iiinova — where your digital self keeps evolving

Maike Morrison @maikemorrison.bsky.social · 28/07/2026

SFI is a blast and I have so enjoyed my first of three years on this fellowship. Please share with the quantitative, interdisciplinary, early-career researchers in your circles!

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Reposted by Maike Morrison

Nastia Lyulina @alyulina.github.io · 06/11/2025

How is functional variation at large-effect loci maintained in natural populations, even as environments change? In a paper led by @mkarag.bsky.social, we tracked known pesticide resistant alleles in outdoor 𝘋. 𝘮𝘦𝘭𝘢𝘯𝘰𝘨𝘢𝘴𝘵𝘦𝘳 cages & inferred selection and dominance from temporal sequencing data.

Glass beads of all sorts balancing on wavy threads.

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Maike Morrison @maikemorrison.bsky.social · 04/11/2025

Rank-choice voting AND a roadrunner sticker? NM has voting figured out.

"I voted! / !Yo voté!" sticker featuring a road runner, a yucca, and a Zia symbol in the background

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Reposted by Maike Morrison

Ben Moran @ben-moran.bsky.social · 01/05/2025

1/9 Excited to share the preprint for the second half of my PhD with @mollyschumer.bsky.social: Connecting human environmental impacts to hybridization in swordtail fish through genomics, GIS, water chemistry, and histology. Thread below! #SciSky www.biorxiv.org/content/10.1...

biorxiv.org

Increased rates of hybridization in swordtail fish are associated with water pollution

Biodiversity loss can occur when disturbance compromises the reproductive barriers between species, causing them to collapse into a single population through hybridization. Recent research has documen...

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Reposted by Maike Morrison

Dr. David Miller 🏳️‍🌈 @davidimiller.bsky.social · 24/04/2025

🚨 Practical URGENT tip for NSF grantees: Out of an abundance of caution, I would right now go into Research.gov and… 1. Download your NSF award letters. 2. Print PDF your annual reports. 3. Screenshot the status table for annual reports. NSF is planning maintenance tomorrow to Research.gov

Due to maintenance, Research.gov (including access to NSF-PAR, GRFP, PES, and ETAP) will be unavailable from Fri., 4/25 at 10:00 PM ET to Sat., 4/26 at 1:00 PM ET. NSF apologizes for any inconvenience.

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Reposted by Maike Morrison

Jeremy Berg @jeremymberg.bsky.social · 24/04/2025

ATTENTION: NSF GRANT RECIPIENTS We received a heads up from a trusted source that you should proactively download/print/screen shot any documentation on research.gov pertaining to your NSF awards, both those that are current and any that have closed in the last 5-6 years. 1/n

media.tenor.com

a cartoon of a man holding a frying pan and a spoon with red alert written above him

ALT: a cartoon of a man holding a frying pan and a spoon with red alert written above him

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Maike Morrison @maikemorrison.bsky.social · 31/03/2025

"The silence from the leaders of our university—at least in public—suggests the assault has already produced the intended chilling effect, but together we can overcome it." Good read from Stanford History profs Jessica Riskin and Priya Satia. stanforddaily.com/2025/03/17/i...

stanforddaily.com

From the Community | Is it 1984 in 2025?

Stanford’s leadership must join with other universities to stand up and fight for American higher education, write Professors Riskin and Satia.

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Maike Morrison @maikemorrison.bsky.social · 17/03/2025

Thanks! Totally! We have a preprint using a similar framework to look at mutational signature heterogeneity across tumors (collab with @nalcala.bsky.social doi.org/10.1101/2023...) and we also used this framework to look at heterogeneity of immune cell infiltration (analysis not published yet).

doi.org

Variability of mutational signatures is a footprint of carcinogens

Understanding the genomic impact of carcinogens is fundamental to cancer biology and prevention. However, recent coordinated efforts to detect such fingerprints have been largely unsuccessful, challen...

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Maike Morrison @maikemorrison.bsky.social · 14/03/2025

8/8 FAVA is the culmination of many conversations and collaborations. Thanks especially to my co-authors, @ksxue.bsky.social and Noah Rosenberg–I truly feel like I won the collaborator/mentor lottery. And thanks to you for reading! Paper is here if you want to read more: doi.org/10.1073/pnas...

doi.org

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

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Maike Morrison @maikemorrison.bsky.social · 14/03/2025

7/ (Ex. 2) In longitudinal microbiome samples from healthy humans taking an antibiotic (collab with @ksxue.bsky.social), FAVA is much higher post-abx than pre-abx, and just half of the 22 subjects return to their baseline FAVA level (computed in 6-sample sliding window) during the 30 days post-abx!

