Steven Hoffman
@hoffmansteven.bsky.social
Lover of my family, Single-cell Sequencing and BBQ. marketing @Ultima Genomics but all posts my own
Reposted by Steven Hoffman
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."
"The results show the damage that cuts in funding can do to research, and the unpredictable nature of the research process."
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
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
September 25, 2025 at 2:49 PM
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."
"The results show the damage that cuts in funding can do to research, and the unpredictable nature of the research process."
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
September 2, 2025 at 3:18 PM
Looking for some best practices for analysis of Ultima Genomics Data: Start Here: link.ultimagenomics.com/199ff0
Reposted by Steven Hoffman
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-...
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
July 17, 2025 at 3:06 PM
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-...
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-...
Reposted by Steven Hoffman
Highly recommended read if you are looking into spatial transcriptomic options.
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
June 23, 2025 at 10:53 AM
Highly recommended read if you are looking into spatial transcriptomic options.
Reposted by Steven Hoffman
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/...
journals.biologists.com/jcs/article/...
June 19, 2025 at 8:56 AM
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/...
journals.biologists.com/jcs/article/...
About 15 yrs ago when I first started doing single-cell genomics plant scientists asked about analyzing single pollen grains - now Keygene demonstrates it!
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...
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
June 12, 2025 at 1:18 PM
About 15 yrs ago when I first started doing single-cell genomics plant scientists asked about analyzing single pollen grains - now Keygene demonstrates it!
Happy to be with Ultima today at the The Houston UGM hosted by @10xgenomics.bsky.social
June 3, 2025 at 3:35 PM
Happy to be with Ultima today at the The Houston UGM hosted by @10xgenomics.bsky.social
Reposted by Steven Hoffman
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
May 19, 2025 at 2:42 AM
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
Reposted by Steven Hoffman
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
May 25, 2025 at 11:00 AM
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...
Reposted by Steven Hoffman
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.
▶️Watch his video pitch to find out more.
March 24, 2025 at 1:36 PM
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.
▶️Watch his video pitch to find out more.
Reposted by Steven Hoffman
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 Steven Hoffman
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!
May 2, 2025 at 8:46 PM
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!
Reposted by Steven Hoffman
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
April 28, 2025 at 9:52 AM
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
Reposted by Steven Hoffman
Glad we have these in the office supply cabinet in case I need to back up a quarter of a phone photo
April 24, 2025 at 3:13 PM
Glad we have these in the office supply cabinet in case I need to back up a quarter of a phone photo
Reposted by Steven Hoffman
🚀 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!
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!
April 24, 2025 at 3:50 PM
🚀 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!
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!
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
April 1, 2025 at 12:36 PM
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...
Reposted by Steven Hoffman
An incredible resource that shows how Federal research funding supports your neighborhood, your neighbors.
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
a 🧵
Find out how your community may be impacted.
Explore more at SCIMaP: scienceimpacts.org
a 🧵
March 28, 2025 at 2:53 AM
An incredible resource that shows how Federal research funding supports your neighborhood, your neighbors.
Reposted by Steven Hoffman
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:
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
March 24, 2025 at 10:18 PM
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:
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:
Reposted by Steven Hoffman
BIG NEWS! The Mosquito Cell Atlas preprint is live! 🦟🧬 My first senior author paper! Massive and accessible snRNA-seq dataset and a lot of cool mosquito biology. A true collaborative achievement! #MCA
biorxiv.org/content/10.1...
See @oliviagoldman.net thread here
biorxiv.org/content/10.1...
See @oliviagoldman.net thread here
March 5, 2025 at 7:02 PM
BIG NEWS! The Mosquito Cell Atlas preprint is live! 🦟🧬 My first senior author paper! Massive and accessible snRNA-seq dataset and a lot of cool mosquito biology. A true collaborative achievement! #MCA
biorxiv.org/content/10.1...
See @oliviagoldman.net thread here
biorxiv.org/content/10.1...
See @oliviagoldman.net thread here
#AGBT25 Ultima Workshop Video is available on-demand www.ultimagenomics.com/resources/?c...
Resources | Ultima Genomics
www.ultimagenomics.com
March 4, 2025 at 6:04 PM
#AGBT25 Ultima Workshop Video is available on-demand www.ultimagenomics.com/resources/?c...
Reposted by Steven Hoffman
Congratulations to Dr. Peter Hotez. I've had conversations with Hotez. Not only is he a brilliant man, but also a very kind human being.
houston.innovationmap.com/peter-hotez-...
houston.innovationmap.com/peter-hotez-...
Houston Nobel Prize nominee earns latest award for public health research
Hotez and his team were selected to receive $500,000 from Lyda Hill Philanthropies to help fund The Texas Virosphere Project.
houston.innovationmap.com
February 26, 2025 at 11:55 PM
Congratulations to Dr. Peter Hotez. I've had conversations with Hotez. Not only is he a brilliant man, but also a very kind human being.
houston.innovationmap.com/peter-hotez-...
houston.innovationmap.com/peter-hotez-...
Reposted by Steven Hoffman
Join @jlemieux.bsky.social and expert panelists -- Catharine Aquino @biomath.bsky.social @jasmineplummer.bsky.social @jessie-no.bsky.social -- as they cover the latest research and novel technologies. #genomics #NGS #spatial #singlecell #AGBTGM #AGBT25 REGISTER: hubs.li/Q036f_3x0
February 26, 2025 at 3:17 PM
Join @jlemieux.bsky.social and expert panelists -- Catharine Aquino @biomath.bsky.social @jasmineplummer.bsky.social @jessie-no.bsky.social -- as they cover the latest research and novel technologies. #genomics #NGS #spatial #singlecell #AGBTGM #AGBT25 REGISTER: hubs.li/Q036f_3x0
Reposted by Steven Hoffman
Watch @thejohnnyyu.bsky.social @therealnima.bsky.social (@vevotherapeutics.bsky.social), @pdhsu.bsky.social , Dave Burke and I (@arcinstitute.org) talking about virtual cells, and how #Tahoe100M, now on. @arcinstitute.org's Virtual Cell Atlas, can change the game!
www.youtube.com/watch?v=ak_f...
www.youtube.com/watch?v=ak_f...
No Priors Ep. 103 | With Vevo Therapeutics and the Arc Institute
YouTube video by No Priors: AI, Machine Learning, Tech, & Startups
www.youtube.com
February 25, 2025 at 1:39 PM
Watch @thejohnnyyu.bsky.social @therealnima.bsky.social (@vevotherapeutics.bsky.social), @pdhsu.bsky.social , Dave Burke and I (@arcinstitute.org) talking about virtual cells, and how #Tahoe100M, now on. @arcinstitute.org's Virtual Cell Atlas, can change the game!
www.youtube.com/watch?v=ak_f...
www.youtube.com/watch?v=ak_f...