Jay Keche G.
@caterpillar-coevo.bsky.social
Evolutionary genetics of plant-insect interactions. Sault Tribe Chippewa. Currently at Arizona State University
Pinned
I guess it's time to reintroduce myself:
I'm Jay. I study the ecology and evolution of plant-insect interactions using a combination of omics approaches and field experimentation. I'm especially interested in how toxic plants in the nightshade family have co-evolved with specialist herbivores.
I'm Jay. I study the ecology and evolution of plant-insect interactions using a combination of omics approaches and field experimentation. I'm especially interested in how toxic plants in the nightshade family have co-evolved with specialist herbivores.
In case anyone needs to learn how to make a computer delete all of your data instead of running an anova in R
The era of coding agents is here. How do we approach this as scientists?
Wednesday Dec 10th at 9am PT I'll livestream an interactive demo of what I have learned (matsen.group/agentic.html) about how to leverage agentic coding to do rigorous science.
www.youtube.com/watch?v=Rbhs...
Wednesday Dec 10th at 9am PT I'll livestream an interactive demo of what I have learned (matsen.group/agentic.html) about how to leverage agentic coding to do rigorous science.
www.youtube.com/watch?v=Rbhs...
Agentic Coding for Scientists (Dec 2025 edition)
YouTube video by Erick Matsen
www.youtube.com
December 3, 2025 at 5:44 AM
In case anyone needs to learn how to make a computer delete all of your data instead of running an anova in R
Reposted by Jay Keche G.
We are recruiting Guest Faculty for the 2026 Amazon Research Initiative for Educators in the Peruvian Amazon!!
🌴 🐸 🐒 🦎 🌱
@morphoinstitute.org
July 11-25, 2026 at the Amazon Conservatory for Tropical Studies (morphoinstitute.org/actsperu/)
For more info and to apply: forms.gle/hxgaiPuYhdfD...
🌴 🐸 🐒 🦎 🌱
@morphoinstitute.org
July 11-25, 2026 at the Amazon Conservatory for Tropical Studies (morphoinstitute.org/actsperu/)
For more info and to apply: forms.gle/hxgaiPuYhdfD...
2026 Amazon Research Initiative for Educators Guest Faculty Questionnaire
When: July 11-25, 2026 in Loreto, Peru
Where: Amazon Conservatory for Tropical Studies in the Napo-Sucusari Biological Reserve, Loreto, Peru (outside of the city of Iquitos)
ARIE Program Details: w...
forms.gle
December 2, 2025 at 8:47 PM
We are recruiting Guest Faculty for the 2026 Amazon Research Initiative for Educators in the Peruvian Amazon!!
🌴 🐸 🐒 🦎 🌱
@morphoinstitute.org
July 11-25, 2026 at the Amazon Conservatory for Tropical Studies (morphoinstitute.org/actsperu/)
For more info and to apply: forms.gle/hxgaiPuYhdfD...
🌴 🐸 🐒 🦎 🌱
@morphoinstitute.org
July 11-25, 2026 at the Amazon Conservatory for Tropical Studies (morphoinstitute.org/actsperu/)
For more info and to apply: forms.gle/hxgaiPuYhdfD...
Reposted by Jay Keche G.
We are excited to present the accepted paper on the Mycetohabitans pangenome now in @genomebiolevol.bsky.social! 🧬🦠
Thanks to @bhuwanabbot.bsky.social
for leading and collaborators:
@raw937.bsky.social @andrabuchan.bsky.social
academic.oup.com/gbe/advance-...
Thanks to @bhuwanabbot.bsky.social
for leading and collaborators:
@raw937.bsky.social @andrabuchan.bsky.social
academic.oup.com/gbe/advance-...
Comparative genomics reveals multipartite genomes undergoing loss in the fungal endosymbiotic genus Mycetohabitans
Abstract. Endosymbiotic bacteria extensively impact phenotypes of their eukaryotic hosts, while experiencing dramatic changes to their own genome as they b
academic.oup.com
December 2, 2025 at 5:16 PM
We are excited to present the accepted paper on the Mycetohabitans pangenome now in @genomebiolevol.bsky.social! 🧬🦠
Thanks to @bhuwanabbot.bsky.social
for leading and collaborators:
@raw937.bsky.social @andrabuchan.bsky.social
academic.oup.com/gbe/advance-...
Thanks to @bhuwanabbot.bsky.social
for leading and collaborators:
@raw937.bsky.social @andrabuchan.bsky.social
academic.oup.com/gbe/advance-...
Reposted by Jay Keche G.
Nothing could be better than bedtools. But maybe something could be bedder…
We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
1/n
1/n
Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 4:45 AM
Nothing could be better than bedtools. But maybe something could be bedder…
Me:
Them: *sends blurry photo of a speck on a wall* "hey do you know what this bug in my house is?"
