Anna Maria Niewiadomska
@amnbio.bsky.social
Science, infectious disease, virology, public health, molecular biology, genomics, bioinformatics. Opinions are my own.
Ever looked at a Sanger trace & thought, “This is going to be a pain to interpret”? Long-read sequencing makes complex genotypes easier to resolve & interpret by separating individual DNA molecules. Try Plasmidsaurus Genotyping Analysis for your project: plasmidsaurus.com/genotyping?u...
🌿 Make the most of #ICOM2026! Join hands-on workshops on Nanopore sequencing and fungal mapping in R, or discover Australia’s mycorrhizal landscapes on our savanna-to-rainforest field trip. 🍄🇦🇺 🔎 Details icom2026.org/workshops/ 🎟️ Register now icom.eventsair.com/icom2026/ext... @icom2026.bsky.social
Without trusted references, methylation data is hard to interpret. Using ATCC Genome Portal resources and nanopore sequencing, this webinar shows how to turn raw microbial modification signals into biological insight. https://bit.ly/4o369uU
Nanopore sequencing provides not just long reads, but the the raw signal data can also be used to identify RNA and DNA modifications. This repository (and the associated review) lists some of the great tools that have been developed www.cell.com/trends/genet...
Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data
Nanopore sequencing provides signal data corresponding to the nucleotide motifs sequenced. Through machine learning-based methods, these signals are translated into long-read sequences that overcome t...
cell.com
Goeke Lab@goekelab.bsky.social · 2mo agoWe’ve updated our awesome-nanopore list! The list is a community-curated list of ONT software tools, please feel free to check it out & contribute: github.com/GoekeLab/awesome-nanopore #Nanopore #Bioinformatics #LongReadSequencing
Volta Labs Launches Automated Library Preparation System for Oxford Nanopore Sequencing Kit V14 #USA #Boston #Volta_Labs #Callisto_System #DNA_Library
Volta Labs Launches Automated Library Preparation System for Oxford Nanopore Sequencing Kit V14
Volta Labs has unveiled its DNA Library Preparation Application designed for the Oxford Nanopore Technologies Ligation Sequencing Kit V14, enhancing lab workflows with automation.
third-news.com
The simplicity and elegance of this solution to protein sequencing rather masks how impressively impactful this can be. What would you do with protein sequencing? @nanopore #nanoporeconf
Look fwd to teach short course (June 1&5) on @nanoporetech.com-based 16S metagenomic sequencing for diagnostics via @ecdc.europa.eu:s #GenEpiBioTrain with @AnnaNoren, Elin Loo, Sofia Stamouli & @lilianderssonli.bsky.social Open to the public! #bioinformatics learning.ecdc.europa.eu/enrol/index....
Milestone day in our new lab at UCLA! Our stellar undergrad Annabelle Conti is celebrating the payoff of a hardworking quarter sequencing 16S microbiomes in our Oxford Nanopore MinIon of local Crustose Coralline Algae and water form the Venice canals 🧪🌎🌊🦠🧬
'A WHO advisory group is due to meet on Tuesday to recommend candidate jabs to prioritise for clinical trials, the global health body said. It will assess data including an analysis by CEPI, which was set up after failures in the international response to a previous Ebola crisis.'
Lethal Ebola virus outbreak triggers urgent international quest for vaccine
World Health Organization experts will meet to recommend candidate jabs for clinical trials
ft.com
Glad to be back at London Calling 2026, and with sunshine this time ☀️ Looking forward to great science and always happy to connect. Feel to say hi if you’re around! #nanoporeconf
Nanopore sequencing is coming to the classroom. 🧬 The DNA Learning Center at Cold Spring Harbor Laboratory is hosting a hands-on educator workshop at Arecibo C3, May 20–22. High school and college faculty may apply. Stipend available. Apply: dnalc.cshl.edu/educatorapps/nanopore-sequencing.html
Our recent preprint: “Interrogating the Escherichia coli epitranscriptome via CRISPR interference and Nanopore native RNA sequencing” www.biorxiv.org/content/10.6...
biorxiv.org
New software enables more accurate and efficient reconstruction of microbial genomes from Nanopore sequencing data, making advanced metagenomic analysis accessible to a wider range of laboratories. doi.org/hbv5j3
Cheaper sequencing, bigger payoff: New software could bring advanced metagenomics to more labs
Metagenomics relies on the use of software programs called assemblers, which can reconstruct tens of thousands of individual microbial genomes from DNA sequencing of samples such as soil, bodily fluids, or clinical swabs from hospitals.
phys.org
We are delighted to have the brilliant Maula Nadia working on her PhD using advanced molecular tricks to combat #illegal #trade in #sharks and #rays! Her 3-peak/amplicon skyline is pure #SciArt! @ljmuimpact.bsky.social @cefasgovuk.bsky.social @nanoporetech.com
Struggling to get complete microbial genomes at scale? Join the webinar to see how a nanopore‑only solution delivers reference‑quality assemblies — resolving plasmids, repeats and AMR genes in a single workflow. https://bit.ly/4lElUYe
Day 4 - part 2 AMR of Bacterial Pathogens - Africa course #AMRBactcourse on the sequencing practical with Nanopore led by @effkay88.bsky.social Huge thanks to the team from @nanoporetech.com South Africa @eventswcs.bsky.social @sangerinstitute.bsky.social
New preprint from the group! Here we use Nanopore dRNA and Ribo-Seq data from multiple yeast species to discover tens of highly conserved microproteins encoded by uORFs in polycistronic transcripts/alternative isoforms. @prbb.org @grib-barcelona.bsky.social www.biorxiv.org/content/10.6...
