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Pat Schloss

@patschloss.bsky.social
2.4K followers 23 following 142 posts

Papa to 9 microbes, mackerel snapper, shepherd, master of sucking. I want to help you learn the skills you'll need to succeed in science.

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Pat Schloss @patschloss.bsky.social · 30/09/2026
Once upon a time (2020), I submitted a paper saying we shouldn't be removing "rare" taxa from microbiome analyses. The reviewers were like, "but you used rarefaction, which is the absolute worst thing ever!"
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Cameron Thrash @jcamthrash.bsky.social · 30/09/2026
Rarefaction is better than robust Aitchison PCA and other compositional data analysis methods at controlling for uneven sequencing effort journals.asm.org/doi/10.1128/... #jcampubs
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Pat Schloss @patschloss.bsky.social · 29/09/2026
Latest from the Schloss Lab is the {strollur} R package at MRA journals.asm.org/eprint/MA3AD...
journals.asm.org
Strollur: an R package for working with amplicon sequence data in R | Microbiology Resource Announcements
Amplicon sequencing projects, including 16S rRNA gene sequence collections, are widely used by microbiologists to analyze diverse microbiomes. These data sets are often large and complicated, making i...
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Pat Schloss @patschloss.bsky.social · 29/09/2026
The number of legends like this in prestigious journals is staggering. Work with people's intuition. For heatmap colors red is hot (positive) and blue is cold (negative). Flipping the colors makes the figure far more challenging for your audience to interpret. From Nature Microbiology...
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Pat Schloss @patschloss.bsky.social · 29/09/2026
It breaks my cold little heart that the IMMSA logo includes a stacked bar chart AND that they clearly didn't use subsampling or rarefaction to control for uneven sampling effort.
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Pat Schloss @patschloss.bsky.social · 18/09/2026
Let me get this straight. There's a title. There's a commentary article. There's an abstract. There's a set of bullet point highlights. There's a graphical abstract. AND YOU STILL THINK I NEED YOUR AI AGENT TO SUMMARIZE THE ARTICLE FOR ME?
AI BS from Cell
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Nichole Broderick, PhD @nabroderick.bsky.social · 16/09/2026
Society journals support the scientific community, including advocacy for funding and science policies. $ to for profit journals just ends up in another shareholders yacht.
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Pat Schloss @patschloss.bsky.social · 25/08/2026
'"At the end of the day ... they're either going to play for you or they're going to play for someone else around the country," Kiffin said at a news conference Monday. "So we've made the decision to recruit them like probably most people are."' - This is exactly what I hear peers say about using AI
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Pat Schloss @patschloss.bsky.social · 31/07/2026
Put one in Central Park or Lincoln Park before putting one in Saline or Ypsilanti Michigan then we might believe you
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Pat Schloss @patschloss.bsky.social · 07/07/2026
"AI is just like..." is a common refrain that absolves people from doing hard work. Read this all the way to the end and then try again. The difference in learning between Serrano's students and classmates is a 1000000000000-fold. Beyond the learning is the humanity www.chronicle.com/article/the-...
chronicle.com
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Ira Blader @bladerlab.bsky.social · 02/07/2026
A poll for principal investigators and group leaders: If a journal compensated reviewers for evaluating a submitted manuscript, would you prefer to 1️⃣ Be paid directly 2️⃣ Use the money as a credit for future publications 📊 Show results
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George O'Toole (he/him/his) @geiselbiofilm.bsky.social · 24/06/2026
Submit to the JB Biofilms Collection! Research Articles & Minireviews on biofilm formation/dispersal, Abx tolerance, polymicrobial interactions, signalling, imaging & more. Submission deadline: 30 September 2026. journals.asm.org/journal/jb/b... @asm.org #JBacteriol #ASMjournals
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Pat Schloss @patschloss.bsky.social · 22/06/2026
Someone recently gushed to me about an undergrad they wrote a letter of recommendation for to med school. He then said he used AI to write the letter. I lost a lot of respect for him and was left dumfounded. Someone else recently asked me how is AI dehumanizing. This.
