Jack Kamm
@snackematician.bsky.social
Statistician working in genomics. https://jackkamm.github.io/
Reposted by Jack Kamm
SINGER, our ARG inference method, is finally published and freely available online:
doi.org/10.1038/s415...
It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
doi.org/10.1038/s415...
It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes - Nature Genetics
SINGER is a method for creating ancestral recombination graphs to understand the genealogical history of genomes. The method has increased speed, and thus scalability, without sacrificing accuracy.
doi.org
September 11, 2025 at 3:50 AM
SINGER, our ARG inference method, is finally published and freely available online:
doi.org/10.1038/s415...
It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
doi.org/10.1038/s415...
It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
Reposted by Jack Kamm
Reposted by Jack Kamm
Disappointing from @janeqiu.bsky.social, who is well aware that scientists haven’t shut down legitimate inquiry into a “lab leak.” No evidence supports it.
Trust is lost not by scientists publishing evidence, but by dishonest actors misrepresenting the evidence.
www.theguardian.com/commentisfre...
Trust is lost not by scientists publishing evidence, but by dishonest actors misrepresenting the evidence.
www.theguardian.com/commentisfre...
The Covid ‘lab leak’ theory isn’t just a rightwing conspiracy – pretending that’s the case is bad for science | Jane Qiu
While figures like Steve Bannon have exploited the issue, scientists have done themselves no favours by shutting down legitimate inquiry, says award-winning science writer Jane Qiu
www.theguardian.com
June 25, 2025 at 1:31 PM
Disappointing from @janeqiu.bsky.social, who is well aware that scientists haven’t shut down legitimate inquiry into a “lab leak.” No evidence supports it.
Trust is lost not by scientists publishing evidence, but by dishonest actors misrepresenting the evidence.
www.theguardian.com/commentisfre...
Trust is lost not by scientists publishing evidence, but by dishonest actors misrepresenting the evidence.
www.theguardian.com/commentisfre...
Reposted by Jack Kamm
Joseph Parker and Matt Pennell propose gene expression programs — sets of co-expressed transcripts that collectively encode cellular subfunctions — as fundamental entities from which novel organismal phenotypes are constructed. www.cell.com/current-biol...
The cellular substrate of evolutionary novelty
Joseph Parker and Matt Pennell propose gene expression programs — sets of co-expressed
transcripts that collectively encode cellular subfunctions — as fundamental entities
from which novel organismal ...
www.cell.com
June 24, 2025 at 1:41 PM
Joseph Parker and Matt Pennell propose gene expression programs — sets of co-expressed transcripts that collectively encode cellular subfunctions — as fundamental entities from which novel organismal phenotypes are constructed. www.cell.com/current-biol...
Reposted by Jack Kamm
On the day of Dr. Fauci's testimony, @nytimes.com decides to run a deeply unethical OpEd with snazzy graphics and snappy headlines about the Lab Leak.
The article itself contains multiple falsehoods and deep mischaracterizations.
Let's take every point in turn 👇🧵
www.nytimes.com/interactive/...
The article itself contains multiple falsehoods and deep mischaracterizations.
Let's take every point in turn 👇🧵
www.nytimes.com/interactive/...
Opinion | Why the Pandemic Probably Started in a Lab, in 5 Key Points
The world must not continue to bear the intolerable risks of research with the potential to cause pandemics.
www.nytimes.com
June 3, 2024 at 11:13 PM
On the day of Dr. Fauci's testimony, @nytimes.com decides to run a deeply unethical OpEd with snazzy graphics and snappy headlines about the Lab Leak.
The article itself contains multiple falsehoods and deep mischaracterizations.
Let's take every point in turn 👇🧵
www.nytimes.com/interactive/...
The article itself contains multiple falsehoods and deep mischaracterizations.
Let's take every point in turn 👇🧵
www.nytimes.com/interactive/...
Reposted by Jack Kamm
A rebuttal of the paper that looked at historical samples and found evidence of natural selection due to the Black Death at immune loci. Multiple lines of evidence, incl that observed freq changes were an artefact.
By Alison Barton, @mathiesoniain.bsky.social et al
www.nature.com/articles/s41...
