Joanna Achinger
@aachinger.bsky.social
Lab head in 3D chromatin organisation at SAiGENCI, University of Adelaide 🇦🇺 | Interested in 3D chromatin structure, gene regulation, transposable elements and cancer | website: achingerlab.com
Pinned
Joanna Achinger
@aachinger.bsky.social
· Dec 23
Androgen stimulation rapidly reorganizes temporal 3D genome and epigenome states to trigger AR-mediated transcription in prostate cancer.
Introduction Androgen receptor (AR)-mediated transcription drives prostate cancer progression and remains a key therapeutic target. AR is activated by androgens, translocating to the nucleus to bind D...
www.biorxiv.org
NEW preprint led by Elyssa Campbell with Susan Clark, where we used MOFA+ to uncover the rapid 3D chromatin and transcription changes triggered by androgens in prostate cancer. (1)
Check it out here: www.biorxiv.org/content/10.1...
Check it out here: www.biorxiv.org/content/10.1...
Reposted by Joanna Achinger
I'm super excited to announce that registrations are now open for the 19th Australian Cell Cycle, DNA Repair and Telomere Workshop. Awesome international speaker line-up, with plenty of locals being invited! Book now to secure your earlybird rate. www.australiancellcycle.org
May 15, 2025 at 5:48 AM
I'm super excited to announce that registrations are now open for the 19th Australian Cell Cycle, DNA Repair and Telomere Workshop. Awesome international speaker line-up, with plenty of locals being invited! Book now to secure your earlybird rate. www.australiancellcycle.org
Reposted by Joanna Achinger
“In all my discussions with scientists across every sector, exactly zero think the journal system works well.”
Some will disagree with aspects of Seemay’s analysis but this point is undoubtedly true open.substack.com/pub/asterain...?
Some will disagree with aspects of Seemay’s analysis but this point is undoubtedly true open.substack.com/pub/asterain...?
Scientific Publishing: Enough is Enough
Why we're no longer funding journal publications
open.substack.com
June 19, 2025 at 1:30 AM
“In all my discussions with scientists across every sector, exactly zero think the journal system works well.”
Some will disagree with aspects of Seemay’s analysis but this point is undoubtedly true open.substack.com/pub/asterain...?
Some will disagree with aspects of Seemay’s analysis but this point is undoubtedly true open.substack.com/pub/asterain...?
Reposted by Joanna Achinger
2nd Meeting on Epigenetics & Epigenomics - 24th - 26th September, Brussels 🇧🇪
Speakers Line-up looks fantastic including @adelmanlab.bsky.social @kjarmache.bsky.social @mariekeoudelaar.bsky.social @tinekelenstra.bsky.social @lucianodicroce.bsky.social
www.xcellsconferences.com/epigenetics2...
Speakers Line-up looks fantastic including @adelmanlab.bsky.social @kjarmache.bsky.social @mariekeoudelaar.bsky.social @tinekelenstra.bsky.social @lucianodicroce.bsky.social
www.xcellsconferences.com/epigenetics2...
Epigenetics 2025 | Xcells Conferences
www.xcellsconferences.com
June 10, 2025 at 10:48 AM
2nd Meeting on Epigenetics & Epigenomics - 24th - 26th September, Brussels 🇧🇪
Speakers Line-up looks fantastic including @adelmanlab.bsky.social @kjarmache.bsky.social @mariekeoudelaar.bsky.social @tinekelenstra.bsky.social @lucianodicroce.bsky.social
www.xcellsconferences.com/epigenetics2...
Speakers Line-up looks fantastic including @adelmanlab.bsky.social @kjarmache.bsky.social @mariekeoudelaar.bsky.social @tinekelenstra.bsky.social @lucianodicroce.bsky.social
www.xcellsconferences.com/epigenetics2...
Reposted by Joanna Achinger
Textbooks: “Enhancers are just a bunch of TFBSs”
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
June 18, 2025 at 5:56 PM
Textbooks: “Enhancers are just a bunch of TFBSs”
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
Reposted by Joanna Achinger
🧬🧪Fiber-seq was developed and originally published by Andrew Stergachis (now at @uwdeptmedicine.bsky.social) in 2020.
It's a very cool method for adding chromatin accessibility data to native LRS experiments.
You should definitely check out the original paper: www.science.org/doi/10.1126/...
It's a very cool method for adding chromatin accessibility data to native LRS experiments.
You should definitely check out the original paper: www.science.org/doi/10.1126/...
Single-molecule regulatory architectures captured by chromatin fiber sequencing
Fiber-seq translates single-molecule chromatin stencils into a readout of the primary architecture of chromatin.
www.science.org
June 18, 2025 at 8:45 PM
🧬🧪Fiber-seq was developed and originally published by Andrew Stergachis (now at @uwdeptmedicine.bsky.social) in 2020.
