https://thestacks.org Latest publications from Arcadia Science https://thestacks.org/publications/dataset-raman-imaging-cerevisiae-mutants We acquired single-cell coherent Raman microscopy data (SRS and CARS) from wild-type budding yeast and two mutants. Our aim was to collect spatially resolved biochemical data on living yeast cells. We’re sharing the data and code for others to visualize and explore it! 2026-02-24 00:33:39 feedback requested resource 2 https://thestacks.org/publications/observation-marine-broth-chlamy Marine Broth induces extreme morphological transformation in _C. smithii_: Cells shift from typical ellipsoid shape to amorphous forms with thin wisp-like appendages containing mitochondria, revealing unexpected cellular plasticity. 2026-02-19 21:48:20 feedback requested observation 2 https://thestacks.org/publications/resource-tractability-atlas We’ve mapped experimental tractability for ~15,000 diverse organisms. By aggregating data on community activity, infrastructure, tooling, throughput, and logistics, our interactive atlas helps researchers navigate trade-offs when deciding which organisms to use for their work. 2026-02-12 23:18:05 feedback requested resource 7 https://thestacks.org/publications/idea-prospective-biology Since biological data are often non-independent, more data doesn't always mean more insight. We argue that a prospective approach is needed to uncover the deepest principles of life. 2026-02-05 20:26:44 feedback requested idea 6 https://thestacks.org/publications/perspective-search-strategy-bio-utility To accurately and efficiently identify instances of useful biological variation, we must establish an evolution-integrated bioprospecting framework. This will enable us to better interpret biological datasets and direct future sampling efforts to solve societal challenges. 2026-02-05 20:25:13 feedback requested perspective 1 https://thestacks.org/publications/result-phylo-analysis-msa-pairformer ​​We characterize how MSA Pairformer encodes phylogenetic relationships. Sequence weights correlate with evolutionary distance, with distinct layers specializing as phylogenetic filters. Yet uniform averaging often outperforms learned weights for contact prediction. 2026-01-30 18:49:31 feedback requested result 2 https://thestacks.org/publications/perspective-linear-mappings-deep-networks Deep networks make accurate predictions, but their nonlinearity makes them a black box, hiding what they have learned. Here, we look inside the black box and analyze the exact relationships they learn for UMAP embeddings and epistasis in a genotype–phenotype dataset. 2025-10-29 18:30:00 Feedback requested Perspective 10 https://thestacks.org/publications/method-qg-nn-decomposition We tested equivalent linear mapping (ELM) on a neural network trained to predict phenotypes from genotypes in simulated data. We show that ELM successfully recapitulates additive and epistatic effects learned by the model, even in data with substantial environmental noise. 2025-10-29 18:30:00 Feedback requested Method 5 https://thestacks.org/publications/method-glass-box-umap We transform UMAP from a black box into a glass box. By learning the embedding function with a certain type of deep network, we can compute equivalent linear mappings of the input features that exactly reconstruct each embedding, revealing the heretofore hidden logic of UMAP. 2025-10-29 18:30:00 Feedback requested Method 4 https://thestacks.org/publications/resource-organism-illustration-library We create vector graphics of model organisms and emerging biological research organisms to enhance our publications. We’re sharing these editable graphics under a CC0 license for other scientists to use in figures, slides, teaching materials, or other outputs. 2025-09-24 18:30:00 Feedback requested Resource 28 https://thestacks.org/publications/open-question-ht-protein-expression-labor-yield We need to test hundreds of *in silico* protein variant designs in the lab. We have automated purification strategies, but expressing enough protein to purify is low-throughput and rate-limiting. Can we crank up expression without big, unwieldy culture flasks and intensive effort? 2025-09-21 18:30:00 Feedback requested Open question Revised after community feedback 71 https://thestacks.org/publications/result-gfp-variant-design-nn We designed novel GFPs using a neural network ensemble. We quickly developed an experimental validation procedure in parallel, confirming that several candidates were functional. This rapid loop of *in silico* generation and lab validation may accelerate protein engineering. 2025-09-10 18:30:00 Feedback requested Iced Result 22 https://thestacks.org/publications/resource-autoopenraman We developed AutoOpenRaman, an automated, inexpensive microscope for Raman spectroscopy. We recapitulated many features of expensive commercial Raman spectroscopy systems using economical hardware and open-source software. 2025-09-08 18:30:00 Feedback requested Resource 4 https://thestacks.org/publications/result-sequence-structure-asgard-archaea-proteins We analyzed 4,064 Asgard protein families, seeking generalizable rules governing sequence–structure relationships. We found a subset of protein families with structural conservation despite phylogenetic and sequence diversity, but no global constraints across the proteome. 