Manu Saraswat
@manusaraswat.bsky.social
Postdoc in ML for genomics with Dana Pe'er and Oliver Stegle
Previously at Genentech, UBC and BITS Pilani
https://scholar.google.com/citations?user=4yUtALcAAAAJ&hl=en&oi=ao
Previously at Genentech, UBC and BITS Pilani
https://scholar.google.com/citations?user=4yUtALcAAAAJ&hl=en&oi=ao
Pinned
Manu Saraswat
@manusaraswat.bsky.social
· May 16
🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇
Excited to be at #ASHG2025 in Boston next week. On Thursday, I will be presenting a poster (1007T) on our latest work on Personalised sequence to expression modelling. Looking forward to meeting new folks and reconnecting with old friends and colleagues.
October 10, 2025 at 2:49 AM
Excited to be at #ASHG2025 in Boston next week. On Thursday, I will be presenting a poster (1007T) on our latest work on Personalised sequence to expression modelling. Looking forward to meeting new folks and reconnecting with old friends and colleagues.
Reposted by Manu Saraswat
September 19, 2025 at 8:12 PM
Excited to be at @aithyra.bsky.social #AIinLifeScience symposium in Vienna. What a gorgeous venue!
Will be presenting posters on my latest work on personalized gene expression prediction and gene regulatory network inference
Will be presenting posters on my latest work on personalized gene expression prediction and gene regulatory network inference
September 8, 2025 at 3:18 PM
Excited to be at @aithyra.bsky.social #AIinLifeScience symposium in Vienna. What a gorgeous venue!
Will be presenting posters on my latest work on personalized gene expression prediction and gene regulatory network inference
Will be presenting posters on my latest work on personalized gene expression prediction and gene regulatory network inference
Dived into past, present & future of human genetics with brilliant students & mentors.Grateful for the chance to present my work on personalized sequence→expression prediction and discussions with @sashagusevposts.bsky.social @bpasaniuc.bsky.social @mashaals.bsky.social @tuuliel.bsky.social & others
Leena Peltonen School of Human Genetics in full-swing!
@gosiatrynka.bsky.social
@dgmacarthur.bsky.social
@bpasaniuc.bsky.social
@tuuliel.bsky.social
@hilarycmartin.bsky.social
@sashagusevposts.bsky.social
@zkutalik.bsky.social
@mashaals.bsky.social
@alemedinarivera.bsky.social
@gosiatrynka.bsky.social
@dgmacarthur.bsky.social
@bpasaniuc.bsky.social
@tuuliel.bsky.social
@hilarycmartin.bsky.social
@sashagusevposts.bsky.social
@zkutalik.bsky.social
@mashaals.bsky.social
@alemedinarivera.bsky.social
August 1, 2025 at 6:07 PM
Dived into past, present & future of human genetics with brilliant students & mentors.Grateful for the chance to present my work on personalized sequence→expression prediction and discussions with @sashagusevposts.bsky.social @bpasaniuc.bsky.social @mashaals.bsky.social @tuuliel.bsky.social & others
Reposted by Manu Saraswat
Our work on "Evaluating the representational power of pre-trained DNA language models for regulatory genomics" led by @AmberZqt with help from @NiraliSomia & @stevenyuyy is finally published in Genome Biology! Check it out!
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
Evaluating the representational power of pre-trained DNA language models for regulatory genomics - Genome Biology
Background The emergence of genomic language models (gLMs) offers an unsupervised approach to learning a wide diversity of cis-regulatory patterns in the non-coding genome without requiring labels of ...
genomebiology.biomedcentral.com
July 16, 2025 at 12:12 PM
Our work on "Evaluating the representational power of pre-trained DNA language models for regulatory genomics" led by @AmberZqt with help from @NiraliSomia & @stevenyuyy is finally published in Genome Biology! Check it out!
