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Elizabeth McDaniel

@lizilla93.bsky.social
412 followers 486 following 44 posts

Scientist passionate about bioinformatics, microbes, and open science. She/her elizabethmcdaniel.com

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Reposted by Elizabeth McDaniel
Claus Wilke @clauswilke.com · 02/07/2025
Now published: Systematic comparison of protein language models for transfer learning. Key points: - You don't need gigantic models. The two smaller ESM C variants work great. - There is huge variability in performance across datasets. We have no idea why. www.nature.com/articles/s41...
Fig. 3 from the paper, showing that model performance levels off around 300M parameters and ESM C variants tend to outperform the other available protein language models.Figure 5 from the paper, showing a wide range of model performance across datasets, with R^2 values ranging from 0.1 to 0.8. Only a small fraction of this variation is explained by either dataset size or protein length.
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Sean Gibbons 🦠💩 @gibbological.bsky.social · 02/07/2025
I started a personal #Substack to cultivate my creative writing skills. Let's see how it goes. Opinions are my own. The first essay: why I think it's probably a bad idea to give 80-year-olds fecal transplants from 20-year-olds. gibbological.substack.com/p/what-the-m... Subscribe if, you're into it
open.substack.com
What the microbiome teaches us about aging gracefully...
...and why we shouldn't necessarily 'turn back the clock'
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Tressie McMillan Cottom @tressiemcphd.bsky.social · 03/06/2025
The way people are talking about the current demolition of research funding and HE legitimacy reminds me of the early days of COVID when I (and others) said it would be at least six years before any normalcy. Rage, despondency, rejection…eventually voting for a dictator just to feel alive.
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Jim Musil Painter @jimmusilpainter.bsky.social · 26/05/2025
My painting WISCONSIN FARM
An acrylic painting by Jim Musil depicting a farm in Wisconsin. A red barn sits at the end of a dirt road in the middle of a verdant green field. A colorful sky dominates the composition.
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Mark Harris @markharris.bsky.social · 14/04/2025
I hate to be that guy, but this is the five-alarm fire, and every elected Democrat and frankly, every Washington reporter should be ringing the bell. If it can happen to him, it can happen to anyone. Nobody with a voice should give this administration a moment’s peace about it.
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Hunter Walker @hunterw.bsky.social · 02/04/2025
In his 1957 filibuster, Strom Thurmond said "Negroes ... are not so well qualified to vote as are the white people.” A Black senator just broke the record Thurmond set with that speech. talkingpointsmemo.com/news/cory-bo...
talkingpointsmemo.com
Cory Booker Just Gave The Longest Speech In The History of The US Senate
Only two men have spoken on the floor of the U.S. Senate...
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Barack Obama @barackobama.bsky.social · 25/03/2025
Right now, there’s an important race happening that will shape the Wisconsin Supreme Court for the next 10 years. Judge Susan Crawford is ready to protect the fundamental rights and freedoms of all Wisconsinites. Make a plan to vote early today — don’t wait until April 1st: wisdems.org/vote
wisdems.org
Find Your Voting Locations | WISDEMS Voter Protection Team
This searchable map shows you early voting and dropbox info for hundreds of villages, towns, and cities across Wisconsin. Enter the address you're registered at and your options will pop up!
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Jacquelyn Gill @jacquelyngill.bsky.social · 16/03/2025
This is so evil that it defies understanding. A transplant surgeon on an H1B visa was deported, despite a court injunction. She had committed no crimes. This must stop. We must stand together to protect immigrants and visitors against state terrorism. www.providencejournal.com/story/news/l...
providencejournal.com
Brown Medicine doctor deported despite federal court order. What we know.
A court order that would have delayed the deportation of Dr. Rasha Alawieh was issued while her plane was on the tarmac, but it took off anyway.
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Hensley Lab @scottehensley.bsky.social · 13/03/2025
Today @natmedicine.bsky.social published our study showing the older individuals born prior to 1968 have more antibodies that cross-react to #H5N1 relative to younger individuals. If H5N1 causes a pandemic, children will likely be the most susceptible. 1/2 www.nature.com/articles/s41...
nature.com
Immune history shapes human antibody responses to H5N1 influenza viruses - Nature Medicine
H5N1 strain-specific antibodies are higher in older individuals and correlate more with birth year than with age, suggesting that younger individuals are potentially more likely to benefit from H5N1 v...
