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. Excellent work by Wen, Shiwei, and Crystal!

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!

Our Giotto paper has been published in Genome Biology. Giotto is a comprehensive and open-source software package for spatial data analysis and visualization. It contains many functionalities such as cell-type identification, deconvolution, spatial pattern detection, cell neighborhood analysis, ligand-receptor detection, and interactive visualization.  We welcome users to check out our project and GitHub websites.

The DNA seqFISH+ paper has been published in Nature. We use super-resolution imaging combined with multiplex DNA barcoding to visualize the 3D chromatin structure in individual cells. We found extensive chromatin structure heterogeneity within transcriptionally similar cell states. It was a great collaboration with Dr. Long Cai’s lab.