It's a very cool method for adding chromatin accessibility data to native LRS experiments.
You should definitely check out the original paper: www.science.org/doi/10.1126/...
It's a very cool method for adding chromatin accessibility data to native LRS experiments.
You should definitely check out the original paper: www.science.org/doi/10.1126/...
Reposted by Joanna Achinger
STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging @cellcellpress.bsky.social @lgmartelotto.bsky.social @hoheyn.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
June 17, 2025 at 4:40 PM
STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging @cellcellpress.bsky.social @lgmartelotto.bsky.social @hoheyn.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Reposted by Joanna Achinger
New review paper written by Jess Chitty in the team just out in Trends in Cancer (@cp-trendscancer.bsky.social) (OpenAccess)
The extracellular matrix in cancer: from understanding to targeting
| → www.sciencedirect.com/science/arti... ← |
The extracellular matrix in cancer: from understanding to targeting
| → www.sciencedirect.com/science/arti... ← |
The extracellular matrix in cancer: from understanding to targeting
Significant advances in matrix biology research have enhanced our understanding of individual matrix components and extracellular matrix (ECM) signall…
www.sciencedirect.com
June 3, 2025 at 11:46 PM
New review paper written by Jess Chitty in the team just out in Trends in Cancer (@cp-trendscancer.bsky.social) (OpenAccess)
The extracellular matrix in cancer: from understanding to targeting
| → www.sciencedirect.com/science/arti... ← |
The extracellular matrix in cancer: from understanding to targeting
| → www.sciencedirect.com/science/arti... ← |
Reposted by Joanna Achinger
Fun writing this piece with @bartegiani.bsky.social!
New online! Searching for the origin of human brain tumours
Searching for the origin of human brain tumours
Nature Reviews Genetics, Published online: 28 May 2025; doi:10.1038/s41576-025-00858-7In this Journal Club, Delilah Hendriks and Benedetta Artegiani recall a 2018 paper by Lee et al. that combined data from human patients and experimental model systems to reveal the complexities of how brain tumours originate.
www.nature.com
May 28, 2025 at 8:37 PM
Fun writing this piece with @bartegiani.bsky.social!
Reposted by Joanna Achinger
Just a nice reminder! 🧪🧬🖥️ I found this GitHub very useful: github.com/cxli233/Frie...
GitHub - cxli233/FriendsDontLetFriends: Friends don't let friends make certain types of data visualization - What are they and why are they bad.
Friends don't let friends make certain types of data visualization - What are they and why are they bad. - GitHub - cxli233/FriendsDontLetFriends: Friends don't let friends make certain ty...
github.com
May 25, 2025 at 7:05 AM
Just a nice reminder! 🧪🧬🖥️ I found this GitHub very useful: github.com/cxli233/Frie...
Reposted by Joanna Achinger
This is very interesting!
Check out our latest work on the evolution of animal genome regulation out today in @nature.com. Nicely summarized below by @ianakim.bsky.social.
www.nature.com/articles/s41...
This is a major output from our ERC-StG project Evocellmap @erc.europa.eu at @crg.eu
www.nature.com/articles/s41...
This is a major output from our ERC-StG project Evocellmap @erc.europa.eu at @crg.eu
May 7, 2025 at 6:25 PM
This is very interesting!
Reposted by Joanna Achinger
(1/n) New preprint from @claricehongky.bsky.social
Fan Fang Varshini Ramanathan in collab w Jie Liu.
Q: How do we get ultra-high-res 3D genome maps?
A: New deep learning model, Cleopatra.
Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution.
Fan Fang Varshini Ramanathan in collab w Jie Liu.
Q: How do we get ultra-high-res 3D genome maps?
A: New deep learning model, Cleopatra.
Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution.
May 7, 2025 at 8:53 PM
(1/n) New preprint from @claricehongky.bsky.social
Fan Fang Varshini Ramanathan in collab w Jie Liu.
Q: How do we get ultra-high-res 3D genome maps?
A: New deep learning model, Cleopatra.
Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution.
Fan Fang Varshini Ramanathan in collab w Jie Liu.
Q: How do we get ultra-high-res 3D genome maps?
A: New deep learning model, Cleopatra.
Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution.
Reposted by Joanna Achinger
@fxquah.bsky.social 's paper is finally out @genomeresearch.bsky.social and we made the cover!! This was only possible due to the brilliant illustration by @sonhita.bsky.social
Paper here:
genome.cshlp.org/content/35/5...
See below for more details 🧵
Paper here:
genome.cshlp.org/content/35/5...
See below for more details 🧵
May 6, 2025 at 1:29 PM
@fxquah.bsky.social 's paper is finally out @genomeresearch.bsky.social and we made the cover!! This was only possible due to the brilliant illustration by @sonhita.bsky.social
Paper here:
genome.cshlp.org/content/35/5...
