Bram Bloemen
@brbloemen.bsky.social
PhD student @ Sciensano, the Belgian National Institute of Health
Reposted by Bram Bloemen
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 11:35 PM
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Reposted by Bram Bloemen
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
September 3, 2025 at 8:39 AM
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Reposted by Bram Bloemen
Very exciting work here from Sanjana Kulkarni, Maha Farhat and team. CNN prediction of MIC, v thoroughwork!!
August 14, 2025 at 7:26 AM
Very exciting work here from Sanjana Kulkarni, Maha Farhat and team. CNN prediction of MIC, v thoroughwork!!
Reposted by Bram Bloemen
Reposted by Bram Bloemen
Joe Rogan might call this a brutal KO, if it wasn't him getting knocked the F out.
A supremely delightful takedown by @climatetown.bsky.social of Rogan's confident, ignorant, and dangerous climate denial.
A supremely delightful takedown by @climatetown.bsky.social of Rogan's confident, ignorant, and dangerous climate denial.
Joe Rogan Doesn't Understand Graphs
YouTube video by Climate Town
www.youtube.com
August 13, 2025 at 7:24 PM
Joe Rogan might call this a brutal KO, if it wasn't him getting knocked the F out.
A supremely delightful takedown by @climatetown.bsky.social of Rogan's confident, ignorant, and dangerous climate denial.
A supremely delightful takedown by @climatetown.bsky.social of Rogan's confident, ignorant, and dangerous climate denial.
Reposted by Bram Bloemen
Didn't realise this nonsensical government advice about deleting emails was now all over the news as top advice. Madness.
www.thetimes.com/uk/environme...
www.telegraph.co.uk/news/2025/08...
www.independent.co.uk/news/delete-...
metro.co.uk/2025/08/12/d...
www.thetimes.com/uk/environme...
www.telegraph.co.uk/news/2025/08...
www.independent.co.uk/news/delete-...
metro.co.uk/2025/08/12/d...
I ran the numbers on the UK government's recommendation to delete old photos and emails to save water in data centers andymasley.substack.com/p/contra-the...
August 14, 2025 at 6:38 AM
Didn't realise this nonsensical government advice about deleting emails was now all over the news as top advice. Madness.
www.thetimes.com/uk/environme...
www.telegraph.co.uk/news/2025/08...
www.independent.co.uk/news/delete-...
metro.co.uk/2025/08/12/d...
www.thetimes.com/uk/environme...
www.telegraph.co.uk/news/2025/08...
www.independent.co.uk/news/delete-...
metro.co.uk/2025/08/12/d...
Reposted by Bram Bloemen
Grateful to @marionkoopmans.bsky.social for writing this thoughtful piece in Nature Rev Micro. We can’t push back against anti-science movements without taking the threat seriously, proactively address our limitations, and engage with the public clearly & candidly.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Anti-science and the science community
Nature Reviews Microbiology - As anti-science sentiment intensifies — aggravated by the pandemic, driven in some parts of the world by political actors and amplified by social media —...
www.nature.com
August 13, 2025 at 8:20 PM
Grateful to @marionkoopmans.bsky.social for writing this thoughtful piece in Nature Rev Micro. We can’t push back against anti-science movements without taking the threat seriously, proactively address our limitations, and engage with the public clearly & candidly.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Bram Bloemen
What a sentence: “One pharma company "is banking on a continuing decline in vaccination rates to fuel [investment]”
What a world.
This is like saying you’re banking on seat belt use declining so you can make money on head injury treatment. It’s logical sure, but what are we even doing here?
What a world.
This is like saying you’re banking on seat belt use declining so you can make money on head injury treatment. It’s logical sure, but what are we even doing here?
As the US hits a 33-year high in measles infections, there is now a "race" to find a treatment for the disease.
One pharma company "is banking on a continuing decline in vaccination rates to fuel a need for measles treatments—and in turn, more investor interest"
🎁 link
www.wsj.com/health/healt...
