Indra
@indrasingh.bsky.social
Aging | Leukemia | HSCs heterogeneity | lineage tracing | Chromatin
Reposted by Indra
Nature research paper: Basal cell of origin resolves neuroendocrine–tuft lineage plasticity in cancer
go.nature.com/3ViRTAP
go.nature.com/3ViRTAP
Basal cell of origin resolves neuroendocrine–tuft lineage plasticity in cancer - Nature
Basal cells, rather than neuroendocrine cells, have been identified as the probable origin of small cell lung cancer and other neuroendocrine–tuft cancers, explaining neuroendocrine–tuft heterogeneity and offering new perspectives for targeting lineage plasticity.
go.nature.com
September 24, 2025 at 12:48 PM
Nature research paper: Basal cell of origin resolves neuroendocrine–tuft lineage plasticity in cancer
go.nature.com/3ViRTAP
go.nature.com/3ViRTAP
Reposted by Indra
Now online in Cancer Discovery @aacrjournals.bsky.social: Development and Prospective Validation of a Cell-free DNA-based Model for the Early Detection of Pancreatic Cancer - by Xiuchao Wang, Hongwei Wang, Meng Zhang, Jun Yu, Chuntao Gao, Yunfeng Cui, Jihui Hao, et al. doi.org/10.1158/2159...
September 24, 2025 at 1:43 PM
Now online in Cancer Discovery @aacrjournals.bsky.social: Development and Prospective Validation of a Cell-free DNA-based Model for the Early Detection of Pancreatic Cancer - by Xiuchao Wang, Hongwei Wang, Meng Zhang, Jun Yu, Chuntao Gao, Yunfeng Cui, Jihui Hao, et al. doi.org/10.1158/2159...
Reposted by Indra
🚨 New preprints from our lab!
First, we introduce Cryo-mtscATAC-seq, led by Maren (@ms-maren.bsky.social ), enabling high-throughput clonal tracing from frozen human samples by isolating nuclei with their mitochondria (“CryoCells”).
👉 www.biorxiv.org/content/10.1...
Cryo-mtscATAC-seq for single-cell mitochondrial DNA genotyping and clonal tracing in archived human tissues
High-throughput clonal tracing of primary human samples relies on naturally occurring barcodes, such as somatic mitochondrial DNA (mtDNA) mutations detected via single-cell ATAC-seq (mtscATAC-seq). Fr...
www.biorxiv.org
September 24, 2025 at 12:39 PM
🚨 New preprints from our lab!
First, we introduce Cryo-mtscATAC-seq, led by Maren (@ms-maren.bsky.social ), enabling high-throughput clonal tracing from frozen human samples by isolating nuclei with their mitochondria (“CryoCells”).
👉 www.biorxiv.org/content/10.1...
Reposted by Indra
EPI-Clone is a transgene-free lineage tracing method that uses single-cell DNA methylation analysis to track hematopoietic stem cell clones over time #NBThighlight www.nature.com/articles/s41...
Clonal tracing with somatic epimutations reveals dynamics of blood ageing - Nature
The discovery that DNA methylation of different CpG sites can serve as digital barcodes of clonal identity led to the development of EPI-Clone, an algorithm that enables single-cell lineage tracing th...
www.nature.com
May 23, 2025 at 8:05 PM
EPI-Clone is a transgene-free lineage tracing method that uses single-cell DNA methylation analysis to track hematopoietic stem cell clones over time #NBThighlight www.nature.com/articles/s41...
Reposted by Indra
CRISPRai simultaneously activates and represses two genes in single cells go.nature.com/4apFU9q
rdcu.be/efe0E
rdcu.be/efe0E
Bidirectional epigenetic editing reveals hierarchies in gene regulation - Nature Biotechnology
CRISPRai simultaneously activates and represses two genes in single cells.
go.nature.com
April 2, 2025 at 2:06 AM
CRISPRai simultaneously activates and represses two genes in single cells go.nature.com/4apFU9q
rdcu.be/efe0E
rdcu.be/efe0E
Reposted by Indra
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 🧵👇
Reposted by Indra
Information storage across a microbial community using universal RNA barcoding - @lauren-stadler.bsky.social @joffsilberg.bsky.social go.nature.com/440gL5E
Information storage across a microbial community using universal RNA barcoding - Nature Biotechnology
Barcoding microbial ribosomal RNA creates a recording of gene transfer events without requiring translation.
go.nature.com
March 18, 2025 at 6:37 PM
Information storage across a microbial community using universal RNA barcoding - @lauren-stadler.bsky.social @joffsilberg.bsky.social go.nature.com/440gL5E
Reposted by Indra
New paper out in @bloodjournal.bsky.social. In this study lead by Daria Karpova and Hector Encabo, we investigated the effect of frequent blood donations (FD) on clonal hematopoiesis (CH). Briefly, FD selects for DNMT3A mutations rendering HSC sensitive to stimulation by EPO. doi.org/10.1182/bloo...
