iiinova — where your digital self keeps evolving

David Bass @davidb256.bsky.social · 28/09/2026

is this the greatest #ratio in modern science

A screenshot of a Google Scholar search result that shows the 2017 paper "DBSCAN revisited, revisited" with more than 10 times as many citations as the 2015 paper "DBSCAN revisited"

David Bass @davidb256.bsky.social · 07/08/2026

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.

Google Maps screenshot showing several miles of the Mississippi–Louisiana border as a dotted line. The line mostly conforms to the river, but contains oxbow shapes that reflect long-gone changes in the River's flow

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David Bass @davidb256.bsky.social · 03/08/2026

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

A map of Spain showing its autonomous communities, which are its first level of regional administration. Ceuta and Melilla, two Spanish exclaves that in the region of North Africa otherwise controlled by Morocco and are in the news, appear as islands instead of parts of North Africa, since the map does not shade in or draw borders for anything not owned by Spain.

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David Bass @davidb256.bsky.social · 14/07/2026

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

Photo of me standing next to my poster at a research conference.

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David Bass @davidb256.bsky.social · 04/03/2026

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

A plot showing the flow of metagenetic material in patients receiving fecal microbiota transplantation. Thick, colorful bands connect a column of donor patients on the left to a column of recipient patients on the right.

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David Bass @davidb256.bsky.social · 09/12/2025

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

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David Bass @davidb256.bsky.social · 05/11/2025

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

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David Bass @davidb256.bsky.social · 10/10/2025

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.)

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

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David Bass @davidb256.bsky.social · 20/08/2025

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

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David Bass @davidb256.bsky.social · 05/08/2025

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.)

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.

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David Bass @davidb256.bsky.social · 23/06/2025

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

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.

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David Bass @davidb256.bsky.social · 16/04/2025

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

An image of Mithrun, an anime character from Dungeon Meshi, photoshopped to be decked out in Maryland gear and hanging out in Baltimore's Innher Harbor. She is non-chalant, but conveys great pride in her state.

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David Bass @davidb256.bsky.social · 08/04/2025

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

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.

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David Bass @davidb256.bsky.social · 26/03/2025

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

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

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David Bass @davidb256.bsky.social · 14/02/2025

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

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.

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David Bass @davidb256.bsky.social · 13/02/2025

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

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.

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David Bass @davidb256.bsky.social · 11/11/2024

this is a rhodopsin structure fan account

3D structure of the Drosophila melanogaster protein RH2, a G-protein coupled receptor homologous to human rhodopsin. As a GPCR, it features seven alpha-helical transmembrane domains; one of them is highlighted.

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David Bass @davidb256.bsky.social · 17/09/2024

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

A dense blue scatterplot of putative introns' lengths versus the count of aligned reads that were spliced over them. A red quadratic regression curve fits poorly, interestingly plunging down below the (positive-valued) y-axis between ~7500 and ~20000 bp in length due to the curve being fit to non-log-transformed data, but then displayed with a log-transformed y-axis.

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David Bass @davidb256.bsky.social · 29/01/2024

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

A graph illustrates the formation of a heterotrimer. The reaction network is parameterized by two stage-specific, rate constants, k_dim and k_tri.

A presentation slide is titled "Kinetic trapping inhibits molecular self-assembly. Three sketches of a cell attempting to complete a sufficiently long microtubule are labelled, respectively, "Cell seeks to span self with microtubule," "Tubulin subunits bind to existing microtubule: No kinetic trapping," and "Tubulin subunits form new microtubule: Kinetic trapping."

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