This page collects items for the course "reading list" (and beyond). The files for the articles can be found in the link you've received throgh the chat. Since the repository is public, we're not able to provide direct downloads as part of the repository but there are some links here to videos or other resources.
- Heather and Chain (2016): The sequence of sequencers
- 2016-01-15___Heather_and_Chain__The-sequence-of-sequencers__Genomics.pdf
- Spinner and Ferguson-Smith (2019): Cytogenetic-Analysis - Chapter from "Principles and Practice of Medical Genetics"
- 2019-07-01___Spinner-and-Ferguson-Smith__Cytogenetic-Analysis__Chapter-from-Principles-Practice-Medical-Genetics.pdf
- Zweig et al (2008): UCSC genome browser tutorial
- 2008-08-01___Zweig_et_al.__UCSC-genome-browser-tutorial__Genomics.pdf
- Schattner (2009): Genomics made easier
- 2009-03-01___Schattner__Genomics-made-easier__Genomics.pdf
- Gao, Huang & Baudis (2018): segment_liftover : a Python tool to convert segments between genome assemblies.
- 1000 Genomes
- 2015-10-01___1000-Genomes-Consortium__A%20global-reference-for-human-genetic-variation__Nature.pdf
- Evans et al: Finding the Rare Pathogenic Variants in a Human Genome
- 2017-05-09___Evans__Clinical_genome_sequencing__JAMA_comment.pdf
- TCGA Project - The Cancer Genome Atlas Pan Cancer analysis project - Nature Genetics
- 2013-10-01___TCGA_Project__The-Cancer-Genome-Atlas-Pan-Cancer-analysis-project__Nature_Genetics.pdf
- den Dunnen and Antonorakis (2000): Mutation Nomenclature Extensions (i.e. "HGVS"
- 2000-01-01___den_Dunnen_and_Antonorakis__Mutation-Nomenclature-Extensions__Human_Mutation.pdf
- den Dunnen et al. (2016): HGVS Nomenclature Update
- 2016-03-02___Dunnen_et_al.__HGVS%20Recommendations_2016-Update__Human_Mutation.pdf
- Sondka et al. - COSMIC Cancer Gene Census - Nature Reviews Cancer (2018-10-09
- 2018-10-09___Sondka-et-al.__COSMIC-Cancer-Gene-Census__Nature-Reviews-Cancer.pdf
- S. Samarajiwa - Genome Browsers (2018-10-09
- 2014-07-27___Samarajiwa__Genome-Browsers__Cambridge-lecture-slides
- Gymrek et al. - Identifying Personal Genomes by Surname Inference (Science, 2013-01-18
- 2013-01-18___Gymrek-et-al.__Identifying-Personal-Genomes-by-Surname-Inference__Science.pdf
- Erlich and Narayanan2 - Routes for breaching and protecting genetic privacy (2014-06-17; Nat Rev Gen
- 2014-06-17___Erlich__Routes_breaching_genetic_privacy__NatRevGen.pdf
- Shringarpure-and-Bustamante - Privacy Risks from Genomic Data-Sharing Beacons
- 2015-10-29___Shringarpure-and-Bustamante__Privacy-Risks-from-Genomic-Data-Sharing-Beacons__American-Journal-of-Human-Genetics.pdf
- 1000 Genomes (2015): A global reference for human genetic variation
- 2015-10-01___1000-Genomes-Consortium__A-global-reference-for-human-genetic-variation__Nature.pdf
- TCGA Project (2013): The Cancer Genome Atlas Pan-Cancer analysis project
- 2013-10-01___TCGA_Project__The-Cancer-Genome-Atlas-Pan-Cancer-analysis-project__Nature_Genetics.pdf
- Griffith et al (2015): CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer
- 2015-07-01___Griffith__CIViC-is-a-community-knowledgebase-for-expert-crowdsourcing-the-clinical-interpretation-of-variants-in-cancer__Nature_Genetics.pdf
- Sunyaev (2012): Inferring causality and functional significance of human coding DNA variants
- 2012-09-06___Sunyaev__Inferring-causality-and-functional-significance-of-human-coding-DNA-variants__Human_Molecular_Genetics.pdf
- Freeman et al (2006): Copy number variation: new insights in genome diversity
- 2006-06-29___Sunyaev__Copy-number-variation-new-insights-in-genome-diversity__Genome_Research.pdf
- Deng et al (2017): Comparative genomic analysis of esophageal squamous cell carcinoma between Asian and Caucasian patient populations
- 2017-11-16___Deng__Comparative-genomic-analysis-of-esophageal-squamous-cell-carcinoma-between-Asian-and-Caucasian-patient-populations__Nature_Communications.pdf
- Zehir et al (2017): Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients
- 2017-05-08___Zehir_et_al.__MSKCC-IMPACT_Panel_Sequencing_more_than_10000_metastatic_cancer_patients__NatMed.pdf
- Koboldt et al (2012): VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
- 2012-02-02___VarScan-2-Somatic-mutation-and-copy-number-alteration-discovery-in-cancer-by-exome-sequencing__Genome_Research.pdf
- Wagner et al (2020): A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer
- 2020-04-03___Wagner-et-al.__A-Harmonized-Meta-Knowledgebase-of-Somatic-Cancer-Variants__Nature-Genetics.pdf
- Nurk et al. (2022): The complete sequence of a human genome
- 2022-04-01___Nurk-et-al__The-complete-sequence-of-a-human-genome__Science.pdf
- Liao, Paten et al. (2023): A draft human pangenome reference
- 2023-05-11___Liao,-Paten-et-al.__A-draft-human-pangenome-reference__Nature.pdf
- Mark Gerstein (Yale): Lecture slides "Analyzing Personal Genomes: Prioritizing High-impact Rare & Somatic Variants"
- 2016-03-29___Gerstein_Personal-Genomes-Prioritizing-High-impact-Variants__slides.pdf
- Harold Varmus: "Approaches to increased equity in the use of genomics"
- GA4GH 2023 keynote (Youtube video)
- Karen Miga: "The Human Pangenome Project"
- GA4GH 2024 keynote (Youtube video )
- CRAM file format presentations