Avril Harder
@avril-m-harder.bsky.social
Computational biologist, Evolutionary Analysis Group @ HudsonAlpha Genome Sequencing Center · working from Birmingham, AL · evolution, genomics, plant pangenomes
Reposted by Avril Harder
1/2 #NearLab @chasedbrownstein.bsky.social described Birmingham Darter Etheostoma birminghamesnse in April 2025 It is under threat from a mega data center. A petition was filed yesterday by the @biologicaldiversity.org to review the species for protection under the ESA
www.wbrc.com/2025/11/14/n...
www.wbrc.com/2025/11/14/n...
National conservation group joining fight against proposed data center
A national conservation group is joining their fight, saying the center will have a major impact on a fish population found only in this area of Alabama.
www.wbrc.com
November 14, 2025 at 1:04 PM
1/2 #NearLab @chasedbrownstein.bsky.social described Birmingham Darter Etheostoma birminghamesnse in April 2025 It is under threat from a mega data center. A petition was filed yesterday by the @biologicaldiversity.org to review the species for protection under the ESA
www.wbrc.com/2025/11/14/n...
www.wbrc.com/2025/11/14/n...
Reposted by Avril Harder
New — with @joannarifkin.bsky.social, @jotlovell.bsky.social, @spicybotrytis.bsky.social, and many more — we created seven new high-quality genomes and explored pangenomic variation in the emerging oilseed crop pennycress (Thlaspi arvense). 1/
Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome
Summary · Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biod...
www.biorxiv.org
September 28, 2025 at 5:25 PM
New — with @joannarifkin.bsky.social, @jotlovell.bsky.social, @spicybotrytis.bsky.social, and many more — we created seven new high-quality genomes and explored pangenomic variation in the emerging oilseed crop pennycress (Thlaspi arvense). 1/
Another hit from @alabamarivers.bsky.social and Southern Exposure
Meet Alabama’s salamanders like you’ve never seen them before and fall for their undeniable charm.
vimeo.com/1114098611/8...
vimeo.com/1114098611/8...
SALABAMA
Meet Alabama’s salamanders like you’ve never seen them before and fall for their undeniable charm. We dive into the salamanders’ hidden world of…
vimeo.com
September 26, 2025 at 1:42 PM
Another hit from @alabamarivers.bsky.social and Southern Exposure
Reposted by Avril Harder
🌿Plant pangenomes🌿 have a LOT of genomic presence-absence-variation.
Or do they???
A new @jgi.doe.gov preprint by @tomasbruna.bsky.social @jotlovell.bsky.social @avril-m-harder.bsky.social Avinash Sreedasyam takes a closer look
www.biorxiv.org/content/10.1...
Or do they???
A new @jgi.doe.gov preprint by @tomasbruna.bsky.social @jotlovell.bsky.social @avril-m-harder.bsky.social Avinash Sreedasyam takes a closer look
www.biorxiv.org/content/10.1...
August 18, 2025 at 6:28 PM
🌿Plant pangenomes🌿 have a LOT of genomic presence-absence-variation.
Or do they???
A new @jgi.doe.gov preprint by @tomasbruna.bsky.social @jotlovell.bsky.social @avril-m-harder.bsky.social Avinash Sreedasyam takes a closer look
www.biorxiv.org/content/10.1...
Or do they???
A new @jgi.doe.gov preprint by @tomasbruna.bsky.social @jotlovell.bsky.social @avril-m-harder.bsky.social Avinash Sreedasyam takes a closer look
www.biorxiv.org/content/10.1...
Reposted by Avril Harder
'Hoods are out!!! Big thank you to @plantevolution.bsky.social for the support throughout. Luisa, @kdm9.bsky.social , @aconga.bsky.social , @hajkdrost.bsky.social it was intellectually stimulating ride with you, so congratulations!!!! #diversity #NLR #immune #pan-genome #graphs #networktheory
Happy to be able to finally share our NLR pangenome paper, out now in CHM.
