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David Bass

@davidb256.bsky.social

he | PhD student doing computational genomics at JHU Dept of Bio and CCB | TRU-UE Local 197 member | quizbowler, PACE member | UVA alumnus

155 Followers  |  214 Following  |  33 Posts  |  Joined: 13.11.2023  |  1.5471

Latest posts by davidb256.bsky.social on Bluesky

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

23.07.2025 13:55 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
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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...

15.07.2025 11:54 β€” πŸ‘ 520    πŸ” 234    πŸ’¬ 17    πŸ“Œ 32

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

14.07.2025 19:14 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

mmmm alignment to transcriptome :)

09.07.2025 01:46 β€” πŸ‘ 3    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

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

25.06.2025 02:20 β€” πŸ‘ 15600    πŸ” 3048    πŸ’¬ 116    πŸ“Œ 97
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.

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

23.06.2025 00:37 β€” πŸ‘ 3    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

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

27.05.2025 18:27 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

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

16.04.2025 21:50 β€” πŸ‘ 10    πŸ” 1    πŸ’¬ 1    πŸ“Œ 0
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Apparently not all my popgen advice is good.

16.04.2025 00:09 β€” πŸ‘ 31    πŸ” 5    πŸ’¬ 3    πŸ“Œ 1
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.

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!

08.04.2025 14:55 β€” πŸ‘ 8    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
A promotional image of MacGyver, looking cool and carrying a missile, for the original '80s TV series.

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

26.03.2025 03:28 β€” πŸ‘ 3    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

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)

16.03.2025 23:26 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

that's my favorite DEST 2.0 lead author 😍

14.03.2025 18:48 β€” πŸ‘ 2    πŸ” 0    πŸ’¬ 1    πŸ“Œ 0
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"The real crisis is not that public health β€” which is fundamentally about policies dictating the distribution of
resources required to protect human life β€” has been politicized. It is that it has not been politicized nearly enough."β€” @ericreinhart.bsky.social
www.nature.com/articles/d41...

11.03.2025 16:48 β€” πŸ‘ 358    πŸ” 110    πŸ’¬ 13    πŸ“Œ 12

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"

10.03.2025 04:27 β€” πŸ‘ 2    πŸ” 0    πŸ’¬ 1    πŸ“Œ 0
Navy background with white text that says "2 days until stand up for science"

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 β˜€οΈ

#standupforscience2025

05.03.2025 14:08 β€” πŸ‘ 351    πŸ” 145    πŸ’¬ 5    πŸ“Œ 31
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.

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 PluviΓ΄se in the year 233, the day of the topologically associating domain

14.02.2025 15:18 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
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.

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

13.02.2025 15:41 β€” πŸ‘ 2    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

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

23.01.2025 18:51 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
A complicated, multi-colored, rectangular visualization of eras of geologic time from the Wikipedia page for the Precambrian. The vertical axis shows time in millions of years ago, and the horizontal axis shows increasing precision of terms in the hierarchy of geologic eras, epochs, eons, whatever, etc.

A complicated, multi-colored, rectangular visualization of eras of geologic time from the Wikipedia page for the Precambrian. The vertical axis shows time in millions of years ago, and the horizontal axis shows increasing precision of terms in the hierarchy of geologic eras, epochs, eons, whatever, etc.

i love these little guys

08.01.2025 15:18 β€” πŸ‘ 3    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

maybe it's NYC workers disproportionately getting to work virtually?

03.01.2025 00:34 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

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

02.01.2025 14:45 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

Contempt (1963)

23.12.2024 23:23 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

it has occurred to me that end-inclusivity is useful for DataFrames with non-numeric indices

17.12.2024 15:06 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

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

17.12.2024 13:54 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 1    πŸ“Œ 0

watched Eyes Wide Shut for the first time this weekend, just had the thought, "I wonder if there's the shitty 'Die Hard is a Christmas movie'-type discourse but for Eyes Wide Shut," and a quick search has confirmed my suspicions; good movie, lots of Christmas trees, maybe not for the whole family

09.12.2024 16:08 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

Motzi Bread in Charles Village is incredible, I've never had more moist (but in a good way!) sourdough

08.12.2024 04:50 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 1    πŸ“Œ 0

it's a "learning the difference between snakemake's -j and -c flags the hard way" kinda morning

02.12.2024 14:00 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

retvrn to charging a reasonable fee for a good service that delivers real value

13.11.2024 17:34 β€” πŸ‘ 1820    πŸ” 71    πŸ’¬ 24    πŸ“Œ 12
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Footprints of worldwide adaptation in structured populations of D. melanogaster through the expanded DEST 2.0 genomic resource Large scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster , we p...

My second-ever publication is now on bioRxiv! I worked with Joaquin Nunez and @berglandalan.bsky.social to perform demographic inference on global D. mel. samples, testing the validity of putative populations within the Americas and Europe. I got to revitalize some of my undergrad work into Text S3.

12.11.2024 14:13 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

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