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Kuba Sawicki

@kubasawicki.bsky.social
842 followers 1.2K following 68 posts

Bryologist, UWM Sequencing Core Lab Researcher at Department of Genetics and Plant Pathophysiology, University of Warmia and Mazury in Olsztyn, Poland

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Kuba Sawicki @kubasawicki.bsky.social · 23/09/2026
How do early land plants switch between water and land? 🌿💧 In our new study in Frontiers in Plant Science, we paired SBS with @nanoporetech.com sequencing to explore alternative splicing and 5mC DNA methylation in Riccia fluitans: doi.org/10.3389/fpls... #PlantGenomics #Epigenetics #Bryophytes
doi.org
Frontiers | Habitat-specific alternative splicing shifts and the 5mC methylation landscape of differentially spliced genes in Riccia fluitans
Phenotypic plasticity in amphibious plants was considered a key evolutionary strategy for survival in fluctuating environments; however, the epigenetic mecha...
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Kuba Sawicki @kubasawicki.bsky.social · 06/09/2026
While our lab mainly focuses on plant genomics, we occasionally step into environmental microbiology. Using long-read metagenomics @nanoporetech.com , we investigated how chlorine disinfection shapes the microbiome, resistome, and mobilome in hospital wastewater www.sciencedirect.com/science/arti...
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Kuba Sawicki @kubasawicki.bsky.social · 17/08/2026
Is the flora of Poland ready for plastome super-barcoding? We assessed GenBank coverage for 3,339 plant & bryophyte species: • 54.4% overall coverage (bryophytes ~76%, vascular plants ~46%) • Most sequenced material is non-European, highlighting the need for local references #Botany #Genomics
mdpi.com
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Kuba Sawicki @kubasawicki.bsky.social · 05/05/2026
We’re hiring! 🌿 Join us as a Principal Investigator in Plant Genomics. Lead your own research group in a friendly environment at UWM. We are looking for innovation and excellence! 🧬 Apply here: www.researchgate.net/job/1036122_... #PlantSci #Genomics #AcademicJobs #ScienceSky
researchgate.net
PRINCIPAL INVESTIGATOR – PLANT GENOMICS at University of Warmia and Mazury in Olsztyn in Olsztyn, POLAND
Mar 17, 2026 | Principal Investigator – Plant Genomics University of Warmia and Mazury in Olsztyn, Poland Scientific Excellence • International Partnerships •... | NEW JOB
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Kuba Sawicki @kubasawicki.bsky.social · 03/05/2026
Can plants "remember" stress without DNA changes? Our new review summarizes 15 years of plant epigenetics, covering rapid adaptation and tools like @nanoporetech.com. Note: huge gaps remain for bryophytes so more to come soon! 📖 OA: doi.org/10.3390/d180... #epigenetics #plants #UWM #liverworts
doi.org
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Kuba Sawicki @kubasawicki.bsky.social · 28/03/2026
New paper alert! 🌿 We sequenced 8 new Pellidae liverwort organellar genomes using @nanoporetech.com . Highlights: 🔹 Radical mitogenome reduction in Apopellia 🔹 Conflicting cp/mt phylogenies 🔹 Insights into ancient plant evolution Link: www.mdpi.com/2223-7747/15...
mdpi.com
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Kuba Sawicki @kubasawicki.bsky.social · 23/03/2026
📢 Job Alert: PI in Data Science/Bioinformatics Are you a Senior Bioinformatician or Researcher ready to run your own group? Lead the charge in high-throughput analysis and computational modeling. 🧬💻 Check it out: www.nature.com/naturecareer... #Bioinformatics #Research #DataScience #CareerMove
nature.com
Principal Investigator - Data Science - Poland (PL) job with University of Warmia and Mazury in Olsztyn | 12856708
Principal Investigator in Data Science for Life Sciences to lead an independent research group using advanced analytics in interdisciplinary research.
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Kuba Sawicki @kubasawicki.bsky.social · 23/03/2026
📢 Job Alert: Principal Investigator in Plant Genomics Looking for your next career move in plant genetics? Great chance to lead a research group and drive innovation in the field. 🧬🌿 Link to apply: www.nature.com/naturecareer... #Research #PlantGenetics #PostdocJobs #Science
nature.com
Principal Investigator – Plant Genomics - Poland (PL) job with University of Warmia and Mazury in Olsztyn | 12856711
Principal Investigator in Plant Genomics to lead an independent research group and advance interdisciplinary genomics and biotechnology research.
