i've been unknowingly abbreviating "alignment" as both "alnmt" and "almnt" and it has finally caught up with me

figure from [Sibley et al. 2015](doi.org/10.1038/natu...) that shows how the brain dominates every other tissue's expression of long genes. each line is essentially a histogram, normalized w.r.t. the brain transcriptome's distribution. cool that neural complexity manifests in such a simple stat

nearly had a crisis of faith in Snakemake today

so much depends upon Cloudflare service even the poetry- foundation dot org.

biblically accurate sequence logo (Hsiao et al. 2018, Genome Res., fig. 2G)

interesting use of popgen in distinguishing SNVs from RNA edit sites: "a pair of SNPs within the mRNA ... possess perfect allelic linkage. In contrast ... RNA editing sites do not generally show significant allelic linkage with each other nor with SNPs" (L-GIREMI, Liu et al. 2023 Genome Biol.)

tfw you get to "A Squeeze of the Hand"

it's the kind of "prepping for union's Labor Day BBQ" morning that reminds a man just how heavy four watermelons can be

NYT Mini seems to be paywalled starting today :/

@jcbnunez.bsky.social et al. present an expanded release of the community-generated resource Drosophila Evolution over Space and Time (DEST 2.0), and showcase it by studying the species' demographic history and signatures of adaptation. 🔗 doi.org/10.1093/molbev/msaf132 #evobio #molbio #drosophila

accidentally applying `.set_xbound(0, 1)` instead of `.set_ybound(0, 1)` turns violin plots into KDE plots that cling to the walls

DEST 2.0 is now up on MBE! academic.oup.com/mbe/article/...

beating the dead horse here, but I just tried my hand at asking GPT-4.1 (JHU gives us access to a bunch of premium LLMs for free) to help me look for a certain type of data, and it told me about four papers, precisely one of which actually exists. impressively wasteful

just read The Unbearable Lightness of Being, and the quote "kitsch is the absolute denial of shit" reminded me of this post about genAI refusing to draw accurate baby birds because they're not cute

fascinated by this plot for listing permutations (namely, the orders in which four introns can be spliced from a given RNA transcript) and denoting their frequencies with line thickness and shade. It avoids needing to enumerate all 4! permutations. from Choquet et al. 2023 (Nat. Struct. Mol. Biol.)

is there a pre-built/easy way to filter a BAM file to the reads that are aligned spliced over a given intron? The best that I can come up with is to do initial filtering with pysam's fetch function, then examine each read's alignment position and CIGAR string

My NYT op-ed this morning I’m a Genocide Scholar. I Know It When I See It. www.nytimes.com/2025/07/15/o...

just learned that you can seamlessly concatenate sequences produced by brace expansion with explicit strings in Bash, e.g. `{1..22} X Y` to list all chromosome names. truly a language of many tricks and wiles

mmmm alignment to transcriptome :)

crush your enemies, see them driven before you, and hear the lamentations of their consultants

today is a good day because I saw the Sucellus statue at the Walters

I just finished Marilynne Robinson's Gilead. Incredible book about living on the edge of political violence and celebrating uncertainty. Makes me want to read the New Testament

the MD pride flowing through my veins today has got me like

Apparently not all my popgen advice is good.

had a great time competing in @naqt.com's Intercollegiate Championship Tournament this weekend with my JHU teammates!

how it feels to zoom out in order to see previous lines of output in a Linux screen after having your (foolish) attempt to scroll rewarded with a bunch of "^]]A"s

my Jupyter notebooks are vibrant ecosystems in which data analysis for my research and Balatro odds calculations coexist side-by-side (the expected xMult from five Bloodstone procs is 3.05)

"The real crisis is not that public health — which is fundamentally about policies dictating the distribution of resources required to protect human life — has been politicized. It is that it has not been politicized nearly enough."— @ericreinhart.bsky.social www.nature.com/articles/d41...

my partner and I just watched Koyaanisqatsi on archive.org and it was reversed, but we didn't notice until after finishing it... I was like "oh cool the music is Einstein on the Beach but backwards" and "wow you don't notice that the space shuttle explodes in reverse until a minute in"

2 DAYS until we STAND UP FOR SCIENCE! More information on local sites available at www.standupforscience2025.org ☀️ #standupforscience2025

it's Sextidi the 26th of Pluviôse in the year 233, the day of the topologically associating domain

French Republican calendar but instead of rural day names it's genomics day names and today is recursive splicing

holding strong opinions about movies that I haven't seen has never been so exhilarating

i love these little guys

may your 2025 return-to-office begin with an error-free `snakemake -n`

am I a data science influencer if I complain about how .loc[] in Pandas is end-inclusive

watched Eyes Wide Shut for the first time this weekend, just had the thought, "I wonder if there's the shitty 'Die Hard is a Christmas movie'-type discourse but for Eyes Wide Shut," and a quick search has confirmed my suspicions; good movie, lots of Christmas trees, maybe not for the whole family

Motzi Bread in Charles Village is incredible, I've never had more moist (but in a good way!) sourdough

it's a "learning the difference between snakemake's -j and -c flags the hard way" kinda morning

retvrn to charging a reasonable fee for a good service that delivers real value

My second-ever publication is now on bioRxiv! I worked with Joaquin Nunez and @berglandalan.bsky.social to perform demographic inference on global D. mel. samples, testing the validity of putative populations within the Americas and Europe. I got to revitalize some of my undergrad work into Text S3.

this is a rhodopsin structure fan account

Interesting shape of a quadratic regression fit to data that is, uh, not particularly quadratic and also log-transformed

it's a `cat head_m0.diff.sam | awk '{print $1}' | sort | uniq -c | awk '{print $1}' | sort -n | uniq -c` kinda afternoon

it's a `mamba install conda-forge::scikit-posthocs` kinda night

My first-ever preprint is up on bioRxiv! I contributed demographic inference of North American and European Daphnia populations to help describe why so many Daphnia alleles are globally maintained despite long-ago divergence times among (sub)species: www.biorxiv.org/content/10.1...

Joined by nearly 1,000 of my grad worker colleagues, I signed my union's strike pledge this week. We will continue to organize until JHU admin recognizes that we will not stop fighting for living wages, our fair share of the profit that we bring to our university.

Happy about these Google Slides illustrations that I made for a rotation project presentation on inference of rate constants from (simulated) experimental data describing kinetic trapping

they did a gay wedding at the chicago rat hole

I really don't understand how I end up on en.wikipedia.org/wiki/Glossar... as often as I do.