iiinova — where your digital self keeps evolving

Reposted by Noor Pratap Singh

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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Ben Langmead @benlangmead.bsky.social · 07/10/2025

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.

youtube.com

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...

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Ben Langmead @benlangmead.bsky.social · 22/08/2025

The Genome Informatics conference (@ Cold Spring Harbor Lab, Nov 5 - 8) abstract deadline is **today**. We welcome your submissions! Topics include: - PanGenomes - Genome Assembly & Seq. Algos. - Algorithmic Evo. Bio - Single Cell & Spatial Omics - Microbial Genomics - AI/ML & Integrative Omics 🙏🙏🙏

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Noor Pratap Singh @noorpratap.bsky.social · 22/08/2025

So excited that this is finally out. This was among the longest and most uncertain (no)pun intended during my PhD, with different challenges, starting my from evaluation metrics to finding the right datasets, to tweak the method and interpreting the results. github.com/NPSDC/mehenDi

github.com

GitHub - NPSDC/mehenDi: R package for the differential testing on RNASeq data for TreeTerminus trees

R package for the differential testing on RNASeq data for TreeTerminus trees - NPSDC/mehenDi

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Rob Patro @robp.bsky.social · 20/08/2025

The 25th iteration of the excellent Conference for Algorithms in Bioinformatics (WABI) starts tomorrow at UMD @umdscience.bsky.social at the Brendan Iribe Center. You can find details at the website wabiconf.github.io/2025/. We'll use the tag #WABI25 for the meeting!

wabiconf.github.io

WABI 2025

WABI Conference on Algorithms in Bioinformatics

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Rob Patro @robp.bsky.social · 30/06/2025

🧬🖥️ oarfish v0.9.0 is out! The big improvement in this version is future-oriented. v0.9.0 allows the user to pass in transcript sequences via the `--annotated` option, the `--novel` option, or both. The provenance will be separately tracked to that later 1/4

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Rob Patro @robp.bsky.social · 31/05/2025

🖥️🧬 The new release (v0.13.0) of piscem is out. However, almost all changes here are transparent to the user (except for the need to rebuild the index before using the new version). I want to take a second to talk about something that often goes unappreciated. 1/x github.com/COMBINE-lab/...

github.com

Release v0.13.0 · COMBINE-lab/piscem

Install piscem 0.13.0 Install prebuilt binaries via shell script curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/piscem/releases/download/v0.13.0/piscem-installer.sh | sh Downl...

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Noor Pratap Singh @noorpratap.bsky.social · 13/03/2025

Excited and nervous at the time!!! Looking forward to it.

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Rob Patro @robp.bsky.social · 25/01/2025

We just released simpleaf v0.19.0 (github.com/COMBINE-lab/...). Make sure to pair it with piscem v0.12 for faster scATAC-seq processing. The other big feature & first explicit @scverse.bsky.social integration point is AnnData format output with the new `--anndata-out` flag!

github.com

Release v0.19.0 · COMBINE-lab/simpleaf

Install simpleaf 0.19.0 Install prebuilt binaries via shell script curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/simpleaf/releases/download/v0.19.0/simpleaf-installer.sh | sh...

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Ben Langmead @benlangmead.bsky.social · 11/12/2024

Very excited to see Movi (by @mohsenzakeri.bsky.social) now out in iScience: www.cell.com/iscience/ful.... Movi builds on the "move structure" pangenome index, a compressed full-text index and close cousin to r-index. Compared to r-index, the move structure is simpler and more cache-efficient.

cell.com

Movi: A fast and cache-efficient full-text pangenome index

Biocomputational method; Classification of bioinformatical subject; Genomic analysis

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