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Kuba Sawicki @kubasawicki.bsky.social · 14/03/2026
How do early land plants adapt to life between water and land? In our new paper in PCRE, we provide the first evidence of environmentally responsive organellar 6mA methylation in Riccia fluitans using @nanoporetech.com native DNA sequencing. 🔗 link.springer.com/article/10.1... #liverworts #UWM
link.springer.com
6 mA methylation differences in Riccia fluitans organellar genomes under flood stress - Plant Cell Reports
Key message The first genome-wide evidence of 6 mA methylation in the organellar genomes of Riccia fluitans was provided by this study, with methylation patterns being shown to differ between aquatic ...
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Kuba Sawicki @kubasawicki.bsky.social · 25/02/2026
Our latest paper, "Revisiting the Pellia sensu lato complex: an integrative review of taxonomic revision, phylogeny, and molecular biology," is now out in ASBP. It’s my final publication affiliated with the Dept. of Botany. Check it out: www.journalssystem.com/asbp/Revisit... #Bryology #Liverworts
journalssystem.com
Revisiting the Pellia sensu lato complex: an integrative review of taxonomic revision, phylogeny, and molecular biology
The genus Pellia sensu lato, a crucial early lineage in land plant phylogeny, has long presented a significant taxonomic challenge. This stemmed from its high phenotypic plasticity and a limited numbe...
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Kuba Sawicki @kubasawicki.bsky.social · 10/02/2026
Something new is coming to our lab 😎
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Kuba Sawicki @kubasawicki.bsky.social · 09/02/2026
Tiny plant, giant genome! 🌱🧬 We’re excited to share the final version of our paper in @GigaScience: the first complete telomere-to-telomere (T2T) assembly of the liverwort Apopellia endiviifolia. Thanks @ncn.gov.pl Check out the full open-access study here: doi.org/10.1093/giga...
doi.org
Giant chromosomes of a tiny plant—the complete telomere-to-telomere genome assembly of the simple thalloid liverwort Apopellia endiviifolia (Jungermanniopsida, Marchantiophyta)
AbstractBackground. The liverwort Apopellia endiviifolia, a dioicous, simple thalloid species, is notable for its cryptic diversity, habitat adaptability,
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Kuba Sawicki @kubasawicki.bsky.social · 26/01/2026
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
journals.asm.org
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...
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Kuba Sawicki @kubasawicki.bsky.social · 21/12/2025
The nap after lunch. #wildlife #Butryny #Poland #Warmia
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Henrik Toft Simonsen @htsbiotechmoss.bsky.social · 05/12/2025
www.consilium.europa.eu/en/press/pre... Awesome
consilium.europa.eu
New genomic techniques: Council and Parliament strike deal to boost the competitiveness and sustainability of our food systems
Council and Parliament reach provisional deal on a set of rules for new genomic techniques, aiming to improve the competitiveness of European agriculture and support the sustainability of our food sys...
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Gregor Mendel Institute of Molecular Plant Biology @gmivienna.bsky.social · 02/12/2025
The @embo.org Workshop at the GMI and the @viennabiocenter.bsky.social has come to a close! From November 25th-27th, researchers attended inspiring talks and engaged in discussions on the topic of plant evolution. #EMBOplantEvo
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Kuba Sawicki @kubasawicki.bsky.social · 29/11/2025
Our paper “Giant chromosomes of a tiny plant” is out in @gigascience.bsky.social! We present a T2T genome assembly of the simple thalloid liverwort Apopellia endiviifolia with truly giant chromosomes. 🌱🧬 #plantgenomics #T2T #liverworts @nanoporetech.com Thanks @ncn.gov.pl ! tinyurl.com/m8tkkxd3
tinyurl.com
Giant chromosomes of a tiny plant - the complete telomere-to-telomere genome assembly of the simple thalloid liverwort Apopellia endiviifolia (Jungermanniopsida, Marchantiophyta)
AbstractBackground. The liverwort A. endiviifolia, a dioicous, simple thalloid species, is notable for its cryptic diversity, habitat adaptability, genomic
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Kuba Sawicki @kubasawicki.bsky.social · 04/10/2025
Our latest study reveals how RNA modifications (m⁶A, m⁵C, and pseudouridine) shape the environmental adaptation of the amphibious liverwort Riccia fluitans. 🌿💧 Using direct RNA @nanoporetech.com sequencing, SBS RNAseq and metabolome. #UMW #Riccia 📄 Read here: www.sciencedirect.com/science/arti...
sciencedirect.com
Epitranscriptomic and expression profiling in Riccia fluitans across diverse environmental conditions
Post-transcriptional RNA modifications, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridine (Ψ), are critical regulators of pl…
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Charles Roussin-Léveillée @charlesrleveillee.bsky.social · 02/10/2025
NEW ARTICLE FROM THE LAB 🎉🍀🧫 Groundbreaking work performed by @hueihsuantsai.bsky.social and all! Please, go have a read! Congrats to making it to the cover!!! www.science.org/doi/10.1126/...
