johnny connolly
@jcons.bsky.social
microbial ecology, metagenomics, science policy and funding.
Ph.D. in systems & computational biology (2024)
Ph.D. in systems & computational biology (2024)
Reposted by johnny connolly
we need a department of kerning
November 13, 2025 at 2:54 AM
we need a department of kerning
Reposted by johnny connolly
NEW method! eComp is a new, #evolution-informed #compression method🗜️ for multiple #sequence alignments (#MSAs)...that outperforms gzip!
Unlike gzip's row-based compression, eComp implements a simple #column-based solution for compression, following how biological information is stored in MSAs
Unlike gzip's row-based compression, eComp implements a simple #column-based solution for compression, following how biological information is stored in MSAs
October 21, 2025 at 3:26 PM
NEW method! eComp is a new, #evolution-informed #compression method🗜️ for multiple #sequence alignments (#MSAs)...that outperforms gzip!
Unlike gzip's row-based compression, eComp implements a simple #column-based solution for compression, following how biological information is stored in MSAs
Unlike gzip's row-based compression, eComp implements a simple #column-based solution for compression, following how biological information is stored in MSAs
data science is my passion
October 28, 2025 at 1:15 AM
data science is my passion
Reposted by johnny connolly
The most mathematically rigorous microbiology papers I read pale in comparison to articles with titles like Composition of Snail Species on New Jersey Beaches (1965)
August 15, 2024 at 1:48 PM
The most mathematically rigorous microbiology papers I read pale in comparison to articles with titles like Composition of Snail Species on New Jersey Beaches (1965)
Reposted by johnny connolly
I find it very funny that people whose job it was to like, count trees in 1960s Wisconsin were well-versed in Information Theory
August 15, 2024 at 1:44 PM
I find it very funny that people whose job it was to like, count trees in 1960s Wisconsin were well-versed in Information Theory
In a hilarious and unfortunate coincidence, two completely unrelated metagenomic methods, both sharing the name "PHLAME", were published this year:
www.sciencedirect.com/science/arti...
www.biorxiv.org/content/10.1...
www.sciencedirect.com/science/arti...
www.biorxiv.org/content/10.1...
Intraspecies associations from strain-rich metagenome samples
Genetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting…
www.sciencedirect.com
October 16, 2025 at 3:01 PM
In a hilarious and unfortunate coincidence, two completely unrelated metagenomic methods, both sharing the name "PHLAME", were published this year:
www.sciencedirect.com/science/arti...
www.biorxiv.org/content/10.1...
www.sciencedirect.com/science/arti...
www.biorxiv.org/content/10.1...
Reposted by johnny connolly
London researchers estimate COVID-19 vaccines cost $79B in 2020–21 but returned $4.8–$37.8T in health and economic benefits.
That is $60–$475 gained for every $1 invested, making them one of the best global investments ever.
www.medrxiv.org/content/10.1...
That is $60–$475 gained for every $1 invested, making them one of the best global investments ever.
www.medrxiv.org/content/10.1...
The global return-on-investment of COVID-19 vaccines in the first year of the vaccination programme
COVID-19 vaccines played a critical role in reducing global health burden during the COVID-19 pandemic, but their rapid development required extraordinary effort. This study aims to evaluate their glo...
www.medrxiv.org
September 5, 2025 at 1:52 PM
London researchers estimate COVID-19 vaccines cost $79B in 2020–21 but returned $4.8–$37.8T in health and economic benefits.
That is $60–$475 gained for every $1 invested, making them one of the best global investments ever.
www.medrxiv.org/content/10.1...
That is $60–$475 gained for every $1 invested, making them one of the best global investments ever.
www.medrxiv.org/content/10.1...
Reposted by johnny connolly
Recently tested some de-novo minibinders against two targets (thanks Adaptyv!) designed using our open-source design library, `mosaic`; our best method got hit rates of 7/10 and 8/10 and affinities as low as single-digit nanomolar. Wrote up some thoughts here: blog.escalante.bio/minibinder-d...
September 2, 2025 at 2:39 PM
Recently tested some de-novo minibinders against two targets (thanks Adaptyv!) designed using our open-source design library, `mosaic`; our best method got hit rates of 7/10 and 8/10 and affinities as low as single-digit nanomolar. Wrote up some thoughts here: blog.escalante.bio/minibinder-d...
Reposted by johnny connolly
Meteorologists now face a Trump ‘loyalty test’ when applying to National Weather Service jobs.
The essay questions — which have nothing to do with meteorology — are part of federal guidelines launched as part of the Trump administration’s efforts to recruit “patriotic Americans” to its workforce.
The essay questions — which have nothing to do with meteorology — are part of federal guidelines launched as part of the Trump administration’s efforts to recruit “patriotic Americans” to its workforce.
