Genetics

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Genetics is the study of genes (encoded in DNA), genetic variation between organisms (differences in DNA sequences), and heredity. It is increasingly relied upon in neuroscience as Genome Wide Association Studies (GWAS) and other massive genomics investigations help uncover genes and variations on genes that affect disease risk and variation in many qualities between the brains of individuals. Molecular genetics remains a strong method of exploring the function of genes indicated by these massive association studies and inform our understanding of cellular mechanisms in the brain. Epigenetics, included at the end of this page, adds another layer of information ‘above’ that encoded in DNA ( ‘epi’ = above, so ‘epigenome’ means above the genome). This helps direct how genes react to environmental context and generate more complex biological interactions from a limited number of genes.

Molecular Genetics

Molecular Genetics– The study of genes at the level of DNA molecules and the mechanisms by which a gene is ‘expressed’. This includes how a gene is ‘read’ from the DNA code, generating messenger RNA molecules from this ‘reading’ to pass the information onwards to several outcomes, including the generation of proteins and noncoding RNAs.

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Learn Genetics: this website offers a comprehensive and well laid out website about genetics with plenty of videos and interactive games throughout. The website includes a section on the basics of genetics (DNA, protein), inheritance (e.g. dominant vs recessive genes) as well as an introduction to gene-targeting technology and epigenetics.

Gene Expression and Regulation: a simple article from Nature that introduces concepts of eukaryotic gene expression and regulation. It contains links to more in-depth subtopics including chromatin structure, transcription factors and transcription regulation as well as basic concepts of DNA, RNA and proteins.

DNA learning center from Cold Spring Harbor: This website provides resources for basic genetics education and has a catalog of resources including 3-D animations of genetic, cellular, and neuroscience concepts.

Genomics

Genomics– A field which uses sequencing technologies and bioinformatics (large data processing for biology) to examine how the entire set of genes in an organism or species work together.

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Genome Wide Association Studies: this page discusses the advantages of whole genome studies as a research tool, including how they can be used to predict disease risk.

DNA Sequencing: The Sanger Method (Video) : A short video illustrating the Sanger Sequencing method, a classical technique more recently superseded by Next-Gen Sequencing.

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Gene Ontology – this database describes genes and gene products in terms of their associated biological processes, cellular components and molecular functions.

Genome Browser: This site contains the reference sequence and working draft assemblies for a large collection of genomes.

Protein Data Bank: Searchable archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies.

Ensembl Genome Browser: This tool can browse various genomes, find SNPs in your sequence, compare genes across species, and provide phenotypic information.

GeneMANIA: This website allows you to visualize close interactions between your gene of interest and other genes, or between sets of genes of interest. You may change the species genome in which you’re searching.

GeneMANIA Help: See this blog for information on how to use GeneMANIA.

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Genome Browser TutorialsThese guides (Level 0 and Level 1) illustrate the basics of using a tool called “Genome Browser” to find databased information about a gene, sequence, regulatory element, or protein of interest.

Find the function of a geneA guide for navigating the National Center for Biotechnology Information (NCBI) website to find known functions of a gene or gene product.

Human Health and Clinical Genetics

Clinical Genetics often has a different focus than molecular and genomic research. Very often, it is used to determine familial disease risk, to diagnose diseases with clear genetic basis (such as Huntington’s), or to recommend treatments with different efficacies for different genotypes.

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Online Mendelian Inheritance in Man: OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily.

Human Gene Database: GeneCards is a searchable, integrative database that provides comprehensive, user-friendly genomic, transcriptomic, proteomic, genetic, clinical and functional information on all annotated and predicted human genes.

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Paper Protein ModelsActivity resources for visualizing 3D protein structures from the Protein Data Bank.

National Human Genome Research Institute: This database provides a broad list of Genetics Education resources from many different sources for educational, clinical, and research purposes.

DNA Files Radio Series: The DNA Files was an award winning radio program (1998-2007) that explored the science of genetics and its ethical, societal, and legal implications.

Special/In Depth pages:

The DNA files (radio) “Minding The Brain”: This episode of the DNA files explored how the brain changes in response to the cultural, social, personal and physical environments in which we live.

Genes to Cognition (Cold Spring Harbor): This website provides a rich, interactive network map of information and resources about cognitive disorders, cognitive processes, and relevant research approaches.

The Science of Addiction: Genetics and the Brain– A learning resource specifically focused on research into the genetics and neuroscience of drug addiction.

Epigenetics

Epigenetics – The information ‘above’ the genome (‘epi’ = above) which governs how the genome responds to environmental and developmental cues to generate complex profiles of gene expression. This can govern how multiple types of tissues arise from a limited set of genes, how environmental contexts can impact cellular function at a molecular level, and even disease outcome.

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What is Epigenetics?A website providing educationally entertaining news about epigenetics research, tools and technology in the field, and tips and techniques for researchers. Includes citations at the bottom of the articles.

Fundamentals of Epigenetics– An article from “What is Epigenetics” describing the fundamentals of epigenetics; what it is, the history of research in the field, epigenetics and the environment, epigenetics in the clinic. A good start for beginners.

Epigenetics Glossary– A glossary of terms provided by “What is Epigenetics”, relevant to epigenetic modifications and mechanisms.

Chromatin Remodeling–An article from “What is Epigenetics” on the mechanisms of chromatin remodeling that contribute to the epigenetic regulation of gene expression.

Histone modifications–An explanation of the role of histone modifications as epigenetic marks regulating gene expression. (from “What is Epigenetics?”)

Noncoding RNA A short article detailing the types of non-coding RNAs involved in epigenetic regulation.  (from “What is Epigenetics?”)

Methylation– A “Scitable” Nature article about the role of methylation in gene expression.

EpiGenie Learning Center–An epigenetics learning resource for people new to the field. Contains background information about key epigenetic readers, writers, and erasers and a compliation of relevant tools and databases.

Learn.Genetics: Epigenetics– A learning resource for basic epigenetics with videos and interactive media.

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Roadmap Epigenomics– A public resource for browsable human epigenomic data and reference epigenomes. The Consortium provides access to standardized protocols, important publications, and downloadable tools.

BiSearch–A primer design and search tool for original and bisulfite converted sequences.

Reverse Complement Tool– This tool will take an inputed sequence and output a reverse sequence, a complementary sequence, or a reverse-complement sequence.

BS Primer Seeker–A tool for finding primers to bisulfite converted sequences. It requires an unconverted sequence input and displays a sequence preview that highlights bisulfite conversion sites and CpG islands.

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