One pharma company "is banking on a continuing decline in vaccination rates to fuel a need for measles treatments—and in turn, more investor interest"
🎁 link
www.wsj.com/health/healt...
The Race to Find a Measles Treatment as Infections Surge
The measles vaccine was so effective the disease was considered eliminated in the U.S., but a resurgence of outbreaks is spurring a need for drugs.
www.wsj.com
August 10, 2025 at 8:48 AM
What a sentence: “One pharma company "is banking on a continuing decline in vaccination rates to fuel [investment]”
What a world.
This is like saying you’re banking on seat belt use declining so you can make money on head injury treatment. It’s logical sure, but what are we even doing here?
What a world.
This is like saying you’re banking on seat belt use declining so you can make money on head injury treatment. It’s logical sure, but what are we even doing here?
Reposted by Bram Bloemen
If I could change one thing about #ScientificPublishing I'd ask funding bodies to stipulate all work they fund be published in non-profit journals.
The knock-on effects would alleviate most of the strain on #AcademicSky.
This isn't hard. It's big, but actually, it's pretty easy.
1/n
The knock-on effects would alleviate most of the strain on #AcademicSky.
This isn't hard. It's big, but actually, it's pretty easy.
1/n
The strain on scientific publishing
Abstract. Scientists are increasingly overwhelmed by the volume of articles being published. The total number of articles indexed in Scopus and Web of Science has grown exponentially in recent years; ...
direct.mit.edu
August 4, 2025 at 8:10 AM
If I could change one thing about #ScientificPublishing I'd ask funding bodies to stipulate all work they fund be published in non-profit journals.
The knock-on effects would alleviate most of the strain on #AcademicSky.
This isn't hard. It's big, but actually, it's pretty easy.
1/n
The knock-on effects would alleviate most of the strain on #AcademicSky.
This isn't hard. It's big, but actually, it's pretty easy.
1/n
Proud to share my second paper!
Metagenomics could be a powerful tool to study antibiotic resistance in entire microbial communities.
Here we tested several new nanopore-enabled methods such as detecting DNA methylation, or strain-haplotyping.
www.frontiersin.org/journals/mic...
Metagenomics could be a powerful tool to study antibiotic resistance in entire microbial communities.
Here we tested several new nanopore-enabled methods such as detecting DNA methylation, or strain-haplotyping.
www.frontiersin.org/journals/mic...
Frontiers | Overcoming challenges in metagenomic AMR surveillance with nanopore sequencing: a case study on fluoroquinolone resistance
IntroductionAntimicrobial resistance is an alarming public health problem, and comprehensive surveillance across environments is required to reduce its impac...
www.frontiersin.org
July 30, 2025 at 10:51 AM
Proud to share my second paper!
Metagenomics could be a powerful tool to study antibiotic resistance in entire microbial communities.
Here we tested several new nanopore-enabled methods such as detecting DNA methylation, or strain-haplotyping.
www.frontiersin.org/journals/mic...
Metagenomics could be a powerful tool to study antibiotic resistance in entire microbial communities.
Here we tested several new nanopore-enabled methods such as detecting DNA methylation, or strain-haplotyping.
www.frontiersin.org/journals/mic...
Reposted by Bram Bloemen
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
July 16, 2025 at 9:59 PM
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
Reposted by Bram Bloemen
Now on YouTube too! youtu.be/mCQLTfEHiS8?...
July 17, 2025 at 6:15 AM
Now on YouTube too! youtu.be/mCQLTfEHiS8?...
Reposted by Bram Bloemen
Hello Bluesky! Our lab is very excited to be here. This is post is a little older but is a really lovely article by the @washingtonpost.com and @shannonosaka.bsky.social about some of the work we are doing on microbiomes to combat climate change!
www.washingtonpost.com/climate-solu...
#microbiome
www.washingtonpost.com/climate-solu...
