Patrick Bohn
@PatrickBohnPB
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Interested in Nanopores, RNA and 3d printing - amphibious (wet and dry lab) Scientist
Joined July 2019
RT @RayanChikhi: 🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of o….
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RT @plasmidsaurus: We’re working hard to accelerate your research! . You can now view the predicted amino acid sequence of each coding regi….
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RT @plasmidsaurus: How can sequencing reveal how viruses spread through hospitals? 🦠. Join CHOP’s Dr. Robert Potter as he shares how he use….
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RT @AlexBoRNA: Interested in joining our growing interdisciplinary team studying viruses, RNA, and condensates? Looking for a postdoctoral….
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RT @naturemethods: Check out the results of the most recent round of the RNA Puzzles endeavor for RNA 3D structure prediction! https://t.co….
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RT @JosephYesselman: 🧬Excited to share our new preprint! DMS chemical mapping, a key technique for studying RNA structure. It is assumed th….
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RT @PoLDresden: Congratulations to PoL postdoc Lukáš Pekárek @LukasPekarek1 from the Jahnel group @jjmajahn for being awarded the prestigio….
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RT @wiepp: 5/6 ⚡️ Processing speed benchmark: WDX4: 2.2 min/100k reads (on 8 CPU cores, decreases linearly with number of cores) https://t.….
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RT @wiepp: 2/6 📊 Performance highlights for RNA004: .- Calibrated performance for difference target accuracy modes (95-99.9%) at high yield….
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Interested in multiplexing samples for nanopore dRNA sequencing with the new chemistry? Check out our newly released RNA4 model! . 4 barcode model available here: .
github.com
Highlights 🎉 Full RNA004 Support with the WDX4 model, achieving 99.5% target accuracy at 95% yield. Features barcode-specific target accuracy confidence score filtering for optimal performance....
1/6 🎉 Excited to announce WarpDemuX v0.4.4 with RNA004 support! Our (@PatrickBohnPB ) WDX4 model achieves 99.5% target accuracy with 95% yield on the latest RNA sequencing kit from @nanopore. Release notes at:
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RT @GDiensthuber: VERY excited to share SeqTagger with the world! If you want to learn more about our super-fast and accurate demultiplexin….
biorxiv.org
Nanopore direct RNA sequencing (DRS) enables direct measurement of RNA molecules, including their native RNA modifications, without prior conversion to cDNA. However, commercial methods for molecular...
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RT @MorghanLucas: Very excited to announce our preprint on adapting the @nanopore Cas9 workflow for R10 flow cells. This is work from the a….
biorxiv.org
Hereditary ataxias, caused by expansions of short tandem repeats, are difficult to diagnose using traditional PCR and Southern blot methods, which struggle to detect complex repeat expansions and...
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RT @biorxiv_bioinfo: End-to-end simulation of nanopore sequencing signals with feed-forward transformers #biorxiv_….
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Conflict-of-interest disclaimer: The involved institutes have filed a patent application related to this project on which I am listed as a co-inventor.
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With this optimization we were able to detect the adapter, classify it and make decisions on reads within 0.4 s after the poly A tail started, often in less than 0.2 s (i.e. 30-15 nts). This means we almost always reject reads while the poly A tail is still in the pore!.
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But we soon realized that MinKNOW was returning data only in 1 second chunks - too slow for our liking (and reducing adaptive sampling efficiency). So we invested a lot of work in getting this chunk size down - finally achieving 0.1 second chunk size 🤏.
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And imho the coolest part of it all: At a lunch meeting in Nov 23 we contemplated whether we could run this fast classifier on live data to make real-time decisions, optimally while the poly A tail is still in the pore . After a very long 3 weeks, we had a working prototype.
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@wiepp Oh, and if you have existing data with DPC barcodes - WDX and its models (including one trained on DPC) are available here:
github.com
direct RNA nanopore sequencing barcode design and demultiplexing - GitHub - KleistLab/WarpDemuX: direct RNA nanopore sequencing barcode design and demultiplexing
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@wiepp I won't go into too much detail on the rational barcode design (check it out in Fig 2), but briefly, we searched the DNA signal space for sets of sequences with high DTW distances between them. We picked a set of 12 bc's to establish WDX, but this is certainly not the limit . .
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