Reading List
Seminar in Computational Genomics, COMS W4995-2
Prof. Itsik Pe’er
1. Human genome sequencing and assembly:
a. Nature 409:860-921 (2001). Initial sequencing and analysis of the human genome International Human Genome Sequencing Consortium
b. Science 291:1304 -1351 (2001). The Sequence of the Human Genome. J. Craig Venter et al.
2. Human genome gene content (same refs)
3. Human genome repeats & GC content (same refs)
4. Human genome variation & recombination (same refs)
5. Science 297:1003-1007 (2002) Recent segmental duplications in the human genome. Bailey, J. A. et al.
6. Nature 420:520-562 (2002) Initial sequencing and comparative analysis of the mouse genome. Mouse Genome Sequencing Consortium
7. Science 297:1301-1310 (2002). Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes Samuel Aparicio, et al.
8. Nature 432, 695 – 716 (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. International Chicken Genome Sequencing Consortium.
9. The Y chromosome:
a. Nature 423:825-837 (2003) The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. H. Skaletsky et al.
b. Nature 423:873-876 (2003) Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. S. Rozen et al.
10. The ‘feminine genome’:
a. PLoS Biology 2: e273 (2004), Continued Colonization of the Human Genome by Mitochondrial DNA. Ricchetti M et al.
b. Nature 434:325-337 (2005) The DNA sequence of the human X chromosome Mark T. Ross et al.
11. Autosome tales:
a. Nature 431:268-274 (2004) The DNA sequence and comparative analysis of human chromosome 5. Jeremy Schmutz et al.
b. Nature 440:671-675 (2006) Analysis of the DNA sequence and duplication history of human chromosome 15. Michael C. Zody et al
12. Conservation I:
a. Nature 423:241-54 (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Manolis Kellis et al.
b. Genome Research 13:813-820 (2003) Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes. Gregory M. Cooper et al.
13. Ultraconservation:
a. Science 304:1321-1325 (2004) Ultraconserved Elements in the Human Genome. Gill Bejerano et al.
b. PNAS 103, 11659-11664 (2006)A family of conserved noncoding elements derived from an ancient transposable element Xiaohui Xie
14. Murids:
a. Nature 428:493-521 (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Rat Genome Sequencing Project Consortium
b.
PLoS Genetics 2:e204
(2006) Genomic Selective Constraints in Murid Noncoding DNA. Gaffney DJ, Keightley
PD
15. Nature 437, 1299-1320 (2005) A haplotype map of the human genome. The International HapMap Consortium
16. Nature 438:803-819 (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Kerstin Lindblad-Toh et al.
17. Structural variation:
a. Nature Genet 37:727-732 (2005) Fine-scale structural variation of the human genome. Tuzun, E. et al.
b. Conrad,
D.F. , Andrews, T.D. , Carter, N.P. ,
18. Structural variation and genetics:
a.
b. Hinds, D.A. , Kloek, A.P. , Jen, M. , Chen, X. & Frazer, K.A. Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat. Genet. 38, 82–85 (2006).
19. Structural variation maps:
a. Nature 444:444-454 (2006) Global variation in copy number in the human genome. Richard Redon et al.
b. PLoS Genetics, e3 (2007) A high resolution map of segmental DNA copy number variation in the mouse genome. Timothy Graubert et al.
20. Nature 437:69-87 (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. The Chimpanzee Sequencing and Analysis Consortium
b. Genome Research 16:576-583 (2006) A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications. Xinwei She et al.
22. Chimp structural changes:
a. Nature 437:88-93 (2005) A genome-wide comparison of recent chimpanzee and human segmental duplications. Ze Cheng et al.
b. PLoS Genet. 1:e56 (2005). Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies. Feuk, L. et al.
23. Conservation II:
a. Genome Research 15:901-913 (2005) Distribution and intensity of constraint in mammalian genomic sequence Gregory M. Cooper et al.
b. Genome Research 15:1373-1378 (2005) Evolutionary constraints in conserved nongenic sequences of mammals Peter D. Keightley et al.
24. Conservation III:
a. Genome Research 15:1034-1050 (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes Adam Siepel et al.
b. Genome Research 16:656-668, 2006 Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Mathieu Blanchette et al.
25. Conservation and annotation:
a. Genome Res. 14, 852–859 (2004).Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment. Dermitzakis, E.T. et al.
b. Nature Genetics 38:1216 - 1220 (2006) Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants, Adnan Derti et al.
26. Mammalian ancestors:
a. Genome Research 14:2412-2423 (2004) Reconstructing large regions of an ancestral mammalian genome in silico. Mathieu Blanchette et al.
b. PLoS Genetics 3:e2 (2006) Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data. Nikolaev S et al.
27. Other forces:
a. PLoS Genetics 2:e168
(2006) Forces Shaping the Fastest Evolving Regions in the Human Genome.
b. Nature 441:1103-1108 (2006) Genetic evidence for complex speciation of humans and chimpanzees. Nick Patterson et al.
28. Neanderthals:
a. Nature 444:330-336 (2006) Analysis of one million base pairs of Neanderthal DNA Richard E. Green et al.
b. Science 314:1113–1118 (2006) Sequencing and Analysis of Neanderthal Genomic DNA. James P. Noonan et al.