Alex Monell

Bioinformatics PhD Student at UC San Diego @GoldrathLab @yeo_lab

[Alex Monell @almonell]

We studied antigen-specific CD8 T cells in the mouse small intestine with spatial transcriptomics out @Nature!

You can find the paper here (https://t.co/ja2hChyRlP) and Max's (https://t.co/xD4AxnDNat) and Miguel's (https://t.co/2js1nRDQ9K) Bluesky threads on our work.

[Journal of Experimental Medicine @JExpMed]

Ferry, @AGoldrath et al. @ucsdbiosciences show that differentiation of tissue-resident memory T cells (TRM) is accompanied by the upregulation of the conventional DC1 (cDC1) chemoattractant, Xcl1. https://t.co/OvQDU1ACmu

#MucosalImmunology #TumorImmunology

[Alex Monell @almonell]

Thanks to the whole team on this project @reinacampos.bsky.social @heeg.io (Bluesky) @GoldrathLab @UCSDChangLab @yeo_lab

@10xGenomics and @vizgen_inc for their spatial transcriptomics technologies

And @elnlnx for the amazing cover art

[Alex Monell @almonell]

We studied antigen-specific CD8 T cells in the mouse small intestine with spatial transcriptomics out @Nature!

You can find the paper here (https://t.co/ja2hChyRlP) and Max's (https://t.co/xD4AxnDNat) and Miguel's (https://t.co/2js1nRDQ9K) Bluesky threads on our work.

[Alex Monell @almonell]

Some press releases from:
UCSD: https://t.co/DvEQ63rn2N
Allen Institute: https://t.co/HOMankhhBR
LJI: https://t.co/pYwwyO3rho
@ljiresearch @AllenInstitute @UCSDHealthSci

[Alex Monell @almonell]

Check out the published version of our paper!

[Tatsuya Nobori @nobolly]

New year, new paper! Now published in @Nature. We identified and characterised diverse immune cell states in plants under pathogen attack. My postdoc work in @JoeEcker lab at @salkinstitute.
https://t.co/YcvFuDpO0U

[Alex Monell @almonell]

Check out Bento, a toolkit for studying sub cellular transcript localization in spatial transcriptomics data led by @mah_clarence @NoorsherAhmed

[Gene Yeo’s Lab at UC San Diego @yeo_lab]

Excited to share research from @mah_clarence and @NoorsherAhmed in my group to enable deeper analysis of subcellular RNA localization from spatial transcriptomics datasets. https://t.co/S96rbRFL6y

[Alex Monell @almonell]

We're excited to receive feedback from the community for this big team effort!
https://t.co/84gVlgExDd

[Alex Monell @almonell]

Our team (@MReinaCampos @MaximilianHeeg @GoldrathLab @UCSDChangLab @yeo_lab) used single-cell spatial transcriptomics to study antigen-specific Cd8 T-Cell (P14) responses to acute systemic viral infection in the small intestine.

Check it out on biorxiv! https://t.co/84gVlgExDd

[Alex Monell @almonell]

Finally, we performed spatial on human terminal ileum samples to draw relevant parallels to our mouse findings.

[Miguel Reina-Campos @MReinaCampos]

How is immunity molded by the tissues it inhabits? Excited to share the latest @GoldrathLab study - a “TRM exposé” - in which we found that CD8 T cell location and functional states are fundamentally intertwined.https://t.co/ZLLTp1RCcz

[Alex Monell @almonell]

Check out our recently published work building a spatial atlas of fetal heart development 🫀

[nature @Nature]

Nature research paper: Spatially organized cellular communities form the developing human heart https://t.co/dJbVm4jC8f

[Nature Biotechnology @NatureBiotech]

AlphaFold2 and RoseTTAFold are limited to predicting the 3D structure of proteins. A new all-atom method models complete biomolecular assemblies, including proteins, nucleic acids, small molecules, metals, and covalent modifications. #NBThighlight https://t.co/a9relIlKLC

[Miguel Reina-Campos @MReinaCampos]

Curious about the Reina Lab? Functional genetic screens, metabolomics, and lots of #spatialtranscriptomics to define the inner workings of T cell tissue immunity in infection and cancer ->
https://t.co/stZKd1Luwu

[Tatsuya Nobori @nobolly]

Our PHYTOMap paper (w/ @JoeEcker @ry_lister @molivarina) has now been published in @NaturePlants 🌱🧬🔬

Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap
https://t.co/Qkzee93vNG

[Alex Monell @almonell]

Well deserved, congrats!

[Tatsuya Nobori @nobolly]

Thrilled to share that I will be opening a lab @TheSainsburyLab next year! My lab will study plant-microbe interactions with cutting-edge technologies that bring genomics and cell biology together. I will post updates on available positions on Twitter. Stay tuned!

[Luca Marconato @LucaMarconato2]

1/9 Excited to share #SpatiaData, a framework for representing spatially-resolved omics technologies. Great colab w/ @g_palla1 @ky396 @ivirshup @HeidariElyas @TreisTim Marcella @rahulbshrestha @harald_voeh @wolfgangkhuber @MoritzGerstung @notjustmoore @fabian_theis @OliverStegle