Jack Bateman
@jbateman01.bsky.social
Biology professor at Bowdoin College. Genetics, flies, chromosomes, weird science 🥰
Pinned
Jack Bateman
@jbateman01.bsky.social
· Nov 12
I thought we could use a Drosophila starter pack, please let me know if you’d like to be added. (I think there is also a more general insect list out there somewhere that i cant find rn..) go.bsky.app/JGggkH3
AI learns from chromatin data to uncover gene interactions www.nature.com/articles/d41...
AI learns from chromatin data to uncover gene interactions
Machine-learning tool for predicting gene expression.
www.nature.com
December 30, 2025 at 6:12 PM
AI learns from chromatin data to uncover gene interactions www.nature.com/articles/d41...
Medical breakthroughs in 2025 www.scientificdiscovery.dev/p/medical-br...
Medical breakthroughs in 2025
... and a happy new year.
www.scientificdiscovery.dev
December 30, 2025 at 4:09 PM
Medical breakthroughs in 2025 www.scientificdiscovery.dev/p/medical-br...
Reposted by Jack Bateman
"A mathematical model is a logical machine for converting assumptions into conclusions. If the model is correct and we believe its assumptions then we must, as a matter of logic, believe its conclusions. "
link.springer.com/article/10.1...
link.springer.com/article/10.1...
Models in biology: ‘accurate descriptions of our pathetic thinking’ - BMC Biology
In this essay I will sketch some ideas for how to think about models in biology. I will begin by trying to dispel the myth that quantitative modeling is somehow foreign to biology. I will then point o...
link.springer.com
December 26, 2025 at 1:01 PM
"A mathematical model is a logical machine for converting assumptions into conclusions. If the model is correct and we believe its assumptions then we must, as a matter of logic, believe its conclusions. "
link.springer.com/article/10.1...
link.springer.com/article/10.1...
Reposted by Jack Bateman
Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm - Nature Cell Biology
Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through the cytoplasm.
www.nature.com
December 22, 2025 at 11:45 AM
Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Jack Bateman
Very happy to share our paper rdcu.be/eUImj out today in @natcellbio.nature.com 🎉🎉🎉
We uncover an unexpected role for endogenous Xist RNA in regulating X-linked genes that escape X-inactivation.
We uncover an unexpected role for endogenous Xist RNA in regulating X-linked genes that escape X-inactivation.
Escape from X inactivation is directly modulated by Xist noncoding RNA
Nature Cell Biology - The authors show that increased Xist RNA levels can induce de novo silencing of genes that normally escape X inactivation. SPEN depletion prevents the silencing of escape...
rdcu.be
December 15, 2025 at 4:22 PM
Very happy to share our paper rdcu.be/eUImj out today in @natcellbio.nature.com 🎉🎉🎉
We uncover an unexpected role for endogenous Xist RNA in regulating X-linked genes that escape X-inactivation.
We uncover an unexpected role for endogenous Xist RNA in regulating X-linked genes that escape X-inactivation.
An integrated view of the structure and function of the human 4D nucleome www.nature.com/articles/s41...
An integrated view of the structure and function of the human 4D nucleome - Nature
The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitatin...
www.nature.com
December 24, 2025 at 10:14 PM
An integrated view of the structure and function of the human 4D nucleome www.nature.com/articles/s41...
Reposted by Jack Bateman
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene | Science www.science.org/doi/10.1126/...
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene
Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...
www.science.org
September 23, 2025 at 9:04 AM
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene | Science www.science.org/doi/10.1126/...
Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions www.cell.com/cell/fulltex...
Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions
Li et al. apply base-pair resolution Micro Capture-C ultra to map chromatin contacts
between individual motifs within cis-regulatory elements and reveal a unified model
of biophysically mediated enhan...
www.cell.com
December 11, 2025 at 11:40 PM
Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions www.cell.com/cell/fulltex...
The evolving landscape of RAS-targeted therapies www.nature.com/articles/s43...
The evolving landscape of RAS-targeted therapies - Nature Cancer
The initial discovery of an inhibitor of KRAS G12C revolutionized the KRAS field. Since then, more-potent G12C-specific inhibitors, newer allele-specific inhibitors and combinations based on KRAS targ...
www.nature.com
December 10, 2025 at 10:28 PM
The evolving landscape of RAS-targeted therapies www.nature.com/articles/s43...
High-fidelity human chromosome transfer and elimination www.science.org/doi/abs/10.1...
High-fidelity human chromosome transfer and elimination
The synthesis of human genomes and other gigabase-scale genomes will require new strategies. Here, we realized key steps in our pipeline for building synthetic human chromosomes. We established: (i) t...
www.science.org
December 10, 2025 at 12:56 AM
High-fidelity human chromosome transfer and elimination www.science.org/doi/abs/10.1...
