7,708Result(s)
withinHuman Genetics
Protocol
Protocol
Simulating Evolution in Asexual Populations with Epistasis
I show how to use OncoSimulR, software for forward-time genetic simulations, to simulate evolution of asexual populations in the presence of epistatic interactions. This chapter emphasizes the specification of...
Protocol
Analysis of Recombination at Yeast Telomeres
Upon telomerase inactivation telomeres are getting shorter at each round of DNA replication and progressively lose capping functions and hence protection against homologous recombination. In addition, telomera...
Protocol
Computational Detection of Plant RNA Editing Events
电脑能够系统地利用RNA-seq data allowing us to efficiently detect RNA editing sites in a genome-wide scale. This chapter introduces a very flexible computational framework for detecti...
Protocol
In Vivo Binding of Recombination Proteins to Non-DSB DNA Lesions and to Replication Forks
Homologous recombination (HR) has been extensively studied in response to DNA double-strand breaks (DSBs). In contrast, much less is known about how HR deals with DNA lesions other than DSBs (e.g., at single-s...
Protocol
A Practical Step-by-Step Guide for Quantifying Retroactivity in Gene Networks
One of the fundamental properties of engineered large-scale complex systems is modularity. In synthetic biology, genetic parts exhibit context-dependent behavior. Here, we describe and quantify a major source ...
Protocol
Ethics of DNAVaccineTransfer for Clinical Research
Several experimental human DNA vaccines are currently undergoing Phase I, II, and III clinical trials in order to investigate their efficacy and safety. Human clinical trials must follow guidelines and procedu...
Protocol
Protocol for Construction of Genome-Wide Epistatic SNP Networks Using WISH-R Package
Epistasis is the interaction between genes or genetic variants (such as Single Nucleotide Polymorphisms or SNPs) that influences a phenotype or a disease outcome. Statistically and biologically, significant ev...
Protocol
Stochastic Differential Equations for Practical Simulation of Gene Circuits
The Chemical Langevin Equation approach allows simple stochastic simulation of gene circuits under many practical situations where the number of molecules of the species involved is not extremely low. Here, we...
Protocol
Analyzing Homologous Recombination at a Genome-Wide Level
Among the types of damage, DNA double-strand breaks (DSBs) (provoked by various environmental stresses, but also during normal cell metabolic activity) are the most deleterious, as illustrated by the variety o...
Protocol
C-to-U RNA Editing: From Computational Detection to Experimental Validation
The AID/APOBEC family of enzymes are cytidine deaminases that act upon DNA and RNA. Among APOBECs, the best characterized family member to act on RNA is the enzyme APOBEC1. APOBEC1-mediated RNA editing plays a...
Protocol
In Vitro Characterization of Sumoylation of HR Proteins
In vitro analysis of posttranslational modifications such as sumoylation provides a great tool to not only identify the target proteins but also to characterize the specific effects of this modification on the...
Protocol
Engineering Protein-Based Parts for Genetic Devices in Mammalian Cells
Synthetic biology has been advancing cellular and molecular biology studies through the design of synthetic circuits capable to examine diverse endogenously or exogenously driven regulatory pathways. While ear...
Protocol
First-Order Correction of Statistical Significance for Screening Two-Way Epistatic Interactions
If one uses data to identify the most likely epistatic interaction between two genetic units, and then tests if the identified interaction is associated with a phenotype, the nominal statistical evidence will ...
Protocol
Automated Biocircuit Design with SYNBADm
SYNBADm is a Matlab toolbox for the automated design of biocircuits using a model-based optimization approach. It enables the design of biocircuits with pre-defined functions starting from libraries of biologi...
Protocol
Adenosine-to-Inosine RNA Editing Enzyme ADAR and microRNAs
RNA is subjected to over 100 different types of chemical modifications inside the cell. These modifications have various effects on its function and expression, resulting in RNA diversity. RNA editing or conve...
Protocol
Fluorescence Microscopy for Analysis of Relocalization of Structure-Specific Endonucleases
The analysis of by fluorescence microscopy has been important for studying processes involved in genome integrity maintenance at the cellular level. are required for genome stability, and work in has rev...
Protocol
Co-transcriptional Analysis of Self-Cleaving Ribozymes and Their Ligand Dependence
Self-cleaving ribozymes are RNA molecules that catalyze a site-specific self-scission reaction. Analysis of self-cleavage is a crucial aspect of the biochemical study and understanding of these molecules. Here...
Protocol
Genome Engineering ofYarrowia lipolyticawith the PiggyBac Transposon System
A mutant excision+/integration−piggyBac transposase can be used to seamlessly excise a chromosomally integrated, piggyBac-compatible selection marker cassette from theYarrowia lipolyticagenome. This piggyBac t...
Protocol
Using C-JAMP to Investigate Epistasis and Pleiotropy
Unraveling the complex biological mechanisms underlying human health and disease is a great challenge. With genomic data, many aspects can be investigated in great detail, such as interactions between differen...
Protocol
Computer-Aided Design and Pre-validation of Large Batches of DNA Assemblies
Type-2S restriction enzymes allow the routine assembly of large batches of synthetic constructs from individual genetic parts. However, design flaws in the part sequence can cause assembly failures, incurring ...
