Valentina Boeva
@valboeva.bsky.social
Computational Cancer Genomics Group
Reposted by Valentina Boeva
#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
@valboeva.bsky.social @bhaibeka.bsky.social
July 12, 2025 at 6:12 PM
#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
@valboeva.bsky.social @bhaibeka.bsky.social
🔥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! 🚀
Ever wondered if you can linearly interpolate between transformers and still get a working model? Now you know how. A breakthrough! 🚀
July 4, 2025 at 3:26 PM
🔥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! 🚀
Ever wondered if you can linearly interpolate between transformers and still get a working model? Now you know how. A breakthrough! 🚀
🚨 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
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
June 11, 2025 at 12:57 PM
🚨 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
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
Reposted by Valentina Boeva
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.
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
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
April 26, 2025 at 11:00 AM
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.
Reposted by Valentina Boeva
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...
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
April 11, 2025 at 5:55 PM
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...
www.nytimes.com/2025/04/11/s...
🥳🔥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
April 10, 2025 at 5:05 PM
🥳🔥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!
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!
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
March 23, 2025 at 11:41 AM
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!
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!
Reposted by Valentina Boeva
🎤 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
🔹Session chaired by @valboeva.bsky.social and @carmonation.bsky.social
👉Interested? Submit your abstract before 27 Feb: tinyurl.com/49w6wthj
February 4, 2025 at 8:38 AM
🎤 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
🔹Session chaired by @valboeva.bsky.social and @carmonation.bsky.social
👉Interested? Submit your abstract before 27 Feb: tinyurl.com/49w6wthj
Reposted by Valentina Boeva
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
February 4, 2025 at 2:40 PM
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
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...
January 13, 2025 at 10:01 AM
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...
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!
January 10, 2025 at 3:26 PM
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!
🌟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 👇
@flobarkmann.bsky.social and Alex Theus 👇
📢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...
Preprint: biorxiv.org/content/10.1...
December 15, 2024 at 8:01 PM
🌟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 👇
@flobarkmann.bsky.social and Alex Theus 👇
📅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
📢 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.
December 13, 2024 at 8:22 AM
📅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
Reposted by Valentina Boeva
A mathematical model clarifies the ABC Score formula used in enhancer-gene prediction https://www.biorxiv.org/content/10.1101/2024.11.29.626072v1
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
December 4, 2024 at 12:48 AM
A mathematical model clarifies the ABC Score formula used in enhancer-gene prediction https://www.biorxiv.org/content/10.1101/2024.11.29.626072v1
Reposted by Valentina Boeva
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....
1/8
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
December 3, 2024 at 8:38 AM
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....
1/8
🚀 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
November 26, 2024 at 1:40 PM
🚀 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
Should now we start doing it for whole human tumors?!
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/...
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/...
November 22, 2024 at 5:26 PM
Should now we start doing it for whole human tumors?!
Reposted by Valentina Boeva
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
tinyurl.com/ymkvk7vn
November 20, 2024 at 8:07 AM
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
tinyurl.com/ymkvk7vn
Reposted by Valentina Boeva
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
November 17, 2024 at 8:47 PM
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/...