Multiscale structure of chromatin condensates explains phase separation and material properties www.science.org/doi/10.1126/...
Multiscale structure of chromatin condensates explains phase separation and material properties
The structure and interaction networks of molecules within biomolecular condensates are poorly understood. Using cryo–electron tomography and molecular dynamics simulations, we elucidated the structur...
www.science.org
December 6, 2025 at 10:15 PM
Multiscale structure of chromatin condensates explains phase separation and material properties www.science.org/doi/10.1126/...
Cohesin drives chromatin scanning during the RAD51-mediated homology search www.science.org/doi/10.1126/...
Cohesin drives chromatin scanning during the RAD51-mediated homology search
Cohesin folds genomes into chromatin loops, the roles of which are under debate. We found that double-strand breaks (DSBs) induce de novo formation of chromatin loops in human cells, with the loop bas...
www.science.org
December 6, 2025 at 1:42 AM
Cohesin drives chromatin scanning during the RAD51-mediated homology search www.science.org/doi/10.1126/...
Reposted by Jack Bateman
"We find that the evidence for in vivo LLPS is often phenomenological and inadequate to discriminate between phase separation and other possible mechanisms. Moreover, the causal relationship and functional consequences of LLPS in vivo are even more elusive"
(2019)
pubmed.ncbi.nlm.nih.gov/31594803/
(2019)
pubmed.ncbi.nlm.nih.gov/31594803/
Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences - PubMed
The idea that liquid-liquid phase separation (LLPS) may be a general mechanism by which molecules in the complex cellular milieu may self-organize has generated much excitement and fervor in the cell biology community. While this concept is not new, its rise to preeminence has resulted in renewed in …
pubmed.ncbi.nlm.nih.gov
November 30, 2025 at 12:08 PM
"We find that the evidence for in vivo LLPS is often phenomenological and inadequate to discriminate between phase separation and other possible mechanisms. Moreover, the causal relationship and functional consequences of LLPS in vivo are even more elusive"
(2019)
pubmed.ncbi.nlm.nih.gov/31594803/
(2019)
pubmed.ncbi.nlm.nih.gov/31594803/
Reposted by Jack Bateman
Check out this beautiful paper by @richardcsilva.bsky.social et al., out now in @natcomms.nature.com. Great new DSB sensors to track DNA break formation and repair in real-time
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Engineered chromatin readers track damaged chromatin dynamics in live cells and animals - Nature Communications
DNA damage threatens genome stability, but its dynamics in living systems remain difficult to track. Here, the authors engineer MCPH1-based protein probes that specifically recognize γH2AX, enabling r...
www.nature.com
November 22, 2025 at 12:13 PM
Check out this beautiful paper by @richardcsilva.bsky.social et al., out now in @natcomms.nature.com. Great new DSB sensors to track DNA break formation and repair in real-time
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Jack Bateman
Some of the eggs laid by Iberian harvester ant queens contain males of another species, the builder harvester ant – and these males father all of the workers in the colony.
Queen ant makes males of another species for daughters to mate with
Bizarrely, Iberian harvester ant queens lay eggs that turn into male builder harvester ants, and some of her offspring are hybrids of the two species
www.newscientist.com
September 9, 2025 at 9:26 AM
Some of the eggs laid by Iberian harvester ant queens contain males of another species, the builder harvester ant – and these males father all of the workers in the colony.
Reposted by Jack Bateman
Identification of optimal fluorophores for use in the Drosophila embryo by Timothy E Saunders and team: www.biorxiv.org/content/10.1...
September 30, 2025 at 2:43 PM
Identification of optimal fluorophores for use in the Drosophila embryo by Timothy E Saunders and team: www.biorxiv.org/content/10.1...
Reposted by Jack Bateman
#Wolbachia has puzzled scientists with its power to rewire insect reproduction. What if I tell you that we found one of the keys Wolbachia use to rewire its host AND a small molecule inhibitor uses this key to mimic what this microbe has mastered for millions of years.
www.cell.com/cell-reports...
www.cell.com/cell-reports...
Beyond Wolbachia—Can a small molecule control insect reproduction?
Kaur et al. demonstrate reduced histone acetylation as a key mechanism underpinning
Wolbachia’s paternal-effect embryonic lethality trait in Drosophila melanogaster.
Recapitulation of this trait by in...
www.cell.com
October 3, 2025 at 12:58 PM
#Wolbachia has puzzled scientists with its power to rewire insect reproduction. What if I tell you that we found one of the keys Wolbachia use to rewire its host AND a small molecule inhibitor uses this key to mimic what this microbe has mastered for millions of years.
www.cell.com/cell-reports...
www.cell.com/cell-reports...
