Daniel Lipka
@dblipka.bsky.social
Physician Scientist at DKFZ & NCT Heidelberg
studying 🩸🧬 #epigenomics #DNAmethylation #singleCell #precisiononcology #JMML
www.translational-cancer-epigenomics.de
studying 🩸🧬 #epigenomics #DNAmethylation #singleCell #precisiononcology #JMML
www.translational-cancer-epigenomics.de
Reposted by Daniel Lipka
The figures from this book are all freely available through
@figshare.com, hopefully helpful for presentations and teaching:
figshare.com/projects/Epi...
Please let me know if you find any inaccuracies and I'll fix them. I've already updated one of the figures.
#EpigeneticsBook
@figshare.com, hopefully helpful for presentations and teaching:
figshare.com/projects/Epi...
Please let me know if you find any inaccuracies and I'll fix them. I've already updated one of the figures.
#EpigeneticsBook
October 24, 2025 at 3:09 PM
The figures from this book are all freely available through
@figshare.com, hopefully helpful for presentations and teaching:
figshare.com/projects/Epi...
Please let me know if you find any inaccuracies and I'll fix them. I've already updated one of the figures.
#EpigeneticsBook
@figshare.com, hopefully helpful for presentations and teaching:
figshare.com/projects/Epi...
Please let me know if you find any inaccuracies and I'll fix them. I've already updated one of the figures.
#EpigeneticsBook
Great to meet friends and colleagues at this year’s EWOG-MDS meeting in Berlin. We had great discussions and developed new project ideas and collaborations with the aim of improving risk stratification and patient care for JMML patients.
#jmml #ewogmds #precisionmedicine www.ewogberlin2025.org
#jmml #ewogmds #precisionmedicine www.ewogberlin2025.org
On the Verge to Malignancy: Cytopenia and Beyond - Ewog Symposium
On the Verge to Malignancy:
Cytopenia and Beyond
International Symposium on
bone marrow failure, predisposition,
MDS and MPD in the Young
Dear colleagues and friends,
we are pleased to wel...
www.ewogberlin2025.org
September 19, 2025 at 5:07 PM
Great to meet friends and colleagues at this year’s EWOG-MDS meeting in Berlin. We had great discussions and developed new project ideas and collaborations with the aim of improving risk stratification and patient care for JMML patients.
#jmml #ewogmds #precisionmedicine www.ewogberlin2025.org
#jmml #ewogmds #precisionmedicine www.ewogberlin2025.org
Reposted by Daniel Lipka
On behalf of @ckadoch.bsky.social and myself, we are pleased to present our upcoming @KeystoneSymposia, #KSEpigenetics26 Epigenetics and Gene Regulation in Health and Disease, March 2-5, in Geneva, Switzerland. keysym.us/KSEpigenetic...
Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities | Keystone Symposia
Join us at the Keystone Symposia on Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities, March 2026, in Geneva, with field leaders!
keysym.us
September 16, 2025 at 4:01 PM
On behalf of @ckadoch.bsky.social and myself, we are pleased to present our upcoming @KeystoneSymposia, #KSEpigenetics26 Epigenetics and Gene Regulation in Health and Disease, March 2-5, in Geneva, Switzerland. keysym.us/KSEpigenetic...
Of interest to the #epigenomics, #dnamethylation, #neurooncology, #oncology and #precisionmedicine communities! 🧬
DNA-methylation-based deconvolution can be a powerful tool for identifying novel disease subgroups. In our paper in Acta Neuropathologica, we show how this can be leveraged in IDH-mutant gliomas - specifically in oligodendrogliomas.
doi.org/10.1007/s004...
doi.org/10.1007/s004...
