Lightnews — Scholar-powered news

Ben Langmead @benlangmead.bsky.social · 2h

Oooo, that's very nice

Ben Langmead @benlangmead.bsky.social · 17h

The generated illustrations are SVGs -- you can load them into Illustrator, Inkscape, Designer, etc, and edit away. I tried to put the components of the image into SVG groups so you can treat them as "layers" in those editors (e.g. you can hide bits you don't need).

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Ben Langmead @benlangmead.bsky.social · 17h

New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....

Illustration of Burrows-Wheeler Transform and many auxiliary structures from the input string how$now$brown$cow$#

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Ben Langmead @benlangmead.bsky.social · 1d

Wow! Very helpful

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Ben Langmead @benlangmead.bsky.social · 5d

Huge congrats, Andre!

Reposted by Ben Langmead

Rob Patro @robp.bsky.social · 6d

Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...

Postdoc Description.docx

Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...

docs.google.com

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Reposted by Ben Langmead

Robert Aboukhalil @robert.bio · 5d

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt

It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

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Ben Langmead @benlangmead.bsky.social · 6d

This playlist (www.youtube.com/playlist?lis...) is from my Coursera course (www.coursera.org/learn/dna-se...) and these are more high level, intended for a broader(er) audience -- may be worth a try.

Algorithms for DNA Sequencing - YouTube

All the lectures and practicals from the "Algorithms for DNA Sequencing" Coursera class: https://www.coursera.org/course/ads1.

www.youtube.com

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Reposted by Ben Langmead

JHU Computer Science @jhucompsci.bsky.social · 6d

10 new CS professors! 🥳

@anandbhattad.bsky.social @uthsav.bsky.social @gligoric.bsky.social @murat-kocaoglu.bsky.social @tiziano.bsky.social

Johns Hopkins Data Science and AI Institute @hopkinsdsai.bsky.social · Aug 25

#HopkinsDSAI welcomes 22 new faculty members, who join more than 150 DSAI faculty members across @jhu.edu in advancing the study of data science, machine learning, and #AI and translation to a range of critical and emerging fields.

ai.jhu.edu/news/data-sc...

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Reposted by Ben Langmead

Rob Patro @robp.bsky.social · 6d

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....

If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

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Ben Langmead @benlangmead.bsky.social · 7d

Thank you!

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Ben Langmead @benlangmead.bsky.social · 7d

I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.

Burrows-Wheeler Indexing - YouTube

Videos on : (a) the Burrows-Wheeler Transform (BWT), (b) the FM Index, which uses the BWT to construct a full-text index, (c) Wheeler graphs, (d) r-index, an...

www.youtube.com

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Reposted by Ben Langmead

AAUP @aaup.org · 14d

BREAKING: WE WON!!!
💥 💥 💥

Federal Judge William G. Young ruled today in our lawsuit against the Trump administration that the policy of arresting, detaining, & deporting noncitizen students & faculty members for their pro-Palestinian advocacy violates the 1st Amendment.

Full ruling here:

Findings of Fact & Conclusions of Law – #261 in American Association of University Professors v. Rubio (D. Mass., 1:25-cv-10685) – CourtListener.com

Judge William G. Young: ORDER entered. FINDINGS OF FACT AND RULINGS OF LAW, PURSUANT TO FED. R. CIV. P. 52(A)(Sonnenberg, Elizabeth) (Additional attachment(s) added on 9/30/2025: # 1 Main Document) (J...

www.courtlistener.com

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Ben Langmead @benlangmead.bsky.social · 15d

Yes, I use the built-in camera on my MacBook Pro, which I've been happy with. It doesn't temporarily lose focus, like I feel like I often see in other YT videos. Lighting is important, at least according to my taste! Which is why I record in a room with lots of windows for outside light.

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Ben Langmead @benlangmead.bsky.social · 15d

I used to use a lavalier (lapel) mic, so any video I posted prior to 2025 is using one of two different lavaliers I tried. I use a lavalier in the classroom too. But starting with these 2025 videos, I have preferred the audio from the pictured mic, which is: www.amazon.com/dp/B0CTJ7PVN...

