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Megan L. Hochstrasser
Director of Publishing
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1 pub in other communities.
Megan L. has published in other PubPub communities. Click to go to their full profile.
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Published: May 31, 2022
If you’re interested in generating proteomics data but your organism of interest doesn’t have a sequenced genome to use as a reference database, it is straightforward and useful to collect a transcriptome instead.
Published: May 31, 2022
Researchers studying any organism with genomic data can follow this simple walkthrough to create sets of barcoded probes for the multiplexed FISH technique called MERFISH. We’re sharing interactive code notebooks that can be adapted to design barcoded FISH probes for any species.
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Published: May 31, 2022
The way you generate a reference database has a real impact on the completeness and results of proteomics experiments.
Published: May 31, 2022
Building on the open-source platform PubPub, we’re sharing the first iteration of our publishing website. In addition to posting our first set of research pubs, we’re documenting our progress in developing this new system for sharing science and hope you’ll provide feedback.
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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
RY
Published: Oct 14, 2022
Quantifying movement is a powerful window into cellular functions. However, cells can generate movement through a variety of complex mechanisms. Here, we generate a flexible framework for comparing an especially variable type of motility: cellular crawling.
Connections
Supplements (1): Code v1.1 - GitHub
BB
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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
Published: Dec 04, 2022
Long protrusions from several microalgal species appear to help cells move, capture prey, transport mitochondria and chloroplasts, and more. Are they filopodia that evolved abilities more like other actin- or microtubule-based structures, or are they something new?
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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.
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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.
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SC
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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.
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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
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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.
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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.
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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.
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Published: Mar 29, 2023
Treating P. tricornutum cells with serine endopeptidases or certain cytoskeletal inhibitors induces the formation of cell wall-free protoplasts and suggests a novel role for actin and myosin in preventing protoplast formation.
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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
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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.
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Published: Jun 15, 2023
Even with many tools available, categorizing species is tough. We used data from Raman spectroscopy, a form of label-free imaging, to infer phylogenetic patterns among several dozen diverse microbial taxa, offering a non-destructive and rapid way to dissect species relationships.
Connections
Supplements (1): Code v1.0 - GitHub
TE
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Published: May 03, 2023
Constraining motile microorganisms for live imaging often requires costly microfluidics or optical traps to keep them in view. We used patterned stamps and agar to make versatile, inexpensive “microchambers” and offer a way to predict the right chamber size for a given organism.
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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.
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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
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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.
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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.
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Published: Sep 29, 2023
We investigated protein structure predictions as an alternative to protein sequence homology for comparing single-cell RNA-seq data across species.
Connections
Supplements (2): Code v0.0.1 - GitHub • Related data - Zenodo
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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
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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.
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Supplements (2): Code v1.0 - GitHub • Clustered nr database and taxonomy files - OSF
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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.
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Supplements (1): Code v1.0.0 - GitHub
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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.
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Supplements (1): Code v1.0 - GitHub
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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.
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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
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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.
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Supplements (1): Code v1.0 - GitHub
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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.
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+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
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Published: Sep 22, 2023
It is commonly assumed that phenotypes arise from the cumulative effects of many independent genes. However, we show that by accounting for dependent and nonlinear biological relationships, we can generate models that predict phenotypes with great accuracy.
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Supplements (2): Data - Zenodo • Code v1.0.1 - GitHub
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Published: Nov 17, 2023
We distilled label-free microscopy data by comparing and implementing feature-detection algorithms. Sobel and Laplacian methods outperformed pixel intensity variance in accuracy.
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Supplements (1): Code v1.0 - GitHub
SC
Published: Nov 02, 2023
Our "icebox" is where we share the projects that we've decided not to continue. We surveyed our company to understand resulting cultural shifts and how others are carrying our iced work forward.
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Published: Dec 02, 2023
Machine learning is a powerful tool for classifying images in a time series, such as the developmental stages of embryos. We built a classifier using only bright-field microscopy images to infer nematode embryonic stages at high throughput.
Connections
Supplements (2): Code v1.0 - GitHub • Data- Time-course images of nematode embryos - Zenodo
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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.
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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.
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Supplements (2): Code v1.0 - GitHub • Data - Zenodo
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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
IK
Published: Dec 02, 2023
Oligo pools can contain millions of unique sequences, but they’re limited by length, error rate, and bias. We propose methods to scalably screen synthetic DNA libraries, so an individual researcher can obtain thousands of error-free synthetic DNA assemblies at low cost.
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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!
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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.
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Published: Mar 05, 2024
We’re seeking feedback on NovelTree, our modular phylogenomic workflow. We’d appreciate your insights into how we can improve gene family inference, incorporate protein structure predictions, and expand to whole-genome data as input.