DNA methylation analysis reveals an epigenetic signature distinctive of high-grade oligodendroglioma - Acta Neuropathologica
IDH-mutant gliomas represent a subtype of diffuse gliomas that primarily affect patients in early to mid-adolescence. These tumors are classified into three distinct CNS WHO grades of malignancy. Accu...
doi.org
September 15, 2025 at 12:29 PM
Of interest to the #epigenomics, #dnamethylation, #neurooncology, #oncology and #precisionmedicine communities! 🧬
Reposted by Daniel Lipka
DNA-methylation-based deconvolution can be a powerful tool for identifying novel disease subgroups. In our paper in Acta Neuropathologica, we show how this can be leveraged in IDH-mutant gliomas - specifically in oligodendrogliomas.
doi.org/10.1007/s004...
doi.org/10.1007/s004...
DNA methylation analysis reveals an epigenetic signature distinctive of high-grade oligodendroglioma - Acta Neuropathologica
IDH-mutant gliomas represent a subtype of diffuse gliomas that primarily affect patients in early to mid-adolescence. These tumors are classified into three distinct CNS WHO grades of malignancy. Accu...
doi.org
September 8, 2025 at 7:07 AM
DNA-methylation-based deconvolution can be a powerful tool for identifying novel disease subgroups. In our paper in Acta Neuropathologica, we show how this can be leveraged in IDH-mutant gliomas - specifically in oligodendrogliomas.
doi.org/10.1007/s004...
doi.org/10.1007/s004...
Reposted by Daniel Lipka
Epigenetics Update - Fluctuating DNA methylation tracks cancer evolution at clinical scale go.nature.com/3Ve4OUy
#Epigenetics #Cancer #DNAme #DNAm
---
Empower your research with high-res epigenetic insights at epigenometech.com
#Epigenetics #Cancer #DNAme #DNAm
---
Empower your research with high-res epigenetic insights at epigenometech.com
September 12, 2025 at 11:49 AM
Epigenetics Update - Fluctuating DNA methylation tracks cancer evolution at clinical scale go.nature.com/3Ve4OUy
#Epigenetics #Cancer #DNAme #DNAm
---
Empower your research with high-res epigenetic insights at epigenometech.com
#Epigenetics #Cancer #DNAme #DNAm
---
Empower your research with high-res epigenetic insights at epigenometech.com
Reposted by Daniel Lipka
Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation. www.biorxiv.org/content/10.1...
August 18, 2025 at 12:23 PM
Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation. www.biorxiv.org/content/10.1...
Still two weeks left to apply to the #postdoc position in my lab via the @dkfz.bsky.social fellowship program.
#epigenomics #hematology #leukemia #computationalbiology #precisiononcology
#epigenomics #hematology #leukemia #computationalbiology #precisiononcology
+++ Postdoc Opportunity +++
My lab is looking for researchers interested in combining cutting edge #genomics, #epigenetics and #AI for precision oncology in pediatric #leukemia.
www.dkfz.de/fileadmin/us...
Applications via the #DKFZ postdoc program:
www.dkfz.de/en/karriere/...
My lab is looking for researchers interested in combining cutting edge #genomics, #epigenetics and #AI for precision oncology in pediatric #leukemia.
www.dkfz.de/fileadmin/us...
Applications via the #DKFZ postdoc program:
www.dkfz.de/en/karriere/...
August 30, 2025 at 10:51 AM
Still two weeks left to apply to the #postdoc position in my lab via the @dkfz.bsky.social fellowship program.
#epigenomics #hematology #leukemia #computationalbiology #precisiononcology
#epigenomics #hematology #leukemia #computationalbiology #precisiononcology
Reposted by Daniel Lipka
Every so often, a paper lands at exactly the right moment. This one’s a gem. Can’t wait to try out this new strategy for delivering CRISPRoff chromatin-editing tools into our favorite cellular model system. Congrats to James K Nuñez and his team: www.nature.com/articles/s41...
