David Bass

A figure panel showing a sketch of how, due to genetic linkage, SNPs are distinguished from RNA editing sites by sharing more mutual information.

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 :/

MBE - Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource

@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

Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource Abstract. Large-scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population g

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

two of the three fake DOI URLs take me to an error page, while the third takes me to "Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines." sounds cool, but very much not what I research

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

A tumblr textpost, which I of course screenshotted from Reddit, that shows two images of "baby pigeons" created by generative "AI." The images are cute, depicting the babies as downsized adults instead of the ugly scruffy things that most baby birds actually are. A tumblr user writes "the ai's aversion to producing anything that's not aesthetically pleasing dentist office artwork leaves it unable to comprehend true beauty" and attaches a real image of a baby bird, which is ugly and lacks feathers.

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

Panel of figure 2 of Choquet et al. 2023 "Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts" (Nat. Struct. Mol. Biol.) that uses zig-zagging lines of different thicknesses and (gray) colors to show frequencies of permutations of splicing order of four introns in a representative transcript.

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

Opinion | I’m a Genocide Scholar. I Know It When I See It.

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

Picture from the Walters Museum of Art of their ~foot-tall bronze statue of the Celtic/Gallo-Roman deity Sucellus, standing in contraposto and holding up a mallet that has been lost to time. Floating behind him is a large mallet with five smaller mallets protruding from its head.

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.

Group photo of the Johns Hopkins University quizbowl team, shortly before round 1 of NAQT's 2025 Intercollegiate Championship Tournament. We are (mostly) wearing matching navy team sweaters. We sit in a large hotel convention space.

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

A promotional image of MacGyver, looking cool and carrying a missile, for the original '80s TV series.

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)

that's my favorite DEST 2.0 lead author 😍

"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"

Navy background with white text that says "2 days until stand up for science"

2 DAYS until we STAND UP FOR SCIENCE!

More information on local sites available at www.standupforscience2025.org ☀️

#standupforscience2025

Figure 1 from Matharu and Ahituv 2015 "Minor Loops in Major Folds" shows (A) a cartoon of chromatin in the nucleus partitioned into differently colored topologically associating domains (TADs), (B) a cartoon of an individual TAD's structure and interactions with the nuclear membrane, and (C) a genetic track displaying regulatory elements, genes, and TAD boundaries within a single (active) TAD compartment, highlighted with a green triangle evocative of HiC heatmap output.

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

Excerpt from Fig. 2a of Sibley et al. 2016's "Lessons from non-canonical splicing" that illustrates the signature "sawtooth" pattern of RNA-seq read coverage in recursively spliced introns.

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