21 papers · ranked by Valyu relevance
David M Emms, Steven Kelly
The correct interpretation of any phylogenetic tree is dependent on that tree being correctly rooted. We present STRIDE, a fast, effective, and outgroup-free method for identification of gene duplication events and species tree root inference in large-scale molecular phylogenetic analyses. STRIDE identifies sets of…
David M. Emms, Steven Kelly
The correct interpretation of a phylogenetic tree is dependent on it being correctly rooted. A gene duplication event at the base of a clade of species is synapamorphic, and thus excludes the root of the species tree from that clade. We present STRIDE, a fast, effective, and outgroup-free method for species tree root…
Ben Bettisworth, Alexandros Stamatakis
In phylogenetic analysis, it is common to infer unrooted trees. Thus, it is unknown which node is the most recent common ancestor of all the taxa in the phylogeny. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such as midpoint…
Jiangsan Zhao, Gernot Bodner, Boris Rewald, Daniel Leitner + 2 more
Title: Highlight A root architecture model accurately predicts mature root systems of distinct pea genotypes from seedling stage phenotyping information of elongation rate and interbranch distance.
Jonas Alle, Roland Gruber, Norbert Wörlein, Norman Uhlmann + 3 more
'Joelle Claußen' 'Thomas Wittenberg' 'Stefan Gerth'] Background The non-invasive 3D-imaging and successive 3D-segmentation of plant root systems has gained interest within fundamental plant research and selectively breeding resilient crops. Currently the state of the art consists of computed tomography (CT) scans and…
Fernando D. K. Tria, Giddy Landan, Devani Romero Picazo, Tal Dagan
The determination of the last common ancestor (LCA) of a group of species plays a vital role in evolutionary theory. Traditionally, an LCA is inferred by the rooting of a fully resolved species tree. From a theoretical perspective, however, inference of the LCA amounts to the reconstruction of just one branch - the…
Harry Crane, Min Xu
Many existing statistical models for networks overlook the fact that most real world networks are formed through a growth process. To address this, we introduce the PAPER (Preferential Attachment Plus Erd˝os–R´enyi) model for random networks, where we let a random network G be the union of a preferential attachment…
Ben Bettisworth, Alexandros Stamatakis
Background In phylogenetic analysis, it is common to infer unrooted trees. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such as molecular clock analysis (including midpoint rooting) or rooting the tree using an outgroup.…
Suha Naser-Khdour, Bui Quang Minh, Robert Lanfear
Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In…
Yuan Tian, Laura Kubatko
Background Phylogenetic tree inference is a fundamental tool to estimate ancestor-descendant relationships among different species. In phylogenetic studies, identification of the root - the most recent common ancestor of all sampled organisms - is essential for complete understanding of the evolutionary relationships.…
Suha Naser-Khdour, Bui Quang Minh, Robert Lanfear, Robert Thomson
Using Nonreversible Models for Mammals Authors: Suha Naser-Khdour, Bui Quang Minh, Robert Lanfear, Robert Thomson Title: Abstract Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide…
Eric V. Strobl, Thomas A. Lasko
Root causal analysis seeks to identify the set of initial perturbations that induce an unwanted outcome. In prior work, we defined sample-specific root causes of disease using exogenous error terms that predict a diagnosis in a structural equation model. We rigorously quantified predictivity using Shapley values.…
Eric V. Strobl
Root causes of disease intuitively correspond to root vertices that increase the likelihood of a diagnosis. This description of a root cause nevertheless lacks the rigorous mathematical formulation needed for the development of computer algorithms designed to automatically detect root causes from data. Prior work…
Anand Seethepalli, Kundan Dhakal, Marcus Griffiths, Haichao Guo + 2 more
Roots are central to the function of natural and agricultural ecosystems by driving plant acquisition of soil resources and influencing the carbon cycle. Root characteristics like length, diameter, and volume are critical to measure to understand plant and soil functions. RhizoVision Explorer is an open-source software…
Joerg Schoenfisch, Janno von Stulpnagel, Jens Ortmann, Christian Meilicke + 1 more
'Christian Meilicke' 'Heiner Stuckenschmidt'] Abstract. In this paper we propose an approach for calculating the most probable root cause for an observed failure in an IT infrastructure. Our approach is based on Markov Logic Networks. While Markov Logic supports a special type of deductive inference, known as maximum a…
Authors not listed
Understanding how plants respond to dynamic and spatially variable stimuli is a key goal in plant sciences. Traditional imaging methods often involve a trade-off between environmental control and spatial resolution, limiting their ability to capture real-time responses in high resolution. Microfluidic technology…
Authors not listed
Global food security and environmental sustainability are closely linked to positive plant-soil feedback, for example through reduced dependence on synthetic agrochemicals. Beyond their nutritional value as protein- and lipid-rich crops, legumes have an essential ecological function by enhancing soil fertility and…
Saad Raza, Troy Sievertsen, Sakiko Okumoto, Josh Vermaas
Competition for soil nutrients and water with other plants foster competition within the biosphere for access to these limited resources. The roots for the common grain sorghum produce multiple small molecules that are released via root exudates into the soil to compete with other plants. Sorgoleone is one such…
Nicole Bidoít, Dario Colazzo, Federico Ulliana
This paper presents a novel static analysis technique to detect XML query-update independence, in the presence of a schema. Rather than types, our system infers chains of types. Each chain represents a path that can be traversed on a valid document during query/update evaluation. The resulting independence analysis is…
Lars-Phillip Spiegel, Jonas Haldimann, Jesse Heyninck, Gabriele Kern-Isberner + 1 more
In nonmonotonic reasoning from conditional belief bases, an inference operator satisfying syntax splitting postulates allows for taking only the relevant parts of a belief base into account, provided that the belief base splits into subbases based on disjoint signatures. Because such disjointness is rare in practice…
Jonas Schaub, Julian Zander, Achim Zielesny, Christoph Steinbeck
The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the…