Sign in

Aaron Pomerantz

@aaronpomerantz.bsky.social
317 followers 349 following 28 posts

Associate Director, Global Segment Marketing @ Oxford Nanopore Technologies - Microbiology, Infectious Disease, Synthetic Biology. The coolest discoveries are the ones you make. Tweets/views are my own.

PostsRepliesMedia
Reposted by Aaron Pomerantz
Steven Robbins @stevenjrobbins.bsky.social · 22/07/2026
It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...
nature.com
The planktonic microbiome of the Great Barrier Reef - Nature
The Great Barrier Reef Microbial Genomes Database compiles prokaryotic, viral and eukaryotic genomes from seawater collected from the Great Barrier Reef, providing a rich resource for the study of mar...
88443
Reposted by Aaron Pomerantz
Oxford Nanopore @nanoporetech.com · 28/05/2026
Join Jim Shaw at #ASMicrobe to uncover how to unlock high-resolution, strain-level microbiome insights. Learn how this is could be crucial to helping deliver more precise diagnostics and treatment in the future. bit.ly/4v4XuKE
185
Reposted by Aaron Pomerantz
Jim Shaw @jimshaw.bsky.social · 29/05/2026
Excited to speak at ASM Microbe 2026 in the Oxford Nanopore session about new tools for long-read metagenomics + 16S sequencing. If you're attending ASM Microbe June 4-7 in D.C. and want to chat, let me know!
1347
Reposted by Aaron Pomerantz
George Olah @georgeolah.bsky.social · 12/11/2025
Our nature note with @philtorres.bsky.social @aaronpomerantz.bsky.social et al. in @ecol-evol.bsky.social was featured in @science.org #ScienceShots written by @sahasmehra.bsky.social #Cyclosa #decoy #spiders #evolution #Peru #Philippines
032
Reposted by Aaron Pomerantz
Jen Cross @jencross.bsky.social · 15/11/2025
Congrats @philtorres.bsky.social and @aaronpomerantz.bsky.social on the paper! I look for these decoy spiders whenever I’m in the rainforest and this is the best example I’ve found. #inverts Cuyabeno Reserve, Ecuador 2022
A spider web with a trash line through the middle leading up to a larger, spider-ish looking patch at the top.
314232
Aaron Pomerantz @aaronpomerantz.bsky.social · 13/11/2025
Hi Steven, here are a few that may be helpful - The nanoMDBG study has some nice comparative datasets www.biorxiv.org/content/10.1... Ultra-deep long-read metagenomics of soil microbes (used R9) www.biorxiv.org/content/10.1... Gut bacteriophage metagenomics pmc.ncbi.nlm.nih.gov/articles/PMC...
000
Reposted by Aaron Pomerantz
Emmanuele Severi @emmseveri.bsky.social · 02/11/2025
#phagesky #phage #microsky www.biorxiv.org/content/10.1...
biorxiv.org
Rolling out plaque-2-sequence: a single plaque sequencing approach enabling rapid, low-cost sequencing of phages directly from plaques
Rapid, accurate, and scalable sequencing of bacteriophage genomes is critical to advance phage therapy, build phage biobanks and understand phage genomic diversity. Current methods are based on sequen...
1156
Reposted by Aaron Pomerantz
Javier Santoyo @jsantoyo.bsky.social · 18/10/2025
Yeast genomes show how large genomic variations affect trait diversity. #YeastGenomes #GenomicVariations #TraitDiversity #LongReads #Sequencing #Pangenome @nature.com 🧬 🖥️ www.nature.com/articles/d41...
012
Reposted by Aaron Pomerantz
Oxford Nanopore @nanoporetech.com · 18/09/2025
Introducing our new Microbial Amplicon Barcoding Kit, which enhances microbial community profiling with an information-rich, rapid & accessible protocol for streamlined identification of bacteria, archaea & fungi — in one go. nanoporetech.com/news/oxford-...
1134
Reposted by Aaron Pomerantz
Sullivan Lab at OSU @sullivan-lab.bsky.social · 12/09/2025
🚨 New tool for viral genomics! Meet CLAE: a high-fidelity Nanopore sequencing strategy that pushes accuracy to Q30, boosts throughput >800 Mb/100 pores, and recovers full-length viral genomes from complex samples 🌊🦠 👉 [doi.org/10.1002/advs.202505978] #viromics #nanopore #genomics
1178
Reposted by Aaron Pomerantz
Hugh Cottingham @hughcottingham.bsky.social · 30/07/2025
Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1 www.medrxiv.org/content/10.1...
