Joe Walker
@evojfwalker.bsky.social
Assistant professor in the biology department at the University of Illinois Chicago. Lab website https://walkerlab-uic.github.io/. All opinions, spelling mistakes, and grammatical errors are still my own.
Reposted by Joe Walker
Another exciting #SSB2026 workshop to highlight:
A Primer for Phylogenetic Causal Inference
with @oschwery.bsky.social & @pseudacris.bsky.social
Also, lots of new info on the website and more soon:
ssb2026.github.io
Follow for the latest updates!
@jembrown.bsky.social @systbiol.bsky.social
A Primer for Phylogenetic Causal Inference
with @oschwery.bsky.social & @pseudacris.bsky.social
Also, lots of new info on the website and more soon:
ssb2026.github.io
Follow for the latest updates!
@jembrown.bsky.social @systbiol.bsky.social
August 15, 2025 at 3:07 PM
Another exciting #SSB2026 workshop to highlight:
A Primer for Phylogenetic Causal Inference
with @oschwery.bsky.social & @pseudacris.bsky.social
Also, lots of new info on the website and more soon:
ssb2026.github.io
Follow for the latest updates!
@jembrown.bsky.social @systbiol.bsky.social
A Primer for Phylogenetic Causal Inference
with @oschwery.bsky.social & @pseudacris.bsky.social
Also, lots of new info on the website and more soon:
ssb2026.github.io
Follow for the latest updates!
@jembrown.bsky.social @systbiol.bsky.social
Not to shamelessly promote lab stuff, but if anyone is teaching evolution or phylogenetics, Karolis’ program has been great for students learning about trees. Its user interface is more like a basic calculator instead of a scientific calculator, which helps when learning. github.com/karolisr/tre...
GitHub - karolisr/treehouse: View and edit gene trees and phylogenies
View and edit gene trees and phylogenies. Contribute to karolisr/treehouse development by creating an account on GitHub.
github.com
August 15, 2025 at 4:17 PM
Not to shamelessly promote lab stuff, but if anyone is teaching evolution or phylogenetics, Karolis’ program has been great for students learning about trees. Its user interface is more like a basic calculator instead of a scientific calculator, which helps when learning. github.com/karolisr/tre...
Reposted by Joe Walker
#phylogenetics Mac users alert: TreeHouse opens trees with >500k+ tips and it is very FAST. The initial version can open, sort, root/unroot, & save multitree newick files (Nexus+ coming soon). Karolis is soliciting features. Apple-certified installer here: github.com/karolisr/tre...
Release v0.3.1 · karolisr/treehouse
This is very much a work in progress. Currently:
TreeHouse will only open files with .tre and .newick extensions, and will treat them as NEWICK (multi-tree files are supported). NEXUS support comi...
github.com
July 14, 2025 at 4:48 PM
#phylogenetics Mac users alert: TreeHouse opens trees with >500k+ tips and it is very FAST. The initial version can open, sort, root/unroot, & save multitree newick files (Nexus+ coming soon). Karolis is soliciting features. Apple-certified installer here: github.com/karolisr/tre...
Glad to see this work by @atyszka.org published, and excited to see the Field Museum on the front of Trends in Plant Sciences this month. Also, a great chance for the lab to collaborate with Drew Larson. www.cell.com/trends/plant...
Sequencing historical RNA: unrealized potential to increase understanding of the plant tree of life
Recent studies have demonstrated that it is a misconception that transcriptome sequencing
requires tissue preserved at ultracold temperatures. Here, we outline the potential
origins of this misconcept...
www.cell.com
July 2, 2025 at 2:43 PM
Glad to see this work by @atyszka.org published, and excited to see the Field Museum on the front of Trends in Plant Sciences this month. Also, a great chance for the lab to collaborate with Drew Larson. www.cell.com/trends/plant...
Reposted by Joe Walker
🚨 I’m thrilled to share that I am starting as an Assistant Professor at Wake Forest University this Fall!
👀 Opportunities coming soon as I re-root my research program in plant ecophysiology and evolution at Wake 🌿 🌲🌱
#NewPI #plantecophys #botany @wfubiology.bsky.social
@wakeforest.bsky.social
👀 Opportunities coming soon as I re-root my research program in plant ecophysiology and evolution at Wake 🌿 🌲🌱
#NewPI #plantecophys #botany @wfubiology.bsky.social
@wakeforest.bsky.social
June 30, 2025 at 12:55 PM
🚨 I’m thrilled to share that I am starting as an Assistant Professor at Wake Forest University this Fall!
