Shubhra Bhattacharya

Single-cell multiomics analysis reveals CTCF as a key regulator of lung morphogenesis and progenitor maintenance | Nature Communications Lung development generates a complex tree-like architecture through proximal-distal patterning and branching morphogenesis. However, the gene regulatory programs governing embryonic lung development remain poorly understood. Here, we present a comprehensive single-cell multi-omics atlas of mouse embryonic lungs, integrating gene expression and chromatin accessibility profiles. Through systematic analysis, we identify 13 distinct cell types and map cis-regulatory elements, peak-to-gene linkages, and transcription factors underlying lung development. Leveraging this multi-modal dataset, we uncover lineage-determining transcription factors driving cell differentiation, including the Activated Protein-1 complex. We further delineate gene regulatory networks involving diverse transcription regulators, including CCCTC-binding factor (CTCF). Using the Ctcf conditional knockout mouse, coupled with histological and multi-omics analyses, we demonstrate that CTCF orchestrates lung progenitor main

Explore 13 cell types in mouse embryo lungs through single-cell multiomics! CTCF emerges as crucial in lung morphogenesis & progenitor maintenance! PMID:41315351, Nat Commun 2025, @NatureComms https://doi.org/10.1038/s41467-025-65757-1 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪

H4K16 acylations destabilize chromatin architecture and facilitate transcriptional response during metabolic perturbations Histone modifications play crucial roles in genome function. However, how chromatin integrates physiological and metabolic responses at the molecular …

Excited to share new manuscript on histone acylations, exploring how H4K16 acylations regulate inter and intranucleosomal interactions and how they confer resilience to metabolic challenges in vivo. Thanks to all authors +1 author @sandrani.bsky.social Enjoy 👇👇
www.sciencedirect.com/science/arti...

We are looking for a senior #bioinformatician.... only 5 days left to apply! careers.carrerasresearch.org/jobs/6552694...

Interesting work led by René! (not on bluesky)
Congrats to everyone involved
@marcusbuschbeck.bsky.social
@dcorujo.bsky.social

Happy to share our latest publication, in which we show that the arrangement of nucleosomes around CTCF sites contributes to higher-order organisation of chromatin into TADs: www.embopress.org/doi/full/10....

MEET THE LAB!

This week our postdoc René Winkler will attend the @febspress.bsky.social workshop 'Molecular and cellular pathways of aging in hematopoiesis' on Crete, Greece.

René will present work led by @shubhra.bsky.social on how cohesin mutations impact MDS progression.

Characterization of induced cohesin loop extrusion trajectories in living cells Nature Genetics - This study introduces a system called TArgeted Cohesin Loader (TACL) that recruits cohesin complexes at defined genomic regions and induces loop extrusion events in living cells,...

The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project!

If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!

rdcu.be/eLiT5

Super cool work!

Introducing ParTIpy, a python package for Pareto Task Inference that scales to large-scale datasets, including single-cell and spatial transcriptomics.
🔗 Manuscript: www.biorxiv.org/content/10.1...
💻 Code: partipy.readthedocs.io

NEW LAB MEMBER!

We welcome ‪@florherbstein.bsky.social who is joining us as a‬ ‪@carrerasleaders.bsky.social‬ Postdoctoral Fellow. She is alumni of #IBioBA-MPSP and the University of Buenos Aires.‬‬
She will study how nuclear metabolism influences proliferation and therapy resistance in AML.

Congratulations to Masahiro Nagano on his new paper on STAG3-cohesin.

STAG3-cohesin has a much shorter residence time which leads to altered 3D genome organization and STAG3-cohesin is important for male germ cell differentiation.
www.nature.com/articles/s41...

Mapping early human blood cell differentiation using single-cell proteomics and transcriptomics Single-cell transcriptomics (scRNA-seq) has facilitated the characterization of cell state heterogeneity and recapitulation of differentiation trajectories. However, the exclusive use of mRNA measurem...

We’re excited to present this integrative analysis of single-cell proteomics and transcriptomics of the human HSPC hierarchy. Now published in @science.org together with @fabiantheis.bsky.social, @erwinschoof.bsky.social, @porsebo.bsky.social.
www.science.org/doi/10.1126/...
🧵

#InterferonPower! Thrilled for our latest work @cp-cell.bsky.social! With @danielboehmer.bsky.social, we dug into tons of papers & created what we hope will be a go-to resource for immunologists & non-immunologist about type I, II, III (& IV😉) #interferons! Free👉 authors.elsevier.com/a/1leKGL7PXu...