Evolutionary emergence and preservation of microproteins encoded by upstream ORFs
The analysis of ribosome profiling (Ribo-Seq) data has provided evidence that many eukaryotic mRNAs contain translated upstream or downstream ORFs (uORFs/dORFs), but the biological significance of this translation activity remains, for the most part, unknown. One of the principal limitations has been the lack of Ribo-Seq data from several closely related species, precluding the identification of cases in which translation is phylogenetically conserved. Here, by combining Ribo-Seq data from 100 different experiments, we identify 2,332 translated uORFs and 1,008 translated dORFs in S. cerevisiae, which result in microproteins that tend to be highly hydrophobic or positively charged. To study their phylogenetic conservation, we have generated Nanopore direct RNA sequencing data, together with Ribo-Seq data, from six additional Saccharomyces species, spanning an evolutionary period of around 16 million years. We have identified 195 translated S. cerevisiae uORFs that are also translated in other Saccharomyces species; these uORFs are translated at levels comparable to the main coding sequence and display signatures of purifying selection at the level of the encoded microproteins. In contrast, dORFs are translated at very low levels and they are rarely conserved, suggesting much more limited microprotein functionalization. We have also discovered that uORF translation is associated with the formation of alternative transcript isoforms encompassing the region containing the uORFs but not the main protein coding sequence, implying that some microproteins can be produced independently of the main protein product. This work significantly advances our understanding of how initially pervasive uORF translation can result in new microproteins, providing many new candidates for further functional studies. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, 101052538 Ministerio de Ciencia, Innovación y Universidades, PID2021- 122726NBI00, PGC2018-094091- B-I00, PID2022-136939OBI00, CEX2024-001431-M, MICIU/AEI/10.13039/501100011033 Generalitat de Catalunya, https://ror.org/01bg62x04, 2021SGR00042, 2021SGR00176
biorxiv.org
At the OHSU School of Dentistry AI in Research Symposium, I presented that AI is a major driver of advances in third-generation sequencing technologies (e.g., Nanopore and PacBio). Our lab is using Nanopore sequencing to study DNA and RNA modifications in oral bacteria. #microbiology #dentistry
Last year, we proposed a model of plasmid evolution via fusion and fragmentation (via mge mediated recombination) generating mosaics, by studying historical isolates. Excited to see a MASSIVE paper from @jrpenades.bsky.social , @epcrocha.bsky.social expanding on this www.biorxiv.org/content/10.6...
ARTIC 2 measles resources are live! As part of the Wellcome Trust funded ARTIC 2 project we have developed a collection of measles virus resources that are now openly available at artic.network/viruses/mev
Long-reads exposed plasmid-driven carbapenem resistance transmission missed by routine diagnostics 📌Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing www.doi.org/10.1099/mgen.0.001644 🖥️🧬💻 #AcademicSky #MicroSky #IDSky 🧪🧫🦠
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 res...
doi.org
Happy our preprint is out🦠: "Evaluation of an Oxford Nanopore sequencing workflow for mycobacteria from primary MGIT culture" We developed and tested a workflow for long-read sequencing of #mycobacteria, including optimising DNA extraction and assessing how #ONT performs compared with #Illumina.
biorxiv.org
"Our findings underscore the importance of GuFi phages with broad host ranges in the gut microbiome, and the utility of long-read sequencing for viral discovery, paving the way for deeper insights into the role of bacteriophages in human health and disease." www.biorxiv.org/content/10.6...
biorxiv.org
Application of Nanopore sequencing to intact caspid-packaged DNA reveals that bacterial DNA encapsulation is widespread in the human gut #microbiome www.nature.com/articles/s41...
Large-scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome - Nature Communications
Here, the authors show that packaging of bacterial DNA by phage-like particles is widespread in the gut microbiome, with activity of gene transfer agents being prominent in Oscillospiraceae and Rumino...
nature.com
Announcing a new tool for "denoising" long-read amplicon sequences: savont. Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay. 1/4 github.com/bluenote-157...
GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads
Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont
github.com
End of an era! 🧬 Our latest paper is out now in Microbiology Spectrum. This marks our final study utilizing the @nanoporetech.com RNA002 chemistry before we transition to RNA004. It’s been a wild ride with those flow cells! 🧪📖 Read it here: journals.asm.org/doi/10.1128/... #Nanopore #DRS #UWM
Epitranscriptomic signatures of m5C, m6A, and pseudouridine in COVID-19 reveal host RNA modifications involved in viral pathogenesis | Microbiology Spectrum
RNA modifications are increasingly recognized as critical regulators of host-virus interactions, yet their specific roles in human viral infections remain largely unexplored. Here, we provide the firs...
journals.asm.org
Interested in virome sequencing on @nanoporetech.com instruments? Check out our latest paper where we publish Twist-ONT, a modified protocol for the Twist Comprehensive Viral Research Panel (by @twistbioscience.com) so that it can be used with ONT. www.sciencedirect.com/science/arti... 🧵1/7 🧪
Twist-ONT: Combining nanopore sequencing with the twist comprehensive viral research panel
The Twist Comprehensive Viral Research Panel (Twist CVRP) is a probe-based hybridization capture enrichment method for whole-genome sequencing, design…
sciencedirect.com
Genotypic Technology invites you to an exclusive webinar on Oxford Nanopore RNA Sequencing, exploring how long-read and direct RNA sequencing overcome the limitations of short-read platforms. Register now shorturl.at/uCc1Q
