iiinova — where your digital self keeps evolving

Reposted by Peter van Galen

Sandra McAllister, PhD @sandramcallister.bsky.social · 15/12/2025

🎀 Age influences breast cancer cell and molecular features 🎀 Congrats to our international team for the work featured in the December @nataging.nature.com issue! @vangalenlab.bsky.social @mgbresearch.bsky.social @harvardmed.bsky.social

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Peter van Galen @vangalenlab.bsky.social · 15/12/2025

🟣🟣🟣 Check out this straightforward method of improving human hematopoietic stem cell expansion by inhibiting ferroptosis 🟣🟣🟣 thanks for including me @bloodgenes.bsky.social #hemesky 🧬🔬🧪

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Peter van Galen @vangalenlab.bsky.social · 06/11/2025

Exciting to see our latest story out in print — with @sandramcallister.bsky.social — on how breast cancer differs between younger and older patients, leading the way to tailored management to improve outcomes 💻🔬🧬🧪

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Reposted by Peter van Galen

Peter van Galen @vangalenlab.bsky.social · 28/09/2025

Congratulations! * Rapid epigenomic classification of acute leukemia* — the most innovative and impactful application of long-read sequencing and machine learning I know. Happy to be included!! #hemesky 🩸🧬💻🔬

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Peter van Galen @vangalenlab.bsky.social · 28/09/2025

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Peter van Galen @vangalenlab.bsky.social · 07/09/2025

This new way of looking at cellular diversity in single-cell sequencing is transformative imo, which is why we've taken a similar approach to study aging blood stem cells. Congratulations @dkotliar.bsky.social and @soumya-boston.bsky.social! 🩸🧪🧬 #hemesky

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Peter van Galen @vangalenlab.bsky.social · 06/09/2025

These findings provide new insight into blood aging at the source, and raise the possibility of targeting inflammatory HSCs to "rejuvenate" blood production in aging 🧪 Thanks Ksenia Safina and collaborators @trowbridgelab.bsky.social @bloodgenes.bsky.social Read more at doi.org/10.1101/2025... 5/5🏁

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Peter van Galen @vangalenlab.bsky.social · 06/09/2025

We discovered a type of stem cells that expand with age and is dominated by a program of inflammation and quiescence (GEP:1 below), which could leave the blood system less able to renew itself 📊 4/5

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Peter van Galen @vangalenlab.bsky.social · 06/09/2025

There is no clear agreement on the effects of aging on HSCs, and how different types of HSCs play into this. So we pulled seven datasets together and re-analyzed them using new bioinformatic methods, revealing a clearer picture 💻 3/5

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Peter van Galen @vangalenlab.bsky.social · 06/09/2025

Aging of blood system leads to health problems such as weakened immunity and a higher risk of anemia. Many of these changes can be traced back to HSCs, which reside in the bone marrow and renew all blood cells 🔬 2/5

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Peter van Galen @vangalenlab.bsky.social · 06/09/2025

Excited to share our latest work on blood aging! To find out why the blood system changes as people age, we started at the source: hematopoietic stem cells (HSCs) #hemesky 🩸🧬 doi.org/10.1101/2025... 🧵 1/5

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Peter van Galen @vangalenlab.bsky.social · 06/09/2025

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Peter van Galen @vangalenlab.bsky.social · 06/09/2025

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Peter van Galen @vangalenlab.bsky.social · 15/08/2025

Online today! *Aging, Immune Fitness and Cancer* 🔬 Learn the latest about the intersection between these processes in @natrevcancer.nature.com 🧬 Great to work with @sandramcallister.bsky.social lab again 😁 doi.org/10.1038/s415...

