Joachim Wolff
@joachimwolff.bsky.social
Bioinformatics researcher, PostDoc in the Heidel Lab, Medical School Hannover. Chromatin architecture, Hi-C, and epigenetics.
Reposted by Joachim Wolff
I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...
Reply to: Reply to: False positives in the study of memory-related gene expression
In the Nature paper “Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory” published on March 14th, 2024, authors Sun et al. claimed to identify cell-type specifi…
liorpachter.wordpress.com
June 16, 2025 at 9:31 PM
I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...
Reposted by Joachim Wolff
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 Joachim Wolff
(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 Joachim Wolff
Want to learn more about chromatin and its dynamics? Read this review by Charlotte and Jolijn in our lab, aimed at giving an overview on this and the ways this is dealt with during transcription, replication and damage repair. Thanks to Biochemistry for inviting us! doi.org/10.1021/acs....
Always on the Move: Overview on Chromatin Dynamics within Nuclear Processes
Our genome is organized into chromatin, a dynamic and modular structure made of nucleosomes. Chromatin organization controls access to the DNA sequence, playing a fundamental role in cell identity and...
doi.org
May 4, 2025 at 7:39 AM
Want to learn more about chromatin and its dynamics? Read this review by Charlotte and Jolijn in our lab, aimed at giving an overview on this and the ways this is dealt with during transcription, replication and damage repair. Thanks to Biochemistry for inviting us! doi.org/10.1021/acs....
Reposted by Joachim Wolff
AI-driven discovery of synergistic drug combinations against pancreatic cancer 🧪 🧬🖥️ www.nature.com/articles/s41...
AI-driven discovery of synergistic drug combinations against pancreatic cancer - Nature Communications
Finding optimal multi-drug combinations for pancreatic cancer remains a complex task. Here, authors across three different groups apply machine learning approaches to predict synergy across 1.6 millio...
www.nature.com
April 29, 2025 at 7:13 PM
AI-driven discovery of synergistic drug combinations against pancreatic cancer 🧪 🧬🖥️ www.nature.com/articles/s41...
Reposted by Joachim Wolff
A call for built-in biosecurity safeguards for generative AI tools go.nature.com/3GIpTlR
A call for built-in biosecurity safeguards for generative AI tools - Nature Biotechnology
Nature Biotechnology - A call for built-in biosecurity safeguards for generative AI tools
go.nature.com
April 28, 2025 at 3:21 PM
A call for built-in biosecurity safeguards for generative AI tools go.nature.com/3GIpTlR
Reposted by Joachim Wolff
The Biomarkers of Aging Consortium would like feedback on its tool Biolearn, which is used for analyses of aging biomarkers data. See the links below to Biolearn and the survey:
bio-learn.github.io
tally.so/r/wovVQO
bio-learn.github.io
tally.so/r/wovVQO
Biolearn
Biolearn enables easy and versatile analyses of biomarkers of aging data. It provides tools to easily load data from publicly available sources like the Gene Expression Omnibus, National Health and...
bio-learn.github.io
April 29, 2025 at 10:10 PM
The Biomarkers of Aging Consortium would like feedback on its tool Biolearn, which is used for analyses of aging biomarkers data. See the links below to Biolearn and the survey:
bio-learn.github.io
tally.so/r/wovVQO
bio-learn.github.io
tally.so/r/wovVQO
Reposted by Joachim Wolff
MYC and AP-1 oncogenes synergistically bind enhancers to rewire transcription https://www.biorxiv.org/content/10.1101/2025.04.28.650480v1
April 30, 2025 at 3:34 AM
MYC and AP-1 oncogenes synergistically bind enhancers to rewire transcription https://www.biorxiv.org/content/10.1101/2025.04.28.650480v1
Reposted by Joachim Wolff
The most-cited papers of the twenty-first century so far include those that describe developments in AI; approaches to improve the quality of research or systematic reviews; cancer statistics & research software
@nature.com
🧪
www.nature.com/articles/d41...
@nature.com
🧪
www.nature.com/articles/d41...
Exclusive: the most-cited papers of the twenty-first century
A Nature analysis reveals the 25 highest-cited papers published this century and explores why they are breaking records.
www.nature.com
April 16, 2025 at 6:09 AM
The most-cited papers of the twenty-first century so far include those that describe developments in AI; approaches to improve the quality of research or systematic reviews; cancer statistics & research software
@nature.com
🧪
www.nature.com/articles/d41...
@nature.com
🧪
www.nature.com/articles/d41...
Reposted by Joachim Wolff
Earnshaw, Goloborodko, Dekker & Mirny labs are excited to present our latest work, "Rules of engagement for condensins and cohesins guide mitotic chromosome formation" - now accepted!!
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
Rules of Engagement
YouTube video by Johan Gibcus
www.youtube.com
April 11, 2025 at 7:45 AM
Earnshaw, Goloborodko, Dekker & Mirny labs are excited to present our latest work, "Rules of engagement for condensins and cohesins guide mitotic chromosome formation" - now accepted!!
