Gavin Woodruff
@weirdworms.bsky.social
๐ค 728
๐ฅ 1139
๐ 343
Development, evolution, worms, gene name etymology. I log interesting papers, questions, and ideas.
Comparative transcriptomics reveals an extracellular worm Argonaute as an ancestral regulator of LTR retrotransposons
academic.oup.com/gbe/advance-...
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Comparative transcriptomics reveals an extracellular worm Argonaute as an ancestral regulator of LTR retrotransposons
Abstract. Safeguarding the genome from non-self elements is essential for development, reproduction, and ageing. One of the major threats to genomic integr
https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evag117/8672763
1 day ago
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Joanna Masel
3 days ago
Our paper unpacking "fitness" is out
doi.org/10.1093/gene...
. How to define fitness depends on what question you ask. Selection acts on organismal vital rates, longer-term outcomes make sense for genetic lineages, models link them. "Invasion fitness" = speed, but sometimes probability matters more.
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๐ Actually, what is a gain-of-function mutation?
doi.org/10.1093/gene...
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Actually, what is a gain-of-function mutation?
Abstract. For more than a century, scientists have worked to characterize, understand, and predict the consequences of mutations. For almost as long, scien
https://doi.org/10.1093/genetics/iyag059
3 days ago
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Jordan Theriault
4 days ago
Put simply: It coordinates action in more varied and context-dependent ways across more complex environments, AND it regulates a more complex internal environment. Highly recommend this chapter from Sterling and Laughlin!
link.springer.com/article/10.1...
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Why an animal needs a brain - Animal Cognition
In Principles of Neural Design (2015, MIT Press), inspired by Charles Darwin, Sterling and Laughlin undertook the unfashionable task of distilling principles from facts in the technique-driven, data-s...
https://link.springer.com/article/10.1007/s10071-023-01825-7
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Richard Lenski
7 days ago
New book "A Primer for Experimental Evolution" with coauthors Michael Rose, Margarida Matos, and Joe Graves.
www.worldscientific.com/worldscibook...
A compact primer for students and colleagues interested in planning and designing experiments to address questions in evolutionary biology.
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A Primer for Experimental Evolution
https://www.worldscientific.com/worldscibooks/10.1142/14651#t=aboutBook
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Microbial genetic screen identifies bacterial genes that compromise Caenorhabditis elegans reproductive fitness
journals.asm.org/doi/full/10....
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Microbial genetic screen identifies bacterial genes that compromise Caenorhabditis elegans reproductive fitness | mSystems
This study identifies a direct causal link between a specific bacterial gene and host reproductive fitness. Systematic screening of Escherichia coli mutants showed that deleting one gene severely impa...
https://journals.asm.org/doi/full/10.1128/msystems.01698-25
7 days ago
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Gavin Woodruff
Mart Krupovic
7 days ago
With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the
#virosphere
. We describe all 10 viral realms and the logic behind them, and so much more. Check it out!
comptes-rendus.academie-sciences.fr/biologies/ar...
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Ashar Malik
9 days ago
New work: Our earlier work showed that Foldseek characters could be adapted for phylogenetic alignment, treating each character as an evolutionary state. That part holds but there's a hidden assumption baked in that needed unpacking. So lets do that.๐งต
#StructuralPhylogenetics
#Evolution
#Protein
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Internalized Evolutionary Inertia on Body Plan Evolution
onlinelibrary.wiley.com/doi/10.1111/...
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Internalized Evolutionary Inertia on Body Plan Evolution
Animal development appears to intrinsically bias phenotypic evolution, though the exact mechanism is unclear. This review discusses potential mechanisms by which animal embryogenesis limits phenotypi...
https://onlinelibrary.wiley.com/doi/10.1111/ede.70041
10 days ago
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Cathepsin B protease mediates high population density-induced mutagenesis to drive genome evolution and competitive growth
www.nature.com/articles/s41...
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Cathepsin B protease mediates high population density-induced mutagenesis to drive genome evolution and competitive growth - Nature Communications
Density-dependent population regulation is widespread in animals. Here, the authors identify cathepsin B cysteine protease as a crowd-responding factor that induces increased genome mutagenesis, leadi...
https://www.nature.com/articles/s41467-026-72521-6
10 days ago
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WormTagDB: a systematic survey of endogenously tagged proteins in Caenorhabditis elegans and roadmap toward the tagged proteome
academic.oup.com/g3journal/ad...
