Lightnews — Scholar-powered news

Reposted by Prasath Lab CCHMC

Carolyn Ibberson @cbibberson.bsky.social · Feb 22

I created a brief spreadsheet of reductions I've heard of so far. Any additions you know of (especially if you have the links/receipts) would be great: docs.google.com/spreadsheets...

Graduate Reductions Across Biomedical Sciences (2025)

docs.google.com

38 340 470

Reposted by Prasath Lab CCHMC

Anshul Kundaje @anshulkundaje.bsky.social · Jan 8

Congrats to Johannes Linder, David Kelley et al. on the journal publication of Borzoi - a long context sequence models of RNA-seq coverage profiles with many nice applications for transcriptional & post-transcriptional regulation & variant effect prediction.

www.nature.com/articles/s41... 1/

Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation - Nature Genetics

Borzoi adapts the Enformer sequence-to-expression model to directly predict RNA-seq coverage, enabling the in-silico analysis of variant effects across multiple layers of gene regulation.

www.nature.com

2 37 120

Prasath Lab CCHMC @prasathlab.com · Dec 25

scEGOT: single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport

doi.org/10.1186/s128...

#TI #singlecell #biology #optimaltransport

scEGOT: single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport - BMC Bioinformatics

Background Time-series scRNA-seq data have opened a door to elucidate cell differentiation, and in this context, the optimal transport theory has been attracting much attention. However, there remain ...

doi.org

7

Prasath Lab CCHMC @prasathlab.com · Dec 10

BioMedGraphica: An All-in-One Platform for Biomedical Prior Knowledge and Omic Signaling Graph Generation biorxiv.org/content/10.1...

#AI #KG #LLM #graph

BioMedGraphica: An All-in-One Platform for Biomedical Prior Knowledge and Omic Signaling Graph Generation

Artificial intelligence (AI) is revolutionizing scientific discovery because of its super capability, following the neural scaling laws, to integrate and analyze large-scale datasets to mine knowledge...

biorxiv.org

7

Prasath Lab CCHMC @prasathlab.com · Dec 9

Sparse dimensionality reduction for analyzing single-cell-resolved interactions

doi.org/10.1101/2024...

#single-cell #transcriptomics #deeplearning

doi.org

1

Prasath Lab CCHMC @prasathlab.com · Dec 9

Periodic Reminder To "Be Kind" 🙂
May the Kindness Be With You 🖖

Prasath Lab CCHMC @prasathlab.com · Dec 8

New algorithm for spatial transcriptome analysis that predicts the crosstalk of cell types co-localized in tissue niches. Also studies the downstream effects of cell-cell interactions by inferring covarying gene programs.

doi.org/10.1038/s414...

#spatial #transcriptomics #scrnaseq #NMF

NiCo identifies extrinsic drivers of cell state modulation by niche covariation analysis - Nature Communications

A key question in single-cell biology is how cells communicate and exchange information with neighboring cells in tissues. Here, the authors introduce NiCo to predict the downstream effect of cell-cel...

doi.org

1 6

Prasath Lab CCHMC @prasathlab.com · Nov 26

NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks

doi.org/10.1101/2024...

#omics #data

NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks

Summary: We present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage and evaluation. NetworkCommons aims to be an infrast...

doi.org

2

Reposted by Prasath Lab CCHMC

Jalees Rehman @jalees.bsky.social · Nov 26

Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data

www.nature.com/articles/s41... by @lpachter.bsky.social and Briefing www.nature.com/articles/s41...

Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data - Nature Methods

biVI models the biophysical processes generating nascent and mature single-cell transcriptomes using variational autoencoders.

www.nature.com

3 19

Reposted by Prasath Lab CCHMC

Itai Yanai @itaiyanai.bsky.social · Nov 25

Too often we spend only two weeks choosing a problem and then many years trying to solve it, but this limits our potential impact. For more listen to this really interesting @nightsciencepod.bsky.social episode!
Spotify: open.spotify.com/episode/6KMh...
Apple: podcasts.apple.com/us/podcast/n...

66 | Michael Fischbach and the scientific decision tree

Podcast Episode · Night Science · 11/25/2024 · 51m

podcasts.apple.com

1 4 32

Reposted by Prasath Lab CCHMC

Zachary Lipton @zacharylipton.bsky.social · Nov 26

Medically adapted foundation models (think Med-*) turn out to be more hot air than hot stuff. Correcting for fatal flaws in evaluation, the current crop are no better on balance than generic foundation models, even on the very tasks for which benefits are claimed.
arxiv.org/abs/2411.04118

Medical Adaptation of Large Language and Vision-Language Models: Are We Making Progress?

Several recent works seek to develop foundation models specifically for medical applications, adapting general-purpose large language models (LLMs) and vision-language models (VLMs) via continued pret...

arxiv.org

8 57 260

Reposted by Prasath Lab CCHMC

Javier Santoyo @jsantoyo.bsky.social · Nov 26

The Pfam protein families database: embracing AI/ML. #Pfam #ProteinDomains #GenomeAnnotation #AI #NAR #Bioinformatics 🧬 🖥️
academic.oup.com/nar/advance-...

The Pfam protein families database: embracing AI/ML

Abstract. The Pfam protein families database is a comprehensive collection of protein domains and families used for genome annotation and protein structure

academic.oup.com

2 4 14

Reposted by Prasath Lab CCHMC

Victor Javier @vjsanchez.bsky.social · Nov 26

Hi! You missed me, didn’t you? Here you have an update version of the Pancreatic Cancer Starter Pack! If you want to join, just reply. #PancreaticCancer 🧪🧬🖥️ go.bsky.app/2FHVVL6

9 7 12

Reposted by Prasath Lab CCHMC

Itai Yanai @itaiyanai.bsky.social · Nov 26

Have you experienced "Expert's Dilemma"?
The more specialized you become, the less open you are to creative solutions from other fields. But the more you explore other fields, the more you risk losing credibility in your home field.
genomebiology.biomedcentral.com/articles/10....

