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Bioinformatics

Coursera · University of California San Diego · 5 HN comments

Join Us in a Top 50 MOOC of All Time! How do we sequence and compare genomes? How do we identify the genetic basis for disease? How do we construct an evolutionary Tree of Life for ...
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This course is offered by University of California San Diego on the Coursera platform.
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If you're a programmer/CS person interesting in genomics/bioinformatics, I can't recommend UCSD's Coursera courses[0] enough.

[0] https://www.coursera.org/specializations/bioinformatics

The UCSD bioinformatics algorithms courses on Coursera are fantastic: https://www.coursera.org/specializations/bioinformatics
https://www.coursera.org/specializations/bioinformatics
Open Source Projects/Platforms:

ADAM (Big Data Genomics, code-base I think worked currently by UC Berkeley AMPLab and Microsoft Research group focused on cancer research) https://github.com/bigdatagenomics/adam/labels/pick%20me%20u...

BioConductor (R package that is very popular for crunching different genomic analysis, RNA-Seq)https://www.bioconductor.org/developers/

Galaxy (Platform for reproducible genomics workflows in the cloud)https://wiki.galaxyproject.org/Support

Public Available Data Sets:

Cancer Genome Atlas (contains expression data for different kinds of cancer) http://cancergenome.nih.gov/

NCBI Short Reads Archive (contains the genome assembly of a lot of published papers): https://www.ncbi.nlm.nih.gov/sra

European Nucleotide Archive: http://www.ebi.ac.uk/ena, e.g.,

For a recent major paper, "The Simons Genome Diversity Project: 300 genomes from 142 diverse populations"; you can grep for "accession code"(http://www.nature.com/nature/journal/vaop/ncurrent/full/natu...), follow the link and download the whole raw assemblies of all samples here: http://www.ebi.ac.uk/ena/data/view/PRJEB9586

MOOC:

https://www.edx.org/xseries/genomics-data-analysis

https://www.coursera.org/specializations/bioinformatics

StackOverflow:

https://www.biostars.org/

http://seqanswers.com/

Jobs:

NYGC, JCVI, CRB, Sanger, BGI, Broad, NIH, NCBI, Janelia Farm; any research group in universities; any informatics job at pharmaceutical or pharma startups.

My all star lineup would be:

The Analytics Edge - https://www.edx.org/course/analytics-edge-mitx-15-071x-0

Design of Computer Programs - https://www.udacity.com/course/design-of-computer-programs--...

Justice - https://www.edx.org/course/justice-harvardx-er22-1x-0

If I had more time I would love to go through the bioinformatics specialization on Coursera. They have 2 books and an exercise site (rosalind.info). It looks like great fun.

https://www.coursera.org/specializations/bioinformatics?utm_...

amykhar
Design of Computer Programs was decidedly the best course I ever took online. I was lucky enough to take it when it was first offered. Peter Norvig was very active in the course forum.
geomark
+1 for The Analytics Edge.

Along the same lines but a more thorough treatment of linear regression and statistical inference is the excellent Data Analysis and Statistical Inference https://www.coursera.org/course/statistics

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