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Reposted by Valentina Boeva

American Association for Cancer Research (AACR) @theaacr.bsky.social · Jul 12

#AACRai25 cochairs Valentina Boeva and Benjamin Haibe-Kains adjourned the AACR Conference on AI and Machine Learning. We thank all of the chairs—including @marzyehghassemi.bsky.social and @bowang87.bsky.social—for developing an outstanding program.
@valboeva.bsky.social @bhaibeka.bsky.social

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Valentina Boeva @valboeva.bsky.social · Jul 4

🔥A very cool piece from Alexander Theus and team is finally on arXiv: arxiv.org/abs/2506.22712

Ever wondered if you can linearly interpolate between transformers and still get a working model? Now you know how. A breakthrough! 🚀

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Valentina Boeva @valboeva.bsky.social · Jun 11

🚨 New preprint out!
We studied deep learning models for high-resolution DNA accessibility prediction from DNA sequence!

Key takeaway: ConvNeXt V2 blocks consistently boost accuracy.

📖 Preprint: biorxiv.org/content/10.1...
🔗Code: github.com/BoevaLab/ASAP
📦 pip install atac-asap

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Reposted by Valentina Boeva

Stein Aerts @steinaerts.bsky.social · Apr 26

Our new call for VIB.AI group leaders is online! Junior and senior positions available to develop innovative ML methods in biology. With professorship at CS or Medical Faculty. Deadline 14th June. DM for more info.

VIB.AI @vibai.bsky.social · Apr 25

We are looking for additional Group Leaders to join the growing computational biology community at VIB.

If you are excited about combining AI and machine learning with fundamental biology, we would love to hear from you!

https://vib.ai/en/opportunities#/job-description/110906

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Reposted by Valentina Boeva

Maxim Greenberg @maxvcg.bsky.social · Apr 11

The Americans are doing to Kseniia what the Russians did to Brittney Griner for having 0.7 grams of cannabis oil. Except no one is coming to negotiate her freedom and Harvard is sitting on their hands. I am so ashamed. Please share this story.
www.nytimes.com/2025/04/11/s...

She Worked in a Harvard Lab to Reverse Aging, Until ICE Jailed Her (Gift Article)

President Trump’s immigration crackdown ensnared Kseniia Petrova, a scientist who fled Russia after protesting its invasion of Ukraine. She fears arrest if she is deported there.

www.nytimes.com

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Valentina Boeva @valboeva.bsky.social · Apr 10

🥳🔥Our study is out in Genome Biology! Conventional filtering out high-mtRNA cells depletes key malignant populations in cancer single-cell studies. Read it here 👉 genomebiology.biomedcentral.com/articles/10.... Thanks to the dream team: Josephine Yates and Agneizska Kraft!

Filtering cells with high mitochondrial content depletes viable metabolically altered malignant cell populations in cancer single-cell studies - Genome Biology

Background Single-cell transcriptomics has transformed our understanding of cellular diversity, yet noise from technical artifacts and low-quality cells can obscure key biological signals. A common pr...

genomebiology.biomedcentral.com

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Valentina Boeva @valboeva.bsky.social · Mar 23

Speakers: Dana Pe’er, Marinka Zitnik, Charlotte Bunne, Raul Rabadan, Christina Curtis, Ben Raphael, Anne Carpenter, Elana J. Fertig, and many others! www.aacr.org/meeting/aacr...

Program

Program overview for AACR Special Conference in Cancer Research: Artificial Intelligence and Machine Learning

www.aacr.org

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Valentina Boeva @valboeva.bsky.social · Mar 23

Interested in cutting-edge ML and AI in cancer research?
Join us at the AACR Special Conference on Artificial Intelligence and Machine Learning in Montreal, July 10–12, 2025:
🔗 www.aacr.org/meeting/aacr...

⏳ Submit your abstract by April 16, 2025 at 1 p.m. ET!

AACR Special Conference in Cancer Research: Artificial Intelligence and Machine Learning

Overview for AACR Special Conference in Cancer Research: Artificial Intelligence and Machine Learning

www.aacr.org

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Reposted by Valentina Boeva

SIB Swiss Institute of Bioinformatics @sib.swiss · Feb 4

🎤 It is a pleasure to welcome Itay Tirosh from the Weizmann Institute at [BC]². Itay will present in the session 'Bioinformatics for cancer research'.

🔹Session chaired by @valboeva.bsky.social and @carmonation.bsky.social

👉Interested? Submit your abstract before 27 Feb: tinyurl.com/49w6wthj

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Reposted by Valentina Boeva

Samuel Kaski @samikaski.bsky.social · Feb 4

I have big news: @ellis.eu has launched its 2nd major research center, @ellisfinland.bsky.social! I have agreed to start as founding director & the first call for PI positions is open. This is a major opportunity for outstanding researchers, join us! ellisinstitute.fi/PI-recruit

Principal Investigator positions at ELLIS Institute Finland | ELLIS Institute Finland

Now recruiting new PIs in artificial intelligence and machine learning

ellisinstitute.fi

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Valentina Boeva @valboeva.bsky.social · Jan 13

Looking forward to meeting the Lausanne AI Center people and giving a talk on predicting enhancer-promoter interactions using our deep ensemble model this Wednesday! memento.epfl.ch/event/ai-cen...