"Pangenomic context reveals the extent of intraspecific plant NLR evolution"
www.cell.com/cell-host-mi...
#plantscience #plantimmunity #pangenomes #science #nlr
"Pangenomic context reveals the extent of intraspecific plant NLR evolution"
www.cell.com/cell-host-mi...
#plantscience #plantimmunity #pangenomes #science #nlr
Pangenomic context reveals the extent of intraspecific plant NLR evolution
Individual- and population-level diversity is required for pathogen defense by nucleotide-binding
site leucine-rich repeat (NLR) proteins. Teasdale et al. leverage annotated, divergent
A. thaliana gen...
www.cell.com
August 14, 2025 at 8:22 PM
'Hoods are out!!! Big thank you to @plantevolution.bsky.social for the support throughout. Luisa, @kdm9.bsky.social , @aconga.bsky.social , @hajkdrost.bsky.social it was intellectually stimulating ride with you, so congratulations!!!! #diversity #NLR #immune #pan-genome #graphs #networktheory
Reposted by Avril Harder
my new idea is to look at runs of homozygosity (ROH) only for mutations that are restricted to heterozygous state in other pops, suggesting they are low freq. and enriched for deleterious stuff. a good measure of inbreeding. I call my new statistic
August 12, 2025 at 9:06 PM
my new idea is to look at runs of homozygosity (ROH) only for mutations that are restricted to heterozygous state in other pops, suggesting they are low freq. and enriched for deleterious stuff. a good measure of inbreeding. I call my new statistic
Reposted by Avril Harder
This began as a @jgi.doe.gov Community Science Program (CSP) project in 2017 with the goal of uniting the diverse sorghum breeding and mapping populations in the framework of a 'pangenome'.
Thanks to a huge efforts across many stakeholders, the article was preprinted today. A 🧵 w/ what we found:
Thanks to a huge efforts across many stakeholders, the article was preprinted today. A 🧵 w/ what we found:
Developing future resilience from signatures of adaptation across the sorghum pangenome https://www.biorxiv.org/content/10.1101/2025.08.01.667986v1
August 6, 2025 at 8:32 PM
This began as a @jgi.doe.gov Community Science Program (CSP) project in 2017 with the goal of uniting the diverse sorghum breeding and mapping populations in the framework of a 'pangenome'.
Thanks to a huge efforts across many stakeholders, the article was preprinted today. A 🧵 w/ what we found:
Thanks to a huge efforts across many stakeholders, the article was preprinted today. A 🧵 w/ what we found:
Reposted by Avril Harder
🚨 We're looking for a #postdoc to join our team at the Center for Bioenergy Innovation at Oak Ridge National Labs, TN 🚨
Project: Advance poplar bioenergy by understanding adaptive trait/genomic variation — breeding/pop gen/bioinformatics
Apply by 18-Aug
Apply here: jobs.ornl.gov/job/Oak-Ridg...
Project: Advance poplar bioenergy by understanding adaptive trait/genomic variation — breeding/pop gen/bioinformatics
Apply by 18-Aug
Apply here: jobs.ornl.gov/job/Oak-Ridg...
Postdoctoral Research Associate - Plant Systems Biology & The Center for Bioenergy Innovation (CBI)
Postdoctoral Research Associate - Plant Systems Biology & The Center for Bioenergy Innovation (CBI)
jobs.ornl.gov
July 21, 2025 at 1:52 PM
🚨 We're looking for a #postdoc to join our team at the Center for Bioenergy Innovation at Oak Ridge National Labs, TN 🚨
Project: Advance poplar bioenergy by understanding adaptive trait/genomic variation — breeding/pop gen/bioinformatics
Apply by 18-Aug
Apply here: jobs.ornl.gov/job/Oak-Ridg...
Project: Advance poplar bioenergy by understanding adaptive trait/genomic variation — breeding/pop gen/bioinformatics
Apply by 18-Aug
Apply here: jobs.ornl.gov/job/Oak-Ridg...
