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Yeast Functional Genomics

Overview of attention for book
Cover of 'Yeast Functional Genomics'

Table of Contents

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    Book Overview
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    Chapter 1 Using RNA-seq for Analysis of Differential Gene Expression in Fungal Species.
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    Chapter 2 Enhancing Structural Annotation of Yeast Genomes with RNA-Seq Data.
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    Chapter 3 Pathogen Gene Expression Profiling During Infection Using a Nanostring nCounter Platform.
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    Chapter 4 Comparative Transcriptomics in Yeasts.
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    Chapter 5 Mapping the Transcriptome-Wide Landscape of RBP Binding Sites Using gPAR-CLIP-seq: Experimental Procedures.
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    Chapter 6 Mapping the Transcriptome-Wide Landscape of RBP Binding Sites Using gPAR-CLIP-seq: Bioinformatic Analysis.
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    Chapter 7 Translation Analysis at the Genome Scale by Ribosome Profiling.
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    Chapter 8 Biotin-Genomic Run-On (Bio-GRO): A High-Resolution Method for the Analysis of Nascent Transcription in Yeast.
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    Chapter 9 Genome-Wide Probing of RNA Structures In Vitro Using Nucleases and Deep Sequencing.
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    Chapter 10 Genome-Wide Chromatin Immunoprecipitation in Candida albicans and Other Yeasts.
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    Chapter 11 ChIPseq in Yeast Species: From Chromatin Immunoprecipitation to High-Throughput Sequencing and Bioinformatics Data Analyses.
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    Chapter 12 Systematic Determination of Transcription Factor DNA-Binding Specificities in Yeast.
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    Chapter 13 Generation and Analysis of Chromosomal Contact Maps of Yeast Species.
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    Chapter 14 A Versatile Procedure to Generate Genome-Wide Spatiotemporal Program of Replication in Yeast Species.
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    Chapter 15 Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae.
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    Chapter 16 Label-Free Quantitative Proteomics in Yeast.
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    Chapter 17 Profiling of Yeast Lipids by Shotgun Lipidomics.
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    Chapter 18 Identification of Links Between Cellular Pathways by Genetic Interaction Mapping (GIM).
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    Chapter 19 On the Mapping of Epistatic Genetic Interactions in Natural Isolates: Combining Classical Genetics and Genomics.
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    Chapter 20 Experimental Evolution and Resequencing Analysis of Yeast.
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    Chapter 21 Reconstruction and Analysis of the Evolution of Modular Transcriptional Regulatory Programs Using Arboretum.
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    Chapter 22 Predicting Gene and Genomic Regulation in Saccharomyces cerevisiae, using the YEASTRACT Database: A Step-by-Step Guided Analysis.
Attention for Chapter 14: A Versatile Procedure to Generate Genome-Wide Spatiotemporal Program of Replication in Yeast Species.
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Chapter title
A Versatile Procedure to Generate Genome-Wide Spatiotemporal Program of Replication in Yeast Species.
Chapter number 14
Book title
Yeast Functional Genomics
Published in
Methods in molecular biology, January 2016
DOI 10.1007/978-1-4939-3079-1_14
Pubmed ID
26483026
Book ISBNs
978-1-4939-3078-4, 978-1-4939-3079-1
Authors

Agier, Nicolas, Fischer, Gilles, Nicolas Agier, Gilles Fischer

Abstract

Here, we describe a complete protocol, comprising both the experimental and the analytical procedures, that allows to generate genome-wide spatiotemporal program of replication and to find the location of chromosomally active replication origins in yeast. The first step consists on synchronizing a cell population by physical discrimination of G1 cells according to their sedimentation coefficient. G1 cells are then synchronously released into S-phase and time-point samples are regularly taken until they reach the G2 phase. Progression through the cell cycle is monitored by measuring DNA content variation by flow cytometry. DNA samples, covering the entire S-phase, are then extracted and analyzed using deep sequencing. The gradual change of DNA copy number is measured to determine the mean replication time along the genome. A simple method of peak calling allows to infer from the replication profile the location of replication origins along the chromosomes. Our protocol is versatile enough to be applied to virtually any yeast species of interest and generate its replication profile.

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X Demographics

The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
 Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 6 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
France 1 17%
Unknown 5 83%

Demographic breakdown

Readers by professional status Count As %
Researcher 4 67%
Student > Master 1 17%
Unknown 1 17%
Readers by discipline Count As %
Agricultural and Biological Sciences 4 67%
Biochemistry, Genetics and Molecular Biology 1 17%
Unknown 1 17%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 21 October 2015.
All research outputs
#15,821,622
of 23,498,099 outputs
Outputs from Methods in molecular biology
#5,527
of 13,368 outputs
Outputs of similar age
#234,750
of 396,908 outputs
Outputs of similar age from Methods in molecular biology
#553
of 1,472 outputs
Altmetric has tracked 23,498,099 research outputs across all sources so far. This one is in the 22nd percentile – i.e., 22% of other outputs scored the same or lower than it.
So far Altmetric has tracked 13,368 research outputs from this source. They receive a mean Attention Score of 3.4. This one is in the 44th percentile – i.e., 44% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 396,908 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 31st percentile – i.e., 31% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 1,472 others from the same source and published within six weeks on either side of this one. This one is in the 47th percentile – i.e., 47% of its contemporaries scored the same or lower than it.

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