Skip to main content
Elizabeth A. McDaniel
Scientist
Scientist interested in computational discovery & reproducible research
SC
+2
Published: Mar 07, 2023
A workflow orchestration framework can streamline repeatable tasks and make workflows broadly usable. From several options, we chose Nextflow due to the ease of deploying across platforms, vibrant nf-core community, and ability to manage and monitor workflows with Nextflow Tower.
Connections
Supplements (1): Nextflow template v1.1.0 - GitHub
RD
TR
Published: Mar 11, 2023
How do you approach getting a microbiome set up in a new lab? We’re sharing protocols for how we collected, stocked, and sequenced a set of cheese rind microbiomes and generated a high-quality metagenomics resource for future computational studies.
TR
Published: Apr 11, 2023
We want to swiftly generate genome assemblies and produce quality control statistics to gauge the need for more curation. We built a Nextflow pipeline that assembles Illumina, Nanopore, or PacBio sequencing reads for a single organism and runs QC checks on the resulting assembly.
Connections
Supplements (1): reads2genome v1.0 - GitHub
RD
MM
+2
Published: May 26, 2023
We want to seamlessly process and summarize metagenomics data from Illumina or Nanopore technologies. We built a Nextflow workflow that handles common metagenomics tasks and produces useful outputs and intuitive visualizations.
RD
+4
Published: Jul 19, 2023
We sampled cheese microbial communities to discover bacteriophages with unusual genome chemistries. We isolated 114 bacterial host strains and 17 phages, and identified one phage with a probable arabinose hypermodification of hydroxymethylcytosine.
Connections
Supplements (11): Raw short reads from 11 cheese communities and one virome - ENA • Taxonomic and functional analysis - MGnify • Raw long reads from one cheese community - ENA • Serratia phage 92A1, complete genome - GenBank • Arthrobacter phage 1191A, complete genome - GenBank • Phage genomes and host 16S data - Zenodo • Protocol - Enriching and isolating phages on agar plates - protocols.io • Protocol - Enriching and isolating phages in liquid culture - protocols.io • Protocol - Propagating Serratia phage 92A1 and host - protocols.io • Biological specimen - Serratia phage 92A1 - DSMZ • Biological specimen - Serratia strain 92 - DSMZ
RD
MM
DS
Published: Aug 15, 2023
Hoping to find proteins that alter physiology in useful ways, we screened venom data sets for toxins fused to domains with additional functionality. We identified candidates, but struggled to infer any novel functions, and none seem well-conserved across venomous species.
Connections
Supplements (2): Code v2.0 - GitHub • Data - Zenodo
SC
RD
+5
Published: Dec 20, 2023
Some human proteins are encoded by genes with repetitive sequences, which, if they expand, damage the nervous system and cause disorders like Huntington’s disease. We found animals with similar proteins that have more repeats than we’ve ever seen in healthy people.
Connections
BB
+3
Published: Oct 06, 2023
Only some bacteria accumulate substantial amounts of polyphosphate (polyP). We thought that despite sequence divergence, polyP synthesis enzymes in these bacteria might have similar structures. We found this is sometimes true but doesn’t fully explain the phenomenon.
Connections
Replies (1): How can we identify the common molecular signatures underlying polyphosphate accumulation?
Supplements (2): Data - Zenodo • Code - GitHub
MD
Published: Dec 20, 2023
Since releasing our pub on polyphosphate-forming proteins in bacteria, we’ve noticed the community has similar problems studying this process in diverse organisms. We’re actively seeking feedback with a focus on advancing basic discoveries and useful tools in this space!
SC
RD
+2
Published: Feb 24, 2024
We previously released a draft genome assembly for the lone star tick, A. americanum. We've now predicted genes from this assembly to use for downstream functional characterization and comparative genomics efforts.
BB
SC
RD
+5
Published: Aug 09, 2024
Inspired by wasps co-opting viral capsids to deliver genes to the caterpillars they parasitize, we looked for capsid-like proteins in other species. We found capsid homologs in ticks and other parasites, suggesting this phenomenon could be wider spread than previously known.
Connections
Replies (1): Code v1.0 - GitHub
Supplements (2): ProteinCartography run data - Zenodo • Data - Zenodo
RC
+1
Published: Aug 22, 2024
This workflow lets you find potential circular DNA in your organism of interest using short-read, whole-genome sequencing data and a reference genome. We applied it to parasitoid wasps and some other parasites and found putative circular DNA.
Connections
Supplements (2): Code v1.0 - GitHub • Data - Zenodo
