16 papers · ranked by Valyu relevance
Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler + 5 more
The identification of large regulatory and signalling networks involved in the control of crucial cellular processes calls for proper modelling approaches. Indeed, models can help elucidate properties of these networks, understand their behaviour, and provide (testable) predictions by performing in silico experiments.…
Vincent Noël, Aurélien Naldi, Laurence Calzone, Loic Paulevé + 1 more
This tutorial provides stepwise instructions to install the 20 tools integrated in the CoLoMoTo software suite, to develop reproducible dynamical analyses of logical models of complex biological molecular networks. The tutorial specifically focuses on the analysis of a previously published model of the regulatory…
Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll + 8 more
Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and…
Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll + 8 more
'Pedro T. Monteiro' 'Claudine Chaouiya' 'Tomáš Helikar' 'Andrei Zinovyev' 'Laurence Calzone' 'Sarah Cohen-Boulakia' 'Denis Thieffry' 'Loïc Paulevé'] Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times with…
Vincent Noël, Aurélien Naldi, Laurence Calzone, Loic Paulevé + 1 more
'Denis Thieffry'] This tutorial provides stepwise instructions to install over 20 tools, written in multiple languages. Their integration in the CoLoMoTo software suite makes them accessible with a single popular language (Python), thereby enabling reproducible and sophisticated dynamical analyses of logical models of…
Nicolas Levy, Aurélien Naldi, Céline Hernandez, Gautier Stoll + 4 more
'Denis Thieffry' 'Andrei Zinovyev' 'Laurence Calzone' 'Loïc Paulevé'] Boolean and multi-valued logical formalisms are increasingly used to model complex cellular networks. To ease the development and analysis of logical models, a series of software tools have been proposed, often with specific assets. However…
Nicolas Levy, Aurélien Naldi, Céline Hernandez, Gautier Stoll + 4 more
Boolean and multi-valued logical formalisms are increasingly used to model complex cellular networks. To ease the development and analysis of logical models, a series of software tools have been proposed, often with specific assets. However, combining these tools typically implies a series of cumbersome software…
Gerhard Mayer
| ASP | Answer Set Programming | | --- | --- | | (Open)BEL | Biological Expression Language | | BioPAX | BIOlogical Pathways eXchange | | CoD | Coefficient of Determination | | | CoLoMoTo Consortium for Logical Models and Tools | | COMBINE | COmputational Modelling in BIology Network | | EBN | Extended Boolean Network…
Songbo Ni, Emanuele Marini, Ivo Buttinoni, Heiko Wolf + 1 more
Active colloids, also known as artificial microswimmers, are self-propelled micro and nanoparticles that convert uniform sources of fuel (e.g. chemical) or uniform external driving fields (e.g. magnetic or electric) into directed motion by virtue of asymmetry in their shape or composition. These materials are currently…
Martin Cheek
A new subgenus, Subg. Disticha is erected for 14 species of simple-leaved Cola sharing unique characters within the genus which are presumed synapomorphies: distichous phyllotaxy; petioles lacking pulvini; petioles of uniformly short length, <10 mm long; male flowers with short androphores <1(– 2) mm long; stamens 4 –…
Authors not listed
Tubulins are among the most successful targets for cancer chemotherapy. However, the emergence of drug resistance stimulates the continuous search for novel chemotherapeutics. Here, we discover that coumarin-30, a widely available laser dye, binds to the colchicine site of tubulin and inhibits microtubule dynamics and…
John L. Clark, Sofía Ballesteros, Laura Clavijo
Field expeditions to the western Andean slopes of Colombia and ongoing herbarium research resulted in the discovery of a new species of Columnea (Gesneriaceae). Columnearubromarginata J.L.Clark & Clavijo, sp. nov. is described from the Chocó Biogeographic Region in the premontane wet forests of Esmeraldas in northern…
John L. Clark, David Lozano-Cifuentes, Jorge Ríos-Cervera, Laura Clavijo + 1 more
'Laura Clavijo' 'Sofía Ballesteros'] Title: Abstract Two new species of Columnea are described based on recent field expeditions and herbarium research. These species are unusual within Columnea for exhibiting a dorsiventral epiphytic habit typical of many northern Andean species, but they lack conspicuous floral…
Mikhail N. Anisimov, Maksim A. Boichenko, Vitaly V. Shorokhov, Julia N. Borzunova + 12 more
Dynamic polymers of tubulin, known as microtubules, are among the most important targets for anti-cancer chemo-therapy. Although several inhibitors of tubulin polymerization are clinically successful, the resistance of cancers to existing drugs urges for the development of novel tubulin-binding substances that can…
Authors not listed
Kurtis D. Bornea, b , Rebecca Boll c , Thomas M. Baumann c , Surjendu Bhattacharyyaa, b , Martin Centurion d , Keyu Chen a , Benjamin Erk e , Alberto De Fanis c , Ruaridh Forbesb, f , Markus Ilchenc,e, g , Edwin Kukk h , Huynh V. S. Lam a , Xiang Li b , Lingyu Ma i , Tommaso Mazza c , Michael Meyer c , Terence…
Authors not listed
The self-organization of colloidal nanoparticles into complex structures, both in equilibrium and out-of-equilibrium, is a critical area in colloidal science with potential applications in creating new functional materials. While equilibrium assemblies yield thermodynamically stable and periodic structures…