Evidence map›Paper›PMID 30077635›Full record

ArticleCell systems2018

The Cell Cycle Browser: An Interactive Tool for Visualizing, Simulating, and Perturbing Cell-Cycle Progression.

David Borland, Hong Yi, Gavin D Grant, Katarzyna M Kedziora, Hui Xiao Chao, Rachel A Haggerty, Jayashree Kumar, Samuel C Wolff, Jeanette G Cook, Jeremy E Purvis

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell systems, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Review
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

David BorlandRenaissance Computing Institute, University of North Carolina, Chapel Hill, 100 Europa Drive, Suite 540, Chapel Hill, NC 27517, USA.
Hong YiRenaissance Computing Institute, University of North Carolina, Chapel Hill, 100 Europa Drive, Suite 540, Chapel Hill, NC 27517, USA.
Gavin D GrantDepartment of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA.
Katarzyna M KedzioraDepartment of Genetics, University of North Carolina, Chapel Hill, Genetic Medicine Building 5061, CB#7264, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA.
Hui Xiao ChaoDepartment of Genetics, University of North Carolina, Chapel Hill, Genetic Medicine Building 5061, CB#7264, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA; Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA.
Rachel A HaggertyDepartment of Genetics, University of North Carolina, Chapel Hill, Genetic Medicine Building 5061, CB#7264, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA; Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA.
Jayashree KumarCurriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA.
Samuel C WolffDepartment of Genetics, University of North Carolina, Chapel Hill, Genetic Medicine Building 5061, CB#7264, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA.
Jeanette G CookDepartment of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA.
Jeremy E PurvisLineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA; Department of Genetics, University of North Carolina, Chapel Hill, Genetic Medicine Building 5061, CB#7264, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA; Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, USA. Electronic address: jeremy_purvis@med.unc.edu.

Funding

UNC Predoc Training Progr in Bioinformatics/Comp BiologyT32GM067553 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI ELSTON, TIMOTHY C · 2005 to 2019
$2.5M
Post-Translational Regulation of DNA Replication Origin Licensing in Human CellsR01GM102413 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI COOK, JEANETTE GOWEN · 2013 to 2021
$2.5M
Controlling Stem Cell Fate through Computational ModelingDP2HD091800 · NICHD · UNIV OF NORTH CAROLINA CHAPEL HILL · PI PURVIS, JEREMY · 2016 to 2018
$2.3M
Defining the quantitative relationship between DNA damage and cell cycle dynamics in CUL9-deficient cellsF30CA213876 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI CHAO, HUI XIAO · 2017 to 2020
$158k
Single-cell dynamics of the OCT4-GATA6 axis in human lung progenitorsF31HL134336 · NHLBI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HAGGERTY, RAYMOND · 2016 to 2018
$96k
NCI NIH HHS F30 CA213876NHLBI NIH HHS F31 HL134336NICHD NIH HHS DP2 HD091800NIGMS NIH HHS R01 GM102413NIGMS NIH HHS T32 GM067553
6 · The paper itself

Abstract

The cell cycle is driven by precise temporal coordination among many molecular activities. To understand and explore this process, we developed the Cell Cycle Browser (CCB), an interactive web interface based on real-time reporter data collected in proliferating human cells. This tool facilitates visualizing, organizing, simulating, and predicting the outcomes of perturbing cell-cycle parameters. Time-series traces from individual cells can be combined to build a multi-layered timeline of molecular activities. Users can simulate the cell cycle using computational models that capture the dynamics of molecular activities and phase transitions. By adjusting individual expression levels and strengths of molecular relationships, users can predict effects on the cell cycle. Virtual assays, such as growth curves and flow cytometry, provide familiar outputs to compare cell-cycle behaviors for data and simulations. The CCB serves to unify our understanding of cell-cycle dynamics and provides a platform for generating hypotheses through virtual experiments.

Indexed as

Cell CycleComputer SimulationModels, BiologicalSoftwareCell ProliferationCell SurvivalFlow CytometryHumansImage Processing, Computer-Assistedcell cyclecomputational modelingdata visualizationlive-cell imagingsingle-cell dynamics

Identifiers

PMID30077635
PMCPMC6214685

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.