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WormTagDB: a systematic survey of endogenously tagged proteins in Caenorhabditis elegans and roadmap toward the tagged proteome
Abstract. Endogenous protein tagging in Caenorhabditis elegans enables the direct visualization and manipulation of proteins in vivo, providing native read
https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag068/8539546
10 days ago
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Differential Phoretic Vector Use Among Sympatric Caenorhabditis Nematodes and an Association With Invasive Nitidulid Beetles in Southwestern Germany
onlinelibrary.wiley.com/doi/full/10....
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Differential Phoretic Vector Use Among Sympatric Caenorhabditis Nematodes and an Association With Invasive Nitidulid Beetles in Southwestern Germany
We show evidence for differential host use among the three sympatric Caenorhabditis, and a novel association with nitidulid beetles for C. apta sp. n. This information adds to our understanding of ho...
https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.73510
10 days ago
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Jeremy S Davis
12 days ago
7 years ago I was incredibly lucky to join
@hoosierflyman.bsky.social
on the great
#Seabattical
Today, you can read in full print
@genetics-gsa.bsky.social
the description of a NEW SPECIES of Drosophila parasitoid and it's really unique biology. I just happened to be the guy who found it! ๐๐๏ธ๐ชฐ
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! High-resolution global recombination mapping in C. elegans reveals sexual dimorphisms shaped by meiotic chromosomal features and structures
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.04.25.720830v1.abstract
12 days ago
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Ali Seleit
13 days ago
(1/15) Thrilled to share new Evo-Devo work where we address the molecular, cellular & morphometric basis of an extreme axis segmentation program in the Japanese eel โ an animal that forms 120 vertebrae.
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https://www.biorxiv.org/content/10.64898/2026.04.29.721344v1
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Marcus Stensmyr
13 days ago
Here is a banger! Our new paper in
@currentbiology.bsky.social
is out! We have used museomics to sequence a 45yr old specimen of Drosophila enhydrobia, a rare and most unusual fly whose larvae are aquatic(!) and predatory(!). Very cool, big success.
authors.elsevier.com/sd/article/S...
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16 days ago
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Kinetochore proteins control microtubule dynamics in postmitotic neurons to regulate the formation of dendritic spines
www.pnas.org/doi/full/10....
17 days ago
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Developmental constraints in the repeated evolution of male tail characters in rhabditid and diplogastrid nematodes
journals.plos.org/plosone/arti...
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Developmental constraints in the repeated evolution of male tail characters in rhabditid and diplogastrid nematodes
A longstanding question in evolutionary biology is how change might be restricted or biased due to developmental constraints. To address this question, we investigated three recurrently evolving chara...
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0348186
17 days ago
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A Trojan horse pathogen breaking through partner-choice barriers in the insect gut
doi.org/10.1073/pnas...
17 days ago
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Chromosome size as a robust predictor of recombination rate: insights from holocentric and monocentric systems
academic.oup.com/genetics/art...
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Chromosome size as a robust predictor of recombination rate: insights from holocentric and monocentric systems
Abstract. Recombination is a fundamental evolutionary process essential for generating genetic diversity, facilitating adaptation, and driving speciation.
https://academic.oup.com/genetics/article/232/1/iyaf247/8321416
17 days ago
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Dr. Brendan "Doesn't-go-to-Ravenholm" Pinto
19 days ago
Happy to announce two-fold news! 1) The SCINKD paper is now published in
@molbioevol.bsky.social
-
doi.org/10.1093/molb...
2) SCINKD [v2.2.4] release has reduced runtimes (about 2x) and the revitalized mode for genomes >5Gb is now live and tested on genomes up to 21Gb! ๐ธ
github.com/DrPintoThe2n...
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Sex chromosome identification and genome curation from a single individual with SCINKD
Abstract. In most animal species, the sex-determining pathway is typically initiated by the presence/absence of a primary genetic cue at a critical point d
https://doi.org/10.1093/molbev/msag067
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Gavin Woodruff
Srinivas Lab
19 days ago
We are happy to share our new bioRxiv pre-print on A-P axis patterning. A great collaboration with Felix Zhou (UT Southwestern) & the Yeomans group (Physics, Oxford)
www.biorxiv.org/content/10.6...
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EvoDevo PanAm
25 days ago
โจA central mission of PASEDB is to foster networking, discussion, and a sense of community We want to highlight new
#EvoDevo
labs in Pan-America. In our first newsletter issue, we highlight: - Roberto Mรกrquez - Anyi Mazo-Vargas
@anyimv.bsky.social
- Bruno Vellutini
@bruvellu.bsky.social
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Looking at the EvoWorm 2026 abstracts--I'm getting excited about this meeting!!
