Jess Chen
@drjesschen.bsky.social
Mom, wife, birder, bike commuter, and microbial bioinformatician.
Reposted by Jess Chen
New blog post: ONT read QC strategies for assembly
rrwick.github.io/2026/02/05/r...
Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.
rrwick.github.io/2026/02/05/r...
Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.
ONT read QC strategies for assembly
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
February 5, 2026 at 3:38 AM
New blog post: ONT read QC strategies for assembly
rrwick.github.io/2026/02/05/r...
Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.
rrwick.github.io/2026/02/05/r...
Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.
Reposted by Jess Chen
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning - Nature Biotechnology
PlasMAAG uses cross-sample information to improve plasmid reconstruction from metagenomic samples.
www.nature.com
February 4, 2026 at 8:20 PM
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
Reposted by Jess Chen
Curious, what's the best-practice tool at this point for taxonomically classifying long reads from metagenomes from less well-characterised environments?
My impression is that Kraken will give lots of false positives and mis-classify taxa not in its database.
Please share around for visibility.
My impression is that Kraken will give lots of false positives and mis-classify taxa not in its database.
Please share around for visibility.
January 28, 2026 at 6:59 PM
Curious, what's the best-practice tool at this point for taxonomically classifying long reads from metagenomes from less well-characterised environments?
My impression is that Kraken will give lots of false positives and mis-classify taxa not in its database.
Please share around for visibility.
My impression is that Kraken will give lots of false positives and mis-classify taxa not in its database.
Please share around for visibility.
Reposted by Jess Chen
We are looking for new editors for Microbiology, the flagship journal of @microbiologysociety.org
Deadline for applications is 16 Feb 2026
microbiologysociety.org/who-we-are/j...
Deadline for applications is 16 Feb 2026
microbiologysociety.org/who-we-are/j...
Jobs
View the current job vacancies at the Microbiology Society.
microbiologysociety.org
January 28, 2026 at 8:44 AM
We are looking for new editors for Microbiology, the flagship journal of @microbiologysociety.org
Deadline for applications is 16 Feb 2026
microbiologysociety.org/who-we-are/j...
Deadline for applications is 16 Feb 2026
microbiologysociety.org/who-we-are/j...
Reposted by Jess Chen
How do you react when your favorite microbe is renamed by taxonomists who are completely outside your field—and who ignore the community that actually works with it? Here is our clear answer re the case of Pseudomonas putida KT2440 👉🏻 journals.asm.org/doi/10.1128/...
The disputed identity of Pseudomonas putida KT2440: when taxonomists rename your favorite microbe | mBio
Names matter; they are not mere labels. They operate as anchors of memory, social coordinates, and references of collective identity. When a name becomes established through long-term
use and broad ad...
journals.asm.org
January 27, 2026 at 4:54 PM
How do you react when your favorite microbe is renamed by taxonomists who are completely outside your field—and who ignore the community that actually works with it? Here is our clear answer re the case of Pseudomonas putida KT2440 👉🏻 journals.asm.org/doi/10.1128/...
Reposted by Jess Chen
⏰ Don’t miss out!
📢 The TARGetAMR Annual Conference 2026 is coming 14–15 May to Birmingham.
🦠 Connect with experts & shape the future of AMR research.
👉 Register now: www.targetamr.org.uk/hdrevents/ta...
#TARGetAMR26
📢 The TARGetAMR Annual Conference 2026 is coming 14–15 May to Birmingham.
🦠 Connect with experts & shape the future of AMR research.
👉 Register now: www.targetamr.org.uk/hdrevents/ta...
#TARGetAMR26
January 28, 2026 at 10:12 AM
⏰ Don’t miss out!
📢 The TARGetAMR Annual Conference 2026 is coming 14–15 May to Birmingham.
🦠 Connect with experts & shape the future of AMR research.
👉 Register now: www.targetamr.org.uk/hdrevents/ta...
#TARGetAMR26
📢 The TARGetAMR Annual Conference 2026 is coming 14–15 May to Birmingham.
🦠 Connect with experts & shape the future of AMR research.
👉 Register now: www.targetamr.org.uk/hdrevents/ta...
#TARGetAMR26
Reposted by Jess Chen
We've got ISSUES. Literally.
We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?
arxiv.org/abs/2601.07563
A 🧵 1/n
We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?
arxiv.org/abs/2601.07563
A 🧵 1/n
January 13, 2026 at 8:27 AM
We've got ISSUES. Literally.
We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?
arxiv.org/abs/2601.07563
A 🧵 1/n
We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?
arxiv.org/abs/2601.07563
A 🧵 1/n
Amazing news!
Epstein-Barr Virus #EBV was linked to #MultipleSclerosis - now a plausible cause has been found, misidentification by longterm memory T-cells that pick on the wrong protein, ANO2, instead of the EBV-antigen. Massive inflection towards the elimination of MS!!!
🧪🧠Cell www.cell.com/cell/fulltex...
🧪🧠Cell www.cell.com/cell/fulltex...
Anoctamin-2-specific T cells link Epstein-Barr virus to multiple sclerosis
Researchers identified anoctamin-2 (ANO2) as a frequent autoimmune target in multiple
sclerosis, with T cell responses against ANO2 occurring in over half of patients.
