Sushmita Roy
@sroyyors.bsky.social
Regulatory genomics, machine learning, networks, systems biology, evolution
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Sushmita Roy
@sroyyors.bsky.social
· Apr 28
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An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
So happy to see this published now! We present TGIF, Tree-Guided Integrated Factorization, based on multi-task NMF to examine dynamics of the 3D genome organization.
genome.cshlp.org/cgi/content/... with rockstar student, now Dr. Erika Da-Inn Lee.
genome.cshlp.org/cgi/content/... with rockstar student, now Dr. Erika Da-Inn Lee.
Reposted by Sushmita Roy
Our new paper is out now in Nature Communications! We uncovered the function of XBP1 in beta cells of a preclinical model of T1D and identified unique and shared gene regulatory networks driven by IRE1 and XBP1.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Defining the role of β-cell IRE1α/XBP1 pathway and its gene regulatory network components in non-obese diabetic mice - Nature Communications
Modulating the unfolded protein response (UPR) can induce protective dedifferentiation of β-cells in non-obese diabetic mice. Here, the authors show that β-cell deletion of UPR transcription factor XB...
www.nature.com
November 26, 2025 at 2:28 PM
Our new paper is out now in Nature Communications! We uncovered the function of XBP1 in beta cells of a preclinical model of T1D and identified unique and shared gene regulatory networks driven by IRE1 and XBP1.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
very cool www.nature.com/articles/s41... Conservation of regulatory elements with highly diverged sequences across large evolutionary distances
Conservation of regulatory elements with highly diverged sequences across large evolutionary distances - Nature Genetics
Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence conservation.
www.nature.com
June 4, 2025 at 2:32 AM
very cool www.nature.com/articles/s41... Conservation of regulatory elements with highly diverged sequences across large evolutionary distances
Reposted by Sushmita Roy
How might AI transform science? DSI Director @kylecranmer.bsky.social will discuss the diverse ways AI could revolutionize scientific practice at this @uwbadgertalks.bsky.social live event in Green Bay. Join us at the Neville Public Museum, June 10, 6pm. www.nevillepublicmuseum.org/events/calen...
As AI expands what’s possible for scientists, why do its effects vary across fields? Join presenter Kyle Cranmer on June 10, 2025, at 6 PM at the Neville Public Museum for a PBS AI Talk Series event. He’ll share how AI is reshaping science with real examples.
For more information: hubs.li/Q03mRJ2K0
For more information: hubs.li/Q03mRJ2K0
June 3, 2025 at 7:07 PM
How might AI transform science? DSI Director @kylecranmer.bsky.social will discuss the diverse ways AI could revolutionize scientific practice at this @uwbadgertalks.bsky.social live event in Green Bay. Join us at the Neville Public Museum, June 10, 6pm. www.nevillepublicmuseum.org/events/calen...
Reposted by Sushmita Roy
Collaborative work shared with: #JasonErnst @juliazeitlinger.bsky.social @shaunmahony.bsky.social @amathelier.bsky.social @sroyyors.bsky.social @ferhatay.bsky.social and #SaurabhSinha
May 13, 2025 at 4:59 PM
Collaborative work shared with: #JasonErnst @juliazeitlinger.bsky.social @shaunmahony.bsky.social @amathelier.bsky.social @sroyyors.bsky.social @ferhatay.bsky.social and #SaurabhSinha
Reposted by Sushmita Roy
Authors include: @juliazeitlinger.bsky.social, @sroyyors.bsky.social, @ferhatay.bsky.social, @amathelier.bsky.social, @alemedinarivera.bsky.social, @shaunmahony.bsky.social
May 14, 2025 at 10:02 AM
Reposted by Sushmita Roy
Our New perspective explores breakthroughs & challenges in regulatory & systems genomics: from cis-regulatory code & 3D chromatin to spatial omics & AI models.
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
Perspective on recent developments and challenges in regulatory and systems genomics
Abstract. Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regul
doi.org
May 13, 2025 at 4:59 PM
Our New perspective explores breakthroughs & challenges in regulatory & systems genomics: from cis-regulatory code & 3D chromatin to spatial omics & AI models.
