Interested in Nanopores, RNA and 3d printing - amphibious (wet and dry lab) Scientist. Accelerating science globally at Plasmidsaurus
Bay Area
Joined July 2019
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So cool to see this being built by our incredible engineers! And there's so much more ...
Patrick Bohn retweeted
Hey dinos 🦖 we’ve been cooking up something new in your library…
Now you can:
1. Quickly align any two sequences from your history or uploads
2. Search across everything you've sequenced with us
We'd love a few of you to try early access & help build this. Reply if you're in!
Patrick Bohn retweeted
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024.07.30.6…
Patrick Bohn retweeted
We’re working hard to accelerate your research!
You can now view the predicted amino acid sequence of each coding region and per-base quality scores directly on your results page, giving you clearer insight into your sequence results at every position.
Patrick Bohn retweeted
How can sequencing reveal how viruses spread through hospitals? 🦠
Join CHOP’s Dr. Robert Potter as he shares how he uses Plasmidsaurus long-read sequencing to investigate norovirus transmission within hospitals.
🗓️ Sept 5th, 10am PT
👉 Register: hubs.ly/Q03FnL-L0
Patrick Bohn retweeted
Interested in joining our growing interdisciplinary team studying viruses, RNA, and condensates? Looking for a postdoctoral position? Please consider joining us in Cambridge, UK, or drop us a line to discuss these opportunities: jobs.cam.ac.uk/job/49901/
Patrick Bohn retweeted
Check out the results of the most recent round of the RNA Puzzles endeavor for RNA 3D structure prediction! nature.com/articles/s41592-0…
Patrick Bohn retweeted
🧬Excited to share our new preprint! DMS chemical mapping, a key technique for studying RNA structure. It is assumed that low DMS reactivity=WC, high=non-WC. However, analyzing 7,500 RNA structures containing known 3D structures reveals it's not simple. doi.org/10.1101/2024.11.21.6…
Patrick Bohn retweeted
Congratulations to PoL postdoc Lukáš Pekárek @LukasPekarek1 from the Jahnel group @jjmajahn for being awarded the prestigious Peter and Traudl Engelhorn Scholarship! Lukáš researches long RNA structure and their changes during phase separation.
Read more: physics-of-life.tu-dresden.d…
Patrick Bohn retweeted
5/6 ⚡️ Processing speed benchmark: WDX4: 2.2 min/100k reads (on 8 CPU cores, decreases linearly with number of cores)
Patrick Bohn retweeted
2/6 📊 Performance highlights for RNA004:
- Calibrated performance for difference target accuracy modes (95-99.9%) at high yields
- Extremely low cross-talk between barcodes
- 10 fold runtime improvement compared to RNA002
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/KleistLab/WarpDem…
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: github.com/KleistLab/WarpDem…
Patrick Bohn retweeted
VERY excited to share SeqTagger with the world! If you want to learn more about our super-fast and accurate demultiplexing tool for direct RNA-sequencing (DRS), check out the thread below. bit.ly/3ClVYxG (1/15) 🧵
Patrick Bohn retweeted
Very excited to announce our preprint on adapting the @nanopore Cas9 workflow for R10 flow cells. This is work from the amazing Veronika Scholz and Veronika Schoenrock and team @MGZMuenchen, and is also my very first senior author paper 🧵biorxiv.org/content/10.1101/…
Patrick Bohn retweeted
End-to-end simulation of nanopore sequencing signals with feed-forward transformers biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
Patrick Bohn retweeted
So happy to see this out today - our ultra-fast genome browser GW v1.0 #Genomics 🚀 biorxiv.org/content/10.1101/…
Finally, meet WarpDemuX!
Our (@wiepp) solution for dRNA multiplexing - so fast it runs on any laptop, and so accurate that we could demux even super low abundance samples with high specificity!
And imho the coolest thing? We've also run dRNA live barcode balancing with it 👀
Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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!