@almonell

Bioinformatics PhD Student at UC San Diego @GoldrathLab @yeo_lab

 San Diego
Joined August 2022
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We studied antigen-specific CD8 T cells in the mouse small intestine with spatial transcriptomics out @Nature! You can find the paper here (bit.ly/42mAwDS) and Max's (bit.ly/3Q9dfOB) and Miguel's (bit.ly/3E8slRA) Bluesky threads on our work.

Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted

Nature - Profiling of the location and transcriptome of tissue-resident memory CD8 T cell formation at single-transcript resolution finds regionalized signalling as the basis of immune diversity in...

nature.com
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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. hubs.la/Q033wDGh0 #MucosalImmunology #TumorImmunology
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Some press releases from: UCSD: bit.ly/4aspGOJ Allen Institute: alleninstitute.org/news/new-… LJI: bit.ly/40MjDBe @ljiresearch @AllenInstitute @UCSDHealthSci

New Research Reveals How Location Influences How Our Immune System Fights Disease

A new study led by a team of scientists reveals how cells known as tissue-resident memory CD8 T cells play unique and specialized roles based on where they are located. The discovery sheds light on...

today.ucsd.edu
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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
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Check out the published version of our paper!
Tatsuya Nobori@nobolly8 Jan 2025
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. nature.com/articles/s41586-0…
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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_lab2 Apr 2024
Excited to share research from @mah_clarence and @NoorsherAhmed in my group to enable deeper analysis of subcellular RNA localization from spatial transcriptomics datasets. link.springer.com/article/10…

Bento: a toolkit for subcellular analysis of spatial transcriptomics data

Genome Biology - The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell–cell interactions, and...

link.springer.com
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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! biorxiv.org/content/10.1101/…
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Finally, we performed spatial on human terminal ileum samples to draw relevant parallels to our mouse findings.
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We're excited to receive feedback from the community for this big team effort! biorxiv.org/content/10.1101/…

Functional Diversity of Memory CD8 T Cells is Spatiotemporally Imprinted

Tissue-resident memory CD8 T cells (TRM) kill infected cells and recruit additional immune cells to limit pathogen invasion at barrier sites. Small intestinal (SI) TRM cells consist of distinct...

biorxiv.org
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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.biorxiv.org/content/10.1101/…

Functional Diversity of Memory CD8 T Cells is Spatiotemporally Imprinted

Tissue-resident memory CD8 T cells (TRM) kill infected cells and recruit additional immune cells to limit pathogen invasion at barrier sites. Small intestinal (SI) TRM cells consist of distinct...

biorxiv.org
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Check out our recently published work building a spatial atlas of fetal heart development 🫀
nature
@Nature13 Mar 2024
Nature research paper: Spatially organized cellular communities form the developing human heart go.nature.com/48Tw92N

Spatially organized cellular communities form the developing human heart

Nature - Combining single-cell RNA-sequencing with high-resolution multiplexed error-robust fluorescence in situ hybridization reveals in detail the cellular interactions and specialization of...

nature.com
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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 science.org/doi/10.1126/scie…

Generalized biomolecular modeling and design with RoseTTAFold All-Atom

Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which combines a residu...

science.org
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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 -> lji.org/labs/reina-lab/

Reina Lab

Dr. Reina-Campos’ lab seeks to understand the underlying principles governing tissue immune networks that enable robust and long-term protection against infection and tumors.

lji.org
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Alex Monell retweeted
Tatsuya Nobori@nobolly12 Jun 2023
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 nature.com/articles/s41477-0…
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Well deserved, congrats!
Tatsuya Nobori@nobolly15 May 2023
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!
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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
The text “SpatialData Framework” along with the SpatialData logo, showing three stacked layers in perspective, at the top a yellow tabular structure, in the middle a dark blue layer with green dots (i.e. cells), and at the bottom a lighter blue layer with a black grid representing a raster image.

ALT The text “SpatialData Framework” along with the SpatialData logo, showing three stacked layers in perspective, at the top a yellow tabular structure, in the middle a dark blue layer with green dots (i.e. cells), and at the bottom a lighter blue layer with a black grid representing a raster image.

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