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1579 Publications visible to you, out of a total of 1579
Semantic Matching of Documents from Heterogeneous Collections: A Simple and Transparent Method for Practical Applications

Abstract

Not specified

Author: Mark-Christoph Müller

Date Published: 23rd May 2019

Publication Type: InProceedings

A new method for the construction of coarse-grained models of large biomolecules from low-resolution cryo-electron microscopy data

Abstract

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Authors: Yuwei Zhang, Kelin Xia, Zexing Cao, Frauke Gräter, Fei Xia

Date Published: 15th May 2019

Publication Type: Journal

Higgs Bundles and Geometric Structures on Manifolds

Abstract (Expand)

Geometric structures on manifolds became popular when Thurston used them in his work on the geometrization conjecture. They were studied by many people and they play an important role in higher Teichmüller … theory. Geometric structures on a manifold are closely related with representations of the fundamental group and with flat bundles. Higgs bundles can be very useful in describing flat bundles explicitly, via solutions of Hitchin’s equations. Baraglia has shown in his Ph.D. Thesis that Higgs bundles can also be used to construct geometric structures in some interesting cases. In this paper, we will explain the main ideas behind this theory and we will survey some recent results in this direction, which are joint work with Qiongling Li.

Author: Daniele Alessandrini

Date Published: 10th May 2019

Publication Type: Journal

Using RAxML-NG in Practice

Abstract

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Authors: Alexey M. Kozlov, Alexandros Stamatakis

Date Published: 6th May 2019

Publication Type: Journal

Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

Abstract (Expand)

High-throughput environmental DNA metabarcoding has revolutionized the analysis of microbial diversity, but this approach is generally restricted to amplicon sizes below 500 base pairs. These short … regions contain limited phylogenetic signal, which makes it impractical to use environmental DNA in full phylogenetic inferences. However, new long-read sequencing technologies such as the Pacific Biosciences platform may provide sufficiently large sequence lengths to overcome the poor phylogenetic resolution of short amplicons. To test this idea, we amplified soil DNA and used PacBio Circular Consensus Sequencing (CCS) to obtain a ~4500 bp region of the eukaryotic rDNA operon spanning most of the small (18S) and large subunit (28S) ribosomal RNA genes. The CCS reads were first treated with a novel curation workflow that generated 650 high-quality OTUs containing the physically linked 18S and 28S regions of the long amplicons. In order to assign taxonomy to these OTUs, we developed a phylogeny-aware approach based on the 18S region that showed greater accuracy and sensitivity than similarity-based and phylogenetic placement-based methods using shorter reads. The taxonomically-annotated OTUs were then combined with available 18S and 28S reference sequences to infer a well-resolved phylogeny spanning all major groups of eukaryotes, allowing to accurately derive the evolutionary origin of environmental diversity. A total of 1019 sequences were included, of which a majority (58%) corresponded to the new long environmental CCS reads. Comparisons to the 18S-only region of our amplicons revealed that the combined 18S-28S genes globally increased the phylogenetic resolution, recovering specific groupings otherwise missing. The long-reads also allowed to directly investigate the relationships among environmental sequences themselves, which represents a key advantage over the placement of short reads on a reference phylogeny. Altogether, our results show that long amplicons can be treated in a full phylogenetic framework to provide greater taxonomic resolution and a robust evolutionary perspective to environmental DNA.

Authors: Mahwash Jamy, Rachel Foster, Pierre Barbera, Lucas Czech, Alexey Kozlov, Alexandros Stamatakis, David Baß, Fabien Burki

Date Published: 5th May 2019

Publication Type: Journal

Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning

Abstract

Not specified

Authors: Ivo Baar, Lukas Hubner, Peter Oettig, Adrian Zapletal, Sebastian Schlag, Alexandros Stamatakis, Benoit Morel

Date Published: 1st May 2019

Publication Type: Proceedings

Exploring the sensitivity of gravitational wave detectors to neutron star physics

Abstract

Not specified

Authors: Denis Martynov, Haixing Miao, Huan Yang, Francisco Hernandez Vivanco, Eric Thrane, Rory Smith, Paul Lasky, William E. East, Rana Adhikari, Andreas Bauswein, Aidan Brooks, Yanbei Chen, Thomas Corbitt, Andreas Freise, Hartmut Grote, Yuri Levin, Chunnong Zhao, Alberto Vecchio

Date Published: 1st May 2019

Publication Type: Journal

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