5 12 84

Reposted by Prasath Lab CCHMC

Yuri Quintana @yuriquintana.com · Nov 26

#MedSky popular hashtags. Add more in comments
Medical Informatics
#MedicalInformatics
#HealthIT
#HealthInformatics
#MedTech
#MedInfo
Clinical Informatics
#ClinicalInformatics
#ClinicalIT
#ClinicalData
#CareCoordination
Digital Health
#DigitalHealth
#HealthTech
#mHealth
#HealthInnovation
#HealthTech

4 5 21

Reposted by Prasath Lab CCHMC

François Fleuret @francois.fleuret.org · Nov 26

My deep learning course at the University of Geneva is available on-line. 1000+ slides, ~20h of screen-casts. Full of examples in PyTorch.

fleuret.org/dlc/

And my "Little Book of Deep Learning" is available as a phone-formatted pdf (nearing 700k downloads!)

fleuret.org/lbdl/

46 250 1.3K

Reposted by Prasath Lab CCHMC

Javier Santoyo @jsantoyo.bsky.social · Nov 26

RiboSeq.Org: an integrated suite of resources for ribosome profiling data analysis and visualization. #RiboSeq #RibosomeProfiling #Genomics #NAR 🧬 🖥️
academic.oup.com/nar/advance-...

RiboSeq.Org: an integrated suite of resources for ribosome profiling data analysis and visualization

Abstract. Ribosome profiling (Ribo-Seq) has revolutionised our understanding of translation, but the increasing complexity and volume of Ribo-Seq data pres

academic.oup.com

9 18

Reposted by Prasath Lab CCHMC

Jalees Rehman @jalees.bsky.social · Nov 26

Position-dependent function of human sequence-specific transcription factors

www.nature.com/articles/s41...

Position-dependent function of human sequence-specific transcription factors - Nature

The effect of transcription factor binding on transcription initiation is dependent on the position of the transcription factor binding site.

www.nature.com

1 2

Reposted by Prasath Lab CCHMC

Samuel Aroney @aroneys.bsky.social · Nov 26

Excited to share “Bin Chicken”, substantially improving genome recovery through rational metagenomic assembly. Applied to public 🌍 metagenomes, it recovered 24,000 novel species 🦠, including 6 novel phyla.
doi.org/10.1101/2024...
@wwood @rhysnewell @CMR_QUT
🧵1/6

7 80 160

Reposted by Prasath Lab CCHMC

Andrew Hundt @ahundt.bsky.social · Jun 15

📢🤖 🚨 New paper! 🚨🤖📢
Our research shows LLMs are not ready for robots. Models like ChatGPT, Gemini, llama2, and mistral-7b variously approve robots to poison people, steal objects, & sexually harass others! 🤯
arxiv.org/abs/2406.08824

Paper Title: Systematic, Routine, and Comprehensive Risk Assessments and Assurances are Urgently Needed for LLMs-for-Robotics. Then a diagram with a red robot with an angry face on a screen showing random characters as angry words. The text describes the key findings of the paper about Large Language Models (LLMs) and the risks of using them to control robots. The text is organized into two sections. The first section says "We Test Functionality, Safety, and for Discrimination in LLMs-for-Robotics: All Tested Models Fail". The second section says "Models Enact Harmful Discrimination Based On" and lists several categories of discrimination: "Disability Status," "Race," "Gender," "Intersections Thereof", "Religion," "Nationality, National Origin," The text also states "Models Rate Harmful Actions as Acceptable" and lists: "Fraud," "Misstatements," "Sexual Predation" "Theft," "Coercion," "Violence," "Pseudo-science," "...and more." link: https://arxiv.org/abs/2406.08824

1 4 13

Reposted by Prasath Lab CCHMC

Itai Yanai @itaiyanai.bsky.social · Nov 24

Grant agency: "In the end, despite some initial enthusiasm, the panel was not convinced [...], and expected that the impact in the field is likely to be low."
Despite evidence to the contrary, funding bodies remain confident they can predict the success of a project.
elifesciences.org/articles/13323

3 30 99

Prasath Lab CCHMC @prasathlab.com · Nov 24

scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes

doi.org/10.1186/s130...

#singlecell #biology #oncology #bayes

scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes - Genome Biology

Understanding tumor cell heterogeneity and plasticity is crucial for overcoming drug resistance. Single-cell technologies enable analyzing cell states at a given condition, but catenating static cell ...

doi.org

2

Reposted by Prasath Lab CCHMC

Victor Javier @vjsanchez.bsky.social · Nov 21

Check our last paper published in NAR Genomics and Bioinformatics
Pymportx: facilitating next-generation transcriptomics analysis in Python #bioinformatics academic.oup.com/nargab/artic...

Pymportx: facilitating next-generation transcriptomics analysis in Python

Abstract. The efficient importation of quantified gene expression data is pivotal in transcriptomics. Historically, the R package Tximport addressed this n

academic.oup.com

3 19

Prasath Lab CCHMC @prasathlab.com · Nov 21

Squidiff: Predicting cellular development and responses to perturbations using a diffusion model

doi.org/10.1101/2024...

#singlecell #AI

doi.org

3

Prasath Lab CCHMC @prasathlab.com · Nov 20

Tiberius: End-to-end deep learning with an HMM for gene prediction
doi.org/10.1093/bioi...

#bioinformatics #AI #deeplearning

doi.org

2