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
Reposted by Sushmita Roy
HAPPY 75th, NSF!
We’re celebrating this milestone by highlighting some of NSF’s most transformative accomplishments—innovations that have shaped our world and continue to drive progress in health, technology, the environment, and beyond.
Read on 🧵(1/11):
We’re celebrating this milestone by highlighting some of NSF’s most transformative accomplishments—innovations that have shaped our world and continue to drive progress in health, technology, the environment, and beyond.
Read on 🧵(1/11):
May 10, 2025 at 8:19 PM
HAPPY 75th, NSF!
We’re celebrating this milestone by highlighting some of NSF’s most transformative accomplishments—innovations that have shaped our world and continue to drive progress in health, technology, the environment, and beyond.
Read on 🧵(1/11):
We’re celebrating this milestone by highlighting some of NSF’s most transformative accomplishments—innovations that have shaped our world and continue to drive progress in health, technology, the environment, and beyond.
Read on 🧵(1/11):
Wow, this paper on interpreting ML models by
@suinlee.bsky.social
and Scott Lundberg came out in 2017 and has 34k citations! Congratulations
@suinlee.bsky.social
and your team, what an achievement :-). arxiv.org/abs/1705.07874
@suinlee.bsky.social
and Scott Lundberg came out in 2017 and has 34k citations! Congratulations
@suinlee.bsky.social
and your team, what an achievement :-). arxiv.org/abs/1705.07874
A Unified Approach to Interpreting Model Predictions
Understanding why a model makes a certain prediction can be as crucial as the prediction's accuracy in many applications. However, the highest accuracy for large modern datasets is often achieved by c...
arxiv.org
May 10, 2025 at 11:18 PM
Wow, this paper on interpreting ML models by
@suinlee.bsky.social
and Scott Lundberg came out in 2017 and has 34k citations! Congratulations
@suinlee.bsky.social
and your team, what an achievement :-). arxiv.org/abs/1705.07874
@suinlee.bsky.social
and Scott Lundberg came out in 2017 and has 34k citations! Congratulations
@suinlee.bsky.social
and your team, what an achievement :-). arxiv.org/abs/1705.07874
Reposted by Sushmita Roy
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...
I'm so excited about this!
www.biorxiv.org/content/10.1...
Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data
Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...
www.biorxiv.org
May 9, 2025 at 10:49 AM
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...
I'm so excited about this!
www.biorxiv.org/content/10.1...
Reposted by Sushmita Roy
In case you have not seen it 😉 Here is our latest paper!
With @arnausebe.bsky.social @ianakim.bsky.social @encent.bsky.social and many more 👏🏻
www.nature.com/articles/s41...
With @arnausebe.bsky.social @ianakim.bsky.social @encent.bsky.social and many more 👏🏻
www.nature.com/articles/s41...
Chromatin loops are an ancestral hallmark of the animal regulatory genome - Nature
The physical organization of the genome in non-bilaterian animals and their closest unicellular relatives is characterized; comparative analysis shows chromatin looping is a conserved feature of ...
www.nature.com
May 8, 2025 at 5:18 PM
In case you have not seen it 😉 Here is our latest paper!
With @arnausebe.bsky.social @ianakim.bsky.social @encent.bsky.social and many more 👏🏻
www.nature.com/articles/s41...
With @arnausebe.bsky.social @ianakim.bsky.social @encent.bsky.social and many more 👏🏻
www.nature.com/articles/s41...
Reposted by Sushmita Roy
Fantastic work Lars and team! 👏🏻👏🏻
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 6:21 PM
Fantastic work Lars and team! 👏🏻👏🏻
Reposted by Sushmita Roy
🧪 Though a doubling of NSF's budget might seem far-fetched, that's exactly what Congress said what's needed to maintain national competitiveness in science & tech.
From the bipartisan CHIPS and Science Act of 2022:
From the bipartisan CHIPS and Science Act of 2022:
May 4, 2025 at 3:04 AM
🧪 Though a doubling of NSF's budget might seem far-fetched, that's exactly what Congress said what's needed to maintain national competitiveness in science & tech.
