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This page lists some of the original literature that are related to genome sequence assembly and analysis.
Background Materials
Background material on BLAST and other computer programs can be found in a number of texts. The following are all useful, depending on the goals of the course and the background of the students.
- "Discovering Genomics, Proteomics, and Bioinformatics" by A.M. Campbell and L.J. Heyer, 2nd edition, 2007, CSHL Press & Pearson Benjamin Cummings, NY.
- "Bioinformatics and Functional Genomics" by R. Pevsner, 2003, J. Wiley & Sons, NJ (also an excellent web site).
- "BLAST" by I. Korf, M. Yandell, J. Bedell, 2003, O'Reilly (recommended for in-depth use of BLAST and interpretation of results).
Sequencing Technology
- Green ED, Guyer MS (2011) Charting a course for genomic medicine from base pairs to bedside. Nature 470: 204-13.
- Mardis, ER. (2011) A decade's perspective on DNA sequencing technology. Nature 470: 198-203.
- André E Minoche, Juliane C Dohm and Heinz Himmelbauer (2011). Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome analyzer systems. Genome Bio 12:R112
- Rothberg, JM et al. (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475: 348-52.
- Treangen, TJ, and Salzberg, SL (2011) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature Rev. Genet. 13: 36-46.
- Koboldt, DC et al. (2010) Challenges of sequencing human genomes. Brief Bioinform. 11: 484-98.
- Mardis, ER. (2010) The $1,000 genome, the $100,000 analysis. Genome Medicine 2:84.
- Cydney B Nielsen, Michael Cantor, Inna Dubchak, David Gordon & Ting Wang. (2010). Visualizing genomes: techniques and challenges. