Arcadia Science

J

Juliana Gil

Affiliation: UC Davis

Pubs Collaborators

Megan L. Hochstrasser 0

0Distinct spatiotemporal movement properties reveal sub-modalities in crawling cell types

0Discovering shared protein structure signatures connected to polyphosphate accumulation in diverse bacteria

0Paired residue prediction dependencies in ESM2

0Designing genome-wide MERFISH probes for understudied species

0Putative horizontal gene transfer events point to candidate genes involved in cross-species neuromodulation

0Raman spectroscopy enables rapid and inexpensive exploration of biology

0Compound 48/80 is toxic in HMC1.2 and RBL-2H3 cells

0How confident should we be in potential targets of tick protease inhibitors predicted by AlphaFold-Multimer?

0The experiment begins: Arcadia publishing 1.0

0Paired long- and short-read metagenomics of cheese rind microbial communities at multiple time points

0How can we biochemically validate protein function predictions with the Ras GTPase family?

0Phenotypic differences between interfertile _Chlamydomonas_ species

0Early update on Arcadia publishing 2.0: Scientists are in charge, speed is an issue

0Identification of capsid-like proteins in venomous and parasitic animals

0Performing mass spectrometry-based proteomics in organisms with minimal reference protein databases

0ProteinCartography: Comparing proteins with structure-based maps for interactive exploration

0NovelTree: Highly parallelized phylogenomic inference

0Speeding up the quality control of raw sequencing data using seqqc, a Nextflow-based solution

0Harnessing genotype-phenotype nonlinearity to accelerate biological prediction

0Using protein language models to predict coding and non-coding transcripts with plm-utils

0Predicted genes from the _Amblyomma americanum_ draft genome assembly

0Streamlining genome assembly and QC with the reads2genome workflow

0How can we biochemically validate protein function predictions with the deoxycytidine kinase family?

0A capsid-based search recovers viral sequences from human brain sequencing data

0Gotta catch ‘em all: Agar microchambers for high-throughput single-cell live imaging

0Applying information theory to genetics can better explain biological phenomena

0A new R package, sourmashconsumr, for analyzing and visualizing the outputs of sourmash

0Rescuing _Chlamydomonas_ motility in mutants modeling spermatogenic failure

0The phenotype-o-mat: A flexible tool for collecting visual phenotypes

0Predicting bioactive peptides from transcriptome assemblies with the peptigate workflow

0Icebox is a science-sharing strategy designed to encourage risk-taking

0Label-free neuroimaging in mice captures sensory activity in response to tactile stimuli and acute pain

0Raman spectra reflect complex phylogenetic relationships

0Chlorarachniophytes form light- and Arp2/3 complex-dependent extensions that are involved in motility and predation

0DIY Raman spectroscopy for biological research

0Creating reproducible workflows for complex computational pipelines

0Exploring the actin family: A case study for ProteinCartography

0The experiment continues: Arcadia publishing 2.0

0A structurally divergent actin conserved in fungi has no association with specific traits

0Clustering the NCBI nr database to reduce database size and enable faster BLAST searches

0Creating a 7,000-strain _E. coli_ genotype dataset with antimicrobial resistance phenotypes

0Identifying candidate accessory domains by mining putative venom protein fusions

0Comparative phylogenomic analysis of chelicerates points to gene families associated with long-term suppression of host detection

0Robust long-read saliva transcriptome and proteome from the lone star tick, _Amblyomma americanum_

0PreHGT: A scalable workflow that screens for horizontal gene transfer within and between kingdoms

0A data-driven approach to match organisms and research problems

0How can we measure and communicate the impact of science?

0Comparing gene expression across species based on protein structure

0Isolation of a phage with an arabinosylated genome from a cheese microbial community

0An experimental and computational workflow to characterize nematode motility behavior

0Automated classification of time-course imaging data applied to nematode embryogenesis

0Challenges of isolating bacteriophage mRNA for chemical analysis

0HiPR-FISH spatial mapping of cheese rind microbial communities

0_De novo_ assembly of a long-read _Amblyomma americanum_ tick genome

0A strategy to validate protein function predictions _in vitro_

0Combinatorial indexing and screening of clonal DNA fragments

0Structure-based protein clustering sometimes, but not always, provides insight into protein function

0How can we improve upon and expand the scope of our phylogenomic inferences?

0Microchamber slide design for cell confinement during imaging

0A workflow to isolate phage DNA and identify nucleosides by HPLC and mass spectrometry

0A high-throughput imaging approach to track and quantify single-cell swimming

0Closing the divide between analysis and publication: The notebook pub

0Streamlining microscopy datasets by enriching for in-focus frames

0Repeat expansions associated with human disease are present in diverse organisms

0Inducing protoplast formation in _Phaeodactylum tricornutum_ by silica deprivation, enzymatic treatment, or cytoskeletal inhibition

0Defining actin: Combining sequence, structure, and functional analysis to propose useful boundaries

0Identifying circular DNA using short-read mapping

0How can we identify the common molecular signatures underlying polyphosphate accumulation?

0Quickly preprocessing and profiling microbial community sequencing data with a Nextflow workflow for metagenomics