Anna Maria Niewiadomska
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Anna Maria Niewiadomska
@amnbio.bsky.social
60 followers 140 following 50 posts
Science, infectious disease, virology, public health, molecular biology, genomics, bioinformatics. Opinions are my own.
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Reposted by Anna Maria Niewiadomska
weisbergaj.bsky.social
Our manuscript comparing Nanopore vs. Illumina reads for population-level variant calling and genotyping is now out: journals.asm.org/doi/10.1128/... . This work was led by Andrea Schiffer and @arftrhmn.bsky.social.
A comparison of short- and long-read whole-genome sequencing for microbial pathogen epidemiology | mSystems
Genome assembly and variant calling are important steps in microbial population studies and epidemiology. Most variant calling and genotyping pipelines are designed for Illumina short sequencing reads...
journals.asm.org
November 13, 2025 at 9:31 PM
Reposted by Anna Maria Niewiadomska
chcrestani.bsky.social
📢 Save the Date!

The 2nd Nanopore Users Day will take place 🗓️10 March 2026 at the Duclaux Amphitheater, Institut Pasteur (Paris). This edition will be open to external participants!

👉 More details and registration info coming soon!

@chloebaum.bsky.social @pasteur.fr @nanoporetech.com
November 7, 2025 at 3:53 PM
Reposted by Anna Maria Niewiadomska
plosone.org
Countering illegal wildlife trade needs rapid, reliable species ID in places such as airports. This study describes VeRIF-ID, a portable nanopore DNA method that identifies vertebrate species on-site with >91 % accuracy, offering a fast, low-cost tool against trafficking.
Rapid on-site universal vertebrate species identification via multi-barcode nanopore sequencing
The growing illegal wildlife trade (IWT) threatens biodiversity and is a conduit for zoonotic disease, yet its risk of detection is low. Once processed, trafficked species are difficult to identify…
plos.io
November 12, 2025 at 1:02 PM
Reposted by Anna Maria Niewiadomska
nanoporetech.com
See how researchers are detecting species in real time using portable Oxford Nanopore sequencing. Learn best practices for eDNA collection to uncover hidden communities — without the need for observation.

Join our live webinar tomorrow. https://bit.ly/47RharD
November 12, 2025 at 1:49 PM
Reposted by Anna Maria Niewiadomska
biorxivpreprint.bsky.social
A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing https://www.biorxiv.org/content/10.1101/2025.11.12.687992v1
November 12, 2025 at 3:20 PM
Reposted by Anna Maria Niewiadomska
livuni-livsrf.bsky.social
Join the Oxford Nanopore Sequencing Symposium at Life Sciences SR1 on 20 Nov 2025 (10:00–15:00). Talks, networking, free pilot project contest & lunch. Hosted by @cgr-uol.bsky.social
Register: nanoporetech.swoogo.com/Nanopore_X_L...
Begin Registration
nanoporetech.swoogo.com
November 4, 2025 at 11:18 AM
Reposted by Anna Maria Niewiadomska
ingrida.bsky.social
RNA Virus Journal Club – Upcoming Talk - this thursday (Nov 6th !)

With @rdrpsummit.bsky.social - excited to announce talk and discussion with Dr Sanguu Kim about HF nanopore sequencing strategy for virology :)

calendar.app.google/oyRVP6v5Tvjg...
CET: 14:00–15:00,
Format: 30 min + 30 min
CLAE: A High‐Fidelity Nanopore Sequencing Strategy for Read‐Level Viral Variant Detection and Environmental RNA Virus Discovery
High-fidelity Nanopore sequencing offers a cost-effective, portable path to uncovering viral dark matter in complex environments—but suffers from severe read-length bias, low throughput, and limited ...
doi.org
November 4, 2025 at 3:10 PM
Reposted by Anna Maria Niewiadomska
pastelbio.bsky.social
Identification of Capture Phases in Nanopore Protein Sequencing... arxiv.org/abs/2511.0...