27 days ago
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Transgenerational inheritance is variable across Caenorhabditis worms
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.04.10.717426v1.abstract
27 days ago
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Global genomic diversity of the selfing nematode Caenorhabditis tropicalis correlates with geography
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.04.05.716573v1.abstract
27 days ago
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! Epigenetic constraints and enhancer innovation link neuronal plasticity to evolutionary adaptation
www.pnas.org/doi/abs/10.1...
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Epigenetic constraints and enhancer innovation link neuronal plasticity to evolutionary adaptation | PNAS
How nervous systems balance the generation of robust neuron types with gene expression plasticity mechanisms and how these processes impact cell-ty...
https://www.pnas.org/doi/abs/10.1073/pnas.2524709123
about 1 month ago
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Gavin Woodruff
Jason Rasgon
about 1 month ago
WAT
www.science.org/doi/10.1126/...
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Science | AAAS
https://www.science.org/doi/10.1126/science.aed1656
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The abstract submission deadline for EvoWorm 2026 is today! Don't forget to submit an abstract!! Share your exciting science at *the* best meeting!!!
evoworm.org
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about 1 month ago
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Are you ready for *the* meeting about the evolutionary biology of Caenorhabditis and other nematodes? The abstract deadline is Wednesday! EvoWorm 2026 will be held at McMaster University from June 16โ19 Abstract deadline: April 15 Registration deadline: June 1 Details can be found at
evoworm.org
about 1 month ago
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Optimal male fertility and fecundity in Caenorhabditis elegans requires Microprocessor and Argonaute gene function
academic.oup.com/g3journal/ad...
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Optimal male fertility and fecundity in Caenorhabditis elegans requires Microprocessor and Argonaute gene function
Abstract. Small RNA pathways play key roles in the regulation of gene expression in the germ line and in somatic cells. The germ line in Caenorhabditis ele
https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag079/8578691
about 1 month ago
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Caenorhabditis elegans populations shape their microbial environment
www.nature.com/articles/s41...
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Caenorhabditis elegans populations shape their microbial environment - npj Biofilms and Microbiomes
npj Biofilms and Microbiomes - Caenorhabditis elegans populations shape their microbial environment
https://www.nature.com/articles/s41522-026-00975-z
about 1 month ago
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Gavin Woodruff
bioRxiv Neuroscience
about 1 month ago
Whole-organism spatial transcriptomics at single-cell resolution in C. elegans
https://www.biorxiv.org/content/10.64898/2026.04.09.717568v1
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Analysis of Nematode Ventral Nerve Cords Suggests Multiple Instances of Evolutionary Changes to Neuron Number
onlinelibrary.wiley.com/doi/10.1111/...
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Analysis of Nematode Ventral Nerve Cords Suggests Multiple Instances of Evolutionary Changes to Neuron Number
โAnalysis of Nematode Ventral Nerve Cords Suggests Multiple Instances of Evolutionary Addition and Loss of Neuronsโ Han et al. DAPI staining of Xiphinema sp. (Clade 2) highlighting the neuronal-like ...
https://onlinelibrary.wiley.com/doi/10.1111/ede.70037
about 1 month ago
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Gavin Woodruff
Sean Bresnahan
about 2 months ago
๐ It's published! Our placental long-read transcriptome is now in
@natcomms.nature.com
! Thank you to
@arjunbhattac.bsky.social
,
@jonhuang.bsky.social
, and
@mikelove.bsky.social
for collaborating on this first project of my postdoc
@mdanderson.bsky.social
. A recap ๐งฌ๐ซ๐งต
www.nature.com/articles/s41...
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Gavin Woodruff
Trends in Genetics
about 1 month ago
"Complexity and Innovation in Carnivorous Plant Genomes" by Victor A. Albert et al. "Here, we review recent research that has uncovered some of the more interesting genomic oddities and specializations among carnivorous plants..." FREE till May 26th at
authors.elsevier.com/a/1muZP_3rsx...
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Gavin Woodruff
Will Ratcliff
about 1 month ago
1/25 New paper out in PNAS! We show that the fitness costs of reproductive specialization, where somatic cells give up reproduction, scale inversely with organism size. Larger organisms can afford far more soma, removing a key barrier to multicellular complexity.
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The fitness costs of reproductive specialization scale inversely with organismal size
https://www.pnas.org/doi/epdf/10.1073/pnas.2536055123
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Rethinking mitochondrial heteroplasmy: selection, conflict and adaptation
royalsocietypublishing.org/rstb/article...
