Cameron Thrash
@jcamthrash
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Professor @USC_MEB, microbe hunter. he/him. Not a bot. @[email protected] @jcamthrash.bsky.social
Los Angeles, CA
Joined June 2011
GhostFold: Accurate protein structure prediction using structure-constrained synthetic coevolutionary signals
biorxiv.org
The accuracy of protein structure prediction models such as AlphaFold2 is tightly coupled to the depth and quality of multiple sequence alignments (MSAs), posing a persistent challenge for proteins...
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Genotype-phenotype modeling of light ecotypes in Prochlorococcus reveals genomic signatures of ecotypic divergence
biorxiv.org
Prochlorococcus is a cyanobacterial genus that exhibits photosynthetic capacity and remarkable genetic diversity. We analyze how Prochlorococcus genomics relate to high vs. low light environment...
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High-Throughput Absolute Quantification Sequencing Advances Characterisation of Microbial Community Ecology
onlinelibrary.wiley.com
High-throughput sequencing has been extensively used in microbial ecology research, but this technology typically generates semi-quantitative relative abundance data. The discrepancies of community...
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Predicting functions of uncharacterized gene products from microbial communities
nature.com
Nature Biotechnology - FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.
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Bacterial Volatile Organic Compound Specialists in the Phycosphere
academic.oup.com
Abstract. Labile dissolved organic carbon in the surface oceans accounts for ~¼ of carbon produced through photosynthesis and turns over on average every t
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METAHIT enables comprehensive and flexible genome-resolved microbiome analysis with metagenomic Hi-C
biorxiv.org
Metagenomic Hi-C (metaHi-C) augments shotgun sequencing with in-cell proximity information, enabling genome-resolved analysis of complex communities. However, computational tools for metaHi-C remain...
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A compact model of Escherichia coli core and biosynthetic metabolism
journals.plos.org
Author summary Metabolism is central to life, influencing microbial function in complex environments. Traditional genome-scale metabolic models offer broad coverage but often lack precision without...
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Microbial oxidation significantly reduces methane export from global groundwaters
pnas.org
Methane is ubiquitous in groundwater, and its release to surface environments through pumping, discharge, or diffusion is an emerging environmental...
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Counting-based inference of mutant growth rates from pooled sequencing across growth regimes
biorxiv.org
Simultaneously inferring the growth rates of thousands of genetically distinct cellular variants coexisting in a single culture is now possible by tracking their relative abundances over time through...
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Phages communicate across species to shape microbial ecosystems
biorxiv.org
Arbitrium is a communication system that helps bacteriophages decide between lysis and lysogeny via secreted peptides. In arbitrium, the AimP peptide binds its cognate AimR receptor to repress aimX...
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Variations in the latitudinal diversity gradients of the ocean microbiome
biorxiv.org
Latitudinal diversity gradients (LDGs), typically declining from the equator to the poles, are among the most pervasive macroecological patterns, yet their generality and underlying drivers in the...
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Dissolved oxygen concentrations influence microbial diversity, abundance and dominant players in an oxygen minimum zone
biorxiv.org
Expansion of marine global oxygen minimum zones (OMZs) can have profound impacts on resident macrofauna. Less obvious is the influence OMZs will have on the diversity and abundance of planktonic...
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μGrowthDB: querying, visualizing, and sharing microbial growth curve data
biorxiv.org
Microbial growth curve data contain valuable information about microorganisms' physiology and metabolism. However, they are currently reported in various formats scattered across publications. A...
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Contrasting greenhouse gas dynamics along a coastal‐to‐oligotrophic ocean continuum
aslopubs.onlinelibrary.wiley.com
The oceans play the dual role of carbon sinks and greenhouse gases (GHGs) sources in global climate change, but there are still gaps in understanding the GHG fluxes and regulation mechanisms across...
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Evolution induced state shifts in a long-term microbial community experiment
biorxiv.org
Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain poorly understood. Understanding how Darwinian...
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Deterministic co-encapsulation of microparticles in droplets via synchronized merging for single-cell genomics
biorxiv.org
Droplet encapsulation of microparticles such as hydrogel beads and cells is fundamental to high-throughput bioanalytical assays, including single-cell genomics. However, co-encapsulation of multiple...
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Database Release: PPSDB, a Linked Open Data Knowledge Base for Protist–Prokaryote Symbioses
onlinelibrary.wiley.com
As the ecological and evolutionary importance of symbiotic interactions between protists (microbial eukaryotes) and prokaryotes (bacteria and archaea) is better appreciated, keeping an overview of...
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Habitat-specificity in SAR11 is associated with a few genes under high selection
academic.oup.com
Abstract. The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages
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Metabolic capacity is maintained despite shifts in microbial diversity in estuary sediments
academic.oup.com
Abstract. Estuaries are highly productive ecosystems where microbial communities drive nutrient and carbon cycling, supporting complex food webs. With inte
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A new family of ribosome hibernation factors in Archaea
biorxiv.org
Ribosome hibernation preserves translation machinery during stress, yet its mechanisms in Archaea remain poorly defined. Here we identify Hib, a previously unrecognized family of archaeal hibernation...
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