
:
383-386
[doi]
KAMIStudio: An Environment for Biocuration of Cellular Signalling Knowledge
Russ Harmer
,
Eugenia Oshurko
.
cmsb 2019
:
322-328
[doi]
Effective Computational Methods for Hybrid Stochastic Gene Networks
Guilherme C. P. Innocentini
,
Fernando Antoneli
,
Arran Hodgkinson
,
Ovidiu Radulescu
.
cmsb 2019
:
60-77
[doi]
Compartmental Modeling Software: A Fast, Discrete Stochastic Framework for Biochemical and Epidemiological Simulation
Christopher W. Lorton
,
Joshua L. Proctor
,
Min K. Roh
,
Philip A. Welkhoff
.
cmsb 2019
:
308-314
[doi]
Symmetry Breaking for GATA-1/PU.1 Model
Lenka Pribylová
,
Barbora Losová
.
cmsb 2019
:
360-363
[doi]
Barbaric Robustness Monitoring Revisited for STL* in Parasim
David Safránek
,
Matej Troják
,
Vojtech Bruza
,
Tomás Vejpustek
,
Jan Papousek
,
Martin Demko
,
Samuel Pastva
,
Ales Pejznoch
,
Lubos Brim
.
cmsb 2019
:
356-359
[doi]
Fast Enumeration of Non-isomorphic Chemical Reaction Networks
Carlo Spaccasassi
,
Boyan Yordanov
,
Andrew Phillips
,
Neil Dalchau
.
cmsb 2019
:
224-247
[doi]
Transcriptional Response of SK-N-AS Cells to Methamidophos (Extended Abstract)
Akos Vertes
,
Albert-Baskar Arul
,
Peter Avar
,
Andrew R. Korte
,
Lida Parvin
,
Ziad J. Sahab
,
Deborah I. Bunin
,
Merrill Knapp
,
Denise Nishita
,
Andrew Poggio
,
Mark-Oliver Stehr
,
Carolyn L. Talcott
,
Brian M. Davis
,
Christine A. Morton
,
Christopher J. Sevinsky
,
Maria I. Zavodszky
.
cmsb 2019
:
368-372
[doi]
Wasserstein Distances for Estimating Parameters in Stochastic Reaction Networks
Kaan Öcal
,
Ramon Grima
,
Guido Sanguinetti
.
cmsb 2019
:
347-351
[doi]
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