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COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

Abstract (Expand)

We hereby describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, … platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. We describe the contents of the map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied to the contents of the COVID-19 Disease Map for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases.

Authors: Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frischman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G. Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E. Ackerman, Jason Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, D. A. B. Rex, Denise Slenter, Marvin Martens, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W. Overall, Dieter Maier, Angela Bauch, Benjamin M. Gyori, John A. Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Peña-Chilet, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Aurélien Dugourd, Aurelien Naldi, Vincent Noel, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C. Freeman, Franck Augé, Jacques S. Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L. Wilighagen, Alexander R. Pico, Chris T. Evelo, Marc E. Gillespie, Lincoln D. Stein, Henning Hermjakob, Peter D’Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider

Date Published: 28th Oct 2020

Publication Type: Unpublished

SoftWipe – a tool and benchmark to assess scientific software quality

Abstract

Not specified

Authors: Adrian Zapletal, Dimitri Höhler, Carsten Sinz, Alexandros Stamatakis

Date Published: 13th Oct 2020

Publication Type: Journal

Mechanical characterization and induced crystallization in nanocomposites of thermoplastics and carbon nanotubes

Abstract (Expand)

Nanocomposites built from polymers and carbon nanotubes (CNTs) are a promising class of materials. Computer modeling can provide nanoscale views of the polymer-CNT interface, which are much needed to … foster the manufacturing and development of such materials. However, setting up periodic nanocomposite models is a challenging task. Here we propose a computational workflow based on Molecular Dynamics simulations. We demonstrate its capabilities and showcase its applications, focusing on two existing nanocomposite materials: polystyrene (PS) with CNT and polyether ether ketone with CNT. The models provide insights into the polymer crystallization inside CNTs. Furthermore, the PS+CNT nanocomposite models are mechanically tested and able to predict an enhancement in Young's modulus due to the addition of highly dispersed CNTs. We accompany those results with experimental tests and provide a prediction model based on Dynamic Quantized Fracture Mechanics theory. Our study proposes representative simulations of polymer-CNT nanocomposites as promising tools to guide the rational design of this class of materials.

Authors: Eduardo R. Cruz-Chú, Gonzalo Villegas-Rodriguez, Tobias Jäger, Luca Valentini, Nicola Pugno, Konstantinos Gkagkas, Frauke Gräter

Date Published: 12th Oct 2020

Publication Type: Journal

SCRAPP : A tool to assess the diversity of microbial samples from phylogenetic placements

Abstract

Not specified

Authors: Pierre Barbera, Lucas Czech, Sarah Lutteropp, Alexandros Stamatakis

Date Published: 9th Oct 2020

Publication Type: Journal

Computation of FRAP recovery times for linker histone – chromatin binding on the basis of Brownian dynamics simulations

Abstract

Not specified

Authors: Mehmet Ali Öztürk, Rebecca C. Wade

Date Published: 1st Oct 2020

Publication Type: Journal

Recent progress in molecular simulation methods for drug binding kinetics

Abstract

Not specified

Authors: Ariane Nunes-Alves, Daria B Kokh, Rebecca C Wade

Date Published: 1st Oct 2020

Publication Type: Journal

A Layered Approach to Robust Determination of Asteroseismic Parameters

Abstract (Expand)

We describe here a layered approach to the robust determination of the broad characteristics of the asteroseismic signal from red-giant stars. No single stringent test can exclude all false results. … The use of multiple, weak tests not only provides robust results but also avoids over-constraining the parameter space.

Authors: Yvonne Elsworth, Nathalie Themeßl, Saskia Hekker, William Chaplin

Date Published: 1st Oct 2020

Publication Type: Misc

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