Meteorologists now face a Trump ‘loyalty test’ when applying to National Weather Service jobs
After firing hundreds of meteorologists, the National Weather Service announced it is filling vacant positions. Applicants are being asked to detail their support for Trump’s policies.
www.sfchronicle.com
August 27, 2025 at 11:52 PM
Meteorologists now face a Trump ‘loyalty test’ when applying to National Weather Service jobs.
The essay questions — which have nothing to do with meteorology — are part of federal guidelines launched as part of the Trump administration’s efforts to recruit “patriotic Americans” to its workforce.
The essay questions — which have nothing to do with meteorology — are part of federal guidelines launched as part of the Trump administration’s efforts to recruit “patriotic Americans” to its workforce.
This was the best case scenario. Unfortunately, we ended up with the Other Thing
I think the best case scenario for the RFK HHS is that he focuses on food additives and chemicals the entire time
August 28, 2025 at 12:21 AM
This was the best case scenario. Unfortunately, we ended up with the Other Thing
Reposted by johnny connolly
Bob Clark, VP of marketing for Herr Foods, Inc., said the company was surprised to see it was mentioned in the press.
“While we can’t speak to the details of the story,” he said, “we can confirm that our Sour Cream & Onion flavor is money.”
www.thecity.nyc/2025/08/21/w...
“While we can’t speak to the details of the story,” he said, “we can confirm that our Sour Cream & Onion flavor is money.”
www.thecity.nyc/2025/08/21/w...
The Chips Fall as Rivals Fry the Mayor
The jokes and jabs are flying as Eric Adams’ closest aides was slapped with new criminal charges the day after another of his longtime allies offered a reporter cash inside a potato chip bag.
www.thecity.nyc
August 21, 2025 at 10:35 PM
Bob Clark, VP of marketing for Herr Foods, Inc., said the company was surprised to see it was mentioned in the press.
“While we can’t speak to the details of the story,” he said, “we can confirm that our Sour Cream & Onion flavor is money.”
www.thecity.nyc/2025/08/21/w...
“While we can’t speak to the details of the story,” he said, “we can confirm that our Sour Cream & Onion flavor is money.”
www.thecity.nyc/2025/08/21/w...
I drafted for a fantasy league that's been going since high school last night. One of the younger guys (2-3 years below me) had to take a call in the middle. When he came back he said "Sorry, my paralegal is out today" I have never felt so old in my entire life
August 19, 2025 at 2:39 PM
I drafted for a fantasy league that's been going since high school last night. One of the younger guys (2-3 years below me) had to take a call in the middle. When he came back he said "Sorry, my paralegal is out today" I have never felt so old in my entire life
Trying to determine when industry will see the damage from lack of new research. I think probably starting in ~4-5 years?
August 16, 2025 at 11:46 PM
Trying to determine when industry will see the damage from lack of new research. I think probably starting in ~4-5 years?
Reposted by johnny connolly
this work saved millions of lives in 2021, won the Nobel Prize in 2023, and is cancelled in 2025
"The U.S. Department of Health and Human Services (HHS) today announced the beginning of a coordinated wind-down of its mRNA vaccine development activities...."
cc: Sen. Bill Cassidy
cc: Sen. Bill Cassidy
August 5, 2025 at 9:58 PM
this work saved millions of lives in 2021, won the Nobel Prize in 2023, and is cancelled in 2025
Looking for an apartment in SF has made me understand why people are so insane about housing there. You have to pay a gajillion dollars for a single room in a house and meanwhile there are no buildings above two stories
July 22, 2025 at 11:55 AM
Looking for an apartment in SF has made me understand why people are so insane about housing there. You have to pay a gajillion dollars for a single room in a house and meanwhile there are no buildings above two stories
Hard to overstate how damaging this will be to science and universities broadly
Grant terminations have grabbed the headlines and have seen legal action, but even more damaging to the US research enterprise has been the massive decrease in number of research grants issued by federal agencies
NIH has seen a decrease of 57% in the number of awards & 63% in value compared to FY24
NIH has seen a decrease of 57% in the number of awards & 63% in value compared to FY24
July 14, 2025 at 10:03 PM
Hard to overstate how damaging this will be to science and universities broadly
Reposted by johnny connolly
Grant terminations have grabbed the headlines and have seen legal action, but even more damaging to the US research enterprise has been the massive decrease in number of research grants issued by federal agencies
NIH has seen a decrease of 57% in the number of awards & 63% in value compared to FY24
NIH has seen a decrease of 57% in the number of awards & 63% in value compared to FY24
July 14, 2025 at 9:21 PM
Grant terminations have grabbed the headlines and have seen legal action, but even more damaging to the US research enterprise has been the massive decrease in number of research grants issued by federal agencies
NIH has seen a decrease of 57% in the number of awards & 63% in value compared to FY24
NIH has seen a decrease of 57% in the number of awards & 63% in value compared to FY24
Reposted by johnny connolly
New Consensus Statement in Nature Microbiology!
