Fascinating story about how genome-based theories of disease clouded our understanding of exposome-based explanations of disease and how those errors are now slowly being corrected.
“Your exposome is the sum of your own personal environmental exposures, from the womb to the casket.”
“Your exposome is the sum of your own personal environmental exposures, from the womb to the casket.”
“No one knows exactly how much of the world’s drinking water is laced with TCE. The CDC reckons the water supply of 4-18% of Americans is contaminated… In Silicon Valley, where TCE was integral to manufacturing of early transistors, a necklace of underground plumes…”
www.wired.com/story/scient...
www.wired.com/story/scient...
Scientists Thought Parkinson’s Was in Our Genes. It Might Be in the Water
New ideas about chronic illness could revolutionize treatment, if we take the research seriously.
www.wired.com
January 11, 2026 at 5:24 AM
Fascinating story about how genome-based theories of disease clouded our understanding of exposome-based explanations of disease and how those errors are now slowly being corrected.
“Your exposome is the sum of your own personal environmental exposures, from the womb to the casket.”
“Your exposome is the sum of your own personal environmental exposures, from the womb to the casket.”
Our paper “A genome-wide atlas of human cell morphology” is finally out today in @naturemethods.bsky.social ! www.nature.com/articles/s41...
(I tweeted about our preprint in 2023 over at the bad place, but deactivated my account, so here we go again!)
(I tweeted about our preprint in 2023 over at the bad place, but deactivated my account, so here we go again!)
A genome-wide atlas of human cell morphology - Nature Methods
An optical pooled cell profiling platform (PERISCOPE) based on Cell Painting and optical sequencing of molecular barcodes was used to develop the first unbiased genome-wide morphology-based perturbati...
www.nature.com
January 27, 2025 at 6:23 PM
Our paper “A genome-wide atlas of human cell morphology” is finally out today in @naturemethods.bsky.social ! www.nature.com/articles/s41...
(I tweeted about our preprint in 2023 over at the bad place, but deactivated my account, so here we go again!)
(I tweeted about our preprint in 2023 over at the bad place, but deactivated my account, so here we go again!)
Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it!
Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time
Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time
July 22, 2026 at 1:36 AM
Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it!
Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time
Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time
GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.
GTDB - Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
gtdb.ecogenomic.org
April 15, 2026 at 2:06 PM
GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.
GTDB Release 10-RS226 (16th April 2025) has been published
gtdb.ecogenomic.org
gtdb.ecogenomic.org
GTDB - Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
gtdb.ecogenomic.org
April 17, 2025 at 12:20 PM
GTDB Release 10-RS226 (16th April 2025) has been published
gtdb.ecogenomic.org
gtdb.ecogenomic.org
Need a genome sequence of your favourite plant? We laid out instructions for a complete workflow based on ONT sequencing:
"Cookbook for plant genome sequences"
doi.org/10.1186/s128...
#Genomics #LongReads #PlantSciences #Bioinformatics
@puckerlab.bsky.social @unibonn.bsky.social
"Cookbook for plant genome sequences"
doi.org/10.1186/s128...
#Genomics #LongReads #PlantSciences #Bioinformatics
@puckerlab.bsky.social @unibonn.bsky.social
February 9, 2026 at 5:56 AM
Need a genome sequence of your favourite plant? We laid out instructions for a complete workflow based on ONT sequencing:
"Cookbook for plant genome sequences"
doi.org/10.1186/s128...
#Genomics #LongReads #PlantSciences #Bioinformatics
@puckerlab.bsky.social @unibonn.bsky.social
"Cookbook for plant genome sequences"
doi.org/10.1186/s128...
#Genomics #LongReads #PlantSciences #Bioinformatics
@puckerlab.bsky.social @unibonn.bsky.social
Bioinformatics folks: check out our @biorxivpreprint on a new, very efficient and accurate system for automated genome annotation, EviAnn, led by my colleague Aleksey Zimin: www.biorxiv.org/content/10.1...
