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Sarah Bagby

@scbagby.bsky.social
1K followers 503 following 79 posts

Environmental microbiologist at Case Western. She/her. bagby-lab.github.io, emerge-bii.github.io

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Sarah Bagby @scbagby.bsky.social · 01/07/2026
The whole issue of Nature Micro is up now, and look at that gorgeous cover! @emerge-bii.bsky.social co-director Ruth Varner took the picture. www.nature.com/nmicrobiol/v...
nature.com
Nature Microbiology - Microbial gene flow through thawing permafrost
This photograph shows the entrance to Stordalen Mire, Sweden, near the Abisko Scientific Research Station in the margin of the permafrost zone. As rising...
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Sarah Bagby @scbagby.bsky.social · 29/06/2026
Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23
Screenshot of an email header with subject line "Crazy ideas"
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Sarah Bagby @scbagby.bsky.social · 08/05/2026
I feel that the local science center could have done with one more round of review before going with "Voices of the Titanic Immersive Experience" for the new exhibit.
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𝙽𝚊𝚜𝚑 𝙸𝚜 𝙷𝚎𝚛𝚎 𝙵𝚘𝚛 𝙸𝚝 @nashishereforit.bsky.social · 17/02/2026
Wow.
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Sarah Bagby @scbagby.bsky.social · 03/11/2025
Microbial eukaryote folks, you've got two more weeks to apply for this TT job: apply.interfolio.com/174456. We're a supportive department with a great breadth of interests, with really sharp students, in a very livable city with the nation's best park system. Come join us!
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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Ben Monreal @benmonreal.bsky.social · 09/08/2025
Fellow Clevelanders will have seen @neorsd.org's update on the end of their Shaker Dam engineering work. I have some technical-detail thoughts about this, as an engineering-adjacent STEM person and a fan of the lake and brook. Keep reading for a summary (incl. links to slides and video): 1/8
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Ben J Woodcroft @benjwoodcroft.bsky.social · 16/07/2025
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
Logo for the Sandpiper website
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The Tennessee Holler @thetnholler.bsky.social · 18/03/2025
NEBRASKA CROWD: “TAX THE RICH! TAX THE RICH!” @USRepMikeFlood: “So your proposal to solve (the debt) is tax the rich?” NEBRASKA CROWD: *CHEERS WILDLY* (not sure this went quite as he planned 😬)
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Joshua Weitz @joshuasweitz.bsky.social · 22/02/2025
No PhD students or severely reduced # of admits -> *undergraduates* looking now to start the next phase of their career in support of research & discovery will be stuck without an option. This is far from the only place in a similar situation, whether announced publicly yet or not.
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Alexandria Ocasio-Cortez @aoc.bsky.social · 21/02/2025
Medicaid is not for sale. NASA is not for sale. The Post Office is not for sale. America is not for sale. We have an obligation to resist kings. We outnumber them. And they can be overwhelmed.
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Scott Delaney @scott-delaney.bsky.social · 21/02/2025
NIH indirects case update: Hearing ongoing now, and I'll try to live tweet some notable exchanges. Prior to more detailed arguments, Judge Kelley starts off with a few point questions to both sides: (I'm paraphrasing here)
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Mike Dickison @adzebill.bsky.social · 01/02/2025
The Internet Archive has to date downloaded 500 terabytes of US government websites, which it crawls at the end of every presidential term. The whole archive is fully searchable. This effort's housed by a donation-funded nonprofit, not a branch of the US government. blog.archive.org/2024/05/08/e...
blog.archive.org
End of Term Web Archive – Preserving the Transition of a Nation | Internet Archive Blogs
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Nicole Bedera @nbedera.bsky.social · 01/02/2025
I know that all these institutions know how to push back because when Obama directed them to enforce pre-existing Title IX law, universities said no. They flat out refused until there was a working group and specific guidelines. And even then, they *still* refused.
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Kelly Zamudio @kzutaustin.bsky.social · 16/01/2025
Everyone, plz share with your stellar undergrads! The UDE program (Undergraduate Diversity at Evolution) pairs students from diverse backgrounds with mentors to attend the Evolution meeting each year. Encourage your undergrads to apply!
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Patrick R. Secor @prsecor.bsky.social · 06/01/2025
Friends, please help spread the word about our microbiology REU program at Montana State University. www.montana.edu/mbi/reu/ Each student receives a stipend ($7000 for 10 wks). Travel compensation, room, and board are also provided. Details in the attached pic--Feb 13 deadline 🧫🧪🦠#microsky
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Ben Vezina @bananabenana.bsky.social · 21/11/2024
(1/6) Our new short paper on incidental bacterial domestication between patient isolation and creation of frozen stock. Geno/phenotype changes are obscured by rich media and more prevalent than we previously thought. #MicroSky
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Vivek Mutalik @vivekmutalik.bsky.social · 21/11/2024
#phagesky Some partnerships are always fun!! Excited to share one such 🎉 product w Simon Roux, perspectives on our favorite “atypical” phages, for special issue to celebrate my former mentor Carol Gross @ UCSF Tapping the treasure trove of atypical phages www.sciencedirect.com/science/arti...
sciencedirect.com
Tapping the treasure trove of atypical phages
With advancements in genomics technologies, a vast diversity of ‘atypical’ phages, that is, with single-stranded DNA or RNA genomes, are being uncover…
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Brooke Conti @brookeconti.bsky.social · 15/11/2024
Ohio friends: consider contacting Gov Dewine to urge him not to sign the "bathroom bill" (SB 104). Educators are in a particularly good position to made the case against this on practical grounds, though I also brought up the specter of conference/business boycotts, as in NC.
