Curriculum 2020

Molecular Biology

Refer to Wikipedia for basic information

High throughput sequencing (HTS)

The sequence of sequencers: The history of sequencing DNA, Heather JM et. al., Genomics 2016

High-Throughput Sequencing Technologies, Reuter JA et. al., Molecular Cell 2015

Sequencing depth and coverage: key considerations in genomic analyses, Sims D et. al., Nature Reviews 2014

RNA-seq differential expression studies: more sequence or more replication?, Liu Y et. al., Bioinformatics 2014

De novo genome assembly

A field guide to whole‐genome sequencing, assembly and annotation, Ekblom and Wolf, Evolutionary Applications 2014

The Theory and Practice of Genome Sequence Assembly, Simpson and Pop, Annual Review of Genomics and Human Genetics 2015

Variant Calling

Genotype and SNP calling from next-generation sequencing data Nielsen et al., Nature Reviews Genetics 2011. This is a review paper that should be easily understandable once the student has taken the variant calling module.

Exome sequencing identifies the cause of a mendelian disorder Ng et al., Nature Genetics 2010. A paper reporting the first resolution of a mendelian disorder using exome capture.

Somatic Variant Calling

Getz, et al. “Advances in understanding cancer genomes through second-generation sequencing”. Nature Reviews Genetics 2010

Machine Learning

Wainberg, et al. Deep learning in biomedicine, Nature Biotechnology 2018