Review: Sex differences in tissue-specific immunity and immunology
www.science.org/doi/10.1126/...

Super cool cover! Especially excited to read more on tissue specific immunity and biological sex here.

PSCS: Unified Sharing of Single-Cell Omics Data, Analyses, and Results Single-cell omics data analyses are complicated to design and difficult to distribute or reproduce. We present a web platform that enables no-code analysis pipeline design, computing, and the sharing ...

If you are doing single cell data analysis please check out our new manuscript in JPR:

PSCS: Unified Sharing of Single-Cell Omics Data, Analyses, and Results | Journal of Proteome Research pubs.acs.org/doi/10.1021/...

Cell cycle duration determines oncogenic transformation capacity Danian Chen, Suying Lu, Katherine Huang, Joel D. Pearson, Marek Pacal, Phillipos Peidis, Sean McCurdy, Tao Yu, Monika Sangwan, Angela Nguyen, Philippe P. Monnier, Daniel Schramek, Liang Zhu, David Santamaria, Mariano Barbacid, Nagako Akeno, Kathryn A. Wikenheiser-Brokamp & Rod Bremner https://www.nature.com/articles/s41586-025-08935-x

A recent paper reveals a surprising insight. The length of the cell cycle in a particular tissue determines the oncogenic transformation capacity of particular oncogenes, with tissues with shorter cell cycles most susceptible 3/n

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

Not exactly a structural bio nerd but still excited about implications of this!!

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...

Out @nature.com: Clonal tracing with somatic epimutations

🧬 Single cell methylome encodes cell state & clonal identity

🔨 EPI-Clone reads out both (+mutations, +RNA) at scale

🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations

doi.org/10.1038/s415...
🧵

MEET THE TEAM!

Today half of the lab is at the @scb.iec.cat attending the 15th Chromatin and Epigenetics Day. Kudos to Albert Jordan for organizing.

This is a fixed event in the lab's calender. In the pic below Ollie is presenting his results.

🧠 What do image-based transcriptomics and blood cancer research have in common?
🫵 You, maybe.
We're after a postdoctoral candidate who thinks outside the box & loves data puzzles.

Contact me to apply.

Is the bone marrow microenvironment the hidden catalyst in malignant haematopoiesis? - Leukemia Leukemia - Is the bone marrow microenvironment the hidden catalyst in malignant haematopoiesis?

Excited to share our perspective just out in @leukemia journal! What is bone marrow niche doing in shaping clonal dynamics in MDS and Leukemias.

www.nature.com/articles/s41...

We're pleased to announce that Dr Ari Melnick has been appointed new Director of the Josep Carreras Institute.

Dr Melnick will lead IJC in our mission to advance #research in #leukaemia and other malignant blood diseases.

Read the full release here: www.carrerasresearch.org/en/news/dr-a...

Something to think about

🚨 Postdoc position open!
Join our organoid engineering team in Heidelberg to advance disease modeling & drug testing in cancer & brain disorders using AI, single-cell tech & assembloids.
🧠 5 yrs funding (CZS)
🌐 Apply: bit.ly/heidelberg-o...
#Postdoc #Organoids #Neuroscience

Mutant CEBPA promotes tolerance to inflammatory stress through deficient AP-1 activation - Nature Communications CEBPA is frequently mutated in acute myeloid leukemia (AML), but the transcriptional impact of the AML-associated isoform remains unclear. Here, the authors show that CEBPA-mutant cells have reduced i...

Extremely happy to share that the first paper from our lab is now published! Driven by the very talented PhD student Maria Cadefau, we studied how CEBPA mutations shape transcriptional programs in AML. A thread 🧵👇

www.nature.com/articles/s41...

Amazing work! Congrats to the lab, cant wait to read it in depth!

Sven Furberg Seminars in Bioinformatics and Statistical Genomics - Bioinformatics in Life Science – BiLS We are pleased to introduce the Sven Furberg Seminars in Bioinformatics and Statistical Genomics, an arena for learning, exchanging ideas, promoting scientific excellence, and triggering collaboration...

Excited to announce the upcoming Furberg seminars in Oslo @ncmbm.bsky.social.

- Damir Baranasic @da-bar.bsky.social Apr 23rd
- Wyeth Wasserman @wywywa.bsky.social on May 22nd
- Jacob Schreiber @jmschreiber91.bsky.social on June 17th

Great line-up of exciting science!

www.mn.uio.no/bils/english...

Interesting!