Chengzhe Tian

Chengzhe Tian
CeMM Research Center for Molecular Medicine | CeMM

PhD Biophysics

About

18
Publications
2,131
Reads
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554
Citations
Citations since 2017
15 Research Items
543 Citations
2017201820192020202120222023050100150
2017201820192020202120222023050100150
2017201820192020202120222023050100150
2017201820192020202120222023050100150
Additional affiliations
June 2017 - March 2022
University of Colorado Boulder
Position
  • PostDoc Position
July 2015 - July 2015
University of Copenhagen
Position
  • Research Assistant
Description
  • Teaching Assistant for Numerical Methods in Physics
April 2015 - June 2015
University of Copenhagen
Position
  • Research Assistant
Description
  • Teaching Assistant for Biological Dynamics
Education
February 2014 - January 2017
University of Copenhagen
Field of study
  • Biophysics
September 2011 - September 2013
ETH Zurich
Field of study
  • Computational Biology and Bioinformatics
September 2008 - July 2011
Peking University
Field of study
  • Computer Softwares

Publications

Publications (18)
Article
Oncogene-induced senescence is a phenomenon in which aberrant oncogene expression causes non-transformed cells to enter a non-proliferative state. Cells undergoing oncogenic induction display phenotypic heterogeneity, with some cells senescing and others remaining proliferative. The causes of heterogeneity remain unclear. We studied the sources of...
Preprint
Full-text available
Oncogene-induced senescence (OIS) is a phenomenon in which aberrant oncogene expression causes non-transformed cells to enter a non-proliferative state. Cells undergoing OIS display phenotypic heterogeneity, with some cells senescing and others remaining proliferative. The causes of the heterogeneity remain poorly understood. We studied the sources...
Article
Full-text available
Despite the increasing number of effective anti-cancer therapies, successful treatment is limited by the development of drug resistance. While the contribution of genetic factors to drug resistance is undeniable, little is known about how drug-sensitive cells first evade drug action to proliferate in drug. Here we track the responses of thousands o...
Article
Full-text available
Time-lapse microscopy provides an unprecedented opportunity to monitor single-cell dynamics. However, tracking cells for long periods remains a technical challenge, especially for multi-day, large-scale movies with rapid cell migration, high cell density, and drug treatments that alter cell morphology/behavior. Here, we present EllipTrack, a global...
Article
Full-text available
Assignment of cell types from single-cell RNA sequencing (scRNA-seq) data remains a time-consuming and error-prone process. Current packages for identity assignment use limited types of reference data and often have rigid data structure requirements. We developed the clustifyr R package to leverage several external data types, including gene expres...
Preprint
Full-text available
Time-lapse microscopy provides an unprecedented opportunity to monitor single-cell dynamics. However, tracking cells for long periods of time remains a technical challenge, especially for multi-day, large-scale movies with rapid cell migration, high cell density, and drug treatments that alter cell morphology/behavior. Here, we present EllipTrack,...
Article
How cells monitor mitogen availability Classical experiments indicated that cells sense the mitogens or growth factors that control cell division within a limited window during the cell cycle. Min et al. reexamined this issue with high-throughput live-cell imaging and temporally controlled perturbations to more closely monitor dynamic signal proces...
Article
Assignment of cell types from single-cell RNA sequencing (scRNA-seq) data remains a time-consuming and error-prone process. Current packages for identity assignment use limited types of reference data and often have rigid data structure requirements. We developed the clustifyr R package to leverage several external data types, including gene expres...
Preprint
Full-text available
Despite increasing numbers of effective anti-cancer therapies, successful treatment is limited by the development of drug resistance. While the contribution of genetic factors to drug resistance is undeniable, little is known about how drug-sensitive cells first evade drug action to proliferate in drug. Here we track the response of thousands of si...
Preprint
Full-text available
Background: In single-cell RNA sequencing (scRNA-seq) analysis, assignment of likely cell types remains a time-consuming, error-prone, and biased process. Current packages for identity assignment use limited types of reference data, and often have rigid data structure requirements. As such, a more flexible tool, capable of handling multiple types o...
Article
Full-text available
Ki67 staining is widely used as a proliferation indicator in the clinic, despite poor understanding of this protein's function or dynamics. Here, we track Ki67 levels under endogenous control in single cells over time and find that Ki67 accumulation occurs only during S, G2, and M phases. Ki67 is degraded continuously in G1 and G0 phases, regardles...
Article
Spontaneous genetic mutations allow an initially drug-sensitive population of cancer cells to acquire a drug-resistant phenotype. However, little is known about how drug-sensitive cells first evade drug action and survive in the presence of drug, referred to as "drug tolerance," a crucial step on the road to resistance. In this study, we combined s...
Article
Full-text available
Toxin–antitoxin (TA) loci are widespread in bacteria including important pathogenic species. Recent studies suggest that TA systems play a key role in persister formation. However, the persistence phenotype shows only weak dependence on the number of TA systems, i.e. they are functionally redundant. We use a mathematical model to investigate the in...
Article
Full-text available
Cells receive a multitude of signals from the environment, but how they process simultaneous signaling inputs is not well understood. Response to infection, for example, involves parallel activation of multiple Toll-like receptors (TLRs) that converge on the nuclear factor κB (NF-κB) pathway. Although we increasingly understand inflammatory respons...
Article
We discuss the transition paths in a coupled bistable system consisting of interacting multiple identical bistable motifs. We propose a simple model of coupled bistable gene circuits as an example and show that its transition paths are bifurcating. We then derive a criterion to predict the bifurcation of transition paths in a generalized coupled bi...
Article
Full-text available
Importance: The early stringent response elicited by amino-acid starvation is controlled by a sharp increase of the cellular (p)ppGpp level. Toxin-antitoxin encoded mRNases are activated by (p)ppGpp through enhanced degradation of antitoxins. The present work shows that this activation happens at a very short time scale, and the activated mRNases...
Article
Full-text available
Synthetic genetic circuits are programmed in living cells to perform predetermined cellular functions. However, designing higher-order genetic circuits for sophisticated cellular activities remains a substantial challenge. Here we program a genetic circuit that executes Pavlovian-like conditioning, an archetypical sequential-logic function, in Esch...

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