Adam visited MIT yesterday to give a talk at the Koch Institute for Integrative Cancer Research on “Modeling stochastic cancer dynamics in complex tumor microenvironments.”
Our paper investigating the origins of sexual dimorphism in the mouse kidney is out now in Developmental Cell. In this collaboration led by the McMahon lab, together with Pachter and Kim labs, we discovered that regulation mediated largely through Androgen receptor (AR) controls the dimorphism of the mouse kidney. This was made possible via bulk RNA-seq temporal data coupled with single-cell multiomics integrated through computational analyses.
Adam visited Kyoto, Japan, this week, to speak at a mathematical biology conference, OKO: from genes to cells to humans.” He presented recent work from the lab on deciphering cell fate decision-making from single-cell multiomic data via GRN inference with popInfer.
Ivy’s paper is out now! In a large collaboration led by the McMahon lab together with our lab & and the labs of Lior Pachter & Junhyong Kim we investigated the origins of sex differences in the mammalian kidney. Did you know that male and female kidneys have highly diverged gene expression programs in proximal tubule cells?! Through time-course RNA-seq coupled with joint multiomics (assaying scRNA-seq + scATAC-seq) of WT and AR-ko kidneys we discovered how Androgen receptor controls the sex dimorphism of cell fates in the kidney.
Megan’s paper is up now on bioRxiv, in which we present popInfer: gene regulatory inference with pseudocells over pseudotime. We developed methods that make use of joint multi-omics (RNA-seq + ATAC-seq from the same single cells) to infer networks controlling lineage-specific cell fate decisions during hematopoiesis. Read more on twitter.
Jesse’s paper in which we model myeloid suppressor cell dynamics and their impact on tumor outcomes in metastatic niches is out now in Cancer Immunology Research.
Our perspective article on why chose Julia as a high-level programming language in the biological sciences is out now in Nature Methods.
