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Empirical Numerical Properties of Maximum Likelihood Phylogenetic Inference

Abstract (Expand)

Phylogenetic trees represent hypothetical evolutionary relationships between organisms. Approaches for inferring phylogenetic trees include the Maximum Likelihood (ML) method. This method relies on … numerical optimization routines that use internal numerical thresholds. We analyze the influence of these thresholds on the likelihood scores and runtimes of tree inferences for the ML inference tools RAxML-NG, IQ-Tree, and FastTree. We analyze 22 empirical datasets and show that we can speed up the tree inference in RAxML-NG and IQ-Tree by changing the default values of two such numerical thresholds. Using 15 additional simulated datasets, we show that these changes do not affect the accuracy of the inferred phylogenetic trees. For RAxML-NG, increasing the likelihood thresholds lh_epsilon and spr_lh_epsilon to 10 and 103 respectively results in an average speedup of 1.9 ± 0.6. Increasing the likelihood threshold lh_epsilon in IQ-Tree results in an average speedup of 1.3 ± 0.4. In addition to the numerical analysis, we attempt to predict the difficulty of datasets, with the aim of preventing an unnecessarily large number of tree inferences for datasets that are easy to analyze. We present our prediction experiments and discuss why this task proved to be more challenging than anticipated.

Author: Julia Haag

Date Published: 31st Oct 2021

Publication Type: Master's Thesis

Disentangling the optical AGN and host-galaxy luminosity with a probabilistic flux variation gradient

Abstract

Not specified

Authors: N. Gianniotis, F. Pozo Nuñez, K. L. Polsterer

Date Published: 29th Oct 2021

Publication Type: Journal

Biomechanical Influences on Mesh-Related Complications in Incisional Hernia Repair

Abstract

Not specified

Authors: Friedrich Kallinowski, Yannique Ludwig, Dominik Gutjahr, Christian Gerhard, Hannah Schulte-Hörmann, Lena Krimmel, Carolin Lesch, Katharina Uhr, Philipp Lösel, Samuel Voß, Vincent Heuveline, Matthias Vollmer, Johannes Görich, Regine Nessel

Date Published: 29th Oct 2021

Publication Type: Journal

Kinetic and structural roles for the surface in guiding SAS-6 self-assembly to direct centriole architecture

Abstract (Expand)

iscovering mechanisms governing organelle assembly is a fundamental pursuit in biology. The centriole is an evolutionarily conserved organelle with a signature 9-fold symmetrical chiral arrangement of … microtubules imparted onto the cilium it templates. The first structure in nascent centrioles is a cartwheel, which comprises stacked 9-fold symmetrical SAS-6 ring polymers emerging orthogonal to a surface surrounding each resident centriole. The mechanisms through which SAS-6 polymerization ensures centriole organelle architecture remain elusive. We deploy photothermally-actuated off-resonance tapping high-speed atomic force microscopy to decipher surface SAS-6 self-assembly mechanisms. We show that the surface shifts the reaction equilibrium by ~104 compared to solution. Moreover, coarse-grained molecular dynamics and atomic force microscopy reveal that the surface converts the inherent helical propensity of SAS-6 polymers into 9-fold rings with residual asymmetry, which may guide ring stacking and impart chiral features to centrioles and cilia. Overall, our work reveals fundamental design principles governing centriole assembly.

Authors: Niccolò Banterle, Adrian P. Nievergelt, Svenja de Buhr, Georgios N. Hatzopoulos, Charlène Brillard, Santiago Andany, Tania Hübscher, Frieda A. Sorgenfrei, Ulrich S. Schwarz, Frauke Gräter, Georg E. Fantner, Pierre Gönczy

Date Published: 26th Oct 2021

Publication Type: Journal

Specifications of standards in systems and synthetic biology: status and developments in 2021.

Abstract (Expand)

This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2021 special issue presents four updates of … standards: Synthetic Biology Open Language Visual Version 2.3, Synthetic Biology Open Language Visual Version 3.0, Simulation Experiment Description Markup Language Level 1 Version 4, and OMEX Metadata specification Version 1.2. This document can also be consulted to identify the latest specifications of all COMBINE standards.

Authors: F. Schreiber, P. Gleeson, M. Golebiewski, T. E. Gorochowski, M. Hucka, S. M. Keating, M. Konig, C. J. Myers, D. P. Nickerson, B. Sommer, D. Waltemath

Date Published: 22nd Oct 2021

Publication Type: Journal

Contact Map Fingerprints of Protein–Ligand Unbinding Trajectories Reveal Mechanisms Determining Residence Times Computed from Scaled Molecular Dynamics

Abstract

Not specified

Authors: Marc Bianciotto, Paraskevi Gkeka, Daria B. Kokh, Rebecca C. Wade, Hervé Minoux

Date Published: 12th Oct 2021

Publication Type: Journal

G Protein-Coupled Receptor–Ligand Dissociation Rates and Mechanisms from τRAMD Simulations

Abstract

Not specified

Authors: Daria B. Kokh, Rebecca C. Wade

Date Published: 12th Oct 2021

Publication Type: Journal

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