Programmable epigenome editing by transient delivery of CRISPR epigenome editor ribonucleoproteins - Nature Communications
Epigenome editing programs gene silencing without inducing DNA breaks but challenges in delivery into human cells limit its broader use. Here, the authors present the RENDER platform, which uses virus...
www.nature.com
August 29, 2025 at 7:27 PM
Every so often, a paper lands at exactly the right moment. This one’s a gem. Can’t wait to try out this new strategy for delivering CRISPRoff chromatin-editing tools into our favorite cellular model system. Congrats to James K Nuñez and his team: www.nature.com/articles/s41...
Reposted by Daniel Lipka
Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....
August 7, 2025 at 4:20 PM
Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....
+++ Postdoc Opportunity +++
My lab is looking for researchers interested in combining cutting edge #genomics, #epigenetics and #AI for precision oncology in pediatric #leukemia.
www.dkfz.de/fileadmin/us...
Applications via the #DKFZ postdoc program:
www.dkfz.de/en/karriere/...
My lab is looking for researchers interested in combining cutting edge #genomics, #epigenetics and #AI for precision oncology in pediatric #leukemia.
www.dkfz.de/fileadmin/us...
Applications via the #DKFZ postdoc program:
www.dkfz.de/en/karriere/...
August 25, 2025 at 8:45 PM
+++ Postdoc Opportunity +++
My lab is looking for researchers interested in combining cutting edge #genomics, #epigenetics and #AI for precision oncology in pediatric #leukemia.
www.dkfz.de/fileadmin/us...
Applications via the #DKFZ postdoc program:
www.dkfz.de/en/karriere/...
My lab is looking for researchers interested in combining cutting edge #genomics, #epigenetics and #AI for precision oncology in pediatric #leukemia.
www.dkfz.de/fileadmin/us...
Applications via the #DKFZ postdoc program:
www.dkfz.de/en/karriere/...
Reposted by Daniel Lipka
Epigenetics Update - Thymic epithelial cells amplify epigenetic noise to promote immune tolerance
go.nature.com/45srCWG
Andrew S. Koh (University of Chicago) reporting in Nature
#Epigenetics #Noise #Chromatin #Immunity
---
High-resolution insights without cell sorting; epigenometech.com
go.nature.com/45srCWG
Andrew S. Koh (University of Chicago) reporting in Nature
#Epigenetics #Noise #Chromatin #Immunity
---
High-resolution insights without cell sorting; epigenometech.com
August 21, 2025 at 8:18 AM
Epigenetics Update - Thymic epithelial cells amplify epigenetic noise to promote immune tolerance
go.nature.com/45srCWG
Andrew S. Koh (University of Chicago) reporting in Nature
#Epigenetics #Noise #Chromatin #Immunity
---
High-resolution insights without cell sorting; epigenometech.com
go.nature.com/45srCWG
Andrew S. Koh (University of Chicago) reporting in Nature
#Epigenetics #Noise #Chromatin #Immunity
---
High-resolution insights without cell sorting; epigenometech.com
Reposted by Daniel Lipka
🧵Radiotherapy immune signaling is modular, redundant — and has a limit.
Together with
@joschakraske
@peterhuber_hd
@halama_immuno
@UKHD_radonc
our new study in fully human systems shows that:
t.co/GzH3N6gElf
1/9
Together with
@joschakraske
@peterhuber_hd
@halama_immuno
@UKHD_radonc
our new study in fully human systems shows that:
t.co/GzH3N6gElf
1/9
August 16, 2025 at 8:01 AM
🧵Radiotherapy immune signaling is modular, redundant — and has a limit.
Together with
@joschakraske
@peterhuber_hd
@halama_immuno
@UKHD_radonc
our new study in fully human systems shows that:
t.co/GzH3N6gElf
1/9
Together with
@joschakraske
@peterhuber_hd
@halama_immuno
@UKHD_radonc
our new study in fully human systems shows that:
t.co/GzH3N6gElf
1/9
Reposted by Daniel Lipka
Plant #epigenetics colleagues, is this the consensus opinion?