From the bipartisan CHIPS and Science Act of 2022:
From the bipartisan CHIPS and Science Act of 2022:
Reposted by Sushmita Roy
multideconv - Integrative pipeline for cell type deconvolution from bulk RNAseq using first and second generation methods https://www.biorxiv.org/content/10.1101/2025.04.29.651220v1
May 4, 2025 at 3:47 AM
multideconv - Integrative pipeline for cell type deconvolution from bulk RNAseq using first and second generation methods https://www.biorxiv.org/content/10.1101/2025.04.29.651220v1
Reposted by Sushmita Roy
From a genomics & bioinformatics perspective, these new NIH policies will likely knock out the pillars of these research fields across the world. No joke. Reseachers everywhere should be aware and **non-US funders need to step up** to fill the big gaps that will appear in the coming months.
How are folks handling NIH’s no foreign subawards policy? Anyone working with big consortia (e.g. Human Protein Atlas, Sweden), this will become a massive problem—some orgs are the only source for rare reagents/proteins, and distribute them at cost. Curious the implications/plans for navigating.
May 3, 2025 at 3:55 PM
From a genomics & bioinformatics perspective, these new NIH policies will likely knock out the pillars of these research fields across the world. No joke. Reseachers everywhere should be aware and **non-US funders need to step up** to fill the big gaps that will appear in the coming months.
So happy to see this published now! We present TGIF, Tree-Guided Integrated Factorization, based on multi-task NMF to examine dynamics of the 3D genome organization.
genome.cshlp.org/cgi/content/... with rockstar student, now Dr. Erika Da-Inn Lee.
genome.cshlp.org/cgi/content/... with rockstar student, now Dr. Erika Da-Inn Lee.
Sign In
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
April 28, 2025 at 2:07 PM
So happy to see this published now! We present TGIF, Tree-Guided Integrated Factorization, based on multi-task NMF to examine dynamics of the 3D genome organization.
genome.cshlp.org/cgi/content/... with rockstar student, now Dr. Erika Da-Inn Lee.
genome.cshlp.org/cgi/content/... with rockstar student, now Dr. Erika Da-Inn Lee.
Reposted by Sushmita Roy
Our new call for VIB.AI group leaders is online! Junior and senior positions available to develop innovative ML methods in biology. With professorship at CS or Medical Faculty. Deadline 14th June. DM for more info.
We are looking for additional Group Leaders to join the growing computational biology community at VIB.
If you are excited about combining AI and machine learning with fundamental biology, we would love to hear from you!
https://vib.ai/en/opportunities#/job-description/110906
If you are excited about combining AI and machine learning with fundamental biology, we would love to hear from you!
https://vib.ai/en/opportunities#/job-description/110906
April 26, 2025 at 11:00 AM
Our new call for VIB.AI group leaders is online! Junior and senior positions available to develop innovative ML methods in biology. With professorship at CS or Medical Faculty. Deadline 14th June. DM for more info.
Reposted by Sushmita Roy
New blog post: let's talk about latents!
sander.ai/2025/04/15/l...
sander.ai/2025/04/15/l...
Generative modelling in latent space
Latent representations for generative models.
sander.ai
April 15, 2025 at 9:40 AM
New blog post: let's talk about latents!
sander.ai/2025/04/15/l...
sander.ai/2025/04/15/l...
Reposted by Sushmita Roy
Our latest work now online in Cell:
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
April 17, 2025 at 6:26 PM
Our latest work now online in Cell:
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
Genomic language models: opportunities and challenges: Trends in Genetics www.cell.com/trends/genet...
Genomic language models: opportunities and challenges
Large language models (LLMs) are having transformative impacts across a wide range
of scientific fields, particularly in the biomedical sciences. Just as the goal of
natural language processing is to ...
www.cell.com
April 13, 2025 at 10:49 PM
Genomic language models: opportunities and challenges: Trends in Genetics www.cell.com/trends/genet...