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#proteomics #prot-preprint
November 4, 2025 at 6:00 PM
Reposted by Anna Maria Niewiadomska
dnarnaresearch.bsky.social
Establishing benchmarks for quantitative mapping of m6A by Nanopore Direct RNA Sequencing
doi.org/10.1101/2025...
Establishing benchmarks for quantitative mapping of m6A by Nanopore Direct RNA Sequencing
Nanopore direct RNA sequencing (DRS) coupled with Dorado modification-aware basecalling enables mapping of epitranscriptomic modifications including N6-methyladenosine (m6A) at the level of individual...
doi.org
November 3, 2025 at 5:49 AM
Reposted by Anna Maria Niewiadomska
earlhaminst.bsky.social
“MARTi has its origins in software we developed for really rapid identification of #pathogens in preterm infants, but we’ve since adapted it to use in a wide range of settings...including in agriculture, and biosurveillance..."

A powerful new tool for real-time analysis of #nanopore #metagenomics 👇
New software tool MARTi fast-tracks identification and response to microbial threats.
Scientists at the Earlham Institute introduce MARTi, a powerful new tool for the real-time analysis of nanopore metagenomics.
buff.ly
November 3, 2025 at 10:00 AM
Reposted by Anna Maria Niewiadomska
bioconf.bsky.social
Upcoming seminar by Ali HAMRAOUI: Les approches bioinformatiques pour l’etude des isoformes en transcriptomique cellule unique couplee au sequencage Nanopore at IBENS, Thursday 06 November 2025 at 14:00. More info
October 22, 2025 at 5:43 AM
Reposted by Anna Maria Niewiadomska
cgconsortium.bsky.social
Join us next week for "Transforming Tumor Methylation Profiling with Oxford Nanopore Direct DNA Sequencing" on October 28, 2025. Click here to learn more and register today: buff.ly/Oxz6OQh
October 22, 2025 at 2:06 PM
Reposted by Anna Maria Niewiadomska
kuhnbobio.bsky.social
Sampled the Winogradsky column today in 6 places and extracted DNA. Looking forward to seeing how much DNA we extracted and Nanopore 16S metabarcoding on Friday.
October 22, 2025 at 10:56 PM
Reposted by Anna Maria Niewiadomska
patrickgoymer.bsky.social
A new study in @plosone.org finds portable nanopore eDNA sequencing recovers comparable biodiversity signals to Illumina in resource-limited settings, increasing accessibility for biodiversity monitoring.

