Jan Gawor
@gaworjan.bsky.social
Sanger / NGS sequencing specialist (love long reads :) / microbial de novo sequencing / Research Associate at http://oligo.pl DNA Sequencing Facility IBB PAS Warsaw, Poland
Pinned
Jan Gawor
@gaworjan.bsky.social
· Nov 14
ICESp1109, a Novel Hybrid Integrative Conjugative Element of Macrolide-Resistant Streptococcus pyogenes Serotype M77 Collected Between 2003 and 2017 in Poland
A novel hybrid 103-kb integrative and conjugative element, ICESp1109, was identified in macrolide- and tetracycline-resistant Streptococcus pyogenes M77/ST
academic.oup.com
I'm super excited to present our recent paper! We identified a novel hybrid Integrative Conjugative Element ICESp1109 in macrolide-resistant Streptococcus pyogenes M77 strains collected between 2003 and 2017 in Poland.
academic.oup.com/jid/advance-...
academic.oup.com/jid/advance-...
Reposted by Jan Gawor
Efficient near telomere-to-telomere assembly of Nanopore Simplex reads
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
doi.org
November 19, 2025 at 4:52 AM
Efficient near telomere-to-telomere assembly of Nanopore Simplex reads
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
doi.org/10.1101/2025...
Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...
Reposted by Jan Gawor
Join us at this exciting Workshop on #LongReads with keynotes from @aphillippy.bsky.social @mydennis.bsky.social
co-organized by @christinebeck.bsky.social and Mark Adams @jacksonlab.bsky.social Register www.jax.org/longread
#RNA #genomics #bioinformatics #cancer #medicine #evolution #neuroscience
co-organized by @christinebeck.bsky.social and Mark Adams @jacksonlab.bsky.social Register www.jax.org/longread
#RNA #genomics #bioinformatics #cancer #medicine #evolution #neuroscience
Long-Read Sequencing Workshop
The program will involve sessions on Genome Evolution, Genome Regulation, Transcriptomics, Rare Diseases, Common Diseases, and Viral and Microbial Genomes. Committed speakers include Adam Phillipy (NH...
www.jax.org
November 14, 2025 at 7:57 PM
Join us at this exciting Workshop on #LongReads with keynotes from @aphillippy.bsky.social @mydennis.bsky.social
co-organized by @christinebeck.bsky.social and Mark Adams @jacksonlab.bsky.social Register www.jax.org/longread
#RNA #genomics #bioinformatics #cancer #medicine #evolution #neuroscience
co-organized by @christinebeck.bsky.social and Mark Adams @jacksonlab.bsky.social Register www.jax.org/longread
#RNA #genomics #bioinformatics #cancer #medicine #evolution #neuroscience
Reposted by Jan Gawor
Easy and interactive taxonomic profiling with Metabuli App.
It integrates database curation, read QC, taxonomic profiling, and visualization right on your desktop.
No command line, server, or internet required.
Now published in Bioinformatics! 🧵1/5
doi.org/10.1093/bioi...
github.com/steineggerla...
It integrates database curation, read QC, taxonomic profiling, and visualization right on your desktop.
No command line, server, or internet required.
Now published in Bioinformatics! 🧵1/5
doi.org/10.1093/bioi...
github.com/steineggerla...
October 16, 2025 at 7:29 AM
Easy and interactive taxonomic profiling with Metabuli App.
It integrates database curation, read QC, taxonomic profiling, and visualization right on your desktop.
No command line, server, or internet required.
Now published in Bioinformatics! 🧵1/5
doi.org/10.1093/bioi...
github.com/steineggerla...
It integrates database curation, read QC, taxonomic profiling, and visualization right on your desktop.
No command line, server, or internet required.
Now published in Bioinformatics! 🧵1/5
doi.org/10.1093/bioi...
github.com/steineggerla...
