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Manu Saraswat

@manusaraswat.bsky.social
261 followers 223 following 41 posts

Postdoc in ML for genomics with Dana Pe'er and Oliver Stegle Previously at Genentech, UBC and BITS Pilani scholar.google.com/citations?user=4…

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Manu Saraswat @manusaraswat.bsky.social · 08/02/2026
Excited to share this work on mapping trans-eQTLs at single-cell resolution! Delighted to have co-conceived this project with lead author @danaivagiaki.bsky.social LIVI enables systematic discovery of genetic effects on gene regulatory networks in population-scale scRNA cohorts. Thread below 🧵👇🏼
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Manu Saraswat @manusaraswat.bsky.social · 10/10/2025
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.
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gokcen.bsky.social @gokcen.bsky.social · 19/09/2025
My team has a postdoc position available now, join us! careers.gene.com/us/en/job/20...
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Manu Saraswat @manusaraswat.bsky.social · 08/09/2025
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
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Manu Saraswat @manusaraswat.bsky.social · 01/08/2025
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
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Peter Koo @pkoo562.bsky.social · 16/07/2025
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
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 ...
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Gherman Novakovsky @gnovakovsky.bsky.social · 30/05/2025
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/)
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Omer Ali Bayraktar @bayraktarlab.bsky.social · 16/05/2025
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 🧵
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Manu Saraswat @manusaraswat.bsky.social · 16/05/2025
🧠 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🧵👇
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Lars Velten @larsplus.bsky.social · 08/05/2025
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... 🧵
cell.com
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...
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Reposted by Manu Saraswat
Niklas Kempynck @niklaskemp.bsky.social · 03/04/2025
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...
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Gavin Sherlock @gsherloc.bsky.social · 15/02/2025
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
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Moritz Mall @moritzmall.bsky.social · 13/02/2025
#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
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Anshul Kundaje @anshulkundaje.bsky.social · 11/02/2025
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.
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Manu Saraswat @manusaraswat.bsky.social · 26/01/2025
Exciting work from @jkpritch.bsky.social lab combining perturbation screens with genetic associations 🚀
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Manu Saraswat @manusaraswat.bsky.social · 12/01/2025
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
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Caleb Lareau @caleblareau.bsky.social · 08/01/2025
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...
nature.com
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...
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Manu Saraswat @manusaraswat.bsky.social · 26/12/2024
Congratulations team @anshulkundaje.bsky.social Can't wait to dive into the details
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Saez-Rodriguez Group @saezlab.bsky.social · 23/12/2024
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
GRETA graphical abstract
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Jeff Spence @jeffspence.github.io · 17/12/2024
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...
biorxiv.org
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...
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Manu Saraswat @manusaraswat.bsky.social · 09/12/2024
We are live now @steglelab.bsky.social
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Manu Saraswat @manusaraswat.bsky.social · 01/12/2024
"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 🤡🤡🤡
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Jacob Schreiber @jmschreiber91.bsky.social · 18/11/2024
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.
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 14/11/2024
Evo: A genomic language model of prokaryote genomes generates functional cas9 proteins and transposons. @brianhiestand.bsky.social www.science.org/doi/10.1126/...
Evo, a 7-billion-parameter genomic foundation model, learns biological complexity from individual nucleotides to whole genomes.
Pretraining a genomic foundation model across prokaryotic life.Fine-tuning on CRISPR-Cas sequences enables generative design of protein-RNA complexes.Fig. 4. Fine-tuning on IS200/IS605 sequences enables generative design of transposable biological systems.
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Manu Saraswat @manusaraswat.bsky.social · 15/11/2024
Hello #genomics #compbio world 🧬 Wasn't expecting this level of activity - great to see the community moving here
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