Chuck Smallwood, PhD
@tinytwigs.bsky.social
Okie sharing science and art to inspire a life of learning
Reposted by Chuck Smallwood, PhD
Evaluation of machine learning-assisted directed evolution across diverse combinatorial landscapes: Cell Systems
#microsky
www.cell.com/cell-systems...
#microsky
www.cell.com/cell-systems...
Evaluation of machine learning-assisted directed evolution across diverse combinatorial landscapes
Machine learning-assisted directed evolution (MLDE) enhances protein engineering by
efficiently identifying high-fitness variants. However, a limited understanding of
MLDE performance across diverse p...
www.cell.com
September 12, 2025 at 9:29 PM
Evaluation of machine learning-assisted directed evolution across diverse combinatorial landscapes: Cell Systems
#microsky
www.cell.com/cell-systems...
#microsky
www.cell.com/cell-systems...
Reposted by Chuck Smallwood, PhD
Global methane footprints growth and drivers 1990-2023 www.nature.com/articles/s41... #jcampubs
Global methane footprints growth and drivers 1990-2023 - Nature Communications
Understanding global methane trends remains limited, especially from a consumption view. This study shows rising emissions, limited decoupling, and shifting trade patterns involving more emerging and ...
www.nature.com
September 3, 2025 at 4:49 PM
Global methane footprints growth and drivers 1990-2023 www.nature.com/articles/s41... #jcampubs
Reposted by Chuck Smallwood, PhD
Wow. Check this out.
Politicians actually trying to solve problems can achieve a lot!
www.washingtonpost.com/climate-solu...
Politicians actually trying to solve problems can achieve a lot!
www.washingtonpost.com/climate-solu...
Paris said au revoir to cars. Air pollution maps reveal a dramatic change.
Air pollution fell substantially as the city restricted car traffic and made way for parks and bike lanes.
www.washingtonpost.com
August 30, 2025 at 9:15 PM
Wow. Check this out.
Politicians actually trying to solve problems can achieve a lot!
www.washingtonpost.com/climate-solu...
Politicians actually trying to solve problems can achieve a lot!
www.washingtonpost.com/climate-solu...
Reposted by Chuck Smallwood, PhD
Reposted by Chuck Smallwood, PhD
Lithium has an essential role in the brain and is deficient early in Alzheimer’s disease, which can be recapitulated in mice and treated with a novel lithium salt that restores the physiological level, according to a paper in Nature. go.nature.com/47mxemu #medsky 🧪
August 10, 2025 at 4:38 PM
Lithium has an essential role in the brain and is deficient early in Alzheimer’s disease, which can be recapitulated in mice and treated with a novel lithium salt that restores the physiological level, according to a paper in Nature. go.nature.com/47mxemu #medsky 🧪
Reposted by Chuck Smallwood, PhD
A periodic table of bacteria?: Mapping bacterial diversity in trait space www.biorxiv.org/content/10.1... #jcampubs
July 18, 2025 at 3:09 PM
A periodic table of bacteria?: Mapping bacterial diversity in trait space www.biorxiv.org/content/10.1... #jcampubs
Reposted by Chuck Smallwood, PhD
A new preprint led by Sonomi Yamaguchi in our lab describes a bacterial anti-phage defense system named Clover that uses nucleotide signals to both activate and inhibit host immunity.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
July 17, 2025 at 8:38 PM
A new preprint led by Sonomi Yamaguchi in our lab describes a bacterial anti-phage defense system named Clover that uses nucleotide signals to both activate and inhibit host immunity.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Chuck Smallwood, PhD
Today's reading: Nature should be the model for microbial sciences journals.asm.org/doi/10.1128/... by @brettbakker.bsky.social @emilyraehyde.bsky.social and @pedroleao.bsky.social
Looks ideal for a talk I am working on on model organisms ...
Looks ideal for a talk I am working on on model organisms ...
Nature should be the model for microbial sciences | Journal of Bacteriology
Historically, our understanding of microbes has been based on laboratory cultures.
Much of what we know at a mechanistic level is based on “model organisms” which are
species that readily grow in labo...
journals.asm.org
July 12, 2025 at 2:06 PM
Today's reading: Nature should be the model for microbial sciences journals.asm.org/doi/10.1128/... by @brettbakker.bsky.social @emilyraehyde.bsky.social and @pedroleao.bsky.social
Looks ideal for a talk I am working on on model organisms ...
