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 http://ncbi.nlm.nih.gov 

You may also want to check Google Scholar http://scholar.google.com

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

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 http://www.omin.org or http://www.ncbi.nlm.nih.gov/omim

For even more info on gene disorders, the University of Washington’s Gene Reviews series are highly recommended and available at http://www.ncbi.nlm.nih.gov/books/NBK1116/

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 https://opensnp.org/
SNPedia is a wiki investigating human genetics. We share information about the effects of variations in DNA, citing peer-reviewed scientific publications.http://www.snpedia.com/

SNPs and other genetic variations (dbSNP): http://www.ncbi.nlm.nih.gov/snp

Genomic structural variation dbVarhttp://www.ncbi.nlm.nih.gov/dbvar
Genomic structural variation DGVhttp://dgv.tcag.ca/dgv/app/home
ALFRED allele frequencies in human populations: http://alfred.med.yale.edu/alfred/index.asp
1000Genomes.org reference on human genome variations: http://www.1000genomes.org/
ClinVar aggregates information about genomic variation and its relationship to human health. http://www.ncbi.nlm.nih.gov/clinvar/
Genecards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. http://www.genecards.org/
Free online books at the US National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov/books/
Mayo Clinic http://www.mayoclinic.org/
Ensemble DNA content of Human Chromosomes:
http://www.ensembl.org/index.html
http://www.ensembl.org/Homo_sapiens/Location/Genome
BLAST / BLAT program http://www.ensembl.org/Homo_sapiens/Tools/Blast?db=core
Homologene – An automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species. http://www.ncbi.nlm.nih.gov/homologene
ATGU Analytic and Translational Genetics Unit Harvard https://www.atgu.mgh.harvard.edu/
PharmaGKB https://www.pharmgkb.org/
KEGG DRUG database http://www.genome.jp/kegg/drug/
PDB (An Information Portal to Biological Macromolecular Structures) http://www.rcsb.org/pdb/home/home.do
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) http://www.drugbank.ca
MEDLINE database  http://www.ncbi.nlm.nih.gov/books/NBK25500/
National Library of Medicine https://www.nlm.nih.gov/databases/journal.html 
Comparative Toxicogenomics Database (CTD) http://ctdbase.org
Toxin, Toxin-Target Database (T3DB) http://www.t3db.ca/
National Health and Nutrition Examination Survey (NHANES) http://www.cdc.gov/nchs/nhanes.htm
Framingham Heart Study <http://www.framingham- heartstudy.org>

Studies on Cancer
COSMIC (Catalog of Somatic Mutations in Cancer) database http://cancer.sanger.ac.uk/cosmic
International Cancer Genome Consortium (TCGA) https://icgc.org/
The Cancer Genome Atlas (TCGA)  http://cancergenome.nih.gov/
UCSC Cancer Genomics Browser https://genome-cancer.ucsc.edu/

SNP Analysis

dbGaP http://www.ncbi.nlm.noh.gov/gap/
GWASCentral http://www.gwascentral.org/
GWASdb http://www.jjwanglab.org/gwasdb/
Human Gene Mutation Database (HGMD) http://www.hmgd.cf.ac.uk/ Interpretome
NextBio http://www.nextbio.com/
NHGRI GWAS Catalog http://www.genome.gov/gwastudies/
OpenSNP http://opensnp.org/
PharmGKB http://www.pharmgkb.org/
SNPedia http://www.snpedia.com/
SNPNexus http://www.snp-nexus.org/
PolyPhen http://genetics.bwh.harvard.edu/pph2/
Interpretome http://www.interpretome.com/#start