By Alison Barton, @mathiesoniain.bsky.social et al
www.nature.com/articles/s41...
Insufficient evidence for natural selection associated with the Black Death - Nature
Nature - Insufficient evidence for natural selection associated with the Black Death
www.nature.com
February 20, 2025 at 6:46 AM
A rebuttal of the paper that looked at historical samples and found evidence of natural selection due to the Black Death at immune loci. Multiple lines of evidence, incl that observed freq changes were an artefact.
By Alison Barton, @mathiesoniain.bsky.social et al
www.nature.com/articles/s41...
By Alison Barton, @mathiesoniain.bsky.social et al
www.nature.com/articles/s41...
Reposted by Jack Kamm
Sharing our work expanding SARS-CoV-2 style tiled amplicon sequencing for whole bacteria genomes directly from clinical samples, showing examples with M.tb (>4 mb) and Strep pneumo (>2 mb).
Led by Chaney Kalinich, Freddy Gonzalez, & Seth Redmond
www.biorxiv.org/content/10.1...
Led by Chaney Kalinich, Freddy Gonzalez, & Seth Redmond
www.biorxiv.org/content/10.1...
December 20, 2024 at 8:45 PM
Sharing our work expanding SARS-CoV-2 style tiled amplicon sequencing for whole bacteria genomes directly from clinical samples, showing examples with M.tb (>4 mb) and Strep pneumo (>2 mb).
Led by Chaney Kalinich, Freddy Gonzalez, & Seth Redmond
www.biorxiv.org/content/10.1...
Led by Chaney Kalinich, Freddy Gonzalez, & Seth Redmond
www.biorxiv.org/content/10.1...
Reposted by Jack Kamm
What do GWAS and rare variant burden tests discover, and why?
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies
Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes. Although these methods are conceptually similar, we show by anal...
www.biorxiv.org
December 17, 2024 at 7:05 AM
What do GWAS and rare variant burden tests discover, and why?
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Reposted by Jack Kamm
scSurv: a deep generative model for single-cell survival analysis https://www.biorxiv.org/content/10.1101/2024.12.10.627659v1
December 16, 2024 at 7:47 AM
scSurv: a deep generative model for single-cell survival analysis https://www.biorxiv.org/content/10.1101/2024.12.10.627659v1
Reposted by Jack Kamm
There is a new alternative to the MCC summary tree in BEAST X - the 'highest independent posterior sub-tree reconstruction' or HIPSTR tree. First implemented over 5 years ago (something distracted us from writing it up) we now have a preprint describing it: www.biorxiv.org/content/10.1...
HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X
In Bayesian phylogenetic and phylodynamic studies it is common to summarise the posterior distribution of trees with a time-calibrated consensus phylogeny. While the maximum clade credibility (MCC) tr...
eur02.safelinks.protection.outlook.com
December 11, 2024 at 1:05 PM
There is a new alternative to the MCC summary tree in BEAST X - the 'highest independent posterior sub-tree reconstruction' or HIPSTR tree. First implemented over 5 years ago (something distracted us from writing it up) we now have a preprint describing it: www.biorxiv.org/content/10.1...
Reposted by Jack Kamm
Divergent reference genomes compromise the reconstruction of demographic histories, selection scans, and population genetic summary statistics https://www.biorxiv.org/content/10.1101/2024.11.26.625554v1
Divergent reference genomes compromise the reconstruction of demographic histories, selection scans, and population genetic summary statistics https://www.biorxiv.org/content/10.1101/2024.11.26.625554v1
Characterizing genetic variation in natural populations is central to evolutionary biology. However,
www.biorxiv.org
November 30, 2024 at 9:31 AM
Divergent reference genomes compromise the reconstruction of demographic histories, selection scans, and population genetic summary statistics https://www.biorxiv.org/content/10.1101/2024.11.26.625554v1
Reposted by Jack Kamm
Since we are here now… A few weeks ago we published in @currentbiology.bsky.social our latest work on bonobos, our closest relatives (w/chimps), endangered and with a small population in the wild.
Foto: Martin Surbeck, Kokolopori Research Project (thank you!).
🧪🧬 #popgen #evolution
Foto: Martin Surbeck, Kokolopori Research Project (thank you!).
