Anthony Shiver
@anthonyshiver.bsky.social
Researcher in the life sciences. Expertise in systems biology, biophysics, applied math.
A special thanks to Gigi Storz for making this article happen!
July 2, 2025 at 10:02 PM
A special thanks to Gigi Storz for making this article happen!
I particularly like the table of online resources, like a database of bacterial genome sequences and a literature search tool for protein sequences.
July 2, 2025 at 10:02 PM
I particularly like the table of online resources, like a database of bacterial genome sequences and a literature search tool for protein sequences.
It has contributions from early-career scientists like @bridgesbio.bsky.social, Leah Guthrie, McKenzie Lehman, Elizabeth Kellogg, @drsamwellie.bsky.social, Andrew Pountain, and Andrew Varble.
July 2, 2025 at 10:02 PM
It has contributions from early-career scientists like @bridgesbio.bsky.social, Leah Guthrie, McKenzie Lehman, Elizabeth Kellogg, @drsamwellie.bsky.social, Andrew Pountain, and Andrew Varble.
Original article: www.biorxiv.org/content/10.1...
Original code: github.com/czbiohub-sf/...
My fork (up-to-date versions of dependencies, some debugging): github.com/AnthonyShive...
Original code: github.com/czbiohub-sf/...
My fork (up-to-date versions of dependencies, some debugging): github.com/AnthonyShive...
www.biorxiv.org
June 18, 2025 at 8:19 PM
Original article: www.biorxiv.org/content/10.1...
Original code: github.com/czbiohub-sf/...
My fork (up-to-date versions of dependencies, some debugging): github.com/AnthonyShive...
Original code: github.com/czbiohub-sf/...
My fork (up-to-date versions of dependencies, some debugging): github.com/AnthonyShive...
Adapting the “Well-Lit” device to our workload, we operated 3 devices assembled at $150 each to do the work—2,760 total transfers—in two days. I refuse to go back to printing out an excel sheet, and I think more people should know about this.
June 18, 2025 at 8:19 PM
Adapting the “Well-Lit” device to our workload, we operated 3 devices assembled at $150 each to do the work—2,760 total transfers—in two days. I refuse to go back to printing out an excel sheet, and I think more people should know about this.
All of our measurements of gene-environment interactions, both in vitro and in vivo, are available through the Fitness Browser: fit.genomics.lbl.gov, which has a lot of nice tools for parsing these large datasets.
A heart-felt thanks to the many co-authors who came together to make this happen!
A heart-felt thanks to the many co-authors who came together to make this happen!
March 13, 2025 at 10:35 PM
All of our measurements of gene-environment interactions, both in vitro and in vivo, are available through the Fitness Browser: fit.genomics.lbl.gov, which has a lot of nice tools for parsing these large datasets.
A heart-felt thanks to the many co-authors who came together to make this happen!
A heart-felt thanks to the many co-authors who came together to make this happen!
We also screened a subset of the ordered mutant collection for small molecule production.
We identified new genes involved in aromatic lactic acid production, an important set of signals to the developing infant, and connected production of these small molecules to growth of bifidobacteria.
We identified new genes involved in aromatic lactic acid production, an important set of signals to the developing infant, and connected production of these small molecules to growth of bifidobacteria.
March 13, 2025 at 10:35 PM
We also screened a subset of the ordered mutant collection for small molecule production.
We identified new genes involved in aromatic lactic acid production, an important set of signals to the developing infant, and connected production of these small molecules to growth of bifidobacteria.
We identified new genes involved in aromatic lactic acid production, an important set of signals to the developing infant, and connected production of these small molecules to growth of bifidobacteria.
We measured the genetic determinants of host colonization in B. breve.
By referencing our metabolic reconstruction, we were able to paint a better picture of growth in the complex environment of the host guts. We learned about persistence in adults and the timing of colonization in infants.
By referencing our metabolic reconstruction, we were able to paint a better picture of growth in the complex environment of the host guts. We learned about persistence in adults and the timing of colonization in infants.
March 13, 2025 at 10:35 PM
We measured the genetic determinants of host colonization in B. breve.
By referencing our metabolic reconstruction, we were able to paint a better picture of growth in the complex environment of the host guts. We learned about persistence in adults and the timing of colonization in infants.
By referencing our metabolic reconstruction, we were able to paint a better picture of growth in the complex environment of the host guts. We learned about persistence in adults and the timing of colonization in infants.
We reconstructed global metabolism in B. breve, clarifying and rewriting several gene-protein-reaction assignments using mutant growth profiles.
With experimentally supported metabolic pathways in hand, we then tackled growth in more complex environments like the gut.
With experimentally supported metabolic pathways in hand, we then tackled growth in more complex environments like the gut.