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Peter van Galen @vangalenlab.bsky.social · 05/08/2025

This may be my favorite paper of the year so far: integrating single-cell leukemia datasets to reveal how differentiation and mutations interact to drive disease, along with a tool that speeds up bone marrow cell annotation from ~4 weeks to ~4 hours..! aacrjournals.org/bloodcancerd... 🔬🩸🧬 #hemesky

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Peter van Galen @vangalenlab.bsky.social · 04/08/2025

Whenever the team @posit.co brings out a new feature, it’s exactly how I wished it would be. AI integration done right 🧠 positron.posit.co/assistant @anthropic.com

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Reposted by Peter van Galen

Vikram Paralkar @paralkarlab.bsky.social · 02/08/2025

📣 New preprint 📣 We present a detailed map of nascent and mature ribosomal RNAs in mouse hematopoiesis and AML (including absolute rRNA molecule numbers), and outline principles of rDNA regulation. Work by Eleanor Sams (@eleanor44.bsky.social) & Victoria Feist (@victoriafeist.bsky.social). (1/x)

biorxiv.org

Dynamics of Ribosomal RNA Transcription and Abundance in Normal and Leukemic Hematopoiesis

Transcription of ribosomal RNAs (rRNAs) from rDNA repeats is the first step of ribosome biogenesis, accounting for a major portion of all cellular transcription. Often regarded as a housekeeping proce...

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Peter van Galen @vangalenlab.bsky.social · 02/08/2025

Had a great time catching up with friends and learning new science at FASEB Hematologic Malignancies! #hemesky @faseborg.bsky.social #HEMSRC

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Reposted by Peter van Galen

Vikram Paralkar @paralkarlab.bsky.social · 30/07/2025

At the FASEB Heme Malignancies meeting with old friends and new - Pam Sung, Peter Van Galen (@vangalenlab.bsky.social), Julia Maxson (@juliamaxson.bsky.social), Johnathon Shafer. Trying out ales at the @treehousebrewing.bsky.social! #HEMSRC

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Peter van Galen @vangalenlab.bsky.social · 22/02/2025

#positron is rapidly replacing programs and websites I used with a customizable multilingual coding environment for data science (local+cluster+virtual machines) #bash #rstats #python @posit.co

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Peter van Galen @vangalenlab.bsky.social · 11/01/2025

Erasmus MC Hematology Lecture speaker lineup never fails to impress! #hemesky 🧪🩸 mcusercontent.com/71bcc0f3bb8a...

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Peter van Galen @vangalenlab.bsky.social · 04/01/2025

Just a reminder of what is easily in my top 5 of favorite papers from 2023 www.cell.com/iscience/ful... @bailee-kain.bsky.social @thekinglab.bsky.social

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Peter van Galen @vangalenlab.bsky.social · 01/01/2025

Congrats! Look forward to using it

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Peter van Galen @vangalenlab.bsky.social · 23/12/2024

Our latest work is now available to read on bioRxiv! Very proud of this and its potential implications for patients with acute myeloid leukemia 🩸 🧪 🔬💊 **eIF4A-mediated translation initiation as an AML cell vulnerability that can be co-targeted with BCL-2 inhibition** www.biorxiv.org/content/10.1...

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Peter van Galen @vangalenlab.bsky.social · 16/12/2024

I2 is likely the cell barcode. This is a common sequencing setup for 10x scATAC: * Read1: 50 (genomic DNA) * P7-i7: 8 (library index) * P5-i5: 24 (spacer [8] + cell barcode [16]) * Read2: 50 (genomic DNA)

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Peter van Galen @vangalenlab.bsky.social · 16/12/2024

Our new review “Insights into Leukemia from Single-Cell Genomics” is out! Great work by Nurefsan Sariipek @nursariipek.bsky.social 📝 www.annualreviews.org/content/jour... #hemesky 🩸🧬

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Peter van Galen @vangalenlab.bsky.social · 05/12/2024

Office plants are watered, almost ready to hit the road #ASH24 🩸🧬 #HemeSky

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Peter van Galen @vangalenlab.bsky.social · 04/12/2024

...setting a transcript threshold that seems appropriate for blood progenitors will eliminate many T cell populations. This is illustrated in our MAESTER paper supplement pubmed.ncbi.nlm.nih.gov/35210612/ Thanks @sandramcallister.bsky.social for sending this along 3/3 #HemeSky 🩸 #GeneSky 🧬