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
Reposted by Manu Saraswat
Excited to share my first contribution here at Illumina! We developed PromoterAI, a deep neural network that accurately identifies non-coding promoter variants that disrupt gene expression.🧵 (1/)
May 29, 2025 at 11:57 PM
Excited to share my first contribution here at Illumina! We developed PromoterAI, a deep neural network that accurately identifies non-coding promoter variants that disrupt gene expression.🧵 (1/)
Reposted by Manu Saraswat
How does tumour heterogeneity arise? How can we predict cancer cell plasticity? In 2 new studies, we trace #glioblastoma heterogeneity to a spatial cancer cell trajectory w. multimodal cell atlassing bit.ly/4mkrWgs & predict plasticity w. snRNA/ATAC+deep learning bit.ly/3FbI6Ic 🧵
May 16, 2025 at 11:44 AM
How does tumour heterogeneity arise? How can we predict cancer cell plasticity? In 2 new studies, we trace #glioblastoma heterogeneity to a spatial cancer cell trajectory w. multimodal cell atlassing bit.ly/4mkrWgs & predict plasticity w. snRNA/ATAC+deep learning bit.ly/3FbI6Ic 🧵
🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇
May 16, 2025 at 10:05 AM
🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇
Reposted by Manu Saraswat
Out in Cell @cp-cell.bsky.social: Design principles of cell-state-specific enhancers in hematopoiesis
🧬🩸 screen of fully synthetic enhancers in blood progenitors
🤖 AI that creates new cell state specific enhancers
🔍 negative synergies between TFs lead to specificity!
www.cell.com/cell/fulltex...
🧵
🧬🩸 screen of fully synthetic enhancers in blood progenitors
🤖 AI that creates new cell state specific enhancers
🔍 negative synergies between TFs lead to specificity!
www.cell.com/cell/fulltex...
🧵
Design principles of cell-state-specific enhancers in hematopoiesis
Screen of minimalistic enhancers in blood progenitor cells demonstrates widespread
dual activator-repressor function of transcription factors (TFs) and enables the model-guided
design of cell-state-sp...
www.cell.com
May 8, 2025 at 4:07 PM
Out in Cell @cp-cell.bsky.social: Design principles of cell-state-specific enhancers in hematopoiesis
🧬🩸 screen of fully synthetic enhancers in blood progenitors
🤖 AI that creates new cell state specific enhancers
🔍 negative synergies between TFs lead to specificity!
www.cell.com/cell/fulltex...
🧵
🧬🩸 screen of fully synthetic enhancers in blood progenitors
🤖 AI that creates new cell state specific enhancers
🔍 negative synergies between TFs lead to specificity!
www.cell.com/cell/fulltex...
🧵
Reposted by Manu Saraswat
We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...
April 3, 2025 at 2:30 PM
We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...
Reposted by Manu Saraswat
On January 6th, 1995, my (now ex) wife and I boarded a flight from Heathrow to JFK on a one way ticket. We had two suitcases and about $900 in cash - this was everything we owned and we were moving to the US. We thought it was maybe for 2-3 years. I had visited the US once, for a conference, and
February 15, 2025 at 5:48 AM
On January 6th, 1995, my (now ex) wife and I boarded a flight from Heathrow to JFK on a one way ticket. We had two suitcases and about $900 in cash - this was everything we owned and we were moving to the US. We thought it was maybe for 2-3 years. I had visited the US once, for a conference, and
Reposted by Manu Saraswat
#CellPlasticity—the ability of cells to change their identity—is vital for tissue growth and repair. But when it goes unchecked, it can fuel #cancer. Our latest study examines how to block #LiverCancer by actively suppressing plasticity. www.nature.com/articles/s41... #CancerBiology
February 13, 2025 at 12:16 PM
#CellPlasticity—the ability of cells to change their identity—is vital for tissue growth and repair. But when it goes unchecked, it can fuel #cancer. Our latest study examines how to block #LiverCancer by actively suppressing plasticity. www.nature.com/articles/s41... #CancerBiology
Reposted by Manu Saraswat
Given that science funding is under attack, it might be as good a time as any to reflect on how we spend our precious dollars. Cutting out expenditure publishing papers in overpriced journals might be a good thing to seriously consider once again.
