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 · 14/09/2026

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!

040

David Bass @davidb256.bsky.social · 06/09/2026

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

000

David Bass @davidb256.bsky.social · 25/08/2026

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

000

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

010

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

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

010

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.

000

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.

060

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

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

000

David Bass @davidb256.bsky.social · 06/04/2026

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"

010

David Bass @davidb256.bsky.social · 05/03/2026

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

000

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.

000

David Bass @davidb256.bsky.social · 24/02/2026

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

010

David Bass @davidb256.bsky.social · 13/02/2026

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

000

David Bass @davidb256.bsky.social · 20/01/2026

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

000

David Bass @davidb256.bsky.social · 18/01/2026

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

000

David Bass @davidb256.bsky.social · 16/12/2025

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

000

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

071

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

nearly had a crisis of faith in Snakemake today

020

David Bass @davidb256.bsky.social · 18/11/2025

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

070

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

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

010

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.

000

David Bass @davidb256.bsky.social · 01/09/2025

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

000

David Bass @davidb256.bsky.social · 28/08/2025

NYT Mini seems to be paywalled starting today :/

100

Reposted by David Bass

Molecular Biology and Evolution @molbioevol.bsky.social · 20/08/2025

@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

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

11910

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

010

David Bass @davidb256.bsky.social · 14/08/2025

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

100

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.

072

David Bass @davidb256.bsky.social · 23/07/2025

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

010

Reposted by David Bass

omerbartov.bsky.social @omerbartov.bsky.social · 15/07/2025

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...

nytimes.com

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

14504224

David Bass @davidb256.bsky.social · 14/07/2025

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

010

David Bass @davidb256.bsky.social · 09/07/2025

mmmm alignment to transcriptome :)

030

Reposted by David Bass

Olúfẹ́mi O. Táíwò @olufemiotaiwo.bsky.social · 25/06/2025

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

113152102955

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.

030

David Bass @davidb256.bsky.social · 27/05/2025

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

000

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.

1101

Reposted by David Bass

Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 16/04/2025

Apparently not all my popgen advice is good.

3315

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.

080

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.

030

David Bass @davidb256.bsky.social · 16/03/2025

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)

010

Reposted by David Bass

Eric Topol @erictopol.bsky.social · 11/03/2025

"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...

12354109

David Bass @davidb256.bsky.social · 10/03/2025

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"

120

Reposted by David Bass

Stand Up for Science! @standupforscience.net · 05/03/2025

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

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

5347144

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.

010

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.

020

David Bass @davidb256.bsky.social · 23/01/2025

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

000

David Bass @davidb256.bsky.social · 02/01/2025

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

010

David Bass @davidb256.bsky.social · 17/12/2024

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

110