"...these methylation marks and epiallelic variations found in natural populations are mainly attributed to genetic variations in epigenetic machinery and transposable element (TE) insertions"
pmc.ncbi.nlm.nih.gov/articles/PMC...
"...these methylation marks and epiallelic variations found in natural populations are mainly attributed to genetic variations in epigenetic machinery and transposable element (TE) insertions"
pmc.ncbi.nlm.nih.gov/articles/PMC...
August 10, 2025 at 2:37 PM
Plant #epigenetics colleagues, is this the consensus opinion?
"...these methylation marks and epiallelic variations found in natural populations are mainly attributed to genetic variations in epigenetic machinery and transposable element (TE) insertions"
pmc.ncbi.nlm.nih.gov/articles/PMC...
"...these methylation marks and epiallelic variations found in natural populations are mainly attributed to genetic variations in epigenetic machinery and transposable element (TE) insertions"
pmc.ncbi.nlm.nih.gov/articles/PMC...
Reposted by Daniel Lipka
I am delighted to share a publication in @natcomms.nature.com. IRX3, linked to obesity via the FTO locus, influences fat vs bone cell fate. It is the result of a wonderful collaboration between S. Dankel, G. Mellgren @unibergen.bsky.social and my lab @biovitenskap.bsky.social 🍾
👉 rdcu.be/ezA5o
👉 rdcu.be/ezA5o
IRX3 controls a SUMOylation-dependent differentiation switch in adipocyte precursor cells
Nature Communications - Here, the authors show that IRX3 is a transcriptional master regulator of multiple histone- and chromatin-remodeling enzymes and the SUMOylation pathway in adipocyte...
rdcu.be
August 6, 2025 at 5:49 PM
I am delighted to share a publication in @natcomms.nature.com. IRX3, linked to obesity via the FTO locus, influences fat vs bone cell fate. It is the result of a wonderful collaboration between S. Dankel, G. Mellgren @unibergen.bsky.social and my lab @biovitenskap.bsky.social 🍾
👉 rdcu.be/ezA5o
👉 rdcu.be/ezA5o
Reposted by Daniel Lipka
There’s still time to apply for one of our five advertised postdoctoral positions in developmental epigenetics!
Click here to find out more and apply: lms.mrc.ac.uk/work/vacanci...
Applications close 12th August
#HiringNow #Jobs #Epigenetics
Click here to find out more and apply: lms.mrc.ac.uk/work/vacanci...
Applications close 12th August
#HiringNow #Jobs #Epigenetics
MRC Postdoctoral Research Scientists x 5 - MRC Laboratory of Medical Sciences
Applications are now open for up to five postdoctoral positions in the area of developmental epigenetics.
lms.mrc.ac.uk
August 5, 2025 at 3:21 PM
There’s still time to apply for one of our five advertised postdoctoral positions in developmental epigenetics!
Click here to find out more and apply: lms.mrc.ac.uk/work/vacanci...
Applications close 12th August
#HiringNow #Jobs #Epigenetics
Click here to find out more and apply: lms.mrc.ac.uk/work/vacanci...
Applications close 12th August
#HiringNow #Jobs #Epigenetics
Reposted by Daniel Lipka
Happy to share our recent publication on benchmarking peak calling methods for CUT&RUN.
academic.oup.com/bioinformati...
Published in @oxunipress.bsky.social Bioinformatics | led by aminnoorani.bsky.social
#Epigenomics #Genomics #Bioinformatics #MachineLearning #CUTandRUN #CompBio #4DNucleome
academic.oup.com/bioinformati...
Published in @oxunipress.bsky.social Bioinformatics | led by aminnoorani.bsky.social
#Epigenomics #Genomics #Bioinformatics #MachineLearning #CUTandRUN #CompBio #4DNucleome
July 16, 2025 at 6:14 PM
Happy to share our recent publication on benchmarking peak calling methods for CUT&RUN.
academic.oup.com/bioinformati...
