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David S. Booth
Affiliation:
University of California, San Francisco
Pubs
Collaborators
Megan L. Hochstrasser
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Prachee Avasthi
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Audrey Bell
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Ryan York
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Seemay Chou
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Dennis A. Sun
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Keith Cheveralls
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Distinct spatiotemporal movement properties reveal sub-modalities in crawling cell types
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_Chlamydomonas cpc1-1_ mutant exhibits unexpected growth phenotypes
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Discovering shared protein structure signatures connected to polyphosphate accumulation in diverse bacteria
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Paired residue prediction dependencies in ESM2
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Designing genome-wide MERFISH probes for understudied species
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A method for computational discovery of viral structural mimics
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Putative horizontal gene transfer events point to candidate genes involved in cross-species neuromodulation
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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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The experiment begins: Arcadia publishing 1.0
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Paired long- and short-read metagenomics of cheese rind microbial communities at multiple time points
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How can we biochemically validate protein function predictions with the Ras GTPase family?
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Phenotypic differences between interfertile _Chlamydomonas_ species
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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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Performing mass spectrometry-based proteomics in organisms with minimal reference protein databases
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ProteinCartography: Comparing proteins with structure-based maps for interactive exploration
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NovelTree: Highly parallelized phylogenomic inference
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Speeding up the quality control of raw sequencing data using seqqc, a Nextflow-based solution
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Harnessing genotype-phenotype nonlinearity to accelerate biological prediction
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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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Predicted genes from the _Amblyomma americanum_ draft genome assembly
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Streamlining genome assembly and QC with the reads2genome workflow
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How can we biochemically validate protein function predictions with the deoxycytidine kinase family?
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A capsid-based search recovers viral sequences from human brain sequencing data
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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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A new R package, sourmashconsumr, for analyzing and visualizing the outputs of sourmash
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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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Icebox is a science-sharing strategy designed to encourage risk-taking
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Label-free neuroimaging in mice captures sensory activity in response to tactile stimuli and acute pain
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Raman spectra reflect complex phylogenetic relationships
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Chlorarachniophytes form light- and Arp2/3 complex-dependent extensions that are involved in motility and predation
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DIY Raman spectroscopy for biological research
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Creating reproducible workflows for complex computational pipelines
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Exploring the actin family: A case study for ProteinCartography
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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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Clustering the NCBI nr database to reduce database size and enable faster BLAST searches
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Creating a 7,000-strain _E. coli_ genotype dataset with antimicrobial resistance phenotypes
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Identifying candidate accessory domains by mining putative venom protein fusions
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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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Robust long-read saliva transcriptome and proteome from the lone star tick, _Amblyomma americanum_
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PreHGT: A scalable workflow that screens for horizontal gene transfer within and between kingdoms
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A data-driven approach to match organisms and research problems
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How can we measure and communicate the impact of science?
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Comparing gene expression across species based on protein structure
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Isolation of a phage with an arabinosylated genome from a cheese microbial community
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An experimental and computational workflow to characterize nematode motility behavior
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Automated classification of time-course imaging data applied to nematode embryogenesis
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Challenges of isolating bacteriophage mRNA for chemical analysis
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HiPR-FISH spatial mapping of cheese rind microbial communities
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_De novo_ assembly of a long-read _Amblyomma americanum_ tick genome
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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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Combinatorial indexing and screening of clonal DNA fragments
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Structure-based protein clustering sometimes, but not always, provides insight into protein function
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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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A workflow to isolate phage DNA and identify nucleosides by HPLC and mass spectrometry
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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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Streamlining microscopy datasets by enriching for in-focus frames
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Repeat expansions associated with human disease are present in diverse organisms
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Inducing protoplast formation in _Phaeodactylum tricornutum_ by silica deprivation, enzymatic treatment, or cytoskeletal inhibition
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Defining actin: Combining sequence, structure, and functional analysis to propose useful boundaries
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Identifying circular DNA using short-read mapping
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How can we identify the common molecular signatures underlying polyphosphate accumulation?
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Quickly preprocessing and profiling microbial community sequencing data with a Nextflow workflow for metagenomics
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The known protein universe is phylogenetically biased
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Leveraging evolution to identify novel organismal models of human biology
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Phylogenies and biological foundation models
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An interactive visualization tool for _Amblyomma americanum_ differential expression data
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Graph neural networks: A unifying predictive model architecture for evolutionary applications
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Predicting antimicrobial resistance phenotypes across 7,000 _E. coli_ genomes
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Epistasis and deep learning in quantitative genetics
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Cross-trait learning with a canonical transformer tops custom attention in genotype–phenotype mapping
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