Quite interesting pipeline for bacterial isolate QC including de novo assembly and contamination detection.
github.com/B-UMMI/INNUca
github.com/B-UMMI/INNUca
GitHub - B-UMMI/INNUca: INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search
INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search - B-UMMI/INNUca
github.com
October 17, 2025 at 12:25 PM
Quite interesting pipeline for bacterial isolate QC including de novo assembly and contamination detection.
github.com/B-UMMI/INNUca
github.com/B-UMMI/INNUca
Reposted by Jan Gawor
Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems.
Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...
Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
www.nature.com
October 1, 2025 at 5:57 PM
Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems.
Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...
Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...
Reposted by Jan Gawor
Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV
Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...
www.biorxiv.org
September 29, 2025 at 7:45 PM
Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
Reposted by Jan Gawor
Nauka i badania, w kraju, który jest 20-tą gospodarką świata, powinny być priorytetem ponad podziałami. Apelujemy do wszystkich, którzy rozumieją potrzebę prowadzenia badań naukowych w Polsce o zapoznanie się z treścią listu i poparcie Apelu.
www.petycjeonline.com/list_otwarty...
www.petycjeonline.com/list_otwarty...
List otwarty do Prezydenta RP, Marszałka Sejmu RP, Marszałka Senatu RP, Prezesa Rady Ministrów oraz Wiceprezesów Rady Ministrów w sprawie finansowania nauki, w tym zwłaszcza Narodowego Centrum Nauki
Szanowni Państwo,
W niniejszej petycji prezentujemy List otwarty, który będzie wysłany do Kancelarii Prezydenta, Marszałków Sejmu i Senatu, Prezesa Rady Ministr&oacut...
www.petycjeonline.com
September 29, 2025 at 12:16 PM
Nauka i badania, w kraju, który jest 20-tą gospodarką świata, powinny być priorytetem ponad podziałami. Apelujemy do wszystkich, którzy rozumieją potrzebę prowadzenia badań naukowych w Polsce o zapoznanie się z treścią listu i poparcie Apelu.
www.petycjeonline.com/list_otwarty...
www.petycjeonline.com/list_otwarty...
Our paper is out! We report the first genome-wide essential gene map of Streptococcus anginosus 980/01, a human commensal & opportunistic pathogen. Using TnSeq, we found 348 essential genes, incl. 40 unique ones, shedding light on its biology & pathogenic potential.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Genome-wide identification of essential genes in the invasive Streptococcus anginosus strain - Scientific Reports
Scientific Reports - Genome-wide identification of essential genes in the invasive Streptococcus anginosus strain
www.nature.com
September 25, 2025 at 2:59 PM
Our paper is out! We report the first genome-wide essential gene map of Streptococcus anginosus 980/01, a human commensal & opportunistic pathogen. Using TnSeq, we found 348 essential genes, incl. 40 unique ones, shedding light on its biology & pathogenic potential.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Jan Gawor
Microbiome sequencing has come so far in 2 decades. In my PhD— I used TRFLP…. am now doing long read sequencing of entire soil metagenomes! This review was great fun- thanks Gitta Szabó @emileyeloe-fadrosh.bsky.social Tanja Woyke of @jgi.doe.gov
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A genomic view of Earth’s biomes - Nature Reviews Genetics
Genome-wide approaches have uncovered the vast microbial and viral diversity across ecosystems. This Review explores advances in metagenomics, single-cell sequencing and functional profiling to elucid...
www.nature.com
September 23, 2025 at 4:14 AM
Microbiome sequencing has come so far in 2 decades. In my PhD— I used TRFLP…. am now doing long read sequencing of entire soil metagenomes! This review was great fun- thanks Gitta Szabó @emileyeloe-fadrosh.bsky.social Tanja Woyke of @jgi.doe.gov
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Jan Gawor
GenMasterTable: a user-friendly desktop application for filtering, summarising, and visualising large-scale annotated genetic variants. #GeneticVariants #VariantExploration #DataVisualization #GUI #BMCbioinformatics 🧬 🖥️
bmcbioinformatics.biomedcentral.com/articles/10....
bmcbioinformatics.biomedcentral.com/articles/10....
