Manthan
@manthan5277.bsky.social
Postdoc @Madapuralab, QMUL
Applying Epigenomics Transposons NGS approaches understanding disease and development
Applying Epigenomics Transposons NGS approaches understanding disease and development
Reposted by Manthan
Despite having been scooped big time by this paper from William Pastor's lab, really quite enjoyed reading it. Congrats to the authors.
Divergent roles of DNA methylation, TRIM28, and p53 surveillance in human embryonic and trophoblast stem cells
Transcriptional regulation of transposons and genes by TRIM28 and 5mC is critical for proper mammalian embryonic development, but the specific roles for these mediators in human embryonic and placenta...
www.biorxiv.org
November 28, 2025 at 10:56 AM
Despite having been scooped big time by this paper from William Pastor's lab, really quite enjoyed reading it. Congrats to the authors.
Reposted by Manthan
Bah, who needs cohesin if you're at the right place (near). Grover once taught us the difference between near and far (my favourite Sesame Street piece), and now amazing work from @elphegenoralab.bsky.social led by @karissalhansen.bsky.social shows us how: www.science.org/doi/10.1126/...
Synergy between regulatory elements can render cohesin dispensable for distal enhancer function
Enhancers are critical genetic elements controlling transcription from promoters, yet how they convey regulatory information across large genomic distances remains unclear. Here, we engineer pluripote...
www.science.org
November 27, 2025 at 7:10 PM
Bah, who needs cohesin if you're at the right place (near). Grover once taught us the difference between near and far (my favourite Sesame Street piece), and now amazing work from @elphegenoralab.bsky.social led by @karissalhansen.bsky.social shows us how: www.science.org/doi/10.1126/...
Reposted by Manthan
#TEsky TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution doi.org/10.1093/nar/...
TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution
Abstract. Transposable elements (TEs) are repetitive DNA sequences typically silenced in normal tissues. Their dysregulation in cancer can significantly im
doi.org
November 27, 2025 at 1:45 PM
#TEsky TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution doi.org/10.1093/nar/...
Reposted by Manthan
1/8🧵 Excited to share two studies in which I was involved within the Bird Lab📄📄 We have explored how the transcription factor SALL4 assembles and shapes chromatin in embryonic stem cells.
@kashyapchhatbar.bsky.social @saragiuliani.bsky.social @drphcb-uoe.bsky.social @edinburghbiology.bsky.social
@kashyapchhatbar.bsky.social @saragiuliani.bsky.social @drphcb-uoe.bsky.social @edinburghbiology.bsky.social
November 26, 2025 at 1:59 PM
1/8🧵 Excited to share two studies in which I was involved within the Bird Lab📄📄 We have explored how the transcription factor SALL4 assembles and shapes chromatin in embryonic stem cells.
@kashyapchhatbar.bsky.social @saragiuliani.bsky.social @drphcb-uoe.bsky.social @edinburghbiology.bsky.social
@kashyapchhatbar.bsky.social @saragiuliani.bsky.social @drphcb-uoe.bsky.social @edinburghbiology.bsky.social
Reposted by Manthan
A new and fascinating story from @bencarty.bsky.social and the group, with crucial help from the teams of @naltemose.bsky.social, Simona Giunta, and @dfachinetti.bsky.social. Many thanks to all for a fantastic collaboration.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
November 25, 2025 at 12:16 PM
A new and fascinating story from @bencarty.bsky.social and the group, with crucial help from the teams of @naltemose.bsky.social, Simona Giunta, and @dfachinetti.bsky.social. Many thanks to all for a fantastic collaboration.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Manthan
#TEsky Copy number and sequence variation in ribosomal DNA and the transposon, Pokey in mutation accumulation lines of Daphnia obtusa doi.org/10.1093/g3jo...
Copy number and sequence variation in ribosomal DNA and the transposon, Pokey in mutation accumulation lines of Daphnia obtusa.
Abstract. Ribosomal DNA (rDNA) occurs as tandem arrays of a repeat unit containing the genes encoding 18S, 5.8S and 28S rRNA separated by spacers. These rR
doi.org
November 24, 2025 at 2:38 PM
#TEsky Copy number and sequence variation in ribosomal DNA and the transposon, Pokey in mutation accumulation lines of Daphnia obtusa doi.org/10.1093/g3jo...
Reposted by Manthan
Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
RNA polymerase II coordinates histone deacetylation at active promoters
Transcription initiation limits histone acetylation and H2AZ incorporation at promoters.
www.science.org
February 12, 2025 at 9:21 PM
Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
Reposted by Manthan
Very excited to share my Phd/early post-doc work, out now in Cancer Research! Using multiomic data from multi-site tumors from ovarian cancer patients, we show that the tumors continue to acquire LINE-1 insertions after metastatic spread and find determinants of LINE-1 permissivity in this disease.
