Alexander Piper
@apiper.bsky.social
Biologist using genes 🧬 and computers 💻 to study evolution and spread of invasive Insect pests. Senior Research Scientist @ Agriculture Victoria. Adjunct Research Fellow @ LaTrobe University 🇦🇺
Pinned
Alexander Piper
@apiper.bsky.social
· Feb 28
Our group is recruiting 3 PhD students for insect IPM projects in Victoria, Australia 🦘
1- Exploring the genomic basis of virulence in grapevine phylloxera 🍇
2- Optimising sampling for surveillance and diagnostics of grain pests. 🌾
3- Investigating the use of biological control in almond IPM 🐞
1- Exploring the genomic basis of virulence in grapevine phylloxera 🍇
2- Optimising sampling for surveillance and diagnostics of grain pests. 🌾
3- Investigating the use of biological control in almond IPM 🐞
Reposted by Alexander Piper
Announcing @official-smbe.bsky.social Australasian Protein Structural Phylogenetics Meeting in Brisbane Feb 15-18, 2026. FREE registration. Join for exciting talks & workshops at the interface of protein structure, function & evolution. biosig.lab.uq.edu.au/strphy26/ #StrPhy26 @strphy.bsky.social
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
biosig.lab.uq.edu.au
October 22, 2025 at 7:56 AM
Announcing @official-smbe.bsky.social Australasian Protein Structural Phylogenetics Meeting in Brisbane Feb 15-18, 2026. FREE registration. Join for exciting talks & workshops at the interface of protein structure, function & evolution. biosig.lab.uq.edu.au/strphy26/ #StrPhy26 @strphy.bsky.social
Reposted by Alexander Piper
Just spotted this paper saying their tree search/genetic algorithm writes better bioinformatics software than SOTA. Does batch correction of scRNAseq, and covid hospitalisation estim.
Noth outside my wheelhouse. Does anyone have expertise and energy to look at it?
arxiv.org/abs/2509.06503
Noth outside my wheelhouse. Does anyone have expertise and energy to look at it?
arxiv.org/abs/2509.06503
An AI system to help scientists write expert-level empirical software
The cycle of scientific discovery is frequently bottlenecked by the slow, manual creation of software to support computational experiments. To address this, we present an AI system that creates expert...
arxiv.org
September 9, 2025 at 8:54 PM
Just spotted this paper saying their tree search/genetic algorithm writes better bioinformatics software than SOTA. Does batch correction of scRNAseq, and covid hospitalisation estim.
Noth outside my wheelhouse. Does anyone have expertise and energy to look at it?
arxiv.org/abs/2509.06503
Noth outside my wheelhouse. Does anyone have expertise and energy to look at it?
arxiv.org/abs/2509.06503
Reposted by Alexander Piper
🚨 🐜 is there a Bluesky starter pack for researchers who don’t study ants but who get lightheaded every time there’s an awesome ant paper? CC @mariusw.bsky.social @jrichardalbert.bsky.social www.nature.com/articles/s41...
One mother for two species via obligate cross-species cloning in ants - Nature
In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same moth...
www.nature.com
September 3, 2025 at 6:47 PM
🚨 🐜 is there a Bluesky starter pack for researchers who don’t study ants but who get lightheaded every time there’s an awesome ant paper? CC @mariusw.bsky.social @jrichardalbert.bsky.social www.nature.com/articles/s41...
Reposted by Alexander Piper
Postdoc position available in insect genetics at USDA-ARS, Hilo, HI. Focus on functional genomics in tephritid pests. Applications via Zintellect until filled. More info: https://www.zintellect.com/Opportunity/Details/USDA-ARS-PWA-2025-0071 #postdoc
Zintellect - U.S. Department of Agriculture (USDA) - USDA-ARS Postdoctoral Fellowship in Insect Genetics and Molecular Biology - USDA-ARS-PWA-2025-0071
Zintellect - U.S. Department of Agriculture (USDA) - USDA-ARS Postdoctoral Fellowship in Insect Genetics and Molecular Biology - USDA-ARS-PWA-2025-0071
www.zintellect.com
August 19, 2025 at 4:21 AM
Postdoc position available in insect genetics at USDA-ARS, Hilo, HI. Focus on functional genomics in tephritid pests. Applications via Zintellect until filled. More info: https://www.zintellect.com/Opportunity/Details/USDA-ARS-PWA-2025-0071 #postdoc
Reposted by Alexander Piper
Our first wheat stripe rust Avr effector story. It is a short one that points to suppressors in this pathosystem while we could not link this Avr effector to a described R gene. www.biorxiv.org/content/10.1...