Reposted by Sushmita Roy
Hey #genomics, #bioinformatics & #algorithms peeps 💻🧬. If you haven't seen the CfP for WABI '25 yet, check out the website wabiconf.github.io/2025/. It will be held at UMD @umdscience.bsky.social with Broňa Brejová & myself as co-chairs! Submit your exciting & late-breaking algorithmic work to WABI
WABI 2025
WABI Conference on Algorithms in Bioinformatics
wabiconf.github.io
April 5, 2025 at 9:05 PM
Hey #genomics, #bioinformatics & #algorithms peeps 💻🧬. If you haven't seen the CfP for WABI '25 yet, check out the website wabiconf.github.io/2025/. It will be held at UMD @umdscience.bsky.social with Broňa Brejová & myself as co-chairs! Submit your exciting & late-breaking algorithmic work to WABI
Reposted by Sushmita Roy
Make sure to also check out the preprint on the new CREsted package: many more sequence-to-function models across different species! … and it works with HyDrop v2 data as well.
Congrats to @niklaskemp.bsky.social & @seppedewinter.bsky.social & all the others working on this super cool project!
Congrats to @niklaskemp.bsky.social & @seppedewinter.bsky.social & all the others working on this super cool project!
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 4, 2025 at 10:04 AM
Make sure to also check out the preprint on the new CREsted package: many more sequence-to-function models across different species! … and it works with HyDrop v2 data as well.
Congrats to @niklaskemp.bsky.social & @seppedewinter.bsky.social & all the others working on this super cool project!
Congrats to @niklaskemp.bsky.social & @seppedewinter.bsky.social & all the others working on this super cool project!
Reposted by Sushmita Roy
We investigate new CREsted models for the mouse cortex, PBMC, glioblastoma, and zebrafish development; and we validated synthetic enhancers for the heart, muscle, and endothelial cells in vivo in zebrafish. We furthermore fine-tune Borzoi to better capture cell type specific enhancer logic.
April 4, 2025 at 9:04 AM
We investigate new CREsted models for the mouse cortex, PBMC, glioblastoma, and zebrafish development; and we validated synthetic enhancers for the heart, muscle, and endothelial cells in vivo in zebrafish. We furthermore fine-tune Borzoi to better capture cell type specific enhancer logic.
Very nice perspective on causal machine learning, perturbations + single cell omics, gene regulatory networks. nature.com/articles/s41... graph-based representations are important for getting to mechanism. This really resonates with me.
Causal machine learning for single-cell genomics - Nature Genetics
This Perspective explores causal machine learning in single-cell genomics, addressing challenges such as generalization, interpretability and cell dynamics, while highlighting advances and the potenti...
nature.com
April 5, 2025 at 10:55 PM
Very nice perspective on causal machine learning, perturbations + single cell omics, gene regulatory networks. nature.com/articles/s41... graph-based representations are important for getting to mechanism. This really resonates with me.
Reposted by Sushmita Roy
📢 new preprint alert: So so excited to share our analysis on the impact of common and rare variants on single-cell gene expression in blood, using WGS and scRNA-seq data from nearly 2,000 individuals and 5.4m cells as part of TenK10K phase 1 🧬 www.medrxiv.org/content/10.1...
🧵👇 (1/n)
🧵👇 (1/n)
March 24, 2025 at 7:47 AM
📢 new preprint alert: So so excited to share our analysis on the impact of common and rare variants on single-cell gene expression in blood, using WGS and scRNA-seq data from nearly 2,000 individuals and 5.4m cells as part of TenK10K phase 1 🧬 www.medrxiv.org/content/10.1...
🧵👇 (1/n)
🧵👇 (1/n)
Reposted by Sushmita Roy
ATTENTION:
Do you or someone you know get fired or have a job offer rescinded because of uncertainty due to the NIH funding freeze?
Please DM me!
THANK YOU!
Do you or someone you know get fired or have a job offer rescinded because of uncertainty due to the NIH funding freeze?
Please DM me!
THANK YOU!
a yellow piece of paper is laying on a brown background
ALT: a yellow piece of paper is laying on a brown background
media.tenor.com
March 19, 2025 at 7:06 PM
ATTENTION:
Do you or someone you know get fired or have a job offer rescinded because of uncertainty due to the NIH funding freeze?
Please DM me!
THANK YOU!
Do you or someone you know get fired or have a job offer rescinded because of uncertainty due to the NIH funding freeze?
Please DM me!
THANK YOU!