2025-08-14 18:30:00 Feedback requested Iced Result 11 https://thestacks.org/publications/resource-automating-mouse-scratch-behavior Itch is a key symptom of many diseases. Drug development for these diseases requires assessing itch to determine if potential drugs work. We developed a workflow to rapidly quantify scratching, a measure of itch, in a pre-clinical animal model to speed drug discovery. 2025-08-14 18:30:00 Feedback requested Resource 19 https://thestacks.org/publications/perspective-approach-bioprospecting-ticks Ticks produce a trove of bioactive molecules. We built a discovery pipeline to find new therapeutics in ticks, but were stymied by compounding challenges in our approach and decided to ice the project. 2025-08-14 18:30:00 Feedback requested Iced Perspective 5 https://thestacks.org/publications/dataset-archaea-giant-virus-protein-annotation We assembled a comprehensive dataset of proteins from Asgard archaea and giant virus genome assemblies. This dataset lets us explore protein sequence and structure relationships more broadly across the tree of life to better understand protein structure and function. 2025-08-11 18:30:00 Dataset Feedback requested 12 https://thestacks.org/publications/result-g-p-atlas G–P Atlas extends genetic analysis with neural networks that model multiple traits simultaneously. By capturing complex interactions between genes and phenotypes, our framework predicts biological outcomes more accurately and reveals genetic influences that traditional methods miss. 2025-08-07 18:30:00 Feedback requested Result 16 https://thestacks.org/publications/result-ancestral-sequences-protein-language-models Protein language models are trained on evolutionarily related sequences, yet the extent to which they capture the underlying evolutionary relationships remains unclear. We explore this question using reconstructed ancestral protein sequences and the ESM2 protein language model. 2025-07-29 18:30:00 Feedback requested Result 4 https://thestacks.org/publications/resource-modeling-human-monogenic-diseases-salpingoeca-rosetta We applied a decision-making framework for identifying tractable genes from our organism selection dataset for pilot experiments in the choanoflagellate *Salpingoeca rosetta*. 2025-06-22 18:30:00 Feedback requested Resource 4 https://thestacks.org/publications/resource-modeling-human-monogenic-diseases-ciona-intestinalis We applied a decision-making framework for identifying tractable genes from our organism selection dataset for pilot experiments in the tunicate *Ciona intestinalis*. 2025-06-22 18:30:00 Feedback requested Resource 10 https://thestacks.org/publications/resource-modeling-human-monogenic-diseases We designed a decision-making framework to find tractable genes from our organism selection dataset for pilot experiments. We focused on genes in two potential models of human monogenic disease, the choanoflagellate *Salpingoeca rosetta* and the tunicate *Ciona intestinalis*. 2025-06-22 18:30:00 Feedback requested Resource 15 https://thestacks.org/publications/perspective-graph-neural-networks-for-evolution The transition from explanatory to predictive models in evolutionary biology is a significant and challenging task. We propose that graph representations and graph neural networks may play a crucial role in this transition. 2025-06-17 18:30:00 Feedback requested Perspective 16 https://thestacks.org/publications/idea-phylogenies-bfms Biological foundation models are, at their core, evolutionary comparisons on massive scales. As with all comparative studies, evolutionary nonindependence determines their power. We chart how this affects biological AI and propose practical routes to set the field on firmer ground. 2025-06-16 18:30:00 Feedback requested Idea 12 https://thestacks.org/publications/result-gp-deep-learning-scaling We explore when deep learning (DL) outperforms linear models in predicting complex phenotypes. We show that DL requires at least 20% as many samples as possible epistatic interactions, and benefits from marker feature selection and multi-task learning on correlated phenotypes. 2025-06-15 18:30:00 Feedback requested Result 4 https://thestacks.org/publications/observation-chlamy-cpc1-growth Comparative analysis of *Chlamydomonas* strains revealed that a *cpc1-1* mutant has three unexpected growth phenotypes across different media types, suggesting possible genetic background contributions beyond characterized mutations. 2025-05-21 18:30:00 Feedback requested Observation 13 https://thestacks.org/publications/result-predicting-detection-suppression-tick-peptides We predicted tick salivary gland peptides that may help the tick evade host detection while feeding. Using phylogenetics and peptide prediction, we identified 12 candidates. However, testing the trait in the lab proved challenging, so we aren’t continuing the project. 2025-05-20 18:30:00 Iced Not actively updating Result 18 https://thestacks.org/publications/method-structural-mimicry Some parasites use mimics of host proteins to manipulate host pathways. We’ve developed a mimicry detection pipeline and benchmarked it using well-studied viral mimics. The pipeline successfully recovers known mimics and is ready for deployment at scale. 