Lightnews — Scholar-powered news

Reposted by Steven Hoffman

Max Kozlov @maxkozlov.bsky.social · 16d

NEW: Nature trained AI to predict which NIH grants from 2014 would have been cut if the Trump admin had its way back then — and what science would have been lost to history.

"The results show the damage that cuts in funding can do to research, and the unpredictable nature of the research process."

Nature @nature.com · 16d

We used machine-learning tools in an attempt to recreate the method for cutting funding, and then applied it to past US NIH grants to reveal the broad-reaching consequences

go.nature.com/4pBArFH

What research might be lost after the NIH’s cuts? Nature trained a bot to find out

We used machine-learning tools in an attempt to recreate the method for cutting funding, and then applied it to past US National Institutes of Health grants to reveal the broad-reaching consequences of such action.

go.nature.com

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Steven Hoffman @hoffmansteven.bsky.social · Sep 2

Looking for some best practices for analysis of Ultima Genomics Data: Start Here: link.ultimagenomics.com/199ff0

Get Started with UG Bioinformatics

Bioinformatic Guides and tutorials for the analysis of Ultima Genomics CRAM files using AWS healthomics workflows for germline and somatic Whole genome sequencing

link.ultimagenomics.com

Reposted by Steven Hoffman

Bethany Brookshire @beebrookshire.bsky.social · Jul 17

Pythons can eat an entire deer.

Whole.

And then...basically liquid comes out. NO skeleton. No BONES. Why doesn't what came out look like what went in?

The answer is sssssssspecial cells. www.sciencenews.org/article/new-...

A newly discovered cell helps pythons poop out the bones of their prey

The cells helps the snakes absorb the bones of their prey — and might show up in other animals that chomp their meals whole.

www.sciencenews.org

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Steven Hoffman @hoffmansteven.bsky.social · Jul 10

Howdy!

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Reposted by Steven Hoffman

Koen De Gelas @kdegelas.bsky.social · Jun 23

Highly recommended read if you are looking into spatial transcriptomic options.

Karsten Rippe @karsten-rippe.bsky.social · Jun 20

1/ Spatial transcriptomics technologies are rapidly evolving. We compared five methods—Visium, RNAscope HiPlex, Molecular Cartography, Merscope, and Xenium—and developed technology-agnostic quality control metrics to guide their use: doi.org/10.1186/s130...

Comparison of spatial transcriptomics technologies using tumor cryosections - Genome Biology

Background Spatial transcriptomics technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor microenvironment by revealing single-cell molecular profiles within the...

doi.org

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Reposted by Steven Hoffman

Journal of Cell Science @jcellsci.bsky.social · Jun 19

In their Cell Science at a Glance article and accompanying poster, Max Grönloh, Werner van der Meer, Merel Tebbens and Jaap van Buul describe the mechanisms regulating transendothelial and trans-pericyte leukocyte migration hotspots during inflammation.
journals.biologists.com/jcs/article/...

JCS poster on Leukocyte transendothelial migration hotspots at a glance

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Steven Hoffman @hoffmansteven.bsky.social · Jun 13

Interesting

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Steven Hoffman @hoffmansteven.bsky.social · Jun 12

About 15 yrs ago when I first started doing single-cell genomics plant scientists asked about analyzing single pollen grains - now Keygene demonstrates it!

KeyGene @keygene.com · Jun 12

Joint research by @keygene.com & Ultima Genomics shows that single-pollen-nuclei sequencing can help plant breeders to improve their breeding by better understanding the recombination of the mother and father DNA during meiosis without raising and analysing an F2.
www.keygene.com/newsitem/sin...

Single pollen nuclei sequencing: profiling of meiotic recombination

KeyGene’s advanced protocols & smart bioinformatics + Ultima Genomics sequencing platform: better understanding DNA recombination in meiosis.

www.keygene.com

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Steven Hoffman @hoffmansteven.bsky.social · Jun 3

Happy to be with Ultima today at the The Houston UGM hosted by @10xgenomics.bsky.social

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Reposted by Steven Hoffman

medRxivpreprint @medrxivpreprint.bsky.social · May 19

Evaluation of the Ultima Genomics UG 100 sequencer for low-cost, high-sensitivity metagenomic pathogen detection from cerebrospinal fluid https://www.medrxiv.org/content/10.1101/2025.05.16.25327810v1

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Reposted by Steven Hoffman

Silvia Domcke @sdomcke.bsky.social · May 25

Expanding Perturb-seq-like screens to multicellular systems also increases the complexity of confounding effects. We encountered this when we perturbed all TFs in mosaic embryoid bodies (EBs) and develop a scalable solution by barcoding monoclonal individuals. 🧵 www.biorxiv.org/content/10.1...

Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens

Genetic screens in organoids hold tremendous promise for accelerating discoveries at the intersection of genomics and developmental biology. Embryoid bodies (EBs) are self-organizing multicellular str...

www.biorxiv.org

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Steven Hoffman @hoffmansteven.bsky.social · May 22

People that like crispy little cabbages (sometimes with balsamic vinegar)

Steven Hoffman @hoffmansteven.bsky.social · May 21

Chicken wings - Brussels sprouts

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Reposted by Steven Hoffman

VIB Training & Conferences @vibtrainconf.bsky.social · Mar 24

Rene Hogers @keygene.com presented his work on establishing single-cell research for crop improvement at #RNGS25.
▶️Watch his video pitch to find out more.

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Reposted by Steven Hoffman

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

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Reposted by Steven Hoffman

Wendy Salmon 🐟🔬🧫 @fishcscells.bsky.social · May 2

Microscopy friends! Anyone know of an online resource that shows how to plate, fix and mount adherent cells using coverslips and slides? I'm digging online but figure I'd see if anyone already had something. TIA!

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Reposted by Steven Hoffman

Chris Ponting @cgatist.bsky.social · Apr 28

Want to use UK Biobank data to study ME/CFS? Can't decide which of the 5,354 UKB participants with evidence of ME/CFS to choose as cases? In this preprint, we consider what case/control definitions to apply. openresearch.nihr.ac.uk/articles/5-3... #pwME #mecfs

NIHR Open Research Article: Defining a High-Quality Myalgic Encephalomyelitis/Chronic Fatigue Syndrome cohort in UK Biobank.

Read the latest article version by Gemma L. Samms, Chris P. Ponting, at NIHR Open Research.

openresearch.nihr.ac.uk

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Reposted by Steven Hoffman

Kevin Ringelman @kevinringelman.bsky.social · Apr 24

Glad we have these in the office supply cabinet in case I need to back up a quarter of a phone photo

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Steven Hoffman @hoffmansteven.bsky.social · Apr 26

I wish we could help more with the library prep, so many of the projects I have helped to vette have much higher costs associated with the library prep than our sequencing

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Reposted by Steven Hoffman

Watchmaker Genomics @watchmakergenomics.bsky.social · Apr 24

🚀 Join Watchmaker Genomics at #AACR25 in Chicago!
Explore high-performance NGS library prep solutions for FFPE, cfDNA & RNA.

Check out our DNA/RNA kits, Equinox amplification, TAPS methylation analysis & quant-free library normalization.

📍Booth 3341 – let’s connect!

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Steven Hoffman @hoffmansteven.bsky.social · Apr 1

Need it!

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Steven Hoffman @hoffmansteven.bsky.social · Apr 1

I am thrilled to be a part of this initiative to help keep science moving forward. If you have samples you can get them sequenced for free with Ultima Genomics: www.genengnews.com/topics/omics...

Ultima Genomics Gives Away Sequencing for Free. Literally.

Ultima Genomics announces that it will provide three trillion DNA sequencing reads free of charge to researchers across the United States and Canada.

www.genengnews.com

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Reposted by Steven Hoffman

Vaughn Cooper @vscooper.micropopbio.org · Mar 28

An incredible resource that shows how Federal research funding supports your neighborhood, your neighbors.

Joshua Weitz @joshuasweitz.bsky.social · Mar 28

Working with an interdisciplinary team, we have developed a website to communicate how the White House's proposed cuts to health research would cause losses of $16B and 68,500 jobs.

Find out how your community may be impacted.

Explore more at SCIMaP: scienceimpacts.org

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US map via scienceimpacts.org visualization of economic loss due to IDC cuts to 15% as part of Feb 7, 2025 executive order, with shading denoting intensity of cuts.

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Reposted by Steven Hoffman

Hani Goodarzi @genophoria.bsky.social · Mar 24

Other links re: Tahoe-100M
Link to the press release: tinyurl.com/vevo-tahoe100
Link to Arc Virtual Cell atlas for download: arcinstitute.org/tools/virtua...
Link to our manuscript:

Vevo Therapeutics Open Sources Tahoe-100M, the World's Largest Single-Cell Dataset, as the Inaugural Contribution to Arc Institute's New Virtual Cell Atlas

/PRNewswire/ -- In a landmark move to advance AI-driven biological research, Arc Institute and Vevo Therapeutics announced today that they have partnered on...

tinyurl.com

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