• International Human Genome Sequencing Consortium
  Initial sequencing and analysis of the human genome.
  Nature. 2001 Feb 15; 409(6822):860-921.
• Venter et al.
  The sequence of the human genome.
  Science. 2001 Feb 16; 291(5507):1304-51. Erratum in: Science 2001 Jun 5 ;292 (5523):1838
• Waterston RH, Lander ES, Sulston JE.
  On the sequencing of the human genome.
  Proc Natl Acad Sci U S A. 2002 Mar 19; 99(6):3712-6. Epub 2002 Mar 05
• Myers EW, Sutton GG, Smith HO, Adams MD, Venter JC.
  On the sequencing and assembly of the human genome.
  Proc Natl Acad Sci U S A. 2002 Apr 2 ;99 (7):4145-6. Epub 2002 Mar 19. Erratum in: Proc Natl Acad Sci U S A 2002 Jun 25; 99(13):9081
• Green P.
  Whole-genome disassembly.
  Proc Natl Acad Sci U S A. 2002 Apr 2; 99(7):4143-4. Epub 2002 Mar 19.
• Waterston RH, Lander ES, Sulston JE.
  More on the sequencing of the human genome.
  Proc Natl Acad Sci U S A. 2003 Mar 18; 100(6):3022-4; author reply 3025-6. Epub 2003 Mar 11.
• International Human Genome Sequencing Consortium.
  Finishing the euchromatic sequence of the human genome.
  Nature. 2004 Oct 21;431(7011):931-45.
• ENCODE Project Consortium.
  The ENCODE (ENCyclopedia Of DNA Elements) Project.
  Science. 2004 Oct 22;306(5696):636-40.
  ENCODE website and databases
• Gibson G and Muse S.
  A Primer of Genome Science (On reserve at Countway and available in the Biophysics office)
  Chapters 1 and 2: sections on the Human Genome Project and Genome Sequencing

Single Sequence Analysis Methods

Genome Sequence Analysis

Required:

• Burge C, Karlin S.
  Prediction of complete gene structures in human genomic DNA.
  J Mol Biol. 1997 Apr 25;268(1):78-94.


• Tringe, SG et al.
  Comparative metagenomics of microbial communities.
  Science. 2005 Apr 22;308(5721):554-7.
  Supplementary Information

• Venter JC et al.
  Environmental genome shotgun sequencing of the Sargasso Sea.
  Science. 2004 Apr 2;304(5667):66-74. Epub 2004 Mar 04.
  Supplementary Online Material
• Eckburg PB et al.
  Diversity of the human intestinal microbial flora. Science. 2005 Jun 10;308(5728):1635-8. Epub 2005 Apr 14.

Suggested Background :

• Durbin, Eddy, Krogh, and Mitchison.
  Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids (On reserve at Countway and available in the Biophysics office)
  Chapters 1 & 3
• Zhang, MQ.
  Computational prediction of eukaryotic protein-coding genes.
  Nat Rev Genet. 2002 Sep;3(9):698-709. Review.

• Gibson G and Muse S.
  A Primer of Genome Science (On reserve at Countway and available in the Biophysics office)
  Box 2.3

Homology Searches, Protein Domains, Substitution Matrices

Protein Sequence Analysis

Required:

• Altschul SF, Boguski MS, Gish W, Wootton JC.
  Issues in searching molecular sequence databases.
  Nat Genet. 1994 Feb; 6(2):119-29. Review.
  
  To be presented together:
• Geer LY, Domrachev M, Lipman DJ, Bryant SH.
  CDART: protein homology by domain architecture.
  Genome Res. 2002 Oct;12(10):1619-23.
• Mott R, Schultz J, Bork P, Ponting CP.
  Predicting protein cellular localization using a domain projection method.
  Genome Res. 2002 Aug;12(8):1168-74.

Protein Domain Databases

Additional Optional Reading:

• Eddy SR. Profile hidden Markov models Bioinformatics. 1998 14(9): 755-83
• Durbin et al. Biological Sequence Analysis
  Chapter 5
• Gibson and Muse
  Box 4.1 (First Edition) or Box 5.1 (Second Edition)

Motif Finding

Required:

• Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, Burge CB.
  Systematic identification and analysis of exonic splicing silencers.
  Cell. 2004 Dec 17;119(6):831-45.


• Crawford GE, et al.
  Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 2006 Jan;16(1):123-31. Epub 2005 Dec 12.

Supplemental Reading:

• Sabo PJ, et al.
  Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries. Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4537-42. Epub 2004 Mar 19.