2025-05-14 18:30:00 Iced Method Not actively updating 11 https://thestacks.org/publications/open-question-protease-inhibitor-target-prediction We want to predict the targets of tick effectors to identify new therapeutic targets for skin diseases. We ran a case study using AlphaFold-Multimer to predict the targets of tick protease inhibitors, but we aren't sold on our method. What other approaches should we consider? 2025-05-01 18:30:00 Iced Not actively updating Open question Result 9 https://thestacks.org/publications/observation-geno-pheno-attention We added standard transformer components, omitted by Rijal et al. (2025) in their attention-based genotype–phenotype mapping. We found that this addition substantially boosts predictive accuracy on their yeast dataset. 2025-05-01 18:30:00 Feedback requested Observation 10 https://thestacks.org/publications/result-48-80-toxicity We found that compound 48/80, an MRGPRX2 agonist and commonly used *in vitro* mast cell activator, is toxic in HMC1.2 (human mast cells) and RBL-2H3 (rat basophils). Researchers should use caution and incorporate a viability test when performing assays in these cell lines. 2025-03-16 18:30:00 Iced Not actively updating Result 4 https://thestacks.org/publications/perspective-raman-spec-comparison We tested several spectrometers for spontaneous Raman spectroscopy as a rapid biological phenotyping tool. We analyzed the spectra from each instrument, comparing the resolution, signal-to-noise ratio, and ability to resolve peaks to determine the best fit for our research. 2025-03-16 18:30:00 Feedback requested Perspective 4 https://thestacks.org/publications/result-paired-token-masking During a quick analysis of the ESM2 model for masked token prediction, we noticed that amino acid probability distributions of residues affect each other in a pattern that mirrors a protein’s 3D contact map. But less so for the larger model sizes. Our question to you is, why? 2025-03-09 18:30:00 Feedback requested Result 0 https://thestacks.org/publications/perspective-notebook-pub-format We're experimenting with treating our computational notebooks as publications themselves. This approach reduces publication burden, encourages faster publishing, and builds in reproducibility. Scientists can publish with minimal extra effort. 2025-03-09 18:30:00 Feedback requested Perspective 26 https://thestacks.org/publications/result-ecoli-amr-popgen-genomic-prediction We explored the genetic basis of antimicrobial resistance (AMR) phenotypes among 7,000 globally distributed strains of *E. coli*. AMR is associated with various genetic architectures that span multiple evolutionary scales. 2025-03-03 18:30:00 Feedback requested Result 26 https://thestacks.org/publications/resource-diy-raman-bio We optimized an open-source Raman spectrometer for solid and liquid biological samples, including microorganisms, organic solvents, and biochemicals. Here, we share a calibration protocol, data processing notebooks, sample prep methods, and a nascent spectral reference library. 2025-02-26 18:30:00 Feedback requested Resource 4 https://thestacks.org/publications/result-pc-validation-dck We asked whether ProteinCartography’s structure-based protein clustering reflects functional features of proteins. We found that proteins often clustered with proteins that have similar functions, but there were cases when this wasn’t the case. 2025-02-13 18:30:00 Feedback requested Result 48 https://thestacks.org/publications/method-nematode-motility 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. 2025-01-07 18:30:00 Method Not actively updating 20 https://thestacks.org/publications/result-chelicerate-detection-suppression 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. 2025-01-01 18:30:00 Feedback requested Result 23 https://thestacks.org/publications/resource-amblyomma-americanum-differential-expression We analyzed RNA-seq data from *Amblyomma americanum* to explore gene expression linked to skin manipulation during tick feeding. We built an interactive app to explore the differential expression results and find patterns related to tick sex, tissue, and time in blood meal. 2025-01-01 18:30:00 Not actively updating Resource Revised after community feedback 16 https://thestacks.org/publications/result-early-publishing-v2-assessment 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. 2024-12-18 18:30:00 Feedback requested Result 31 https://thestacks.org/publications/result-evolutionary-organismal-selection Researching just a handful of organisms limits biological discovery. We developed an approach pairing organisms with biological questions to expand research biodiversity. 2024-12-13 18:30:00 Feedback requested Result 50 https://thestacks.org/publications/result-chlamy-spgf 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. 2024-12-13 18:30:00 Feedback requested Iced Result 10 https://thestacks.org/publications/idea-selecting-better-models 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. 2024-12-13 18:30:00 Feedback requested Idea 38 https://thestacks.org/publications/resource-swimtracker-htp-swimming-assay 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. 2024-11-05 18:30:00 Feedback requested Resource 24 https://thestacks.org/publications/method-circular-dna-id 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. 2024-08-21 18:30:00 Iced Method Not actively updating 8 https://thestacks.org/publications/dataset-ecoli-amr-genotype-phenotype 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. 