Biology subjects

Chlenski, P.

Publications and source records attributed to Chlenski, P..

3 recordsLinked to original sources

bioRxiv2021

MiSDEED: a synthetic multi-omics engine for microbiome power analysis and study design

SummaryMiSDEED is a command-line tool for generating synthetic longitudinal multi-omics data from simulated microbial environments. It generates relative-abundance timecourses under perturbations for an arbitrary number of samples and patients. All simulation parameters are exposed to the user to facilitate rapid power analysis and aid in study design. Users who want additional flexibility may also use MiSDEED as a Python package. Availability and implementationMiSDEED is written in Python and is freely available at https://github.com/pchlenski/misdeed. Contactpac@cs.columbia.edu

bioinformatics↗

bioRxiv2021

Accurate and robust inference of microbial growth dynamics from metagenomic sequencing

Patterns of sequencing coverage along a bacterial genome--summarized by a peak-to-trough ratio (PTR)--have been shown to accurately reflect microbial growth rates, revealing a new facet of microbial dynamics and host-microbe interactions. Here, we introduce CoPTR (Compute PTR): a tool for computing PTRs from complete reference genomes and assemblies. We show that CoPTR is more accurate than the current state-of-the-art, while also providing more PTR estimates overall. We further develop theory formalizing a biological interpretation for PTRs. Using a reference database of 2935 species, we applied CoPTR to a case-control study of 1304 metagenomic samples from 106 individuals with irritable bowel disease. We show that PTRs have high inter-individual variation, are only loosely correlated with relative abundances, and are associated with disease status. We conclude by demonstrating how PTRs can be combined with relative abundances and metabolomics to investigate their effect on the microbiome. AvailabilityCoPTR is available from https://github.com/tyjo/coptr, with documentation on https://coptr.readthedocs.io.

bioinformatics↗

bioRxiv2019

Extraction of near-complete genomes from metagenomic samples: a new service in PATRIC

BackgroundLarge volumes of metagenomic samples are being processed and submitted to PATRIC for analysis as reads or assembled contigs. Effective analysis of these samples requires solutions to a number of problems, including the binning of assembled, mixed, metagenomically-derived contigs into taxonomic units. DescriptionThe PATRIC metagenome binning service utilizes the PATRIC database to furnish a large, diverse set of reference genomes. Reference genomes are assigned based on the presence of single-copy universal marker proteins in the sample, and contigs are assigned to the bin corresponding to the most similar reference genome. Each set of binned contigs represents a draft genome that will be annotated by RASTtk in PATRIC. A structured-language binning report is provided containing quality measurements and taxonomic information about the contig bins. ConclusionWe provide a new service for rapid and interpretable metagenomic contig binning and annotation in PATRIC.

genomics↗