Matt Johnson, PhD

Here is a link to a video of the speech.

xcancel.com/netflix/stat...

Guess who’s got two thumbs, a sword, and tenure? 🎉🍾 grateful to the wonderful friends and colleagues and collaborators who have enabled me getting here 💕 @mossmatters.bsky.social

Good news is hard to come by, so I must celebrate a great week:
• Paper accepted
• Paper submitted
• 3 of my lab undergrads got into grad school
• Scholarship offers to both of my prospective PhD students
• My faculty development leave approved for Spring 2027
• @lisalimeri.bsky.social got tenure!

SPrOUT: A computational and targeted sequencing approach for mixed plant DNA identification with Angiosperms353 https://www.biorxiv.org/content/10.64898/2026.02.20.707031v1

GitHub - nhu92/SPrOUT: A computational pipeline designed for predicting species taxonomic information from single and mixed plant samples, using target sequencing arrays. A computational pipeline designed for predicting species taxonomic information from single and mixed plant samples, using target sequencing arrays. - nhu92/SPrOUT

Github page: github.com/nhu92/SPrOUT

logo for SPrOUT: Species Prediction of Unknown Taxa - a line drawing of a plant with two green leaves emerging from a flask containing multiple DNA helices. Logo designed by Lisa Limeri, with images from the Noun Project flask from Noun Project user Humam flower from Noun Project user Vanicon studio DNA from Noun Project user Akhmad Zaini

Figure from the linked preprint, showing the relationship between the number of Angiosperms353 reference genes and Accuracy of detecting plant families in mixed reads. Based on several z-score values, SPrOUT is generally at 98% accuracy with fewer than 100 genes.

New from our lab! Introducing SPrOUT: Species Prediction of Unknown Taxa.

We developed and tested a novel method to ID plants in mixed DNA with Angiosperms353 using cumulative phylogenetic distances. >98% accuracy to family level for in silico and real test data.

www.biorxiv.org/content/10.6...

Well well well. We witch, ya?

roses are red
violets are blue
anthocyanin!
(betalain, too)

It was "orgo" for us at Duke in the 00s, "o-chem" at Texas Tech since I've been here. In my Bio department, "organic" would get it confused with our "Organic Evolution" course.

Texas Tech struggles with new policy on gender, race The system’s chancellor meant to instill clarity and accountability, but three weeks into the spring semester, some instructors say the standards have led to “censorship.”

www.texastribune.org/2026/02/04/t...

A number of our students got the following comment back on a rejection for the NSF GFRP. They are in an eligible STEM field. Is this something people in other places are getting too? Is it a quirk or targeted?

This must be weird news to see if you’re one of the literally hundreds or even thousands of university administrators who preemptively censored faculty, scrubbed websites, changed the names of centers, etc.

A curved stone bench with a chiseled inscription: "Our lives begin to end the day we become silent about things that matter" - Rev Dr Martin Luther King Jr

Reflecting today on this quote etched into a bench on campus, as I wonder how many on that campus understand its message.

"You died when you refused to stand up for right, you died when you refused to stand up for truth, you died when you refused to stand up for justice." youtu.be/pOjpaIO2seY?...

Stop scrolling and post two characters who bring you happiness.

If not equally important, did they give a ratio of importance? Or generally how broader impacts would be evaluated?

Here to stay, I’m afraid

Promotional graphic on a red background featuring two black-and-white raglan shirts from the Botanical Society of America’s “Stranger Plants” collection. One shirt shows a large illustrated plant scene; the other displays a grid of illustrated unusual plants. White text reads “We love the Stranger Plants BSA SWAG!” Below, descriptive text explains that the shirts highlight strange plants, with common and scientific names listed on the back in a concert-style format. A QR code labeled “Scan to Shop” appears at the lower right, along with BSA logos and text promoting additional BSA apparel.

We 💚 the Stranger Plants—and now they’re on #BSAswag!

The shirts feature bold illustrations by BSA’s own Catrina Adams, with a list of each species by common & scientific name on the back.