September 1, 2025 at 7:05 PM
GenMasterTable: a user-friendly desktop application for filtering, summarising, and visualising large-scale annotated genetic variants. #GeneticVariants #VariantExploration #DataVisualization #GUI #BMCbioinformatics 🧬 🖥️
bmcbioinformatics.biomedcentral.com/articles/10....
bmcbioinformatics.biomedcentral.com/articles/10....
Reposted by Jan Gawor
Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports...
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
August 15, 2025 at 4:33 PM
Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports...
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
Reposted by Jan Gawor
I'm offering a new workshop that's part instruction, part group coaching. This program will focus on the design principles we should consider when generating visuals. There won't be any coding so don't let that hold you back shop.riffomonas.org/products/tra...
Transform your data visualizations in 5 weeks - no judgement, no code
shop.riffomonas.org
July 31, 2025 at 10:14 PM
I'm offering a new workshop that's part instruction, part group coaching. This program will focus on the design principles we should consider when generating visuals. There won't be any coding so don't let that hold you back shop.riffomonas.org/products/tra...
Reposted by Jan Gawor
The software updates on NovaSeq X Series really do improve performance, quality and output. It's all documented in the #illumina blog- sapac.illumina.com/science/geno...
NovaSeq X software update 1.3 improves data quality and customer usability
The first shipments of the NovaSeq X Series introduced XLEAP-SBS chemistry on Illumina’s next-generation high-throughput platform. With the 25B flow cell, NovaSeq X software update 1.2 enabled up to 1...
sapac.illumina.com
July 16, 2025 at 6:24 AM
The software updates on NovaSeq X Series really do improve performance, quality and output. It's all documented in the #illumina blog- sapac.illumina.com/science/geno...
Reposted by Jan Gawor
NEW publication: Super happy to see the ClipKIT web application now published in Nucleic Acids Research @narjournal.bsky.social!!
Trim your alignments for FREE on us :D
Application: clipkit.genomelybio.com#/
Manuscript: academic.oup.com/nar/article/...
#phylogenetics #evolution #bioinformatics
Trim your alignments for FREE on us :D
Application: clipkit.genomelybio.com#/
Manuscript: academic.oup.com/nar/article/...
#phylogenetics #evolution #bioinformatics
ClipKIT in the browser: fast online trimming of multiple sequence alignments for phylogenetics
Abstract. Multiple sequence alignment trimming can help improve phylogenetic signal and reduce computational load. ClipKIT trims multiple sequence alignmen
academic.oup.com
July 14, 2025 at 8:44 PM
NEW publication: Super happy to see the ClipKIT web application now published in Nucleic Acids Research @narjournal.bsky.social!!
Trim your alignments for FREE on us :D
Application: clipkit.genomelybio.com#/
Manuscript: academic.oup.com/nar/article/...
#phylogenetics #evolution #bioinformatics
Trim your alignments for FREE on us :D
Application: clipkit.genomelybio.com#/
Manuscript: academic.oup.com/nar/article/...
#phylogenetics #evolution #bioinformatics
Our paper is out!🦠
The S. aureus phage ASZ22RN can infect or lyse all tested strains and efficiently transfer plasmids—even in strains with phage defenses. Its unique ability to bypass intracellular barriers makes it a valuable tool for genetic delivery into clinical isolates.
The S. aureus phage ASZ22RN can infect or lyse all tested strains and efficiently transfer plasmids—even in strains with phage defenses. Its unique ability to bypass intracellular barriers makes it a valuable tool for genetic delivery into clinical isolates.
Characterization of a novel Phietavirus genus bacteriophage and its potential for efficient transfer of modified shuttle plasmids to Staphylococcus aureus strains of different clonal complexes - PubMe...
This study highlights the capacity of a newly isolated staphylococcal <i>Phietavirus</i>, ASZ22RN, to transfer a low-copy-number shuttle <i>Staphylococcus aureus</i>-<i>Escherichia coli</i> plasmid to...
pubmed.ncbi.nlm.nih.gov
July 14, 2025 at 9:16 PM
Our paper is out!🦠
The S. aureus phage ASZ22RN can infect or lyse all tested strains and efficiently transfer plasmids—even in strains with phage defenses. Its unique ability to bypass intracellular barriers makes it a valuable tool for genetic delivery into clinical isolates.
