David Bass
@davidb256.bsky.social
he/him | PhD student doing computational genomics at JHU Dept of Bio and CCB | TRU-UE Local 197 member | quizbowler, PACE member | UVA alumnus
`|=` is a valid operator in Python for replacing a list with its union with another list, e.g. `x |= y` !!!!
February 13, 2026 at 3:13 AM
`|=` 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__":`
January 20, 2026 at 1:29 PM
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
January 18, 2026 at 9:01 PM
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
December 16, 2025 at 6:14 PM
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
December 9, 2025 at 9:15 PM
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
December 9, 2025 at 9:08 PM
nearly had a crisis of faith in Snakemake today
so much depends
upon
Cloudflare
service
even the
poetry-
foundation
dot org.
upon
Cloudflare
service
even the
poetry-
foundation
dot org.
November 18, 2025 at 2:25 PM
so much depends
upon
Cloudflare
service
even the
poetry-
foundation
dot org.
upon
Cloudflare
service
even the
poetry-
foundation
dot org.
biblically accurate sequence logo (Hsiao et al. 2018, Genome Res., fig. 2G)
November 5, 2025 at 3:17 PM
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.)
October 10, 2025 at 2:59 PM
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"
September 29, 2025 at 6:47 PM
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
September 1, 2025 at 1:23 PM
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 :/
August 28, 2025 at 3:53 PM
NYT Mini seems to be paywalled starting today :/
Reposted by David Bass
@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
🔗 doi.org/10.1093/molbev/msaf132
#evobio #molbio #drosophila
August 20, 2025 at 5:52 PM
@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
🔗 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
August 20, 2025 at 7:39 PM
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/...
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
academic.oup.com
August 19, 2025 at 12:56 PM
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
August 14, 2025 at 8:49 PM
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
August 12, 2025 at 2:04 PM
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.)
August 5, 2025 at 5:21 PM
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
July 23, 2025 at 1:55 PM
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
Reposted by David Bass
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...
I’m a Genocide Scholar. I Know It When I See It. www.nytimes.com/2025/07/15/o...
Opinion | I’m a Genocide Scholar. I Know It When I See It.
www.nytimes.com
July 15, 2025 at 11:54 AM
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...
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
July 14, 2025 at 7:14 PM
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 :)
July 9, 2025 at 1:46 AM
mmmm alignment to transcriptome :)
Reposted by David Bass
crush your enemies, see them driven before you, and hear the lamentations of their consultants
June 25, 2025 at 2:20 AM
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
June 23, 2025 at 12:37 AM
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
May 27, 2025 at 6:27 PM
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