Lightnews — Scholar-powered news

Reposted by Caleb Lareau

Michele Frison @frisophagy.bsky.social · 1d

How can mitophagy be an effective quality control mechanism if mtDNA mutations reach high enough levels to cause disease?

This question led us into a dark path, full of concepts of evolutionary genetics, germline stem cell biology and mito-nuclear compatibility.

www.science.org/doi/10.1126/...

Ubiquitin-mediated mitophagy regulates the inheritance of mitochondrial DNA mutations

Mitochondrial synthesis of adenosine triphosphate is essential for eukaryotic life but is dependent on the cooperation of two genomes: nuclear and mitochondrial DNA (mtDNA). mtDNA mutates ~15 times as...

www.science.org

4 17 37

Reposted by Caleb Lareau

Jacob Schreiber @jmschreiber91.bsky.social · 3d

Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!

The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.

5 26 41

Reposted by Caleb Lareau

Jörg Vogel @jorg-vogel-lab.bsky.social · 2d

Two group leader positions available in the broader areas of RNA science, RNA technologies, and RNA medicine. Attractive packages and a great environment. Come and join us at Helmholtz RNA Würzburg, Bavaria.

1 76 63

Reposted by Caleb Lareau

Ryan Flynn @raflynn5.bsky.social · 3d

We’re excited to report work led by postdoc Jennifer Porat in the lab, finding that DNA accumulates on the surface of living cells and that the secreted extracellular protein DNASE1L3 can modulate its levels on B and T cells. With a new twist for ATAC-seq as well www.biorxiv.org/content/10.1...

DNASE1L3 surveils mitochondrial DNA on the surface of distinct mammalian cells

The extracellular space is a critical environment for discriminating self versus non-self nucleic acids and initiating the appropriate immune responses through signaling cascades to relay information ...

www.biorxiv.org

3 21 70

Reposted by Caleb Lareau

BK. Titanji @boghuma.bsky.social · 4d

A new Nature Medicine study analyzing health records from >100 million people in the US offers compelling evidence that reactivation of varicella-zoster virus (VZV) ,the same virus that causes chickenpox and shingles may contribute to dementia risk.
www.nature.com/articles/s41...

Varicella-zoster virus reactivation and the risk of dementia - Nature Medicine

Large-scale longitudinal health records reveal consistent association of varicella-zoster virus reactivation with dementia.

www.nature.com

8 83 220

Reposted by Caleb Lareau

Nature @nature.com · 4d

BREAKING: The Nobel Prize in Physiology or Medicine has been awarded jointly to Mary E. Brunkow, Fred Ramsdell, and Shimon Sakaguchi "for their discoveries concerning peripheral immune tolerance"

Stay tuned for more.
#NobelPrize

1 98 230

Reposted by Caleb Lareau

Jenna Norton @jenna-m-norton.bsky.social · 7d

Great article from @stephaniemlee.bsky.social at @chronicle.com on the NIH Autism Data Science Initiative (ADSI) www.chronicle.com/article/what...

ADSI funding went to reputable scientists because and only because dedicated NIH civil servants fought hard to ensure a rigorous, science-based process.

What It’s Like to Be an Autism Scientist Funded by the Trump Administration

The government is funding respected scholars to study autism’s causes, at a time when experts say it’s also sowing misinformation about the same topic.

www.chronicle.com

1 5 24

Reposted by Caleb Lareau

Duncan Kountz @dkountz.bsky.social · 13d

Does anyone have a good, reasonably up-to-date review of cryo-EM uses and methodology for (relatively) high-resolution protein structure determination? For someone who doesn't have a cryo-EM background.

4 16 13

Reposted by Caleb Lareau

I-75 Scientist @flscitriguy.bsky.social · 14d

Reminder starting in October NIH NOFOs won’t be posted in the Guide for grants and contracts.

Tips on how to search for opportunities & set up a subscription for custom searches here: grants.nih.gov/news-events/...

New Tool to Explore NIH Grant Opportunities | Grants & Funding

grants.nih.gov

20 25

Reposted by Caleb Lareau

Kushal K. Dey @kanishkadey.bsky.social · 15d

Introducing Spacelink, a unified framework for identifying and prioritizing spatially variable gene programs at tissue and cell type resolution and linking them to disease GWAS studies. Led by Hanbyul Lee & Haochen Sun www.biorxiv.org/content/10.1...

2 4

Reposted by Caleb Lareau

Leif S. Ludwig @leifludwig.bsky.social · 16d

🚨 New preprints from our lab! First, we introduce Cryo-mtscATAC-seq, led by Maren (@ms-maren.bsky.social ), enabling high-throughput clonal tracing from frozen human samples by isolating nuclei with their mitochondria (“CryoCells”). 👉 www.biorxiv.org/content/10.1...

Cryo-mtscATAC-seq for single-cell mitochondrial DNA genotyping and clonal tracing in archived human tissues

High-throughput clonal tracing of primary human samples relies on naturally occurring barcodes, such as somatic mitochondrial DNA (mtDNA) mutations detected via single-cell ATAC-seq (mtscATAC-seq). Fr...

www.biorxiv.org

2 10 22

Reposted by Caleb Lareau

Kamil Slowikowski @slowkow.com · 18d

I'd like to announce the medRxiv preprint of our latest work:

A multimodal atlas of COVID-19 severity identifies hallmarks of dysregulated immunity.

www.medrxiv.org/content/10.1...