Them: *sends blurry photo of a speck on a wall* "hey do you know what this bug in my house is?"
What’s the worst question someone can ask after you tell them your profession? For linguists, it’s definitely “how many languages do you speak?”, but I’m curious what else is happening to the rest of y’all out there?!
December 2, 2025 at 8:35 AM
Me:
Them: *sends blurry photo of a speck on a wall* "hey do you know what this bug in my house is?"
Them: *sends blurry photo of a speck on a wall* "hey do you know what this bug in my house is?"
Very proud to named in this article. It's exciting times for the study of species interactions!
www.cell.com/trends/genet...
www.cell.com/trends/genet...
Extended phenotypes: a new generation
The concept of extended phenotypes – the effects of genes outside of an individual
organism – was formulated by the evolutionary biologist Richard Dawkins over 40 years
ago. Driven by modern molecular...
www.cell.com
December 2, 2025 at 7:44 AM
Very proud to named in this article. It's exciting times for the study of species interactions!
www.cell.com/trends/genet...
www.cell.com/trends/genet...
Reposted by Jay Keche G.
CryoET of symbiotic cell-cell interfaces 🦑🦠
🔗 www.biorxiv.org/content/10.1...
🔗 www.biorxiv.org/content/10.1...
December 1, 2025 at 9:45 AM
CryoET of symbiotic cell-cell interfaces 🦑🦠
🔗 www.biorxiv.org/content/10.1...
🔗 www.biorxiv.org/content/10.1...
Reposted by Jay Keche G.
We all wish peer review to be rapid and professional: doesn’t always go like that. But I am relieved to finally see Helixer by @alisandra-denton.bsky.social and team published in Nature Method. Congratulations! www.nature.com/articles/s41...
Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods
By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and invertebrat...
www.nature.com
November 28, 2025 at 4:58 AM
We all wish peer review to be rapid and professional: doesn’t always go like that. But I am relieved to finally see Helixer by @alisandra-denton.bsky.social and team published in Nature Method. Congratulations! www.nature.com/articles/s41...
Reposted by Jay Keche G.
"Runctitiononal features"? "Medical fymblal"? "1 Tol Line storee"? This gets worse the longer you look at it. But it's got to be good, because it was published in Nature Scientific Reports last week: www.nature.com/articles/s41... h/t @asa.tsbalans.se
November 27, 2025 at 9:30 AM
"Runctitiononal features"? "Medical fymblal"? "1 Tol Line storee"? This gets worse the longer you look at it. But it's got to be good, because it was published in Nature Scientific Reports last week: www.nature.com/articles/s41... h/t @asa.tsbalans.se
Reposted by Jay Keche G.
One of the most exciting projects I have ever been involved in: Project Psyche! Read all about our ambitions and aims. It's ground breaking stuff, just mind blowing and even surreal (27 years ago we did single genes for lep phylogenetics)! @projectpsyche.bsky.social
www.cell.com/trends/ecolo...
www.cell.com/trends/ecolo...
Project Psyche: reference genomes for all Lepidoptera in Europe
Project Psyche is a transnational initiative to generate and study chromosome-level
reference genomes of all ~11 000 species of Lepidoptera (butterflies and moths) found
in Europe. Here, we describe t...
www.cell.com
November 27, 2025 at 8:46 AM
One of the most exciting projects I have ever been involved in: Project Psyche! Read all about our ambitions and aims. It's ground breaking stuff, just mind blowing and even surreal (27 years ago we did single genes for lep phylogenetics)! @projectpsyche.bsky.social
www.cell.com/trends/ecolo...
www.cell.com/trends/ecolo...
This is an incredible tool. I've been using for a couple years already and it has worked amazingly well for everything I've thrown at it.
Except weevils. It's pretty bad at annotating my weevil genomes.
Except weevils. It's pretty bad at annotating my weevil genomes.
AI model Helixer predicts eukaryotic genes ab initio, directly from a plain text FASTA file.
No RNA-seq.
No protein homology.
No repeats, hints, or curated evidence.
Raw genome → accurate gene models.
Deep learning + HMM, published in @natmethods.nature.com
www.nature.com/articles/s41...
No RNA-seq.
No protein homology.
No repeats, hints, or curated evidence.
Raw genome → accurate gene models.
Deep learning + HMM, published in @natmethods.nature.com
www.nature.com/articles/s41...
Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods
By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and invertebrat...
www.nature.com
November 27, 2025 at 8:09 AM
This is an incredible tool. I've been using for a couple years already and it has worked amazingly well for everything I've thrown at it.