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Anna Rogers @annarogers.bsky.social · 15/11/2024
Shameless plug: a post on 'writing as thinking' that I wrote for my own students hackingsemantics.xyz/2024/writing/
hackingsemantics.xyz
On AI-assisted writing in graduate school
What is the proper role of AI ‘assistance’ in graduate student writing? It depends on what you mean by ‘graduate’.
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Agata Starosta @agatastarosta.bsky.social · 14/11/2024
Our first B. subtilis paper, published at NatureComms. Translation in Bacillus subtilis is spatially and temporally coordinated during sporulation. #subtiwiki #bacillus www.nature.com/articles/s41... Funded by FNP_org_pl and EMBO_YIP
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Erin Reed @erininthemorning.com · 13/11/2024
Governor Andy Beshear, in a Trump +30 state, gives advice to Democrats: Do not throw LGBTQ+ people under the bus, it will not work. His advice to dems: Lead on your values. This man ran on a fully inclusive campaign in 2023 and won. He received the same kind of ads Harris did.
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Dr Adrian Bass @aquaticcarbon.bsky.social · 11/11/2024
We are looking for a dynamic, motivated, interdisciplinary researcher to join our new project RESPECT: Rapid Engagement with Stressed Peatland Environments and Communities in Transformation. Field & lab components working in a cross-disciplinary group. 1/2
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Jennifer Biddle @jenbiddle.bsky.social · 04/11/2024
My department is looking for an assistant professor in fisheries and conservation: careers.udel.edu/cw/en-us/job... Please repost! #marinesky #oceanography #STEM #fisheries
careers.udel.edu
University of Delaware - Details - Assistant Professor in Fisheries and Conservation at the School of Marine Science and Policy, University of Delaware
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Will Ratcliff @wcratcliff.bsky.social · 04/11/2024
Excited to share: The inaugural Alma Dal Co School on Collective Behavior is coming to Venice (Sep 29-Oct 4, 2025). This unique school honors Alma (1989-2022), whose brilliant work bridging physics and microbiology revealed how metabolic interactions structure microbial communities. 1/12
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Sarah Bagby @scbagby.bsky.social · 04/11/2024
n o p e
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Stephen Wolf @stephenwolf.bsky.social · 03/11/2024
It's great that turnout here seems high, but a long line is also a sign of voter suppression because Ohio's GOP limited early voting to just 1 site per county regardless of population. Franklin County's 1.3 million people (heavily Dem) & Vinton County's 12,000 people (heavily GOP) each get 1 site
Tweet from Ohio reporter Karen Kasler with a short video embedded of voters waiting in line to vote early. The text says, "Last day of early voting in Ohio and the line at the Franklin County Board of Elections is insane - it’s backed around itself multiple times. I have been covering early voting since Ohio started it in 2005 and I’ve never seen anything close to this"
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Joel Sachs @sachslab.bsky.social · 01/11/2024
I'm so excited to announce that my department is now hiring TWO ECOLOGISTS at the Assistant Professor Level. We will be really excited to substantially expand research in ecology in our EEOB Department at UCR. Please Repost and share widely! aprecruit.ucr.edu/JPF01983
aprecruit.ucr.edu
Assistant Professor of Ecology
University of California, Riverside is hiring. Apply now!
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Fuse Washington @fusewashington.org · 28/10/2024
If this is you, you need to request a replacement ballot in case yours was damaged in this MAGA arson. You can request a replacement ballot by: - Calling the auditor's office at (564) 397-2241 - Emailing elections@clark.wa.gov - Visiting this link: clark.wa.gov/elections/ne...
clark.wa.gov
Need a Replacement Ballot? | Clark County
Click this link to access Votewa.gov for you replacement ballot
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Gina Lewin @ginalewin.bsky.social · 25/10/2024
Hi BlueSky friends! Postdoc(s) available in my lab! Multiple projects on how bacterial genomic and functional diversity impacts microbial interactions & disease. 🦠🧫 See www.thelewinlab.com/join-us/post... for more information. Please RT & share. #Postdoc #Microbiology #OralMicro #VaginalMicro
Ad for postdoc position
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Sarah Bagby @scbagby.bsky.social · 25/09/2024
We're hiring! The Department of Biology at Case Western Reserve University is a welcoming and supportive place for junior faculty. If you work on eukaryotic microbes, especially environment- or host-microbe interactions, we want to hear from you. Deadline 11/18. apply.interfolio.com/155519
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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Simon Roux @simrouxvirus.bsky.social · 02/10/2024
New pipeline alert: if you would like to explore what viruses/phages are in your metagenomes or metatransciptomes, but don't know where to start, we have (an) MVP for you now \o/ - journals.asm.org/doi/epub/10.... Welcoming feedback/suggestion of improvement!
