scholarly journals Integrative analysis of genome‐wide experiments in the context of a large high‐throughput data compendium

2005 ◽  
Vol 1 (1) ◽  
Author(s):  
Amos Tanay ◽  
Israel Steinfeld ◽  
Martin Kupiec ◽  
Ron Shamir
Keyword(s):  
High Throughput ◽  
Integrative Analysis ◽  
High Throughput Data ◽  
Genome Wide

scholarly journals ZetaSuite, A Computational Method for Analyzing Multi-dimensional High-throughput Data, Reveals Genes with Opposite Roles in Cancer Dependency

2021 ◽  
Author(s):  
Yajing Hao ◽  
Changwei Shao ◽  
Guofeng Zhao ◽  
Xiang-Dong Fu
Keyword(s):  
High Throughput ◽  
Regulatory Networks ◽  
Cell Types ◽  
Computational Method ◽  
Two Dimensional ◽  
Experimental Conditions ◽  
Term Survival ◽  
High Throughput Data ◽  
Genome Wide ◽  
Different Cell Types

AbstractThe rapid advance of high-throughput technologies has enabled the generation of two-dimensional or even multi-dimensional high-throughput data, e.g., genome-wide siRNA screen (1st dimension) for multiple changes in gene expression (2nd dimension) in many different cell types or tissues or under different experimental conditions (3rd dimension). We show that the simple Z-based statistic and derivatives are no longer suitable for analyzing such data because of the accumulation of experimental noise and/or off-target effects. Here, we introduce ZetaSuite, a statistical package designed to score and rank hits from two-dimensional screens, construct regulatory networks based on response similarities, and eliminate off-targets. Applying this method to two large cancer dependency screen datasets, we identify not only genes critical for cell fitness, but also those required for constraining cell proliferation. Strikingly, most of those cancer constraining genes function in DNA replication/repair checkpoint, suggesting that cancer cells also need to protect their genomes for long-term survival.

scholarly journals High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sarah E. Pierce ◽  
Jeffrey M. Granja ◽  
William J. Greenleaf
Keyword(s):  
Transcription Factor ◽  
Single Cell ◽  
Cancer Cells ◽  
High Throughput ◽  
Regulatory Networks ◽  
Temporal Dynamics ◽  
Chromatin Accessibility ◽  
Regulatory Regions ◽  
Factor Binding ◽  
Genome Wide

AbstractChromatin accessibility profiling can identify putative regulatory regions genome wide; however, pooled single-cell methods for assessing the effects of regulatory perturbations on accessibility are limited. Here, we report a modified droplet-based single-cell ATAC-seq protocol for perturbing and evaluating dynamic single-cell epigenetic states. This method (Spear-ATAC) enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at once. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations reveals the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles.

scholarly journals A high-throughput genome-wide RNAi screen identifies modifiers of survival motor neuron protein

Cell Reports ◽  
2021 ◽  
Vol 35 (6) ◽  
pp. 109125
Author(s):  
Nikki M. McCormack ◽  
Mahlet B. Abera ◽  
Eveline S. Arnold ◽  
Rebecca M. Gibbs ◽  
Scott E. Martin ◽  
...  
Keyword(s):  
Motor Neuron ◽  
High Throughput ◽  
Rnai Screen ◽  
Survival Motor Neuron ◽  
Survival Motor Neuron Protein ◽  
Genome Wide ◽  
Motor Neuron Protein

High Throughput Data Mapping for Coarse-Grained Reconfigurable Architectures

2011 ◽  
Vol 30 (11) ◽  
pp. 1599-1609 ◽  
Author(s):  
Yongjoo Kim ◽  
Jongeun Lee ◽  
A. Shrivastava ◽  
J. W. Yoon ◽  
Doosan Cho ◽  
...  
Keyword(s):  
High Throughput ◽  
Coarse Grained ◽  
Reconfigurable Architectures ◽  
Data Mapping ◽  
High Throughput Data

scholarly journals Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping

2011 ◽  
Vol 59 (1) ◽  
pp. 206-224 ◽  
Author(s):  
Dorothy A. Steane ◽  
Dean Nicolle ◽  
Carolina P. Sansaloni ◽  
César D. Petroli ◽  
Jason Carling ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
High Throughput ◽  
Population Genetic ◽  
Phylogeny Reconstruction ◽  
Population Genetic Analysis ◽  
Genome Wide

Genome-wide high throughput analysis of DNA methylation in eukaryotes

Methods ◽  
2009 ◽  
Vol 47 (3) ◽  
pp. 142-150 ◽  
Author(s):  
Kyle R. Pomraning ◽  
Kristina M. Smith ◽  
Michael Freitag
Keyword(s):  
Dna Methylation ◽  
High Throughput ◽  
High Throughput Analysis ◽  
Throughput Analysis ◽  
Genome Wide

scholarly journals Genome-wide C-SWAT library for high-throughput yeast genome tagging

2018 ◽  
Vol 15 (8) ◽  
pp. 598-600 ◽  
Author(s):  
Matthias Meurer ◽  
Yuanqiang Duan ◽  
Ehud Sass ◽  
Ilia Kats ◽  
Konrad Herbst ◽  
...  
Keyword(s):  
High Throughput ◽  
Yeast Genome ◽  
Genome Wide
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