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Pat Schloss @patschloss.bsky.social · 15/06/2026
I don't even know what to do with this. Both my worst scores and best scores ever. All for the same proposal. 🤣
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Pat Schloss @patschloss.bsky.social · 10/06/2026
Currently responding to reviewers' critiques that I'm sure were written by generative AI. We complain that reviewers don't seem to read what we give them, but these are so much worse. So hard to take the comments seriously. I don't like what this is doing to me.
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Pat Schloss @patschloss.bsky.social · 14/05/2026
Reminder that R is not RStudio. Just read a paper that performed their analysis "using RStudio (v.4.1.2, v.4.3.0)". Those are R versions (and why two different versions?), not RStudio versions. RStudio versions look like "2026.04.0". Regardless, the R version is more important than the RStudio
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Pat Schloss @patschloss.bsky.social · 04/05/2026
So @biorender.bsky.social wants to tap into the prism market? Can't wait for all the figure legends to have the biorender attribution text and the same soulless appearance. I think I'd rather re-learn how to make plots in Excel than use either.
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Pat Schloss @patschloss.bsky.social · 22/04/2026
In case you were wondering...
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Mark O. Martin @markowenmartin.bsky.social · 22/04/2026
New episode of #MattersMicrobial! This time, Dr. Joe Zackular joins the #QualityQuorum to discuss the wily bacterium Clostridiodes difficile (also known as C. diff) which can cause serious disease in humans. Informative session! Please spread the #GoodMicrobialWord! youtu.be/9oSR01l-EkY?...
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Pat Schloss @patschloss.bsky.social · 02/04/2026
April 1st seems to have become World AI Day, eh? Let that sink in the next time that you use AI for something: we suspect that what you say and show as your own is a lie.
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Pat Schloss @patschloss.bsky.social · 12/03/2026
My next newsletter "What is the most common form of 'chartjunk' in the scientific literature? " is coming out tomorrow morning. Subscribe to get it and stay in the loop on everything I'm up to in helping scientists make the most effective data visualization! shop.riffomonas.org/posts/
shop.riffomonas.org
Riffomonas Professional Development
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Pat Schloss @patschloss.bsky.social · 02/03/2026
Looking for someone to give a talk to your group on the problems with AI for culture, society, or education? I'm a STEM professor at the U of Michigan and would be happy to give that talk.
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Mark O. Martin @markowenmartin.bsky.social · 27/02/2026
I always always tried to get students to see this. In fact, they are so much more.
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Pat Schloss @patschloss.bsky.social · 23/02/2026
When I scan through open peer reviews I'm surprised by how rarely people comment on the design of visuals. I've been working to develop a constructive approach to critique and have been trying them out on the Tube. Here's the latest www.youtube.com/watch?v=zWpt...
youtube.com
How would you improve upon this set of pie charts published in Nature Microbiology (CC401)
YouTube video by Riffomonas Project
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Jacquelyn Gill @jacquelyngill.bsky.social · 23/02/2026
The fundamental premise behind AI-enabled cheating is that coursework is merely busy work, because your'e just doing it for professors. We would never say that showing up for football practice is merely busy work because you're just doing it for your coaches.
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Pat Schloss @patschloss.bsky.social · 17/02/2026
Each Monday I post a video critiquing a figure from recently published paper and on Wednesday (9AM Eastern) I do a livestream either recreating the figure or refactoring it. This week's figure has a problem that is too common in science youtu.be/DNop0UjdfFg
youtu.be
How to improve the structure of a data visualization to be aligned with your text (CC399)
YouTube video by Riffomonas Project
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Pat Schloss @patschloss.bsky.social · 21/01/2026
Because I'm ranting... Please figure out how to replace "_" with " " in your taxa names. Then figure out how to italicize them. Not sure how difficult this is to do in Prism, but it's pretty straightforward with stringr/ggplot2/ggtext in R. How do plots like this appear in journals with 20 JIFs?
