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Arun Das

@arun-das.bsky.social
76 followers 88 following 36 posts

Working on computer science solutions to genomic problems. More info: arundas.org . Previously: PhD, Schatz Lab @ JHU; CS @ Brown. He/His/Him. #YNWA 🍉

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Reposted by Arun Das
Aurelien Mondon @aurelmondon.com · 14/09/2026
"When a bridge collapses, you don’t analyze whether the bridge was ethical or sentient or why it decided to collapse. You ask, who is the person who built this bridge to be so flimsy?" Excellent from @timnitgebru.blacksky.app www.wired.com/story/one-of...
wired.com
One of AI’s Fiercest Critics Says All the Doom Talk Is ‘Meant to Distract Us’
Timnit Gebru argues that AI companies are stoking fears of extinction to avoid discussing actual harms, like autonomous weapons.
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Adam Phillippy @aphillippy.bsky.social · 06/08/2026
For the past 30 years, “whole-genome sequencing” has been a misnomer. Today the T2T Consortium publishes a dozen papers heralding a future of truly complete genomes for humans and nearly any vertebrate 👨‍🔬🐒🐦🐀🦒🐎🫏🐹🐟 (sorry, no salamanders): www.cell.com/consortium/t... 🧵[1/15]
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Marina Purkiss @marina-purkiss.bsky.social · 19/07/2026
Finding this quite hard to stomach from a country that is bombing the shit out of other countries…
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Sina Majidian @sinamajidian.bsky.social · 09/07/2026
JOB ALERT! I'm hiring two postdocs in Computational Genomics to join our lab in beautiful Gothenburg, Sweden. Please share and repost! CGRLab.github.io/research/
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Reposted by Arun Das
Jeff Sharlet @jeffsharlet.bsky.social · 16/06/2026
At the end of the term I asked my college creative wriing students to submit anonymous thoughts on AI. No real surprises: Mood ranges from resignation to despair, capitulation from embittered erosion of standards to total, feelings of betrayal from deep to furious. 1/
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Aaron Reichlin-Melnick @reichlinmelnick.bsky.social · 22/05/2026
🚨 🚨 🚨 NEW: A shocking @USCIS memo seems to declare that hundreds of thousands of immigrants living in this country and applying for green cards must instead apply for visas abroad; which could MASSIVELY disrupt lives. 🧵 on what we know, and what we don’t.
U.S. Citizenship and Immigration
Services
PM-602-0199
May 21, 2026
Policy Memorandum
SUBJECT: Adjustment of Status is a Matter of Discretion and Administrative Grace, and an Extraordinary Relief that Permits Applicants to Dispense with the Ordinary Consular Visa Process
Purpose
This memorandum reminds officers and the public that adjustment of status under section 245 of the Immigration and Nationality Act (INA) is a matter of discretion and administrative grace not designed to supersede the regular consular processing of immigrant visas. U.S. Citizenship and Immigration Services (USCIS) reaffirms this consistent and longstanding approach and declares as a matter of general policy its intention to faithfully apply the statutes consistently with this understanding.
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JHU Computer Science @jhucompsci.bsky.social · 12/03/2026
Congratulations, @vikramshivakumar.bsky.social!
Congratulations! Vikram Shivakumar successfully defended his dissertation “Scalable Sequence Analysis Using Compressed Pangenome Indexing” under the guidance of advisor Ben Langmead. Vikram plans to pursue a joint postdoctoral fellowship at the European Bioinformatics Institute, the Wellcome Sanger Institute, and the University of Cambridge. We in the department are extremely proud of our students who have successfully completed their PhD. Congratulations on this achievement and best wishes as you begin an exciting new phase of life!