Site-specific DNA insertion into the human genome with engineered recombinases www.nature.com/articles/s41...
Site-specific DNA insertion into the human genome with engineered recombinases - Nature Biotechnology
Engineered DNA recombinases efficiently and specifically insert genetic cargos without the use of landing pads.
www.nature.com
November 12, 2025 at 11:10 PM
Site-specific DNA insertion into the human genome with engineered recombinases www.nature.com/articles/s41...
Heterozygosity at a conserved candidate sex determination locus is associated with female development in the clonal raider ant (Ooceraea biroi) elifesciences.org/articles/106...
Heterozygosity at a conserved candidate sex determination locus is associated with female development in the clonal raider ant (Ooceraea biroi)
A complementary sex determination locus is conserved in ants and dates back to approximately 112 million years ago.
elifesciences.org
November 10, 2025 at 1:55 PM
Heterozygosity at a conserved candidate sex determination locus is associated with female development in the clonal raider ant (Ooceraea biroi) elifesciences.org/articles/106...
Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions www.cell.com/cell/fulltex...
Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions
Li et al. apply base-pair resolution Micro Capture-C ultra to map chromatin contacts
between individual motifs within cis-regulatory elements and reveal a unified model
of biophysically mediated enhan...
www.cell.com
November 9, 2025 at 3:42 PM
Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions www.cell.com/cell/fulltex...
Bacterial tubular networks channel carbohydrates in insect endosymbiosis www.cell.com/cell/fulltex...
Bacterial tubular networks channel carbohydrates in insect endosymbiosis
Bacteria with an intracellular lifestyle need to feed from inside their host cells.
This study shows an adaptation of certain symbiotic bacteria, allowing them to actively
retrieve nutrients from the ...
www.cell.com
October 29, 2025 at 11:05 AM
Bacterial tubular networks channel carbohydrates in insect endosymbiosis www.cell.com/cell/fulltex...
Reposted by Jack Bateman
Ever noticed that #CRISPR editing results differ between cells? Awesome PhD student Moritz Schlapansky developed "scOUT-seq" to measure single cell transcriptomes + editing. 1.2 million cells, 74 cell types, living 🐭. Cell subtypes differ wildly from bulk average! www.biorxiv.org/content/10.1...
Cell-stereotyped DNA repair outcomes are widespread during genome editing
Genome editing outcomes are governed by DNA repair pathways that vary with cell type and state. We developed scOUT-seq (single-cell Outcomes Using Transcript sequencing), a scalable approach that join...
www.biorxiv.org
October 24, 2025 at 8:44 AM
Ever noticed that #CRISPR editing results differ between cells? Awesome PhD student Moritz Schlapansky developed "scOUT-seq" to measure single cell transcriptomes + editing. 1.2 million cells, 74 cell types, living 🐭. Cell subtypes differ wildly from bulk average! www.biorxiv.org/content/10.1...
Transcriptional interference gates monogenic odorant receptor expression in ants www.cell.com/current-biol...
Transcriptional interference gates monogenic odorant receptor expression in ants
Ant pheromone communication relies on an expanded odorant receptor repertoire, with
many genes in large genomic tandem arrays. Glotzer et al. describe a novel mechanism,
conserved across ants and othe...
www.cell.com
October 20, 2025 at 11:23 PM
Transcriptional interference gates monogenic odorant receptor expression in ants www.cell.com/current-biol...
Reposted by Jack Bateman
High levels of Cas9 are toxic in sensory neurons. Reducing Cas9 levels with uORFs avoids toxicity and is compatible with efficient editing. From @thompsonpeerlab.bsky.social. Fly lines @vdrc-flies.bsky.social
#CRISPR #Drosophila
www.biorxiv.org/content/10.1...
#CRISPR #Drosophila
www.biorxiv.org/content/10.1...
October 4, 2025 at 9:10 PM
High levels of Cas9 are toxic in sensory neurons. Reducing Cas9 levels with uORFs avoids toxicity and is compatible with efficient editing. From @thompsonpeerlab.bsky.social. Fly lines @vdrc-flies.bsky.social
#CRISPR #Drosophila
www.biorxiv.org/content/10.1...
#CRISPR #Drosophila
www.biorxiv.org/content/10.1...
Kinetic organization of the genome revealed by ultraresolution multiscale live imaging www.science.org/doi/10.1126/...
Kinetic organization of the genome revealed by ultraresolution multiscale live imaging
Genome function requires regulated genome motion. However, tools to directly observe this motion in vivo have been limited in coverage and resolution. Here we introduce an approach to tile mammalian c...
www.science.org
September 19, 2025 at 9:54 AM
Kinetic organization of the genome revealed by ultraresolution multiscale live imaging www.science.org/doi/10.1126/...