10 papers · ranked by Valyu relevance
Marco Matthies, Ryan Krueger, Andrew Torda, Max Ward
Ribonucleic acid (RNA) is an essential molecule in a wide range of biological functions. In 1990, McCaskill introduced a dynamic programming algorithm for computing the partition function of an RNA sequence. This forward model is widely used for understanding the thermodynamic properties of a given RNA. In this work…
Luke Trinity, Sebastian Will, Yann Ponty, Ulrike Stege + 1 more
RNA molecules fold into biologically important functional structures. Efficient dynamic programming RNA (secondary) structure prediction algorithms restrict the search space to evade NP-hardness of general pseudoknot prediction. While such prediction algorithms can be extended to provide a stochastic view on RNA…
Jana Obšteter, Justin Holl, John M. Hickey, Gregor Gorjanc
In this paper we present the AlphaPart R package, an open-source software that implements a method for partitioning breeding values and genetic trends to identify sources of genetic gain. Breeding programmes improve populations for a set of traits, which can be measured with a genetic trend calculated from averaged…
Torsti Schulz, Marjo Saastamoinen, Jarno Vanhatalo
Variance partitioning is a common tool for statistical analysis and interpretation in both observational and experimental studies in ecology. Its popularity has led to a proliferation of methods with sometimes confusing or contradicting interpretations. Here, we present variance partitioning as a general tool in a…
Leah McPhillips, Govind Chandra, Thomas C. McLean, Ngat T. Tran + 1 more
Low-copy-number plasmids often rely on dedicated maintenance mechanisms, such as partitioning systems, to ensure stable inheritance across generations. These partition systems actively segregate sister plasmid copies during cell division and are classified by the NTPase types they encode. While the distribution and…
Carey E. Priebe, Joshua T. Vogelstein, Florian Engert, Christopher M. White
We present modern machine learning, focusing on the state-of-the-art classification methods of decision forests and deep networks, as partition and vote schemes. This illustrative presentation allows for both a unified basic understanding of how these methods work from the perspective of classical statistical pattern…
Pablo Castro Sánchez-Bermejo, Joaquín Hortal, Esben Moland Olsen, Cristina Ronquillo + 2 more
Equivalent numbers represent biodiversity as the effective number of equally distinct units, typically species, and can be partitioned across scales. In practice, they summarize each unit of biodiversity by a single value and compare units pairwise, misrepresenting units that are better described as distributions and…
Constantin Scholl, Kassian Kobert, Tomáš Flouri, Alexandros Stamatakis
Motivated by load balance issues in parallel calculations of the phylogenetic likelihood function, we recently introduced an approximation algorithm for efficiently distributing partitioned alignment data to a given number of CPUs. The goal is to balance the accumulated number of sites per CPU, and, at the same time…
Muyang Lu, Kevin Winner, Walter Jetz
The quantification of Hutchison’s n-dimensional hypervolume has enabled substantial progress in community ecology, species niche analysis and beyond. While non-parametric methods for quantifying and comparing hypervolumes are popular, they do not support a partitioning of the different components and drivers of…
Philipp S. L. Schäfer, Leoni Zimmermann, Paul L. Burmedi, Avia Walfisch + 7 more
Trade-offs between different functions or tasks are pervasive across scales in biological systems. For example, individual cells cannot perform all possible functions simultaneously; instead they allocate limited resources to specialize in subsets of tasks by activating specific gene expression programs. Pareto Task…