March 13, 2025 at 10:35 PM
We reconstructed global metabolism in B. breve, clarifying and rewriting several gene-protein-reaction assignments using mutant growth profiles.
With experimentally supported metabolic pathways in hand, we then tackled growth in more complex environments like the gut.
With experimentally supported metabolic pathways in hand, we then tackled growth in more complex environments like the gut.
To start, we created a hyper-saturated, randomly-barcoded transposon pool in B. breve.
We used this pool to conduct a chemical-genomic screen and converted the transposon pool into an ordered mutant collection.
We then tackled multiple aspects of bifidobacterial biology with these resources.
We used this pool to conduct a chemical-genomic screen and converted the transposon pool into an ordered mutant collection.
We then tackled multiple aspects of bifidobacterial biology with these resources.
March 13, 2025 at 10:35 PM
To start, we created a hyper-saturated, randomly-barcoded transposon pool in B. breve.
We used this pool to conduct a chemical-genomic screen and converted the transposon pool into an ordered mutant collection.
We then tackled multiple aspects of bifidobacterial biology with these resources.
We used this pool to conduct a chemical-genomic screen and converted the transposon pool into an ordered mutant collection.
We then tackled multiple aspects of bifidobacterial biology with these resources.
Bifidobacteria have been associated with myriad health outcomes, but many questions are still unanswered, and many causal links remain to be drawn. Genetic analysis in the genus has been difficult, contributing to the mystery. We wanted to turn this weakness into a strength.
How did we do this?
How did we do this?
March 13, 2025 at 10:35 PM
Bifidobacteria have been associated with myriad health outcomes, but many questions are still unanswered, and many causal links remain to be drawn. Genetic analysis in the genus has been difficult, contributing to the mystery. We wanted to turn this weakness into a strength.
How did we do this?
How did we do this?
We measured the genetic determinants of host colonization in B. breve.
By referencing our metabolic reconstruction, we were able to paint a better picture of growth in the complex environment of the host guts. We learned about persistence in adults and the timing of colonization in infants.
By referencing our metabolic reconstruction, we were able to paint a better picture of growth in the complex environment of the host guts. We learned about persistence in adults and the timing of colonization in infants.
March 13, 2025 at 10:04 PM
We measured the genetic determinants of host colonization in B. breve.
By referencing our metabolic reconstruction, we were able to paint a better picture of growth in the complex environment of the host guts. We learned about persistence in adults and the timing of colonization in infants.
By referencing our metabolic reconstruction, we were able to paint a better picture of growth in the complex environment of the host guts. We learned about persistence in adults and the timing of colonization in infants.
We reconstructed global metabolism in B. breve, clarifying and rewriting several gene-protein-reaction assignments using mutant growth profiles.
With experimentally supported metabolic pathways in hand, we then tackled growth in more complex environments like the gut.
With experimentally supported metabolic pathways in hand, we then tackled growth in more complex environments like the gut.
March 13, 2025 at 10:04 PM
We reconstructed global metabolism in B. breve, clarifying and rewriting several gene-protein-reaction assignments using mutant growth profiles.
With experimentally supported metabolic pathways in hand, we then tackled growth in more complex environments like the gut.
With experimentally supported metabolic pathways in hand, we then tackled growth in more complex environments like the gut.
To start, we created a hyper-saturated, randomly-barcoded transposon pool in B. breve.
We used this pool to conduct a chemical-genomic screen and converted the transposon pool into an ordered mutant collection.
We then tackled multiple aspects of bifidobacterial biology with these resources.
We used this pool to conduct a chemical-genomic screen and converted the transposon pool into an ordered mutant collection.
We then tackled multiple aspects of bifidobacterial biology with these resources.
March 13, 2025 at 10:04 PM
To start, we created a hyper-saturated, randomly-barcoded transposon pool in B. breve.
We used this pool to conduct a chemical-genomic screen and converted the transposon pool into an ordered mutant collection.
We then tackled multiple aspects of bifidobacterial biology with these resources.
We used this pool to conduct a chemical-genomic screen and converted the transposon pool into an ordered mutant collection.
We then tackled multiple aspects of bifidobacterial biology with these resources.
Bifidobacteria have been associated with myriad health outcomes, but many questions are still unanswered, and many causal links remain to be drawn. Genetic analysis in the genus has been difficult, contributing to the mystery. We wanted to turn this weakness into a strength.
How did we do this?
How did we do this?
March 13, 2025 at 10:04 PM
Bifidobacteria have been associated with myriad health outcomes, but many questions are still unanswered, and many causal links remain to be drawn. Genetic analysis in the genus has been difficult, contributing to the mystery. We wanted to turn this weakness into a strength.
How did we do this?
How did we do this?