A conserved stripe rust effector elicits variable resistance responses in wheat
Plant resistance (R) and pathogen avirulence (Avr) gene interactions are central to pathogen recognition and disease resistance in crops. However, functional characterisation of Avr effectors in Pucci...
www.biorxiv.org
August 3, 2025 at 2:41 AM
Our first wheat stripe rust Avr effector story. It is a short one that points to suppressors in this pathosystem while we could not link this Avr effector to a described R gene. www.biorxiv.org/content/10.1...
Reposted by Alexander Piper
Commercial isothermal fluorimeters are pricey & unsuitable for field work, limiting their use in low-resource settings. @jenny-molloy.bsky.social &co develop an #open-source, #low-cost, portable isothermal #fluorimeter designed for various biotech applications @plosbiology.org 🧪 plos.io/3FA7Fmn
May 29, 2025 at 8:18 AM
Commercial isothermal fluorimeters are pricey & unsuitable for field work, limiting their use in low-resource settings. @jenny-molloy.bsky.social &co develop an #open-source, #low-cost, portable isothermal #fluorimeter designed for various biotech applications @plosbiology.org 🧪 plos.io/3FA7Fmn
Reposted by Alexander Piper
Excited to announce that we're collaborating with Citizens of the Sea!
www.citizensofthesea.org/news/citizen...
It's an amazing citizen science effort to equip ocean cruisers, racers, commercial vessels with #eDNA collection devices. So much data from so many vessels and locations!
www.citizensofthesea.org/news/citizen...
It's an amazing citizen science effort to equip ocean cruisers, racers, commercial vessels with #eDNA collection devices. So much data from so many vessels and locations!
Citizens of the Sea partners with Minderoo Foundation — Citizens of the Sea
Citizens of the Sea has been given a significant boost from Minderoo Oceanomics from Western Australia. “We are thrilled to welcome Minderoo to our family of supporters,” says Adele Fitzpatrick, Execu...
www.citizensofthesea.org
May 23, 2025 at 5:27 AM
Excited to announce that we're collaborating with Citizens of the Sea!
www.citizensofthesea.org/news/citizen...
It's an amazing citizen science effort to equip ocean cruisers, racers, commercial vessels with #eDNA collection devices. So much data from so many vessels and locations!
www.citizensofthesea.org/news/citizen...
It's an amazing citizen science effort to equip ocean cruisers, racers, commercial vessels with #eDNA collection devices. So much data from so many vessels and locations!
Reposted by Alexander Piper
Happy to share this collaborative effort on recommendations for #genomics of #type specimens
academic.oup.com/sysbio/advan...
academic.oup.com/sysbio/advan...
Type genomics: a Framework for integrating Genomic Data into Biodiversity and Taxonomic research
academic.oup.com
May 21, 2025 at 7:01 AM
Happy to share this collaborative effort on recommendations for #genomics of #type specimens
academic.oup.com/sysbio/advan...
academic.oup.com/sysbio/advan...
Reposted by Alexander Piper
Our new paper on the parallel evolution of insecticide resistance is online now at @elife.bsky.social
doi.org/10.7554/eLif...
Pest: the two spotted spider mite
doi.org/10.7554/eLif...
Pest: the two spotted spider mite
May 7, 2025 at 11:02 PM
Our new paper on the parallel evolution of insecticide resistance is online now at @elife.bsky.social
doi.org/10.7554/eLif...
Pest: the two spotted spider mite
doi.org/10.7554/eLif...
Pest: the two spotted spider mite
Our group is recruiting 3 PhD students for insect IPM projects in Victoria, Australia 🦘
1- Exploring the genomic basis of virulence in grapevine phylloxera 🍇
2- Optimising sampling for surveillance and diagnostics of grain pests. 🌾
3- Investigating the use of biological control in almond IPM 🐞
1- Exploring the genomic basis of virulence in grapevine phylloxera 🍇
2- Optimising sampling for surveillance and diagnostics of grain pests. 🌾
3- Investigating the use of biological control in almond IPM 🐞
February 28, 2025 at 12:11 AM
Our group is recruiting 3 PhD students for insect IPM projects in Victoria, Australia 🦘
1- Exploring the genomic basis of virulence in grapevine phylloxera 🍇
2- Optimising sampling for surveillance and diagnostics of grain pests. 🌾
3- Investigating the use of biological control in almond IPM 🐞
1- Exploring the genomic basis of virulence in grapevine phylloxera 🍇
2- Optimising sampling for surveillance and diagnostics of grain pests. 🌾
3- Investigating the use of biological control in almond IPM 🐞
Reposted by Alexander Piper
Reposted by Alexander Piper
Immediately assigning this new paper to my pop gen students! Waples publishes some real hits - "What is a population?" is another instant classic onlinelibrary.wiley.com/doi/10.1111/...
