Luciano Martelotto
@lgmartelotto.bsky.social
Sc/St-Omics pro-aficionado. Knowledge sharing is my thing. Views, opinions and comments are my own and do not represent those of my employer. Like/Share ≠ endorse Favorite quote: “Be curious, not judgmental”
www.biorxiv.org/content/10.6...
Spatial microRNA profiling at single-cell resolution by in situ barcoded extension
The spatial organization of post-transcriptional regulation is a fundamental yet difficult to access layer of tissue biology. MicroRNAs (miRNAs) are small RNAs with a key role in post-transcriptional ...
biorxiv.org
Spatiotemporal transcriptome atlas of human embryos after gastrulation www.nature.com/articles/s41...
Spatiotemporal transcriptome atlas of human embryos after gastrulation - Nature
A spatiotemporal transcriptome atlas of whole-human embryos after gastrulation and previously transcriptionally undescribed stages of human development are reported.
nature.com
3D multi-omics tumour atlases: from technology to biology and clinical translation www.nature.com/articles/s41...
3D multi-omics tumour atlases: from technology to biology and clinical translation - Nature Reviews Cancer
In this Review, Liu et al. describe the established and emerging tools for the generation of comprehensive 3D tumour atlases, the analysis of which has the potential to uncover novel biomarkers for ri...
nature.com
www.science.org/doi/10.1126/...
TranscriptFormer: A generative cell atlas across 1.5 billion years of evolution
Single-cell transcriptomics is revolutionizing our understanding of cellular diversity, yet comparing transcriptional programs across the tree of life remains challenging. We developed TranscriptForme...
science.org
It's cool to see we aren't the only ones that think rationally designed probes + gapfilling is the future. Check out a corroborating workflow from @mgrillo.bsky.social, @lgmartelotto.bsky.social, Anna Nam, and colleagues: bsky.app/profile/mgri... 7/n
Marco Grillo@mgrillo.bsky.social · 6mo agoCapturing somatic mutations in single-cell probe-based assays (ie. 10X Flex) is a hard task, especially if you don't know *exactly* the mutations you want to capture, or if your target sequence is a mutational hotspot with many possible alternative alleles. Here's the way we pulled this off. Enjoy!
I had the “Filling” this week was going to be great! Brought to you by @danapeer.bsky.social @ronanchaligne.bsky.social and @caleblareau.bsky.social Sydney Blattman = ⭐️ Genotyping in fixed transcriptomes resolves clonal heterogeneity via single-cell sequencing. www.biorxiv.org/content/10.6...
biorxiv.org
New work from our @mgrillo.bsky.social with @lgmartelotto.bsky.social and others. Capture somatic mutations in single-cell assays via RNA-targeted gap filling. Check it out!
Marco Grillo@mgrillo.bsky.social · 6mo agoCapturing somatic mutations in single-cell probe-based assays (ie. 10X Flex) is a hard task, especially if you don't know *exactly* the mutations you want to capture, or if your target sequence is a mutational hotspot with many possible alternative alleles. Here's the way we pulled this off. Enjoy!
Capturing somatic mutations in single-cell probe-based assays (ie. 10X Flex) is a hard task, especially if you don't know *exactly* the mutations you want to capture, or if your target sequence is a mutational hotspot with many possible alternative alleles. Here's the way we pulled this off. Enjoy!
Luciano Martelotto@lgmartelotto.bsky.social · 6mo agoWe GoT a Filling…uuuuhoooo 𝗧𝗮𝗿𝗴𝗲𝘁𝗲𝗱 𝘀𝗲𝗾𝘂𝗲𝗻𝗰𝗶𝗻𝗴 𝗼𝗳 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻𝘀 𝘃𝗶𝗮 𝗥𝗡𝗔-𝘁𝗲𝗺𝗽𝗹𝗮𝘁𝗲𝗱 𝗴𝗮𝗽 𝗳𝗶𝗹𝗹𝗶𝗻𝗴 𝗼𝗳 𝗼𝗹𝗶𝗴𝗼𝗻𝘂𝗰𝗹𝗲𝗼𝘁𝗶𝗱𝗲𝘀 𝗳𝗼𝗿 𝘀𝗶𝗻𝗴𝗹𝗲-𝗰𝗲𝗹𝗹 𝗥𝗡𝗔-𝘀𝗲𝗾 www.biorxiv.org/content/10.6...
We GoT a Filling…uuuuhoooo 𝗧𝗮𝗿𝗴𝗲𝘁𝗲𝗱 𝘀𝗲𝗾𝘂𝗲𝗻𝗰𝗶𝗻𝗴 𝗼𝗳 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻𝘀 𝘃𝗶𝗮 𝗥𝗡𝗔-𝘁𝗲𝗺𝗽𝗹𝗮𝘁𝗲𝗱 𝗴𝗮𝗽 𝗳𝗶𝗹𝗹𝗶𝗻𝗴 𝗼𝗳 𝗼𝗹𝗶𝗴𝗼𝗻𝘂𝗰𝗹𝗲𝗼𝘁𝗶𝗱𝗲𝘀 𝗳𝗼𝗿 𝘀𝗶𝗻𝗴𝗹𝗲-𝗰𝗲𝗹𝗹 𝗥𝗡𝗔-𝘀𝗲𝗾 www.biorxiv.org/content/10.6...
biorxiv.org
Why so serious? 🃏 Marco Grillo, Anna Nam and yours truly 𝗚𝗼𝗧 𝗮 𝗙𝗶𝗹𝗹𝗶𝗻𝗴 that will make you happy 😃 No more limitations. Maximum flexibility. Something is coming. Stay tuned. #singlecellwithaplus
2026 HCA Asia Meeting in the land of Oz! 🫶🫶🫶 events.humancellatlas.org/2026asia/Home
Home
events.humancellatlas.org
Enjoyed writing this Preview with Jonas Gudera on GoT-Multi 🪄 A powerful #singlecell approach from the teams of Anna Nam and @lgmartelotto.bsky.social Preview: www.cell.com/cell-genomic... Paper: www.cell.com/cell-genomic...