👀 Opportunities coming soon as I re-root my research program in plant ecophysiology and evolution at Wake 🌿 🌲🌱
#NewPI #plantecophys #botany @wfubiology.bsky.social
@wakeforest.bsky.social
👀 Opportunities coming soon as I re-root my research program in plant ecophysiology and evolution at Wake 🌿 🌲🌱
#NewPI #plantecophys #botany @wfubiology.bsky.social
@wakeforest.bsky.social
Reposted by Joe Walker
Excited to share a new paper with Sandra Guerrero-Rubio and @docbroc.bsky.social on the convergent evolution of betalains, now published in @newphyt.bsky.social! nph.onlinelibrary.wiley.com/doi/10.1111/.... A 🧵
Multiple transitions to high l‐DOPA 4,5‐dioxygenase activity reveal molecular pathways to convergent betalain pigmentation in Caryophyllales
Many specialized metabolic pathways have evolved convergently in plants, but distinguishing multiple origins from alternative evolutionary scenarios can be difficult. Here, we explore the evolution .....
nph.onlinelibrary.wiley.com
May 6, 2025 at 12:24 PM
Excited to share a new paper with Sandra Guerrero-Rubio and @docbroc.bsky.social on the convergent evolution of betalains, now published in @newphyt.bsky.social! nph.onlinelibrary.wiley.com/doi/10.1111/.... A 🧵
Reposted by Joe Walker
New Postdoc position (2yrs) available in our #EvoMPMI lab @JohnInnesCentre. Come and work with on harnessing the diversity of immune mechanisms to protect plants. jobs.jic.ac.uk/Details.asp?va…
June 30, 2025 at 1:12 PM
New Postdoc position (2yrs) available in our #EvoMPMI lab @JohnInnesCentre. Come and work with on harnessing the diversity of immune mechanisms to protect plants. jobs.jic.ac.uk/Details.asp?va…
Reposted by Joe Walker
I’m extremely proud of all of our undergrads who undertook the difficult journey of producing scientific material and learning how to process transcriptomic data! Check out the culmination of our work on BioRxiv!! @evojfwalker.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Going green: Recycling transcriptomes to infer evolutionary relationships, gene duplication, gene tree conflict, and patterns of molecular evolution in the Apocynaceae
Background and Aims: The flowering plant family Apocynaceae exhibits diverse adaptations with biological and pharmaceutical significance, many of which have been studied with RNA-seq. However, despite...
www.biorxiv.org
June 27, 2025 at 5:06 AM
I’m extremely proud of all of our undergrads who undertook the difficult journey of producing scientific material and learning how to process transcriptomic data! Check out the culmination of our work on BioRxiv!! @evojfwalker.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
@shawn-anthony.bsky.social helped ~20 undergrads learn transcriptomics in this budget friendly investigation into the dogbane family. A fun way to investigate the molecular evolution of the group. Also, a chance to collaborate with @phylonatworks.bsky.social and Jarrad! doi.org/10.1101/2025...
Going green: Recycling transcriptomes to infer evolutionary relationships, gene duplication, gene tree conflict, and patterns of molecular evolution in the Apocynaceae
Background and Aims: The flowering plant family Apocynaceae exhibits diverse adaptations with biological and pharmaceutical significance, many of which have been studied with RNA-seq. However, despite...
doi.org
June 26, 2025 at 3:43 PM
@shawn-anthony.bsky.social helped ~20 undergrads learn transcriptomics in this budget friendly investigation into the dogbane family. A fun way to investigate the molecular evolution of the group. Also, a chance to collaborate with @phylonatworks.bsky.social and Jarrad! doi.org/10.1101/2025...
Reposted by Joe Walker
Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants
Very happy to share the published version of our work on natural Marchantia-Pseudomonas interactions.
Out now in Current Biology: www.cell.com/current-biol...
Very happy to share the published version of our work on natural Marchantia-Pseudomonas interactions.
Out now in Current Biology: www.cell.com/current-biol...
Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants
Robinson et al. identify pathogenic Pseudomonas viridiflava in wild Marchantia polymorpha
liverworts and interrogate the mechanisms enabling virulence in non-flowering and
flowering plants. Their resu...
www.cell.com
April 1, 2025 at 7:12 PM
Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants
Very happy to share the published version of our work on natural Marchantia-Pseudomonas interactions.
Out now in Current Biology: www.cell.com/current-biol...
Very happy to share the published version of our work on natural Marchantia-Pseudomonas interactions.
Out now in Current Biology: www.cell.com/current-biol...
Reposted by Joe Walker
I am honored to be elected an AAAS fellow! news.umich.edu/13-u-m-facul...
13 U-M faculty named as 2024 AAAS fellows
Thirteen University of Michigan faculty members earned election to the American Association for the Advancement of Science in 2024.
news.umich.edu
March 27, 2025 at 10:43 PM
I am honored to be elected an AAAS fellow! news.umich.edu/13-u-m-facul...
Reposted by Joe Walker
Are you analyzing genotype data via PCA or MDS, in particular including ancient DNA samples? Here is a novel easy-to-use tool to assess the stability of these analyses by bootstrapping the SNPs: academic.oup.com/bioinformati...
Pandora: A Tool to Estimate Dimensionality Reduction Stability of Genotype Data
AbstractMotivation. Genotype datasets typically contain a large number of single nucleotide polymorphisms for a comparatively small number of individuals.
academic.oup.com
March 6, 2025 at 4:04 PM
Are you analyzing genotype data via PCA or MDS, in particular including ancient DNA samples? Here is a novel easy-to-use tool to assess the stability of these analyses by bootstrapping the SNPs: academic.oup.com/bioinformati...