34629
Reposted by Aaron Pomerantz
Jonathan Jacobs @bioinformer.bsky.social · 25/06/2025
🧵🦠🖥️🧬🧪 Please RePost 🙏 We just released reference genomes for another 250 strains to the ATCC Genome Portal (genomes.ATCC.org)! We now have assemblies for _5,750 microbial genomes_ AND all assemblies w/ @nanoporetech.com data will include DNA methylation profiles too (details👇) #genomics 1/
genomes.atcc.org
Home | ATCC Genome Portal
The ATCC Genome Portal is a repository of high-quality, authenticated microbial reference genomes.
13119
Reposted by Aaron Pomerantz
Oxford Nanopore @nanoporetech.com · 23/06/2025
We’re bringing #ASMMicrobe 2025 to you, virtually. Join Robert James, Angela Hickey, and Jose Alexander as they share how real-time, Oxford Nanopore sequencing is transforming microbiology—from single bacterial isolates to the complexities of the microbiome. nanoporetech.com/about/events...
233
Reposted by Aaron Pomerantz
Jonathan Jacobs @bioinformer.bsky.social · 19/06/2025
Need bacterial DNA methylation data? Well, we’ve been re-basecalling all ONT data for the ATCC Genome Portal to get it. A huge effort, but as of today we have Mthyl data for ~1,500 bacterial strains. Attending #ASMicrobe? happy to chat IRL about it too. i.e. > genomes.atcc.org/genomes/67e8...
genomes.atcc.org
ATCC® 9945a™ | Bacillus paralicheniformis | ATCC Genome Portal
Bacillus paralicheniformis is a strain of bacteria in the Bacillus genus. This genome was published to the ATCC Genome Portal on 2022-04-02
2309
Reposted by Aaron Pomerantz
Josh Quick @scalene.bsky.social · 19/06/2025
Francisella tularensis identified using @articnetwork.bsky.social SMART-9N metagenomics and @nanoporetech.com sequencing. Amazing work!
193
Reposted by Aaron Pomerantz
Emma Waters @emmabeansworth.bsky.social · 23/06/2025
What a great key note presentation from @mariechattaway.bsky.social looking at the evolution of #AMR in #Salmonella over the lifetime of #publichealth surveillance. If you enjoyed Marie's talk, then there are many posters featuring work from others @ukhsa.bsky.social's surveillance team here at #I3S
0115
Reposted by Aaron Pomerantz
Samuel Lampa @smllmp.bsky.social · 19/06/2025
Very cool!
131
Aaron Pomerantz @aaronpomerantz.bsky.social · 16/06/2025
Each year at @asm.org I'm blown away by the growing amount of presentations and posters leveraging @nanoporetech.com. This year we identified nearly 100 abstracts, ranging from clinical micro & public health applications to environmental research. See you there! nanoporetech.com/about/events...
022
Reposted by Aaron Pomerantz
Heng Li @lh3lh3.bsky.social · 28/05/2025
New metagenome assembler for ONT R10 and PacBio HiFi reads, from Jim Shaw. See Jim's thread for details
03213
Reposted by Aaron Pomerantz
Steven Robbins @stevenjrobbins.bsky.social · 25/05/2025
Short-read metagenomic sequencing cannot recover genomes from many abundant marine prokaryotes due to high strain heterogeneity and platform-inherent GC bias (likely viruses, too), but Nanopore long reads can address this. A results thread on our recent preprint 🧵.
14423
Reposted by Aaron Pomerantz
Nick Loman @pathogenomenick.bsky.social · 22/05/2025
Absolutely thrilled to announce the launch of ARTIC2 - a £5.5M 5 year project funded by @wellcometrust.bsky.social to build on the ARTIC approach of low-cost, globally accessible genome sequencing for surveillance of outbreaks, epidemics and endemic diseases: www.birmingham.ac.uk/news/2025/am...