Clonal Hematopoiesis Landscape in Frequent Blood Donors
Key Points. CH Analysis of a unique and uniform cohort of exclusively healthy individuals exposed to a novel type of selection pressureIdentification of no
doi.org
March 12, 2025 at 8:03 AM
New paper out in @bloodjournal.bsky.social. In this study lead by Daria Karpova and Hector Encabo, we investigated the effect of frequent blood donations (FD) on clonal hematopoiesis (CH). Briefly, FD selects for DNMT3A mutations rendering HSC sensitive to stimulation by EPO. doi.org/10.1182/bloo...
Reposted by Indra
🚀 Join the #ISCO2025 community at @mdc-berlin.bsky.social on May 12-13! 🚀
Don't miss this incredible opportunity to connect with top #singlecell & #spatial omics experts and participate in a special Workshop led by @itaiyanai.bsky.social.
⏳Abstract submissions: March 21)
www.isco-conference.eu
Don't miss this incredible opportunity to connect with top #singlecell & #spatial omics experts and participate in a special Workshop led by @itaiyanai.bsky.social.
⏳Abstract submissions: March 21)
www.isco-conference.eu
ISCO - ISCO
www.isco-conference.eu
March 12, 2025 at 3:36 PM
🚀 Join the #ISCO2025 community at @mdc-berlin.bsky.social on May 12-13! 🚀
Don't miss this incredible opportunity to connect with top #singlecell & #spatial omics experts and participate in a special Workshop led by @itaiyanai.bsky.social.
⏳Abstract submissions: March 21)
www.isco-conference.eu
Don't miss this incredible opportunity to connect with top #singlecell & #spatial omics experts and participate in a special Workshop led by @itaiyanai.bsky.social.
⏳Abstract submissions: March 21)
www.isco-conference.eu
Reposted by Indra
New spatial method, Perturb-FISH, combines imaging-based spatial transcriptomic measurements with CRISPR screening to reveal effects within and between cells. #Science
New technology puts a spatial lens on CRISPR screening
Perturb-FISH reveals impacts of perturbations on gene expression and phenotype with single-cell, spatial resolution, allowing study of effects within and between cells.
broad.io
March 12, 2025 at 5:10 PM
New spatial method, Perturb-FISH, combines imaging-based spatial transcriptomic measurements with CRISPR screening to reveal effects within and between cells. #Science
Reposted by Indra
Want to track clonality in organoids, cancer models, or in vivo transplants? Try our STRACK barcoding libraries from Addgene: www.addgene.org/233208/ www.addgene.org/233210/ www.addgene.org/233209/. If you need help establishing it, reach out—happy to collaborate and troubleshoot
Addgene: pLARRYv2-EGFP
Plasmid pLARRYv2-EGFP from Dr. Alejo Rodriguez-Fraticelli's lab is published in Cell Stem Cell. 2025 Apr. doi: 10.1016/j.stem.2025.01.012 This plasmid is available through Addgene.
www.addgene.org
February 27, 2025 at 1:48 AM
Want to track clonality in organoids, cancer models, or in vivo transplants? Try our STRACK barcoding libraries from Addgene: www.addgene.org/233208/ www.addgene.org/233210/ www.addgene.org/233209/. If you need help establishing it, reach out—happy to collaborate and troubleshoot
Beyond excited to say my first PhD paper is out today in @CellStemCell 📷. Here, we explored the role of epigenetic heterogeneity on malignant expansion, using a new approach called STRACK
www.cell.com/cell-stem-ce...
www.cell.com/cell-stem-ce...
Pre-existing stem cell heterogeneity dictates clonal responses to the acquisition of leukemic driver mutations
Singh, Fernandez-Perez, et al. use hematopoietic stem cell barcoding to study clones
with and without activation of cancer driver mutations, identifying that pre-existing
stem cell states can dictate ...
www.cell.com
February 27, 2025 at 1:48 AM
Beyond excited to say my first PhD paper is out today in @CellStemCell 📷. Here, we explored the role of epigenetic heterogeneity on malignant expansion, using a new approach called STRACK
www.cell.com/cell-stem-ce...
www.cell.com/cell-stem-ce...
Reposted by Indra
🧪New technique reveals how the same mutations give rise to very different types of #leukaemia.
📰 Cell Stem Cell, supported by #CRISContraelCáncer.
✍️ Indranil Singh, Daniel Fernández-Pérez, Pedro Sánchez Sánchez, @alejofraticelli.bsky.social.