Reposted by Joe Walker
In recognizing that lots of students (undergrads and grads) are unaware of the dire situation created by the recent executive / DOGE actions, I am trying to compile a list of how these will impact folks so I can make materials and spread the word and get more advocates. 1/2
March 2, 2025 at 4:49 PM
In recognizing that lots of students (undergrads and grads) are unaware of the dire situation created by the recent executive / DOGE actions, I am trying to compile a list of how these will impact folks so I can make materials and spread the word and get more advocates. 1/2
Reposted by Joe Walker
🎙️Season 2 of our podcast is here! Kicking things off with the mind-blowing study below.
This research shatters the assumption that herbarium specimens are unsuitable for transcriptomics, successfully extracting mRNA from historical plant samples:
open.spotify.com/episode/1cqA...
This research shatters the assumption that herbarium specimens are unsuitable for transcriptomics, successfully extracting mRNA from historical plant samples:
open.spotify.com/episode/1cqA...
February 18, 2025 at 2:57 AM
🎙️Season 2 of our podcast is here! Kicking things off with the mind-blowing study below.
This research shatters the assumption that herbarium specimens are unsuitable for transcriptomics, successfully extracting mRNA from historical plant samples:
open.spotify.com/episode/1cqA...
This research shatters the assumption that herbarium specimens are unsuitable for transcriptomics, successfully extracting mRNA from historical plant samples:
open.spotify.com/episode/1cqA...
Reposted by Joe Walker
RNA from herbarium specimens is more stable than you think. Cool new study from @atyszka.org @evojfwalker.bsky.social and team. @khongsamchia.bsky.social and I were happy to contribute by functionally validating an NLR immune receptor last expressed in 1956 : www.biorxiv.org/content/10.1...
February 17, 2025 at 2:23 PM
RNA from herbarium specimens is more stable than you think. Cool new study from @atyszka.org @evojfwalker.bsky.social and team. @khongsamchia.bsky.social and I were happy to contribute by functionally validating an NLR immune receptor last expressed in 1956 : www.biorxiv.org/content/10.1...
Getting quality transcriptome assemblies from Herbarium samples is possible doi.org/10.1101/2025.... Work led by @atyszka.org. Another fun collaboration with @philcarella.bsky.social and @khongsamchia.bsky.social, who functionally validated an NLR immune receptor from a sample collected in 1956.
Herbaria provide a valuable resource for obtaining informative mRNA
While DNA has built the framework for molecular insights from museum collections, the utility of archival RNA remains largely unexplored. Likely a consequence of the known instability of RNA relative ...
doi.org
February 17, 2025 at 3:49 PM
Getting quality transcriptome assemblies from Herbarium samples is possible doi.org/10.1101/2025.... Work led by @atyszka.org. Another fun collaboration with @philcarella.bsky.social and @khongsamchia.bsky.social, who functionally validated an NLR immune receptor from a sample collected in 1956.
A former undergraduate, Miles Woodcock-Girard, made a transcriptome assembly pipeline (doi.org/10.1093/bioi...) and is looking for features people may want. He’s a big advocate for maintaining software, so please reach out to him on GitHub if there’s anything you would find helpful.
Semblans: automated assembly and processing of RNA-seq data
AbstractMotivation. Recent advancements in parallel sequencing methods have precipitated a surge in publicly available short-read sequence data. This has e
doi.org
February 12, 2025 at 3:57 PM
A former undergraduate, Miles Woodcock-Girard, made a transcriptome assembly pipeline (doi.org/10.1093/bioi...) and is looking for features people may want. He’s a big advocate for maintaining software, so please reach out to him on GitHub if there’s anything you would find helpful.
Reposted by Joe Walker
Very happy to share the final version of our work on the evolution of broad host virulence in Pseudomonas out now @cellhostmicrobe It’s just in time for the holidays 🎄🦠 www.cell.com/cell-host-mi...
A necrotizing toxin enables Pseudomonas syringae infection across evolutionarily divergent plants
Grenz et al. interrogate the Pseudomonas syringae species complex for its capacity to infect evolutionarily divergent host plants. Their results demonstrate that broad host isolates from phylogroup 2 rely on the lipopeptide toxin syringomycin to promote host necrosis and enhance bacterial growth in plants.
www.cell.com
December 19, 2024 at 4:10 PM
Very happy to share the final version of our work on the evolution of broad host virulence in Pseudomonas out now @cellhostmicrobe It’s just in time for the holidays 🎄🦠 www.cell.com/cell-host-mi...
Reposted by Joe Walker
New pre-print from the lab on the natural history, phylogenomics, and allopolyploidy of North American Drosera. This work was from the pre-COVID field work graduate student Rebekah Mohn did in peatlands across the US and fell into muddy pits many, many times.
January 23, 2025 at 3:28 PM
New pre-print from the lab on the natural history, phylogenomics, and allopolyploidy of North American Drosera. This work was from the pre-COVID field work graduate student Rebekah Mohn did in peatlands across the US and fell into muddy pits many, many times.