Suggested Background :

• Gibson G and Muse S.
  A Primer of Genome Science (On reserve at Countway and available in the Biophysics office)
  Box 3.3. (First Edition) or Box 4.4 (Second Edition)
• Ladd AN, Cooper TA.
  Finding signals that regulate alternative splicing in the post-genomic era.
  Genome Biol. 2002 Oct 23; 3(11):reviews0008. Review.
• Tompa M et al.
  Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol. 2005 Jan;23(1):137-44.

Comparative Genomics

Required:

• Siepel et al.
  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. Epub 2005 Jul 15.


• Rhoades et al.
  Prediction of plant microRNA targets. Cell. 2002 Aug 23;110(4):513-20
  

Suggested Background :

• Miller W, Makova KD, Nekrutenko A, Hardison RC.
  Comparative Genomics
  Annu Rev Genomics Hum Genet. 2004;5:15-56. Review.
• Boffelli D, Nobrega MA, Rubin EM.
  Comparative genomics at the vertebrate extremes.
  Nat Rev Genet. 2004 Jun;5(6):456-65. Review
  

Supplemental Reading:

• Cooper et al.
  Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005 Jul;15(7):901-13. Epub 2005 Jun 17.

Genome Comparison and Regulation

Required:

• Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES.
  Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003 May 15; 423(6937):241-54.
  Supplementary Material


• Extension of Analysis to Mammals:
  Xie X et al.
  Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature. 2005 Mar 17;434(7031):338-45.


• Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM.
  Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science. 2003 Feb 28; 299(5611):1391-4.
  Supplementary Material
  

Suggested Background (as an intro to clustering):

• Jain AK, Murty MN, Flynn PJ.
  Data Clustering: A Review.
  ACM Computing Surveys, Vol. 31, No. 3, September 1999.
• Gibson G and Muse S.
  A Primer of Genome Science
  Chapter 3, Box 3.2 (First Edition) or Box 4.3 (Second Edition)

Additional Optional Reading:

• Bulyk ML
  Computational prediction of transcription-factor binding site locations
  Genome Biology. 2003 Dec 23;5(1): 201.
• Kellis M, Birren BW, Lander ES.
  Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae.
  Nature. 2004 Apr 8;428(6983):617-24. Epub 2004 Mar 07.
• Lynch M, Katju V.
  The altered evolutionary trajectories of gene duplicates. Trends Genet. 2004 Nov;20(11):544-9.
• Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M.
  Finding functional features in Saccharomyces genomes by phylogenetic footprinting.
  Science. 2003 Jul 4;301(5629):71-6. Epub 2003 May 29.

Transcriptional Analysis

Required:

• Hughes TR et al.
  Functional discovery via a compendium of expression profiles.
  Cell. 2000 Jul 7; 102(1):109-26.
  Supplemental Data

• Beer MA, Tavazoie S.
  Predicting gene expression from sequence.
  Cell. 2004 Apr 16;117(2):185-98.
  Supplementary Figures

Supplemental Reading:

• Stolc V, et al.
  A gene expression map for the euchromatic genome of Drosophila melanogaster.
  Science. 2004 Oct 22;306(5696):655-60.
  Supplementary Material
• Bertone P, et al.
  Global identification of human transcribed sequences with genome tiling arrays.
  Science. 2004 Dec 24;306(5705):2242-6. Epub 2004 Nov 11.

Background Reading:

• Lockhart DJ and Winzeler EA
  Genomics, gene expression and DNA arrays. Nature. 2000 June 15;405: 827-836.
• Stoughton RB.
  Applications of DNA microarrays in biology. Annu Rev Biochem. 2005;74:53-82. Review.
• Gibson and Muse
  Chapter 3 (first edition) or Chapter 4 (second edition)

Epigenome Analysis

Required:

• Cheng YW, Shawber C, Notterman D, Paty P, Barany F.
  Multiplexed profiling of candidate genes for CpG island methylation status using a flexible PCR/LDR/Universal Array assay.
  Genome Res. 2005 Dec 20; [Epub ahead of print]

• Yuan GC et al.
  Genome-scale identification of nucleosome positions in S. cerevisiae.
  Science. 2005 Jul 22;309(5734):626-30. Epub 2005 Jun 16.
  
  
• Liu CL et al.
  Single-nucleosome mapping of histone modifications in S. cerevisiae.
  PLoS Biol. 2005 Oct;3(10):e328. Epub 2005 Aug 30.

