How would you design a *multithreaded*, *concurrent* & *dynamic* hash table if you are focused specifically on common k-mer workloads, where streaming query & insertion are common? Jamshed, Prashant and I explore this in kache-hash, a cache-friendly k-mer hash table!
www.biorxiv.org/content/10.6...
I feel it quite possible that those relying on AI from the very start may form a different skill set that will accelerate some software, but result in key regressions (without the expertise to address them) in other types. combine-lab.github.io/blog/2026/02... see the caveats section hereβ¦
CVs are broadly distributed across the department. Evaluations are kept to people on the hiring committee (though there is some flexibility around that). I don't know if there are any formal restrictions on the statements, but in practice they are typically shared with people who express interest
depends on the materials (letters are treated more confidentially than research statements than CVs)
At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...
π¨UPCOMING DEADLINESπ¨
RECOMB-CG: 13 February
RECOMB-RSG: 15 February
RECOMB-Privacy: 9 March
RECOMB-Seq: 12 March (abstract registration)
RECOMB-Arch: 12 March (abstract registration)
RECOMB-Genetics: 13 March
#RECOMB2026 #deadlines
There is still many Amish villages around where Penn State is. Local farmer markets often carry their produce. I think they speak some form of Germanic, IIRC.
But its not rare in the US that states used to speak the language of the colonizers (cali->spanish, louisiana->french)
Time for a thread on our Christmas preprint βOrigin and evolution of acrocentric chromosomes in human and great apesβ. I had so much fun with this project and paper. It will be hard to summarize in a thread, but Iβll try www.biorxiv.org/content/10.6... [1/21]
PREPRINT ALERT
I heard you craving for more combinatorics, here are some more for y'all !
Preprint alert!
arxiv.org/abs/2602.03525
TLDR:
ZOR filters are STATIC filters with false positives.
-Almost memory optimal: <1% overhead over the theoretical lower bound (!!!)
-Fast queries: ~100 ns
-Construction cannot fail
A thread:
If you are an Israeli PhD student and are interested in a postdoc at Harvard Medical (my lab included!), I strongly recommend looking into the Kalaniyot fellowship program, providing 2-3 years of full support:
globalprograms.hms.harvard.edu/kalaniyot-hm...
The 12th edition of the 2-days workshop βData Structures in Bioinformaticsβ (DSB) will take place in Venice (Italy) on February 18-19th, 2026: dsb-meeting.github.io/DSB2026/
This thread gives really interesting and relevant history!
Kraken 2 (K2) community: we are giving more attention to our new `k2` wrapper, and a NEW functionality since 2.17.0 is: you can build several component K2 indexes, e.g. each covering a different Refseq database, and then query them all at once...
github.com/DerrickWood/... 1/6
Preprint alert!
We introduce new ideas to revisit the notion of sampling with window guarantees, also known as minimizers.
A thread:
Interested in a post-doc in Israel? The deadline for the Azrieli International Postdoctoral Fellowship is November 19. The fellowship offers generous funding for postdocs to conduct research in any academic discipline at eligible Israeli institutions: azrielifoundation.org/fellows/inte...
Haonan Wu gives a talk on "A k-mer-based estimator of the substitution rate between repetitive sequences"
www.biorxiv.org/content/10.1...
This work tackles the issue of Mash which ignores repeats in the genome, providing better distance estimation #GI2025
After years of research and continuous refinement, weβre thrilled to share that our paper on the MetaGraph framework β enabling Petabase-scale search across sequencing data β has been published today in Nature (www.nature.com/articles/s41...)
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!
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.
Sounds like someone is trying to solve a bidirected flow problem..
i've let the person in charge know
There seems to be a self-contradiction within the CFP, since it also says: "Submissions to peer-reviewed journals other than the partnering ones are also allowed.."
Our preprint on our new metagenomic HiFi assembler Alice is out π₯³ Based on a *new sketching method* (π§΅1/6)
π Preprint www.biorxiv.org/content/10.1...
π Github github.com/rolandfaure/...
Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching https://www.biorxiv.org/content/10.1101/2025.09.29.679204v1
It could be. Or it could be that the decision process is not consistent? Hard to tell...
I see. Do you know if the list of papers that are posted there get disseminated somehow through mail lists or social media?
They do, but they did not accept our paper. From what we understood, it was because it was a review paper and not novel research
#RECOMB2026 will be in Thessaloniki, Greece on May 26-29, 2026. Satellites on May 24-25. Save the date!
΀ο ΟΟ
Ξ½ΞΞ΄ΟΞΉΞΏ #RECOMB2026 ΞΈΞ± ΟΟΞ±Ξ³ΞΌΞ±ΟΞΏΟοιηθΡί ΟΟΞ· ΞΞ΅ΟΟαλονίκη, ΟΟΞΉΟ 26-29 ΞΞ±ΞΞΏΟ
2026. ΞΞΉ δοΟΟ
ΟΞΏΟΞΉΞΊΞΟ Ξ΅ΞΊΞ΄Ξ·Ξ»ΟΟΞ΅ΞΉΟ ΞΈΞ± διΡξαΟΞΈΞΏΟΞ½ ΟΟΞΉΟ 24-25 ΞΞ±ΞΞΏΟ
2026. ΣημΡιΟΟΟΞ΅ ΟΞ·Ξ½ Ξ·ΞΌΞ΅ΟΞΏΞΌΞ·Ξ½Ξ―Ξ±!
Hi Gaurav, I'm not sure what you mean. (But it sounds like you are asking for a library with all these implemented in one place? That would be quite an undertaking! As these things are always evolving, I'd guess it would also not age well.