See below for more details 🧵
Paper here:
genome.cshlp.org/content/35/5...
See below for more details 🧵
Reposted by Joanna Achinger
I am excited to share our lab's first review out with in Blood Cancer Journal. We discuss the impact of transposable elements on genome regulation and variation in both normal
haematopoietic processes and haematological cancers. www.nature.com/articles/s41...
haematopoietic processes and haematological cancers. www.nature.com/articles/s41...
Transposable elements as genome regulators in normal and malignant haematopoiesis - Blood Cancer Journal
Blood Cancer Journal - Transposable elements as genome regulators in normal and malignant haematopoiesis
www.nature.com
May 6, 2025 at 4:31 PM
I am excited to share our lab's first review out with in Blood Cancer Journal. We discuss the impact of transposable elements on genome regulation and variation in both normal
haematopoietic processes and haematological cancers. www.nature.com/articles/s41...
haematopoietic processes and haematological cancers. www.nature.com/articles/s41...
Reposted by Joanna Achinger
Super excited to share the first 3D genome paper from my lab @narjournal.bsky.social , led by my smart and hardworking student Carlos (joint with @LuLaboratory) with assists from a brilliant summer intern Narjis. (1/n) academic.oup.com/nar/article/...
pC-SAC: A method for high-resolution 3D genome reconstruction from low-resolution Hi-C data
Abstract. The three-dimensional (3D) organization of the genome is crucial for gene regulation, with disruptions linked to various diseases. High-throughpu
academic.oup.com
April 14, 2025 at 5:02 PM
Super excited to share the first 3D genome paper from my lab @narjournal.bsky.social , led by my smart and hardworking student Carlos (joint with @LuLaboratory) with assists from a brilliant summer intern Narjis. (1/n) academic.oup.com/nar/article/...
Reposted by Joanna Achinger
📣 A reminder about an open postdoctoral position in our group!
🧫 Are you interested in mechanisms of gene regulation, human facial development and disease? How our DNA shapes the way we look? Do you love chromatin and enhancers? 🧬
If so, reach out for an informal chat! 💬
longlab.co.uk
🧫 Are you interested in mechanisms of gene regulation, human facial development and disease? How our DNA shapes the way we look? Do you love chromatin and enhancers? 🧬
If so, reach out for an informal chat! 💬
longlab.co.uk
Postdoctoral Researcher
Our research is focused on understanding how genetic changes in the non-coding genome can impact gene regulatory mechanisms, alter developmental processes and ultimately affect human craniofacial shap...
elxw.fa.em3.oraclecloud.com
April 15, 2025 at 9:17 AM
📣 A reminder about an open postdoctoral position in our group!
🧫 Are you interested in mechanisms of gene regulation, human facial development and disease? How our DNA shapes the way we look? Do you love chromatin and enhancers? 🧬
If so, reach out for an informal chat! 💬
longlab.co.uk
🧫 Are you interested in mechanisms of gene regulation, human facial development and disease? How our DNA shapes the way we look? Do you love chromatin and enhancers? 🧬
If so, reach out for an informal chat! 💬
longlab.co.uk
Reposted by Joanna Achinger
A beautiful example of how cautious interpretation of an artifact leads to important results for the scientific community👇Congrats @konrad-chudzik.bsky.social @drmrobson.bsky.social and all authors!
🚨 Preprint alert 🚨
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...
Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomics
Antibodies (Ab) are essential for detecting specific epitopes in microscopy and genomics, but can produce artifacts leading to erroneous interpretations. Here, we characterize a novel artifact, Ab-tra...
doi.org
April 15, 2025 at 10:30 AM
A beautiful example of how cautious interpretation of an artifact leads to important results for the scientific community👇Congrats @konrad-chudzik.bsky.social @drmrobson.bsky.social and all authors!
Reposted by Joanna Achinger
Great to see that sawfish, our new HiFi SV caller, is accepted for publication in Bioinformatics! Sawfish emphasizes local haplotype modeling to improve SV representation and genotyping in both single and joint-sample analysis. Advance-access article now available: (1/n)
doi.org/10.1093/bioi...
doi.org/10.1093/bioi...
Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling
AbstractMotivation. Structural variants (SVs) play an important role in evolutionary and functional genomics but are challenging to characterize. High-accu
doi.org
April 10, 2025 at 3:41 PM
Great to see that sawfish, our new HiFi SV caller, is accepted for publication in Bioinformatics! Sawfish emphasizes local haplotype modeling to improve SV representation and genotyping in both single and joint-sample analysis. Advance-access article now available: (1/n)
doi.org/10.1093/bioi...
doi.org/10.1093/bioi...
