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RB
KH
+2
Published: Aug 23, 2022
Cells can be highly motile, moving in and out of a microscope’s field of view. Understanding complex life cycles is difficult without continuous observation. To overcome this challenge, we’ve developed a 3D-printed microchamber device to confine cells for long-term visualization.
Connections
Supplements (7): 3D-printing files - NIH 3D Print Exchange • Code v1.1 - GitHub • Imaging data - C. steinii cyst rotation - Zenodo • Imaging data - C. steinii early encystment - Zenodo • Imaging data - C. steinii in a 384-well plate or microwells - Zenodo • Imaging data - C. steinii reanimation experiment - Zenodo • Imaging data - T. rostrata timelapse - Zenodo
BB
TR
Published: Dec 01, 2022
The process of deciding whether a candidate actin homolog represents a “true” actin is tricky. We propose clear and data-driven criteria to define actin that highlight the functional importance of this protein while accounting for phylogenetic diversity.
Connections
Supplements (2): Code v2.0 - GitHub • Data outputs - Zenodo
TR
+1
Published: Dec 19, 2022
This pub details a process for phage amplification and concentration, DNA extraction, and HPLC and MS analysis of phage nucleosides. We optimized the approach with model phages known to use non-canonical nucleosides in their DNA, but plan to apply it for other phages.
SC
TR
Published: Feb 21, 2023
seqqc is a Nextflow pipeline for quality control of short- or long-read sequencing data. It quickly assesses the quality of sequencing data so that it can be posted to a public repository before analysis for biological insights. Faster open data, faster knowledge for everyone.
Connections
SC
RD
TR
+1
Published: Feb 21, 2023
The sourmash Python package produces many outputs that describe the content and similarity of sequencing data. We developed a new R package, sourmashconsumr, that lets a wider range of users easily load, analyze, and visualize those outputs in R.
Connections
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: Mar 14, 2023
We struggled to isolate enough phage mRNA for HPLC as we searched for new nucleoside chemistries. Ribodepleting the abundant extracted rRNA introduced contaminating DNA, and we were still left with more bacterial mRNA than phage transcripts. We suggest an alternative approach.
SC
TD
BF
KP
TR
+2
Published: Mar 30, 2023
We generated a whole-genome assembly for the lone star tick to serve as a reference for downstream efforts where whole-genome maps are required. We created our assembly using pooled DNA from salivary glands of 50 adult female ticks that we sequenced using PacBio HiFi reads.
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
TR
Published: Apr 26, 2023
Seeing how microbes are organized within a community can inspire hypotheses about how species interact with each other. We used HiPR-FISH spatial imaging to look at the distribution of microbes within five distinct microbial communities growing on the surface of aged cheeses.
Connections
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
KP
TR
Published: Jul 20, 2023
We are interested in neuroactive metabolites that influence animal behavior. Some fungi have horizontally transferred neuroactive metabolite pathways between species. We used a horizontal gene transfer detection pipeline to screen for novel fungal genes tied to neuroactivity.
Connections
Supplements (1): Code v1.0 - GitHub
RD
+4
Published: Jul 20, 2023
Horizontal gene transfer (HGT) is the exchange of DNA between species. It can lead to the acquisition of new gene functions, so finding HGT events can reveal genome novelty. preHGT is a pipeline that uses multiple existing methods to quickly screen for transferred genes.
Connections
Supplements (1): Code v1.0.0 - GitHub
TR
Published: Jul 19, 2023
The increasingly large number of sequences available in public databases makes searches slower and slower. We clustered the NCBI non-redundant protein database and calculated taxonomic info for each cluster. This collapses similar sequences and reduces the database by over half.
Connections
Supplements (2): Code v1.0 - GitHub • Clustered nr database and taxonomy files - OSF
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
SC
+4
Published: Sep 29, 2023
We want to find and use evolutionary innovations to solve present-day problems. We developed NovelTree, an efficient phylogenomic workflow that will empower us to decode the evolutionary traces of these innovations across the tree of life.
RD
KP
TR
Published: Aug 25, 2023
We implemented a lightweight method to identify viruses in 342 human brain bulk and single-cell sequencing data sets, and identified two glioblastoma cells from a single patient that contained deltapolyomavirus sequences.
Connections
Supplements (1): Code v1.0 - GitHub
DM
DM
TR
+1
Published: Sep 27, 2023
Genetic models of complex traits often rely on incorrect assumptions that drivers of trait variation are additive and independent. An information theoretic framework for analyzing trait variation can better capture phenomena like allelic dominance and gene-gene interaction.
BB
KC
RD
+14
Published: Sep 29, 2023
The ProteinCartography pipeline identifies proteins related to a query protein using sequence- and structure-based searches, compares all protein structures, and creates a navigable map that can be used to look at protein relationships and make hypotheses about function.
Connections
Supplements (3): ProteinCartography v0.5.0 - GitHub • ProteinCartography v0.4.2 - GitHub • Data - Zenodo
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
BB
TE
+7
Published: Jun 23, 2023
We’re crossing C. reinhardtii and C. smithii algae for high-throughput genotype-phenotype mapping. In preparation, we’re comparing the parents to uncover unique species-specific phenotypes.
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
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
TR
DS
+1
Published: Feb 14, 2024
We've applied ProteinCartography, a tool for protein family exploration, to the well-studied actin family. We’re able to categorize actins and related proteins into distinguishable functional buckets, and we uncovered some surprising hypotheses that could prompt further study.
Connections
Supplements (2): Code v1.0 - GitHub • Data - Zenodo
BB
IK
DM
+5
Published: Mar 06, 2024
We outline a comparative approach to investigate protein function by correlating the presence or absence of a protein with species-level phenotypes. We applied this strategy to a novel actin isoform in fungi but didn’t find an association with any of the phenotypes we considered.
Connections
Supplements (2): Data - Zenodo • Code v1.0 - GitHub
DM
TR
+1
Published: Apr 24, 2024
We’ve developed an easy-to-assemble apparatus and software for the automated collection of visible biological phenotypes such as growth, macroscopic morphology, motion, reflectance, and fluorescence.
KC
GM
+1
Published: Aug 08, 2024
We explored the use of embeddings from protein language models to distinguish between genuine and putative coding open reading frames (ORFs). We found that an embeddings-based approach (shared as a small Python package called plm-utils) improves identification of short ORFs.
Connections
Supplements (2): Code v1.0.0 - GitHub • Evaluation and training code - GitHub
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
KC
SC
+2
Published: Aug 08, 2024
Peptigate predicts bioactive peptides from transcriptomes. It integrates existing tools to predict sORF-encoded peptides, cleavage peptides, and RiPPs, then annotates them for bioactivity and other properties. We welcome feedback on expanding its capabilities.
Connections
Supplements (2): Code v1.0.0 - GitHub • Evaluation code and data v1.0 - GitHub
