Senior Data Scientist - Bayraktar Group at @sangerinstitute
Cambridge, England
Joined September 2011
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Absolutely over the moon to share our COVID-19 study is now featured on @NatureComms Editors’ Highlights for Microbiology & Infectious Diseases! Huge thanks to @Lake_Octopus for choosing our work as one of the 50 BEST papers in this field. 💡Check it out: nature.com/collections/jedgc…
our work mapping the molecular + cellular progression of lung damage in severe COVID-19 is out @NatureComms ! A covid side project that turned into a labour of love over the years & really happy @THJimmyLee & Sam pushed this collaboration over the line. nature.com/articles/s41467-0…
📢 @bayraktar_lab @mo_lotfollahi & colabs at @sangerinstitute are assembling the @OpenTargets funded Neuroimmune Team 🧠🧬
Leverage AI to uncover neurodegeneration
Tech Spec: sanger.wd103.myworkdayjobs.c…
Postdoc AI: sanger.wd103.myworkdayjobs.c…
#SpatialTranscriptomics #Neurodegeneration
Jimmy Lee retweeted
🚨 We’re hiring @sangerinstitute!
Join us as a Postdoc or ML Scientist to build generative & foundation models for biology.
🧬 Spatial + single-cell omics
🧠 Diffusion, transformers, multimodal data
💊 Drug discovery via Open Targets
Apply:
Postdocs in computational biology and AI for biology 👉 lnkd.in/dk6PAp8y
ML scientist (sequence modelling) 👉 lnkd.in/dKEYJSNj
ML scientist (Foundation model) 👉 lnkd.in/dsp-CtcV
🔁 RT to help us find amazing people!
#AI #ML #genomics #bioinformatics #postdoc #foundationmodels #computationalbiology #hiring
Jimmy Lee retweeted
Alzheimer’s disease 🧠starts with a molecular domino effect - but what triggers the first piece to fall?
In our new study we cracked open the black box of early protein aggregation, and the findings could reshape how we fight neurodegeneration. 🧵👇
science.org/doi/10.1126/scia…
Very cool study that discovers novel recessive signals in a Exome sequencing of British South Asians population! 🧬
#Bioinformatics #exome #exomesequencing #populationgenetics #Genetics #datascience
Preprint alert! 🚨
Our manuscript on Exome sequencing and analysis of 44,028 British South Asians (Genes & Health) is now live @medrxivpreprint! Among great findings, and I’m thrilled to highlight the pieces I worked on 🧵
doi.org/10.1101/2025.06.05.2…
Amazing work by the GBM-SPACE team atlassing one of the deadliest cancers #glioblastoma at multimodality, & coupled the elegant scDORI framework. Revealing a high-res spatiotemporal cell trajectory from tumour heterogeneity & plasticity at both cellular and molecular levels
#GBM
How does tumour heterogeneity arise? How can we predict cancer cell plasticity? In 2 studies, we trace #glioblastoma heterogeneity to a spatial cancer cell trajectory w. atlassing bit.ly/4mkrWgs & predict plasticity w. snRNA/ATAC+deep learning bit.ly/3FbI6Ic 🧵
Ever wondered what a snapshot of single cell/spatial dataset can reveal?
scCellFie - a scalable tool that goes beyond gene expression, making metabolic analysis possible
3-2-1 Say GENES🤳
BioRxiv doi.org/10.1101/2025.05.09.6…
TRY NOW sccellfie.readthedocs.io
#DataScience #Bioinformatics
I’m happy to share that our scCellFie manuscript is finally on bioRxiv — a project that was an amazing opportunity to return to my roots in metabolism!
We infer metabolic activity from single-cell & spatial transcriptomics 🧬
Read the pre-print here👇
📄 doi.org/10.1101/2025.05.09.6…
Jimmy Lee retweeted
How can causal machine learning help answer causal questions in single-cell genomics—like how genes interact and influence phenotypes? Our latest @NatureGenet paper explores this challenge, along with approaches to generalizability, interpretability, and modeling cell dynamics.
Jimmy Lee retweeted
Amazing news for @humancellatlas
⭐ Huge NEWS for the Human Cell Atlas! ⭐
The Human Cell Atlas signs a partnership with the UNESCO. @humancellatlas @UNESCO
Tremendous recognition of the Human Cell Atlas (HCA) project's vision, ethical standards, and global impact. UNESCO, renowned worldwide for promoting open science, educational development, and ethical frameworks, now formally acknowledges the HCA’s efforts and mission. This collaboration honors HCA’s commitment to building a truly representative atlases of the global human population, underscoring our dedication to inclusivity, openness, and equity in scientific research.
As we move forward into the next exciting phase, developing also disease-specific atlases, this partnership with the UNESCO will empower us to tackle significant global health challenges, including diseases endemic to regions and worldwide pandemics.
