Advanced search

Filter By:

Journal Check one or more journals to show results from those journals only.

Choose more journals

Article type Check one or more article types to show results from those article types only.
Subject Check one or more subjects to show results from those subjects only.
Date Choose a date option to show results from those dates only.

Custom date range

Clear all filters
Sort by:
Showing 1–18 of 18 results
Advanced filters: Author: Todd J. Treangen Clear advanced filters

  • CLASSIC is a high-throughput genetic profiling platform that combines long- and short-read next-generation-sequencing modalities to quantitatively assess pools of constructs of arbitrary length containing diverse genetic part compositions.

    • Kshitij Rai
    • Ronan W. O’Connell
    • Caleb J. Bashor
    Research
    Nature
    P: 1-10

  • Here the authors report asperigimycins, fungal ribosomally synthesized and post-translationally modified peptides with a heptacyclic scaffold. After chemically modifying them for nanomolar anticancer activity, CRISPR screening identifies SLC46A3 as a key transporter for their uptake in cells.

    • Qiuyue Nie
    • Fanglong Zhao
    • Xue Gao
    Research
    Nature Chemical Biology
    Volume: 21, P: 1938-1947

  • The assignment of genetic variants to the two copies of the genome present in cells (phasing) is crucial for predicting the consequences, interaction and inheritance of variants, but is limited by the length of sequencing reads and stretches of homozygosity in the genome. Here the authors develop a method that utilizes DNA methylation signals from Oxford Nanopore Technologies sequencing data to improve phasing.

    • Yilei Fu
    • Sergey Aganezov
    • Fritz J. Sedlazeck
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-12

  • Tiled amplicon sequencing is an essential tool for tracking the spread and evolution of pathogens, including SARS-CoV-2, however existing methods for tiled amplicon design require slow and costly downstream manual optimization. Here the authors present Olivar, a first step towards fully automated, variant-aware design of tiled amplicons for pathogen genomes.

    • Michael X. Wang
    • Esther G. Lou
    • Todd J. Treangen
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-12

  • Wastewater surveillance has the potential to be used for early detection of new SARS-CoV-2 lineages. Here, the authors present Crykey, a computational method for detecting cryptic SARS-CoV-2 mutations in wastewater that co-occur on the same sequencing read, potentially representing new lineages.

    • Yunxi Liu
    • Nicolae Sapoval
    • Lauren B. Stadler
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-13

  • Contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low biomass environments. Here the authors describe Squeegee, a computational approach designed to detect microbial contamination within low microbial biomass microbiomes and identify microbial contaminants in publicly available datasets that lack negative controls.

    • Yunxi Liu
    • R. A. Leo Elworth
    • Todd J. Treangen
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-14

  • Tracking low frequency intra-host variants has helped understanding within-host viral population dynamics and transmission. Precise tracking, however, depends partially on the error rate of the sequencing platforms used. Here, Liu et al. present Variabel, a method to rescue low frequency intra-host variants from Oxford Nanopore Technologies (ONT) platforms and validate their approach on Ebola virus, norovirus, and SARS-CoV-2 datasets.

    • Yunxi Liu
    • Joshua Kearney
    • Todd J. Treangen
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-9

    • Todd J. Treangen
    • Moshe Y. Vardi
    Correspondence
    Nature Biotechnology
    Volume: 41, P: 1373-1374

  • The Human Microbiome Project Consortium has established a population-scale framework to study a variety of microbial communities that exist throughout the human body, enabling the generation of a range of quality-controlled data as well as community resources.

    • Barbara A. Methé
    • Karen E. Nelson
    • Owen White
    ResearchOpen Access
    Nature
    Volume: 486, P: 215-221

  • Repeat sequences in DNA remain one of the most challenging aspects of next-generation sequencing data analysis and interpretation. This Review explains the problems and current strategies for handling repeats; ignoring repeats risks missing important biological information.

    • Todd J. Treangen
    • Steven L. Salzberg
    Reviews
    Nature Reviews Genetics
    Volume: 13, P: 36-46

  • The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.

    • Curtis Huttenhower
    • Dirk Gevers
    • Owen White
    ResearchOpen Access
    Nature
    Volume: 486, P: 207-214