Working with low-biomass microbiome samples? From deep subsurface rocks to human lungs, contamination is a major challenge. We offer field-to-data analysis guidelines to help keep your results clean.
📖 doi.org/10.1038/s415...
Working with low-biomass microbiome samples? From deep subsurface rocks to human lungs, contamination is a major challenge. We offer field-to-data analysis guidelines to help keep your results clean.
📖 doi.org/10.1038/s415...
Guidelines for preventing and reporting contamination in low-biomass microbiome studies - Nature Microbiology
In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize contaminants.
doi.org
June 23, 2025 at 4:54 PM
New Consensus Statement in Nature Microbiology!
Working with low-biomass microbiome samples? From deep subsurface rocks to human lungs, contamination is a major challenge. We offer field-to-data analysis guidelines to help keep your results clean.
📖 doi.org/10.1038/s415...
Working with low-biomass microbiome samples? From deep subsurface rocks to human lungs, contamination is a major challenge. We offer field-to-data analysis guidelines to help keep your results clean.
📖 doi.org/10.1038/s415...
Reposted by johnny connolly
🥁NEW publication from our lab:
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer - Nature Medicine
An analysis of 18 metagenomic datasets of individuals with colorectal cancer, adenomas and healthy controls yields improved cancer prediction accuracy based solely on gut metagenomics, as well as the ...
www.nature.com
June 3, 2025 at 10:43 AM
🥁NEW publication from our lab:
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
Reposted by johnny connolly
Slow grant making continues. Here is a graph through May 1st.
2/n
2/n
May 12, 2025 at 11:00 AM
Slow grant making continues. Here is a graph through May 1st.
2/n
2/n
Reposted by johnny connolly
"This cross-sectional study of the oral microbiome in US adults showed that a few genera were universally present and a different set of genera explained a high percentage of oral microbiome diversity across the population."
Oral Microbiome Profile of the US Population
This cross-sectional study examines the demographic, socioeconomic, behavioral, anthropometric, metabolic, and clinical characteristics of the oral microbiome of US adults.
jamanetwork.com
May 9, 2025 at 4:33 PM
"This cross-sectional study of the oral microbiome in US adults showed that a few genera were universally present and a different set of genera explained a high percentage of oral microbiome diversity across the population."
Reposted by johnny connolly
The “brain drain” will be a primarily domestic phenomenon, w/ STEM-trained people moving into non-STEM occupations.
There are not remotely enough STEM jobs abroad for our *millions* scientists, and even if there were, moving is hard, expensive & dependent on multiple intersecting privileges.
There are not remotely enough STEM jobs abroad for our *millions* scientists, and even if there were, moving is hard, expensive & dependent on multiple intersecting privileges.
May 4, 2025 at 2:35 PM
The “brain drain” will be a primarily domestic phenomenon, w/ STEM-trained people moving into non-STEM occupations.
There are not remotely enough STEM jobs abroad for our *millions* scientists, and even if there were, moving is hard, expensive & dependent on multiple intersecting privileges.
There are not remotely enough STEM jobs abroad for our *millions* scientists, and even if there were, moving is hard, expensive & dependent on multiple intersecting privileges.
Reposted by johnny connolly
There are a lot of questions being asked about the awarding of a $500M grant to an #NIH team to develop a new (old) vaccine platform that could be used for a "universal" #flu vaccine. www.statnews.com/2025/05/03/n...
Scientists question NIH project’s use of 20th century technology to make a universal flu vaccine
$500 million NIH program to make vaccines against pathogens that can trigger pandemics uses approach pioneered in last century
www.statnews.com
May 4, 2025 at 3:33 PM
There are a lot of questions being asked about the awarding of a $500M grant to an #NIH team to develop a new (old) vaccine platform that could be used for a "universal" #flu vaccine. www.statnews.com/2025/05/03/n...
Reposted by johnny connolly
NSF has two kinds of grants, standard (where all of the awarded $ is issued up front) and continuing (where the awarded $ is issued in yearly increments). It sounds like they're freezing any expenditures on awarded continuing grants and not making any new awards for now. Disastrous for US science. 🧪
BREAKING: NSF has frozen all grant funding, as of yesterday. It's unclear when they will resume funding awards, or why the pause has been put in place. www.nature.com/articles/d41...
Exclusive: NSF stops awarding new grants and funding existing ones
US science funder also plans to screen grant applications for compliance with ‘agency priorities’.
www.nature.com
May 2, 2025 at 1:40 AM
NSF has two kinds of grants, standard (where all of the awarded $ is issued up front) and continuing (where the awarded $ is issued in yearly increments). It sounds like they're freezing any expenditures on awarded continuing grants and not making any new awards for now. Disastrous for US science. 🧪