The Idiot's Guide to Effective Population Size
This is a reference manual for the elegant, yet hideously complex concept of effective population size (Ne), inspired by a classic, self-published manual of automotive repair ‘for the compleat idiot’...
onlinelibrary.wiley.com
February 17, 2025 at 5:35 PM
Immediately assigning this new paper to my pop gen students! Waples publishes some real hits - "What is a population?" is another instant classic onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Alexander Piper
Hi everyone on Bluesky working in #genomics #NGS. Today is Valentines day. How many of you are more excited about Feb 20th?!
Read my new post on Enseqlopedia Roche emerges from the Lazarus pit to take on Illumina
enseqlopedia.com/2025/02/roch...
Read my new post on Enseqlopedia Roche emerges from the Lazarus pit to take on Illumina
enseqlopedia.com/2025/02/roch...
Roche emerges from the Lazarus pit
Is Roche going to "knock it out of the park" or "jump the shark"? Everyone I know is excited, even if many of them are sceptical, about the Feb 20th webinar and what we will learn about SBX. Alex Dick...
enseqlopedia.com
February 14, 2025 at 10:46 AM
Hi everyone on Bluesky working in #genomics #NGS. Today is Valentines day. How many of you are more excited about Feb 20th?!
Read my new post on Enseqlopedia Roche emerges from the Lazarus pit to take on Illumina
enseqlopedia.com/2025/02/roch...
Read my new post on Enseqlopedia Roche emerges from the Lazarus pit to take on Illumina
enseqlopedia.com/2025/02/roch...
Reposted by Alexander Piper
Here are some thoughts and suggestions from me as to how barcoding (particularly of dark taxa at scale) and taxonomy might better come together.
doi.org/10.1111/mec....
@biogeneurope.bsky.social
doi.org/10.1111/mec....
@biogeneurope.bsky.social
Delimiting Species—Prospects and Challenges for DNA Barcoding
Discovering, describing and cataloguing global species diversity remains a fundamental challenge both for biodiversity research and for the management and conservation of biodiversity. Among animals,....
doi.org
February 6, 2025 at 4:26 PM
Here are some thoughts and suggestions from me as to how barcoding (particularly of dark taxa at scale) and taxonomy might better come together.
doi.org/10.1111/mec....
@biogeneurope.bsky.social
doi.org/10.1111/mec....
@biogeneurope.bsky.social
Reposted by Alexander Piper
Want to use your #statistics, ML/AI or #bioinformatics skills to solve problems in #agriculture?
We are seeking 3 postdocs (up to 3 years) to join at ANU Biological Data Science Institute as part of Analytics for 🇦🇺 Grains industry by 📅 19 Jan
We now also have a (WIP) website!
🌐 anu-aagi.github.io
We are seeking 3 postdocs (up to 3 years) to join at ANU Biological Data Science Institute as part of Analytics for 🇦🇺 Grains industry by 📅 19 Jan
We now also have a (WIP) website!
🌐 anu-aagi.github.io
January 2, 2025 at 3:37 AM
Want to use your #statistics, ML/AI or #bioinformatics skills to solve problems in #agriculture?
We are seeking 3 postdocs (up to 3 years) to join at ANU Biological Data Science Institute as part of Analytics for 🇦🇺 Grains industry by 📅 19 Jan
We now also have a (WIP) website!
🌐 anu-aagi.github.io
We are seeking 3 postdocs (up to 3 years) to join at ANU Biological Data Science Institute as part of Analytics for 🇦🇺 Grains industry by 📅 19 Jan
We now also have a (WIP) website!
🌐 anu-aagi.github.io
Reposted by Alexander Piper
If your partner complains about a lack of #intimacy: Platynothrus peltifer has gone 20 million years without #sex. With clever genome management (and no dates), this #mite cheats evolution like a pro. 🕷️
#Evolution #Science
www.science.org/doi/10.1126/...
#Evolution #Science
www.science.org/doi/10.1126/...
Chromosome-scale genome dynamics reveal signatures of independent haplotype evolution in the ancient asexual mite Platynothrus peltifer
Haplotype independence contributes to genome evolution under ancient asexuality.
www.science.org
January 29, 2025 at 5:13 PM
If your partner complains about a lack of #intimacy: Platynothrus peltifer has gone 20 million years without #sex. With clever genome management (and no dates), this #mite cheats evolution like a pro. 🕷️
#Evolution #Science
www.science.org/doi/10.1126/...
#Evolution #Science
www.science.org/doi/10.1126/...