Looks ideal for a talk I am working on on model organisms ...
Reposted by Chuck Smallwood, PhD
Plastic Biofilms as Hotspots of Nitrogen Cycling in Estuarine Ecosystems: Comparative Ecological, Genomic, and Transcriptomic Analysis Across Substrates onlinelibrary.wiley.com/doi/10.1111/... #jcampubs 🌊
Plastic Biofilms as Hotspots of Nitrogen Cycling in Estuarine Ecosystems: Comparative Ecological, Genomic, and Transcriptomic Analysis Across Substrates
Plastic surfaces in estuarine waters serve as unexpected hotspots for microbial activity, significantly enhancing nitrogen cycling compared to natural substrates and surrounding seawater. By combinin...
onlinelibrary.wiley.com
July 8, 2025 at 1:11 PM
Plastic Biofilms as Hotspots of Nitrogen Cycling in Estuarine Ecosystems: Comparative Ecological, Genomic, and Transcriptomic Analysis Across Substrates onlinelibrary.wiley.com/doi/10.1111/... #jcampubs 🌊
Reposted by Chuck Smallwood, PhD
Ten simple rules for faculty members building just and equitable environments in academic science journals.plos.org/ploscompbiol... #jcampubs
Ten simple rules for faculty members building just and equitable environments in academic science
journals.plos.org
July 8, 2025 at 1:25 PM
Ten simple rules for faculty members building just and equitable environments in academic science journals.plos.org/ploscompbiol... #jcampubs
Reposted by Chuck Smallwood, PhD
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities academic.oup.com/ismej/advanc... #jcampubs
July 7, 2025 at 4:51 PM
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities academic.oup.com/ismej/advanc... #jcampubs
Reposted by Chuck Smallwood, PhD
Defining ultra-slow-growing extremophilic microorganisms as aeonophiles #USC_earth #USC_MEB #jcampubs www.nature.com/articles/s41...
Defining ultra-slow-growing extremophilic microorganisms as aeonophiles - Nature Microbiology
In environments like the deep subsurface, microorganisms with long doubling times can remain metabolically active for millions of years — we propose referring to this class of extremophile as aeonophi...
www.nature.com
June 20, 2025 at 5:14 PM
Defining ultra-slow-growing extremophilic microorganisms as aeonophiles #USC_earth #USC_MEB #jcampubs www.nature.com/articles/s41...
Reposted by Chuck Smallwood, PhD
The Study of Microbial Physiology Under Microoxic Conditions Is Critical but Neglected enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs
The Study of Microbial Physiology Under Microoxic Conditions Is Critical but Neglected
Microbial physiology is mainly studied under aerobic or anaerobic/anoxic conditions, neglecting microbial behaviours in diverse microoxic conditions. The current article revisits the definition of mi....
enviromicro-journals.onlinelibrary.wiley.com
June 19, 2025 at 2:38 PM
The Study of Microbial Physiology Under Microoxic Conditions Is Critical but Neglected enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs
Reposted by Chuck Smallwood, PhD
🧑🚀💫Our July issue is now live! Read it here ⬇️
nature.com/nrmicro/volumes/23/issues/7
Inside:
🛰️Phage satellites
🧬Mobile genetic element interactions and evolution in bacteria
💊Bacterial metabolism and antimicrobial resistance
🎯SARS-CoV-2 spike
...and more!
nature.com/nrmicro/volumes/23/issues/7
Inside:
🛰️Phage satellites
🧬Mobile genetic element interactions and evolution in bacteria
💊Bacterial metabolism and antimicrobial resistance
🎯SARS-CoV-2 spike
...and more!
June 18, 2025 at 10:25 PM
🧑🚀💫Our July issue is now live! Read it here ⬇️
nature.com/nrmicro/volumes/23/issues/7
Inside:
🛰️Phage satellites
🧬Mobile genetic element interactions and evolution in bacteria
💊Bacterial metabolism and antimicrobial resistance
🎯SARS-CoV-2 spike
...and more!
nature.com/nrmicro/volumes/23/issues/7
Inside:
🛰️Phage satellites
🧬Mobile genetic element interactions and evolution in bacteria
💊Bacterial metabolism and antimicrobial resistance
🎯SARS-CoV-2 spike
...and more!