➡️ bit.ly/3QyrAnJ
📌 doi.org/10.1016/j.st...
📰 Cell Stem Cell, supported by #CRISContraelCáncer.
✍️ Indranil Singh, Daniel Fernández-Pérez, Pedro Sánchez Sánchez, @alejofraticelli.bsky.social.
➡️ bit.ly/3QyrAnJ
📌 doi.org/10.1016/j.st...
February 25, 2025 at 4:08 PM
🧪New technique reveals how the same mutations give rise to very different types of #leukaemia.
📰 Cell Stem Cell, supported by #CRISContraelCáncer.
✍️ Indranil Singh, Daniel Fernández-Pérez, Pedro Sánchez Sánchez, @alejofraticelli.bsky.social.
➡️ bit.ly/3QyrAnJ
📌 doi.org/10.1016/j.st...
📰 Cell Stem Cell, supported by #CRISContraelCáncer.
✍️ Indranil Singh, Daniel Fernández-Pérez, Pedro Sánchez Sánchez, @alejofraticelli.bsky.social.
➡️ bit.ly/3QyrAnJ
📌 doi.org/10.1016/j.st...
Reposted by Indra
Here is a growing list of conferences and schools in gene regulation for 2025 generegulation.org/conferences-.... You can order/filter this list by the date, deadline, location. Please reply here to suggest new events*
*should be specific to gene regulation
*should be specific to gene regulation
Conferences & Schools – 2025 – Gene Regulation – Teif Lab
generegulation.org
January 14, 2025 at 7:14 PM
Here is a growing list of conferences and schools in gene regulation for 2025 generegulation.org/conferences-.... You can order/filter this list by the date, deadline, location. Please reply here to suggest new events*
*should be specific to gene regulation
*should be specific to gene regulation
Reposted by Indra
Epidemiological studies have linked dirty air to dementia and other brain disorders. Nature reports on how researchers are trying to determine how pollutants do their damage, and how much harm they cause. 🧪
Air pollution and brain damage: what the science says
Epidemiological studies have linked dirty air to dementia and other brain disorders. Now researchers are trying to determine how pollutants do their damage, and how much harm they cause.
go.nature.com
January 18, 2025 at 10:37 PM
Epidemiological studies have linked dirty air to dementia and other brain disorders. Nature reports on how researchers are trying to determine how pollutants do their damage, and how much harm they cause. 🧪
Reposted by Indra
Very interesting work - @alejofraticelli.bsky.social @shalinhnaik.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
High-resolution, noninvasive single-cell lineage tracing in mice and humans based on DNA methylation epimutations - Nature Methods
This work presents a computational tool MethylTree to infer cell lineages based on epimutations on DNA methylation.
www.nature.com
January 16, 2025 at 2:05 PM
Very interesting work - @alejofraticelli.bsky.social @shalinhnaik.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Indra
Excited to share James Jusuf's preprint:
By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%)
We quantify mESC 36k loops: are generally rare (2.3%)
www.biorxiv.org/content/10.1...
By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%)
We quantify mESC 36k loops:
www.biorxiv.org/content/10.1...
January 16, 2025 at 1:35 PM
Excited to share James Jusuf's preprint:
By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%)
We quantify mESC 36k loops: are generally rare (2.3%)
www.biorxiv.org/content/10.1...
By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%)
We quantify mESC 36k loops:
www.biorxiv.org/content/10.1...
Reposted by Indra
Sometimes, the exciting papers with more surprising findings have a harder time in the current scientific community. This is such an example. I think how cells remember past exposures and how this impacts their future fates is still poorly understood.
Hidden among our immune system's seeds, scientists found special ones that could revolutionize cancer treatments and vaccines.
@deekshadeep @danapeer.bsky.social @jexpmed.bsky.social
t.co/k5lwZHxzxi
#ImmunoSky 🧪
@deekshadeep @danapeer.bsky.social @jexpmed.bsky.social
t.co/k5lwZHxzxi
#ImmunoSky 🧪
December 31, 2024 at 4:17 PM
Sometimes, the exciting papers with more surprising findings have a harder time in the current scientific community. This is such an example. I think how cells remember past exposures and how this impacts their future fates is still poorly understood.
Reposted by Indra
Chromatin-based memory as a self-stabilizing influence on cell identity | Genome Biology
#Chromatin #CellFate #Review
genomebiology.biomedcentral.com/articles/10....
#Chromatin #CellFate #Review
genomebiology.biomedcentral.com/articles/10....
Chromatin-based memory as a self-stabilizing influence on cell identity - Genome Biology
Cell types are traditionally thought to be specified and stabilized by gene regulatory networks. Here, we explore how chromatin memory contributes to the specification and stabilization of cell states...
genomebiology.biomedcentral.com
December 31, 2024 at 7:08 AM
Chromatin-based memory as a self-stabilizing influence on cell identity | Genome Biology
#Chromatin #CellFate #Review
genomebiology.biomedcentral.com/articles/10....