🧪🧬 #popgen #evolution
November 23, 2024 at 4:01 PM
Since we are here now… A few weeks ago we published in @currentbiology.bsky.social our latest work on bonobos, our closest relatives (w/chimps), endangered and with a small population in the wild.
Foto: Martin Surbeck, Kokolopori Research Project (thank you!).
🧪🧬 #popgen #evolution
Foto: Martin Surbeck, Kokolopori Research Project (thank you!).
🧪🧬 #popgen #evolution
Reposted by Jack Kamm
THEY'RE BACK
The Fast and the Furious: Tokyo Drift Barrier Hypothesis
November 23, 2024 at 3:47 AM
THEY'RE BACK
Reposted by Jack Kamm
If this is 2016 sci twitter redux can we get popgengoogling back plz?
November 22, 2024 at 9:52 PM
If this is 2016 sci twitter redux can we get popgengoogling back plz?
Reposted by Jack Kamm
My BlueSky 'inaugural' post is our classic rotating embryo video from our recently published Zebrahub paper
www.cell.com/cell/fulltex...
“Zebrahub | Supp. Video 3: Light-sheet time-lapse of Tg(h2afva:h2afva-mcherry ; mezzo:eGFP) embryo starting at 50% epiboly.”
on #Vimeo vimeo.com/803719225
www.cell.com/cell/fulltex...
“Zebrahub | Supp. Video 3: Light-sheet time-lapse of Tg(h2afva:h2afva-mcherry ; mezzo:eGFP) embryo starting at 50% epiboly.”
on #Vimeo vimeo.com/803719225
Zebrahub | Supp. Video 3: Light-sheet time-lapse of Tg(h2afva:h2afva-mcherry ; mezzo:eGFP) embryo starting at 50% epiboly.
This is "Zebrahub | Supp. Video 3: Light-sheet time-lapse of Tg(h2afva:h2afva-mcherry ; mezzo:eGFP) embryo starting at 50% epiboly." by Loic A. Royer on…
vimeo.com
November 20, 2024 at 9:29 PM
My BlueSky 'inaugural' post is our classic rotating embryo video from our recently published Zebrahub paper
www.cell.com/cell/fulltex...
“Zebrahub | Supp. Video 3: Light-sheet time-lapse of Tg(h2afva:h2afva-mcherry ; mezzo:eGFP) embryo starting at 50% epiboly.”
on #Vimeo vimeo.com/803719225
www.cell.com/cell/fulltex...
“Zebrahub | Supp. Video 3: Light-sheet time-lapse of Tg(h2afva:h2afva-mcherry ; mezzo:eGFP) embryo starting at 50% epiboly.”
on #Vimeo vimeo.com/803719225
Reposted by Jack Kamm
My group's work dissecting the contribution of common variants to rare neurodevelopmental conditions is now out at nature.com/articles/s41..., led by co-first authors Qinqin Huang (not yet on blue sky) and @emiliewigdor.bsky.social . See below for Emilie's tweetorial.
November 20, 2024 at 4:15 PM
My group's work dissecting the contribution of common variants to rare neurodevelopmental conditions is now out at nature.com/articles/s41..., led by co-first authors Qinqin Huang (not yet on blue sky) and @emiliewigdor.bsky.social . See below for Emilie's tweetorial.
Reposted by Jack Kamm
For me, the most incredible artefacts from the ancient world are the letters people wrote on clay tablets and sent to one another over thousands of years in Mesopotamia, going back to more than 5,000 years ago.
They contain recognisable humanity, warmth and humour. Here's a thread of my favourites.
They contain recognisable humanity, warmth and humour. Here's a thread of my favourites.
November 17, 2024 at 11:14 AM
For me, the most incredible artefacts from the ancient world are the letters people wrote on clay tablets and sent to one another over thousands of years in Mesopotamia, going back to more than 5,000 years ago.
They contain recognisable humanity, warmth and humour. Here's a thread of my favourites.
They contain recognisable humanity, warmth and humour. Here's a thread of my favourites.