Efficient evidence-based genome annotation with EviAnn
For many years, machine learning-based ab initio gene finding approaches have been the central components of eukaryotic genome annotation pipelines, and they remain so today. The reliance on these app...
www.biorxiv.org
May 13, 2025 at 5:52 PM
Bioinformatics folks: check out our @biorxivpreprint on a new, very efficient and accurate system for automated genome annotation, EviAnn, led by my colleague Aleksey Zimin: www.biorxiv.org/content/10.1...
super cool from the @peterfineran.bsky.social et al Defining the essential genome of diverse phages with phage Tn-seq
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Defining the essential genome of diverse phages with phage Tn-seq - Nature Microbiology
Phage Tn-seq uses Tn5 transposon mutagenesis with anti-CRISPR-based selection and deep sequencing as a method to generate unbiased, genome-wide mutations across diverse phages
www.nature.com
October 6, 2026 at 7:15 AM
super cool from the @peterfineran.bsky.social et al Defining the essential genome of diverse phages with phage Tn-seq
www.nature.com/articles/s41...
www.nature.com/articles/s41...
🚨Research alert! A new study based on the largest bat genome and fossil study ever conducted has found that bats most likely arose in Europe around 65 million years ago, overturning previous assumptions.
Read more.👇
Read more.👇
New Study Points to Bats Originating in Europe | AMNH
New bat genome and fossil study, the largest ever, finds bats likely originated in Europe around 65 million years ago before going global.
amnh.link
September 24, 2026 at 3:12 PM
🚨Research alert! A new study based on the largest bat genome and fossil study ever conducted has found that bats most likely arose in Europe around 65 million years ago, overturning previous assumptions.
Read more.👇
Read more.👇
A DNA language model based on multispecies alignment predicts the effects of genome-wide variants - @yun-s-song.bsky.social go.nature.com/4gWppWg
A DNA language model based on multispecies alignment predicts the effects of genome-wide variants - Nature Biotechnology
A language model predicts the effects of genetic variants in the human genome.
go.nature.com
January 2, 2025 at 4:18 PM
A DNA language model based on multispecies alignment predicts the effects of genome-wide variants - @yun-s-song.bsky.social go.nature.com/4gWppWg
If you are looking for web-based phage annotation, phage-annotation.org is live. Upload a genome to run Pharokka, Phold and Phynteny sequentially (see our recent protocols paper doi.org/10.1002/cpz1...). If you have feedback, please reach out
Thanks to @ardc.edu.au for making this possible!
Thanks to @ardc.edu.au for making this possible!
Phage Annotation Server -- phage genome annotation
Free automated phage genome annotation -- pharokka, phold and phynteny in one pipeline.
phage-annotation.org
August 7, 2026 at 1:18 AM
If you are looking for web-based phage annotation, phage-annotation.org is live. Upload a genome to run Pharokka, Phold and Phynteny sequentially (see our recent protocols paper doi.org/10.1002/cpz1...). If you have feedback, please reach out
Thanks to @ardc.edu.au for making this possible!
Thanks to @ardc.edu.au for making this possible!
"In fact, 5 of those 20 changes are based on mutations known to produce light coats in grey wolves, Shapiro told New Scientist. Only 15 are based on the dire wolf genome directly and are intended to alter the animals’ size, musculature and ear shape."
finally some real fucking journalism lol
finally some real fucking journalism lol
April 7, 2025 at 10:34 PM
"In fact, 5 of those 20 changes are based on mutations known to produce light coats in grey wolves, Shapiro told New Scientist. Only 15 are based on the dire wolf genome directly and are intended to alter the animals’ size, musculature and ear shape."
finally some real fucking journalism lol
finally some real fucking journalism lol
Based on some quick math, this alone could fund the NSF Plant Genome Research Program for ~4 years; the NSF Postdoctoral Research Fellowship in Biology, which was totally axed in the NSF budget request, for ~9 years; and ~ half the total NSF GRFP budget
BREAKING: The Pentagon said the deployment of National Guard members and Marines to protests over immigration raids in LA will cost $134 million.
Hegseth faces sharp questions from Congress on deploying troops to Los Angles and Pentagon chaos
Defense Secretary Pete Hegseth has been quickly met with sharp questions and criticism by lawmakers who pressed him about his early moves to fire key military leaders and and purge diversity programs.
bit.ly
June 10, 2025 at 4:19 PM
Based on some quick math, this alone could fund the NSF Plant Genome Research Program for ~4 years; the NSF Postdoctoral Research Fellowship in Biology, which was totally axed in the NSF budget request, for ~9 years; and ~ half the total NSF GRFP budget
A genome-based phylogeny for Mollusca is concordant with fossils and morphology | Science www.science.org/doi/10.1126/...
