Directed and Scaleable Evolution

Ravikumar Liu 768x523

In a study published November 8, 2018 in the journal Cell, CCBS associated researchers, Chang Liu and Arjun Ravikumar,  reported that they have accelerated and simplified directed evolution by having live cells do most of the heavy lifting. By inserting a specially engineered DNA replication system into yeast, the scientists were able to coax selected genes to rapidly and stably mutate and evolve as the host yeast cells reproduced. 


Interdisciplinary Case Study: Mathematicians and Biologists Found Order in Cellular Noise

Rackauckas Nie Schilling

During development, cells take cues from their immediate environment to decide their fate, but it is not always easy to “hear” the relevant information among all the genetic and molecular activities that are taking place. Cells will quiet this noise so that they can make accurate calls on how to behave. Using the zebrafish hindbrain as a testing ground, three University of California, Irvine (UCI), scientists—applied mathematician Christopher Rackauckas (now at MIT), developmental biologist Thomas Schilling, and mathematical biologist Qing Nie—identified a strategy called intermediate states that cells use to control noise. Their paper is one of the first examples of how a specific cellular protein can tone noise down to levels necessary for developmental activities. THIS article is the backstory for “Mean-Independent Noise Control of Cell Fates via Intermediate States,” published on April 10 in iScience (

Internet of Bodies

MaryLee    Former MCSB/CCBS graduate student, Mary Lee, a mathematician with biology training, has written an interesting op-ed entitled  "The Internet of Bodies"  published in Washington Post's World Post.


2018 Opportunity Awards

Congratulations to the winners of this year's CCBS Opportunity Awards competition based on the theme of Cell States and Transitions! Each winning proposal will receive $10,000 to be shared between the faculty for lab project expenses; and a $1,000 award for research supplies to be shared between student and/or postdoctoral participants. We look forward to hearing about the projects at next year's annual CCBS retreat scheduled March 29 - 31, 2019 at the Sheraton Universal in Los Angeles!

Characterizing the Transition Between Naïve and Primed States of Pluripotent ESCs in Different Mammalian Species Christina Wilcox, Kate Williams PI - Ali Mortazavi Developmental & Cell Biology
Linh Vuong, PI - Peter Donovan Developmental & Cell Biology
Transcriptomic analysis of MCF-10A mammary epithelial acini in normal and invasive states Sorena Rahmanian, PI - Ali Mortazavi Developmental & Cell Biology
Qingda Hu, PI - Elliot Botvinick Biomedical Engineering and Surgery
Understanding cellular state transitions in the mammary gland microenvironment from a control theory perspective Kevin Nee, PI - Kai Kessenbrock Biological Chemistry
Suoqin Jin, PI - Qing Nie  Mathematics and Developmental & Cell Biology
Transitional states regulating macrophage heterogeneity in dystrophic muscle Nick Pervolarakis, Quy Nguyen, PI - Kai Kessenbrock Biological Chemistry
Jenna Kastenschmidt, PI - S. Armando Villalta  Physiology & Biophysics
Methylation pseudotime: a novel tool for observing protein-DNA interactions Julien Morival, PI - Tim Downing Biomedical Engineering
Adam MacLean, PI - Qing Nie  Mathematics  and Developmental & Cell Biology 
Label-free, non-destructive determination of cell state using high throughput characterization of cell physical properties Matt Bovyn, PI - Jun Allard Physics and Astronomy and Mathematics
Cody Combs, PI - Zuzanna Siwy Physics and Astronomy
Optimal experimental design for feedback models of hematopoiesis Luis Martinez-Lomeli, PI - Babak Shahbaba/Volodymyr Minin Statistics
Abdon Iniguez, Shuxiong Wang, PI - John Lowengrub  Mathematics, Biomedical Engineering and Chemical Engineering & Material Science
Prasanthi Tata, PI - Richard Van Etten Hematology/Oncology, Department of Medicine

$3.3 million NIH grant awarded for the study of scarless wound healing

wound healing trio

The National Institutes of Health has awarded a five-year, $3.3 million grant to UCI’s Qing Nie, Chancellor’s Professor of mathematics and developmental & cell biology; Maksim Plikus, associate professor of developmental & cell biology; and Xing Dai, professor of biological chemistry. They will blend cutting-edge, single-cell techniques with mathematical modeling to study wound healing.  Read More...

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