The S. aureus phage ASZ22RN can infect or lyse all tested strains and efficiently transfer plasmids—even in strains with phage defenses. Its unique ability to bypass intracellular barriers makes it a valuable tool for genetic delivery into clinical isolates.
Delighted to share a new preprint from the lab!
We identified essential genes in S. anginosus, a bloodstream isolate, under optimal laboratory conditions using a transposon mutagenesis combined with Transposon-Directed Insertion Site Sequencing (TraDIS).
www.biorxiv.org/content/10.1...
We identified essential genes in S. anginosus, a bloodstream isolate, under optimal laboratory conditions using a transposon mutagenesis combined with Transposon-Directed Insertion Site Sequencing (TraDIS).
www.biorxiv.org/content/10.1...
Genome-Wide Identification of Essential Genes in the Invasive Streptococcus anginosus Strain
Background: Streptococcus anginosus, part of the Streptococcus anginosus group (SAG), is a human commensal increasingly recognized as an opportunistic pathogen responsible for abscesses formation and ...
www.biorxiv.org
June 10, 2025 at 12:02 PM
Delighted to share a new preprint from the lab!
We identified essential genes in S. anginosus, a bloodstream isolate, under optimal laboratory conditions using a transposon mutagenesis combined with Transposon-Directed Insertion Site Sequencing (TraDIS).
www.biorxiv.org/content/10.1...
We identified essential genes in S. anginosus, a bloodstream isolate, under optimal laboratory conditions using a transposon mutagenesis combined with Transposon-Directed Insertion Site Sequencing (TraDIS).
www.biorxiv.org/content/10.1...
Reposted by Jan Gawor
Explore microbial evolution with AutoMLST2, a web server for automated phylogenetic analysis for bacterial & archaeal genomes. PMID:40357641, Nucleic Acids Res 2025, @NAR_Open https://doi.org/10.1093/nar/gkaf397 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
https://doi.org/10.1093/nar/gkaf397
No description available
doi.org
May 28, 2025 at 5:10 AM
Reposted by Jan Gawor
Excited to share our latest work on comparing and visualizing multiple genome assemblies to identify conservation and structural variation in pangenomes with Mumemto! Check out poster 250 at #bog25 if you are here. New preprint coming very soon 👀
May 9, 2025 at 4:26 PM
Excited to share our latest work on comparing and visualizing multiple genome assemblies to identify conservation and structural variation in pangenomes with Mumemto! Check out poster 250 at #bog25 if you are here. New preprint coming very soon 👀
Reposted by Jan Gawor
🌐Our @nature.com paper is out! Researchers from IIMCB and other Polish institutions show how TENT5A boosts mRNA vaccine efficacy by stabilizing therapeutic mRNAs and enhancing antigen production. A step toward better therapies for cancer and beyond! 🧬
👉Read the story: bit.ly/3XYvQkI
#Nature #mRNA
👉Read the story: bit.ly/3XYvQkI
#Nature #mRNA
IIMCB
bit.ly
April 16, 2025 at 6:00 PM
🌐Our @nature.com paper is out! Researchers from IIMCB and other Polish institutions show how TENT5A boosts mRNA vaccine efficacy by stabilizing therapeutic mRNAs and enhancing antigen production. A step toward better therapies for cancer and beyond! 🧬
👉Read the story: bit.ly/3XYvQkI
#Nature #mRNA
👉Read the story: bit.ly/3XYvQkI
#Nature #mRNA
The best food choices for healthy aging! Huge cohort - 105,000 people tracked over 30 years. Eat fruit and vegetables and avoid red meat. Wine is quite good.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Optimal dietary patterns for healthy aging - Nature Medicine
In two longitudinal cohorts followed for 30 years, the associations of eight different dietary patterns with healthy aging—encompassing cognitive, physical and mental health—were studied, identifying ...
www.nature.com
March 24, 2025 at 9:56 PM
The best food choices for healthy aging! Huge cohort - 105,000 people tracked over 30 years. Eat fruit and vegetables and avoid red meat. Wine is quite good.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Our first paper this year is out!
