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 π 1 π 0 π¬ 0 π 0
Opinion | Iβm a Genocide Scholar. I Know It When I See It.
My NYT op-ed this morning
Iβm a Genocide Scholar. I Know It When I See It. www.nytimes.com/2025/07/15/o...
15.07.2025 11:54 β π 520 π 234 π¬ 17 π 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 π 1 π 0 π¬ 0 π 0
mmmm alignment to transcriptome :)
09.07.2025 01:46 β π 3 π 0 π¬ 0 π 0
crush your enemies, see them driven before you, and hear the lamentations of their consultants
25.06.2025 02:20 β π 15600 π 3048 π¬ 116 π 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.
today is a good day because I saw the Sucellus statue at the Walters
23.06.2025 00:37 β π 3 π 0 π¬ 0 π 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 π 0 π 0 π¬ 0 π 0
the MD pride flowing through my veins today has got me like
16.04.2025 21:50 β π 10 π 1 π¬ 1 π 0
Apparently not all my popgen advice is good.
16.04.2025 00:09 β π 31 π 5 π¬ 3 π 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.
had a great time competing in @naqt.com's Intercollegiate Championship Tournament this weekend with my JHU teammates!
08.04.2025 14:55 β π 8 π 0 π¬ 0 π 0
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 π 3 π 0 π¬ 0 π 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 π 1 π 0 π¬ 0 π 0
that's my favorite DEST 2.0 lead author π
14.03.2025 18:48 β π 2 π 0 π¬ 1 π 0
"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 π 358 π 110 π¬ 13 π 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 π 2 π 0 π¬ 1 π 0
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 βοΈ
#standupforscience2025
05.03.2025 14:08 β π 351 π 145 π¬ 5 π 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.
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 π 1 π 0 π¬ 0 π 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.
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 π 2 π 0 π¬ 0 π 0
holding strong opinions about movies that I haven't seen has never been so exhilarating
23.01.2025 18:51 β π 0 π 0 π¬ 0 π 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.
i love these little guys
08.01.2025 15:18 β π 3 π 0 π¬ 0 π 0
maybe it's NYC workers disproportionately getting to work virtually?
03.01.2025 00:34 β π 0 π 0 π¬ 0 π 0
may your 2025 return-to-office begin with an error-free `snakemake -n`
02.01.2025 14:45 β π 1 π 0 π¬ 0 π 0
Contempt (1963)
23.12.2024 23:23 β π 0 π 0 π¬ 0 π 0
it has occurred to me that end-inclusivity is useful for DataFrames with non-numeric indices
17.12.2024 15:06 β π 0 π 0 π¬ 0 π 0
am I a data science influencer if I complain about how .loc[] in Pandas is end-inclusive
17.12.2024 13:54 β π 1 π 0 π¬ 1 π 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 π 1 π 0 π¬ 0 π 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 π 1 π 0 π¬ 1 π 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 π 1 π 0 π¬ 0 π 0
retvrn to charging a reasonable fee for a good service that delivers real value
13.11.2024 17:34 β π 1820 π 71 π¬ 24 π 12
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 π 1 π 0 π¬ 0 π 0
Hoping to be: Minneapolis Mayor. Currently: State Senator for the Southside, husband, renter, son of Somali immigrants, long-time advocate for working people.
Official Bluesky account for NOAA's National Weather Service.
Incoming assistant professor at University of Maryland, College Park β’ NSF PRFB postdoc β’ PhD from Bhattacharya lab @RutgersU β’ Passionate about algae / protists + genomics + evolutionary biology + microscopy β’ vanettenlab.org #NewPI
Opinions are my own.
economist // former Charlottesville state rep ποΈ // UVa prof // election reform πΊπΈ // I write about bright lights for democracy β¨
Day job on climate change policy. Writing about landscape and the arts in the occasional spare moment...
Research Scientist at Johns Hopkins University, interested in molecular biology and genetics (that's as specific as possible), mom, reading fanatic (she/her/hers, my views are my own)
UAW members are leading the fight for economic justice. This UAW account is administered by union members represented by the NewsGuild-CWA 34022. https://linktr.ee/uawunion
I'm an associate professor @UofUBiology
gagnonlab.org | fish stuff in and out of the tank
Professor of planetary science at Johns Hopkins. Titanβs biggest fan. Pomeranian wrangler. Runner. Love many, trust few, always paddle your own canoe. She/her. sarahhorst.com
Planetdr.26 on signal
Assemblymember. Democratic Nominee for Mayor of NYC. Running to freeze the rent, make buses fast + free, and deliver universal childcare. Democratic Socialist. zohranfornyc.com
Physics of membranes and self-assembly || Biophysics postdoc at Johns Hopkins || Previously Penn State -> Carnegie Mellon || views are now yours, good luck || /dΚΙͺf/ ||
www.samuelfoley.com
Associate Professor of Biophysics at Johns Hopkins. Theory, modeling, and computation. Living systems and statistical mechanics. https://sites.krieger.jhu.edu/johnson-lab/
Scientist working in computer science and genomics. arundas.org
PhD from Schatz Lab @ JHU CS. Brown '18. He/His/Him. #YNWA π
Evolutionary biologist at Yale University. https://dunnlab.org
Worker-owned radical bookstore and cafe in Baltimore, the greatest city in America
PhD candidate at Johns Hopkins | Alexis Battle lab | Computational Biology | Machine Learning | He/Him
Running for Congress (IL-09) because we deserve Democrats who actually do something | katforillinois.com
Associate Professor
DFCI & HMS
Professor at UVA Law, sometimes civil rights / criminal defense lawyer, full-time Ruth wrangler (RIP Haley). Stuff I write here: https://papers.ssrn.com/sol3/cf_dev/AbsByAuth.cfm?per_id=1785600
Comp Bio @ UMich | Incoming PhD @ Cornell | NSF Graduate Research Fellow | popgen.dev