Reposted by Avril Harder
Ok, fine I'm willing to admit it now: Mimulus is interesting www.authorea.com/doi/full/10....
June 10, 2025 at 10:15 PM
Ok, fine I'm willing to admit it now: Mimulus is interesting www.authorea.com/doi/full/10....
Reposted by Avril Harder
That time in 2013 when this crabeater seal decided to see what this noisy orange menace was doing in its territory....In 2013 near Peter I Island in #Antarctica on our research cruise (LMG 13-12). Bonus (the 'wait for it' at the end): amazing sunset/sunrise around 1am that night :) 🧪🌎🦑🐧🇦🇶
May 22, 2025 at 11:22 AM
That time in 2013 when this crabeater seal decided to see what this noisy orange menace was doing in its territory....In 2013 near Peter I Island in #Antarctica on our research cruise (LMG 13-12). Bonus (the 'wait for it' at the end): amazing sunset/sunrise around 1am that night :) 🧪🌎🦑🐧🇦🇶
Reposted by Avril Harder
Wow, the cover looks great!
Nice work Patrice and @roederlab.bsky.social
The GENESPACE plot uses our new @jgi.doe.gov Pennycress and Brassica rapa genomes built in collaboration with @spicybotrytis.bsky.social & Katie Greenham, hosted on phytozome
Nice work Patrice and @roederlab.bsky.social
The GENESPACE plot uses our new @jgi.doe.gov Pennycress and Brassica rapa genomes built in collaboration with @spicybotrytis.bsky.social & Katie Greenham, hosted on phytozome
Check out the beautiful cover to our focus issue on Translational research from Arabidopsis to crop plants and beyond. More articles coming shortly. Congrats Patrice Salome and @jotlovell.bsky.social. @theplantcell.bsky.social academic.oup.com/plcell/issue...
May 14, 2025 at 1:39 PM
Wow, the cover looks great!
Nice work Patrice and @roederlab.bsky.social
The GENESPACE plot uses our new @jgi.doe.gov Pennycress and Brassica rapa genomes built in collaboration with @spicybotrytis.bsky.social & Katie Greenham, hosted on phytozome
Nice work Patrice and @roederlab.bsky.social
The GENESPACE plot uses our new @jgi.doe.gov Pennycress and Brassica rapa genomes built in collaboration with @spicybotrytis.bsky.social & Katie Greenham, hosted on phytozome
Reposted by Avril Harder
Clever new BUSCO-like method to evaluate the quality of pangenome graphs www.biorxiv.org/content/10.1...
PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers
Motivation Pangenome graphs integrate multiple assemblies to represent non-redundant genetic diversity. However, current evaluations of pangenome graph quality rely primarily on technical parameters (...
www.biorxiv.org
May 13, 2025 at 10:56 PM
Clever new BUSCO-like method to evaluate the quality of pangenome graphs www.biorxiv.org/content/10.1...
Reposted by Avril Harder
Quick break from the doom and gloom for science! We're really proud of this one. We found that two major effect loci on duplicated versions of the same ancestral chromosome play a major role in run timing diversity across four species of salmon (pink, chum, sockeye, coho) shorturl.at/GISX2
Diversification of large-effect loci in a duplicated genomic region leads to complex phenotypes
Whole genome duplication provides evolutionary opportunities to increase biological complexity and phenotypic diversity by selective retention of duplicated genes. We identify a small genomic region a...
shorturl.at
April 22, 2025 at 2:06 AM
Quick break from the doom and gloom for science! We're really proud of this one. We found that two major effect loci on duplicated versions of the same ancestral chromosome play a major role in run timing diversity across four species of salmon (pink, chum, sockeye, coho) shorturl.at/GISX2
Reposted by Avril Harder
longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/lon...