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
Reposted by Joachim Wolff
Review | Epigenetics and individuality: from concepts to causality across timescales www.nature.com/articles/s41...
Epigenetics and individuality: from concepts to causality across timescales - Nature Reviews Genetics
Recent genomic approaches are providing unprecedented opportunity to disentangle how genotype and environment affect organismal traits. The authors review the role of epigenetic variation in mediating...
www.nature.com
January 12, 2025 at 8:58 PM
Review | Epigenetics and individuality: from concepts to causality across timescales www.nature.com/articles/s41...
Reposted by Joachim Wolff
Quantum Computing Inches Closer to Reality After Another Google Breakthrough
Google unveiled an experimental machine capable of tasks that a traditional supercomputer could not master in 10 septillion years. (That’s older than the universe.)
www.nytimes.com/2024/12/09/t...
Google unveiled an experimental machine capable of tasks that a traditional supercomputer could not master in 10 septillion years. (That’s older than the universe.)
www.nytimes.com/2024/12/09/t...
Google Makes New Quantum Computing Breakthrough
Google unveiled an experimental machine capable of tasks that a traditional supercomputer could not master in 10 septillion years. (That’s older than the universe.)
www.nytimes.com
December 10, 2024 at 2:14 AM
Quantum Computing Inches Closer to Reality After Another Google Breakthrough
Google unveiled an experimental machine capable of tasks that a traditional supercomputer could not master in 10 septillion years. (That’s older than the universe.)
www.nytimes.com/2024/12/09/t...
Google unveiled an experimental machine capable of tasks that a traditional supercomputer could not master in 10 septillion years. (That’s older than the universe.)
www.nytimes.com/2024/12/09/t...
Reposted by Joachim Wolff
By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12
Redirecting
doi.org
December 2, 2024 at 4:44 PM
By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12
Reposted by Joachim Wolff
After we reach advanced age, around 80, the propensity to develop cancer is markedly reduced. A discovery reported at Nature today about aged stem cells and iron insufficiency may help explain this advantage
www.nature.com/articles/d41...
www.nature.com/articles/d41...
December 4, 2024 at 6:06 PM
After we reach advanced age, around 80, the propensity to develop cancer is markedly reduced. A discovery reported at Nature today about aged stem cells and iron insufficiency may help explain this advantage
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Reposted by Joachim Wolff
Overwhelmed by all of the exciting new research on chromatin modifiers in AML? Find it hard to keep track of all the new menin inhibitors? Well good news, we’ve just published the perfect review for you in SCTM!
@alexkschurer.bsky.social
@gritsmanlab.bsky.social
academic.oup.com/stcltm/advan...
@alexkschurer.bsky.social
@gritsmanlab.bsky.social
academic.oup.com/stcltm/advan...
Targeting chromatin modifying complexes in acute myeloid leukemia
Abstract. Acute myeloid leukemia (AML) is a devastating hematologic malignancy with high rates of relapse, which can, in part, be attributed to the dysregu
academic.oup.com
December 4, 2024 at 3:20 AM
Overwhelmed by all of the exciting new research on chromatin modifiers in AML? Find it hard to keep track of all the new menin inhibitors? Well good news, we’ve just published the perfect review for you in SCTM!
@alexkschurer.bsky.social
@gritsmanlab.bsky.social
academic.oup.com/stcltm/advan...
@alexkschurer.bsky.social
@gritsmanlab.bsky.social
academic.oup.com/stcltm/advan...
Reposted by Joachim Wolff
Enhancer cooperativity can compensate for loss of activity over large genomic distances www.cell.com/molecular-ce...
Enhancer cooperativity can compensate for loss of activity over large genomic distances
Thomas, Feng, et al. introduce a synthetic platform that allows the building of complex
regulatory landscapes. Integrating the same enhancer at different distances from a
promoter uncovered that activ...
www.cell.com
December 3, 2024 at 2:33 AM
Enhancer cooperativity can compensate for loss of activity over large genomic distances www.cell.com/molecular-ce...
Reposted by Joachim Wolff
Thank you for the comment and letting me know for the link. Here it is: www.biorxiv.org/content/10.1...
A Scaffolding Element Rewires Local 3D Chromatin Architecture During Differentiation
Upon differentiation chromatin rewires to reflect its new cellular identity and function. While it is widely known that this process involves cooperative changes in transcription, chromatin compositio...
www.biorxiv.org
December 1, 2024 at 5:15 PM
Thank you for the comment and letting me know for the link. Here it is: www.biorxiv.org/content/10.1...
Reposted by Joachim Wolff
Honoured to be invited for the Emerging Leaders Edition of Oncogene! This review, spearheaded by my postdoc Julia Scott, explores cohesin-STAG2’s roles in chromatin architecture, transcriptional regulation, and cancer biology. Read it here: www.nature.com/articles/s41...