Reposted by Jack Kamm
I made one for stats papers
November 18, 2024 at 4:02 AM
I made one for stats papers
Reposted by Jack Kamm
Large protein language models can learn complex epistatic interactions, but how much does that help with predicting variant effects? In this NeurIPS article, we show that classical independent-sites phylogenetic models can outperform pLMs on this task.
1/7
openreview.net/forum?id=H7m...
1/7
openreview.net/forum?id=H7m...
Ultrafast classical phylogenetic method beats large protein...
Amino acid substitution rate matrices are fundamental to statistical phylogenetics and evolutionary biology. Estimating them typically requires reconstructed trees for massive amounts of aligned...
openreview.net
November 16, 2024 at 8:42 PM
Large protein language models can learn complex epistatic interactions, but how much does that help with predicting variant effects? In this NeurIPS article, we show that classical independent-sites phylogenetic models can outperform pLMs on this task.
1/7
openreview.net/forum?id=H7m...
1/7
openreview.net/forum?id=H7m...
Reposted by Jack Kamm
We are here! All future seminar announcements will be posted here.
November 16, 2024 at 3:50 PM
We are here! All future seminar announcements will be posted here.
Reposted by Jack Kamm
Explore the scverse Starter Pack!
Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place.
go.bsky.app/UvFMa8d
Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place.
go.bsky.app/UvFMa8d
November 16, 2024 at 1:59 PM
Explore the scverse Starter Pack!
Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place.
go.bsky.app/UvFMa8d
Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place.
go.bsky.app/UvFMa8d
Reposted by Jack Kamm
Restarting a previous discussion on here:
How convinced are #SingleCell people by cell-cell communication methods? I'm still at "not very" 😅
I see them used everywhere, but I don't know of any really good way to validate them...
More importantly, I don't know of any *non-simulated* training data.
How convinced are #SingleCell people by cell-cell communication methods? I'm still at "not very" 😅
I see them used everywhere, but I don't know of any really good way to validate them...
More importantly, I don't know of any *non-simulated* training data.
November 15, 2024 at 10:27 AM
Restarting a previous discussion on here:
How convinced are #SingleCell people by cell-cell communication methods? I'm still at "not very" 😅
I see them used everywhere, but I don't know of any really good way to validate them...
More importantly, I don't know of any *non-simulated* training data.
How convinced are #SingleCell people by cell-cell communication methods? I'm still at "not very" 😅
I see them used everywhere, but I don't know of any really good way to validate them...
More importantly, I don't know of any *non-simulated* training data.
Reposted by Jack Kamm
In a new paper with co-authors @courtsmithrun.bsky.social , Julie Zhu, @jeffspence.bsky.social, and @jkpritch.bsky.social, I explore why this occurs: www.medrxiv.org/content/10.1...
Buffering and non-monotonic behavior of gene dosage response curves for human complex traits
The genome-wide burdens of deletions, loss-of-function mutations, and duplications correlate with many traits. Curiously, for most of these traits, variants that decrease expression have the same geno...
www.medrxiv.org
November 12, 2024 at 6:10 AM
In a new paper with co-authors @courtsmithrun.bsky.social , Julie Zhu, @jeffspence.bsky.social, and @jkpritch.bsky.social, I explore why this occurs: www.medrxiv.org/content/10.1...
Reposted by Jack Kamm
How to pronounce #rstats symbols:
~ squiggle
<- pretentious equals
; mouthless wink
%>% poop
! AHH (you have to shout it)
$ cha ching
[ subset
[[ subset and I really mean it!
(reposting an old tweet sparked by @amelia.mn)
~ squiggle
<- pretentious equals
; mouthless wink
%>% poop
! AHH (you have to shout it)
$ cha ching
[ subset
[[ subset and I really mean it!
(reposting an old tweet sparked by @amelia.mn)
November 14, 2024 at 3:30 PM
How to pronounce #rstats symbols:
~ squiggle
<- pretentious equals
; mouthless wink
%>% poop
! AHH (you have to shout it)
$ cha ching
[ subset
[[ subset and I really mean it!
(reposting an old tweet sparked by @amelia.mn)
~ squiggle
<- pretentious equals
; mouthless wink
%>% poop
! AHH (you have to shout it)
$ cha ching
[ subset
[[ subset and I really mean it!
(reposting an old tweet sparked by @amelia.mn)