2024-08-21 18:30:00 Dataset Feedback requested 36 https://thestacks.org/publications/result-venom-capsids 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 more widespread than previously known. 2024-08-08 18:30:00 Iced Not actively updating Result 32 https://thestacks.org/publications/resource-plm-utils 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. 2024-08-07 18:30:00 Not actively updating Resource 21 https://thestacks.org/publications/resource-peptigate 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. 2024-08-07 18:30:00 Not actively updating Resource 23 https://thestacks.org/publications/result-protein-universe-phylogenetic-bias Many protein prediction and design models rely on evolutionary comparisons. We show that popular databases are phylogenetically biased, influencing the statistical utility of the known protein universe in important ways. 2024-07-31 18:30:00 Feedback requested Result 40 https://thestacks.org/publications/result-sensory-neuroimaging 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. 2024-07-25 18:30:00 Iced Not actively updating Result 24 https://thestacks.org/publications/perspective-publishing-version-two 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. 2024-06-12 18:30:00 Feedback requested Perspective 20 https://thestacks.org/publications/result-easy-raman-spectroscopy 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). 2024-05-30 18:30:00 Feedback requested Result 16 https://thestacks.org/publications/open-question-rasgtpase-proteincartography 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. 2024-05-30 18:30:00 Not actively updating Open question 10 https://thestacks.org/publications/open-question-dck-proteincartography 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. 2024-05-30 18:30:00 Not actively updating Open question 15 https://thestacks.org/publications/idea-how-to-validate-proteincartography 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. 2024-05-30 18:30:00 Idea Not actively updating 31 https://thestacks.org/publications/method-automated-phenotype-imaging 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. 2024-04-23 18:30:00 Feedback requested Resource 17 https://thestacks.org/publications/open-question-measuring-reuse 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. 2024-03-28 18:30:00 Feedback requested Open question 68 https://thestacks.org/publications/negative-data-divergent-fungal-actins 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. 2024-03-05 18:30:00 Negative data Not actively updating 8 https://thestacks.org/publications/open-question-noveltree-extensions 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. 2024-03-04 18:30:00 Not actively updating Open question 15 https://thestacks.org/publications/dataset-amblyomma-americanum-predicted-genes 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. 2024-02-23 18:30:00 Dataset Not actively updating 0 https://thestacks.org/publications/result-actin-structural-clustering 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. 2024-02-13 18:30:00 Feedback requested Result 6 https://thestacks.org/publications/result-neurodegeneration-repeat-expansion-homology 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. 2023-12-19 18:30:00 Iced Not actively updating Result 2 https://thestacks.org/publications/open-question-polyphosphate-discovery 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! 2023-12-19 18:30:00 Not actively updating Open question 0 https://thestacks.org/publications/resource-nematode-classifier 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. 2023-12-01 18:30:00 Iced Not actively updating Resource 1 https://thestacks.org/publications/idea-htp-dna-screening 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. 2023-12-01 18:30:00 Iced Idea Not actively updating 8 https://thestacks.org/publications/resource-filtering-in-focus-frames We distilled label-free microscopy data by comparing and implementing feature-detection algorithms. Sobel and Laplacian methods outperformed pixel intensity variance in accuracy. 2023-11-16 18:30:00 Not actively updating Resource 6 https://thestacks.org/publications/perspective-icebox-lessons 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. 2023-11-01 18:30:00 Not actively updating Perspective 6 https://thestacks.org/publications/result-ppk1-homology 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. 2023-10-05 18:30:00 Not actively updating Result Revised after community feedback 9 https://thestacks.org/publications/resource-protein-cartography 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. 2023-09-28 18:30:00 Feedback requested Resource 42 https://thestacks.org/publications/resource-noveltree 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. 2023-09-28 18:30:00 Feedback requested Resource 13 https://thestacks.org/publications/idea-structure-based-expression-comparison We investigated protein structure predictions as an alternative to protein sequence homology for comparing single-cell RNA-seq data across species. 2023-09-28 18:30:00 Iced Idea Not actively updating 14 https://thestacks.org/publications/perspective-genetics-and-information-theory 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. 