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.
Statistical genomics¶
Colocalization analyses of genomic elements: approaches, recommendations and challenges, Kanduri et. al., Bioinformatics 2018.
Quinlan, Aaron R., and Ira M. Hall. “BEDTools: a flexible suite of utilities for comparing genomic features.” Bioinformatics 26.6 (2010): 841-842.
Optional reading for those interested: Salvatore, Stefania, et al. “Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis.” Briefings in bioinformatics 21.5 (2020): 1523-1530
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