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Rethinking mitochondrial heteroplasmy: selection, conflict and adaptation
Abstract. Mitochondrial DNA (mtDNA) variation is increasingly recognized for its role in shaping evolutionary changes at the species and population levels.
https://royalsocietypublishing.org/rstb/article/381/1947/20250079/481187
about 1 month ago
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Gavin Woodruff
Needhi Bhalla ๐ ๐ฝ
about 2 months ago
The two papers:
www.science.org/doi/10.1126/...
and
www.science.org/doi/10.1126/...
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Gavin Woodruff
Olivia Ghosh
about 2 months ago
Really excited that this major work from my PhD is finally published in
@plosbiology.org
! In it, we were trying to tackle a fundamental question in evolution - how do genetic mutations map onto evolutionary fitness? (1/n)
journals.plos.org/plosbiology/...
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Genotype-fitness mapping of adaptive mutants reveals shifting low-dimensional structure across divergent environments
Predicting the effect of a genetic mutation on fitness is a major challenge in evolutionary biology. This study uses fitness effects of a large collection of adaptive yeast mutants in multiple lab env...
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003618
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Gavin Woodruff
Enrico Sandro Colizzi
about 2 months ago
How common is multicellularity in bacteria? And archaea? And how does it evolve? We wrote a short review "On the architecture and evolution of prokaryotic multicellularity". Preprint link:
bit.ly/4ta06Gq
Sharing and comments are much appreciated. 1/4
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Reconsidering cytonuclear discordance in the genomic age
academic.oup.com/evolut/artic...
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Reconsidering cytonuclear discordance in the genomic age
Abstract. Historically, phylogenetic datasets had relatively few loci but were over-represented for cytoplasmic sequences (mitochondria and chloroplast) be
https://academic.oup.com/evolut/article/80/1/1/8276722
about 2 months ago
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Gavin Woodruff
Dmitri Petrov
about 2 months ago
A question for biologists: we often talk about evolutionary novelty. What does โnoveltyโ mean for you? Whatโs your favorite definition if any? Or just a rule of thumb for what is and isnโt novel.
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Gavin Woodruff
Roli Roberts
about 2 months ago
Back in the noughties when I was an academic, my lab did quite a bit of work on (conserved) alternative transcripts. This study in
@plosbiology.org
presents compelling evidence that most alternative transcripts are deleterious noise
journals.plos.org/plosbiology/...
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Transcript diversity reflects deleterious RNA processing errors shaped by population size in metazoans
Alternative transcription initiation, splicing and polyadenylation generate extensive transcript diversity in eukaryotes, but its evolutionary significance has been disputed. This study analyses 166 t...
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003671
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Intraspecific variation in the duration of epigenetic inheritance in wild isolates of C. elegans
www.cell.com/current-biol...
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Intraspecific variation in the duration of epigenetic inheritance in wild isolates of C. elegans
Frejacques, Saglio, et al. demonstrate variation among C. elegans wild isolates in the multigenerational memory of an initial RNA interference trigger. Genetic polymorphisms and environmental variable...
https://www.cell.com/current-biology/abstract/S0960-9822(26)00227-7
about 2 months ago
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Tissue-specific DNA Repair Strategies Underlie Apparent High Transposon Activity in the C. elegans Soma
academic.oup.com/g3journal/ad...
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Tissue-specific DNA Repair Strategies Underlie Apparent High Transposon Activity in the C. elegans Soma
Abstract. Transposons are parasitic nucleic acids that threaten genome integrity in all organisms. DNA transposons mobilize via a cut-and-paste mechanism,
https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag054/8527922
about 2 months ago
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Gavin Woodruff
Joshua Weitz
2 months ago
The data is in: the NIH goalposts have shifted. What were once almost certain fundable scores have become coin flips and what used to be likely grants have become aspirational, leading to fewer awards. Another manifestation of how HHS policies have led to fewer awards and less science.
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Gavin Woodruff
Sasha Gusev
2 months ago
Here is the "effective payline" for each institute, estimated (by Claude) as the percentile where one can expect 80% probability of funding from a logistic regression fit. The effective payline has gone from a historic ~12% to 6% in 2025.
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Cells & Development
2 months ago
Two complementary articles from the lab of Anming Meng and Katie McDole discussing the history and biology of organizer in ๐, ๐ธ, and ๐ญ. Even after more than 100 years since its discovery, major questions remain, especially for mammals.
doi.org/10.1016/j.cd...
doi.org/10.1016/j.cd...
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