GitHub - yangao07/longcallD: A local-haplotagging-based small and structural variant caller
A local-haplotagging-based small and structural variant caller - yangao07/longcallD
github.com
March 24, 2025 at 4:53 PM
longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/lon...
Reposted by Avril Harder
"Our results reveal substantial differences between pipelines, with many inversions either misrepresented or lost. Most notably, recovery rates remain strikingly low, even with the most simple simulated genome sets, highlighting major challenges in analyzing inversions in pangenomic approaches."
Investigating the topological motifs of inversions in pangenome graphs https://www.biorxiv.org/content/10.1101/2025.03.14.643331v1
March 18, 2025 at 4:53 PM
"Our results reveal substantial differences between pipelines, with many inversions either misrepresented or lost. Most notably, recovery rates remain strikingly low, even with the most simple simulated genome sets, highlighting major challenges in analyzing inversions in pangenomic approaches."
Reposted by Avril Harder
Our paper on the past, present, and genomics-enabled future of American chestnut (Castanea dentata) tree breeding for resistance to invasive pathogens is on BioRxiv.
🧵with some background and a few things we found 👇 bsky.app/profile/bior...
🧵with some background and a few things we found 👇 bsky.app/profile/bior...
Improving American chestnut resistance to two invasive pathogens through genome-enabled breeding https://www.biorxiv.org/content/10.1101/2025.01.30.635736v1
February 3, 2025 at 9:23 PM
Our paper on the past, present, and genomics-enabled future of American chestnut (Castanea dentata) tree breeding for resistance to invasive pathogens is on BioRxiv.
🧵with some background and a few things we found 👇 bsky.app/profile/bior...
🧵with some background and a few things we found 👇 bsky.app/profile/bior...
Reposted by Avril Harder
A new version of our variation graphs (vg) tool, "Boccaleone," is now available! Updates include:
🔵 HiFi and Oxford Nanopore read support to the Giraffe read mapper
🔵 Faster read sorting
🔵 New Unix manual page
Link: github.com/vgteam/vg/re...
🔵 HiFi and Oxford Nanopore read support to the Giraffe read mapper
🔵 Faster read sorting
🔵 New Unix manual page
Link: github.com/vgteam/vg/re...
January 29, 2025 at 5:18 PM
A new version of our variation graphs (vg) tool, "Boccaleone," is now available! Updates include:
🔵 HiFi and Oxford Nanopore read support to the Giraffe read mapper
🔵 Faster read sorting
🔵 New Unix manual page
Link: github.com/vgteam/vg/re...
🔵 HiFi and Oxford Nanopore read support to the Giraffe read mapper
🔵 Faster read sorting
🔵 New Unix manual page
Link: github.com/vgteam/vg/re...
Reposted by Avril Harder
Welcome to Day 2 of #PAG32 | #PAG2025. Today's cant miss session is Comparative Genomics hosted by Vijay Tiwari and John Lovell. It is 10:30 - 12:40 in Pacific A. pag.confex.com/pag/32/meeti...
Comparative Genomics
The availability of genomes for many plant and animal species provides opportunities to compare genomes. These comparisons provide insights into the variability of genome structure and content within ...
pag.confex.com
January 11, 2025 at 4:31 PM
Welcome to Day 2 of #PAG32 | #PAG2025. Today's cant miss session is Comparative Genomics hosted by Vijay Tiwari and John Lovell. It is 10:30 - 12:40 in Pacific A. pag.confex.com/pag/32/meeti...
Reposted by Avril Harder
Are you headed to #PAG32 and interested in plant reproduction? 🌼 Come check out my talk in the “Sex Chromosomes and Sex Determination” session on Saturday!
I’ll be talking about ancient ZW sex chromosomes, the impact of polyploidy on sexual system evolution, “leaky” dioecy, and much more.
I’ll be talking about ancient ZW sex chromosomes, the impact of polyploidy on sexual system evolution, “leaky” dioecy, and much more.