Dynamic and Ongoing De Novo L1 Retrotransposition Contributes to Genome Plasticity and Intrapatient Heterogeneity in Ovarian Cancer
Abstract. L1 retrotransposons are the only protein-coding active transposable elements in the human genome. While typically silenced in normal cells, they are highly expressed in many human epithelial...
aacrjournals.org
November 20, 2025 at 10:54 PM
Very excited to share my Phd/early post-doc work, out now in Cancer Research! Using multiomic data from multi-site tumors from ovarian cancer patients, we show that the tumors continue to acquire LINE-1 insertions after metastatic spread and find determinants of LINE-1 permissivity in this disease.
Reposted by Manthan
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics
Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.
www.nature.com
November 18, 2025 at 12:00 PM
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Reposted by Manthan
My first preprint is out! Excited to share a major part of my PhD work, now shaped as a finalised story.
If you’re interested in epigenetics and cardiovascular research, go check it out!
#Preprint #OpenScience #Epigentics #FunctionalGenomics #CardiovascularResearch
www.biorxiv.org/content/10.1...
If you’re interested in epigenetics and cardiovascular research, go check it out!
#Preprint #OpenScience #Epigentics #FunctionalGenomics #CardiovascularResearch
www.biorxiv.org/content/10.1...
An epigenomic investigation of atrial fibrillation in a matched left and right atrial human cohort
As the most prevalent cardiac arrythmia, atrial fibrillation is an important contributor to cardiovascular morbidity and mortality. Human population findings increasingly support its complex genetic a...
www.biorxiv.org
November 15, 2025 at 6:54 PM
My first preprint is out! Excited to share a major part of my PhD work, now shaped as a finalised story.
If you’re interested in epigenetics and cardiovascular research, go check it out!
#Preprint #OpenScience #Epigentics #FunctionalGenomics #CardiovascularResearch
www.biorxiv.org/content/10.1...
If you’re interested in epigenetics and cardiovascular research, go check it out!
#Preprint #OpenScience #Epigentics #FunctionalGenomics #CardiovascularResearch
www.biorxiv.org/content/10.1...
Reposted by Manthan
🚨 New preprint alert!
Our latest work from @immler.bsky.social lab 🐟🧬
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
#TESky #TE #piRNA #miRNA #zebrafish #DanioDigest
🔗 Read here www.biorxiv.org/content/10.1...
A thread 🧵...
Our latest work from @immler.bsky.social lab 🐟🧬
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
#TESky #TE #piRNA #miRNA #zebrafish #DanioDigest
🔗 Read here www.biorxiv.org/content/10.1...
A thread 🧵...
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
Environmental fluctuations influence heritable phenotypes through complex molecular mechanisms. In zebrafish (Danio rerio), the interplay between temperature variation, transposable element (TE) activ...
www.biorxiv.org
November 16, 2025 at 10:18 AM
🚨 New preprint alert!
Our latest work from @immler.bsky.social lab 🐟🧬
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
#TESky #TE #piRNA #miRNA #zebrafish #DanioDigest
🔗 Read here www.biorxiv.org/content/10.1...
A thread 🧵...
Our latest work from @immler.bsky.social lab 🐟🧬
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
#TESky #TE #piRNA #miRNA #zebrafish #DanioDigest
🔗 Read here www.biorxiv.org/content/10.1...
A thread 🧵...
Reposted by Manthan
🗨️ Just published in Nature Biotechnology: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper here: www.nature.com/articles/s41.... Annotated walkthrough in a thread below (1/11)
November 11, 2025 at 12:52 PM
🗨️ Just published in Nature Biotechnology: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper here: www.nature.com/articles/s41.... Annotated walkthrough in a thread below (1/11)
Reposted by Manthan
☕ @katerinakraft.bsky.social @sedonamurphy.bsky.social @mattjones.bsky.social et al. identify extrachromosomal DNA(ecDNA)-interacting elements (EIEs) enriched for #TransposableElements in #ColorectalCancer. EIE 14 integrated within ecDNA acts as an enhancer to promote cancer fitness.
bit.ly/49iFC7C
bit.ly/49iFC7C
Enhancer activation from transposable elements in extrachromosomal DNA - Nature Cell Biology
Kraft, Murphy, Jones et al. identify extrachromosomal DNA (ecDNA)-interacting elements (EIEs) enriched for transposable elements within ecDNA in colorectal cancer cells. They show that EIE 14 integrat...
bit.ly
November 16, 2025 at 8:29 AM
☕ @katerinakraft.bsky.social @sedonamurphy.bsky.social @mattjones.bsky.social et al. identify extrachromosomal DNA(ecDNA)-interacting elements (EIEs) enriched for #TransposableElements in #ColorectalCancer. EIE 14 integrated within ecDNA acts as an enhancer to promote cancer fitness.
bit.ly/49iFC7C
bit.ly/49iFC7C
Reposted by Manthan
I'm excited to introduce our new workflow for detecting endogenous viral elements - HI-FEVER. 🖥️🧬
academic.oup.com/bioinformati...