• Fazzari MJ, Greally JM.
  Epigenomics: beyond CpG islands. Nat Rev Genet. 2004 Jun;5(6):446-55. Review.
• Laird PW.
  Cancer epigenetics. Hum Mol Genet. 2005 Apr 15;14 Spec No 1:R65-76. Review.
• Felsenfeld G, Groudine M.
  Controlling the double helix. Nature. 2003 Jan 23;421(6921):448-53. Review.

Transcriptional Regulatory Networks

Required:

• Stuart JM, Segal E, Koller D, Kim SK.
  A gene coexpression network for global discovery of conserved genetic modules.
  Science. 2003 Oct 10; 302(5643):249-55. Epub 2003 Aug 21.
  Supplementary Material


• Foat BC, Houshmandi SS, Olivas WM, Bussemaker HJ.
  Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc Natl Acad Sci U S A. 2005 Dec 6;102(49):17675-80. Epub 2005 Nov 29.
  Supplementary Material


• Carson, JP. et al.
  A Digital Atlas to Characterize the Mouse Brain
  Transcriptome.
  PLoS Comput Biol. 2005 Sep 23;1(4):e41
  

• Bar-Joseph Z et al.
  Computational discovery of gene modules and regulatory networks. Nat Biotechnol. 2003 Nov;21(11):1337-42. Epub 2003 Oct 12.

Regulomics

Required:

• Simon I et al.
  Serial regulation of transcriptional regulators in the yeast cell cycle.
  Cell. 2001 Sep 21; 106(6):697-708.
  Supplemental Website
  
  
• Rajewski et al.
  Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics. 2002 Oct 24;3:30. Epub 2002 Oct 24.

Additional Background Reading:

• Schroeder MD et al.
  Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol. 2004 Sep;2(9):E271. Epub 2004 Aug 31.
  (Specifically helpful to presenter of Rajewsky et al.)

Hypergeometric Distribution Information:

• Tavazoie S, et al.
  Systematic determination of genetic network architecture. Nat Genet. 1999 Jul;22(3):281-5. hypergeometric distribution equation on p. 5
• MathWorld description of hypergeometric distribution

Introduction to Proteomics

Required:

• Huang J, Zhu H, Haggarty SJ, Spring DR, Hwang H, Jin F, Snyder M, Schreiber SL
  Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips.
  Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16594-9. Epub 2004 Nov 11.
  Supplementary Tables


• Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R
  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags.
  Nat Biotechnol . 1999 Oct; 17(10):994-9.


• Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK.
  Global analysis of protein localization in budding yeast.
  Nature. 2003 Oct 16; 425(6959):686-91.
  Supplementary Material

Additional Background Reading:

• Zhu H, et al.
  Global analysis of protein activities using proteome chips. Science. 2001 Sep 14;293(5537):2101-5. Epub 2001 Jul 26.
  Supplementary Material
• Zhou H, Ranish JA, Watts JD, Aebersold R.
  Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry.
  Nat Biotechnol. 2002 May;20(5):512-5.

Proteomics

Required:

To be presented together:
• Gavin AC, et al.
  Proteome survey reveals modularity of the yeast cell machinery. Nature. 2006 Jan 22; [Epub ahead of print]
  
• Ho Y, Gruhler A, Heilbut A, Bader GD, ...Mann M, Hogue CW, Figeys D, Tyers M.
  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002 Jan 10; 415(6868):180-3.
  Supplementary Material


• Neduva V, Linding R, Su-Angrand I, Stark A, De Masi F, Gibson TJ, Lewis J, Serrano L, Russell RB.
  Systematic discovery of new recognition peptides mediating protein interaction networks.
  PLoS Biol. 2005 Dec;3(12):e405. Epub 2005 Nov 15.

• Gavin AC, Bosche M, Krause R, ...Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G.
  Functional organization of the yeast proteome by systematic analysis of protein complexes.
  Nature. 2002 Jan 10; 415(6868):141-7.
  Supplementary Material

• Cusick ME, Klitgord N, Vidal M, Hill DE.
  Interactome: gateway into systems biology. Hum Mol Genet. 2005 Oct 15;14 Spec No. 2:R171-81. Epub 2005 Sep 14. Review.
• Gibson G and Muse S.
  A Primer of Genome Science
  p. 202-204 (first edition) or p. 283-289 (second edition)

Pathways

Required:

• Monod J, Jacob F.
  Teleonomic mechanisms in cellular metabolism, growth, and differentiation.
  Cold Spring Harb Symp Quant Biol. 1961; 26:389-401.


• Elowitz MB, Leibler S.
  A synthetic oscillatory network of transcriptional regulators.
  Nature. 2000 Jan 20; 403(6767):335-8.