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Elizabeth McDaniel @lizilla93.bsky.social · 13/03/2025
My college symphony orchestra director Dr. Robert Mueller passed away last week, and he was an incredibly passionate musician and teacher. Some of my most cherished memories were very small acts of kindness on his behalf. He will be incredibly missed. news.uark.edu/articles/769...
news.uark.edu
Department of Music Mourns Passing of Robert Mueller; Memorial Scheduled for March 12
Professor Robert Kent Mueller, a beloved member of the U of A community for 37 years, died March 6. A visitation will be held today at Good Shepherd Lutheran Church with a memorial on Wednesday.
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Stephen Turner @stephenturner.us · 07/03/2025
geneviewer - Gene Cluster Visualizations in R. Imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. github.com/nvelden/gene... #Rstats
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Carl Zimmer @carlzimmer.com · 05/03/2025
I'm on the new episode of Tyler Cowen's podcast talking about AIR-BORNE, plus some of my other books. Listen here: conversationswithtyler.com/episodes/car...
conversationswithtyler.com
Carl Zimmer on the Hidden Life in the Air We Breathe (Ep. 235)
From the mysteries of airborne disease to the search for extraterrestrial life, what are we missing about the unseen world around us?
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Sarah Karlin-Smith @sarahkarlin-smith.bsky.social · 26/02/2025
Breaking: FDA's March meeting to select flu shot strains for 2025-2026 season has been canceled per email sent to committee members, a VRBPAC member told me. drug companies need about 6 months leeway to make shots in time for fall vax campaigns. #healthpolicy
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Science Friday @scifri.bsky.social · 23/02/2025
Last October, we took a trip to the World Forestry Center in Portland, Oregon, for a daylong exploration of lichen—the fuzzy growths often found on trees, roofs, and gravestones. Two experts joined us to discuss the fascinating world of lichen and their role in a changing climate.
buff.ly
What Lichen Tell Us About Ecology, Air Quality, And More
Ira is joined on stage by experts in Portland, Oregon, to talk about the amazing world of lichen and their role in a changing climate.
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Michael Baym @baym.lol · 21/02/2025
Legitmately thrilled to share our latest work, in which @fernpizza.bsky.social solved an experimental challenge in plasmid biology as old as the field: measuring how plasmids compete and evolve within individual cells!
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Ameet Pinto @watermicrobe.bsky.social · 06/01/2025
I had the pleasure of being interviewed by @markowenmartin.bsky.social on his Fantastic "Microbial Matters" podcast about my group's work on the #drinkingwatermicrobiome. You can watch it here. www.youtube.com/watch?v=JDAU...
youtube.com
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Ferris Jabr @ferrisjabr.bsky.social · 06/01/2025
In winter through early spring, you can sometimes find unspoiled, still-bright groundcherries sitting in the latticed remnants of their husks, like hearts suspended in paper ribcages
A photo of groundcherries (Alkekengi) in a garden in winter. The round, orange, cherry tomato-like fruits are suspended in the center of pendulous, vaguely heart-shaped husks made of networks of dried beige veins. The husks have a delicate, skeletal, lattice-like structure, reminiscent of laser-cut papercraft.
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Ákos T Kovács @evolvedbiofilm.bsky.social · 05/01/2025
Ten species comprise half of the bacteriology literature, leaving most species unstudied @biorxiv-microbiol.bsky.social by Paul A Jensen www.biorxiv.org/content/10.1... B. subtilis is #6 😍, anyhow, the literature is biased to models Would publications on plants or animals be similarly biased?
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Stephen King @stephenking.bsky.social · 01/01/2025
There are really only two "mystery box" shows that I felt were worth my time last year and this coming year (for "mystery box shows," think LOST): FROM and SILO. As always, your mileage may differ.
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The Trandalorian @charliejaneanders.com · 30/12/2024
We're doing an *emergency* Bookstore and Chocolate Crawl on Saturday Jan. 11. We'll visit Medicine For Nightmares and Adobe, which suffered massive flood damage recently. Then we'll hit East Bay Booksellers, recovering from a fire. Plus Pegasus! Details/RSVP: www.eventbrite.com/e/emergency-...
eventbrite.com
EMERGENCY Bookstore and Chocolate Crawl!