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Matthew Nguyen @mnguyen667.bsky.social · 09/03/2026
1/ Excited to share my first first-author preprint from my PhD! We introduce Perseus, a lineage-aware confidence estimation framework for taxonomic classification in long-read metagenomics. Preprint: www.biorxiv.org/content/10.6... Code: github.com/matnguyen/Pe...
biorxiv.org
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Alondra Nelson @alondra.bsky.social · 24/01/2026
🚨🚨🚨 "At least 63 times since 2007, data from some of the 28 human genomic repositories that the N.I.H. controls was improperly released to researchers, used for unapproved purposes or made vulnerable to theft..." (Gift Link) www.nytimes.com/2026/01/24/u...
nytimes.com
Genetic Data From Over 20,000 U.S. Children Misused for ‘Race Science’
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Rajiv McCoy @rajivmccoy.bsky.social · 21/01/2026
Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk. First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
nature.com
Common variation in meiosis genes shapes human recombination and aneuploidy - Nature
Analysis of data from pre-implantation genetic testing sheds light on the genetic basis of meiotic-origin aneuploidy, the leading cause of human pregnancy loss, identifying common genetic variants ass...
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Arun Das @arun-das.bsky.social · 15/12/2025
Appalling. This whole situation has been handled so poorly, without any care for the community at Brown, the community and people that live in and around the university, and the larger Providence community.
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Arun Das @arun-das.bsky.social · 13/12/2025
Just awful, awful news. Sending all my love and thoughts to those affected, and to the many on campus who never should have had to experience this.
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Terry McGlynn @hormiga.bsky.social · 07/11/2025
Hey folks, as news of Watson's demise spreads, please don't set aside his weighty legacy of misogyny and racism. He was truly among the worst of us. www.vox.com/2019/1/15/18...
vox.com
DNA scientist James Watson has a remarkably long history of sexist, racist public comments
“People say it would be terrible if we made all girls pretty,” he said in 2003. “I think it would be great.”
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JHU Computer Science @jhucompsci.bsky.social · 04/11/2025
Check out the cool work being presented by our students at Genome Informatics! This year’s event was co-organized by @benlangmead.bsky.social, & features talks from @vikramshivakumar.bsky.social & more, plus posters from @alexsweeten.bsky.social, @maojanlin.bsky.social, & @sinamajidian.bsky.social:
cs.jhu.edu
Johns Hopkins researchers to present at Genome Informatics 2025
Students from the Department of Computer Science will give talks and present posters on their research in genome informatics.
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Reposted by Arun Das
Sina Majidian @sinamajidian.bsky.social · 06/11/2025
Fantastic talk by @vikramshivakumar.bsky.social Mumemto—Scalable multi-MUM finding for pangenomes Papers biorxiv.org/content/10.1101/2025.05.20.654611 & doi.org/10.1186/s13059-025-03644-0 Code: github.com/vikshiv/mume... Very efficient pangenome visualization tool, revealing synteny and variations!
Figure 1: (A) Anchor-based merging requires a common sequence (red) present in each partition. Multi-MUMs are merged by identifying overlaps between partition-specific matches in the anchor coordinate space, and a uniqueness threshold determines if a MUM is still unique in each partition after truncation. (B) String-based merging enables compu- tation of multi-MUMs between partitions without a common sequence. An example tree (left) is shown, highlighting the use case where partial multi-MUMs specific to internal nodes (starred) can be computed by merging subclade-based partitions up a tree. (right) MUM overlaps are computed by running Mumemto on the MUM sequences, and the uniqueness threshold array ensures overlaps remain unique across the merged dataset. (C) An example Burrows-Wheeler Transform (BWT), matrix (BWM), and Longest Com- mon Prefix (LCP) array, with sequence IDs for each suffix shown (ID). A non-maximal unique match (UM) is shown, and the uniqueness threshold for this match is found us- ing the flanking LCP values. (D) A partial multi-MUM (in blue) is found in all-but-one sequence (excluded in red). Using two anchor sequences (red and orange), all-but-one partial MUMs can be computed using an augmented anchor-based merging method (sec- tion 2.6).
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Arun Das @arun-das.bsky.social · 04/11/2025
Today, for no particular reason at all, it is worth sharing this, as a reminder of what one man's lies can do. Taken from this resource from my alma mater: costsofwar.watson.brown.edu (Specific page is: costsofwar.watson.brown.edu/costs/human/...)
