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721
Modeling bi-modality improves characterization of cell cycle on gene expression in single cells
- PLoS Comput. Biol
, 2014
"... Advances in high-throughput, single cell gene expression are allowing interrogation of cell heterogeneity. However, there is concern that the cell cycle phase of a cell might bias characterizations of gene expression at the single-cell level. We assess the effect of cell cycle phase on gene expressi ..."
Abstract
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Cited by 3 (0 self)
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, wherein the expression of otherwise abundant genes is either strongly positive, or undetectable within individual cells. This bi-modality is likely both biologically and technically driven. Irrespective of its source, we show that it should be modeled to draw accurate inferences from single cell
regulation at the single-cell level
- Science
, 2005
"... The quantitative relation between transcription factor concentrations and the rate of protein production from downstream genes is central to the function of genetic networks. Here we show that this relation, which we call the gene regulation function (GRF), fluctuates dynamically in individual livin ..."
Abstract
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Cited by 84 (3 self)
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the effective single-cell GRF. These results can form a basis for quantitative modeling of natural gene circuits and for design of synthetic ones. The operation of transcriptional genetic cir-
Modelling and analysis of gene regulatory networks,
- Nat Rev Mol Cell Biol
, 2008
"... The genome encodes thousands of genes whose pro ducts enable cell survival and numerous cellular func tions. The amounts and the temporal pattern in which these products appear in the cell are crucial to the pro cesses of life. Gene regulatory networks govern the levels of these gene products. A ge ..."
Abstract
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Cited by 118 (2 self)
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with an associated probability. Modelling and analysis of gene regulatory networks Guy Karlebach and Ron Shamir Abstract | Gene regulatory networks have an important role in every process of life, including cell differentiation, metabolism, the cell cycle and signal transduction. By understanding the dynamics
Improved Fourier Transform Method for Unsupervised Cell-cycle Regulated Gene Prediction
"... Motivation: Cell-cycle regulated gene prediction using microarray time-course measurements of the mRNA expression levels of genes has been used by several researchers. The popularly employed approach is Fourier transform (FT) method in conjunction with the set of known cell-cycle regulated genes. In ..."
Abstract
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Cited by 1 (0 self)
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bias the prediction. Results: In this paper we propose an Improved Fourier Transform (IFT) method which takes care of several factors such as monotonic additive component of the cell-cycle expression, irregular or partial-cycle sampling of gene expression. The proposed algorithm does not need any known
Tracking the herd: resynchronization analysis of cell-cycle gene expression d ata
- in Saccharomyces cerevisiae. Conf. Proc. IEEE Eng. Med. Biol. Soc
, 2005
"... Abstract — Identification of genes expressed in a cell-cyclespecific periodical manner is of great interest to understand cyclic systems which play a critical role in many biological processes. However, identification of cell-cycle regulated genes by microarray gene expression data is complicated by ..."
Abstract
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Cited by 3 (1 self)
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by the factor of synchronization loss, thus remains a challenging problem. Decomposing the expression measurements will allow to better represent the single-cell behavior and improve the accuracy in identifying periodically expressed genes. In this paper, we propose a resynchronization-based algorithm
Modelling regulatory pathways in E. coli from time series expression profiles
, 2002
"... Motivation: Cells continuously reprogram their gene expression network as they move through the cell cycle or sense changes in their environment. In order to understand the regulation of cells, time series expression profiles provide a more complete picture than single time point expression profiles ..."
Abstract
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Cited by 66 (1 self)
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Motivation: Cells continuously reprogram their gene expression network as they move through the cell cycle or sense changes in their environment. In order to understand the regulation of cells, time series expression profiles provide a more complete picture than single time point expression
Genome-wide analysis of core cell cycle genes in Arabidopsis. Plant Cell 14: 903–916
, 2002
"... Cyclin-dependent kinases and cyclins regulate with the help of different interacting proteins the progression through the eukaryotic cell cycle. A high-quality, homology-based annotation protocol was applied to determine the core cell cycle genes in the recently completed Arabidopsis genome sequenc ..."
Abstract
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Cited by 45 (4 self)
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products were again validated or modified by comparing them with those of other family members in a multiple alignment. With this additional approach, we could determine clearly whether the predicted genes were similar to a certain class of cell cycle genes. To characterize subclasses within the gene
BIOINFORMATICS Polynomial Model Approach for Resynchronization Analysis of Cell-Cycle Gene Expression Data
"... Motivation: Identification of genes expressed in a cell-cycle-specific periodical manner is of great interest to understand cyclic systems which play a critical role in many biological processes. However, identification of cell-cycle regulated genes by raw microarray gene expression data directly is ..."
Abstract
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is complicated by the factor of synchroni-zation loss, thus remains a challenging problem. Decomposing the expression measurements and extracting synchronized expression will allow to better represent the single-cell behavior and improve the accuracy in identifying periodically expressed genes. Results
New candidate genes to predict pregnancy outcome in single embryo transfer cycles when using cumulus cell gene expression
"... Objective: To relate the gene expression in cumulus cells surrounding an oocyte to the potential of the oocyte, as evaluated by the embryo morphology (days 3 and 5) and pregnancy obtained in single-embryo transfer cycles. Design: Retrospective analysis of individual human cumulus complexes using qu ..."
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Objective: To relate the gene expression in cumulus cells surrounding an oocyte to the potential of the oocyte, as evaluated by the embryo morphology (days 3 and 5) and pregnancy obtained in single-embryo transfer cycles. Design: Retrospective analysis of individual human cumulus complexes using
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721