• Suel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB.
  An excitable gene regulatory circuit induces transient cellular differentiation. Nature. 2006 Mar 23;440(7083):545-50.
  
• ICSB Meeting Lecture Videos

Networks

Required:

To be presented together:
• Albert R, Jeong H, Barabasi AL.
  Error and attack tolerance of complex networks
  Nature. 2000 Jul 27; 406(6794):378-82.
• Jeong H, Mason SP, Barabasi AL, Oltvai ZN.
  Lethality and centrality in protein networks.
  Nature. 2001 May 3; 411(6833):41-2.
  Supplementary Methods
  Supplementary Results



• Aloy P et al.
  Structure-based assembly of protein complexes in yeast.
  Science. 2004 Mar 26;303(5666):2026-9.
  Supplementary Material



• Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U.
  Network motifs: simple building blocks of complex networks. Science. 2002 Oct 25;298(5594):824-7.
  Supplementary Material

Networks

Required:

• Jones RB, Gordus A, Krall JA, MacBeath G.
  A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature. 2006 Jan 12;439(7073):168-74. Epub 2005 Nov 6.

• Becskei A, Kaufmann BB, van Oudenaarden A.
  Contributions of low molecule number and chromosomal positioning to stochastic gene expression.
  Nat Genet. 2005 Sep;37(9):937-44. Epub 2005 Aug 7.
  Supplementary Material

• Ozbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A
  Regulation of noise in the expression of a single gene. Nat Genet. 2002 May;31(1):69-73. Epub 2002 Apr 22.

Function Prediction

Required:

• Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N.
  The use of gene clusters to infer functional coupling.
  Proc Natl Acad Sci USA . 1999 Mar 16; 96(6):2896-901.
  Supplementary Material



• Lee I, Date SV, Adai AT, Marcotte EM.
  A probabilistic functional network of yeast genes. Science. 2004 Nov 26;306(5701):1555-8
  Supplementary Material



• Wilson CA, Kreychman J, Gerstein M.
  Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.
  J Mol Biol. 2000 Mar 17;297(1):233-49.

Supplemental Reading:

• Marcotte EM et al.
  Detecting protein function and protein-protein interactions from genome sequences.
  Science. 1999 Jul 30; 285(5428):751-3
  
• Tian W, Skolnick J.
  How well is enzyme function conserved as a function of pairwise sequence identity?
  J Mol Biol. 2003 Oct 31;333(4):863-82

Networks and Function Prediction

Required:

• Yeang CH, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T.
  Validation and refinement of gene-regulatory pathways on a network of physical interactions.
  Genome Biol. 2005;6(7):R62. Epub 2005 Jul 1.
  Supplementary Information


• Jim K, Parmar K, Singh M, Tavazoie S.
  A cross-genomic approach for systematic mapping of phenotypic traits to genes.
  Genome Res. 2004 Jan;14(1):109-15.
  Supplementary Information


• Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T.
  Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):1974-9. Epub 2005 Feb 1.
  Supplementary Information

• Suthram S, Sittler T, Ideker T.
  The Plasmodium protein network diverges from those of other eukaryotes.Nature. 2005 Nov 3;438(7064):108-12.
  Supplementary Information

Metabolomics

Required:

• Allen J, Davey HM, Broadhurst D, Heald JK, Rowland JJ, Oliver SG, Kell DB.
  High-throughput classification of yeast mutants for functional genomics using metabolic footprinting .
  Nat Biotechnol . 2003 Jun ;21 (6):692-6. Epub 2003 May 12.
  Supplementary Material


• Famili I, Forster J, Nielsen J, Palsson BO.
  Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network.
  Proc Natl Acad Sci U S A. 2003 Nov 11; 100(23):13134-9. Epub 2003 Oct 24
  Supplementary Material


• Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD.
  Computational prediction of human metabolic pathways from the complete human genome. Genome Biol. 2005;6(1):R2. Epub 2004 Dec 22.
  

Supplemental Reading:

• Green ML, Karp PD.
  A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics. 2004 Jun 9;5:76.
• Raamsdonk LM, et al.
  A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations.
  Nat Biotechnol. 2001 Jan;19(1):45-50.
• Forster J, Famili I, Fu P, Palsson BO, Nielsen J.
  Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.
  Genome Res. 2003 Feb;13(2):244-53.
• Gibson G and Muse S.
  A Primer of Genome Science
  Chapter 6 p. 301-308 (first edition) p. 333-339 (second edition)

Phenotyping

Required:

• Giaever G, et al.
  Functional profiling of the Saccharomyces cerevisiae genome.
  Nature. 2002 Jul 25; 418(6896):387-91.
  Supplemental Data
  Supplementary Methods
  
  To be presented together:
  
• Nolan PM et al.
  A systematic, genome-wide, phenotype-driven mutagenesis programme for gene function studies in the mouse.
  Nat Genet. 2000 Aug;25(4):440-3.
• Bacon Y, et al.
  Screening for novel ENU-induced rhythm, entrainment and activity mutants. Genes Brain Behav. 2004 Aug;3(4):196-205.