Today, I'm feeling even prouder to be part of the HCA! 🧡 Looking forward to contributing further to building this remarkable effort in an inclusive, equitable, and truly global manner.
humancellatlas.org/news/the-…
Thrilled to share our new @NatureComms study w/ Sam from @NosedaLab on early vs late #COVID19 lung damage 🫁. Using single-cell & histopathology-informed #SpatialTranscriptomics, we uncovered key biomarkers & immune patterns. Thanks to collaborators & @UKCICstudy @humancellatlas
our work mapping the molecular + cellular progression of lung damage in severe COVID-19 is out @NatureComms ! A covid side project that turned into a labour of love over the years & really happy @THJimmyLee & Sam pushed this collaboration over the line. nature.com/articles/s41467-0…
Jimmy Lee retweeted
Interested in exploring @vevo_ai’s massive Tahoe-100M single-cell perturbation dataset? #Scanpy now supports out-of-core analysis, powered by Dask—allowing you to seamlessly work with a single huge AnnData object without loading everything into memory.
🔗 theislab.github.io/vevo_Taho…
Very excited to see this work out at @naturemethods Our lab's RNA velocity toolkit cell2fate ✅all the boxes if you're 1⃣looking for complex & weak dynamical signals 2⃣driver gene programmes 3⃣Cell fates in Spatial Transcriptomics! See the "X"torial shared below:
#bioinformatics
happy to see our cell2fate model out at @naturemethods. It is a completely new take on RNA velocity to disentangle complex cell trajectories from scRNA data & we have some very cool applications coming up! nature.com/articles/s41592-0…
Absolutely amazing!
Thrilled to share LUNA🌕 – our new generative AI model that reassembles tissues from dissociated cells! Think of it as AlphaFold for cells 🧬
From the MERFISH mouse brain atlas to the scRNA-seq atlas & Slide-tags datasets, LUNA is widely applicable. Bringing us closer to virtual tissue modeling 🧠
Super proud of @yistyu – what a way to start her PhD!🙌 And huge thanks also to all our collaborators @thecekbote @stephanedascoli @pafrossard Nikita Morozov Jiashuo Fan
Curious about LUNA? Check out our paper Tissue Reassembly with Generative AI: biorxiv.org/content/10.1101/…
Jimmy Lee retweeted
Are you keen to work with an exciting team? We are advertising a postdoc position jobs.ac.uk/job/DLW091/resear…
Looking forward to see great applicants!
@ImperialNHLI @imperialcollege
Jimmy Lee retweeted
Really fun to write this paper on spatial transcriptomics with @SarahBuddenborg . It’s an exciting technique that has a lot of potential in Parasitology for new insights.
In our Jan issue: Entering the #spatial age of parasite #genomics, authored by @SarahBuddenborg & @stephenrdoyle highlighting Simone Haeberlein & colleagues’ @NatureComms article. #Transcriptomics #Helminths #Fasciola #hepatica @sangerinstitute @jlugiessen
cell.com/trends/parasitology…
Jimmy Lee retweeted
Today we’re sharing an initial set of cell models that bring together #SingleCell & imaging data in a centralized place.
They come with a suite of resources so they’re easy to run + further develop to quickly uncover the mechanics of how cells work czi.co/4g1jTSa
It was a pleasure to give a talk at the #HCA2024Asia @humancellatlas meeting. I really enjoyed catching up with some @sangerinstitute alumni and had some fascinating discussions with amazing scientists like @drneavin
#HumanCellAtlas #Neuroscience #SingleCell #Bioinformatics
Final talk now in the #HCA2024Asia neuro track is from @THJimmyLee on cellular vulnerabilities in ALS
Jimmy Lee retweeted
What an atlas from the @TeichLab and @NosedaLab! 🤯
Sam Barnett (@sn_barnett), @Ana_Cujba, and Ling Yang (@edenling3) developed a #vascular cell atlas integrating #SingleCell data of 19 organs and tissues.
🔖 @NatureMedicine: go.nature.com/3Ou3B8e
💬: bit.ly/4g70Sxm
Jimmy Lee retweeted
Super proud of the vascular atlas team @sn_barnett @ana_cujba @teichlab Lu(Ling) Yang @LabAnna @NosedaLab @ImperialNHLI @imperialcollege @ImperialMed
What an epic achievement and great data demonstrating the diversity of human vascular cells
nature.com/articles/s41591-0…
Jimmy Lee retweeted
Latest paper out in @Nature this week: an atlas integrating 36 single-cell transcriptomic datasets spanning 26 protocols for making neural hashtag#organoids
Effort led by @TreutleinLab @fabian_theis and @GrayCampLab
In Figure 4 you can also find the pojection of the neural organoid morphogen screen developed by Neal @neal_amin and Kevin @kevinwkelley in the lab
