Synthetic recording and in situ readout of lineage information in single cells

KL Frieda, JM Linton, S Hormoz, J Choi, KHK Chow…�- Nature, 2017 - nature.com
Reconstructing the lineage relationships and dynamic event histories of individual cells
within their native spatial context is a long-standing challenge in biology. Many biological�…

[HTML][HTML] Dynamic heterogeneity and DNA methylation in embryonic stem cells

ZS Singer, J Yong, J Tischler, JA Hackett, A Altinok…�- Molecular cell, 2014 - cell.com
Cell populations can be strikingly heterogeneous, composed of multiple cellular states, each
exhibiting stochastic noise in its gene expression. A major challenge is to disentangle these�…

[HTML][HTML] Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming

DH Kim, GK Marinov, S Pepke, ZS Singer, P He…�- Cell stem cell, 2015 - cell.com
Cellular reprogramming highlights the epigenetic plasticity of the somatic cell state. Long
noncoding RNAs (lncRNAs) have emerging roles in epigenetic regulation, but their potential�…

[HTML][HTML] Inferring cell-state transition dynamics from lineage trees and endpoint single-cell measurements

S Hormoz, ZS Singer, JM Linton, YE Antebi…�- Cell systems, 2016 - cell.com
As they proliferate, living cells undergo transitions between specific molecularly and
developmentally distinct states. Despite the functional centrality of these transitions in�…

Rapid screening of engineered microbial therapies in a 3D multicellular model

T Harimoto, ZS Singer, OS Velazquez…�- Proceedings of the�…, 2019 - National Acad Sciences
Synthetic biology is transforming therapeutic paradigms by engineering living cells and
microbes to intelligently sense and respond to diseases including inflammation, infections�…

[HTML][HTML] Quantitative measurements of early alphaviral replication dynamics in single cells reveals the basis for superinfection exclusion

ZS Singer, PM Ambrose, T Danino, CM Rice�- Cell systems, 2021 - cell.com
While decades of research have elucidated many steps of the alphavirus lifecycle, the
earliest replication dynamics have remained unclear. This missing time window has�…

Sindbis Macrodomain Poly-ADP-Ribose Hydrolase Activity Is Important for Viral RNA Synthesis

EG Aguilar, G Paniccia, C Adura, ZS Singer…�- Journal of�…, 2022 - Am Soc Microbiol
ABSTRACT ADP-ribosylation is a highly dynamic posttranslational modification frequently
studied in stress response pathways with recent attention given to its role in response to viral�…

Segmentation with residual attention u-net and an edge-enhancement approach preserves cell shape features

N Zhu, C Liu, B Forsyth, ZS Singer…�- 2022 44th Annual�…, 2022 - ieeexplore.ieee.org
The ability to extrapolate gene expression dynamics in living single cells requires robust cell
segmentation, and one of the challenges is the amorphous or irregularly shaped cell�…

Engineered bacteria launch and control an oncolytic virus

ZS Singer, J Pabon, H Huang, CM Rice, T Danino�- bioRxiv, 2023 - biorxiv.org
The ability of bacteria and viruses to selectively replicate in tumors has led to synthetic
engineering of new microbial therapies. Here we design a cooperative strategy whereby S�…

Spatial control of bacteria using screen printing

S Moon, IL Fritz, ZS Singer, T Danino�- 3D Printing and Additive�…, 2016 - liebertpub.com
Synthetic biology has led to advances in both our understanding and engineering of genetic
circuits that affect spatial and temporal behaviors in living cells. A growing array of native�…