These ANO2-specific T cells shar...
www.cell.com
January 15, 2026 at 3:12 AM
Amazing news!
GLP-1s are a game changer for those who can tolerate them and it’s great to see all the evidence around their effectiveness. I’ve personally been on a GLP-1 for a little over two years and have lost 50 lb, prediabetes is in remission, and my anxiety for whatever reason is greatly decreased.
A 5★ new review of the GLP-1 drugs, what they have achieved, and where the field is headed with so many new molecules and combinations
@thelancet.com
thelancet.com/journals/lan...
@thelancet.com
thelancet.com/journals/lan...
January 15, 2026 at 1:38 AM
GLP-1s are a game changer for those who can tolerate them and it’s great to see all the evidence around their effectiveness. I’ve personally been on a GLP-1 for a little over two years and have lost 50 lb, prediabetes is in remission, and my anxiety for whatever reason is greatly decreased.
Reposted by Jess Chen
Reposted by Jess Chen
Just making sure that 2025 is definitely over
January 1, 2026 at 4:43 AM
Just making sure that 2025 is definitely over
Sliding into the last 2 weeks of 2025 with this energy.
December 22, 2025 at 2:29 PM
Sliding into the last 2 weeks of 2025 with this energy.
i changed a light fixture and didnt electrocute myself!!!!
December 6, 2025 at 5:43 PM
i changed a light fixture and didnt electrocute myself!!!!
Had to sprint to the shuttle this morning. Man I’m out of practice in this getting to work thing….
November 13, 2025 at 1:34 PM
Had to sprint to the shuttle this morning. Man I’m out of practice in this getting to work thing….
Reposted by Jess Chen
BIOLOG question: is there a good pipeline or program to compare biolog results (either in terms of absorbance reads or carbon sources/antibiotics/etc) to KEGG outputs from whole genome sequencing? Right now our tech is doing am manual comparison but there has to be an easier way. 🦠🧬
November 10, 2025 at 7:49 PM
BIOLOG question: is there a good pipeline or program to compare biolog results (either in terms of absorbance reads or carbon sources/antibiotics/etc) to KEGG outputs from whole genome sequencing? Right now our tech is doing am manual comparison but there has to be an easier way. 🦠🧬
Furlough day, I’ve lost count. More sanding.
November 6, 2025 at 4:46 PM
Furlough day, I’ve lost count. More sanding.
Reposted by Jess Chen
CDC Figures It Easier To Start Tracking People Without Measles
CDC Figures It Easier To Start Tracking People Without Measles
ATLANTA—As the agency struggles to manage a measles caseload that has erupted to its largest size in decades, the Centers for Disease Control and Prevention stated Monday that at this point, it would ...
theonion.com
November 4, 2025 at 9:00 PM
CDC Figures It Easier To Start Tracking People Without Measles
Excepted day 2: Only bike at the rack.
November 4, 2025 at 9:18 PM
Excepted day 2: Only bike at the rack.
Furlough day 30: refinishing a table.
October 30, 2025 at 9:47 PM
Furlough day 30: refinishing a table.
Paper mache volcano Robin and I made. Most of the supplies from #Scraplanta.
October 26, 2025 at 1:22 PM
Paper mache volcano Robin and I made. Most of the supplies from #Scraplanta.
Reposted by Jess Chen
Updating my LEGO White House
October 23, 2025 at 2:51 AM
Updating my LEGO White House
Furlough day 17. Doors. 🚪
October 17, 2025 at 4:21 PM
Furlough day 17. Doors. 🚪
Reposted by Jess Chen
In honour of spooky month, share a 4 word horror story that only someone in your profession would understand.
rm -rf ~/
rm -rf ~/
"The chancellor approved it"
In honour of spooky month, share a 4 word horror story that only someone in your profession would understand.
“a supply chain attack”
“a supply chain attack”
October 12, 2025 at 6:36 AM
In honour of spooky month, share a 4 word horror story that only someone in your profession would understand.
rm -rf ~/
rm -rf ~/
Reposted by Jess Chen
🚨Fed PSA🚨
Print off employee docs before the shut down.
CDC’s union (AFGE2883) has put together a RIF guide detailing what docs may be needed if firings occur: www.afge2883ga.org/_files/ugd/9...
More info on joining AFGE👉https://afge2883ga.org
Check furlough status👉 wcps.cdc.gov (intranet only)
Print off employee docs before the shut down.
CDC’s union (AFGE2883) has put together a RIF guide detailing what docs may be needed if firings occur: www.afge2883ga.org/_files/ugd/9...
More info on joining AFGE👉https://afge2883ga.org
Check furlough status👉 wcps.cdc.gov (intranet only)
September 29, 2025 at 2:36 PM
🚨Fed PSA🚨
Print off employee docs before the shut down.
CDC’s union (AFGE2883) has put together a RIF guide detailing what docs may be needed if firings occur: www.afge2883ga.org/_files/ugd/9...
More info on joining AFGE👉https://afge2883ga.org
Check furlough status👉 wcps.cdc.gov (intranet only)
Print off employee docs before the shut down.
CDC’s union (AFGE2883) has put together a RIF guide detailing what docs may be needed if firings occur: www.afge2883ga.org/_files/ugd/9...
More info on joining AFGE👉https://afge2883ga.org
Check furlough status👉 wcps.cdc.gov (intranet only)