Reposted by Chuck Smallwood, PhD
Just out in Nature Reviews Genetics!
From twin studies to microbiome GWAS to cutting-edge transcriptomics, we explore the cross-talk between our genes and the microbiome!
Fun working together with
@pamferretti.bsky.social @blekhman.bsky.social Kelsey Johnson
www.nature.com/articles/s41...
From twin studies to microbiome GWAS to cutting-edge transcriptomics, we explore the cross-talk between our genes and the microbiome!
Fun working together with
@pamferretti.bsky.social @blekhman.bsky.social Kelsey Johnson
www.nature.com/articles/s41...
Genomics of host–microbiome interactions in humans - Nature Reviews Genetics
In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome on host gene regulation.
www.nature.com
June 5, 2025 at 6:47 PM
Just out in Nature Reviews Genetics!
From twin studies to microbiome GWAS to cutting-edge transcriptomics, we explore the cross-talk between our genes and the microbiome!
Fun working together with
@pamferretti.bsky.social @blekhman.bsky.social Kelsey Johnson
www.nature.com/articles/s41...
From twin studies to microbiome GWAS to cutting-edge transcriptomics, we explore the cross-talk between our genes and the microbiome!
Fun working together with
@pamferretti.bsky.social @blekhman.bsky.social Kelsey Johnson
www.nature.com/articles/s41...
Reposted by Chuck Smallwood, PhD
Research Saves Lives
At Hopkins, we just went live with an expansive website showing the extraordinary value of research, the impact of cuts to research, what's at stake, resources for our research community, etc.
Check it out: researchsaveslives.jhu.edu
At Hopkins, we just went live with an expansive website showing the extraordinary value of research, the impact of cuts to research, what's at stake, resources for our research community, etc.
Check it out: researchsaveslives.jhu.edu
June 2, 2025 at 9:24 PM
Research Saves Lives
At Hopkins, we just went live with an expansive website showing the extraordinary value of research, the impact of cuts to research, what's at stake, resources for our research community, etc.
Check it out: researchsaveslives.jhu.edu
At Hopkins, we just went live with an expansive website showing the extraordinary value of research, the impact of cuts to research, what's at stake, resources for our research community, etc.
Check it out: researchsaveslives.jhu.edu
Reposted by Chuck Smallwood, PhD
Starship giant transposable elements cluster by host taxonomy using k-mer-based phylogenetics. #TransposableElements #TEs #Kmer #Phylogenetics #Genomics #Bioinformatics #G3 🧬 🖥️
academic.oup.com/g3journal/ad...
academic.oup.com/g3journal/ad...
June 2, 2025 at 5:06 PM
Starship giant transposable elements cluster by host taxonomy using k-mer-based phylogenetics. #TransposableElements #TEs #Kmer #Phylogenetics #Genomics #Bioinformatics #G3 🧬 🖥️
academic.oup.com/g3journal/ad...
academic.oup.com/g3journal/ad...
Reposted by Chuck Smallwood, PhD
BONCAT-Live for isolation and cultivation of active environmental bacteria www.biorxiv.org/content/10.1... #jcampubs
BONCAT-Live for isolation and cultivation of active environmental bacteria
In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including in association with plants and animals. Their physiological...
www.biorxiv.org
May 15, 2025 at 1:05 PM
BONCAT-Live for isolation and cultivation of active environmental bacteria www.biorxiv.org/content/10.1... #jcampubs
Reposted by Chuck Smallwood, PhD
Frank Santoriello showed how phage φVP882 make life-or-death decisions using bacterial quorum sensing. Depending on host density and whether cells are on a surface or in liquid, the phage toggles between lysis & lysogeny. For more: wix.to/1Cx2fsI #Microbiology #Princeton #PhageBiology #QuorumSensing
Phage with a Sixth Sense: Francis Santoriello Reveals How φVP882 Uses Quorum Signals and Surfaces to Decide Its Fate
At the 2025 Theobald Smith Society Spring Symposium, postdoctoral researcher Francis Santoriello of the Bassler Lab at Princeton University delivered a fascinating talk on how a bacterial virus (phage...
wix.to
May 15, 2025 at 10:36 PM
Frank Santoriello showed how phage φVP882 make life-or-death decisions using bacterial quorum sensing. Depending on host density and whether cells are on a surface or in liquid, the phage toggles between lysis & lysogeny. For more: wix.to/1Cx2fsI #Microbiology #Princeton #PhageBiology #QuorumSensing
Reposted by Chuck Smallwood, PhD
Today "a milestone in the evolution of personalized therapies for rare & ultra-rare inborn errors of metabolism"
—the 1st human to undergo custom genome editing
—from decades of NIH funded research
www.nejm.org/doi/full/10....