#microbiome
Scientists may have found a radical solution for making your hamburger less bad for the planet
Scientists are studying how to genetically modify the makeup of cows’ gut microbiomes to prevent their planet-warming methane emissions.
www.washingtonpost.com
July 9, 2025 at 3:12 AM
Hello Bluesky! Our lab is very excited to be here. This is post is a little older but is a really lovely article by the @washingtonpost.com and @shannonosaka.bsky.social about some of the work we are doing on microbiomes to combat climate change!
www.washingtonpost.com/climate-solu...
#microbiome
www.washingtonpost.com/climate-solu...
#microbiome
Reposted by Bram Bloemen
Frank Stahl died today at 95. He and his colleague Matt Meselson found a way to demonstrate how DNA replicated. Their lab experiment has been called the "most beautiful experiment". Here's a video of them describing how they did it. Video h/t NYT. #science
www.youtube.com/watch?v=7-tn...
www.youtube.com/watch?v=7-tn...
The Most Beautiful Experiment: Meselson and Stahl
YouTube video by Science Communication Lab
www.youtube.com
July 8, 2025 at 12:14 AM
Frank Stahl died today at 95. He and his colleague Matt Meselson found a way to demonstrate how DNA replicated. Their lab experiment has been called the "most beautiful experiment". Here's a video of them describing how they did it. Video h/t NYT. #science
www.youtube.com/watch?v=7-tn...
www.youtube.com/watch?v=7-tn...
Reposted by Bram Bloemen
Springer Nature--pioneering the new world of science where facts can be made up and citations generated to support them
July 3, 2025 at 8:31 PM
Springer Nature--pioneering the new world of science where facts can be made up and citations generated to support them
Reposted by Bram Bloemen
Interesting paper on precisely detecting species of interest in metagenomes. I thought this was a thoughtful investigation for a problem that most folks don't discuss much, but implicitly think about often.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Comparative performance of reference-based metagenomic tools to identify species-level taxa among families of bacteria: benchmarking Mycobacteriaceae and Neisseriaceae
Hypotheses concerning the ecology and evolution of bacteria commonly relate to the presence and abundance of species in various settings and conditions. Shotgun metagenomics may address these hypothes...
www.biorxiv.org
July 3, 2025 at 9:09 PM
Interesting paper on precisely detecting species of interest in metagenomes. I thought this was a thoughtful investigation for a problem that most folks don't discuss much, but implicitly think about often.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Bram Bloemen
Just for clarity: Fortunate Son is an anti-Vietnam song specifically about those who dodge the draft.
I did not edit this, this is the actual parade with the actual music being played.
CINEMATIC
CINEMATIC
June 15, 2025 at 6:56 AM
Just for clarity: Fortunate Son is an anti-Vietnam song specifically about those who dodge the draft.
Reposted by Bram Bloemen
Beautiful work from my friend @kiranrpatil.bsky.social . Gut bacteria can accumulate Forever chemicals and help us get rid of them! Happy we could contribute! www.nature.com/articles/s41...
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances - Nature Microbiology
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances (PFAS), commonly known as forever chemicals, in intracellular aggregates. Colonization of gnotobiotic mice with bioaccumulating bac...
www.nature.com
July 1, 2025 at 11:25 AM
Beautiful work from my friend @kiranrpatil.bsky.social . Gut bacteria can accumulate Forever chemicals and help us get rid of them! Happy we could contribute! www.nature.com/articles/s41...
Reposted by Bram Bloemen
A new paper in The Lancet, one of the world’s foremost peer reviewed medical journals, estimates that USAID prevented 91 million deaths across 133 countries over 20 years.
The paper estimates that Elon Musk’s DOGE funding cuts to USAID will lead to 14 million deaths by 2030 (4.5 million children).
The paper estimates that Elon Musk’s DOGE funding cuts to USAID will lead to 14 million deaths by 2030 (4.5 million children).