journals.asm.org
MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes
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George Matsumoto @georgeimatsumoto.bsky.social · 01/10/2024
🧪📍 🌊 🦑 Applications are now being accepted from undergraduate students, graduate students, post-docs, and early-career scientists to participate in an NSF-funded research cruise aboard the R/V Marcus G. Langseth mailchi.mp/ldeo/langset...
mailchi.mp
Call for Participation: R/V Langseth Research Cruise
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Sarah Bagby @scbagby.bsky.social · 25/09/2024
We're hiring! The Department of Biology at Case Western Reserve University is a welcoming and supportive place for junior faculty. If you work on eukaryotic microbes, especially environment- or host-microbe interactions, we want to hear from you. Deadline 11/18. apply.interfolio.com/155519
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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Ben Monreal @benmonreal.bsky.social · 23/09/2024
I just took a survey that would have benefited from the modified 2-D Likert scale I just invented
Likert survey form with options
"strongly agree - agree - neutral - disagree - strongly disagree", or
"grudgingly agree - meh - grudgingly disagree", or 
"this question is annoying"
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JL Weissman @jlw-ecoevo.bsky.social · 16/09/2024
A little over two weeks left to apply!
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Sarah Bagby @scbagby.bsky.social · 12/05/2024
Me: What about when you get together with someone? 6yo child of scientists: Oh! COLLABORATE!
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Binning Singletons @binningsingletons.com · 24/04/2024
We're taking registrations for attendees of #ASMicrobe in the ATL! forms.gle/dMgXp8zqU4rS...
7 boxes explaining Binning Singletons.
1: Binning singletons is a mentoring and networking program for attendees seeking community in a large meeting
2: Participants self-identify as singletons (often solo and 1st time attendees)
3: We group Singletons into bins based on common interests
4: Each bin has a mentor
5: The mentor is a meeting coach and helps with logistics and networking
6: We bring the different bins together to grow the community
7: We support singletons by promoting their presentations, hosting meet-ups, attending vendor events, organizing social activities, and providing assistance throughout the meeting
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Carl T. Bergstrom @carlbergstrom.com · 17/03/2024
A new arXiv preprint from James Zou suggests that quite a few academics are also using ChatGPT to write their peer reviews. I don't have to explain what an utter shitshow this is going to be, do I?
arxiv.org
Monitoring AI-Modified Content at Scale: A Case Study on the...
We present an approach for estimating the fraction of text in a large corpus which is likely to be substantially modified or produced by a large language model (LLM). Our maximum likelihood model...
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Zamin Iqbal @zaminiqbal.bsky.social · 11/03/2024
First step in a community project to provide a uniformly assembled, annotated and searchable set of bacterial genomes, our preprint on our initial release of 1.9 million genome assemblies+taxonomic estimates. (figure compares with previous 661k dataset) www.biorxiv.org/content/10.1... #microsky
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Sarah Bagby @scbagby.bsky.social · 09/02/2024
I think it's now late enough that I can say: SPOILER, Ezersky, jeez
A Spelling Bee grid, showing the word DORY as "Already found"
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Sarah Bagby @scbagby.bsky.social · 03/02/2024
I've had a soft spot for the effects of synonymous mutations ever since learning about cotranslational folding in my first year of grad school---just how extremely like capital-L Life to exploit this channel for information. So this is a fun 🦠 read: doi.org/10.1073/pnas... #microbiomesky
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Jennifer Biddle @jenbiddle.bsky.social · 26/01/2024
If anyone sees a position for a remote bioinformatics person, ideally in industry or longer term in academia, HMU. I am trying to help someone stay with their family and they are fantastic at science, I give them my highest recommendation. They are based in US.
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Sarah Bagby @scbagby.bsky.social · 26/01/2024
This is lovely. @baym.lol hits the nail on the head when he talks about how much fun it is to do collaborative science---just a wildly better experience than constant worry about sharp-elbowed competition. Kudos to @relenski.bsky.social for helping make it happen.
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Dan Udwary @danudwary.secondarymetabolism.com · 17/11/2023
The JGI’s Secondary Metabolism Collaboratory, SMC, version 1.0 is released! This is JGI’s database of natural product BGCs. The current version contains BGC info from AntiSMASH 7 and EmeraldBGC for as many bacteria as we could find (~1.3M genomes). smc.jgi.doe.gov or secondarymetabolism.com 1/n 🧪🧬🖥️
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Chenxin Li, PhD @chenxinli2.bsky.social · 08/11/2023
Not enough people know about bioicons.com Open source vector graphics. Free alternatives to BioRender.
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Sarah Bagby @scbagby.bsky.social · 20/10/2023
my name is DALL, and wen i bak i wisk the potper with the vedk. i sift the miilk into the kek. i brek the fear. i pour the eg.
Misbegotten DALL-E 3 annotation of the ingredients it expects a cake to require.
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