Except weevils. It's pretty bad at annotating my weevil genomes.
Except weevils. It's pretty bad at annotating my weevil genomes.
Reposted by Jay Keche G.
It’s fellowship season in UK and many postdocs will be looking for host institutions. This is a very critical step. Approach at least 3-4 hosts. Make sure there is genuine interest in hiring you. Many institutions claim to support fellows into long term careers but most actually don’t. #UKRIFLF
November 23, 2025 at 8:48 PM
It’s fellowship season in UK and many postdocs will be looking for host institutions. This is a very critical step. Approach at least 3-4 hosts. Make sure there is genuine interest in hiring you. Many institutions claim to support fellows into long term careers but most actually don’t. #UKRIFLF
Reposted by Jay Keche G.
Latest work out today in @currentbiology.bsky.social
We find the fly development gene bicoid is much older than previously thought (~20 million yrs older!) 🪰🧬
To pinpoint its origins we tackled the Diptera phylogeny, providing some resolution (many open questions remain).
🔗 tinyurl.com/2vyuevpy
We find the fly development gene bicoid is much older than previously thought (~20 million yrs older!) 🪰🧬
To pinpoint its origins we tackled the Diptera phylogeny, providing some resolution (many open questions remain).
🔗 tinyurl.com/2vyuevpy
Revised evolutionary relationships within Brachycera and the early origin of bicoid in flies
Mulhair et al. uncover a functional bicoid in non-cyclorrhaphan flies, pushing the
gene's origin back by ∼20 million years. Reassessing the Diptera phylogeny using the
largest dataset to date permits ...
www.cell.com
October 17, 2025 at 3:14 PM
Latest work out today in @currentbiology.bsky.social
We find the fly development gene bicoid is much older than previously thought (~20 million yrs older!) 🪰🧬
To pinpoint its origins we tackled the Diptera phylogeny, providing some resolution (many open questions remain).
🔗 tinyurl.com/2vyuevpy
We find the fly development gene bicoid is much older than previously thought (~20 million yrs older!) 🪰🧬
To pinpoint its origins we tackled the Diptera phylogeny, providing some resolution (many open questions remain).
🔗 tinyurl.com/2vyuevpy
Reposted by Jay Keche G.
New study out in Ecology Letters 🌱🐑!
Using long-term Åland monitoring data, we found that herbivory increases plant diversity across scales and flips the diversity–area relationship: a positive relationship is found in grazed sites while a negative one in ungrazed sites.
🔗 doi.org/10.1111/ele....
Using long-term Åland monitoring data, we found that herbivory increases plant diversity across scales and flips the diversity–area relationship: a positive relationship is found in grazed sites while a negative one in ungrazed sites.
🔗 doi.org/10.1111/ele....
Herbivory Modifies the Role of Spatial Processes in a Grassland Plant Metacommunity
We empirically examined how mammalian herbivory interacts with habitat size and connectivity to affect plant diversity in a natural grassland metacommunity. We found that herbivory increased plant di...
doi.org
November 24, 2025 at 8:30 AM
New study out in Ecology Letters 🌱🐑!
Using long-term Åland monitoring data, we found that herbivory increases plant diversity across scales and flips the diversity–area relationship: a positive relationship is found in grazed sites while a negative one in ungrazed sites.
🔗 doi.org/10.1111/ele....
Using long-term Åland monitoring data, we found that herbivory increases plant diversity across scales and flips the diversity–area relationship: a positive relationship is found in grazed sites while a negative one in ungrazed sites.
🔗 doi.org/10.1111/ele....
Reposted by Jay Keche G.
TIL: conchologists
Search is on for the German hairy snail in London
Conchologists, and citizen scientists team up to seek out endangered mollusc species along River Thames
www.theguardian.com
November 24, 2025 at 10:25 AM
TIL: conchologists
Reposted by Jay Keche G.
Excited that our new collaborative work on Amazonian frogs with giant meiotic chains of 8–12 😲 #SexChromosomes now is out in @commsbio.nature.com! 🐸🧬
Investigating the evolution of large meiotic rings of multiple X and Y chromosomes in two Leptodactylus species
🔗 www.nature.com/articles/s42...
Investigating the evolution of large meiotic rings of multiple X and Y chromosomes in two Leptodactylus species
🔗 www.nature.com/articles/s42...
November 22, 2025 at 12:12 AM
Excited that our new collaborative work on Amazonian frogs with giant meiotic chains of 8–12 😲 #SexChromosomes now is out in @commsbio.nature.com! 🐸🧬
Investigating the evolution of large meiotic rings of multiple X and Y chromosomes in two Leptodactylus species
🔗 www.nature.com/articles/s42...
