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1579 Publications visible to you, out of a total of 1579
Glycosaminoglycans: What Remains To Be Deciphered?

Abstract

Not specified

Authors: Serge Perez, Olga Makshakova, Jesus Angulo, Emiliano Bedini, Antonella Bisio, Jose Luis de Paz, Elisa Fadda, Marco Guerrini, Michal Hricovini, Milos Hricovini, Frederique Lisacek, Pedro M. Nieto, Kevin Pagel, Giulia Pairardi, Ralf Richter, Sergey A. Samsonov, Romain A. Vivès, Dragana Nikitovic, Sylvie Ricard Blum

Date Published: 27th Mar 2023

Publication Type: Journal

Convergence of forecast distributions in a 100,000‐member idealised convective‐scale ensemble

Abstract

Not specified

Authors: Kirsten I. Tempest, George C. Craig, Jonas R. Brehmer

Date Published: 22nd Mar 2023

Publication Type: Journal

The power and limitations of species tree-aware phylogenetics

Abstract (Expand)

Abstract Species tree-aware phylogenetic methods model how gene trees are generated along the species tree by a series of evolutionary events, including the duplication, transfer and loss of genes. …fer and loss of genes. Over the past ten years these methods have emerged as a powerful tool for inferring and rooting gene and species trees, inferring ancestral gene repertoires, and studying the processes of gene and genome evolution. However, these methods are complex and can be more difficult to use than traditional phylogenetic approaches. Method development is rapid, and it can be difficult to decide between approaches and interpret results. Here, we review ALE and GeneRax, two popular packages for reconciling gene and species trees, explaining how they work, how results can be interpreted, and providing a tutorial for practical analysis. It was recently suggested that reconciliation-based estimates of duplication and transfer frequencies are unreliable. We evaluate this criticism and find that, provided parameters are estimated from the data rather than being fixed based on prior assumptions, reconciliation-based inferences are in good agreement with the literature, recovering variation in gene duplication and transfer frequencies across lineages consistent with the known biology of studied clades. For example, published datasets support the view that transfers greatly outnumber duplications in most prokaryotic lineages. We conclude by discussing some limitations of current models and prospects for future progress. Significance statement Evolutionary trees provide a framework for understanding the history of life and organising biodiversity. In this review, we discuss some recent progress on statistical methods that allow us to combine information from many different genes within the framework of an overarching phylogenetic species tree. We review the advantages and uses of these methods and discuss case studies where they have been used to resolve deep branches within the tree of life. We conclude with the limitations of current methods and suggest how they might be overcome in the future.

Authors: Tom A. Williams, Adrian A. Davin, Benoit Morel, Lénárd L. Szánthó, Anja Spang, Alexandros Stamatakis, Philip Hugenholtz, Gergely J. Szöllősi

Date Published: 17th Mar 2023

Publication Type: Journal

A “two-in-one hit” model of shortcut carcinogenesis in MLH1 Lynch syndrome carriers

Abstract

Not specified

Authors: Aysel Ahadova, Albrecht Stenzinger, Toni Seppälä, Robert Hüneburg, Matthias Kloor, Hendrik Bläker, Jan-Niklas Wittemann, Volker Endris, Leonie Gerling, Veit Bertram, Marie Theres Neumuth, Johannes Witt, Sebastian Graf, Glen Kristiansen, Oliver Hommerding, Saskia Haupt, Alexander Zeilmann, Vincent Heuveline, Daniel Kazdal, Johannes Gebert, Magnus von Knebel Doeberitz, Jukka-Pekka Mecklin, Jacob Nattermann

Date Published: 11th Mar 2023

Publication Type: Journal

Model diagnostics and forecast evaluation for quantiles

Abstract

Not specified

Authors: Tilmann Gneiting, Daniel Wolffram, Johannes Resin, Kristof Kraus, Johannes Bracher, Timo Dimitriadis, Veit Hagenmeyer, Alexander I. Jordan, Sebastian Lerch, Kaleb Phipps, Melanie Schienle

Date Published: 10th Mar 2023

Publication Type: Journal

Bringing Stellar Evolution and Feedback Together: Summary of Proposals from the Lorentz Center Workshop

Abstract (Expand)

Stars strongly impact their environment, and shape structures on all scales throughout the universe, in a process known as "feedback." Due to the complexity of both stellar evolution and the … physics of larger astrophysical structures, there remain many unanswered questions about how feedback operates and what we can learn about stars by studying their imprint on the wider universe. In this white paper, we summarize discussions from the Lorentz Center meeting "Bringing Stellar Evolution and Feedback Together" in 2022 April and identify key areas where further dialog can bring about radical changes in how we view the relationship between stars and the universe they live in.

Authors: Sam Geen, Poojan Agrawal, Paul A. Crowther, B. W. Keller, Alex de Koter, Zsolt Keszthelyi, Freeke van de Voort, Ahmad A. Ali, Frank Backs, Lars Bonne, Vittoria Brugaletta, Annelotte Derkink, Sylvia Ekström, Yvonne A. Fichtner, Luca Grassitelli, Ylva Götberg, Erin R. Higgins, Eva Laplace, Kong You Liow, Marta Lorenzo, Anna F. McLeod, Georges Meynet, Megan Newsome, G. André Oliva, Varsha Ramachandran, Martin P. Rey, Steven Rieder, Emilio Romano-Díaz, Gautham Sabhahit, Andreas A. C. Sander, Rafia Sarwar, Hanno Stinshoff, Mitchel Stoop, Dorottya Szécsi, Maxime Trebitsch, Jorick S. Vink, Ethan Winch

Date Published: 9th Mar 2023

Publication Type: Journal

An artificial neural network model to predict structure-based protein–protein free energy of binding from Rosetta-calculated properties

Abstract

An artificial neural network protocol to compute protein–protein free energy of binding.

Authors: Matheus V. F. Ferraz, José C. S. Neto, Roberto D. Lins, Erico S. Teixeira

Date Published: 8th Mar 2023

Publication Type: Journal

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