The human cost of the post 9/11 wars on people in Afghanistan, Pakistan, Iraq, Syria and Yemen. Between indirect and direct deaths, 4.5-4.7 million people have died, and tens of millions have been displaced.
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Reposted by Arun Das
Adam Phillippy @aphillippy.bsky.social · 22/09/2025
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
biorxiv.org
A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
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Arun Das @arun-das.bsky.social · 20/09/2025
Small victories, but this doesn’t seem to apply to those currently on an H-1B visa. Wish it was made clear in the initial “proclamation”, before we spent the entire day panicking while trying to figure out a way to get a friend back to the US before midnight.
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Arun Das @arun-das.bsky.social · 20/09/2025
This is catastrophic. So, so many people I know and love are going to find it impossible to stay and work in the US, and it makes it almost impossible for people like me to stay and work here in the longer term, no matter how qualified we are.
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Reposted by Arun Das
Heng Li @lh3lh3.bsky.social · 12/09/2025
New blog post – A quick look at Roche's SBX lh3.github.io/2025/09/11/a...
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Arun Das @arun-das.bsky.social · 30/07/2025
Extremely disappointed in my alma mater, who have chosen to fold without a fight and endanger the most vulnerable members of our community instead of standing up for them. Spineless and shameful.
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JHU Computer Science @jhucompsci.bsky.social · 24/06/2025
Getting into computational biology this summer? 🏖️ 📖 Check out “Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References” by @arun-das.bsky.social‬, @mikeschatz.bsky.social, and more for a great introduction to the field:
annualreviews.org
Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References | Annual Reviews
The Human Genome Project was an enormous accomplishment, providing a foundation for countless explorations into the genetics and genomics of the human species. Yet for many years, the human genome ref...
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Vikram Shivakumar @vikramshivakumar.bsky.social · 27/05/2025
Excited to share a new update to Mumemto, scaling MUM and conserved element finding to any size pangenome! Preprint out now w/ @benlangmead.bsky.social. Mumemto scales to the new HPRC v2 release and beyond, and can merge in future assemblies without any recomputation! 1/n
biorxiv.org
Partitioned Multi-MUM finding for scalable pangenomics
Pangenome collections are growing to hundreds of high-quality genomes. This necessitates scalable methods for constructing pangenome alignments that can incorporate newly-sequenced assemblies. We prev...
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Arun Das @arun-das.bsky.social · 16/05/2025
Easily the most important thing happening next week. Come and watch my friend Sara defend her PhD!
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Reposted by Arun Das
Arjun Biddanda @aabiddanda.github.io · 15/05/2025
Really cool work from @arun-das.bsky.social on recovering sequence from unmapped reads (even with T2T reference or HPRC pangenomes!). Can recover a decent amount of sequence per individual using these approaches. Check it out!
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Rajiv McCoy @rajivmccoy.bsky.social · 15/05/2025
@arun-das.bsky.social's thesis research demonstrates that short-read mapping-based approaches, even using complete linear (T2T-CHM13) and pangenome (HPRC) references, miss a lot of variation that can be recovered from unmapped reads.
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Arun Das @arun-das.bsky.social · 15/05/2025
Our pre-print on investigating variation in South Asian genomes is now out! Thank you to @mikeschatz.bsky.social, @rajivmccoy.bsky.social and @aabiddanda.bsky.social for all their work on this. 🧵 A thread on the key results and takeaways from our work:
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Arun Das @arun-das.bsky.social · 09/05/2025
Happening at 2pm in Biondi - come and check out Vikram’s great work!
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Arun Das @arun-das.bsky.social · 02/05/2025
Thank you to everyone who attended, and thank you to everyone who got me to this point - I appreciate you all. I'm on the job market this summer, so please send any interesting opportunities my way 😃
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Arun Das @arun-das.bsky.social · 21/04/2025
Hello Bluesky 👋🏾 I’m going to be defending my thesis on Wednesday, so I thought this was as good a time as any to introduce myself and my work. I’m Arun Das, I’m a PhD student in Schatz Lab @ JHU, and my work broadly focuses on algorithms to improve accessibility and representation in genomics.
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