Published in @oxunipress.bsky.social Bioinformatics | led by aminnoorani.bsky.social
#Epigenomics #Genomics #Bioinformatics #MachineLearning #CUTandRUN #CompBio #4DNucleome
academic.oup.com/bioinformati...
Published in @oxunipress.bsky.social Bioinformatics | led by aminnoorani.bsky.social
#Epigenomics #Genomics #Bioinformatics #MachineLearning #CUTandRUN #CompBio #4DNucleome
Reposted by Daniel Lipka
📢 Announcing the MOPITAS Autumn School on Spatial Transcriptomics Data Analysis – taking place November 12–14, in Munich. Don't miss this excellent opportunity to deepen your expertise in data science and multi-OMICS analysis - especially as a PhD student in the data science community.
July 4, 2025 at 7:20 PM
📢 Announcing the MOPITAS Autumn School on Spatial Transcriptomics Data Analysis – taking place November 12–14, in Munich. Don't miss this excellent opportunity to deepen your expertise in data science and multi-OMICS analysis - especially as a PhD student in the data science community.
Reposted by Daniel Lipka
Now online in Cancer Discovery: Detection of Cancers Three Years Prior to Diagnosis Using Plasma Cell-Free DNA - by Yuxuan Wang, Nickolas Papadopoulos, Elizabeth Platz, Bert Vogelstein, and colleagues doi.org/10.1158/2159...
May 27, 2025 at 4:19 PM
Now online in Cancer Discovery: Detection of Cancers Three Years Prior to Diagnosis Using Plasma Cell-Free DNA - by Yuxuan Wang, Nickolas Papadopoulos, Elizabeth Platz, Bert Vogelstein, and colleagues doi.org/10.1158/2159...
Reposted by Daniel Lipka
Flybase lost all of the NIH support overnight - it is a disaster for the community. Please consider donating. I just did! www.philanthropy.cam.ac.uk/give-to-camb...
Drosophila Genetic Database
The Drosophila Genetic Database, FlyBase, is on the brink of collapse due to the sudden termination of the FlyBase NIH grant, which includes salaries for 5 literature curators based at the University ...
www.philanthropy.cam.ac.uk
June 3, 2025 at 6:23 PM
Flybase lost all of the NIH support overnight - it is a disaster for the community. Please consider donating. I just did! www.philanthropy.cam.ac.uk/give-to-camb...
Reposted by Daniel Lipka
How does metabolism act through generic chromatin modifiers promote specific cellular states? Simultaneous modification of transcription factors and chromatin, enhancing epigenetic signal to noise ratios.
www.embopress.org/doi/full/10....
www.embopress.org/doi/full/10....
Altering metabolism programs cell identity via NAD+-dependent deacetylation | The EMBO Journal
imageimageHow alterations in cell metabolism translate into specific developmental gene programs remains a major question. This study shows that forcing OXPHOS metabolism reprograms mouse embryonic stem cells (ESCs) to a more inner cell mass (ICM)-...
www.embopress.org
April 25, 2025 at 3:26 PM
How does metabolism act through generic chromatin modifiers promote specific cellular states? Simultaneous modification of transcription factors and chromatin, enhancing epigenetic signal to noise ratios.
www.embopress.org/doi/full/10....
www.embopress.org/doi/full/10....
Reposted by Daniel Lipka
1/ 🧬 A Hitchhiker’s Guide to Long-Read Genomic Analysis is out now!
This mini-review walks through the latest advances in long-read DNA sequencing — from assemblies to variant calling to epigenetics.
Link 🔗 genome.cshlp.org/content/35/4...
🧵👇
This mini-review walks through the latest advances in long-read DNA sequencing — from assemblies to variant calling to epigenetics.
Link 🔗 genome.cshlp.org/content/35/4...
🧵👇
May 5, 2025 at 2:08 PM
1/ 🧬 A Hitchhiker’s Guide to Long-Read Genomic Analysis is out now!
