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Emanuel ebioman@genomic.social
@ebioman
kinda skilled in NGS data analysis, 
programming, father of 2 monsters 
programming, father of 2 monsters SwitzerlandJoined June 2009
Emanuel ebioman@genomic.social’s Tweets
#rust_bio 1.2 has been released, adding banded partial order alignments (POA) and the ability to obtain a consensus sequence from the POA.
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8 papers with big data to mine for (epi)genomics. Bookmark this thread for data reusing 👇 🧵
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We recorded the talks! youtube.com/watch?v=TaoRZY
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Next week in Memphis: #MemPANG23 pangenome.github.io/MemPanG23/, a workshop on the theory and practice of working with lots of genomes. Join us online next Friday June 2nd from 9:00-16:00 (CDT/UTC-5) for 6 talks on pangenomics (webinar tennesseehipaa.zoom.us/j/92881122014?)
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As a preview to the upcoming MAS-Seq for bulk Iso-Seq, here's a HG002 MAS bulk x Revio dataset for you to play with! 38 million full-length HiFi reads on 1 Revio SMRT Cell! Enjoy :) More to come. downloads.pacbcloud.com/public/dataset
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A meticulous effort by in integrating FPGA-accelerated chaining into Minimap2 doi.org/10.1101/2023.0
Mapping accuracy is near identical.
end-to-end runtime improves ~10-80% (depend on type of data/parameters).
code+pre-built aws binaries
github.com/kisarur/minima
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cPeaks: Consensus peaks of chromatin accessibility in the human genome biorxiv.org/content/10.110
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Combining reference genomes into a pangenome graph improves accuracy and reduces bias. #PangenomeGraph #MultipleGenomeAlignment #StructuralVariants
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Great way to start the holiday weekend with a new lab preprint from the exceptional co-led with and Ludmila Danilova developing SpliceMutr to characterize tumor-specific neoantigens from splice variants doi.org/10.1101/2023.0 1/
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Next week in Memphis: #MemPANG23 pangenome.github.io/MemPanG23/, a workshop on the theory and practice of working with lots of genomes. Join us online next Friday June 2nd from 9:00-16:00 (CDT/UTC-5) for 6 talks on pangenomics (webinar tennesseehipaa.zoom.us/j/92881122014?)
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Beautiful data Viz : finally managed to add one more interval 😎
Our Chromoscope preprint is now online!
Chromoscope helps you to seamlessly visualize/analyze whole-genome structural variants (SVs) at multiple scales
- Preprint: osf.io/pyqrx/
- Document: chromoscope.bio/docs
- Demo: chromoscope.bio
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PSA: if you happen to be using the rust-wfa2 bindings to do alignments (especially gap-affine), please use our updated version with bug fixes:
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Whole-genome long-read sequencing downsampling and its effect on variant calling precision and recall biorxiv.org/cgi/content/sh #biorxiv_genomic
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I’m excited to see the release of our pre-print on HiPhase, a new tool for *jointly* phasing SNVs, indels, and structural variants from HiFi datasets! If you want to read about our results and some cool algorithms, follow along… 1/n
Repo: github.com/PacificBioscie
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HiPhase: Jointly phasing small and structural variants from HiFi sequencing biorxiv.org/cgi/content/sh #bioRxiv
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Results from GO enrichment are often dominated by one type of terms, often the large ones if you sort by P-value.
If you include more terms (top50) and organize them like this, you can find that there are groups of terms related to G1/S & G2/M transition, and response to… Show more
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and I just finished our paper on exact global alignment using A*.
A*PA is now faster than both Edlib and BiWFA when aligning noisy long reads 🎉
We do this using the 'gap-chaining seed heuristic'. 1/6
biorxiv.org/content/10.110
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The genome-wide mutational consequences of DNA hypomethylation. #Hypomethylation #DNAmethylation #GenomicStability
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Again great atmosphere for the 20km Lausanne, and objective less than 2h achieved 🤙
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DivBrowse—interactive visualization and exploratory data analysis of variant call matrices. #VariantCalls #VariantVisualization #InteractiveVisualization #WebApp
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Some last evening intervals before the 20km Lausanne on Sunday
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Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data genomebiology.biomedcentral.com/articles/10.11
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A fascinating paper suggesting that aneuploidy can be measured in ctDNA #liquidbiopsy in #pancreatic #Cancer patients.
genomemedicine.biomedcentral.com/articles/10.11
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When the amazing scientist moves on from your client....
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pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls genomebiology.biomedcentral.com/articles/10.11
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Very proud to announce the release of Cytosine-AI. It's a 120 layer, 500,000 parameter convolutional ResNet that has been trained to detect Cytosines in a DNA sequence. This is the day genomics changed forever. #PyTorch #Bioinformatics #Regex
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Really striking how every AI hype tweet is explicitly trying to induce FOMO. "You're getting left behind. All your competitors are using this. Everyone else is making more money than you. Everyone else is more productive. If you're not using the latest XYZ you're missing out."
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✨DON’T MISS THIS REVIEW ARTICLE – “Moving pan-cancer studies from basic research toward the clinic” by #FengChen #MichaelCWendl #MatthewAWyczalkowski #MatthewHBailey #YizeLi & #LiDing.
Find it here👇
nature.com/articles/s4301
rdcu.be/c77O3
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