A genome-based phylogeny for Mollusca is concordant with fossils and morphology
Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups—gastropods, bivalves, and cephalopods—e...
www.science.org
February 27, 2025 at 8:09 PM
A genome-based phylogeny for Mollusca is concordant with fossils and morphology | Science www.science.org/doi/10.1126/...
if u were a nucleic acid based genome would u wear your genes like this or like this
August 9, 2025 at 5:14 AM
if u were a nucleic acid based genome would u wear your genes like this or like this
A paper in Nature presents an updated phylogeny of bats based on new genome assemblies and many ancient fossils. The findings could resolve long-standing controversies in bat biology and provide new insights into the evolutionary history and trait diversification of bats. go.nature.com/4hJWfvI 🧪
October 8, 2026 at 1:54 AM
A paper in Nature presents an updated phylogeny of bats based on new genome assemblies and many ancient fossils. The findings could resolve long-standing controversies in bat biology and provide new insights into the evolutionary history and trait diversification of bats. go.nature.com/4hJWfvI 🧪
Happy to share results of the @bat1kgenomes.bsky.social phase 1, providing reference genomes covering 21 bat families. New insights into bat phylogeny, ancestral genome reconstruction, European origin & ancestral echolocation. Great work by a team of 100+ colleagues www.nature.com/articles/s41...
Reference genomes and fossils revise bat family phylogeny and biogeography - Nature
An updated phylogeny of bats is presented, based on new genome assemblies and many ancient fossils and including all known bat families.
www.nature.com
September 23, 2026 at 4:53 PM
Happy to share results of the @bat1kgenomes.bsky.social phase 1, providing reference genomes covering 21 bat families. New insights into bat phylogeny, ancestral genome reconstruction, European origin & ancestral echolocation. Great work by a team of 100+ colleagues www.nature.com/articles/s41...
Genome editing of phylogenetically distinct bacteria using cross-species retron-mediated recombineering - @seth-shipman.bsky.social @gladstoneinst.bsky.social go.nature.com/4tZluOU
Genome editing of phylogenetically distinct bacteria using cross-species retron-mediated recombineering - Nature Biotechnology
Retron-based systems for genome editing are functional across bacterial species.
go.nature.com
April 23, 2026 at 1:21 PM
Genome editing of phylogenetically distinct bacteria using cross-species retron-mediated recombineering - @seth-shipman.bsky.social @gladstoneinst.bsky.social go.nature.com/4tZluOU
In a @currentbiology.bsky.social paper earlier this year, led by @laurawesseldijk.bsky.social, we analysed Beethoven’s genome with a polygenic index related to musicality, as a way to communicate limits of genetic predictions at the individual level & the complexity of links between DNA & behaviour:
Notes from Beethoven’s genome
Wesseldijk et al. compare the genomic information collected from Ludwig van Beethoven with population-based datasets used to quantify musical achievement.
www.cell.com
December 5, 2024 at 8:45 PM
In a @currentbiology.bsky.social paper earlier this year, led by @laurawesseldijk.bsky.social, we analysed Beethoven’s genome with a polygenic index related to musicality, as a way to communicate limits of genetic predictions at the individual level & the complexity of links between DNA & behaviour:
We now have genome browsers on our UCSC mirror at genome.senckenberg.de for the 1033 mammal and 866 bird assemblies, showing spliceAi, reference-based and ref-integrated TOGA2 tracks.
Tables with links to all browsers are genome.senckenberg.de/TOGA2Mammali... & genome.senckenberg.de/TOGA2Aves.html
Tables with links to all browsers are genome.senckenberg.de/TOGA2Mammali... & genome.senckenberg.de/TOGA2Aves.html
Hiller Lab UCSC Genome Browser
Senckenberg Genome Browser
genome.senckenberg.de
May 8, 2026 at 6:27 AM
We now have genome browsers on our UCSC mirror at genome.senckenberg.de for the 1033 mammal and 866 bird assemblies, showing spliceAi, reference-based and ref-integrated TOGA2 tracks.
