Curriculum and supporting material 2022¶
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. (2016), Genomics.
High-Throughput Sequencing Technologies, Reuter JA et. al. (2015) Molecular Cell.
Sequencing depth and coverage: key considerations in genomic analyses, Sims D et. al. (2014) Nature Reviews.
Long-read human genome sequencing and its applications Logsdon, G.A., Vollger, M.R. & Eichler, E.E. (2020) Nat Rev Genet 21, 597–614.
Nanopore sequencing technology, bioinformatics and applications, Wang, Y., Zhao, Y., Bollas, A. et al. (2021) Nat Biotechnol 39, 1348–1365.
The long reads ahead: de novo genome assembly using the MinION, de Lannoy, C., de Ridder, D. & Risse, J. (2017) F1000Research 2017, 6:1083.
De novo genome assembly¶
A field guide to whole-genome sequencing, assembly and annotation, Ekblom and Wolf (2014), Evolutionary Applications.
The Theory and Practice of Genome Sequence Assembly, Simpson and Pop (2015) Annual Review of Genomics and Human Genetics.
The present and future of de novo whole-genome assembly, Jang-il Sohn, Jin-Wu Nam (2018) Briefings in Bioinformatics, 19 (1), 23-40.
A survey on de novo assembly methods for single-molecular sequencing, Ying Chen, Chuan-Le Xiao (2020) Quant. Biol., 8, 3, 203-215.
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.)
Variant calling: Considerations, practices, and developments, Zverinova, S., & Guryev, V. (2022) Human Mutation, 43, 976-985.
Best practices for variant calling in clinical sequencing, Koboldt, D.C. (2020) Genome Med 12, 91.
Advances in understanding cancer genomes through second-generation sequencing Getz, et al. (2010) Nature Reviews Genetics 2010.
A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data Chang Xu (2018), Computational and Structural Biotechnology Journal, 16, 15-24.
Statistical genomics¶
Colocalization analyses of genomic elements: approaches, recommendations and challenges, Kanduri et. al. (2018) Bioinformatics.
GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome, Simovski et al. (2017) GigaScience, 6, 1–12.
BEDTools: a flexible suite of utilities for comparing genomic features, Quinlan, Aaron R., and Ira M. Hall. (2010) Bioinformatics 26, 6, 841-842.
Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis, Salvatore, Stefania, et al. (2020) Briefings in bioinformatics 21, 5, 1523-1530 (optional reading for those interested).
Machine Learning¶
Deep learning in biomedicine, Wainberg, et al. (2018) Nature Biotechnology.
DOME: recommendations for supervised machine learning validation in biology, Walsh, I., Fishman, D., Garcia-Gasulla, D. et al. (2021) Nat Methods 18, 1122–1127.
Navigating the pitfalls of applying machine learning in genomics, Whalen, S., Schreiber, J., Noble, W.S. et al. (2022) Nat Rev Genet 23, 169–181.