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Peter van Galen @vangalenlab.bsky.social · 04/12/2024

Fundamentally, I would not recommend any universal QC pipeline across tissues and technologies. Datasets should be thoroughly evaluated by an expert with biological and computational expertise with a defined question. Simple example: cell types can have vastly different numbers of transcripts 👇🏻 2/3

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Peter van Galen @vangalenlab.bsky.social · 04/12/2024

Interesting BMC Genomics paper filters "nucleus-free" low-quality cells using the number of intronic reads. MALAT1 expression may provide a shortcut, but I would be wary of filtering out meaningful data 1/3 🩸🧬 @tmontsay.bsky.social @annaesteveco.bsky.social www.ncbi.nlm.nih.gov/pubmed/39574...

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Peter van Galen @vangalenlab.bsky.social · 04/12/2024

For example, setting a transcript threshold that seems appropriate for blood cell progenitors will eliminate many T cell populations. This is illustrated in this figure from our MAESTER paper supplement pubmed.ncbi.nlm.nih.gov/35210612/ Thanks @sandramcallister.bsky.social for sending this along 3/3

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Peter van Galen @vangalenlab.bsky.social · 04/12/2024

Fundamentally, I would not recommend any universal QC pipeline across tissues and technologies. Datasets should be thoroughly evaluated by an expert with biological and computational expertise with a defined question. For one, cell types can have vastly different numbers of transcripts: 2/3

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Peter van Galen @vangalenlab.bsky.social · 28/11/2024

On Thanksgiving day, what is the effect of frequent blood donations? Donors may have a higher prevalence of EPO-responsive clonal hematopoiesis, but there is no increased risk for malignant clones, underscoring safety of repetitive blood donations. www.medrxiv.org/content/10.1... 🩸🧪 #hemesky

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Peter van Galen @vangalenlab.bsky.social · 21/11/2024

This may be just what we need for our current question. Thanks! 🩸🧪

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Reposted by Peter van Galen

Fabian Theis @fabiantheis.bsky.social · 20/11/2024

1/ 🧬 Single-cell genomics reveals biological variations beyond cell types. Unveiling these in separate latent dim’s is known as disentanglement. Led by @AmirAliMoinfar, we develop DRVI to learn nonlinear, disentangled & interpretable latent spaces. biorxiv.org/content/10.1101/2024.11.06.622266v1

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Peter van Galen @vangalenlab.bsky.social · 18/11/2024

Bad use case 🫠 (and reminder to carefully check everything ChatGPT generates)

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Reposted by Peter van Galen

Kellie Machlus @kmachlus.bsky.social · 17/11/2024

Finally- the starter pack we have all been waiting for is here … Hematopoiesis 🎉❤️🩸🦴 So excited to have reached a critical mass of this community on here. 🙌🏻 Let me know if you want to be added!! go.bsky.app/KWdX5w7

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Peter van Galen @vangalenlab.bsky.social · 16/11/2024

Not many papers change the way I think about AML, but this exceptional work shows how cell states and genetics intertwine to mediate venetoclax resistance, unifying previous studies by identifying RAS-mutated LSCs that are primed to produce myeloid cells #hemesky 🩸🧪 www.nature.com/articles/s41...

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Peter van Galen @vangalenlab.bsky.social · 15/11/2024

Ok let’s give social media another try. I’ll share advances in blood/cancer/aging/bioinformatics research and pictures of my daily commute along Boston’s Esplanade like this one

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Peter van Galen @vangalenlab.bsky.social · 24/02/2024

Python ≠ my forte, but with the help of ChatGPT I created this nice little script to count files stored in Google Cloud Storage (GCS) buckets, categorized by their storage class (e.g., STANDARD, NEARLINE, COLDLINE, ARCHIVE). I hope it helps someone like it does me! 🐍 github.com/petervangale...