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About
James R. Golden
Affiliation:
Arcadia Science
ORCID:
https://orcid.org/0000-0002-9411-9680
Pubs
Collaborators
Audrey Bell
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Ryan York
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Keith Cheveralls
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George Sandler
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Evan Kiefl
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AutoOpenRaman: Low-cost, automated Raman spectroscopy
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_Chlamydomonas cpc1-1_ mutant exhibits unexpected growth phenotypes
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G–P Atlas: A neural network framework for mapping genotypes to many phenotypes
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An interactive visualization tool for _Amblyomma americanum_ differential expression data
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Automating identification and quantification of mouse scratch behavior in video recordings
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A method for computational discovery of viral structural mimics
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A quantitative-genetic decomposition of a neural network
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Raman spectroscopy enables rapid and inexpensive exploration of biology
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Compound 48/80 is toxic in HMC1.2 and RBL-2H3 cells
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How confident should we be in potential targets of tick protease inhibitors predicted by AlphaFold-Multimer?
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How can we biochemically validate protein function predictions with the Ras GTPase family?
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Early update on Arcadia publishing 2.0: Scientists are in charge, speed is an issue
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Identification of capsid-like proteins in venomous and parasitic animals
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Leveraging evolution to identify novel organismal models of human biology
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Using protein language models to predict coding and non-coding transcripts with plm-utils
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A framework for modeling human monogenic diseases by deploying organism selection
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How can we biochemically validate protein function predictions with the deoxycytidine kinase family?
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A free, open-access library of high-quality organism illustrations for science communication
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Modeling human monogenic diseases using the choanoflagellate _Salpingoeca rosetta_
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Rescuing _Chlamydomonas_ motility in mutants modeling spermatogenic failure
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The phenotype-o-mat: A flexible tool for collecting visual phenotypes
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Predicting bioactive peptides from transcriptome assemblies with the peptigate workflow
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Label-free neuroimaging in mice captures sensory activity in response to tactile stimuli and acute pain
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From black box to glass box: Making UMAP interpretable with exact feature contributions
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DIY Raman spectroscopy for biological research
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Predicting peptides from tick salivary glands that suppress host detection
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The experiment continues: Arcadia publishing 2.0
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A structurally divergent actin conserved in fungi has no association with specific traits
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Graph neural networks: A unifying predictive model architecture for evolutionary applications
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Phylogenies and biological foundation models
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Mapping the spectrum of archaeal protein sequence–structure relationships
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Creating a 7,000-strain _E. coli_ genotype dataset with antimicrobial resistance phenotypes
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Predicting antimicrobial resistance phenotypes across 7,000 _E. coli_ genomes
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Lessons from our approach to bioprospecting in ticks
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Comparative phylogenomic analysis of chelicerates points to gene families associated with long-term suppression of host detection
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How do we balance labor and yield in high-throughput protein expression?
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Efficient GFP variant design with a simple neural network ensemble
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A data-driven approach to match organisms and research problems
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An experimental and computational workflow to characterize nematode motility behavior
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A strategy to validate protein function predictions _in vitro_
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Modeling human monogenic diseases using the tunicate _Ciona intestinalis_
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Structure-based protein clustering sometimes, but not always, provides insight into protein function
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Epistasis and deep learning in quantitative genetics
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A high-throughput imaging approach to track and quantify single-cell swimming
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Closing the divide between analysis and publication: The notebook pub
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Assembling and annotating an Asgard archaea and giant virus dataset of over 840,000 proteins
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Identifying circular DNA using short-read mapping
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Distinct spatiotemporal movement properties reveal sub-modalities in crawling cell types
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Cross-trait learning with a canonical transformer tops custom attention in genotype–phenotype mapping
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The known protein universe is phylogenetically biased
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Do protein language models understand evolution? Mixed evidence from ancestral sequences and ESM2
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Phenotypic differences between interfertile _Chlamydomonas_ species
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NovelTree: Highly parallelized phylogenomic inference
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Harnessing genotype-phenotype nonlinearity to accelerate biological prediction
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Gotta catch ‘em all: Agar microchambers for high-throughput single-cell live imaging
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Applying information theory to genetics can better explain biological phenomena
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Raman spectra reflect complex phylogenetic relationships
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Exploring the actin family: A case study for ProteinCartography
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Comparing gene expression across species based on protein structure
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How can we improve upon and expand the scope of our phylogenomic inferences?
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Microchamber slide design for cell confinement during imaging
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Equivalent linear mappings of deep networks are a promising path for biology
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Paired residue prediction dependencies in ESM2
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ProteinCartography: Comparing proteins with structure-based maps for interactive exploration
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Automated classification of time-course imaging data applied to nematode embryogenesis
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Streamlining microscopy datasets by enriching for in-focus frames
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