SOFTWARE
Bioinformatics and Genome Browser http://genome.ucsc.edu/
GenomeBrowse GenomeBrowse
GET-Evidence http://evidence.pgp-hms.org/about
Promethease http://www.snpedia.com/index.php/Promethease
Circos http://circos.ca
myKaryoView http://mykaryoview.com/
Scribl http://chmille4.github.io/Scribl/
Cytoscape http://www.cytoscape.org/
MitoWheel http://mitowheel.org/mitowheel.html
SNPduo http://pevsnerlab.kennedykrieger.org/SNPduo/
Integrative Genomics Viewer (IGV) http://www.broad- institute.org/igv/
Generic Genome Browser (GBrowse) http://gmod.org/wiki/GBrowse
Genomes Unzipped public personal genomics custom browser http://www.genomesunzipped.org/jbrowse/
Dalliance interactive genome viewer http://www.biodalliance.org/
University of Tokio Genome Browser http://utgenome.org/
JBrowse Genome Browser http://jbrowse.org/
Phylotreee phylogenetic tree of global human mitochondrial DNA variation http://www.phylotree.org/
HaploGrep2 automatic classification of mitochondrial DNA profiles http://haplogrep.uibk.ac.at/
mtHap Haplogroup analysis http://dna.jameslick.com/mthap/
ChromoPainter http://paintmychromosomes.com/
GenAbel a free framework for collaborative, robust, transparent, open-source based development of statistical genomics http://www.genabel.org/
Genetic Power Calculator http://pngu.mgh.harvard.edu/~purcell/gpc/
HaploView http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview
LDSC (LD Score) http://github.com/bulik/ldsc/
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. http://pngu.mgh.harvard.edu/~purcell/plink/
PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. http://pngu.mgh.harvard.edu/~purcell/plink/
GRAIL is a tool to examine relationships between genes in different disease associated loci. http://www.broadinstitute.org/mpg/grail/
DAPPLE stands for Disease Association Protein-Protein Link Evaluator. http://www.broadinstitute.org/mpg/dapple/
xBrowse is a software tool we use for searching for causal variants in Mendelian disease families. https://github.com/macarthur-lab/xbrowse
LOFTEE is a plugin for the Ensembl Variant Effect Predictor that improves the detection and filtering of candidate protein-truncating variants. https://github.com/konradjk/loftee
igv_plotter automates the generation of IGV screenshots for sequencing reads at variant sites of interest. https://github.com/macarthur-lab/igv_plotter
exac_browser is the code behind our ExAC browser. https://github.com/konradjk/exac_browser
clinvar provides tools to parse NCBI’s ClinVar database, and a flat file representation thereof. https://github.com/macarthur-lab/clinvar
gene_lists is a collection of gene lists for genome-wide analyses. https://github.com/macarthur-lab/gene_lists
minimal_representation is a collection of scripts for canonicalizing the representation of genomic variants. https://github.com/ericminikel/minimal_representation
denovolyzeR is an R package for testing the gene-wise burden of de novo variants in disease families compared to random mutational expectations. https://cran.r-project.org/web/packages/denovolyzeR/index.html
Jmol visualization software http://jmol.sourceforge.net
PyMol visualization software http://www.pymol.org/
Autodock (molecular docking simulation) http://autodock.scripps.edu/
Biological enrichment analysis tools:
WebGestalt http://bioinfo.vanderbilt.edu/webgestalt/ Free
DAVID https://david.ncifcrf.gov/ Free
Onto-Express http://vortex.cs.wayne.edu/projects.htm Free
GOMiner http://discover.nci.nih.gov/gominer/index.jsp Free
Ingenuity Pathway Analysis http://www.ingenuity.com/products/ipa Commercial
GeneGO Metacore http://lsresearch.thomsonreuters.com/pages/solutions Commercial

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

Genome Analysis Toolkit (GATK) https://software.broadinstitute.org/gatk/
Condel http://bg.upf.edu/fannsdb/
MAPP http://mendel.stanford.edu/SidowLab/downloads/MAPP/index.html
MutationTaster http://www.mutationtaster.org/
nsSNP Analyzer http://snpanalyzer.uthsc.edu/
PANTHER http://www.pantherdb.org
PhD-SNP http://snps.biofold.org/phd-snp/phd-snp.html
PolyPhen2 http://genetics.bwh.harvard.edu/pph2
SIFT http://sift.jcvi.org/
SNAP  https://rostlab.org/services/snap/
SNPs3D http://www.snps3d.org/
VAAST http://www.yandell-lab.org/software/vaast.html