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Kuba Sawicki @kubasawicki.bsky.social · 28/09/2025
We just published TAILcaller 🧬 — an R package for analyzing poly(A) tail length directly from @nanoporetech.com Dorado BAMs. ✅ Works with dRNA & cDNA ✅ PCA, volcano/MA plots, heatmaps ✅ Adaptive tests beyond Wilcoxon Case studies: 🌱 Riccia fluitans #liverworts #UWM academic.oup.com/bioinformati...
academic.oup.com
TAILcaller: an R package for analyzing differences in poly(A) tail length for Oxford Nanopore RNA sequencing
AbstractMotivation. Changes in poly(A) tail length were identified as a key post-transcriptional mechanism that controls protein synthesis. The length of t
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Kuba Sawicki @kubasawicki.bsky.social · 26/09/2025
Our new study on the liverwort Riccia sorocarpa reveals its thallus is a microbial biodiversity hotspot. We found a significantly richer and more functionally specialized microbiome on the plant compared to the surrounding soil. Read more: doi.org/10.1007/s117... #Microbiome #Liverworts #UWM
doi.org
Taxonomic and functional differentiation of soil and thallus microbiomes in Riccia sorocarpa - Biologia
Liverworts, as early-diverging land plants, host unique and ecologically important microbiomes, yet remain largely understudied in microbial ecology. In this study, we investigated the taxonomic and functional composition of microbial communities associated with Riccia sorocarpa, focusing on the thallus and adjacent rhizosphere soil. Using nanopore sequencing and metagenomic analysis, we reveal a significantly higher microbial diversity and functional specialization in the thallus microbiome compared to soil. Despite a shared core microbiota, specific bacterial and fungal taxa are selectively enriched in the thallus, likely driven by host-derived factors. Functional profiling highlights an overrepresentation of nitrogen and sulfur cycling, phototrophy, and plant-associated pathways in the thallus, whereas soil communities are dominated by heterotrophic decomposition processes. These findings support the concept of R. sorocarpa as a holobiont and emphasize the ecological and biotechnological potential of liverwort-associated microbiomes. Our results provide new insights into plant-microbe interactions in early land plants and their roles in ecosystem function and resilience.
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Kuba Sawicki @kubasawicki.bsky.social · 29/07/2025
We're diving deep into the world of plant biology by studying the liverwort Apopellia endiviifolia. Our team will be using the cutting-edge Stereo-seq technology from Stomics to explore its spatial transcriptomics. #Bryology #Botany #UWM #Stomics #Transcriptomics #Apopellia #liverworts
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Kuba Sawicki @kubasawicki.bsky.social · 15/06/2025
Excited to share our new paper in BMC Bioinformatics! We present RSCUcaller, a user-friendly R package to analyze synonymous codon usage bias. It's a versatile tool for genomics & molecular biology research. #RStats #Bioinformatics #CodonUsage bmcbioinformatics.biomedcentral.com/articles/10....
bmcbioinformatics.biomedcentral.com
RSCUcaller: an R package for analyzing differences in relative synonymous codon usage (RSCU) - BMC Bioinformatics
Background Synonymous codon usage bias, a significant factor in gene expression and genome evolution, was extensively studied in genomics and molecular biology. Although the genetic code is universal,...
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Rasmus Kirkegaard @kirk3gaard.bsky.social · 04/06/2025
Got a chance to take the @nanoporetech.com hyp(er accuracy) model for a spin. Pretty decent improvement in read quality 🚀 but expect to spend quite some more GPU hours 😉 (Reads were mapped with minimap2 and identity scores from nanoplot were used for phred score calculations)
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Kuba Sawicki @kubasawicki.bsky.social · 29/05/2025
New paper in Cladistics explores the tricky phylogeny of feather grasses (Stipeae) using mitochondrial genomes.The study features the first fully assembled mitogenome in the tribe using @nanoporetech.com sequencing: #Botany #UWM onlinelibrary.wiley.com/doi/10.1111/...
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Phil Carella @philcarella.bsky.social · 01/04/2025
Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants Very happy to share the published version of our work on natural Marchantia-Pseudomonas interactions. Out now in Current Biology: www.cell.com/current-biol...
cell.com
Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants
Robinson et al. identify pathogenic Pseudomonas viridiflava in wild Marchantia polymorpha liverworts and interrogate the mechanisms enabling virulence in non-flowering and flowering plants. Their resu...