Investigating the evolution of large meiotic rings of multiple X and Y chromosomes in two Leptodactylus species
🔗 www.nature.com/articles/s42...
Reposted by Jay Keche G.
Hey folks, we (the School of Life Sciences at Arizona State University) are looking for an Assistant Teaching Professor in microbiology and immunology. Please pass this on to anyone you think might be interested, or check it out if you are interested yourself!
apply.interfolio.com/176994
apply.interfolio.com/176994
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
November 19, 2025 at 4:59 PM
Hey folks, we (the School of Life Sciences at Arizona State University) are looking for an Assistant Teaching Professor in microbiology and immunology. Please pass this on to anyone you think might be interested, or check it out if you are interested yourself!
apply.interfolio.com/176994
apply.interfolio.com/176994
My time attempting to homebrew Kombucha convinced me that fruit flies may, in fact, spontaneously generate from a mixture of tea and sugar
It's not hard to see how the idea of spontaneous generation came about.
November 19, 2025 at 7:55 PM
My time attempting to homebrew Kombucha convinced me that fruit flies may, in fact, spontaneously generate from a mixture of tea and sugar
Reposted by Jay Keche G.
We are hiring!! Biological Sciences as UNC Charlotte has a broad search for a new assistant professor.
Apps reviewed 12/15.
Please spread the word! 💚⛏️
#PlantSci 🧪🦠🧬
jobs.charlotte.edu/postings/65141
Apps reviewed 12/15.
Please spread the word! 💚⛏️
#PlantSci 🧪🦠🧬
jobs.charlotte.edu/postings/65141
Assistant Professor
Applicants should possess a Ph.D. in the biological sciences or related fields.Candidates are expected to document expertise in their specialty by a record of postdoctoral training, peer reviewed publ...
jobs.charlotte.edu
November 17, 2025 at 2:52 PM
We are hiring!! Biological Sciences as UNC Charlotte has a broad search for a new assistant professor.
Apps reviewed 12/15.
Please spread the word! 💚⛏️
#PlantSci 🧪🦠🧬
jobs.charlotte.edu/postings/65141
Apps reviewed 12/15.
Please spread the word! 💚⛏️
#PlantSci 🧪🦠🧬
jobs.charlotte.edu/postings/65141
Reposted by Jay Keche G.
🧬 PhD Position: Evolutionary & Comparative Genomics 🕷️
Join us at @uni-goettingen.de for a 3-year PhD (65% TV-L E13).
We will investigate the genomic & phenotypic impact of gene duplication across 233 arthropod genomes!
More infos 👇 and s.gwdg.de/eDrAAY
#Evolution #Genomics #Bioinformatics
Join us at @uni-goettingen.de for a 3-year PhD (65% TV-L E13).
We will investigate the genomic & phenotypic impact of gene duplication across 233 arthropod genomes!
More infos 👇 and s.gwdg.de/eDrAAY
#Evolution #Genomics #Bioinformatics
Posnien - Georg-August-Universität Göttingen
Webseiten der Georg-August-Universität Göttingen
s.gwdg.de
November 18, 2025 at 7:04 AM
🧬 PhD Position: Evolutionary & Comparative Genomics 🕷️
Join us at @uni-goettingen.de for a 3-year PhD (65% TV-L E13).
We will investigate the genomic & phenotypic impact of gene duplication across 233 arthropod genomes!
More infos 👇 and s.gwdg.de/eDrAAY
#Evolution #Genomics #Bioinformatics
Join us at @uni-goettingen.de for a 3-year PhD (65% TV-L E13).
We will investigate the genomic & phenotypic impact of gene duplication across 233 arthropod genomes!
More infos 👇 and s.gwdg.de/eDrAAY
#Evolution #Genomics #Bioinformatics
Reposted by Jay Keche G.
Wow
For example, you can cut a huge gash and pull out most of the cytoplasm in Stentor and it will flow back in
pubmed.ncbi.nlm.nih.gov/24378633/
pubmed.ncbi.nlm.nih.gov/24378633/
November 11, 2025 at 8:33 PM
Wow
Reposted by Jay Keche G.
New paper is online! We used single cell RNA-seq & phylogenetics to identify 2 additional cell type specific TFs that control late-stage vinca alkaloid biosynthesis. The key insights originated from Camptotheca, another species that produces alkaloids. doi.org/10.1111/nph.... #PlantScience #SecMet
November 10, 2025 at 1:29 PM
New paper is online! We used single cell RNA-seq & phylogenetics to identify 2 additional cell type specific TFs that control late-stage vinca alkaloid biosynthesis. The key insights originated from Camptotheca, another species that produces alkaloids. doi.org/10.1111/nph.... #PlantScience #SecMet