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Lucas Czech
Heidelberg Institute for Theoretical Studies
17Publications
7H-index
150Citations
Publications 18
Newest
High‐throughput DNA metabarcoding of amplicon sizes below 500 bp has revolutionized the analysis of environmental microbial diversity. However, these short regions contain limited phylogenetic signal, which makes it impractical to use environmental DNA in full phylogenetic inferences. This lesser phylogenetic resolution of short amplicons may be overcome by new long‐read sequencing technologies. To test this idea, we amplified soil DNA and used PacBio Circular Consensus Sequencing (CCS) to obtai...
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#1Xiaofan Zhou (SCAU: South China Agricultural University)H-Index: 18
#2Sarah Lutteropp (Heidelberg Institute for Theoretical Studies)H-Index: 1
Last.Antonis Rokas (Vandy: Vanderbilt University)H-Index: 55
view all 6 authors...
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Background: The exponential decrease in molecular sequencing cost generates unprecedented amounts of data. Hence, scalable methods to analyze these data are required. Phylogenetic (or Evolutionary) Placement methods identify the evolutionary provenance of anonymous sequences with respect to a given reference phylogeny. This increasingly popular method is deployed for scrutinizing metagenomic samples from environments such as water, soil, or the human gut. Novel methods: Here, we present novel an...
4 CitationsSource
#1Lucas Czech (Heidelberg Institute for Theoretical Studies)H-Index: 7
#2Pierre Barbera (Heidelberg Institute for Theoretical Studies)H-Index: 3
Last.Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
view all 3 authors...
The ever increasing amount of genomic and meta-genomic sequence data has transformed biology into a data-driven and compute-intensive discipline. Hence, there is a need for efficient algorithms and scalable implementations thereof for analysing such data. We present genesis, a library for working with phylogenetic data, and gappa, an accompanying command line tool for conducting typical analyses on such data. While our tools primarily target phylogenetic trees and phylogenetic placements, they a...
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#1Mahwash Jamy (Uppsala University)H-Index: 1
#2Rachel Foster (Natural History Museum)H-Index: 2
Last.Fabien Burki (Uppsala University)H-Index: 3
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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 re...
1 CitationsSource
#1Lucas Czech (Heidelberg Institute for Theoretical Studies)H-Index: 7
#2Pierre Barbera (Heidelberg Institute for Theoretical Studies)H-Index: 3
Last.Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
view all 3 authors...
5 CitationsSource
#1Pierre Barbera (Heidelberg Institute for Theoretical Studies)H-Index: 3
#2Alexey M. Kozlov (Heidelberg Institute for Theoretical Studies)H-Index: 12
Last.Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
view all 7 authors...
Next generation sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification of sequences obtained from diverse microbial environments. Phylogenetic placement methods determine how these sequences fit into an evolutionary context. Previous implementations of phylogenetic placement algorithms, such as the evolutionary placement algorithm (EPA) included in RAxML, or PPLACE...
23 CitationsSource
#1David Bass (Centre for Environment, Fisheries and Aquaculture Science)H-Index: 34
#2Lucas Czech (Heidelberg Institute for Theoretical Studies)H-Index: 7
Last.Thomas Williams (UoB: University of Bristol)H-Index: 85
view all 9 authors...
Some protists with microsporidian‐like cell biological characters, including Mitosporidium, Paramicrosporidium, and Nucleophaga, have SSU rRNA gene sequences that are much less divergent than canonical Microsporidia. We analysed the phylogenetic placement and environmental diversity of microsporidian‐like lineages that group near the base of the fungal radiation and show that they group in a clade with metchnikovellids and canonical microsporidians, to the exclusion of the clade including Rozell...
14 CitationsSource
#1Lucas Czech (Heidelberg Institute for Theoretical Studies)H-Index: 7
#2Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
The exponential decrease in molecular sequencing cost generates unprecedented amounts of data. Hence, scalable methods to analyze these data are required. Phylogenetic (or Evolutionary) Placement methods identify the evolutionary provenance of anonymous sequences with respect to a given reference phylogeny. This increasingly popular method is deployed for scrutinizing metagenomic samples from environments such as water, soil, or the human gut. Here, we present novel and, more importantly, highly...
3 CitationsSource
#1Lucas Czech (Heidelberg Institute for Theoretical Studies)H-Index: 7
#2Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
Motivation: In most metagenomic sequencing studies, the initial analysis step consists in assessing the evolutionary provenance of the sequences. Phylogenetic (or Evolutionary) Placement methods can be employed to determine the evolutionary position of sequences with respect to a given reference phylogeny. These placement methods do however face certain limitations: The manual selection of reference sequences is labor-intensive; the computational effort to infer reference phylogenies is substant...
1 CitationsSource
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