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Pat Schloss @patschloss.bsky.social · 21/01/2026
I'm seeing more and more of this: broken y-axes. Regardless of what you think about them (I'm "anti"), examples like this one don't need them! You could easily put ticks every 5000 units without a break
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Pat Schloss @patschloss.bsky.social · 07/01/2026
New paper up on bioRxiv! This is my third and hopefully final paper on rarefaction. It's still better than the other available methods. www.biorxiv.org/content/10.6...
biorxiv.org
Rarefaction is better than robust Aitchison PCA and other compositional data analysis methods at controlling for uneven sequencing effort
Amplicon sequencing typically results in a wide distribution in the number of sequences obtained from each sample. How best to account for this variation has been a persistent problem in the microbial...
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Pat Schloss @patschloss.bsky.social · 19/12/2025
The annual freak out is on over the university no longer paying for GraphPad Prism...
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Pat Schloss @patschloss.bsky.social · 19/12/2025
Healthy organizations have competitive elections.
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Pat Schloss @patschloss.bsky.social · 15/12/2025
The last time you reviewed a paper for a journal, did you comment on the design of any of the figures?
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Pat Schloss @patschloss.bsky.social · 29/10/2025
Just FYI: people are anti-vaxxers for their kids. It's also for their pets and livestock. They've gone so far off the rails. People ask us about mRNA vaccines for sheep an other animals worried something weird might happen to the meat. I wish! We can't get enough vaccines approved for meat animals
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Pat Schloss @patschloss.bsky.social · 24/10/2025
We've all heard seminar speakers say (myself included), "I know this is too small for you to read, but..." This usually happens because people are repurposing panels from their papers without adjusting for the medium (1/20)
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Pat Schloss @patschloss.bsky.social · 10/10/2025
I'm editing and putting the finishing touches on a grant proposal. The though of having AI write the whole thing or even a part of it is pretty unthinkable. When you write you see what you truly know. It forces you to think and troubleshoot your logic. (1/3)
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Pat Schloss @patschloss.bsky.social · 30/08/2025
My google skills are failing... Back in 2011, NCBI (started to?) close the SRA. The SRA is still with us. Anyone know of any articles from around then about how they saw the light? For those that this is news to... genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com
Closure of the NCBI SRA and implications for the long-term future of genomics data storage - Genome Biology
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Pat Schloss @patschloss.bsky.social · 15/08/2025
I know things are hard right now. But, if you are going to review proposals submitted to a special PA, please at least read the PA before reviewing proposals submitted to the PA. I mean, if it says no biological questions allowed, don't ding me for not proposing to answer biological questions.
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Pat Schloss @patschloss.bsky.social · 31/07/2025
I'm offering a new workshop that's part instruction, part group coaching. This program will focus on the design principles we should consider when generating visuals. There won't be any coding so don't let that hold you back shop.riffomonas.org/products/tra...
shop.riffomonas.org
Transform your data visualizations in 5 weeks - no judgement, no code
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Vaughn Cooper @vscooper.micropopbio.org · 08/06/2025
Sharing the most significant work from my group, led by the @evolvingstem.bsky.social team. Come for the discoveries of how Pseudomonas adapts in biofilms, stay for the story of how they were discovered by thousands of young scientists in grades 9-12. 🧪🧫🧬🧵 www.biorxiv.org/content/10.1...
biorxiv.org
Student-led experimental evolution reveals novel biofilm regulatory networks underlying adaptations to multiple niches
We established a research-education partnership known as EvolvingSTEM that provides secondary school students the opportunity to conduct authentic research experiments centered on microbial evolution....
