Lightnews — Scholar-powered news

Sushmita Roy @sroyyors.bsky.social · Jun 4

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

4

Reposted by Sushmita Roy

UW–Madison Data Science Institute @uwdsi.bsky.social · Jun 3

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...

Badger Talks @uwbadgertalks.bsky.social · Jun 3

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

3 7

Reposted by Sushmita Roy

Alejandra Medina-Rivera @alemedinarivera.bsky.social · May 13

Collaborative work shared with: #JasonErnst @juliazeitlinger.bsky.social @shaunmahony.bsky.social @amathelier.bsky.social @sroyyors.bsky.social @ferhatay.bsky.social and #SaurabhSinha

1 1 4

Reposted by Sushmita Roy

Bioinformatics Advances @bioinfoadv.bsky.social · May 14

Authors include: @juliazeitlinger.bsky.social, @sroyyors.bsky.social, @ferhatay.bsky.social, @amathelier.bsky.social, @alemedinarivera.bsky.social, @shaunmahony.bsky.social

2 4

Reposted by Sushmita Roy

Alejandra Medina-Rivera @alemedinarivera.bsky.social · May 13

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

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

1 11 23

Reposted by Sushmita Roy

Stand Up for Science! @standupforscience.bsky.social · May 10

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):

A chocolate cake with red and white decorations and lit candles shaped as the number 75. Bold text reads: ‘The NSF Turns 75 Today. What has it done over the past 7 decades?’ The background is a celebratory red with a spray-paint texture.

8 410 800

Sushmita Roy @sroyyors.bsky.social · May 10

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

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

1 3

Reposted by Sushmita Roy

Erik van Nimwegen @erikvannimwegen.bsky.social · May 9

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...

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

9 100 320

Sushmita Roy @sroyyors.bsky.social · May 9

Congratulations!

1

Reposted by Sushmita Roy

Marc A. Marti-Renom @mamartirenom.bsky.social · May 8

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...

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

1 14

Sushmita Roy @sroyyors.bsky.social · May 8

I had a great time visiting and learning about the cutting edge basic and translational research going on at the Fred! Thank you for inviting me Manu Setty!

1

Reposted by Sushmita Roy

Marc A. Marti-Renom @mamartirenom.bsky.social · May 8

Fantastic work Lars and team! 👏🏻👏🏻

Lars Velten @larsplus.bsky.social · May 8

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...
🧵

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

1 1 6

Reposted by Sushmita Roy

Dr. David Miller 🏳️‍🌈 @davidimiller.bsky.social · May 4

🧪 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:

CHIPS and Science authorization for FY26 = $17.8B

White House skinny budget = $3.9B

2 95 190

Reposted by Sushmita Roy

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · May 4

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

1 1

Sushmita Roy @sroyyors.bsky.social · May 4

its based on this report www.gao.gov/products/gao... that was linked off the nih directors announcement. But just stopping to fund grants with a foreign component without a policy in place seems to fly in the face of efficiency and mindful use of federal resources.

Grants Management: Recent Guidance Could Enhance Subaward Oversight

Some federal grant recipients pass some of their award funding to subrecipients. However, there have been issues with the completeness and accuracy of...

www.gao.gov

Reposted by Sushmita Roy

Mike Inouye @mikeinouye.bsky.social · May 3

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.

Emma Chory, Ph.D. @chorye.bsky.social · May 3

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.

2 8 21

Sushmita Roy @sroyyors.bsky.social · May 3

haha.. no :-)😀 (thankfully)

3

Sushmita Roy @sroyyors.bsky.social · Apr 30

very nice.. NMF++ based methods shine for their elegance and interpretability.. was curious about its comparison to MEFISTO www.nature.com/articles/s41...

Nonnegative spatial factorization applied to spatial genomics - Nature Methods

This paper presents nonnegative spatial factorization, a general framework for spatially aware and interpretable dimension reduction for high-dimensional spatial data, and its application to spatial t...

www.nature.com

Sushmita Roy @sroyyors.bsky.social · Apr 29

Its behind a paywall, but our biorxiv version is updated .. www.biorxiv.org/content/10.1...

Examining dynamics of three-dimensional genome organization with multi-task matrix factorization

Three-dimensional (3D) genome organization, which determines how the DNA is packaged inside the nucleus, has emerged as a key component of the gene regulation machinery. High-throughput chromosome con...

www.biorxiv.org

2

Sushmita Roy @sroyyors.bsky.social · Apr 28

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.

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

1 5

Sushmita Roy @sroyyors.bsky.social · Apr 27

I am a little late introducing myself.. I am at the University of Wisconsin-Madison. We are interested in #ML methods to understand gene regulation & regulatory networks from bulk and single cell omic data.

3

Reposted by Sushmita Roy

Stein Aerts @steinaerts.bsky.social · Apr 26

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.

VIB.AI @vibai.bsky.social · Apr 25

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

21 32

Reposted by Sushmita Roy

Sander Dieleman @sedielem.bsky.social · Apr 15

New blog post: let's talk about latents!
sander.ai/2025/04/15/l...

Generative modelling in latent space

Latent representations for generative models.

sander.ai

3 18 74

Reposted by Sushmita Roy

Jesse Engreitz @jengreitz.bsky.social · Apr 17

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 👇

1 28 120

Sushmita Roy @sroyyors.bsky.social · Apr 13

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

1 14