Tables with links to all browsers are genome.senckenberg.de/TOGA2Mammali... & genome.senckenberg.de/TOGA2Aves.html
Tables with links to all browsers are genome.senckenberg.de/TOGA2Mammali... & genome.senckenberg.de/TOGA2Aves.html
Very excited to share the first paper out of my Postdoc @CMR:
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities.
@sjmcilroy.bsky.social @jamesvolmer.bsky.social @benjwoodcroft.bsky.social
doi.org/10.1093/isme...
🧵1/7
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities.
@sjmcilroy.bsky.social @jamesvolmer.bsky.social @benjwoodcroft.bsky.social
doi.org/10.1093/isme...
🧵1/7
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities
Abstract. Fluorescence in situ hybridisation (FISH) is a powerful tool for visualising the spatial organisation of microbial communities. However, traditio
doi.org
July 8, 2025 at 2:30 AM
Very excited to share the first paper out of my Postdoc @CMR:
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities.
@sjmcilroy.bsky.social @jamesvolmer.bsky.social @benjwoodcroft.bsky.social
doi.org/10.1093/isme...
🧵1/7
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities.
@sjmcilroy.bsky.social @jamesvolmer.bsky.social @benjwoodcroft.bsky.social
doi.org/10.1093/isme...
🧵1/7
RFK's speech is actually a speech so at least it doesn't start off sounding like horrifying word salad.
RFK however is saying like studying the genetics of autism is "like studying the genetics of lung cancer" a thing that, famously, we do. /gen
Here, from Nature:
www.nature.com/articles/s41...
RFK however is saying like studying the genetics of autism is "like studying the genetics of lung cancer" a thing that, famously, we do. /gen
Here, from Nature:
www.nature.com/articles/s41...
Non-coding genetic elements of lung cancer identified using whole genome sequencing in 13,722 Chinese - Nature Communications
Here, the authors conducted a whole genome sequencing (WGS)-based genome-wide scan for non-small cell lung cancer in 13,722 Chinese individuals and identified genes including PARPBP, PLA2G4C, and RITA...
www.nature.com
September 22, 2025 at 9:02 PM
RFK's speech is actually a speech so at least it doesn't start off sounding like horrifying word salad.
RFK however is saying like studying the genetics of autism is "like studying the genetics of lung cancer" a thing that, famously, we do. /gen
Here, from Nature:
www.nature.com/articles/s41...
RFK however is saying like studying the genetics of autism is "like studying the genetics of lung cancer" a thing that, famously, we do. /gen
Here, from Nature:
www.nature.com/articles/s41...
Our new genome annotation method relies almost entirely on transcriptome and alignment evidence, and as a result outperforms pretty much all other de novo pipelines. Check out the just-published paper led by Aleksey Zimin: rdcu.be/frSOg
Efficient evidence-based genome annotation with EviAnn
Nature Methods - EviAnn surpasses existing genome annotation methods by leveraging gene expression and protein sequence homology evidence to achieve higher accuracy and efficiency.
rdcu.be
July 7, 2026 at 2:10 PM
Our new genome annotation method relies almost entirely on transcriptome and alignment evidence, and as a result outperforms pretty much all other de novo pipelines. Check out the just-published paper led by Aleksey Zimin: rdcu.be/frSOg
With sequencing of Hitler's DNA making headlines, time for a reminder: analysing a polygenic score from a dead historically-significant figure won't give new insights into that person's behaviour. In a brief paper last year, we used Beethoven's genome to directly illustrate the fallacies involved.🧪👇
Notes from Beethoven’s genome
Wesseldijk et al. compare the genomic information collected from Ludwig van Beethoven
with population-based datasets used to quantify musical achievement.
www.cell.com
November 13, 2025 at 11:26 AM
With sequencing of Hitler's DNA making headlines, time for a reminder: analysing a polygenic score from a dead historically-significant figure won't give new insights into that person's behaviour. In a brief paper last year, we used Beethoven's genome to directly illustrate the fallacies involved.🧪👇