🧵
Big thanks to @ariskatzourakis.bsky.social, @humanceae.bsky.social, José Gabriel and Cormac for bringing this from conception to fruition!
academic.oup.com/bioinformati...
🧵
Big thanks to @ariskatzourakis.bsky.social, @humanceae.bsky.social, José Gabriel and Cormac for bringing this from conception to fruition!
HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements
AbstractSummary. Endogenous viral elements (EVEs) offer valuable insights into virus and host evolution, but their detection remains computationally and bi
academic.oup.com
November 13, 2025 at 11:14 AM
I'm excited to introduce our new workflow for detecting endogenous viral elements - HI-FEVER. 🖥️🧬
academic.oup.com/bioinformati...
🧵
Big thanks to @ariskatzourakis.bsky.social, @humanceae.bsky.social, José Gabriel and Cormac for bringing this from conception to fruition!
academic.oup.com/bioinformati...
🧵
Big thanks to @ariskatzourakis.bsky.social, @humanceae.bsky.social, José Gabriel and Cormac for bringing this from conception to fruition!
Reposted by Manthan
Having a lot of fun at #EMBOMobileGenome 😃
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Young KRAB-zinc finger gene clusters are highly dynamic incubators of ERV-driven genetic heterogeneity in mice - Nature Communications
KRAB-zinc finger proteins repress retrotransposons and rapidly evolve in mammals. Here, the authors show that ERV insertions drive the emergence and diversification of new KZFP genes in mice, revealin...
www.nature.com
November 6, 2025 at 9:40 AM
Having a lot of fun at #EMBOMobileGenome 😃
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Reposted by Manthan
"We are pleased to inform you that your Article "A disrupted compartment boundary underlies abnormal cardiac patterning and congenital heart defects" has now been accepted for publication"....... coming soon! But in the meantime see updated preprint: www.biorxiv.org/content/10.1...
A disrupted compartment boundary underlies abnormal cardiac patterning and congenital heart defects
Failure of septation of the interventricular septum (IVS) is the most common congenital heart defect (CHD), but mechanisms for patterning the IVS are largely unknown. Here, we show that a Tbx5+/Mef2cA...
www.biorxiv.org
November 4, 2025 at 4:04 PM
"We are pleased to inform you that your Article "A disrupted compartment boundary underlies abnormal cardiac patterning and congenital heart defects" has now been accepted for publication"....... coming soon! But in the meantime see updated preprint: www.biorxiv.org/content/10.1...
Reposted by Manthan
Interesting new work modeling human cholinergic circuitry! Researchers generated nbM organoids from hPSCs and fused them with cortical organoids to form functional nbM–cortical assembloids. This provides a platform to study deficits seen in Down syndrome. @cp-cellstemcell.bsky.social
November 4, 2025 at 5:14 PM
Interesting new work modeling human cholinergic circuitry! Researchers generated nbM organoids from hPSCs and fused them with cortical organoids to form functional nbM–cortical assembloids. This provides a platform to study deficits seen in Down syndrome. @cp-cellstemcell.bsky.social
Reposted by Manthan
Our latest paper on comparative analysis of HiChIP data is now online! HiChIP is one of the most useful/practical assays to profile 3D genome organization and chromatin loops but has its challenges in the data analysis especially when it comes to comparative analysis.
November 4, 2025 at 10:58 PM
Our latest paper on comparative analysis of HiChIP data is now online! HiChIP is one of the most useful/practical assays to profile 3D genome organization and chromatin loops but has its challenges in the data analysis especially when it comes to comparative analysis.
Reposted by Manthan
Reposted by Manthan
Reposted by Manthan
How do pluripotent stem cells resist harmful interferon responses to safeguard development? Through total epigenetic lockdown of ligands, sensors and effectors of IFN-I. In our preprint, James Holt shares his PhD discoveries on the ground state of immune evasion 😊: www.biorxiv.org/cgi/content/...
Epigenetic lockdown of type I interferon sensing and signalling in human pluripotent cells.
