David Bass

is this the greatest #ratio in modern science

My first preprint of grad school is up on bioRxiv. It's been an exciting journey, from getting inspired by a conversation about squid polymerases ~1.5 years ago, presenting at ISMB this summer, and now submitting for peer review!

the real sea people are the ones who violated Zeus' Law along the way

google sheets does not let you simultaneously underline and strikethrough text in a cell... oppression of my shift+alt+5-based lifestyle

the Mississippi–Louisiana border was drawn at the Mississippi River, but a Mississippi River long past. Extinct oxbows are visible all along the border on Google Maps.

why is it the "roof" of your mouth and not the "ceiling"

the map on the Wikipedia page "Autonomous communities of Spain" (Habbit 2007) abstracts out Morocco into just a word, making Melilla and Ceuta appear as islands

it was exciting to get so many good (and tough!) questions yesterday! #ISMB2026

excited for #ISMB next week! come talk to me about recursive splicing on Monday at poster A-171

the Wikipedia page for the United States Central Command specifies that the United States Space Command "is among four [commands] that are headquartered outside their area of operations"

daily inspo: Push an API key to GitHub! You can do it!

apparently this variant of the Sankey diagram is called an "alluvial plot" (fig. from Behling et al. 2024, doi.org/10.1186/s401...)

matplotlib's `wheat` color is a 10/10

`|=` is a valid operator in Python for replacing a list with its union with another list, e.g. `x |= y` !!!!

the #1 reason not to use inline suggestions from Copilot is to preserve the joy of typing `if __name__ == "__main__":`

no other choice is a great movie and contains a lot of really fun camera tricks with phone/tablet screens

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.)

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/...

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`