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.
The project, Computational methods to predict gene regulatory network dynamics and cell state transitions is funded by the NIGMS at the NIH. We will investigate fundamental processes underlying cell state transitions using theoretical modeling, statistical inference, and machine learning.
Our paper Modeling the competing effects of the immune system and EMT on tumor development is out now in Communications Biology. This large collaborative effort included multiscale evolutionary modeling led by Daniel Bergman and Bayesian data analysis led by Matt Karikomi. The paper was featured on the mathematical oncology blog with a write-up from Daniel.
Congratulations to Nikith, who received a Trudi Berwin Student Support Fellowship from the USC Bridge Institute to complete a BUGS summer research project in the lab. Nikith’s work on novel regulators of the Wnt signaling pathway paves the way for future research in the lab. Well done, Nikith!
Welcome to Ivy and Jesse who join the lab as postdoctoral researchers.
Ivy recently completed her PhD at the University of Oxford, studying the interplay between inherited and somatic genetic variants in cancer.
Jesse recently completed his PhD at the University of California, Irvine, modeling viral dynamics using various approaches including hybrid stochastic-deterministic methods.
Our editorial The diverse landscape of modeling in single-cell biology is out now in Physical Biology. This accompanies a special issue guest edited by Adam and Qing Nie, full of exciting recent advances in theoretical and biophysical modeling for single-cell biology.