Evaluating the impact of two decades of USAID interventions and projecting the effects of defunding on mortality up to 2030: a retrospective impact evaluation and forecasting analysis
USAID funding has significantly contributed to the reduction in adult and child mortality
across low-income and middle-income countries over the past two decades. Our estimates
show that, unless the a...
www.thelancet.com
July 1, 2025 at 10:43 AM
A new paper in The Lancet, one of the world’s foremost peer reviewed medical journals, estimates that USAID prevented 91 million deaths across 133 countries over 20 years.
The paper estimates that Elon Musk’s DOGE funding cuts to USAID will lead to 14 million deaths by 2030 (4.5 million children).
The paper estimates that Elon Musk’s DOGE funding cuts to USAID will lead to 14 million deaths by 2030 (4.5 million children).
Reposted by Bram Bloemen
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
myloasm-docs.github.io
myloasm - metagenomic assembly with (noisy) long reads
myloasm-docs.github.io
May 28, 2025 at 5:54 PM
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
myloasm-docs.github.io
Reposted by Bram Bloemen
Amazing @nytimes project on NIH cuts and grant freezes to cancer, alzheimer's, diabetes and other research:
“I would like to cure brain cancer,” Dr. Tanner said. “I think that's not particularly controversial.”
GIFT: www.nytimes.com/interactive/...
“I would like to cure brain cancer,” Dr. Tanner said. “I think that's not particularly controversial.”
GIFT: www.nytimes.com/interactive/...
Here are the nearly 2,500 medical research grants canceled or delayed by Trump (Gift Article)
Some cuts have been starkly visible, but the country’s medical grant-making machinery has also radically transformed outside the public eye.
www.nytimes.com
June 4, 2025 at 2:02 PM
Amazing @nytimes project on NIH cuts and grant freezes to cancer, alzheimer's, diabetes and other research:
“I would like to cure brain cancer,” Dr. Tanner said. “I think that's not particularly controversial.”
GIFT: www.nytimes.com/interactive/...
“I would like to cure brain cancer,” Dr. Tanner said. “I think that's not particularly controversial.”
GIFT: www.nytimes.com/interactive/...
www.biorxiv.org/content/10.1...
Gotta love this excerpt from @shenwei356.bsky.social and @zaminiqbal.bsky.social’s lexicmap preprint
Gotta love this excerpt from @shenwei356.bsky.social and @zaminiqbal.bsky.social’s lexicmap preprint
June 4, 2025 at 12:08 PM
www.biorxiv.org/content/10.1...
Gotta love this excerpt from @shenwei356.bsky.social and @zaminiqbal.bsky.social’s lexicmap preprint
Gotta love this excerpt from @shenwei356.bsky.social and @zaminiqbal.bsky.social’s lexicmap preprint
Reposted by Bram Bloemen
Man comes to the US from Lebanon. Starts out delivering pizzas, becomes a Nobel winning neuroscientist. Trump freezes his funding, he gets an email from China offering to move his lab “any city, any university I want" with guaranteed funding for 20 years.
What are we doing?
What are we doing?
June 3, 2025 at 7:49 PM
Man comes to the US from Lebanon. Starts out delivering pizzas, becomes a Nobel winning neuroscientist. Trump freezes his funding, he gets an email from China offering to move his lab “any city, any university I want" with guaranteed funding for 20 years.
What are we doing?
What are we doing?
Reposted by Bram Bloemen
Unicore is now published on GBE 🚀
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109
June 3, 2025 at 6:55 AM
Unicore is now published on GBE 🚀
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109
Reposted by Bram Bloemen
Bigger not necessarily better. The right small (<150) person conference can produce more networking opportunities than a big one, particularly for students just getting started
May 27, 2025 at 2:47 PM
Bigger not necessarily better. The right small (<150) person conference can produce more networking opportunities than a big one, particularly for students just getting started