We're calling on you to help two bookstores that were flooded in recent storms, plus another bookstore that just reopened after a nasty fire
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Works in Progress @worksinprogress.bsky.social · 05/12/2024
Our latest issue is now out! - Animals as chemical factories - How housing shortages cause homelessness - Where the glamour of progress went - How big data created the modern dairy cow - Urbanist cruise ships - Functionalism - How Madrid built its Metro
worksinprogress.co
Home - Works in Progress
Works in Progress is an online magazine dedicated to sharing new and underrated ideas to improve the world, and features original writing from some of the most interesting thinkers in the world.
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Jonathan Eisen @phylogenomics.bsky.social · 28/12/2024
Well, this was a bit surprising. First, I have been going to Yolo Bypass near Davis, CA very very often and always dream of getting a good raptor pic with the "Hunter Check Station" sign. And I got one today of a kestrel sitting on that sign. Yes, this is a hunter check station.
Picture of an American Kstrel holding something in its talons while perched on a large rectangular wooden sign that reads "HUNTER CHECK STATION" in large yellow letters. The sign also has a yellow arrow pointing up. There is blue sky behind the sign and kestrel at the top of the picture and brown platns / grasses behind the sign in the lower part of the picture. The sigs woos is mostly dark brown with some lighter regions. The sign is held up by two large wooden posts at each end.
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Dmitri Petrov @petrovadmitri.bsky.social · 26/12/2024
It is that time of the year again when @odedrechavi.bsky.social and I do our annual “your favorite paper of the year” thread. Now only on Bluesky! Please link to your favorite paper in the comments and say a few words why you loved it so much. Happy holidays and happy reading!
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Elizabeth McDaniel @lizilla93.bsky.social · 15/12/2024
A Saturday full of knitting, cat snuggles, and the NCAA Women's Volleyball tournament.
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Reposted by Elizabeth McDaniel
Michael Fischbach @mfgrp.bsky.social · 11/12/2024
Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55
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Saloni @scientificdiscovery.dev · 09/12/2024
New post: My substack is back, finally! I meant to keep this to 1,000 words but I failed. In any case, here's a round up of 5 major medical breakthroughs in 2024.
scientificdiscovery.dev
Five medical breakthroughs in 2024
It's December, and time for a retrospective on some breakthroughs in medical innovation this year.
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Elizabeth McDaniel @lizilla93.bsky.social · 09/12/2024
"Science (and other creative endeavors) are rather like animal life in a Darwinian world. There are many more ways to be dead than alive...To succeed—more exactly, to not yet have failed—is to still be in the game; to flourish is simply to not yet to be extinct."
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Bird account @dialecticbio.bsky.social · 02/12/2024
Nitrogenase structural evolution across Earth’s history www.biorxiv.org/content/10.1... Huge paper in protein evolution!
Figure 1. Overview of the methodological pipeline for massive protein structure prediction and experimental crystallographic analysis of extant and ancestral nitrogenase enzymes.Figure 3. Nitrogenase structure variation in a phylogenetic context.Figure 4. Phylogenetic patterns of nitrogenase structural attributes calculated across DDKK proteins.
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 23/11/2024
Our Big Fantastic Virus Database (BFVD) is now published NAR! It contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web. 🌐 bfvd.foldseek.com 💾 bfvd.steineggerlab.workers.dev 📄 academic.oup.com/nar/advance-...
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Ray Newman @raynewman.bsky.social · 03/12/2024
I really need to get better at finding pleasure in being alive and simply existing, rather than constantly thinking "If I can just get through this ordeal..." and "If I can just get past that deadline..." Then what? The next ordeal or deadline, and repeat, until death?
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Elizabeth McDaniel @lizilla93.bsky.social · 03/12/2024
Interesting find related to this, a website that aggregates book recommendations from podcast guests: lennysbookshelf.replit.app I like that you can sort by most mentioned and can see what episodes/guests mentioned the book
lennysbookshelf.replit.app
Lenny's Bookshelf
Curated book recommendations from Lenny's Podcast guests
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Cameron Thrash @jcamthrash.bsky.social · 27/11/2024
Extraordinary physiology of polyphosphate-accumulating Beggiatoa mats suggests a key role for phosphate buffering in marine sediments www.biorxiv.org/content/10.1... #jcampubs
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Michael Nielsen @michaelnielsen.bsky.social · 01/12/2024
New essay: "How to be a wise optimist about science and technology?" michaelnotebook.com/optimism/ind...
michaelnotebook.com
How to be a wise optimist about science and technology?