Phenotyping

Required:

• Hartman JL 4th, Tippery NP.
  Systematic quantification of gene interactions by phenotypic array analysis. Genome Biol. 2004;5(7):R49. Epub 2004 Jun 29
  Supplementary Material


• Kamath RS, et al.
  Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature. 2003 Jan 16; 421(6920):231-7.
  Supplementary Material


• Perlman ZE, Slack MD, Feng Y, Mitchison TJ, Wu LF, Altschuler SJ.
  Multidimensional drug profiling by automated microscopy.
  Science. 2004 Nov 12;306(5699):1194-8.
  Supplementary Material
  

Genetic Networks

• Parsons AB, Brost RL, Ding H, Li Z, Zhang C, Sheikh B, Brown GW, Kane PM, Hughes TR, Boone C.
  Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways.
  Nat Biotechnol. 2004 Jan;22(1):62-9. Epub 2003 Dec 07
  Supplementary Material


• Tong AH, et al.
  Global mapping of the yeast genetic interaction network.
  Science. 2004 Feb 6;303(5659):808-13.
  Supplementary Material


• Zupan B, Demsar J, Bratko I, Juvan P, Halter JA, Kuspa A, Shaulsky G.
  GenePath: a system for automated construction of genetic networks from mutant data.
  Bioinformatics. 2003 Feb 12;19(3):383-9.
  GenePath Website

Additional Optional Reading:

• Tong AH, et al.
  Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science. 2001 Dec 14;294(5550):2364-8.
• Pan X, et al.
  A robust toolkit for functional profiling of the yeast genome. Mol Cell. 2004 Nov 5;16(3):487-96.
• Juvan P, Demsar J, Shaulsky G, Zupan B.
  GenePath: from mutations to genetic networks and back. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W749-52.
  Supplementary Information
• Gibson and Muse
  Box 5.2 (second edition)

Variation

Required:

• Jeon Y, et al.
  Temporal profile of replication of human chromosomes. Proc Natl Acad Sci U S A. 2005 May 3;102(18):6419-24. Epub 2005 Apr 21.


• Altshuler D, Brooks LD, Chakravarti A, Collins FS, Daly MJ, Donnelly P; International HapMap Consortium.
  A haplotype map of the human genome. Nature. 2005 Oct 27;437(7063):1299-320.
  Supplementary Material
  

Optional Reading:

• Pollack JR, et al.
  Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors.
  Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12963-8. Epub 2002 Sep 24.
• Peacock E, Whiteley P.
  Perlegen sciences, inc. Pharmacogenomics. 2005 Jun;6(4):439-42.

• Carlson CS, Eberle MA, Kruglyak L, Nickerson DA.
  Mapping complex disease loci in whole-genome association studies. Nature. 2004 May 27;429(6990):446-52. Review.
• Gibson G and Muse S.
  A Primer of Genome Science
  Chapter 5 (first edition) or Chapter 3 (second edition)

SNPs, Variation

Future Directions of Genomics

Variation

Required:

• Stranger BE, et al.
  Genome-Wide Associations of Gene Expression Variation in Humans. PLoS Genet. 2005 Dec 16;1(6):e78 [Epub ahead of print]
  


• Schadt EE, et al.
  An integrative genomics approach to infer causal associations between gene expression and disease.
  Nat Genet. 2005 Jul;37(7):710-7. Epub 2005 Jun 19.
  

• Bustamante C, et al.
  Natural selection on protein-coding genes in the human genome. Nature. 2005 Oct 20;437(7062):1153-7.
• Williamson SH, et al.
  Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc Natl Acad Sci U S A. 2005 May 31;102(22):7882-7. Epub 2005 May 19.

• Xie L, Bourne PE
  Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models. PLoS Comput Biol. 2005 Aug 19;1(3):e31 [Epub ahead of print]
• Chandonia JM, Brenner SE.
  The impact of structural genomics: expectations and outcomes. Science. 2006 Jan 20;311(5759):347-51. Review.

Course Wrap-Up / Outlook