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Rob Patro

@robp.bsky.social
4.4K followers 560 following 3.3K posts

Professor of CS @ University of Maryland. Proud Rust advocate! I ♥ science & compiled, statically-typed programming languages! Views are my own. Tech stack: github.com/rob-p/tech-stack.

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Rob Patro @robp.bsky.social · 18m
As a millennial, I can absolutely say that for US, it's "this is your brain on drugs".
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Rob Patro @robp.bsky.social · 3h
Relatively niche problem, but worth discussing anyway. Reddit’s /r/bioinformatics doesn’t take posts about new tools or methods (?!?! again, WTAF), and /r/bioinformaticstools has measly throughput and community size. What do we do to address this problem? Cc @curiouscoding.nl @psy-fer.bsky.social
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ISCB News @iscb.bsky.social · 5h
Hoping to present at #ISMBECCB2027 in July? Here's a sneak peek at the upcoming submission deadlines for the biggest bioinformatics and computational biology conference of the year!
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Stephanie Hicks @stephaniehicks.bsky.social · 29/09/2026
Excited to share that @jhubiostat.bsky.social is hiring for postdoctoral fellows and tenure-track Assistant Professors! Details below and committees will start reviewing for both on Oct 1! 🎉
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Rob Patro @robp.bsky.social · 27/09/2026
Tangentially, @jermp.bsky.social also points out @recombconf.bsky.social is listed as B tier in CORE portal.core.edu.au/conf-ranks/?.... This is something that we should figure out how to address. RECOMB is a premiere conference in comp bio, & it is highly selective. It is `A` tier without question.
portal.core.edu.au
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Rob Patro @robp.bsky.social · 25/09/2026
Because.....? Honestly, what relevance does that have, whatsoever?
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Rob Patro @robp.bsky.social · 25/09/2026
@richardsever.bsky.social : what are the potential impediments to having the ability to collect manuscripts (at specific "versions") into approved/signed "Volumes" in the context of @biorxivpreprint.bsky.social ? For context: bsky.app/profile/robp...
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Rob Patro @robp.bsky.social · 25/09/2026
Ok comp. bio / bioinformatics / genomics friends. Let's talk about @recombconf.bsky.social and, specifically, the way in which the "proceedings" have evolved. This seems like something that we, as a community, should address. RECOMB now has no "published" proceedings in the classic sense.
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Rob Patro @robp.bsky.social · 25/09/2026
Cuttlefish 3.0.3 is out! github.com/COMBINE-lab/... Fun little jaunt with Opus 5.5 to substantially reduce the memory requirement (especially at moderate thread counts). Now it's both non-trivially faster *and* more memory-frugal than the initial C++ implementation!
github.com
Release 3.0.3 · COMBINE-lab/cuttlefish
Release Notes Colored builds use far less memory at low and moderate thread counts. On 149,998 Salmonella assemblies at 16 threads, peak RSS falls from 22.4 GB to 8.9 GB (C++ Cuttlefish 3: 11.5 GB...
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Niema Moshiri @niema.net · 24/09/2026
Work with @robp.bsky.social! His lab does awesome stuff 😄
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Rob Patro @robp.bsky.social · 24/09/2026
If you are a US citizen or permanent resident looking for a postdoc, the President's Postdoctoral Fellowship Program is a great opportunity faculty.umd.edu/presidentspo...! If you are eligible, working in computational genomics, and interested in my lab, let me know!
faculty.umd.edu
President's Postdoctoral Fellowship Program | Office of Faculty Affairs
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Steven Salzberg @stevensalzberg.bsky.social · 24/09/2026
Check our new @biorxiv-genomic.bsky.social preprint on a method for masking low-complexity regions in genome databases, led by Yuchin (Peter) Ge in my lab. Also includes a new release of a very large, pre-masked microbial database: www.biorxiv.org/content/10.6...
biorxiv.org
Improving Metagenomics Classification with Kmask: Entropy-Based Masking of Low-Complexity Regions
Abstract Accurate taxonomic classification in metagenomics is often compromised by low-complexity sequences, which lead to chance matches that in turn cause sequences to be misclassified. Here we pres...