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Pat Schloss @patschloss.bsky.social · 16/04/2025
If you've been putting off learning how to make plots in R with ggplot2, then have I got what you need! I'll be teaching a zoom-based workshop on just that subject. This will be a one day all ggplot2 workshop on May 9th shop.riffomonas.org/products/int...
shop.riffomonas.org
Introduction to ggplot2 and the grammar of graphics
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Pat Schloss @patschloss.bsky.social · 16/04/2025
If the folks at @umich.edu need help with web design I'm sure the designers of harvard.edu would be happy to help
harvard.edu
Harvard University
Harvard University is devoted to excellence in teaching, learning, and research, and to developing leaders who make a difference globally.
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Pat Schloss @patschloss.bsky.social · 27/02/2025
Just to be clear... there are two editorials. I appreciate the love for the other one on supporting science, but I don't want this one on diversifying science to get lost
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Pat Schloss @patschloss.bsky.social · 27/02/2025
My editorial simultaneously published in all of @asm.org's journals addresses the ongoing effort by the administration to halt efforts to diversify science. It should be obvious from ASM Journals' efforts over the years, but we aren't fans journals.asm.org/doi/10.1128/...
journals.asm.org
A call for healing and unity | mBio
Executive orders signed since 20 January 2025 aim to end programs intended to diversify the scientific workforce via equitable and inclusive practices and processes; cut federal funding for research and innovation; and stifle scientific communications. They represent a stunning reversal of policies that have been the bedrock of the U.S. scientific research enterprise and its leadership in the world, and therefore not surprisingly they have been met with a number of legal challenges. Some of the executive orders have been blocked by temporary restraining orders, and others are pending judicial review.
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Pat Schloss @patschloss.bsky.social · 27/02/2025
The @asm.org Journals Committee has published a response to the recent disruptions in science in the US... A call for the United States to continue investing in science | mBio journals.asm.org/doi/10.1128/...
journals.asm.org
A call for the United States to continue investing in science | mBio
The U.S. life science research mission is critical not only to human health and understanding the natural world but also to agriculture and food production, technological innovations, socioeconomic pr...
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Pat Schloss @patschloss.bsky.social · 21/02/2025
Hey folks! Over the past few weeks I've been posting videos recreating several of W.E.B. DuBois's "data portraits" from the 1900 Paris Exhibition in #Rstats using only {tidyverse} and {showtext}. I have 4 up now and there will be 4 more over the next 2 weeks www.youtube.com/playlist?lis...
youtube.com
DuBois recreations - YouTube
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Jo Handelsman, PhD @johandelsman.bsky.social · 13/02/2025
"Make America Great Again. Make America Healthy Again. These were promises made by candidate Trump in his campaign to be president of the United States of America. What in this campaign platform should have prepared us for a war on discovery?"
wisconsintechnologycouncil.com
Guest column: “The war on discovery” is antithesis of campaign pledge to make America great again - Wisconsin Technology Council
By Jo Handelsman MADISON, Wis. – Make America Great Again. Make America Healthy Again. These were promises made by candidate Trump in his campaign to be president of the United States of America. What...
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Pat Schloss @patschloss.bsky.social · 14/01/2025
Happy to share that a manuscript describing my {phylotypr} R package has been released on Microbiology Resource Announcements. {phylotypr} is an R-based implementation of the naive Bayesian classifier, aka the RDP classifier: journals.asm.org/doi/epdf/10....
journals.asm.org
phylotypr: an R package for classifying DNA sequences
You have to enable JavaScript in your browser's settings in order to use the eReader.
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Pat Schloss @patschloss.bsky.social · 07/01/2025
My first thing on this platform (what are the things called?).
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Pat Schloss @patschloss.bsky.social · 07/01/2025
What's your favorite plot that you've seen recently? What's the most 🔥💩 plot that you've seen recently? I'm getting headaches looking through 42 part figures that are full of over bolded prism plots, 58 by 287 heat maps with attached dendrograms, or balls of yarn attempting to show interactions
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