January 8, 2025 at 2:02 PM
Are you headed to #PAG32 and interested in plant reproduction? 🌼 Come check out my talk in the “Sex Chromosomes and Sex Determination” session on Saturday!
I’ll be talking about ancient ZW sex chromosomes, the impact of polyploidy on sexual system evolution, “leaky” dioecy, and much more.
I’ll be talking about ancient ZW sex chromosomes, the impact of polyploidy on sexual system evolution, “leaky” dioecy, and much more.
Reposted by Avril Harder
What's better than one polyploid genome? Twelve polyploid genomes! We report a pangenome of the hexaploid oilseed crop Camelina sativa and investigate pangenomic variation and genome evolution in a complex allopolyploid genome. www.biorxiv.org/content/10.1...
August 17, 2024 at 5:30 PM
What's better than one polyploid genome? Twelve polyploid genomes! We report a pangenome of the hexaploid oilseed crop Camelina sativa and investigate pangenomic variation and genome evolution in a complex allopolyploid genome. www.biorxiv.org/content/10.1...
Reposted by Avril Harder
Our groups' goal is to produce genomes that are useful; this does not always mean 'telomere-to-telomere' assemblies. The hybrid sugarcane genome is a nice example of this. The article is out this week in Nature: www.nature.com/articles/s41...
March 29, 2024 at 5:14 PM
Our groups' goal is to produce genomes that are useful; this does not always mean 'telomere-to-telomere' assemblies. The hybrid sugarcane genome is a nice example of this. The article is out this week in Nature: www.nature.com/articles/s41...
Reposted by Avril Harder
@ksamuk.bsky.social pointed this out on the other site, but I don't see much discussion here.
GATK will now encode missing genotypes as "0/0", or homozygous ref, instead of "./." in VCF files. To identify sites with missing data, you'll have to check the DP field.
GATK will now encode missing genotypes as "0/0", or homozygous ref, instead of "./." in VCF files. To identify sites with missing data, you'll have to check the DP field.
GenotypeGVCFs and the death of the dot
If you have been keeping up with our GATK release notes, then you know that we have been rolling out a number of backend changes, tools, and features to GATK that we are hoping will improve the eff...
gatk.broadinstitute.org
February 7, 2024 at 3:18 PM
@ksamuk.bsky.social pointed this out on the other site, but I don't see much discussion here.
GATK will now encode missing genotypes as "0/0", or homozygous ref, instead of "./." in VCF files. To identify sites with missing data, you'll have to check the DP field.
GATK will now encode missing genotypes as "0/0", or homozygous ref, instead of "./." in VCF files. To identify sites with missing data, you'll have to check the DP field.
Reposted by Avril Harder
🚨We're hiring🚨
We are looking for a scientist to bridge the gap between genomics and breeding, focusing on traditionally under-invested crops and regions. It's physically located at Colorado State University in beautiful Ft. Collins, CO.
Pls share!
hudsonalpha.applicantpro.com/jobs/3211389
We are looking for a scientist to bridge the gap between genomics and breeding, focusing on traditionally under-invested crops and regions. It's physically located at Colorado State University in beautiful Ft. Collins, CO.
Pls share!
hudsonalpha.applicantpro.com/jobs/3211389
HudsonAlpha - Staff Scientist - Genome Sequencing Center - Huntsville, AL
Position: STAFF-SCIENTIST: Evolutionary gen
hudsonalpha.applicantpro.com
January 30, 2024 at 5:37 PM
🚨We're hiring🚨
We are looking for a scientist to bridge the gap between genomics and breeding, focusing on traditionally under-invested crops and regions. It's physically located at Colorado State University in beautiful Ft. Collins, CO.
Pls share!
hudsonalpha.applicantpro.com/jobs/3211389
We are looking for a scientist to bridge the gap between genomics and breeding, focusing on traditionally under-invested crops and regions. It's physically located at Colorado State University in beautiful Ft. Collins, CO.
Pls share!
hudsonalpha.applicantpro.com/jobs/3211389