Amazon.com: Shure MV7+ Podcast Dynamic Microphone. OBS Certified, Enhanced Audio, LED Touch Panel, USB-C & XLR Outputs, Auto Level Mode, Digital Pop Filter, Reverb Effects, Podcasting, Streaming, Reco...

Buy Shure MV7+ Podcast Dynamic Microphone. OBS Certified, Enhanced Audio, LED Touch Panel, USB-C & XLR Outputs, Auto Level Mode, Digital Pop Filter, Reverb Effects, Podcasting, Streaming, Recording -B...

www.amazon.com

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Reposted by Ben Langmead

RECOMB Conference Series @recombconf.bsky.social · 18d

#RECOMB2026 will be in Thessaloniki, Greece on May 26-29, 2026. Satellites on May 24-25. Save the date!

Το συνέδριο #RECOMB2026 θα πραγματοποιηθεί στη Θεσσαλονίκη, στις 26-29 Μαΐου 2026. Οι δορυφορικές εκδηλώσεις θα διεξαχθούν στις 24-25 Μαΐου 2026. Σημειώστε την ημερομηνία!

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Reposted by Ben Langmead

Jason Williams @jasonwilliamsny.bsky.social · 19d

Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment.

The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP

jasonjwilliamsny.github.io/grfp2025/

An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program

jasonjwilliamsny.github.io

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Reposted by Ben Langmead

Jason Williams @jasonwilliamsny.bsky.social · 19d

The next 48 hours may be a critical time to get attention and awareness on this before the next crisis lets this fade into the background. Everyone holding similar #NSFGRFP writing workshops takes time to sign this letter and reach out to officials.

Kevin Wright @kevinmawright.bsky.social · 19d

Thanks for organizing this! It has been incredibly frustrating to see these delays. We spent 5 weeks running a workshop for our incoming graduate students on writing a GRFP fellowship, and now we're wondering if they'll even be able to submit anything.

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Reposted by Ben Langmead

Adam Phillippy @aphillippy.bsky.social · 22d

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]

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 ...

www.biorxiv.org

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Reposted by Ben Langmead

Sina Majidian @sinamajidian.bsky.social · 23d

EvANI benchmarking workflow for evolutionary distance estimation academic.oup.com/bib/article/...

An great teamwork by @mohsenzakeri.bsky.social, @stephenhwang.bsky.social and me, with the excellent mentorship of @benlangmead.bsky.social

EvANI benchmarking workflow for evolutionary distance estimation

Abstract. Advances in long-read sequencing technology have led to a rapid increase in high-quality genome assemblies. These make it possible to compare gen

academic.oup.com

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Reposted by Ben Langmead

Pete Buttigieg @petebuttigieg.bsky.social · 24d

Donald Trump is way less popular than he wants you to believe.

And you are significantly more powerful than he wants you to think.

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Reposted by Ben Langmead

Kat Abughazaleh @katmabu.bsky.social · 24d

That’s me in the video. And a Fox News host just celebrated me being assaulted by ICE.

If ICE will do this to a congressional candidate with a big platform, just imagine what they’re doing to the people they’re kidnapping.

Acyn @acyn.bsky.social · 25d

Ingraham: A Democrat congressional candidate was thrown to the ground by an ICE agent. Good work

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Reposted by Ben Langmead

Piali Sengupta @senguptalab.bsky.social · 29d

A huge shoutout to all the dedicated grants management specialists at the NIH who are working around the clock to push grants out before the Sep 30 deadline. And also to the POs responding to frantic emails.
Not an easy job under the best of circumstances and right now it's the pits.
Thank you!

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Reposted by Ben Langmead

Heng Li @lh3lh3.bsky.social · Sep 12

New blog post – A quick look at Roche's SBX
lh3.github.io/2025/09/11/a...

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Ben Langmead @benlangmead.bsky.social · Sep 9

First new one up (continuing an r-index series that I'd left dormant a while): youtu.be/XwhFRiUAGmc. Here's a link to that playlist: www.youtube.com/playlist?lis...

BWT for repetitive texts, part 4a: locate queries

YouTube video by Ben Langmead

youtu.be

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