Teaching

MAR581: Applications of Next Generation Sequencing in Functional Genomics

Course Description: Integrative genomics is a new area of  research that seeks to understand the structure and function of an organism’s genes. This course provides an integrated view of how these methods can be used to answer questions regarding marine organisms evolution, biology and ecology. Over the course of the semester, examples will cover various topics including marine biodiversity, population structures, environmental adaptation, stress responses, phylogeny of animals, Aquaculture and fisheries, interaction between species (predation, parasitism, mutualism…). A particular accent is given to the role of Next Generation Sequencing technologies in answering questions related to these topics.

This course prepares the new generation of students to the use of new technologies, regardless of the research topic they are interested in. At the interface between ecology, evolution, cellular biology, microbiology and genomics, the course of functional and integrative marine genomics addresses Stony Brook University goal of an interdisciplinary graduate education. The course will familiarize students with the latest techniques and prepare them to adapt to the ever-evolving technologies as they conduct their own research. This course is an attractive addition to the curriculum within the graduate program for all students interested in biological sciences.

LEARNING OBJECTIVES:

By the end of the semester students shall be able to

  • Define terms used in structural genomics and functional genomics
  • Understand how genomics methods work
  • Interpret data presented in a scientific paper and evaluate its content
  • Read and understand the operating manuals of NGS tools
  • Choose between different methods to answer a biological question
  • Acquire a broad knowledge of how these methods can be used to answer questions related to the evolution, ecology and biology of marine organisms

These objectives are met through participation in lectures, reading assignments, discussions, practical bioinformatics sessions, preparing and presenting a literature review, and preparing illustrated fact sheets on various topics. When possible, the course  also includes a visit to a Genome Center and discussion with some of its members.

Topics covered (in order over the course of the semester): Second and Third generation sequencing techniques, Genome assembly, Comparative genomics, Population genomics, Epigenomics, Transcriptomics, Metagenomics and Metatranscriptomics

Fact Sheets from Fall 2016 students

cod do better

 

 

Detecting epigenetic modifications by single molecule real time (SMRT) sequencing

 

DNA nanoball sequencing

 

 

 

Genomics shed light on Mysteries of evolution

 

Methods to fragment DNA for Next generation sequencing

 

 

RADseq A powerful new tool for Next generation applications

 

Single cell genome sequencing

 

 

The future of medicine

 

 

Whole genome resequencing reveals population history

 

 

Connecting Epigenetics and Phenotypic Variation in Ecology

 

 

Applications of transcriptomics in Ecotoxicology

 

From Ocean to Octane

 

 

The Marine Eukaryote Transcriptome Sequencing Project is an incredible1

 

Nutrigenomics

 

 

The Metabolic crystal ball

 

 

 

Sumoylation and repression of gene expression

 

Temperature and epigenomics in marine fish

 

Exploring the three-dimensioinal organization of genomes

 

Fact Sheets from Fall 2015 students

multivariateStatistics Multivariate Statistics in Marine Genomics

 

 

NGSForensicSciencesWhat’s eating you? Using Next Generation Sequencing in Forensic Science

 

holobiontMicrobiome importance in the plant holobiont

 

 

metapathways Metapathways

 

 

Epigenomics Epigenomics and its connection to Evolution

 

 

StructuralProteomics Structural proteomics

 

 

WholeGenomeChrStructureVisualizing Wholed Genome Chromosome Structure

 

 

Viromics 2Viromics 

 

 

Viral purification for metagenomic analysis Viral purification for metagenomic analysis

 

 

The MinION The MinION

 

 

XpansionWatch out Pac Bio? Sequencing by Xpansion (SBX)

 

 

mRNAEnrichmentforProkaryotes mRNA enrichment techniques for Prokaryotes

 

 

Bisulfite Sequencing Bisulfite Sequencing

 

 

deep sequencing Deep Sequencing

 

 

 

 

 

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