birmingham.ac.uk
Ambitious project to develop low-cost genome sequencing for pathogens known and unknown - University of Birmingham
Project will build on research that helped diagnostic labs to adopt sequencing capacity for COVID-19 and permit characterisation of future infectious threats
722980
Aaron Pomerantz @aaronpomerantz.bsky.social · 24/05/2025
Hope you enjoyed this London Calling 2025 #NanoporeConf recap. As always, it's the people - my colleagues and the community - who make all of this possible and drive the field forward, even in challenging times
000
Aaron Pomerantz @aaronpomerantz.bsky.social · 24/05/2025
Last but certainly not least, we're taking these applications beyond research into applied industries & biopharma, including plasmid, AAV, mRNA manufacturing and adventitious viral agent contamination, provider deeper insight & faster TAT for these critical biological materials
100
Aaron Pomerantz @aaronpomerantz.bsky.social · 24/05/2025
Direct RNA sequencing is also coming into the limelight for micro, highlighted by Chloé Baum at Pasteur Institute with dengue & chikungunya. Now with 24 barcodes coming for direct RNA multiplexing, this will become a critical tool for novel insights without biases of cDNA
100
Aaron Pomerantz @aaronpomerantz.bsky.social · 24/05/2025
Bonus post sneaking in eukaryotes! High-quality, telomere-to-telomere (T2T) assemblies have potential to set a new gold standard, but were challenging & resource intensive. That's now changing thanks to new software like hifiasm-ONT - check out these amazing assemblies in 🐝🌽🐮
110
Aaron Pomerantz @aaronpomerantz.bsky.social · 24/05/2025
I also believe that the next frontier is Microbial Epigenomics. Detection of base modifications is best-in-class with @nanoporetech.com & the data is already right there every time you sequence a microbial sample directly without PCR. What discoveries are lurking right under our noses?
121
Aaron Pomerantz @aaronpomerantz.bsky.social · 24/05/2025
This extends beyond microbial isolates into complex microbiomes. @sisseljuul.bsky.social and @dorylophile.bsky.social showcased beautiful benchmarking data on superior genome recovery and strain-level resolution in the ZymoBIOMICS Fecal Reference with ONT compared to alternative sequencing platforms
111
Aaron Pomerantz @aaronpomerantz.bsky.social · 24/05/2025
The ability to resolve closed microbial genomes & plasmids has been a critical case for long-reads, but our teams have been pushing to make ONT all you need - thanks to updates in basecalling/polishing, you now get best of both worlds: high-quality assemblies with high-accuracy
100
Aaron Pomerantz @aaronpomerantz.bsky.social · 24/05/2025
bsky.app/profile/nano...
100
Aaron Pomerantz @aaronpomerantz.bsky.social · 24/05/2025
Michael Wiley from Nebraska Public Health shared his great experience with the ElysION device on automated sample-to-answer microbial isolate WGS for hospital-acquired infections, finding that ONT served as a faster, cost-effective, accurate platform to support HAI investigations
100
Aaron Pomerantz @aaronpomerantz.bsky.social · 24/05/2025
bsky.app/profile/nano...
100
Aaron Pomerantz @aaronpomerantz.bsky.social · 24/05/2025
Our community members presented incredible ONT use cases, including Judith Breuer showcasing how rapid metagenomics is faster than standard microbiology for identifying respiratory infections & how new targeted methods increase sensitivity & speed for sterile sites www.medrxiv.org/content/10.1...
101
Aaron Pomerantz @aaronpomerantz.bsky.social · 24/05/2025
One of the new kits I am personally very excited about is the Microbial Amplicon Barcoding Kit - a library prep approach for fast, flexible, full-length amplicon sequencing. If interested, please check out our registration page while we ramp production register.nanoporetech.com/microbial-am...
110
Aaron Pomerantz @aaronpomerantz.bsky.social · 24/05/2025
@rsinclairdokos.bsky.social then highlighted our maturing portfolio of End-to-End solutions in this segment, including full-length 16S/ITS, viral WGS, bacterial & fungal isolate WGS, metagenomics, & synthetic construct verification. You can check out the full tech update youtube.com/watch?v=OYql...
100
Aaron Pomerantz @aaronpomerantz.bsky.social · 24/05/2025
Every year there so many amazing @nanoporetech.com updates at London Calling. Here I'll focus on some of my top picks for Microbiology & Infectious Disease 🦠 First, we saw how the technology continued to advance research in 2024 with ~2/3 of ONT publications in micro/infectious #nanoporeconf
131
Aaron Pomerantz @aaronpomerantz.bsky.social · 19/05/2025
This is going to be an incredible resource for the microbiology community!
010
Reposted by Aaron Pomerantz
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 25/04/2025
High-quality metagenome assembly from nanopore reads with nanoMDBG www.biorxiv.org/content/10.1101/202…
01517
Reposted by Aaron Pomerantz
Sean McKenzie @dorylophile.bsky.social · 25/04/2025
It's been a good month for Nanopore assembly preprints! This time metagenomic assembly with nanoMDBG: hundreds of high-quality MAGs from high-complexity communities
063
Reposted by Aaron Pomerantz
Jonathan Jacobs @bioinformer.bsky.social · 19/04/2025
One thing I’m looking forward to this year: Updating the ATCC Genome Portal to be able to deliver the DNA methylation data we have on over 5,000 bacteria and fungi… We just finished rebasecalling all of the raw @nanoporetech.com data we’ve produced since 2019 with the latest version of Dorado.🙃
081
Reposted by Aaron Pomerantz
Hasindu Gamaarachchi @hasindu2008.bsky.social · 19/04/2025
This new Hifiasm --ont option is amazing. It worked like a charm for us in the nanopore adaptive sampling based assembly paradigm we introduced in a preprint recently. www.biorxiv.org/content/10.1...
biorxiv.org
Adaptively integrated sequencing and assembly of near-complete genomes
Recent advances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals, plants and other eukaryotes. However, there...