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Rob Patro @robp.bsky.social · 24/09/2026
What is "thought", how do you *know* there is none? Is it only thought if humans do it? Only if neurons are the substrate? We shouldn't anthropomorphize machines, of course, but we also should accept that we'll eventually have to grapple with hard questions, like what are thought & intelligence.
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Stephen Turner @stephenturner.us · 22/09/2026
Went on live TV news last night talking about AI safety and #biosecurity
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Rob Patro @robp.bsky.social · 22/09/2026
Apropos of nothing, I've decided that I will start referring to human intelligence as "Ultra intelligence, extreme platinum edition".
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Rob Patro @robp.bsky.social · 22/09/2026
For the Tuesday morning crowd!
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bioRxivpreprint @biorxivpreprint.bsky.social · 21/09/2026
Gravlax: an annotation-independent molecular evidence archive for single-cell RNA-seq www.biorxiv.org/content/10.64898/20…
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 21/09/2026
Uniformly processed transcriptome-wide alternative splicing profiles for pediatric cancer research www.biorxiv.org/content/10.64898/20…
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 21/09/2026
A single-cell RNA-seq catalog of ground truth gene coregulation www.biorxiv.org/content/10.64898/20…
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Charlie Vaske @seavaske.com · 21/09/2026
I love this representation of scRNA data, showing yet again that compression leads to some of the best insights on data.
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 21/09/2026
Gravlax: an annotation-independent molecular evidence archive for single-cell RNA-seq www.biorxiv.org/content/10.64898/20…
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Rob Patro @robp.bsky.social · 21/09/2026
What excites me most about gravlax is that it breaks the dichotomy between tiny but *very limited* count matrix data that is shared and reanalyzed on a near constant basis and huge and compute intensive raw read/bam artifacts that are often too inconvenient for people to routinely reuse.
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Rob Patro @robp.bsky.social · 21/09/2026
Explainer posts here: bsky.app/profile/robp...
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#SingleCell preprints @prepub-singlecell.bsky.social · 21/09/2026
Uniformly processed transcriptome-wide alternative splicing profiles for pediatric cancer research #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20…
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Rob Patro @robp.bsky.social · 21/09/2026
It's here! new preprint: Gravlax, an annotation-independent molecular evidence archive for scRNA-seq. A count matrix freezes one annotation. Molecules never change. Instead, gravlax keeps the evidence. Requantify, query, and discover under any annotation. 🧵 www.biorxiv.org/content/10.6...
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Rob Patro @robp.bsky.social · 21/09/2026
Any @biorxivpreprint.bsky.social mods willing to give `BIORXIV/2026/752708` a little nudge if possible :P ?
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William B. Fuckley @opinionhaver.bsky.social · 20/09/2026
The thesis of this piece is that it’s fine to turn the country’s largest and best public university system into a diploma mill where the degree doesn’t mean anything because it’s more equitable.
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Rob Patro @robp.bsky.social · 20/09/2026
Robert Oppenheimer was, indeed, a physicist youtu.be/PIwWsHy9RfE?...
youtu.be
Bessent: “Robert Oppenheimer was not a physicist...”
YouTube video by American Bridge 21st Century
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Rob Patro @robp.bsky.social · 20/09/2026
Waiting for this to drop; very excited about it 😀!
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Rob Patro @robp.bsky.social · 20/09/2026
Noice!
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Rob Patro @robp.bsky.social · 20/09/2026
Go Terps!
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Rob Patro @robp.bsky.social · 19/09/2026
That magical feeling when you’ve submitted a @biorxivpreprint.bsky.social preprint and you’re awaiting screening so you can share the work with everyone. BioRxiv preprint screening is like “stochastic Christmas morning” 🤣.
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Rob Patro @robp.bsky.social · 17/09/2026
For the Thurs. morning crowd!
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Rob Patro @robp.bsky.social · 16/09/2026
"That looks like a stray Vim :w." Yes, Claude, it was.
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Rob Patro @robp.bsky.social · 16/09/2026
Our bramble preprint is out. Here's a thread about this work and why I think it's exciting! bsky.app/profile/robp...
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Rob Patro @robp.bsky.social · 16/09/2026
New preprint led by Zoe Rudnick: bramble 🌿 RNA-seq quantification makes you pick a side. Align to the transcriptome and your quantifier is happy, but reads from unannotated transcripts get misassigned to annotated ones. Align to the genome and you keep discovery, but limit quantification choices.