New revolutionary hack about to change our molecular tool-box! Thanks @ioavlachos.bsky.social for sharing this! Rapid evolution of a highly efficient RNA polymerase by homologous recombination www.nature.com/articles/s41...
academic.oup.com/nargab/artic...
Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies
Abstract. The rapid development of updated and new commercially available single-cell transcriptomics platforms provides users with a range of experimental
academic.oup.com
Join us to the last #GESTALT seminar the year! Free for all GESTALT member. If you are interested in anything #spatialbiology come be part of our growing community GESTALT Seminar Series globalspatial.org/seminar-seri... December 19 10am EST @ioavlachos.bsky.social @lgmartelotto.bsky.social
Seminar Series – GESTALT – Global Alliance for Spatial Technologies
globalspatial.org
Thanks @natbiotech.nature.com for the shoutout and supporting our work at attempting QC in this emerging field of #spatial #transcriptomics @lgmartelotto.bsky.social @christophermason.bsky.social
Nature Biotechnology@natbiotech.nature.com · 10mo agoSpatial Touchstone brings quality control to spatial transcriptomics #NBTintheNews via @stjuderesearch.bsky.social www.stjude.org/media-resour...
Goliath effort to help with standards in spatial trancriptomics-can only be more amazing when done with @lgmartelotto.bsky.social @christophermason.bsky.social 🚀 Paper: nature.com/articles/s4158… Touchstone portal: spatialtouchstone.org Spatial touchstone protocols: protocols.io/view/spatial-t���
nature.com
St. Jude Children's Research Hospital@stjuderesearch.bsky.social · 10mo agoA collaborative project led by St. Jude has established a comprehensive framework for standardizing spatial transcriptomics. The Spatial Touchstone project integrates publicly available imaging data with newly curated datasets across six tissue types. ow.ly/Ghrg50XBkr6
Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets - @jasmineplummer.bsky.social @lgmartelotto.bsky.social go.nature.com/4rBC1Z0
Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets - Nature Biotechnology
A multi-institute, multi-platform initiative generates standard metrics and best practices for spatial transcriptomics analysis.
go.nature.com
advanced.onlinelibrary.wiley.com/doi/10.1002/...
Single‐Cell Profiling: Any Scale, Any Size, All at Once
Traditional single-cell technologies are constrained by cellular dimension and throughput scale, in addition to its inability preserve spatial information. With recent innovations, these technologies...
advanced.onlinelibrary.wiley.com
Calling all #singlecell #spatial officianados. Join GESTALT team in our workshop at NextGenOmics Spatial & Data 2025 Naveed Ishaque Musa Mhlanga Silas Maniatis Ahmet Coskun Free registration for GESTALT members Nov 13-14 in London UK! @jasmineplummer.bsky.social @ioavlachos.bsky.social
iSCALE www.nature.com/articles/s41...
Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE - Nature Methods
iSCALE leverages histology and spatial transcriptomics to infer gene expression at super resolution in large tissues.
nature.com
Must read from Nick Navin’s lab! www.cell.com/cell/abstrac...
Coalescing single-cell genomes and transcriptomes to decode breast cancer progression
wellDR-seq allows single-cell whole-genome and transcriptome co-profiling at scale, enabling dissections of complex relationships between copy-number alterations and gene expression that inform our un...
cell.com
www.biorxiv.org/content/10.1...
anndataR improves interoperability between R and Python in single-cell transcriptomics
Many single-cell transcriptomics datasets are stored in the HDF5-backed AnnData (H5AD) file format, as popularised by the Python scverse ecosystem. However, accessing these datasets from R, allowing u...
biorxiv.org
New online! Imaging-based multimodal profiling of single cells with STAMP
Imaging-based multimodal profiling of single cells with STAMP
Nature Reviews Genetics, Published online: 21 August 2025; doi:10.1038/s41576-025-00891-6In this Tools of the Trade article, Kellie Wise and Anna Pascual-Reguant introduce STAMP (single-cell transcriptomics analysis and multimodal profiling), which harnesses imaging to measure RNA and/or protein expression in fixed cells or nuclei.
nature.com
Very proud of these two! Anna Pascual Reguant | Kellie Wise A beautiful collaboration with Jasmine Plummer & Holger Heyn CNAG | St Jude Children’s Research Hospital #STAMP Imaging-based multimodal profiling of single cells with STAMP | Nature Reviews Genetics www.nature.com/articles/s41...
Imaging-based multimodal profiling of single cells with STAMP - Nature Reviews Genetics
In this Tools of the Trade article, Kellie Wise and Anna Pascual-Reguant introduce STAMP (single-cell transcriptomics analysis and multimodal profiling), which harnesses imaging to measure RNA and/or ...
nature.com
www.biorxiv.org/content/10.1...
Integrating 12 Spatial and Single Cell Technologies to Characterise Tumour Neighbourhoods and Cellular Interactions in three Skin Cancer Types
Cutaneous squamous cell carcinoma (cSCC), basal cell carcinoma (BCC), and melanoma, the three major types of skin cancer, account for over 70% of all cancer cases. Despite their prevalence, the skin c...
biorxiv.org
Counting my lucky stars⭐️that not only do I get to work with these amazing scientists Jiwoon Park @christophermason.bsky.social but also give fun @cshlnews.bsky.social lectures together💪.Big thank you to @lgmartelotto.bsky.social Nicholas Navin Julea Vlassakis for uniting this #singlecell #dreamteam
