π§ Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at endπ§΅π
16.05.2025 10:04 β π 76 π 29 π¬ 1 π 6
How does tumour heterogeneity arise? How can we predict cancer cell plasticity? In 2 new studies, we trace #glioblastoma heterogeneity to a spatial cancer cell trajectory w. multimodal cell atlassing bit.ly/4mkrWgs & predict plasticity w. snRNA/ATAC+deep learning bit.ly/3FbI6Ic π§΅
16.05.2025 11:42 β π 71 π 31 π¬ 6 π 5
Iβm happy to share that our scCellFie manuscript is finally on bioRxiv β a project that was an amazing opportunity to return to my roots in metabolism!
We infer metabolic activity from single-cell & spatial transcriptomics π§¬
Read the pre-print hereπ
π doi.org/10.1101/2025...
15.05.2025 08:21 β π 6 π 1 π¬ 1 π 1
Our review "Predicting gene expression from DNA sequence using deep learning models" is finally out! π€
14.05.2025 15:43 β π 43 π 11 π¬ 4 π 2
Thrilled to share our new @naturecomms.bsky.social study with @sam-n-barnett.bsky.social on early vs late #COVID19 lung damage π«.
Using single-cell & histopathology-informed #SpatialTranscriptomics, we uncovered key biomarkers & immune patterns. Thanks to collaborators, UKCIC & @humancellatlas.org
12.03.2025 06:35 β π 5 π 1 π¬ 0 π 1
Another great computational method out of the Bayraktar lab!
Alexander Aivazidis has been a great colleague in our lab and it's amazing to see the capstone of his PhD is now published.
03.03.2025 13:16 β π 1 π 0 π¬ 0 π 0
Feri's fundraiser for Refuge
Help Feri Torabi raise money to support Refuge
And the talented PhD student Feri from @mhaniffa.bsky.socialβs
lab is running for Refuge:
supporting women and their children to overcome the impact of domestic abuse.
www.justgiving.com/page/feri-to...
01.03.2025 14:00 β π 2 π 0 π¬ 0 π 0
Jimmy's fundraiser for Alzheimer's Research UK
Help Jimmy Lee raise money to support Alzheimer's Research UK
Our labβs computational wizard @drjimmylee.bsky.social is supporting Alzheimerβs Research UK: www.justgiving.com/page/jimmy4a...
01.03.2025 14:00 β π 2 π 0 π¬ 1 π 0
Next weekend I will run the Cambridge half marathon with @sangerinstitute.bsky.social colleagues πββοΈ
Two amazing people are running for charities, please support them!
01.03.2025 14:00 β π 2 π 1 π¬ 1 π 1
This is really horrific. These single cell reference atlases are widely used as is to train all kinds of models! This is one of the reasons I've constantly harping about uniform reprocessing & extremely careful QC of large atlases. 1/
04.12.2024 07:06 β π 145 π 41 π¬ 9 π 4
Prof of Computer Science and Life Sciences @ EPFL Previously @ Stanford
MLπ€+Bio𧬠https://brbiclab.epfl.ch/
A scientific journal publishing cutting-edge methods, tools, analyses, resources, reviews, news and commentary, supporting life sciences research. Posts by the editors.
Assistant Professor @YaleMed | tissue biology, computation, systems biology |
www.hattiechunglab.bio
PhD Candidate @Cambridge_Uni @sangerinstitute @TrinityHallCamb | learning enthusiast | allergic to mediocrity.
Ψ¨Ψ±Ψ§Ϋ Ψ’Ψ²Ψ§Ψ―Ϋ
Politicoloog en parttime prins. Book on Dutch neoliberal turn due to appear spring 2026 @Verso Books. Columns @DeGroene. βOh god, deze man, hou op! Deze Oudenampsen is een dwaas.β - Frits Bolkestein
website: https://merijnoudenampsen.org/
Researcher at Heidelberg University @saezlab.bsky.social | #ML and AI in #single-cell and #spatial #omics
New here.
Doppelganger. This Changes Everything. The Shock Doctrine. No Logo. On Fire.
UBC Professor of Climate Justice.
π naomiklein.org
π¬ news.naomiklein.org/newsletter
PhD student @EMBL, Stegle group.
Deep learning on single-cell genomics, genetics and electronic health records to understand disease and improve human health.
https://orcid.org/0000-0002-1674-5141
We are a research lab at the Netherlands Cancer Institute. We develop and apply new genomics tools to study genome biology and gene regulation.
Scientist at DKFZ and EMBL in Heidelberg, loving stats, genomics and genetics. @OliverStegle@genomic.social. For group news see @steglelab.bluesky.social
Historicus | Spartaan | Sufisticated πΏ | De Groene Amsterdammer | ex-NRC | Auteur van βGeneratie 9/11β
Chileno π¨π± - Postdoc at the Wellcome Sanger Institute. PhD in Bioinformatics & Systems Biology from UC San Diego.
https://earmingol.github.io
PhD candidate in ML for genomics in Heidelberg, Germany with Oli Stegle
Previously at Genentech, UBC and BITS Pilani
https://scholar.google.com/citations?user=4yUtALcAAAAJ&hl=en&oi=ao
PhD student within the Functional Genomics group (Franke lab), University Medical Centre Groningen. Interested in gene networks, sequence-based models and non-coding somatic mutations
PhD student. Studying gene regulation using AI models | UMCU + NKI, The Netherlands
Anthropologist - Bayesian modeling - organic modem converting poetry into code - cat and cooking content too - Director @ MPI for evolutionary anthropology https://www.eva.mpg.de/ecology/staff/richard-mcelreath/
PhD student at Bioinformatics and Cellular Genomics group @SVIResearch
Group leader
@sangerinstitute.bsky.social Neural diversity, spatial transcriptomics, glia, GBM
Mats Nilsson's team at Stockholm University and Scilifelab, researching molecular diagnostics and in-situ spatial transcriptomics
EMBO postdoc @teichlab @SCICambridge | Single-cell genomics and gene regulation | PhD in evodevo genomics @kaessmannlab @UniHeidelberg