This mini-review walks through the latest advances in long-read DNA sequencing — from assemblies to variant calling to epigenetics.
Link 🔗 genome.cshlp.org/content/35/4...
🧵👇
This mini-review walks through the latest advances in long-read DNA sequencing — from assemblies to variant calling to epigenetics.
Link 🔗 genome.cshlp.org/content/35/4...
🧵👇
Few days left to apply for a #postdoctoral position in my team investigating the pathomechanism of IDH1 mutations at the interface of #metabolism and #epigenomics!
Hey #HemeSky and #EpiSci folks! We are hiring!
For our Translational Cancer Epigenomics team @dkfz.bsky.social and @nct-heidelberg.bsky.social we are looking for a talented postdoc interested in research on heme malignancies and #epigenetics.
Interested?
👉See jobs.dkfz.de/en/jobs/1676... or DM me!
For our Translational Cancer Epigenomics team @dkfz.bsky.social and @nct-heidelberg.bsky.social we are looking for a talented postdoc interested in research on heme malignancies and #epigenetics.
Interested?
👉See jobs.dkfz.de/en/jobs/1676... or DM me!
Postdoctoral Researcher
jobs.dkfz.de
May 3, 2025 at 10:35 AM
Few days left to apply for a #postdoctoral position in my team investigating the pathomechanism of IDH1 mutations at the interface of #metabolism and #epigenomics!
Reposted by Daniel Lipka
We are recruiting! Senior postdoc in computational cancer genomics/epigenomics @ludwigcancer.bsky.social @ox.ac.uk. Lead research into epigenetic drivers of secondary AML with rich omics data + strong clinical/wet-lab collaborations.
cutt.cx/YUoB
We look forward hearing from you!
#epigenetics #jobs
cutt.cx/YUoB
We look forward hearing from you!
#epigenetics #jobs
April 28, 2025 at 2:59 PM
We are recruiting! Senior postdoc in computational cancer genomics/epigenomics @ludwigcancer.bsky.social @ox.ac.uk. Lead research into epigenetic drivers of secondary AML with rich omics data + strong clinical/wet-lab collaborations.
cutt.cx/YUoB
We look forward hearing from you!
#epigenetics #jobs
cutt.cx/YUoB
We look forward hearing from you!
#epigenetics #jobs
Reposted by Daniel Lipka
Want to work with us on DNA methylation and rare genetic disease? Fully funded PhD project with deadline 16th May:
www.findaphd.com/phds/project...
Excited to collaborate with @hannahlong.bsky.social and Daria Bunina (@uoe-igc.bsky.social/@mdc-berlin.bsky.social).
Please share 🙏
#epigenetics
www.findaphd.com/phds/project...
Excited to collaborate with @hannahlong.bsky.social and Daria Bunina (@uoe-igc.bsky.social/@mdc-berlin.bsky.social).
Please share 🙏
#epigenetics
Fully Funded PhD Studentship in Human Genetics, Genomics and Disease: Dissecting DNMT3B functions in Immunodeficiency-centromeric instability facial anomalies syndrome at University of Edinburgh on Fi...
PhD Project - Fully Funded PhD Studentship in Human Genetics, Genomics and Disease: Dissecting DNMT3B functions in Immunodeficiency-centromeric instability facial anomalies syndrome at University of E...
www.findaphd.com
April 23, 2025 at 9:49 AM
Want to work with us on DNA methylation and rare genetic disease? Fully funded PhD project with deadline 16th May:
www.findaphd.com/phds/project...
Excited to collaborate with @hannahlong.bsky.social and Daria Bunina (@uoe-igc.bsky.social/@mdc-berlin.bsky.social).
Please share 🙏
#epigenetics
www.findaphd.com/phds/project...
Excited to collaborate with @hannahlong.bsky.social and Daria Bunina (@uoe-igc.bsky.social/@mdc-berlin.bsky.social).
Please share 🙏
#epigenetics