Ben Williams (@WilliamsSci) header
Ben Williams (@WilliamsSci) profile picture

Ben Williams

@WilliamsSci

Assistant Professor @PMB_Berkeley. Fascinated by epigenetics, evolution, genomes, and all aspects of plant biology.

 Berkeley, California
williamsplantlab.com/
Joined February 2013
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Everyone watch this space regarding DNA methlyation and memory. Shawn knows his stuff -- and the genetic evidence is hard to argue with!!
Shawn Liu (@ShawnLiu_Lab) profile pictureShawn Liu@ShawnLiu_LabOct 30
Ever wonder how memory is consolidated during sleep at the molecular level? We reported Sleep-dependent DNA methylation remodeling in basolateral amygdala to consolidate fear memory. Check out the paper by Dr Tracy Chen from our labs! sciencedirect.com/science/ar…
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Excited to post my lab's latest pre-print, led by the phenomenal Anna Dmitrieva! Anna asked the question - what happens to epigenetic inheritance when you lose (almost) all DNA demethylation activity? biorxiv.org/content/10.64898…
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So without demethylases, the DNA methylation pathways (especially RdDM) clearly create an unstable system. I don't think that last sentence was particularly surprising/new, but I was surprised to see how dramatic the instability is
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This is not "a few epimutations here and there" levels of instability. It's "drift towards death within 10 generations" levels of instability
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We could all save ourselves so much time... Imagine you submit a paper and within 24h you have reasonable and thorough reviews. We all know humans can be bad reviewers and that there is huge variance in review quality. Time to embrace the future!
Ruslan Rust (@rust_ruslan) profile pictureRuslan Rust
@rust_ruslanOct 28
Lots of debate this week on whether journals should ban AI in peer review. We actually tested this in our new preprint, and the results were pretty clear to me. For context, I've reviewed for most of the big journals and evaluated 1,000 human reviews as an editor. I love to read and evaluate science. TLDR: From now on I won't do any peer review without AI. For clinical trials, I'd even call human-only review dangerous 🧵
Image from Ruslan Rust (@rust_ruslan)
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Ben Williams retweeted
Marina Oliva (@molivarina) profile picture
Marina Oliva@molivarinaOct 22
Are plant roots really made up of concentric layers of homogeneous, differentiating cell types? In our new study, out now in @Nature, we show a more complex picture: two distinct cell states within root lineages, shaped in part by the environment. 🧵👇 nature.com/articles/s41586-0…
An environmentally regulated dichotomy in cell lineages of the root

An environmentally regulated dichotomy in cell lineages of the root

Nature - An environment-regulated state is identified across multiple cell types at the root tip, revealing a shared dichotomy between cells with and without this state.

nature.com
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In the LLM era systematic literature reviews by humans may become obsolete, but my lab still believes forward-thinking and thought-provoking opinion papers will be very valuable, so we wrote one!
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In our new Current Opinion paper, we pull together a few strands of research on the scenarios in which epigenetic fidelity is compromised in plants & what this might mean for gene editing and crop improvement sciencedirect.com/science/ar…
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For busy people, it's a short read and at the very least can point you towards some papers that are influencing our thinking. For anyone interested or frustrated by tissue culture, transformation or somaclonal variation - it's worth reading!
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Dogs lose methylation at transposons during aging - just like plants :) science.org/doi/10.1126/scie…
Epigenetic aging and transposon dysregulation reflect size-related lifespan compression in dogs

Epigenetic aging and transposon dysregulation reflect size-related lifespan compression in dogs

The extraordinary lifespan variation in domestic dogs provides a natural experiment for testing how intrinsic rates of biological aging shape lifespan. Using 1640 methylomes from 894 dogs, we...

science.org
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I like the paper and don't want to be too critical... but how can "promoters lose methylation during age" make it to the abstract when the data looks like this (blue = regions that lose methylation, purple = gain methylation):
Image from Ben Williams (@WilliamsSci)
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Seems to happen all the time in the epigenetics field where we pick one-sentence conclusions (e.g. mark X represses transcription) that are just not backed up by the complexity we see in reality
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André Marques (@marques_et_al) profile picture
André Marques@marques_et_alSep 16
Out today in Nature: sex without crossovers. Rhynchospora tenuis makes pollen, fertilises and sets seed, yet 0 crossovers in 10,997 pollen nuclei. Chromosome drive and ~87% seed abortion rebuild the mother's genotype, so the offspring are clones. doi.org/10.1038/s41586-026-1…
Image from André Marques (@marques_et_al)
André Marques (@marques_et_al) profile pictureAndré Marques@marques_et_alJan 27
A new extreme of meiotic evolution: ✔️ no crossovers ✔️ no gene conversion ✔️ normal meiosis & fertility Sex mimics clonality without becoming asexual, in the holocentric multicellular eukaryote 𝘙𝘩𝘺𝘯𝘤𝘩𝘰𝘴𝘱𝘰𝘳𝘢 𝘵𝘦𝘯𝘶𝘪𝘴. more about it: biorxiv.org/content/10.64898…
Image from André Marques (@marques_et_al)
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Completely anecdotal of course but even in the last ~6 years I've noticed a shift from students that approach questions primarily with a "forward-genetic dissection" lens to students whose whole outlook is to approach problems with omics
NIMI VASHI (bio/acc to infinity & beyond) (@nimivashi15) profile pictureNIMI VASHI (bio/acc to infinity & beyond)
@nimivashi15Sep 2
Unpopular opinion: the age of omics and high throughput data in Biology took us away from very good fundamental questions. The omics failed to have outsized returns as they were thought to and now we have a generation that’s trained to not think simple.
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Come and join our department!! We are hiring for a tenure track Assistant Professor studying Plant Responses to Environmental Changes. Please share!! aprecruit.berkeley.edu/JPF05…
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Ruslan Rust (@rust_ruslan) profile picture
Ruslan Rust
@rust_ruslanJul 1
How much does a scientific claim actually change between the preprint and the final published paper? We used a large language model to track it across all available 72,644 bioRxiv -> journal pairs from 2018 - 2025 in this new work with @HaoYin. 🧵
Image from Ruslan Rust (@rust_ruslan)
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