Rob Patro @robp.bsky.social · 18mAs a millennial, I can absolutely say that for US, it's "this is your brain on drugs". 000
Rob Patro @robp.bsky.social · 3hRelatively 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 160
Reposted by Rob PatroISCB News @iscb.bsky.social · 5hHoping 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! 021
Reposted by Rob PatroStephanie Hicks @stephaniehicks.bsky.social · 29/09/2026Excited 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! 🎉 1810
Rob Patro @robp.bsky.social · 27/09/2026Tangentially, @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 043
Rob Patro @robp.bsky.social · 25/09/2026Because.....? Honestly, what relevance does that have, whatsoever? 080
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... 100
Rob Patro @robp.bsky.social · 25/09/2026Ok 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. 195
Rob Patro @robp.bsky.social · 25/09/2026Cuttlefish 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.comRelease 3.0.3 · COMBINE-lab/cuttlefishRelease 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... 1134
Reposted by Rob PatroNiema Moshiri @niema.net · 24/09/2026Work with @robp.bsky.social! His lab does awesome stuff 😄 061
Rob Patro @robp.bsky.social · 24/09/2026If 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.eduPresident's Postdoctoral Fellowship Program | Office of Faculty Affairs 099
Reposted by Rob PatroSteven Salzberg @stevensalzberg.bsky.social · 24/09/2026Check 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.orgImproving Metagenomics Classification with Kmask: Entropy-Based Masking of Low-Complexity RegionsAbstract 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... 063
Rob Patro @robp.bsky.social · 24/09/2026What 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. 131
Reposted by Rob PatroStephen Turner @stephenturner.us · 22/09/2026Went on live TV news last night talking about AI safety and #biosecurity 3202
Rob Patro @robp.bsky.social · 22/09/2026Apropos of nothing, I've decided that I will start referring to human intelligence as "Ultra intelligence, extreme platinum edition". 260
Reposted by Rob PatrobioRxivpreprint @biorxivpreprint.bsky.social · 21/09/2026Gravlax: an annotation-independent molecular evidence archive for single-cell RNA-seq www.biorxiv.org/content/10.64898/20… 022
Reposted by Rob PatrobioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 21/09/2026Uniformly processed transcriptome-wide alternative splicing profiles for pediatric cancer research www.biorxiv.org/content/10.64898/20… 021
Reposted by Rob PatrobioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 21/09/2026A single-cell RNA-seq catalog of ground truth gene coregulation www.biorxiv.org/content/10.64898/20… 044
Reposted by Rob PatroCharlie Vaske @seavaske.com · 21/09/2026I love this representation of scRNA data, showing yet again that compression leads to some of the best insights on data. 261
Reposted by Rob PatrobioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 21/09/2026Gravlax: an annotation-independent molecular evidence archive for single-cell RNA-seq www.biorxiv.org/content/10.64898/20… 032
Rob Patro @robp.bsky.social · 21/09/2026What 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. 1142
Reposted by Rob Patro#SingleCell preprints @prepub-singlecell.bsky.social · 21/09/2026Uniformly processed transcriptome-wide alternative splicing profiles for pediatric cancer research #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20… 011
Rob Patro @robp.bsky.social · 21/09/2026It'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... 33413
Rob Patro @robp.bsky.social · 21/09/2026Any @biorxivpreprint.bsky.social mods willing to give `BIORXIV/2026/752708` a little nudge if possible :P ? 020
Reposted by Rob PatroWilliam B. Fuckley @opinionhaver.bsky.social · 20/09/2026The 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. 3054549
Rob Patro @robp.bsky.social · 20/09/2026Robert Oppenheimer was, indeed, a physicist youtu.be/PIwWsHy9RfE?...youtu.beBessent: “Robert Oppenheimer was not a physicist...”YouTube video by American Bridge 21st Century 5132
Rob Patro @robp.bsky.social · 19/09/2026That 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” 🤣. 1151
Rob Patro @robp.bsky.social · 16/09/2026Our bramble preprint is out. Here's a thread about this work and why I think it's exciting! bsky.app/profile/robp... 092
Reposted by Rob PatroRob Patro @robp.bsky.social · 16/09/2026New 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. 12913
Rob Patro @robp.bsky.social · 16/09/2026Look at Giulia, continuing to kick ass and take names (and she's almost out of names)! Congrats! 121
Rob Patro @robp.bsky.social · 16/09/2026New 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. 12913
Rob Patro @robp.bsky.social · 16/09/2026I 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. 250
Reposted by Rob PatroJim Shaw @jimshaw.bsky.social · 15/09/2026The 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.ioDocumentation for sylph - ultrafast, precise metagenomic profiling 26330
Reposted by Rob PatroRECOMB 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.orgCall for PapersRECOMB 2027 065
Reposted by Rob PatroRob Patro @robp.bsky.social · 14/09/2026I 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? 101
Rob Patro @robp.bsky.social · 14/09/2026I 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? 101
Reposted by Rob PatroSteven Salzberg @stevensalzberg.bsky.social · 13/09/2026Check 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.orgLarge-scale analysis of transcript data reveals thousands of recursive splicing events in human intronsRecursive 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... 1267
Rob Patro @robp.bsky.social · 13/09/2026Derrick Henry will come for you, and you will do nothing, because you can do nothing. 🐦⬛ 020
Rob Patro @robp.bsky.social · 12/09/2026It 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. 000
Reposted by Rob PatroMichael Love @mikelove.bsky.social · 12/09/2026I wrote a post about how slice_sample() and other slice_* functions work in #tidyomics #Bioconductor tidyomics.github.io/tidyomicsBlo...tidyomics.github.ioSlicing in tidyomics – tidyomicsBlogHow to use dplyr-style slice operations on omics data objects in the tidyomics project. 02113
Rob Patro @robp.bsky.social · 12/09/2026Single-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. 🧵 1143
Rob Patro @robp.bsky.social · 11/09/2026There 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.orgDeclaration — Math and AIRead the declaration and add your name. 1121