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Elizabeth McDaniel @lizilla93.bsky.social · 01/12/2024
Related to increased readership in romance/romantasy genres, I do wonder if AI publishing tools will work in this market. Given the demand and relative success of self-published books, I could see it working here. amp.theguardian.com/books/2024/n...
amp.theguardian.com
Writers condemn startup’s plans to publish 8,000 books next year using AI | Books | The Guardian
Publisher Spines will charge authors between $1,200 and $5,000 to have their books proofread, designed and distributed with the help of artificial intelligence
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Elizabeth McDaniel @lizilla93.bsky.social · 01/12/2024
Something I’ve been thinking about a lot lately is how inefficient my book-finding process is compared to platforms I use for discovering new music/shows/movies. I highly rely on conversations with friends, Twitter, podcasts, & random finds at the bookstore to find new & interesting reads.
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Linda Holmes @lindaholmes.bsky.social · 25/11/2024
I don’t always have good news to share first thing in the morning BUT… IT’S BOOKS WE LOVE DAY!!!!! apps.npr.org/best-books/#...
apps.npr.org
Books We Love
Here are 350+ great reads from 2024 hand-picked just for you by NPR staff and trusted critics.
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Linda Holmes @lindaholmes.bsky.social · 23/11/2024
If you’re concerned that people aren’t reading, the best thing you can do is be expansively open-hearted about their habits when they *do* choose to read. When it comes to format, timing, genre, and so forth, you will get so much farther by welcoming enthusiasm instead of trying to mold it.
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Fatima Pereira @fatimacpereira.bsky.social · 21/11/2024
Our study on drug-gut microbiome interactions is out! 🦠💊 We show that the #Parkinson's drug entacapone induces iron deficiency in microbes, leading to selective inhibition of microbial activity. @cemess.bsky.social @sotonbiosciences.bsky.social #BostonUni Check the full story here: rdcu.be/d0ZAQ
rdcu.be
The Parkinson’s disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration
Nature Microbiology - Entacapone, a Parkinson’s disease medication, sequesters iron resulting in a selective inhibition of gut microbial activity.
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Jonathan Eisen @phylogenomics.bsky.social · 17/11/2024
From Daniel Park on Twitter: x.com/Daniel_E_Par... "A trio of Novavax preprints, showing 1) remarkable durability >6 months, 2) cross protection against newer variants, and 3) low reactogenicity (side effects), supporting NVX as an excellent booster platform."
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Stephen Turner @stephenturner.us · 16/11/2024
Bluesky for Science Starter packs for genomics, bioinformatics, #Rstats, Nextflow. Moderation lists. Feeds. Let's rebuild the old scitwitter community and keep this place nice blog.stephenturner.us/p/bluesky-fo... 🧬🖥️🧪
blog.stephenturner.us
Bluesky for Science
Bluesky starter packs for genomics, bioinformatics, R, and Nextflow
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Ethan White @ethanwhite.weecology.org · 17/01/2024
I just saw that @blkwomencompbio.bsky.social is here on Bluesky! Want to support Black women in computational biology? Give them a follow, pick up a great looking shirt www.bonfire.com/store/shop-b... (I ordered two!), and consider making a donation www.blackwomencompbio.org/donate
bonfire.com
shop --bwcb-threads | Official Merchandise | Bonfire
The official merchandise hub of the Black Women in Computational Biology Network
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Elizabeth McDaniel @lizilla93.bsky.social · 04/01/2024
Since writing this, I've found others studying polyP's role in everything from pathogen virulence to blood clotting. Would it be useful for us to uncover basic mechanisms + make tools to study polyP accumulation in bacteria? Join the convo! research.arcadiascience.com/pub/open-que...
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Cameron Thrash @jcamthrash.bsky.social · 26/10/2023
Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium www.nature.com/articles/s41... #jcampubs
nature.com
Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing c...
The ISME Journal - Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium
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Ryan Ziels @ryanziels.bsky.social · 25/10/2023
~70% of CH4 in anoxic ecosystems comes from acetate, but what microbes are catalyzing its oxidation, and how? We shed some new light on this question using long-term enrichments along with metabolic modeling informed by SIP-metaproteogenomics. #MicrobiomeSky www.nature.com/articles/s41...
nature.com
Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing c...
The ISME Journal - Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium
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Elizabeth McDaniel @lizilla93.bsky.social · 09/10/2023
The enzymes for polyphosphate formation are present in nearly all bacteria, but only some store large amounts of polyP. Why? @ArcadiaScience we tackled this problem by looking at structural similarity of the protein catalyzing polyP formation Pub: research.arcadiascience.com/pub/result-p...
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