The Human Silencing Hub (HUSH) complex safeguards genome integrity in human somatic cells by repressing transposable elements and regulating type I interferon (IFN-I) induction. In early development, ...
www.biorxiv.org
October 29, 2025 at 6:03 PM
How do pluripotent stem cells resist harmful interferon responses to safeguard development? Through total epigenetic lockdown of ligands, sensors and effectors of IFN-I. In our preprint, James Holt shares his PhD discoveries on the ground state of immune evasion 😊: www.biorxiv.org/cgi/content/...
Reposted by Manthan
Very happy to see our paper published online natcomms.nature.com. Thank you to @wellcometrust.bsky.social for funding this work during my time with @robklose.bsky.social and David Booth! Thanks also to collaborators @garcialabms.bsky.social @alexdemendoza.bsky.social and the other authors!
Chromatin profiling identifies putative dual roles for H3K27me3 in regulating cell type-specific genes and transposable elements in choanoflagellates
Nature Communications - Here, the authors investigate chromatin-based gene regulation in the closest relative of animal, choanoflagellates. They uncover a putative dual role for the histone...
rdcu.be
October 29, 2025 at 1:40 PM
Very happy to see our paper published online natcomms.nature.com. Thank you to @wellcometrust.bsky.social for funding this work during my time with @robklose.bsky.social and David Booth! Thanks also to collaborators @garcialabms.bsky.social @alexdemendoza.bsky.social and the other authors!
Reposted by Manthan
📣 New preprint from the Jakobsson lab!
We describe a detailed protocol to inhibit the expression of transposable elements in human pluripotent stem cells, developed thanks to @asapresearch.parkinsonsroadmap.org funding.
Special shoutout to @anitaada.bsky.social!
www.biorxiv.org/content/10.1...
We describe a detailed protocol to inhibit the expression of transposable elements in human pluripotent stem cells, developed thanks to @asapresearch.parkinsonsroadmap.org funding.
Special shoutout to @anitaada.bsky.social!
www.biorxiv.org/content/10.1...
A framework for efficient CRISPRi-mediated silencing of retrotransposons in human pluripotent stem cells
This protocol describes the workflow for transcriptional silencing of transposable elements (TEs) in human induced pluripotent stem cells (hiPSCs). The protocol illustrates how to design gRNAs to targ...
www.biorxiv.org
October 29, 2025 at 8:24 AM
📣 New preprint from the Jakobsson lab!
We describe a detailed protocol to inhibit the expression of transposable elements in human pluripotent stem cells, developed thanks to @asapresearch.parkinsonsroadmap.org funding.
Special shoutout to @anitaada.bsky.social!
www.biorxiv.org/content/10.1...
We describe a detailed protocol to inhibit the expression of transposable elements in human pluripotent stem cells, developed thanks to @asapresearch.parkinsonsroadmap.org funding.
Special shoutout to @anitaada.bsky.social!
www.biorxiv.org/content/10.1...
Reposted by Manthan
H3NGST: a fully automated, web-based platform for end-to-end ChIP-seq analysis. #ChIPseq #WebTool #Bioinformatics #Genomics #BMCbioinformatics 🧪🧬 🖥️
bmcbioinformatics.biomedcentral.com/articles/10....
bmcbioinformatics.biomedcentral.com/articles/10....
October 27, 2025 at 4:03 PM
H3NGST: a fully automated, web-based platform for end-to-end ChIP-seq analysis. #ChIPseq #WebTool #Bioinformatics #Genomics #BMCbioinformatics 🧪🧬 🖥️
bmcbioinformatics.biomedcentral.com/articles/10....
bmcbioinformatics.biomedcentral.com/articles/10....
Reposted by Manthan
🚀 Excited to share my latest paper on using SHAP, to predict direct target genes of chromatin-associated factors! Check it out for insights into gene regulation and the power of explainable AI in genomics! #XAI #SHAP #Genomics
doi.org/10.1371/jour...
Let's break down what we found! 👇
doi.org/10.1371/jour...
Let's break down what we found! 👇
Modelling transcription with explainable AI uncovers context-specific epigenetic gene regulation at promoters and gene bodies
Author summary Genes are turned on or off through complex processes involving many proteins that interact with DNA wrapped histones and modify their structure. These changes, known as epigenetic modif...
doi.org
October 24, 2025 at 11:37 AM
🚀 Excited to share my latest paper on using SHAP, to predict direct target genes of chromatin-associated factors! Check it out for insights into gene regulation and the power of explainable AI in genomics! #XAI #SHAP #Genomics
doi.org/10.1371/jour...
Let's break down what we found! 👇
doi.org/10.1371/jour...
Let's break down what we found! 👇