Reposted by Joanna Achinger
Colossal is back with their totally BS claims. They reverse engineered snps into 14 GENES and claim they changed a grey wolf into a dire wolf. 1/n
time.com/7274542/colo...
time.com/7274542/colo...
The Return of the Dire Wolf
Colossal Biosciences has genetically engineered the first dire wolf to live in over 10,000 years. Here's what that means for other extinct species.
time.com
April 7, 2025 at 4:26 PM
Colossal is back with their totally BS claims. They reverse engineered snps into 14 GENES and claim they changed a grey wolf into a dire wolf. 1/n
time.com/7274542/colo...
time.com/7274542/colo...
Reposted by Joanna Achinger
Interesting paper on using long-read sequencing to consider accessibility at repetitive elements.
Chromatin accessibility landscape of mouse early embryos revealed by single-cell NanoATAC-seq2
www.science.org/doi/full/10....
Chromatin accessibility landscape of mouse early embryos revealed by single-cell NanoATAC-seq2
www.science.org/doi/full/10....
www.science.org
March 31, 2025 at 1:20 PM
Interesting paper on using long-read sequencing to consider accessibility at repetitive elements.
Chromatin accessibility landscape of mouse early embryos revealed by single-cell NanoATAC-seq2
www.science.org/doi/full/10....
Chromatin accessibility landscape of mouse early embryos revealed by single-cell NanoATAC-seq2
www.science.org/doi/full/10....
Reposted by Joanna Achinger
Good Lord. EWAS w/ n's in the tens? This nonsense has to stop. Trauma leaves marks across generations but they're not epigenetic.
🧬 Violence Leaves DNA Marks Across Generations
A new study found war-related trauma changes DNA in Syrian refugee families, affecting children and grandchildren.
Could this explain how trauma is inherited?
🔗 www.nature.com/articles/s41...
#SciComm #Trauma 🧪
A new study found war-related trauma changes DNA in Syrian refugee families, affecting children and grandchildren.
Could this explain how trauma is inherited?
🔗 www.nature.com/articles/s41...
#SciComm #Trauma 🧪
Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees - Scientific Reports
Scientific Reports - Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees
www.nature.com
March 1, 2025 at 8:08 AM
Good Lord. EWAS w/ n's in the tens? This nonsense has to stop. Trauma leaves marks across generations but they're not epigenetic.
Reposted by Joanna Achinger
I can't believe we're still allowing completely inadequate and uninterpretable Epigenome-Wide Association Studies (EWAS) to be published.
I don't care that this study is probably well-intentioned, and probably trying to draw attention to awful events in Syria.
www.nature.com/articles/s41...
I don't care that this study is probably well-intentioned, and probably trying to draw attention to awful events in Syria.
www.nature.com/articles/s41...
Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees - Scientific Reports
Scientific Reports - Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees
www.nature.com
March 1, 2025 at 4:51 PM
I can't believe we're still allowing completely inadequate and uninterpretable Epigenome-Wide Association Studies (EWAS) to be published.
I don't care that this study is probably well-intentioned, and probably trying to draw attention to awful events in Syria.
www.nature.com/articles/s41...
I don't care that this study is probably well-intentioned, and probably trying to draw attention to awful events in Syria.
www.nature.com/articles/s41...
Reposted by Joanna Achinger
Reposted by Joanna Achinger
Celebrating 10 years of our lab with a new preprint:
www.biorxiv.org/content/10.1...
How does enhancer location within a TAD control transcriptional bursts from a cognate promoter?
Experiments by Jana Tünnermann and modelling by Gregory Roth
www.biorxiv.org/content/10.1...
How does enhancer location within a TAD control transcriptional bursts from a cognate promoter?
Experiments by Jana Tünnermann and modelling by Gregory Roth
March 29, 2025 at 12:46 PM
Celebrating 10 years of our lab with a new preprint:
www.biorxiv.org/content/10.1...
How does enhancer location within a TAD control transcriptional bursts from a cognate promoter?
Experiments by Jana Tünnermann and modelling by Gregory Roth
www.biorxiv.org/content/10.1...
How does enhancer location within a TAD control transcriptional bursts from a cognate promoter?
Experiments by Jana Tünnermann and modelling by Gregory Roth
Reposted by Joanna Achinger
Check out our preprint "De-repression of Transposable Elements by Histone Hyperacetylation Leads to Sterile Inflammation in Preeclampsia" www.researchsquare.com/article/rs-6...
March 26, 2025 at 10:08 AM
Check out our preprint "De-repression of Transposable Elements by Histone Hyperacetylation Leads to Sterile Inflammation in Preeclampsia" www.researchsquare.com/article/rs-6...
Reposted by Joanna Achinger
1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
March 17, 2025 at 11:56 AM
1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