@nejm.org
www.nejm.org/doi/full/10....
www.nytimes.com/2025/05/15/h...
—the 1st human to undergo custom genome editing
—from decades of NIH funded research
www.nejm.org/doi/full/10....
@nejm.org
www.nejm.org/doi/full/10....
www.nytimes.com/2025/05/15/h...
May 15, 2025 at 6:05 PM
Today "a milestone in the evolution of personalized therapies for rare & ultra-rare inborn errors of metabolism"
—the 1st human to undergo custom genome editing
—from decades of NIH funded research
www.nejm.org/doi/full/10....
@nejm.org
www.nejm.org/doi/full/10....
www.nytimes.com/2025/05/15/h...
—the 1st human to undergo custom genome editing
—from decades of NIH funded research
www.nejm.org/doi/full/10....
@nejm.org
www.nejm.org/doi/full/10....
www.nytimes.com/2025/05/15/h...
Reposted by Chuck Smallwood, PhD
Hydrogen-dependent dissimilatory nitrate reduction to ammonium enables growth of Campylobacterota isolates academic.oup.com/ismej/advanc... #jcampubs
May 15, 2025 at 1:15 PM
Hydrogen-dependent dissimilatory nitrate reduction to ammonium enables growth of Campylobacterota isolates academic.oup.com/ismej/advanc... #jcampubs
Reposted by Chuck Smallwood, PhD
Two types of brains have emerged in nature: solid (ours) and liquid (ant colonies, immune system). What can be computed by liquid brains? How complex are they? Check our paper on the statistical physics of liquid brains @jordipinero.bsky.social royalsocietypublishing.org/doi/full/10....
May 8, 2025 at 9:16 AM
Two types of brains have emerged in nature: solid (ours) and liquid (ant colonies, immune system). What can be computed by liquid brains? How complex are they? Check our paper on the statistical physics of liquid brains @jordipinero.bsky.social royalsocietypublishing.org/doi/full/10....
Reposted by Chuck Smallwood, PhD
The antiviral cytokine interferon is thought to act through the induction of hundreds of genes. In this #PLOSBiology Perspective, @jschoggins.bsky.social highlights recent findings that instead suggest distinct viruses are targeted by small subsets of the induced gene repertoire. 🧪
plos.io/4m7hOYi
plos.io/4m7hOYi
Old cytokine, new tricks: A refined model of interferon’s antiviral activity
Interferon is a central component of the vertebrate antiviral immune response, thought to act through induction of hundreds of interferon-stimulated genes, with some redundancy. This Perspective highl...
plos.io
May 8, 2025 at 9:41 AM
The antiviral cytokine interferon is thought to act through the induction of hundreds of genes. In this #PLOSBiology Perspective, @jschoggins.bsky.social highlights recent findings that instead suggest distinct viruses are targeted by small subsets of the induced gene repertoire. 🧪
plos.io/4m7hOYi
plos.io/4m7hOYi
Reposted by Chuck Smallwood, PhD
Our newest on using genomic and phylogenetic information to predict microbial maximum growth rates www.nature.com/articles/s41... with @liangxu.bsky.social
Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information - Nature Communications
Microbial maximum growth rates vary widely across species, and their measurement is challenging, especially for uncultivated organisms. Here, Xu, Zakem & Weissman present Phydon, a framework for g...
www.nature.com
May 7, 2025 at 6:09 PM
Our newest on using genomic and phylogenetic information to predict microbial maximum growth rates www.nature.com/articles/s41... with @liangxu.bsky.social
Reposted by Chuck Smallwood, PhD
we got three great unofficial great news this week! Celebrate what you can, be happy for your brethren, find joy in the small and the big things! Love one another and be good to one another as we continue to do great science and make the world a better place.
May 8, 2025 at 2:52 AM
we got three great unofficial great news this week! Celebrate what you can, be happy for your brethren, find joy in the small and the big things! Love one another and be good to one another as we continue to do great science and make the world a better place.