Reposted by Alexander Piper
#Mosquito #genome chromatin architecture #evolution - extremely long-ranged looping interactions, conserved for ~100 million years www.nature.com/articles/s41...
Anopheles mosquitoes reveal new principles of 3D genome organization in insects - Nature Communications
Anopheles mosquitoes are vectors of human malaria, and better understanding of them has implications for public health. Here, the authors apply Hi-C, FISH, RNA-seq, and ChIP-seq techniques to comprehe...
www.nature.com
January 26, 2025 at 10:07 AM
#Mosquito #genome chromatin architecture #evolution - extremely long-ranged looping interactions, conserved for ~100 million years www.nature.com/articles/s41...
Reposted by Alexander Piper
Excited to share GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities.
@sjmcilroy.bsky.social, @benjwoodcroft.bsky.social, @jamesvolmer.bsky.social
doi.org/10.21203/rs....
🧵1/6
@sjmcilroy.bsky.social, @benjwoodcroft.bsky.social, @jamesvolmer.bsky.social
doi.org/10.21203/rs....
🧵1/6
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities
Fluorescence in situ hybridisation (FISH) is a powerful tool for visualising the spatial organisation of microbial communities. However, traditional FISH has several limitations, including limited p...
doi.org
December 19, 2024 at 5:17 PM
Excited to share GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities.
@sjmcilroy.bsky.social, @benjwoodcroft.bsky.social, @jamesvolmer.bsky.social
doi.org/10.21203/rs....
🧵1/6
@sjmcilroy.bsky.social, @benjwoodcroft.bsky.social, @jamesvolmer.bsky.social
doi.org/10.21203/rs....
🧵1/6
Reposted by Alexander Piper
Biosecurity urges people to report Oriental fruit fly findings - fruit fly found in Papatoetoe.
Here's hoping our Biosecurity services can handle this effectively after all the cuts in 2024.
www.rnz.co.nz/news/nationa...
Here's hoping our Biosecurity services can handle this effectively after all the cuts in 2024.
www.rnz.co.nz/news/nationa...
Biosecurity urges people to report Oriental fruit fly findings
Controls have now been imposed on the movement of fruit and vegetables in Papatoetoe, Auckland, where an Oriental fruit fly was found yesterday.
www.rnz.co.nz
January 4, 2025 at 1:58 AM
Biosecurity urges people to report Oriental fruit fly findings - fruit fly found in Papatoetoe.
Here's hoping our Biosecurity services can handle this effectively after all the cuts in 2024.
www.rnz.co.nz/news/nationa...
Here's hoping our Biosecurity services can handle this effectively after all the cuts in 2024.
www.rnz.co.nz/news/nationa...
Reposted by Alexander Piper
The use of iconPCR for 16S library preparation improves data quality and workflow https://www.biorxiv.org/content/10.1101/2024.12.18.629279v1
December 22, 2024 at 12:35 AM
The use of iconPCR for 16S library preparation improves data quality and workflow https://www.biorxiv.org/content/10.1101/2024.12.18.629279v1
Reposted by Alexander Piper
New #phylogeography preprint is out, just in time for the holidays! Here we explore glacial lineages, mito-nuclear discordance and local ancestry tract detection using low-coverage WGS (2X), all in Arctic Char of course! 🐟🏔️ @jeansebmoore.bsky.social @michaelmhansen.bsky.social #PopGen
December 16, 2024 at 7:07 PM
New #phylogeography preprint is out, just in time for the holidays! Here we explore glacial lineages, mito-nuclear discordance and local ancestry tract detection using low-coverage WGS (2X), all in Arctic Char of course! 🐟🏔️ @jeansebmoore.bsky.social @michaelmhansen.bsky.social #PopGen
Reposted by Alexander Piper
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:
Reposted by Alexander Piper
Over the last century, milk productivity by the average U.S. dairy cow has risen 6-fold!
Full story worksinprogress.co/issue/how-bi... 🧪
Full story worksinprogress.co/issue/how-bi... 🧪
December 5, 2024 at 8:19 PM
Over the last century, milk productivity by the average U.S. dairy cow has risen 6-fold!
Full story worksinprogress.co/issue/how-bi... 🧪
Full story worksinprogress.co/issue/how-bi... 🧪
Reposted by Alexander Piper
🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips.
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience
November 11, 2024 at 7:29 PM
🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips.
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience
Reposted by Alexander Piper
Letter sent in to the Editor of the Guardian on brain microbiome nonsense.
December 3, 2024 at 10:01 AM
Letter sent in to the Editor of the Guardian on brain microbiome nonsense.