#Chromatin #CellFate #Review
genomebiology.biomedcentral.com/articles/10....
Reposted by Indra
Happy to share the latest work from Preeti Sahu, with Adriana Sanchez-Danes on the biomechanics of cell fate choices during tumor initiation! We implement/test a 3D vertex model with proliferation and fate choices for multilayered tissues! See 🧵 below (1/n) bit.ly/3ZXxJzk
December 17, 2024 at 2:11 PM
Happy to share the latest work from Preeti Sahu, with Adriana Sanchez-Danes on the biomechanics of cell fate choices during tumor initiation! We implement/test a 3D vertex model with proliferation and fate choices for multilayered tissues! See 🧵 below (1/n) bit.ly/3ZXxJzk
Reposted by Indra
The big 4 of grant writing:
1. Credibility: The topic fits your expertise
2. Narrative: It's clear what is the problem, the solution, and why you’re the right person for it
3. Juicy details: Flex your mastery of the topic
4. The concept: You connect every part to the big question
1. Credibility: The topic fits your expertise
2. Narrative: It's clear what is the problem, the solution, and why you’re the right person for it
3. Juicy details: Flex your mastery of the topic
4. The concept: You connect every part to the big question
December 29, 2024 at 4:01 AM
The big 4 of grant writing:
1. Credibility: The topic fits your expertise
2. Narrative: It's clear what is the problem, the solution, and why you’re the right person for it
3. Juicy details: Flex your mastery of the topic
4. The concept: You connect every part to the big question
1. Credibility: The topic fits your expertise
2. Narrative: It's clear what is the problem, the solution, and why you’re the right person for it
3. Juicy details: Flex your mastery of the topic
4. The concept: You connect every part to the big question
Reposted by Indra
Extremely cool system for in vitro culture!
Synthetic organizer cells, engineered to spatially self-assemble around stem cells, can be used to create specific
morphogen gradients and systematically guide in vitro development
Congrats to everyone involved!
www.cell.com/cell/abstrac...
Synthetic organizer cells, engineered to spatially self-assemble around stem cells, can be used to create specific
morphogen gradients and systematically guide in vitro development
Congrats to everyone involved!
www.cell.com/cell/abstrac...
Synthetic organizer cells guide development via spatial and biochemical instructions
Synthetic organizer cells, engineered to spatially self-assemble around stem cells, can be used to create specific morphogen gradients and systematically guide in vitro development.
www.cell.com
December 19, 2024 at 8:01 PM
Extremely cool system for in vitro culture!
Synthetic organizer cells, engineered to spatially self-assemble around stem cells, can be used to create specific
morphogen gradients and systematically guide in vitro development
Congrats to everyone involved!
www.cell.com/cell/abstrac...
Synthetic organizer cells, engineered to spatially self-assemble around stem cells, can be used to create specific
morphogen gradients and systematically guide in vitro development
Congrats to everyone involved!
www.cell.com/cell/abstrac...
Reposted by Indra
Reposted by Indra
This is a really amazing study!
rRNA fingerprinting by Nanopore sequencing reveals cell type biosignatures. 🧪 #RNASky www.cell.com/molecular-ce...
Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures
Milenkovic et al. demonstrate that rRNA modifications are differentially modified across tissues, developmental stages, and in disease. The authors show that rRNA modification patterns, also termed “epitranscriptomic rRNA fingerprints,” are sufficient to accurately identify tissue of origin and tumorigenicity, from as few as 250 reads.
www.cell.com
December 12, 2024 at 1:52 AM
This is a really amazing study!
Reposted by Indra
www.biorxiv.org/content/10.1...
Our study published today on #bioRxiv describe the identification of a deaminase that converts 5mC to T, enabling direct sequencing of the human methylome and genome. This achievement was made possible through a collaborative effort across all departments at #NEB.
Our study published today on #bioRxiv describe the identification of a deaminase that converts 5mC to T, enabling direct sequencing of the human methylome and genome. This achievement was made possible through a collaborative effort across all departments at #NEB.
December 9, 2024 at 2:12 PM
www.biorxiv.org/content/10.1...
Our study published today on #bioRxiv describe the identification of a deaminase that converts 5mC to T, enabling direct sequencing of the human methylome and genome. This achievement was made possible through a collaborative effort across all departments at #NEB.
Our study published today on #bioRxiv describe the identification of a deaminase that converts 5mC to T, enabling direct sequencing of the human methylome and genome. This achievement was made possible through a collaborative effort across all departments at #NEB.