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Valentina Boeva @valboeva.bsky.social · Jan 10

Looking forward to presenting our recent (and yet unpublished) work at UNIL/CHUV next Thursday! If you're in Lausanne and would like to meet, ping me—I’ll be around from Tuesday to Friday!

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Valentina Boeva @valboeva.bsky.social · Dec 15

🌟If you are at #NeurIPS2024, stop by our poster on the first single-cell #cancer foundation model. Amazing work by
@flobarkmann.bsky.social and Alex Theus 👇

Florian Barkmann @flobarkmann.bsky.social · Dec 15

📢If you are interested in single-cell foundation models (scFMs), stop by our poster (West 109) at the AiDrugX Workshop at Neurips 2024. We will present CancerFoundation, a scFM tailored for studying cancer biology🧬.
Preprint: biorxiv.org/content/10.1...

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Valentina Boeva @valboeva.bsky.social · Dec 13

📅Are you attending #NeurIPS2024 and curious about the latest in self-supervised learning (SSL) for biology? - Stop by our poster on applying SSL on single-cell data: SSL workshop on Saturday! Work by amazing team of @oovcharenko.bsky.social, P. Toma, Imant D., J. Vogt and @flobarkmann.bsky.social

Olga Ovcharenko @oovcharenko.bsky.social · Dec 12

📢 Our benchmark on self-supervised learning for single-cell data🧬 is accepted at the #NeurIPS2024 SSL workshop. We take a first step towards establishing best practices for SSL methods for single-cell data, and benchmark 8 SSL methods on 3 downstream tasks across 8 datasets.

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Reposted by Valentina Boeva

bioRxiv Biophysics @biorxiv-biophys.bsky.social · Dec 4

A mathematical model clarifies the ABC Score formula used in enhancer-gene prediction https://www.biorxiv.org/content/10.1101/2024.11.29.626072v1

Enhancers are discrete DNA elements that regulate the expression of eukaryotic genes. They are impor

www.biorxiv.org

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Reposted by Valentina Boeva

Tomàs Montserrat Ayuso @tmontsay.bsky.social · Dec 3

Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
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High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics

The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...

bmcgenomics.biomedcentral.com

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Valentina Boeva @valboeva.bsky.social · Nov 27

Hi Fena, please add me.

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Valentina Boeva @valboeva.bsky.social · Nov 26

🧬UseUniversalEPI for in-silico 3D chromatin modeling in your favorite model! Examples of applications: studies on genetic diseases, cell differentiation, and the regulatory impacts of non-coding variants.

Valentina Boeva @valboeva.bsky.social · Nov 26

- Tracks chromatin dynamics in processes like macrophage reprogramming and cancer transcriptional states.
- Scalable for both bulk and single-cell chromatin accessibility data.

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Valentina Boeva @valboeva.bsky.social · Nov 26

🔬 Key Highlights:
- Predicts chromatin interactions across unseen cell types with no retraining.
- Outperforms state-of-the-art models like C.Origami and ChromaFold with Spearman’s Rho > 0.92 in unseen cell types.

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Valentina Boeva @valboeva.bsky.social · Nov 26

🚀 New preprint from our lab, Ekaterina Krymova, and @fabiantheis.bsky.social: UniversalEPI, an attention-based method to predict enhancer-promoter interactions from DNA sequence and ATAC-seq🌟 Read the full preprint: www.biorxiv.org/content/10.1... by @aayushgrover.bsky.social, L. Zhang & I.L. Ibarra

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Valentina Boeva @valboeva.bsky.social · Nov 22

Should now we start doing it for whole human tumors?!

Johanna Joyce @johannajoyce.bsky.social · Nov 22

Whole-brain spatial transcriptional analysis at cellular resolution

Incredible study - 3D single cell imaging of the entire mouse brain - also on the cover of this week's #Science
🧪🔬🤯

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

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Reposted by Valentina Boeva

Dominic Grün @dominicgrun.bsky.social · Nov 20

Hiring! I'm looking for a postdoc in machine learning of spatial single-cell data. Exciting project to develop methods for modelling cellular circuits in disease and regeneration of heart, liver and bone marrow using Xenium data from our lab.
tinyurl.com/ymkvk7vn

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Reposted by Valentina Boeva

Sten Linnarsson @sten.linnarsson.org · Nov 17

Before I go to bed let me post an amazing paper by Filipe Pereira’s group (Ervin Ascic et al) for your enjoyment. I think this is a likely fundamental breakthrough in cancer immunotherapy: personalized, yet generic and probably pan-cancer. www.science.org/doi/10.1126/...

In vivo dendritic cell reprogramming for cancer immunotherapy

Immunotherapy can lead to long-term survival for some cancer patients, yet generalized success has been hampered by insufficient antigen presentation and exclusion of immunogenic cells from the tumor ...

www.science.org

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