Shubhra Bhattacharya
@shubhra.bsky.social
PhD candidate studying cohesin in context of MDS, AML.
Scientific interests :Bioinformatics, Statistics,immune-system.
Scientific interests :Bioinformatics, Statistics,immune-system.
Reposted by Shubhra Bhattacharya
We are looking for a senior #bioinformatician.... only 5 days left to apply! careers.carrerasresearch.org/jobs/6552694...
November 10, 2025 at 10:12 PM
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
Congrats to everyone involved
@marcusbuschbeck.bsky.social
@dcorujo.bsky.social
NEW PAPER
Out in Science Advances: We have dissected the physiological role of all macroH2A histone variants. In mice, loss of macroH2A1.1 specifically results in profound metabolic reprogramming and kidney pathology.
DOI: 10.1126/sciadv.adz1242
Thread 1/7
Out in Science Advances: We have dissected the physiological role of all macroH2A histone variants. In mice, loss of macroH2A1.1 specifically results in profound metabolic reprogramming and kidney pathology.
DOI: 10.1126/sciadv.adz1242
Thread 1/7
October 30, 2025 at 5:53 PM
Interesting work led by René! (not on bluesky)
Congrats to everyone involved
@marcusbuschbeck.bsky.social
@dcorujo.bsky.social
Congrats to everyone involved
@marcusbuschbeck.bsky.social
@dcorujo.bsky.social
Reposted by Shubhra Bhattacharya
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....
October 27, 2025 at 11:49 AM
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....
Reposted by Shubhra Bhattacharya
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.
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.
October 20, 2025 at 9:38 AM
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.
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.
Reposted by Shubhra Bhattacharya
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
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
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,...
rdcu.be
October 16, 2025 at 8:17 PM
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
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!
Very proud on our stellar Alina Ritter for her frist first-author paper:
Targeting CXADR-mediated AKT signaling suppresses tumorigenesis and enhances #chemotherapy efficacy in #Ewing #sarcoma
tinyurl.com/3kcs3bc9
@dkfz.bsky.social
@uniheidelberg.bsky.social
@nct-heidelberg.bsky.social
Targeting CXADR-mediated AKT signaling suppresses tumorigenesis and enhances #chemotherapy efficacy in #Ewing #sarcoma
tinyurl.com/3kcs3bc9
@dkfz.bsky.social
@uniheidelberg.bsky.social
@nct-heidelberg.bsky.social
October 11, 2025 at 4:35 PM
Super cool work!
Reposted by Shubhra Bhattacharya
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
🔗 Manuscript: www.biorxiv.org/content/10.1...
💻 Code: partipy.readthedocs.io
September 15, 2025 at 8:40 AM
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
🔗 Manuscript: www.biorxiv.org/content/10.1...
💻 Code: partipy.readthedocs.io
Reposted by Shubhra Bhattacharya
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.
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.
August 27, 2025 at 2:22 PM
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.
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.
Reposted by Shubhra Bhattacharya
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...
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...
August 26, 2025 at 4:18 PM
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...
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...
Reposted by Shubhra Bhattacharya
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/...
🧵
www.science.org/doi/10.1126/...
🧵
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...
www.science.org
August 22, 2025 at 6:03 AM
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/...
🧵
www.science.org/doi/10.1126/...
🧵
Reposted by Shubhra Bhattacharya
#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...
August 21, 2025 at 3:20 PM
#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...
Reposted by Shubhra Bhattacharya
Review: Sex differences in tissue-specific immunity and immunology
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
August 7, 2025 at 7:30 PM
Review: Sex differences in tissue-specific immunity and immunology
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Super cool cover! Especially excited to read more on tissue specific immunity and biological sex here.
This week @science.org examines the wonders of the immune system! From molecular defences that co-evolved with pathogens to specialised cells that are intricately linked with physiology, the immune system is attuned to biological sex and different stages of life.
A new special issue of Science explores the immune system at the molecular and cellular level and how it has evolved to govern multiple facets of human health.
Learn more: scim.ag/3IYhnk7
Learn more: scim.ag/3IYhnk7
August 7, 2025 at 8:07 PM
Super cool cover! Especially excited to read more on tissue specific immunity and biological sex here.
Reposted by Shubhra Bhattacharya
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/...
PSCS: Unified Sharing of Single-Cell Omics Data, Analyses, and Results | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
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 ...
pubs.acs.org
August 2, 2025 at 5:00 PM
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/...
PSCS: Unified Sharing of Single-Cell Omics Data, Analyses, and Results | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
Reposted by Shubhra Bhattacharya
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
July 26, 2025 at 2:14 PM
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
Reposted by Shubhra Bhattacharya
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
Not exactly a structural bio nerd but still excited about implications of this!!
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
June 28, 2025 at 10:12 AM
Not exactly a structural bio nerd but still excited about implications of this!!
Reposted by Shubhra Bhattacharya
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...
🧵
🧬 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...
🧵
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...
doi.org
May 21, 2025 at 3:44 PM
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...
🧵
🧬 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...
🧵
Reposted by Shubhra Bhattacharya
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.
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.
May 8, 2025 at 11:50 AM
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.
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.
Reposted by Shubhra Bhattacharya
🧠 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.
🫵 You, maybe.
We're after a postdoctoral candidate who thinks outside the box & loves data puzzles.
Contact me to apply.
📢Looking for a #postdoc in blood cancers?
The CarrerasLeaders Call 4 is OPEN for exceptional applicants at @carrerasijc.bsky.social.
📅 Apply by June 1, 2025
✨World-class researchers supervision
✨International secondments
✨Top-tier research infrastructures
More details at carrerasleaders.eu
The CarrerasLeaders Call 4 is OPEN for exceptional applicants at @carrerasijc.bsky.social.
📅 Apply by June 1, 2025
✨World-class researchers supervision
✨International secondments
✨Top-tier research infrastructures
More details at carrerasleaders.eu
May 6, 2025 at 1:46 PM
🧠 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.
🫵 You, maybe.
We're after a postdoctoral candidate who thinks outside the box & loves data puzzles.
Contact me to apply.
Reposted by Shubhra Bhattacharya
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...
www.nature.com/articles/s41...
Is the bone marrow microenvironment the hidden catalyst in malignant haematopoiesis? - Leukemia
Leukemia - Is the bone marrow microenvironment the hidden catalyst in malignant haematopoiesis?
www.nature.com
May 1, 2025 at 5:59 AM
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...
www.nature.com/articles/s41...
Reposted by Shubhra Bhattacharya
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...
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...
April 22, 2025 at 2:05 PM
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...
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
I am reading this from @lazappi.bsky.social while reviewing a paper that includes a lot of benchmarks to showcase new software. I’m not sure if I can trust the benchmarks now 🤔
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Feature selection methods affect the performance of scRNA-seq data integration and querying - Nature Methods
This Registered Report presents a benchmarking study evaluating the impact of feature selection on scRNA-seq integration.
www.nature.com
April 16, 2025 at 6:17 PM
Something to think about
Reposted by Shubhra Bhattacharya
🚨 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
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
April 16, 2025 at 2:29 PM
🚨 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
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
Reposted by Shubhra Bhattacharya
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...
www.nature.com/articles/s41...
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...
www.nature.com
April 14, 2025 at 1:33 PM
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...
www.nature.com/articles/s41...