In new work in collaboration with Roy Wollman at UCLA, Xiaojun leads work developing methods for parameter inference of Ca2+ dynamics in single cells, making use of the unique information gained from jointly measuring the dynamic Ca2+ responses and the single-cell gene expression in the same single cells. Through clustering of the posterior distributions, we discover that differences in gene expression can inform key differences in the dynamic cellular responses. Code is available here. Read the preprint here.
Giuseppe Torrisi from the lab of Linus Schumacher at the University of Edinburgh visited us this week. We enjoyed deep discussions on the theory of gene regulatory networks: models, principles, and dynamics. We also enjoyed Southern Italian food… probably dangerous to try in Los Angeles with a Sicilian guest, but it seems we got away with it.
MeiLu and Adam visited Lund University in Sweden for the 2022 ELLIIT Focus Period on Data-driven modelling and learning for cancer immunotherapy. The goals were to ”unite young international scholars, ELLIIT researchers and other top international academics active in domains such as systems biology, cancer treatment, machine learning and dynamical systems,” and indeed the participants were diverse! From clinicians to a Fields medalist. Yet we managed to find common ground across these broad domains.
Congratulations to Nikith, undergraduate researcher in the lab, who has been awarded a Summer 2022 Provost’s Research Fellowship to continue his research in the lab this summer. Nikith is developing new models of Wnt shuttling and chaperone mechanisms that impact neurodegenerative disorders.
Our paper: Age-dependent effects of Igf2bp2 on gene regulation, function, and aging of hematopoietic stem cells in mice, is out now in Blood. In this work, Megan led the computational analyses of bulk and single-cell RNA-sequencing data of HSCs to study the role of RNA-binding protein Igf2bp2. We discovered a complex role for Igf2bp2 in aging-associated HSC phenotypes, whereby it positively regulates oxidative metabolism in young mice, yet its loss may ameliorate aging-related deteriorations in hematopoietic function.
Our paper: Single-cell transcriptomic analysis of zebrafish cranial neural crest reveals spatiotemporal regulation of lineage decisions during development, is out now in Cell Reports. In this work, Xiaojun led the computational analyses of temporal gene expression patterns in zebrafish development.
Our paper: A single-cell resolved cell-cell communication model explains lineage commitment in hematopoiesis, is out now in Development. Coverage of this work includes features in the highlights of the journal and in USC Dornsife news. The same issue of Development also features an interview with the authors.
Ivy, Jesse, and Xiaojun were awarded an opportunity award grant together with Stephenson Chea at UC Irvine. It will study cell fate decisions in a model of Cornelia de Lange Syndrome. This proposal grew out of the annual symposium held at the UC Irvine NSF-Simons Center, congratulations all!
We attended the 2021 QCB departmental retreat in Ventura, CA. It was great to cautiously gather again in person for talks and tacos under the pelicans fishing for lunch. In envy of the lab t-shirts of our neighbors (Edge lab), Adam was surprised by these great hand-drawn creations.