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Statistical and Biological Data Analysis Using Programming Languages
Rapid progress in high throughput sequencing technologies has generated an unprecedented huge amount of complex and heterogeneous biological data and...
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Trait Based Association Mapping in Plants
Genome-wide association studies (GWAS) estimate the likelihood of association between genotype and phenotype in any large collection of material and...
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Statistical and Quantitative Genetics Studies
Quantitative genetics and plant breeding are non-exclusive and these disciplines has been benefited from each other for the past 100 years. As a...
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Mapping of Quantitative Traits Loci: Harnessing Genomics Revolution for Dissecting Complex Traits
With the onset of the genomic era, mapping of Quantitative Traits Loci (QTLs) appears to be a feasible solution for dissecting the complex...
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Meta-analysis of Mapping Studies: Integrating QTLs Towards Candidate Gene Discovery
Meta-analysis consists of pooling results from multiple studies, and allows prediction of more precise and meaningful data. A plethora of QTL mapping...
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Assembly, Annotation and Visualization of NGS Data
The next-generation sequencing technologies have revolutionized the field of agriculture with the advent of ever-evolving chemistries and a reduction...
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Overview of the Bioinformatics Databases and Tools for Genome Research and Crop Improvement
The advancement of sequencing technologies and molecular techniques has generated a huge amount of biological data which needs to be analyzed and...
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Measuring Transcription Dynamics of Individual Genes Inside Living Cells
Transcription is a highly dynamic process, which, for many genes, occurs in stochastic bursts. Studying what regulates these stochastic bursts...
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Unfolding and Refolding Proteins Using Single-Molecule AFM
Single-molecule atomic force microscopy (AFM) allows capturing the conformational dynamics of an individual molecule under force. In this chapter, we...
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Atomic Force Microscopy: An Introduction
Imaging of nano-sized particles and sample features is crucial in a variety of research fields, for instance, in biological sciences, where it is...
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Single-Cell Measurements Using Acoustic Force Spectroscopy (AFS)
Single-molecule force spectroscopy is a powerful tool to investigate the forces and motions related to interactions of biological molecules. Acoustic...
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Single-Molecule FRET-Resolved Protein Dynamics – from Plasmid to Data in Six Steps
Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for the detection of conformational dynamics of biomolecules....
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Insect Cell-Based Expression of Cytoskeletal Motor Proteins for Single-Molecule Studies
Cytoskeletal motor proteins are essential molecular machines that hydrolyze ATP to generate force and motion along cytoskeletal filaments. Members of...
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Quantitative Live Imaging of Zebrafish Scale Regeneration: From Adult Fish to Signaling Patterns and Tissue Flows
In regeneration, a damaged body part grows back to its original form. Understanding the mechanisms and physical principles underlying this process...
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In Vivo Optogenetic Phase Transition of an Intrinsically Disordered Protein
Proteins containing intrinsically disordered regions (IDRs) control a wide variety of cellular processes by assembly of membrane-less organelles via...
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Functional Genomics of Novel Rhabdomyosarcoma Fusion-Oncogenes Using Zebrafish
Clinical sequencing efforts continue to identify novel putative oncogenes with limited strategies to perform functional validation in vivo and study...
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Holographic Optogenetic Activation of Neurons Eliciting Locomotion in Head-Embedded Larval Zebrafish
Understanding how motor circuits are organized and recruited in order to perform complex behavior is an essential question of neuroscience. Here we...
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Methods to Study Liver Disease Using Zebrafish Larvae
Liver disease affects millions of people worldwide, and the high morbidity and mortality is attributed in part to the paucity of treatment options....
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Isolation and Culture of Human Umbilical Vein Endothelial Cells (HUVECs)
This protocol describes a simple and an economical method for isolation of endothelial cells from human umbilical vein. Umbilical cord is easily...
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Imaging and Analysis of the Dynamics of Filamentous Actin Structures in Live Endothelial Cells
The ability to view and record the movements of subcellular structures is a powerful tool that has accelerated the discovery and understanding of...