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Sophien Kamoun @kamounlab.bsky.social · 24/03/2025
Engineering resistance with help from Liverworts, Mosses and Ferns @Phil_Carella @JohnInnesCentre www.jic.ac.uk/research-imp...
jic.ac.uk
Engineering resistance with help from Liverworts, Mosses and Ferns | John Innes Centre
Plant diversity and synthetic biology offer solutions to the global challenge of crop protection Non-flowering plants such as liverworts, mosses, and ferns belong to divergent lineages with ancient…
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Kuba Sawicki @kubasawicki.bsky.social · 08/03/2025
The first run of @nanoporetech.com RNA004 in our lab. Big leap forward in quality and output. The times like this I wish we have Promethion24 and run all 8 flow cells in parallel. #liverworts #epitranscriptomics #Apopellia
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Dr. Katja Thieme (she/they) @katjathieme.bsky.social · 25/11/2024
Elsevier products: ScienceDirect, Scopus, Mendeley, SciVal, SSRN, Pure, Interfolio. . .and that's not all. "They know what you are working on, they know what you are submitting, they know the results of your peer reviews. They control every part of the process and register every action you take."
ukrant.nl
Elsevier’s stranglehold on academia: How publishers get rich off our data
Academic publishers’ most valuable asset used to be their journals. Now, it’s the data they collect from researchers and then sell. That is extremely concerning, a growing group of Groningen researche...
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PM Delaux @pierremarcdelaux.bsky.social · 17/02/2025
1/6 Super excited to share with you our work on Marchantia intra-specific diversity and pan-genomics, just out @naturegenet.bsky.social www.nature.com/articles/s41... Everything on the discoveries in the thread by @chloe-beaulieu.bsky.social I want to emphasize 5 additional points:
nature.com
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Kuba Sawicki @kubasawicki.bsky.social · 10/02/2025
Sex chromosime evolution in complex thalloid #liverworts from the perspective of #Riccia genomics. Both Riccia genomes were assembled using @nanoporetech.com Pore-C and native DNA sequencing: nph.onlinelibrary.wiley.com/doi/full/10....
nph.onlinelibrary.wiley.com
Evolution of sexual systems and regressive evolution in Riccia
The genus Riccia is the most speciose of the Marchantiopsida, the complex thalloid liverworts. In contrast to the predicted ancestral liverwort and the majority of extant liverworts that are dioicou...
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Kuba Sawicki @kubasawicki.bsky.social · 24/01/2025
Seriously? 1M$ for Q20 short read machine?
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Chris Seymour @iiseymour.bsky.social · 21/01/2025
Huge performance update in today’s dorado v0.9.1 release on Ampere 8.6/8.7 & Ada Lovelace 8.9 nvidia GPUs with up to 2x increase in throughput with hac calling and 3x sup! 🚀 Plus a whole bunch of updates for dorado polish and the odd misc bug fix. github.com/nanoporetech...
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Schmitt-Mechulam Lab @tbioc.bsky.social · 16/01/2025
We are pleased to share our work on the evolution of translation initiation now published in Nature Communications. Take a look at leaderless mRNAs and eS26 in the small ribosomal subunit of Saccharolobus solfataricus. rdcu.be/d5pgg
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Kuba Sawicki @kubasawicki.bsky.social · 21/01/2025
Mk1 family of @nanoporetech.com sequencers
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Kuba Sawicki @kubasawicki.bsky.social · 20/01/2025
New kid on the block 😎 Upgrade of our @nanoporetech.com mk1c
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Kuba Sawicki @kubasawicki.bsky.social · 19/01/2025
The first T2T assembly and annotation of #liverwort Riccia sorocarpa genome using only @nanoporetech.com technology. Done using 2 Promethion flow cells and one minion for cDNA sequencing. More to come soon... www.nature.com/articles/s41...
nature.com
Chromosome-scale telomere to telomere genome assembly of common crystalwort (Riccia sorocarpa Bisch.) - Scientific Data
Scientific Data - Chromosome-scale telomere to telomere genome assembly of common crystalwort (Riccia sorocarpa Bisch.)
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Kuba Sawicki @kubasawicki.bsky.social · 15/01/2025
Some insight into biology and organellar genomics of rare #liverwort Arnellia fennica. Genomic data generates sorely using @nanoporetech.com technology: www.nature.com/articles/s41...
nature.com
Reproductive and persistence strategy of the liverwort Arnellia fennica after the last glaciation in the area of disjunction in Central Europe (Polish Tatra Mountains, carpathians) - Scientific Report...