Plot showing longitudinal microbiome composition for three individuals who took an antibiotic, along with corresponding plots showing FAVA computed in sliding windows. For all subjects, FAVA increases during the antibiotic window. In one subject (XDA) we see that FAVA can return to stability (low FAVA) without returning to the pre-abx composition.

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Maike Morrison @maikemorrison.bsky.social · 14/03/2025

6/ (Ex. 1) In microbiome samples collected along the GI tracts of individuals from 7 ruminant species, FAVA peaks in the small intestine–so lots of variability would have been missed by stool sampling! We also find taxonomic variability >> functional variability–evidence for functional redundancy.

Plot showing FAVA computed with genus or CAZYme abundances across ruminant host individuals. FAVA is much higher for genus than CAZyme abundances. For both data types, FAVA peaks in the small intestine and is quite low in the large intestine, suggesting much variation across individuals would be missed with stool sampling.

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Maike Morrison @maikemorrison.bsky.social · 14/03/2025

5/ FAVA can account for phylogenetic similarity among taxa and can differentially weight samples, which is especially useful for time series data (Fig. 3). FAVA can be computed in sliding windows to see how variability changes over space or time (Fig. 4). We demonstrate FAVA in 2 examples.

Diagram showing that FAVA can incorporate a matrix giving the similarity between each pair of taxa, as well as a vector of weights for each sample, which can be particularly useful for time series data with uneven sampling times.

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Maike Morrison @maikemorrison.bsky.social · 14/03/2025

4/ FAVA can analyze any relative abundance data, including taxonomic categories like OTUs and species, and functional categories like CAZymes and COGs. You can directly compare FAVA values computed on data with different numbers of categories (e.g., variability of bacterial species vs. families).

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Maike Morrison @maikemorrison.bsky.social · 14/03/2025

3/ FAVA extends the pop-gen statistic FST (which traditionally measures variability of allele frequencies across multiple populations) to instead measure variability of taxonomic or functional abundances across multiple microbiome samples (Fig. 1). All it needs is an OTU table, or similar.

Schematic showing that FAVA measures variability across all rows of an OTU table at once, while other methods measure the diversity of one sample or the distance between a pair of samples.

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Maike Morrison @maikemorrison.bsky.social · 14/03/2025

2/ FAVA is implemented in an R package available for download from CRAN (just run install.packages("FAVA") in R). For detailed guidance on the analysis of microbiome data with FAVA, check out the tutorial on the package website: maikemorrison.github.io/FAVA/article...

maikemorrison.github.io

Analysis of microbiome data with FAVA

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Maike Morrison @maikemorrison.bsky.social · 14/03/2025

1/ Hey y'all, I'm excited to share my latest paper, which is out now in PNAS! We introduce FAVA, a statistical framework to measure compositional variability across microbiome samples. If you want to measure variability across a stacked bar plot, FAVA is for you! Paper: doi.org/10.1073/pnas...

5 relative abundance plots arranged to have increasing compositional variability (variability across relative abundance samples, here vertical bars)

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Maike Morrison @maikemorrison.bsky.social · 14/03/2025

6/ (Ex. 1) In microbiome samples collected along the GI tracts of individuals from 7 ruminant species, FAVA peaks in the small intestine–so lots of variation would have been missed by stool sampling! We also find taxonomic variability >> functional variability, evidence for functional redundancy!

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Maike Morrison @maikemorrison.bsky.social · 14/03/2025

5/ FAVA can account for phylogenetic similarity among taxa and can differentially weight samples, which is especially useful for time-series data (Fig. 3). FAVA can be computed in sliding windows to see how variability changes over space or time (Fig. 4). We demonstrate FAVA in 2 examples:

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Maike Morrison @maikemorrison.bsky.social · 14/03/2025

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Maike Morrison @maikemorrison.bsky.social · 14/03/2025

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Maike Morrison @maikemorrison.bsky.social · 14/03/2025

I've been tremendously fortunate to work with @ksxue.bsky.social during her time as a postdoc at Stanford. She's not only a brilliant scientist and an excellent mentor/collaborator, but also a wonderful human being. You should totally join her lab!

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Reposted by Maike Morrison

Doran Goldman @goldmandoran.bsky.social · 11/03/2025

I’m thrilled to share my first ever publication, now published in PNAS! www.pnas.org/doi/10.1073/... With mentorship from the amazing @ksxue.bsky.social, I looked at how the outcomes of species introductions to microbial communities are influenced by the number of introduced microbes.

pnas.org

PNAS

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Maike Morrison @maikemorrison.bsky.social · 12/03/2025

Reading "The Science Bargain" by Rush Holt: "Democracy is at risk when it becomes simply a contest of opinions not grounded in evidence. When one opinion is as good as another–each asserted as strongly or even as deceptively as possible–democracy cannot survive. This is a call to science."