2023-09-26 18:30:00 Feedback requested Perspective Revised after community feedback 6 https://thestacks.org/publications/result-nonlinear-phenotypes 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. 2023-09-21 18:30:00 Feedback requested Result Revised after community feedback 19 https://thestacks.org/publications/result-viral-search-brain-seq-data 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. 2023-08-24 18:30:00 Iced Not actively updating Result 0 https://thestacks.org/publications/result-venom-toxin-accessory-sequences 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. 2023-08-14 18:30:00 Iced Not actively updating Result 3 https://thestacks.org/publications/result-hgt-neuromodulators 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. 2023-07-19 18:30:00 Iced Not actively updating Result 10 https://thestacks.org/publications/resource-prehgt 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. 2023-07-19 18:30:00 Not actively updating Resource 2 https://thestacks.org/publications/result-arabinosylated-phage-genome 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. 2023-07-18 18:30:00 Iced Not actively updating Result 12 https://thestacks.org/publications/resource-nr-clustering 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. 2023-07-18 18:30:00 Not actively updating Resource 5 https://thestacks.org/publications/result-chlamydomonas-phenotypes 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. 2023-06-22 18:30:00 Feedback requested Result Revised after community feedback 26 https://thestacks.org/publications/result-raman-taxonomy 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. 2023-06-14 18:30:00 Feedback requested Result 12 https://thestacks.org/publications/resource-metagenomics-workflow 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. 2023-05-25 18:30:00 Not actively updating Resource 0 https://thestacks.org/publications/resource-agar-microchambers 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. 2023-05-02 18:30:00 Not actively updating Resource 17 https://thestacks.org/publications/data-set-hipr-fish-spatial-imaging-cheese 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. 2023-04-25 18:30:00 Dataset Iced Not actively updating 4 https://thestacks.org/publications/resource-reads2genome 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. 2023-04-10 18:30:00 Not actively updating Resource 2 https://thestacks.org/publications/dataset-amblyomma-americanum-genome 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. 2023-03-29 18:30:00 Dataset Not actively updating 13 https://thestacks.org/publications/result-phaeodactylum-morphology-cytoskeleton 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. 2023-03-27 18:30:00 Iced Not actively updating Result 6 https://thestacks.org/publications/negative-data-phage-rna-isolation 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. 2023-03-13 18:30:00 Iced Negative data Not actively updating 3 https://thestacks.org/publications/data-set-metagenomics-timecourse-cheese 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. 2023-03-10 18:30:00 Dataset Iced Not actively updating 7 https://thestacks.org/publications/perspective-reproducible-workflows 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. 2023-03-06 18:30:00 Not actively updating Perspective 11 https://thestacks.org/publications/resource-sourmashconsumr 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. 2023-02-20 18:30:00 Not actively updating Resource 0 https://thestacks.org/publications/resource-seqqc 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. 2023-02-20 18:30:00 Not actively updating Resource 0 https://thestacks.org/publications/method-phage-nucleoside-analysis 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. 2022-12-18 18:30:00 Iced Method Not actively updating Revised after community feedback 7 https://thestacks.org/publications/result-chlorarachniophyte-extensions 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? 2022-12-03 18:30:00 Iced Not actively updating Result 9 https://thestacks.org/publications/idea-defining-actin 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. 2022-11-30 18:30:00 Feedback requested Idea Revised after community feedback 44 https://thestacks.org/publications/result-comparative-crawling 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. 2022-10-13 18:30:00 Not actively updating Result 4 https://thestacks.org/publications/resource-microchamber-slide 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. 2022-08-22 18:30:00 Not actively updating Resource Revised after community feedback 10 https://thestacks.org/publications/resource-spatial-genomics-probe-pipeline 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. 2022-05-30 18:30:00 Iced Not actively updating Resource 1 https://thestacks.org/publications/perspective-publishing-round-one 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. 2022-05-30 18:30:00 Not actively updating Perspective 116 https://thestacks.org/publications/method-mass-spec-proteomics-transcriptomics 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. 2022-05-30 18:30:00 Method Not actively updating 12 https://thestacks.org/publications/data-set-transcriptome-proteome-amblyomma-americanum The way you generate a reference database has a real impact on the completeness and results of proteomics experiments. 2022-05-30 18:30:00 Dataset Not actively updating 15