Scientific Reports - Reproductive and persistence strategy of the liverwort Arnellia fennica after the last glaciation in the area of disjunction in Central Europe (Polish Tatra Mountains,...
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Marc Somssich @somssich.bsky.social · 15/01/2025
📜 Diverse plant RNAs coat Arabidopsis leaves and are distinct from apoplastic RNAs 🧑‍🔬 @luciaborniego.bsky.social, @msr20.bsky.social, @inneslab.bsky.social, et al. 📔 @pnas.org 🔗 www.pnas.org/doi/10.1073/... #️⃣ #PlantScience #PlantImmunity #PlantRNAs
pnas.org
Diverse plant RNAs coat Arabidopsis leaves and are distinct from apoplastic RNAs | PNAS
Transgenic expression of a double-stranded RNA in plants can induce silencing of homologous mRNAs in fungal pathogens. Although such host-induced g...
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Kuba Sawicki @kubasawicki.bsky.social · 14/01/2025
Adenine DNA methylation associated to transcription is widespread across eukaryotes prelights.biologists.com/highlights/a...
prelights.biologists.com
Adenine DNA methylation associated to transcription is widespread across eukaryotes - preLights
Breaking paradigms: Finding 6mA DNA methylation in eukaryotes.
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 13/01/2025
grepq: A Rust application that quickly filters FASTQ files by matching sequences to a set of regular expressions www.biorxiv.org/content/10.1101/202…
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Jan Broder Engler @jbengler.de · 11/01/2025
Dendrograms in ggplot2 heatmaps 🔥 Check out the great `legendry` package by @teunbrand.bsky.social github.com/teunbrand/le...
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Nature Plants @natplants.nature.com · 09/01/2025
New Article: "Quantitative RNA pseudouridine maps reveal multilayered translation control through plant rRNA, tRNA and mRNA pseudouridylation" rdcu.be/d5Mrn Comprehensive and quantitative mapping of pseudouridine sites across four plant species. #PlantScience
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Kuba Sawicki @kubasawicki.bsky.social · 08/01/2025
I wonder if we'll be able to run #dorado @nanoporetech.com basecaller on it: www.nvidia.com/en-us/projec...
nvidia.com
NVIDIA Project DIGITS: The World’s Smallest AI Supercomputer.
Reserve yours today.
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Anna Dewar @annadewar.bsky.social · 08/01/2025
Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2 We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets. These methods must be considered an essential part of the comparative genomics toolkit. @lauriebelch.bsky.social @stuwest.bsky.social
rdcu.be
A phylogenetic approach to comparative genomics
Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 06/01/2025
Mumemto: efficient maximal matching across pangenomes www.biorxiv.org/content/10.1101/202…
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 05/01/2025
ModiDeC: a multi-RNA modification classifier for direct nanopore sequencing www.biorxiv.org/content/10.1101/202…
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PM Delaux @pierremarcdelaux.bsky.social · 01/01/2025
Really pleased to transition from 2024 to 2025 with Tatiana Vernie's work on the evolution of the common symbiosis pathway published @pnas.org 🔽 We finally demonstrate that ☘️ have maintained a genetic pathway to engage with🍄for half a billion years! www.pnas.org/doi/10.1073/...
pnas.org
Conservation of symbiotic signaling since the most recent common ancestor of land plants | PNAS
Plants have colonized lands 450 million years ago. This terrestrialization was facilitated by developmental and functional innovations. Recent evo-...
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Kuba Sawicki @kubasawicki.bsky.social · 30/12/2024
Some insights into Ribes organellar genomics with long-reads @nanoporetech.com assembly using single MinION R10.4.1 flow cell: link.springer.com/article/10.1...
link.springer.com
Organellar genome evolution in Ribes L.: hotspots of mutation, sequence transfer, codon usage, and phylogenetic context - Tree Genetics & Genomes
Ribes genus from the Grossulariaceae family, have been used in the food industry and for medicinal purposes for years. Despite the valuable medicinal values and the widespread occurrence of Ribes, man...
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Kuba Sawicki @kubasawicki.bsky.social · 28/12/2024
I'm going to collect and dry some local Radula species ;) nph.onlinelibrary.wiley.com/doi/10.1111/...
nph.onlinelibrary.wiley.com
Unique bibenzyl cannabinoids in the liverwort Radula marginata: parallels with Cannabis chemistry
The potential of cannabinoids to address public health challenges has stimulated exploration into alternative sources and production technologies. Radula marginata, an endemic Aotearoa/New Zealand l...
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