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Maike Morrison @maikemorrison.bsky.social · 08/03/2025

It's been easy to feel powerless these past few months, but the @standupforscience.bsky.social rally in SF this afternoon was an important reminder that the fight is not over!

Maike holding a sign in front of SF city hall. Sign is a parody of the Gadsden flag. Text on bottom says, "don't tread on me." Snake usually on Gadsden flag is replaced with a caterpillar phylogenetic tree.

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Maike Morrison @maikemorrison.bsky.social · 23/07/2024

Today's small joy was discovering the latex package "etaremune," which you can use in place of "enumerate" to count in reverse

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Maike Morrison @maikemorrison.bsky.social · 09/07/2024

I'm stoked to be at #SMBE2024! If you're interested in variability/diversity, microbiomes, and/or non-traditional applications of FST, I would love to chat! Poster Weds #44, title: Quantifying the stability of microbiomes and the timescale of antibiotic perturbation with FAVA

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Maike Morrison @maikemorrison.bsky.social · 09/02/2024

Just bought some science stamps! Now we only need a theory edition... store.usps.com/store/produc...

A sheet of colorful stamps titled "life magnified." Stamps include a moth antenna, mold spores, barnacle legs, and diatoms arranged like a snowflake.

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Maike Morrison @maikemorrison.bsky.social · 07/02/2024

I think this is something I asked students about when I was interviewing for grad programs? I know expectations about conference travel can vary a lot between labs and institutions.

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Maike Morrison @maikemorrison.bsky.social · 06/02/2024

I've been really fortunate to have a great PI and have been able to go to whatever conferences we decide make sense for me to attend.

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Maike Morrison @maikemorrison.bsky.social · 05/02/2024

I can't believe we didn't put TAGC on this list, a bunch of us are going this year!! 🤦‍♀️ Thanks for adding!

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Maike Morrison @maikemorrison.bsky.social · 05/02/2024

Summer Schools: CGSI - computationalgenomics.bioinformatics.ucla.edu Santa Fe Institute Complex Systems Summer School - www.santafe.edu/engage/learn...

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Maike Morrison @maikemorrison.bsky.social · 05/02/2024

Conference organizers to check: Cold Spring Harbor Laboratory - meetings.cshl.edu/meetingshome... Gordon Research Conferences - www.grc.org/find-a-confe... Keystone Symposia - www.keystonesymposia.org/conferences/...

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Maike Morrison @maikemorrison.bsky.social · 05/02/2024

Evolution - www.evolutionmeetings.org International Society for Evolution, Medicine, and Public Health (ISEMPH) - isemph.org New Zealand Phylogenomics Meeting - simonelinz.wordpress.com/wai/ Phylomania - www.maths.utas.edu.au/phylomania/p... SMBE - smbe2024.org

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Maike Morrison @maikemorrison.bsky.social · 05/02/2024

AABA - bioanth.org/meetings-and... Analysis of Algorithms Conference - www.math.aau.at/AofA2024/ ASHG - www.ashg.org Cultural Evolution Society- ces2024.webspace.durham.ac.uk EEID - web.cvent.com/event/b9c7e6... ESA - www.esa.org/longbeach2024/ Evolution - www.evolutionmeetings.org

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Maike Morrison @maikemorrison.bsky.social · 05/02/2024

It's conference application season! We in the Rosenberg Lab recently assembled a list of conferences and I thought it could be helpful for other folks doing theoretical population biology. List is below -- feel free to add any we missed!

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егор @egorlappo.me · 15/11/2023

my work on cultural evolution and transmission biases in chess is out today in Proceedings B! royalsocietypublishing.org/doi/10.1098/... humsci.stanford.edu/feature/stud...

humsci.stanford.edu

Study reveals how cultural factors influence chess move choice

A new Stanford study that used population and statistical models to analyze 3.45 million chess games by master players reveals how cultural biases can influence

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Reposted by Maike Morrison

Jonathan Pritchard @jkpritch.bsky.social · 01/10/2023

I'm delighted to release the first half of my new textbook in human genetics: web.stanford.edu/group/pritch... "An Owner's Guide to the Human Genome: an introduction to human population genetics, variation and disease"

web.stanford.edu

An Owner's Guide to the Human Genome

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Randall Munroe @xkcd.com · 12/09/2023

Brassica xkcd.com/2827

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Maike Morrison @maikemorrison.bsky.social · 29/08/2023

In less than 24 hours, we're 3 for 3!

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Maike Morrison @maikemorrison.bsky.social · 28/08/2023

Today I contacted authors of three papers asking them to share data with me. I wasn't optimistic after seeing various Twitter horror stories, but I've received two kind, helpful, generous replies in just a few hours! Cheers to reproducibility!

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