Noor Pratap Singh
@noorpratap.bsky.social
CS PhD student at UMD. Interested in Computational Biology. Views driven by an unknown combination of previously consumed material (weights are dynamic).
Previously at Genentech, IIIT-Hyderabad
Previously at Genentech, IIIT-Hyderabad
Reposted by Noor Pratap Singh
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
October 7, 2025 at 2:17 PM
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.
Reposted by Noor Pratap Singh
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
🙏🙏🙏
- PanGenomes
- Genome Assembly & Seq. Algos.
- Algorithmic Evo. Bio
- Single Cell & Spatial Omics
- Microbial Genomics
- AI/ML & Integrative Omics
🙏🙏🙏
August 22, 2025 at 3:00 PM
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
🙏🙏🙏
- PanGenomes
- Genome Assembly & Seq. Algos.
- Algorithmic Evo. Bio
- Single Cell & Spatial Omics
- Microbial Genomics
- AI/ML & Integrative Omics
🙏🙏🙏
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/NPSDC/mehenDi
August 22, 2025 at 1:21 PM
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/NPSDC/mehenDi
Reposted by Noor Pratap Singh
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!
WABI 2025
WABI Conference on Algorithms in Bioinformatics
wabiconf.github.io
August 20, 2025 at 2:45 AM
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!
Reposted by Noor Pratap Singh
🧬🖥️ 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
June 29, 2025 at 11:39 PM
🧬🖥️ 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
Reposted by Noor Pratap Singh
🖥️🧬 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/COMBINE-lab/...
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...
github.com
May 31, 2025 at 7:16 PM
🖥️🧬 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/COMBINE-lab/...
Excited and nervous at the time!!! Looking forward to it.
On Thurs, March 13 at 9AM (ET), @noorpratap.bsky.social will be defending his dissertation!
If you want to learn more about tree-based quantification & differential testing, or scATAC-seq preprocessing; tune in!
Talk link: umd.zoom.us/j/9873133564...
Abstract: talks.cs.umd.edu/talks/4137
If you want to learn more about tree-based quantification & differential testing, or scATAC-seq preprocessing; tune in!
Talk link: umd.zoom.us/j/9873133564...
Abstract: talks.cs.umd.edu/talks/4137
Talks
talks.cs.umd.edu
March 13, 2025 at 3:05 AM
Excited and nervous at the time!!! Looking forward to it.
Reposted by Noor Pratap Singh
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!
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...
github.com
January 25, 2025 at 3:04 PM
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!
Reposted by Noor Pratap Singh
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.
Movi: A fast and cache-efficient full-text pangenome index
Biocomputational method; Classification of bioinformatical subject; Genomic analysis
www.cell.com
December 11, 2024 at 4:48 PM
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.