Published: Mar 29, 2024
How can we measure the true impact of science? We're seeking feedback on indicators of the utility and rigor of publications beyond traditional journal metrics. Your input will help shape the future of our publishing experiment.
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Published: May 31, 2024
To test its utility in analyzing biological samples, we built an open-source Raman spectrometer and collected spectra from chilis, beer, and algae. We could stratify samples, classify replicates, and link spectra with quantitative traits of beer (ABV) and chilis (perceived heat).
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Supplements (1): Code and data - GitHub
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Published: May 31, 2024
We’re using the well-studied superfamily of small monomeric GTPases, the Ras GTPases, to evaluate our structure-based clustering tool, ProteinCartography. We’re seeking feedback on working with this protein family and determining which individual proteins to study.
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Supplements (1): Data - Zenodo
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Published: May 31, 2024
We aim to validate ProteinCartography, a tool for structure-based protein clustering, by evaluating two foundational hypotheses: that proteins within a cluster have similar functions and proteins in different clusters have differing functions.
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How can we biochemically validate protein function predictions with the deoxycytidine kinase family?
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Published: May 31, 2024
The human deoxycytidine kinase, a member of the nucleoside salvage pathway, has been studied extensively. We’ll use this family to assess our structure-based protein clustering tool, ProteinCartography. We’d love feedback on how we might work with this protein for validation.
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Supplements (1): Data - Zenodo
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Published: Jun 13, 2024
Two years into our publishing experiment, we’ve learned a lot. We built internal processes that worked but inadvertently decreased scientists' agency and creativity. Now, we’re minimizing process in an effort to empower our scientists to share their work how they see fit.
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Published: Jul 26, 2024
Sensory disorders are clinically common, debilitating conditions. But mouse behavioral models are often insufficient. We demonstrate that label-free, minimally-invasive brain imaging in mice could be a promising avenue for sensory research or drug discovery efforts.
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Supplements (2): Code v1.0.1 - GitHub • Imaging data - Zenodo
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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.
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Supplements (2): Code v1.0.0 - GitHub • Evaluation and training code - GitHub
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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.
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Replies (1): Code v1.0 - GitHub
Supplements (2): ProteinCartography run data - Zenodo • Data - Zenodo
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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.
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Supplements (2): Code v1.0.0 - GitHub • Evaluation code and data v1.0 - GitHub
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Published: Aug 22, 2024
We assembled a comprehensive E. coli antimicrobial resistance phenotype-genotype resource. This dataset will aid large-scale genetic studies on anti-microbial resistance and support research in phylogenetics and other fields.
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Supplements (2): Code v1.0 - GitHub • Data - Zenodo
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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
KC
Published: Dec 19, 2024
Since starting v2 of our publishing model to restore scientist agency, pub “quality” has been similar, and this approach is more efficient overall. The major downside is that pubs take longer. We’re pursuing solutions to this and other problems but feel we’re on the right track.
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Supplements (1): Code v1.0 - GitHub
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Published: Nov 06, 2024
Live imaging of swimming cells can yield insight into an organism’s viability and responses to environmental stimuli. We developed a microscopy workflow and image analysis pipeline, SwimTracker, to track motility phenotypes from swimming cells in high throughput.
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Supplements (2): Code v1.1 - GitHub • Data - BioImage Archive
RY
Published: Dec 14, 2024
What if we could select research organisms that are far more relevant to human biology or more likely to unearth biological solutions not found in humans? With more sequence data, structural prediction, and phylogenetic comparative methods, a richer framework is possible.
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Published: Dec 14, 2024
We used Chlamydomonas reinhardtii motility mutants with disrupted genes homologous to human SPEF2 or DNALI1 to model spermatogenic failure disorders SPGF43 and SPGF83, respectively. We recovered aspects of wild-type motility in these mutants with a small-scale drug screen.
Connections
Supplements (2): Code v1.0 - GitHub • Microscopy data - BioImage Archive
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Published: Jan 02, 2025
We investigated patterns of gene family evolution across ticks and other parasites. We used phylogenetic profiling and trait-association tests to identify gene families that may enable parasitic species to feed on hosts undetected for prolonged periods.
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Supplements (2): Code v1.0 - GitHub • Data - Zenodo
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Published: Jan 08, 2025
We used straightforward microscopy and computational analyses to reproducibly characterize a nematode motility phenotype with interpretable features. This method should be scalable for high-throughput phenotypic screening.
Connections
Supplements (6): Code v1.0 - GitHub • Protocol - Genotyping C. elegans - protocols.io • Protocol - C. elegans culture and maintenance - protocols.io • Protocol - Bleach life-stage synchronization of C. elegans - protocols.io • Protocol - Preparing C. elegans for image acquisition - protocols.io • Imaging data - BioImage Archive