doi.org/10.1371/jour...
Evaluation of nanopore sequencing for increasing accessibility of eDNA studies in biodiverse countries
Biodiversity loss is a global challenge of the 21st century. Environmental DNA (eDNA)-based metabarcoding offers a cost- and time-efficient alternative to conventional biodiversity surveys, enabling d...
doi.org
October 17, 2025 at 10:58 AM
Reposted by Anna Maria Niewiadomska
ribozyme.bsky.social
My lightning talk on “Uncovering Genomic Diversity in the African Diaspora via Long-Read Nanopore Sequencing” will be presented at 1:45 PM in Room 206AB (Level 2). #ASHG25
October 17, 2025 at 3:20 PM
Reposted by Anna Maria Niewiadomska
phypapers.bsky.social
Validation of High-throughput Oxford Nanopore Technology for HIV-1 Transmitted/Founder Virus Identification https://pubmed.ncbi.nlm.nih.gov/41109409/
October 20, 2025 at 9:09 AM
Reposted by Anna Maria Niewiadomska
nanoporetech.com
Our abstract submissions for London Calling 2026 are now open! If you’ve been using Oxford Nanopore technology to power the bigger and bolder research questions, we want to hear about it. Submit your abstract here: nanoporetech.com/about/events... #nanoporeconf
October 20, 2025 at 10:11 AM
Reposted by Anna Maria Niewiadomska
hggadvances.bsky.social
📣New from Wang & colleagues!
📑Fine Mapping Regulatory Variants by Characterizing Native CpG Methylation with Nanopore Long-Read Sequencing
👉 bit.ly/4o8qMoY
Fine Mapping Regulatory Variants by Characterizing Native CpG Methylation with Nanopore Long-Read Sequencing
This study introduces a nanopore long-read sequencing approach to identify functional SNPs by jointly profiling DNA methylation and genetic variation on the same molecules. By examining epigenetic cha...
bit.ly
October 20, 2025 at 5:40 PM
Reposted by Anna Maria Niewiadomska
stefanbarakat.bsky.social
New paper from our ultra-rapid WGS project published @ejhg-journal.bsky.social :
"Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making"
#raredisease #WGS @nanoporetech.com @erasmusmc.bsky.social
www.nature.com/articles/s41...
Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making - European Journal of Human Genetics
European Journal of Human Genetics - Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making
www.nature.com
October 21, 2025 at 2:48 PM
2️⃣ 4️⃣ hours left until our microbial amplicon barcoding webinar!
Learn how to sequence full length 16S and ITS genes with Oxford Nanopore's latest kit. Recordings also sent out after signup.
nanoporetech.com/about/events... #16S #ITS #metagenomics #metabarcoding
Webinar: How to sequence 16S and ITS microbial amplicons
Join us for a deep dive into our end-to-end microbial amplicon barcoding workflow
nanoporetech.com
October 21, 2025 at 3:13 PM
Reposted by Anna Maria Niewiadomska
genewiz.bsky.social
Hope you had a chance to chat with Max at @nanoporetech.com Biopharma Day Philadelphia. We had a great time discussing:
- Plasmid EZ: Easy as 1, 2, 3
- Nanopore Technology Applications at Azenta Life Sciences
- Benefits of mixed platform multiomics

#BiopharmaDay #Nanopore #NGS #ONT
October 10, 2025 at 1:51 PM
"near-complete de novo assembly of chromosomes and plasmids by long-read nanopore sequencing allowed for high-resolution strain identification, plasmid profiling, and antibiotic resistance gene detection"
www.biorxiv.org/content/10.1...
#AMR #Nanopore #PublicHealth #GenomicSurveillance
Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing
The growing resistance of Enterobacterales to last-resort antibiotics such as carbapenems puts a significant burden on healthcare systems, also due to plasmids driving a rapid spread of carbapenem…
buff.ly
October 14, 2025 at 6:55 PM
Cool talk on microbial isolation and metagenomics at Kalk Bay in S. Africa, to screen previously uncharacterised genomes to search for novel antimicrobial compounds
📺 You can watch here: www.youtube.com/watch?v=t5cQ...
#LongReads #AMR #antimicrobial #metagenomics #microbiome #nanopore
Microbial isolation at Kalk Bay and the value of DNA sequencing.
Careers in Marine Sciences Academic Talk: "Microbial isolation at Kalk Bay and the value of DNA sequencing." Speaker: Dr Lonnie van Zyl, Chief Officer – IMBM
buff.ly
October 9, 2025 at 5:00 PM
Reposted by Anna Maria Niewiadomska
virus-metagenomics.bsky.social
Just under 6 weeks until the metagenomic virus discovery workshop kicks off in Stellenbosch, South Africa. We're excited to be bringing together a fantastic group of speakers and teachers with expertise in all aspects of virus discovery from around the world.
October 7, 2025 at 7:04 AM
New TB genomics study! Culture-free Mycobacterium tuberculosis WGS using nanopore sequencing directly from sputum. Faster, simpler, and actionable for public health.
biorxiv.org/content/10.1101/2025.09.23.678181v1

#NanoporeSequencing #Genomics #TB
Direct nanopore sequencing of M. tuberculosis on sputa and rescue of suboptimal results to enhance transmission surveillance
Whole-genome sequencing (WGS) enhances precision in predicting antimicrobial resistance and tracking Mycobacterium tuberculosis (MTB) transmission. Due to MTB’s slow-growing nature, genomic results…
www.biorxiv.org
October 8, 2025 at 7:24 PM