We studied the occurrence and diversity of fungi on the skin of Atopic dermatitis patients and healthy volunteers by using a two-pronged strategy (culture-dependent and NGS-based).
onlinelibrary.wiley.com/doi/10.1111/...
We studied the occurrence and diversity of fungi on the skin of Atopic dermatitis patients and healthy volunteers by using a two-pronged strategy (culture-dependent and NGS-based).
onlinelibrary.wiley.com/doi/10.1111/...
The Skin Mycobiome of Patients With Atopic Dermatitis and Healthy Volunteers: A Case–Control Study
Atopic dermatitis (AD) is a common inflammatory skin disease, for which dysbiosis of the skin mycobiome is considered a triggering factor. The aim of this study was to explore the skin mycobiome of A...
onlinelibrary.wiley.com
March 23, 2025 at 8:12 PM
Our first paper this year is out!
We studied the occurrence and diversity of fungi on the skin of Atopic dermatitis patients and healthy volunteers by using a two-pronged strategy (culture-dependent and NGS-based).
onlinelibrary.wiley.com/doi/10.1111/...
We studied the occurrence and diversity of fungi on the skin of Atopic dermatitis patients and healthy volunteers by using a two-pronged strategy (culture-dependent and NGS-based).
onlinelibrary.wiley.com/doi/10.1111/...
Has anyone of you know how to speed up docker compose? I run the Phastest phage identification pipeline in docker and it is really slow due to running on single thread. Interestingly first sample in my batch is runing faster on multiple cores. Any hints?
March 5, 2025 at 11:15 AM
Has anyone of you know how to speed up docker compose? I run the Phastest phage identification pipeline in docker and it is really slow due to running on single thread. Interestingly first sample in my batch is runing faster on multiple cores. Any hints?
Reposted by Jan Gawor
A link between yogurt intake and reduce risk of colon cancer, from cohort of over 130,00 participants, with inverse relationship to Bifidobacterium in gut microbiome
www.tandfonline.com/doi/full/10.... open-access
www.tandfonline.com/doi/full/10.... open-access
February 12, 2025 at 6:18 PM
A link between yogurt intake and reduce risk of colon cancer, from cohort of over 130,00 participants, with inverse relationship to Bifidobacterium in gut microbiome
www.tandfonline.com/doi/full/10.... open-access
www.tandfonline.com/doi/full/10.... open-access
Reposted by Jan Gawor
Highly multiplexed spatial transcriptomics in bacteria https://www.science.org/doi/10.1126/science.adr0932
January 29, 2025 at 7:30 PM
Highly multiplexed spatial transcriptomics in bacteria https://www.science.org/doi/10.1126/science.adr0932
Reposted by Jan Gawor
In 2014 Dutch scientists left a hamster wheel outside, to see if wild animals would use it like their domesticated counterparts.
The answer: hell yes! 734 visits from wild mice - plus rats, shrews, slugs ("running" being subjective here) & even frogs and snails.
The apparent reason: fun. Just fun.
The answer: hell yes! 734 visits from wild mice - plus rats, shrews, slugs ("running" being subjective here) & even frogs and snails.
The apparent reason: fun. Just fun.
January 27, 2025 at 7:50 PM
In 2014 Dutch scientists left a hamster wheel outside, to see if wild animals would use it like their domesticated counterparts.
The answer: hell yes! 734 visits from wild mice - plus rats, shrews, slugs ("running" being subjective here) & even frogs and snails.
The apparent reason: fun. Just fun.
The answer: hell yes! 734 visits from wild mice - plus rats, shrews, slugs ("running" being subjective here) & even frogs and snails.
The apparent reason: fun. Just fun.