2166
Reposted by Aaron Pomerantz
Heng Li @lh3lh3.bsky.social · 18/04/2025
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
biorxiv.org
Efficient near telomere-to-telomere assembly of Nanopore Simplex reads
Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads w...
513977
Aaron Pomerantz @aaronpomerantz.bsky.social · 19/04/2025
Couple resources you might be interested in @stevenjrobbins.bsky.social Presentation by our ML team gives a little more background on the models - your organism doesn’t necessarily need to be in the training dataset to see improvements youtu.be/rRFREd8qxgs?... nanoporetech.com/resource-cen...
youtu.be
Bacterial isolate and plasmid sequencing
YouTube video by Oxford Nanopore Technologies
130
Reposted by Aaron Pomerantz
Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 03/02/2025
First genome sequence from the Ugandan Ebolavirus outbreak with analysis: virological.org/t/990 and first filovirus genome submitted to Pathoplexus database: pathoplexus.org/seq/PP_0011C.... Great (and rapid) work from the National Health Laboratory, UVRI and partners.
virological.org
Near Real-Time Genomic Characterization of the 2025 Sudan Ebolavirus Outbreak in Uganda’s Index Case: Insights into Evolutionary Origins
Introduction Case History: On January 30, 2025, the Ministry of Health declared an outbreak of Sudan Ebola Virus (SUDV) Disease in Kampala, Uganda, following the death of a healthcare worker at Mula...
310165
Reposted by Aaron Pomerantz
Sean McKenzie @dorylophile.bsky.social · 19/12/2024
Check out our new Apps Note on metagenomic assembly of the Zymo fecal reference with nanopore sequencing and metaMDBG. Almost 200 Gb of metagenomic sequence data from a single PromethION flowcell, yeilding hundreds of high-quality metagenome assembled genomes: nanoporetech.com/resource-cen...
nanoporetech.com
Application note: Oxford Nanopore sequencing provides superior MAG recovery and strain-level resolution from a complex microbiome | Oxford Nanopore Technologies
In this application note, we demonstrate the capabilities of Oxford Nanopore metagenomics by sequencing and analysing the well-characterised ZymoBIOMICS Fecal Reference.
084
Aaron Pomerantz @aaronpomerantz.bsky.social · 15/01/2025
Several references & resources: Hebert et al. (2024) onlinelibrary.wiley.com/doi/10.1111/... Yen et al. (2024) www.biorxiv.org/content/10.1... Vuyk et al. (2024) www.protocols.io/view/whole-g... Oxford Nanopore at PAG 2025 nanoporetech.com/about/events... nanoporetech.com/resource-cen...
nanoporetech.com
Oxford Nanopore at PAG 2025
Visit Oxford Nanopore Technologies at PAG 2025
000
Aaron Pomerantz @aaronpomerantz.bsky.social · 15/01/2025
Advancements in T2T genomes were also highlighted by Sergey Koren at PAG, noting significant progress in Oxford Nanopore sequencing quality as a standalone-dataset for high-quality assemblies, without need for PacBio HiFi data. Can't wait to see even further exciting updates in 2025 🌱
100
Aaron Pomerantz @aaronpomerantz.bsky.social · 15/01/2025
Last but certainly not least, Kevin Fengler (Corteva) shared amazing progress in telomere-to-telomere (T2T) plant genome assemblies, which has has finally become a reality thanks to high-accuracy @nanoporetech.com & assembly methods such as Hifiasm, now producing better assemblies than PacBio HiFi
100
Aaron Pomerantz @aaronpomerantz.bsky.social · 15/01/2025
Eugenie 'Charley' Yen (Queen Mary U of London) then shared her beautiful work using Oxford Nanopore sequencing for genomic & epigenomic approaches for conservation of endangered loggerhead sea turtles - even taking the P2 device into the field to deploy methylation-based biomarkers in real-time!
151
Aaron Pomerantz @aaronpomerantz.bsky.social · 15/01/2025
Next, we had Andrew Lail (O'Connor Lab, U Wisconsin-Madison) share their important work developing methods to enhance H5N1 genomic surveillance by sequencing milk samples, noting how Oxford Nanopore is a useful as a faster, efficient method over short-read platforms for timely avian influenza WGS
100