Genetics and Genomics

Links of interest related to Genetics and Genomic

If you want to stay updated, the US National Center for Biotechnology Information (NCBI) makes available scientific research articles 

You may also want to check Google Scholar


Getting Genetics done, Staying current in bioinformatics & genomics 2017 Edition

Applied Computational Genomics Course at UU: Spring 2017 

Kellis Lab at MIT Computer Science and Broad Institute 

MIT Computational Biology: Genomes, Networks, Evolution, Health – Fall 2018 

Machine Learning Approaches to Decode the Human Genome, CS 522 by Anshul Kundaje, Stanford

MIT Computational Biology: Genomes, Networks, Evolution, Health – Fall 2018 – 6.047/6.878/HST.507  Prof. Manolis Kellis


Genome Analysis Workshop by University of Colorado School of Medicine

The OMIM (Online Mendelian Inheritance in Man database) provides more information on single gene disorders or

For even more info on gene disorders, the University of Washington’s Gene Reviews series are highly recommended and available at

Other very useful resources.
SNP (pronounced ‘snip’) is the short term for Single Nucleotide Polymorphism.
The importance of SNPs comes from their ability to influence disease risk, drug efficacy and side-effects, tell you about your ancestry, and predict aspects of how you look and even act. SNPs are probably the most important category of genetic changes influencing common diseases. And in terms of common diseases, 9 of the top 10 leading causes of death have a genetic component and thus most likely one or more SNPs influence your risk.

The Rs1815739 SNP for example will tell you whether you are likely a sprinter or an endurance athlete.

OpenSNP is a non-profit, open-source project that is about sharing genetical and phenotypic information. You can find info on SNPs
SNPedia is a wiki investigating human genetics. We share information about the effects of variations in DNA, citing peer-reviewed scientific publications.

SNPs and other genetic variations (dbSNP):

Genomic structural variation dbVar
Genomic structural variation DGV
ALFRED allele frequencies in human populations: reference on human genome variations:
ClinVar aggregates information about genomic variation and its relationship to human health.
Genecards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes.
Free online books at the US National Center for Biotechnology Information (NCBI)
Mayo Clinic
Ensemble DNA content of Human Chromosomes:
BLAST / BLAT program
Homologene – An automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species.
ATGU Analytic and Translational Genetics Unit Harvard
KEGG DRUG database
PDB (An Information Portal to Biological Macromolecular Structures)
DrugBank (bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information)
MEDLINE database
National Library of Medicine 
Comparative Toxicogenomics Database (CTD)
Toxin, Toxin-Target Database (T3DB)
National Health and Nutrition Examination Survey (NHANES)
Framingham Heart Study <http://www.framingham->

Studies on Cancer
COSMIC (Catalog of Somatic Mutations in Cancer) database
International Cancer Genome Consortium (TCGA)
The Cancer Genome Atlas (TCGA)
UCSC Cancer Genomics Browser

SNP Analysis

Human Gene Mutation Database (HGMD) Interpretome

Bioinformatics and Genome Browser
GenomeBrowse GenomeBrowse
Integrative Genomics Viewer (IGV) http://www.broad-
Generic Genome Browser (GBrowse)
Genomes Unzipped public personal genomics custom browser
Dalliance interactive genome viewer
University of Tokio Genome Browser
JBrowse Genome Browser
Phylotreee phylogenetic tree of global human mitochondrial DNA variation
HaploGrep2 automatic classification of mitochondrial DNA profiles
mtHap Haplogroup analysis
GenAbel a free framework for collaborative, robust, transparent, open-source based development of statistical genomics
Genetic Power Calculator
LDSC (LD Score)
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data.
GRAIL is a tool to examine relationships between genes in different disease associated loci.
DAPPLE stands for Disease Association Protein-Protein Link Evaluator.
xBrowse is a software tool we use for searching for causal variants in Mendelian disease families.
LOFTEE is a plugin for the Ensembl Variant Effect Predictor that improves the detection and filtering of candidate protein-truncating variants.
igv_plotter automates the generation of IGV screenshots for sequencing reads at variant sites of interest.
exac_browser is the code behind our ExAC browser.
clinvar provides tools to parse NCBI’s ClinVar database, and a flat file representation thereof.
gene_lists is a collection of gene lists for genome-wide analyses.
minimal_representation is a collection of scripts for canonicalizing the representation of genomic variants.
denovolyzeR is an R package for testing the gene-wise burden of de novo variants in disease families compared to random mutational expectations.
Jmol visualization software
PyMol visualization software
Autodock (molecular docking simulation)
Biological enrichment analysis tools:
WebGestalt Free
Onto-Express Free
GOMiner Free
Ingenuity Pathway Analysis Commercial
GeneGO Metacore Commercial

Functional Prediction tools: for evaluating and predicting the functional effect of variants

Genome Analysis Toolkit (GATK)
nsSNP Analyzer