Emerging roles of cohesin-STAG2 in cancer - Oncogene
Oncogene - Emerging roles of cohesin-STAG2 in cancer
www.nature.com
November 29, 2024 at 5:22 PM
Honoured to be invited for the Emerging Leaders Edition of Oncogene! This review, spearheaded by my postdoc Julia Scott, explores cohesin-STAG2’s roles in chromatin architecture, transcriptional regulation, and cancer biology. Read it here: www.nature.com/articles/s41...
Reposted by Joachim Wolff
Transposable element 5mC methylation state of blood cells predicts age and disease - Nature Aging https://www.nature.com/articles/s43587-024-00757-2
November 30, 2024 at 1:00 PM
Transposable element 5mC methylation state of blood cells predicts age and disease - Nature Aging https://www.nature.com/articles/s43587-024-00757-2
Reposted by Joachim Wolff
Enhanced SNP Genotyping with Symmetric Multinomial Logistic Regression https://www.biorxiv.org/content/10.1101/2024.11.28.625807v1
Enhanced SNP Genotyping with Symmetric Multinomial Logistic Regression https://www.biorxiv.org/content/10.1101/2024.11.28.625807v1
In genotyping, determining Single Nucleotide Polymorphisms (SNPs) is standard practice, but it becom
www.biorxiv.org
November 30, 2024 at 2:33 AM
Enhanced SNP Genotyping with Symmetric Multinomial Logistic Regression https://www.biorxiv.org/content/10.1101/2024.11.28.625807v1
Reposted by Joachim Wolff
Excited to share our work @science.org. led by our incredible @tommyz626.bsky.social at @rockefelleruniv.bsky.social! By profiling 21 million single cells across life stages, we reveal aging as distinct, development-like transitions, with dramatic cell population changes in specific time windows!
A panoramic view of cell population dynamics in mammalian aging
To elucidate aging-associated cellular population dynamics, we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissues across different life stages, se...
tinyurl.com
November 29, 2024 at 4:17 PM
Excited to share our work @science.org. led by our incredible @tommyz626.bsky.social at @rockefelleruniv.bsky.social! By profiling 21 million single cells across life stages, we reveal aging as distinct, development-like transitions, with dramatic cell population changes in specific time windows!
Reposted by Joachim Wolff
🔺🔺🔺RED TRIANGLE ALERT 🔺🔺🔺
Ever wonder how #TADs compare across the tree of life?Look no further & read our Review!!!
Find out what genes & 3D chromatin can & can't do in Bacteria! Archeae! Yeast! Plants! Animals!
SMCs & RNA-Pol are the only thing they have in common
www.nature.com/articles/s41...
Ever wonder how #TADs compare across the tree of life?Look no further & read our Review!!!
Find out what genes & 3D chromatin can & can't do in Bacteria! Archeae! Yeast! Plants! Animals!
SMCs & RNA-Pol are the only thing they have in common
www.nature.com/articles/s41...
Evolution and function of chromatin domains across the tree of life - Nature Structural & Molecular Biology
Szalay et al. discuss cross-kingdom similarities and differences in 3D chromatin folding in relation to gene regulation, including in bacteria, archaea, mammals and plants. This comparison reveals cer...
www.nature.com
November 28, 2024 at 12:48 PM
🔺🔺🔺RED TRIANGLE ALERT 🔺🔺🔺
Ever wonder how #TADs compare across the tree of life?Look no further & read our Review!!!
Find out what genes & 3D chromatin can & can't do in Bacteria! Archeae! Yeast! Plants! Animals!
SMCs & RNA-Pol are the only thing they have in common
www.nature.com/articles/s41...
Ever wonder how #TADs compare across the tree of life?Look no further & read our Review!!!
Find out what genes & 3D chromatin can & can't do in Bacteria! Archeae! Yeast! Plants! Animals!
SMCs & RNA-Pol are the only thing they have in common
www.nature.com/articles/s41...
Reposted by Joachim Wolff
Generalized AI models for genomics applications www.nature.com/articles/s41...
Generalized AI models for genomics applications - Nature Methods
The Nucleotide Transformer is a series of foundation models pre-trained on DNA sequences through self-supervised learning that extracts context-specific representations of nucleotide sequences. These ...
www.nature.com
November 28, 2024 at 9:43 PM
Generalized AI models for genomics applications www.nature.com/articles/s41...
Reposted by Joachim Wolff
🔖New paper from the lab!
'Evolution of 3D Chromatin Folding' | Annual Reviews - go.shr.lc/3B60kZF
'Evolution of 3D Chromatin Folding' | Annual Reviews - go.shr.lc/3B60kZF
November 28, 2024 at 5:44 PM
🔖New paper from the lab!
'Evolution of 3D Chromatin Folding' | Annual Reviews - go.shr.lc/3B60kZF
'Evolution of 3D Chromatin Folding' | Annual Reviews - go.shr.lc/3B60kZF
Reposted by Joachim Wolff
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
www.nature.com
November 27, 2024 at 4:13 AM
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...