February 11, 2025 at 6:06 PM
Given that science funding is under attack, it might be as good a time as any to reflect on how we spend our precious dollars. Cutting out expenditure publishing papers in overpriced journals might be a good thing to seriously consider once again.
Exciting work from @jkpritch.bsky.social lab combining perturbation screens with genetic associations 🚀
Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
January 26, 2025 at 4:16 PM
Exciting work from @jkpritch.bsky.social lab combining perturbation screens with genetic associations 🚀
Huge shoutout to @avantikalal.bsky.social (Grelu) and @jmschreiber91.bsky.social (tangermeme) for making sequence model training, evaluation, interpretation and de-novo design so seamless. Finally getting rid of my own clunky scripts i have been using for years for each of these tasks separately
January 12, 2025 at 7:50 AM
Huge shoutout to @avantikalal.bsky.social (Grelu) and @jmschreiber91.bsky.social (tangermeme) for making sequence model training, evaluation, interpretation and de-novo design so seamless. Finally getting rid of my own clunky scripts i have been using for years for each of these tasks separately
Reposted by Manu Saraswat
Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing - Nature Genetics
Programmable Enrichment via RNA FlowFISH by sequencing (PERFF-seq) isolates rare cells based on RNA marker transcripts for single-cell RNA sequencing profiling of complex tissues, with applicability t...
www.nature.com
January 8, 2025 at 1:30 PM
Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Congratulations team @anshulkundaje.bsky.social
Can't wait to dive into the details
Can't wait to dive into the details
Our ChromBPNet preprint out!
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
December 26, 2024 at 10:34 AM
Congratulations team @anshulkundaje.bsky.social
Can't wait to dive into the details
Can't wait to dive into the details
Reposted by Manu Saraswat
We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
December 23, 2024 at 8:43 AM
We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
Reposted by Manu Saraswat
What do GWAS and rare variant burden tests discover, and why?
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies
Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes. Although these methods are conceptually similar, we show by anal...
www.biorxiv.org
December 17, 2024 at 7:05 AM
What do GWAS and rare variant burden tests discover, and why?
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?
Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)
www.biorxiv.org/content/10.1...
We are live now
@steglelab.bsky.social
@steglelab.bsky.social
We are the Stegle Lab: A bioinformatics group advancing computational methods to study molecular variations and their impact on phenotypes. We are jointly hosted at the German Cancer Research Center (@dkfz.bsky.social) and the European Molecular Biology Laboratory (@embl.org) in Heidelberg, Germany.
December 9, 2024 at 4:58 PM
We are live now
@steglelab.bsky.social
@steglelab.bsky.social
"Postdocs receive an annual salary increase following successful completion of their annual review"
The increase -
• 0 years of experience = $66,300
• 1 year = $66,810
• 2 years = $67,320
🤡🤡🤡
The increase -
• 0 years of experience = $66,300
• 1 year = $66,810
• 2 years = $67,320
🤡🤡🤡
December 1, 2024 at 7:49 AM
"Postdocs receive an annual salary increase following successful completion of their annual review"
The increase -
• 0 years of experience = $66,300
• 1 year = $66,810
• 2 years = $67,320
🤡🤡🤡
The increase -
• 0 years of experience = $66,300
• 1 year = $66,810
• 2 years = $67,320
🤡🤡🤡
Reposted by Manu Saraswat
My goal is to understand the regulatory role of every nucleotide in the genome, and how this changes across every cell in the human body.
If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
November 18, 2024 at 6:22 PM
My goal is to understand the regulatory role of every nucleotide in the genome, and how this changes across every cell in the human body.
If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
Reposted by Manu Saraswat
Evo: A genomic language model of prokaryote genomes generates functional cas9 proteins and transposons.
@brianhiestand.bsky.social
www.science.org/doi/10.1126/...
@brianhiestand.bsky.social
www.science.org/doi/10.1126/...
November 14, 2024 at 8:53 PM
Evo: A genomic language model of prokaryote genomes generates functional cas9 proteins and transposons.
@brianhiestand.bsky.social
www.science.org/doi/10.1126/...
@brianhiestand.bsky.social
www.science.org/doi/10.1126/...