Our Giotto Suite paper has just been published in Nature Methods! In this paper, we showcased its power as a multiscale, extensible, and technology-agnostic ecosystem for spatial multi-omics data analysis. Key advances include: multiscale analysis, cross-technology integration, multi-omics integration, scalability, and interoperability. This is the result of a multi-year fantastic collaboration between the Guo-Cheng Yuan and Ruben Dries Labs. Congratulations to the co-first authors: Jiaji George Chen, Joselyn C. Chávez-Fuentes, and other members in the Yuan and Dries labs for their terrific contribution! More background information can be found in the accompanied Mount Sinai news release article.

We are excited to present ONTraC . This is a new method for analyzing spatial omics data, focusing on reconstructing spatial niche trajectories. The software is available at GitHub.

We are proud to release Giotto Suite after several years’ preparation. Giotto Suite greatly extends the functionality, flexibility, scalability, and interoperability compared to the original Giotto package. It implements a completely new design of the core data framework allowing technology-agnostic, multi-scale spatial multi-omic data analysis. This has been a great collaboration with Ruben Dries’ lab at Boston University. Many thanks to Jiaji (George) Chen, Joselyn Chavez, and the entire Giotto team!

We have received a new NIH RF1 grant to develop computational tools to facilitate harmonizing spatial transcriptomics data and integrating with additional data types for the BRAIN Initiative. We are recruiting a new postdoc to join in this effort.

DWLS is a cell-type deconvolution method previously developed by Daphne Tsoucas from our lab. To make this tool readily accessible to the broad community,  we have now converted it to a CRAN package which can be located here. Great work by Adriana!

The detailed protocol of our Giotto package has been published in Current Protocols in Bioinformatics. We provide step-by-step instructions, examples, and, markdown R scripts to help potential users access and apply Giotto in spatial transcriptomics analysis. Great effort by Natalie, George, and Ruben!

We have received a new RF1 grant to create a regulome and transcriptome atlas of fetal and adult human neurogenesis in collaboration with Profs. Roussos, Cai, and Hof labs. We are excited to join in the NIH BICCN network and look forward to collaborating other investigators in the consortium.

Our review paper has been published in the single-cell genomics special issue of Genome Research. In this paper, we provide a comprehensive review of the state-of-the-art computational methods and integrative pipelines on spatial transcriptomic data analysis. Great effort by Ruben, George, Natalie, Muzamil, and Adriana!

Our collaborative paper with Dr. Long Cai’s lab has been published in Science. In this paper, we applied integrative spatial genomics to investigate the single-cell nuclear structure across cell types in the mouse brain. Congrats to Yodai, Long, and our own Shiwei!