Overview of a research study about COVID-19. The study includes three cohorts: (1) 351 acute COVID-19 patients across 5 severity levels and 3 time points profiled by multiple modalities, (2) 4 acute COVID-19 patients treated with tocilizumab, (3) 73 patients, 43 of whom were previously infected with SARS-CoV-2 3 months ago. The overview shows the general study design and visualizations of the single-cell RNA sequencing data analyzed in this study.

1 3 11

Reposted by Caleb Lareau

derek guy @dieworkwear.bsky.social · 18d

my mom took tylenol when she was pregnant, which made me super focused on menswear and now i have a million followers on twitter

470 2.7K 32K

Reposted by Caleb Lareau

bioRxiv Genomics @biorxiv-genomic.bsky.social · 20d

Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting https://www.biorxiv.org/content/10.1101/2025.09.19.676866v1

1 2

Reposted by Caleb Lareau

Jesse Engreitz @jengreitz.bsky.social · 22d

New preprint from our lab!

What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?

Find out here: www.biorxiv.org/content/10.1...

👇

1/

bioRxiv - An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq

1 17 57

Reposted by Caleb Lareau

Nature Methods @natmethods.nature.com · 22d

GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio

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

GPU-accelerated homology search with MMseqs2 - Nature Methods

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

www.nature.com

21 81

Reposted by Caleb Lareau

Sanford Burnham Prebys NCI-Designated Cancer Center @sbpcancercenter.bsky.social · 24d

Today 62 National Cancer Institute (NCI)-Designated Cancer Centers released a statement reinforcing the importance of HPV vaccination.

HPV vaccination is safe and protects against six types of cancer – including oropharyngeal, cervical, and anal cancers.

#HPVvaccine #HPVvax #EndHPVCancers

2 4

Reposted by Caleb Lareau

Collins Genomics Lab @collinsgenomics.bsky.social · 24d

📢We are hiring!

The Collins Genomics Lab @danafarber.bsky.social is looking to hire two postdoctoral fellows

One in hereditary and early-onset adult cancers:
careers.dana-farber.org/job/12158/po...

1/2🧵

Research Laboratory Job: Postdoctoral Research Fellow - Computational Biologist at Dana-Farber Cancer Institute in 450 Brookline Ave, Boston, MA

Postdoctoral Research Fellow - Computational Biologist job

careers.dana-farber.org

1 2 2

Reposted by Caleb Lareau

MSKEducation @mskeducation.bsky.social · 25d

🎉 Congratulations to our 10 MSK Postdoc Slam finalists! 👏 You were all fantastic and it was truly inspiring to learn about the incredible and diverse work happening at @mskcancercenter.bsky.social. Our #MSKPostdocs gave the judges a real challenge… choosing winners was no easy task! 🤗 #NPAW2025

1 4 21

Reposted by Caleb Lareau

Danwei Huangfu @danweihuangfu.bsky.social · 29d

Now accepting applications for our 2026 Cancer Biology & Cancer Engineering programs. Aspiring scientists & engineers will solve fundamental problems in biology & conduct research & develop technology that will help understand, diagnose, & treat cancer.
bit.ly/3WUiuo1

1 4

Reposted by Caleb Lareau

Memorial Sloan Kettering Cancer Center @mskcancercenter.bsky.social · Sep 7

MSK’s Gerstner Sloan Kettering Graduate School of Biomedical Sciences is now accepting applications for its Cancer Biology and Cancer Engineering #PhD programs for the 2026 academic year. Apply below:

Admission to the PhD Programs

Gerstner Sloan Kettering offers a unique opportunity to train with some of the world’s leading researchers while developing a deep understanding of today’s clinical challenges. We are looking for high...

www.sloankettering.edu

5 9

Caleb Lareau @caleblareau.bsky.social · Sep 3

The totality of humanity’s (public) sequencing data is now at your fingertips. This is an absolutely monumental resource for genomics research! Congratulations @rayanchikhi.bsky.social @rnalab.bsky.social on this incredible feat!!!

Rayan Chikhi @rayanchikhi.bsky.social · Sep 3

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

8

Reposted by Caleb Lareau

Rayan Chikhi @rayanchikhi.bsky.social · Sep 3

Logan rapidly accesses the tapestry of Life’s genetic diversity and can help solve global issues.

To tackle the microplastic crisis, we searched Logan for new versions of the 213 known plastic-degrading enzymes. We identified 200+ million homologs 🤯, including new high-efficiency enzymes 🥤🔥

1 2 4

Reposted by Caleb Lareau

Rayan Chikhi @rayanchikhi.bsky.social · Sep 3

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

3 120 220

Reposted by Caleb Lareau

Fred Hutch Innovation Lab @hutchinnovation.bsky.social · Sep 2

Banking fixed samples before sorting improves experiment planning & instrument scheduling. 10x GEM-X DSP-based fixation recommends sorting before fixing cells. We attempted to stain, fix, and freeze cells before sorting & generating GEMs for 5' libraries. SFFS = STAIN FIX FREEZE SORT (1/7)

1 1 4