scholarly journals Joining high-throughput technology with in silico modelling advances genome-wide screening towards targeted discovery

2006 ◽  
Vol 5 (1) ◽  
pp. 32-36 ◽  
Author(s):  
T. Werner
Keyword(s):  
High Throughput ◽  
In Silico ◽  
Genome Wide ◽  
High Throughput Technology ◽  
In Silico Modelling

scholarly journals epiTAD: a web application for visualizing high throughput chromosome conformation capture data in the context of genetic epidemiology

2018 ◽  
Author(s):  
Jordan H. Creed ◽  
Garrick Aden-Buie ◽  
Alvaro N. Monteiro ◽  
Travis A. Gerke
Keyword(s):  
High Throughput ◽  
Genetic Epidemiology ◽  
In Silico ◽  
Web Application ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Web Based ◽  
Genome Wide ◽  
Public Data ◽  
Complex Scale

AbstractThe increasing availability of public data resources coupled with advancements in genomic technology has created greater opportunities for researchers to examine the genome on a large and complex scale. To meet the need for integrative genome wide exploration, we present epiTAD. This web-based tool enables researchers to compare genomic structures and annotations across multiple databases and platforms in an interactive manner in order to facilitate in silico discovery. epiTAD can be accessed at https://apps.gerkelab.com/epiTAD/.

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

A novel compound active against SARS-CoV-2 targeting Uridylate-specific endoribonuclease (NendoU/NSP15): In silico and in vitro investigations

2021 ◽  
Author(s):  
Sumit Kumar ◽  
Yash Gupta ◽  
Samantha Zak ◽  
Charu Upadhyay ◽  
Neha Sharma ◽  
...  
Keyword(s):  
Virtual Screening ◽  
High Throughput ◽  
In Silico ◽  
Specific Enzyme ◽  
Cyclic Phosphates ◽  
High Throughput Virtual Screening

NendoU (NSP15) is an Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond. Our in-house library was subjected to high throughput virtual screening (HTVS) to identify compounds...

scholarly journals In-silico modelling of fullerene and fullerene adsorbed by nO2 molecules (n(O2)@Cm with n = 1, 2, 4 and m = 48 and 60) as potential SARS-CoV-2 inhibitors

2021 ◽  
Vol 44 (3) ◽  
Author(s):  
Meziane Brahimi ◽  
Djamila SELLAM ◽  
Afaf Bouchoucha ◽  
Yassamina Arbia ◽  
Hadjer Merazka ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Modelling

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
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