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Rob Patro @robp.bsky.social · 16/09/2026
Look at Giulia, continuing to kick ass and take names (and she's almost out of names)! Congrats!
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Rob Patro @robp.bsky.social · 16/09/2026
New preprint led by Zoe Rudnick: bramble 🌿 RNA-seq quantification makes you pick a side. Align to the transcriptome and your quantifier is happy, but reads from unannotated transcripts get misassigned to annotated ones. Align to the genome and you keep discovery, but limit quantification choices.
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Rob Patro @robp.bsky.social · 16/09/2026
I hope that one widespread realization that emerges from whatever happens with AI over the coming months and years is that utilitarianism is, empirically, a failed philosophy and that value ethics is vastly superior in both theory and practice.
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Jim Shaw @jimshaw.bsky.social · 15/09/2026
The sylph metagenome profiler is v1.0.0! sylph-docs.github.io A new DB format + approach --> huge performance gains: GTDB-R232 (200k species) now takes < 5 GB of RAM and ~30s (2GB fq.gz). Huge thanks to @benjwoodcroft.bsky.social and his ongoing performance efforts (github.com/wwood/weebill)
sylph-docs.github.io
Documentation for sylph - ultrafast, precise metagenomic profiling
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RECOMB Conference Series @recombconf.bsky.social · 15/09/2026
#RECOMB2027 is now accepting submissions and we'd love to see your best work! 📌 Abstract registration: October 28 📌 Full paper submission: November 4 📜More info: recomb.org/recomb2027/c...
recomb.org
Call for Papers
RECOMB 2027
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Rob Patro @robp.bsky.social · 14/09/2026
I unfortunately cracked the front face of my Amazfit smart watch. I'm looking for an android ecosystem smart watch to replace it, and am particularly interested in value for $ rather than the absolute best feature set. Any recommendations?
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Rob Patro @robp.bsky.social · 14/09/2026
I unfortunately cracked the front face of my Amazfit smart watch. I'm looking for an android ecosystem smart watch to replace it, and am particularly interested in value for $ rather than the absolute best feature set. Any recommendations?
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Steven Salzberg @stevensalzberg.bsky.social · 13/09/2026
Check out our new preprint on thousands of novel recursive exons in the human genome (if you don't know about recursive exons, they are pretty cool), led by PhD student David Bass @davidb256.bsky.social : www.biorxiv.org/content/10.6...
biorxiv.org
Large-scale analysis of transcript data reveals thousands of recursive splicing events in human introns
Recursive splicing (RS) is a process in which an intron is removed from a nascent RNA molecule in two or more splicing events rather than one. We introduce a novel approach for detecting recursive spl...
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Rob Patro @robp.bsky.social · 13/09/2026
Derrick Henry will come for you, and you will do nothing, because you can do nothing. 🐦‍⬛
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Rob Patro @robp.bsky.social · 13/09/2026
Go Ravens 🐦‍⬛🐦‍⬛!
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Rob Patro @robp.bsky.social · 12/09/2026
It is, perhaps, unsurprising that, accelerationists being the ultimate utilitarians, they are content to push progress in a direction that may lead directly to the repugnant conclusion (or the repugnant conclusion 2.0 if you prefer) with no forethought. Seems obvious in retrospect.
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Michael Love @mikelove.bsky.social · 12/09/2026
I wrote a post about how slice_sample() and other slice_* functions work in #tidyomics #Bioconductor tidyomics.github.io/tidyomicsBlo...
tidyomics.github.io
Slicing in tidyomics – tidyomicsBlog
How to use dplyr-style slice operations on omics data objects in the tidyomics project.
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Rob Patro @robp.bsky.social · 12/09/2026
Single-cell RNA-seq count matrices bake in one gene annotation the day you build them. Annotations change several times a year; your molecules never do. Gravlax captures the molecular evidence once, so you can requantify under any future annotation. Align once, query forever. 🧵
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Rob Patro @robp.bsky.social · 11/09/2026
There are some silly, but unfortunately, not unsurprising takes on the mathandai.org statement. I'm decidedly not anti-AI & not opposed to "disruption". But if you think you know the point of math better than these people, or their concerns are silly, you're just wrong.
mathandai.org
Declaration — Math and AI
Read the declaration and add your name.
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