Literature and Links to sites mentioned in Lectures 8 and 9

Literature

Telomere to Telomere special issue:

• https://www.science.org/toc/science/376/6588

T2T-CHM13 paper:

• The complete sequence of a human genome
  Nurk S et al, T2T Consortium
  Science. 2022 376(6588):44-53

Article on comparison of mouse WGS to tiling path sequencing:

• Lineage-specific biology revealed by a finished genome assembly of the mouse.
  Church DM et al., Mouse Genome Sequencing Consortium.
  PLoS Biol. 2009 7(5):e1000112

Genome round one:

• Initial sequencing and analysis of the human genome.
  Lander ES et al. International Human Genome Sequencing Consortium.
  Nature. 2001 409(6822):860-921.
• The sequence of the human genome.
  Venter JC, et al (Celera)
  Science. 2001 291(5507):1304-51.

Genome round two:

• On the sequencing of the human genome.
  Waterston RH, Lander ES, Sulston JE. (International Human Genome Sequencing Consortium)
  PNAS 2002 99(6):3712-6.
• On the sequencing and assembly of the human genome.
  Myers EW, Sutton GG, Smith HO, Adams MD, Venter JC. (Celera)
  PNAS 2002 99(7):4145-6.
• Whole-genome disassembly
  Phil Green (commentary in favor of the public project)
  PNAS 2002 99:4143-4144

Genome round three:

• Explanation of Round Three
  Revisiting the independence of the publicly and privately funded drafts of the human genome
  N. R. Cozzarelli
  PNAS 2003 100:3021
• More on the sequencing of the human genome.
  Waterston RH, Lander ES, Sulston JE. (International Human Genome Sequencing Consortium)
  PNAS 2003 100(6):3022-4
• The independence of our genome assemblies (Celera)
  MD Adams, GG Sutton, HO Smith, EW Myers, and JC Venter
  PNAS 2003 100:3025-3026

Celera true WGS:

• Whole-genome shotgun assembly and comparison of human genome assemblies
  Istrail S et al. (Celera)
  PNAS 2004 101(7):1916-21.

• A comparative analysis of HGSC and Celera human genome assemblies and gene sets.
  Li S, Cutler G, Liu JJ, Hoey T, Chen L, Schultz PG, Liao J, Ling XB.
  Bioinformatics. 2003 19(13):1597-605.
• The map problem: a comparison of genetic and sequence-based physical maps.
  DeWan AT, Parrado AR, Matise TC, Leal SM.
  Am J Hum Genet. 2002 70(1):101-7.
• The Unified DataBase (UDB): a novel genome integration concept
  Chalifa-Caspi,V., Rebhan,M., Prilusky,J. and Lancet,D
  Genome Digest. (1997) 4:15-16

Some papers on inbred mice and genetic variation:

• The Genome of C57BL/6J “Eve”, the Mother of the Laboratory Mouse Genome Reference Strain
  Sarsani VK, Raghupathy N, Fiddes IT, Armstrong J, Thibaud-Nissen F, Zinder O, Bolisetty M, Howe K, Hinerfeld D, Ruan X, Rowe L, Barter M, Ananda G, Paten B, Weinstock GM, Churchill GA, Wiles MV, Schneider VA, Srivastava A, Reinholdt LG
  G3 Genes|Genomes|Genetics (2019) 9(6):1795-1805
• Lessons from Sequencing Eve C57BL/6J
  Dolores Garcia Arocena
  Jackson Labs blog, July 29, 2019
• Inbred lab mice are not isogenic: genetic variation within inbred strains used to infer the mutation rate per nucleotide site
  Chebib J, Jackson BC, Lopez-Cortegano E, Tautz D, Keightley PD
  Heredity (2021) 126:107-116

Links

• Gold Genome Database: http://www.genomesonline.org
• Genome Reference Consortium: https://www.ncbi.nlm.nih.gov/grc
• T2T Consortium: https://sites.google.com/ucsc.edu/t2tworkinggroup
• National Human Genome Research Institute T2T: https://www.genome.gov/about-genomics/telomere-to-telomere

• UCSC Genome Browser: http://genome.ucsc.edu
• NCBI Genome Data Viewer: https://www.ncbi.nlm.nih.gov/genome/gdv/
• Ensembl Genome Browser: http://www.ensembl.org

• DOE Joint Genome Institute: https://jgi.doe.gov/
• TAIR - Arabidopsis Genome Database: http://www.arabidopsis.org
• Saccharomyces Genome Database (SGD): http://www.yeastgenome.org
• Berkley Drosophila Genome Project (BDGP): http://www.fruitfly.org/

• Dolan DNA Learning Center, CSH: http://www.dnalc.org/
• YourGenome, Sanger: http://www.yourgenome.org/