BSA members (exp. 2026+) get 10% off—email aneely@botany.org for code.

www.bonfire.com/store/bsa-wi...

If Stranger Things were released today, it would be set in 1992. Feeling old yet?

Will also feature Sofia Rodriguez, an undergraduate researcher in my lab who attended COP30. Should be a fun conversation!

Link below👇

A banner for the event listing the title "Inside COP30" and headshots of the four participants.

Join me and my @texastech.bsky.social Climate Center colleagues for a breakdown of all things COP30, in an hour.

Nick is an ecologist, Ting is an engineer, Bryan is a humanities scholar, and you know me: so it should be a great discussion.

Free & virtual!

www.eventbrite.com/e/inside-cop...

Giant chromosomes of a tiny plant - the complete telomere-to-telomere genome assembly of the simple thalloid liverwort Apopellia endiviifolia (Jungermanniopsida, Marchantiophyta) AbstractBackground. The liverwort A. endiviifolia, a dioicous, simple thalloid species, is notable for its cryptic diversity, habitat adaptability, genomic

Our paper “Giant chromosomes of a tiny plant” is out in @gigascience.bsky.social! We present a T2T genome assembly of the simple thalloid liverwort Apopellia endiviifolia with truly giant chromosomes. 🌱🧬 #plantgenomics #T2T #liverworts @nanoporetech.com
Thanks @ncn.gov.pl !

tinyurl.com/m8tkkxd3

Since I had baked a loaf of bread in anticipation of leftovers, I mourned the loss of turkey that evening

Everyone is sure to remind my dad of the time he packed up the leftover turkey in Ziploc bags but for lack of counter space placed them… in the open dishwasher.

This was discovered only hours later after the dishwasher ran.

The Ziploc bags were open.

The frequency and importance of polyploidy in tropical rainforest tree radiations The presence of two or more copies of the genome in an organism, termed ‘polyploidy’, is a crucial force in plant evolution, generating genetic, phenotypic and ecological diversity. The Amazonian tr...

New paper just posted with @rschley.bsky.social et al: doi.org/10.1111/nph.... (1/n)

Update: the university is now allegedly offering compensation to faculty who move their exams because of a football game we're not even guaranteed to play in yet.

1-panel SMBC comic update - Two people are talking while seated at computers. One of them says : "Wait! Look, if we change our hypothesis a little, run this other model, and then make a few tweaks to the variables... BAM! No need to publish. The weekend if free." A caption below the panel reads as follows : "New scientific trend: reverse p-hacking. P-hacking is the practice of manipulating data until a statistically significant result is found, here they are doing the opposite to avoid work.

There's got to be SOME hypothesis that makes our experiment useless. THINK!

COMIC ◆ www.smbc-comics.com/comic/stats-3
PATREON ◆ www.patreon.com/ZachWeinersm...
STORE ◆ smbc-store.myshopify.com

We do use student eval scores (among many other things) in T&P decisions. I was thinking the opposite, by releasing this guidance now any faculty who DOESN'T change their final (to value 🎓over 🏈) will now be blasted in their student evals. And faculty have to decide before evals close...

Man in a Duke t-shirt with face painted blue and white, arm outstretched at the 2010 National Championship game

Look, I get being a fan. This is me at the 2010 National Championship game. Despite winning on a weeknight, Duke did not cancel classes. I know because I had get someone to fill in as a TA because I was in Indianapolis. Nobody asked the faculty to pretty please let academics take a back seat.

Exempt the final exam for students who have maintained a high average in the course. Give students a choice to adjust grading by weighting another exam more heavily or revising the grading schema. Contact [email redacted] for assistance with changes in RaiderCanvas. Replace the final exam with an alternative assignment that meets the course’s learning goals. Move the final exam online and consider a broader testing window. Continue with your scheduled exam time on Saturday, Dec. 6.

Because the Big XII championship game is during final exams, our Provost suggests faculty choose from ideas including "exempt students from the exam" and "change your whole method of assessment" with 1 week notice

More than usual I'm feeling I work for a football team with a school on the side.

Wahlund Effect Wednesdays?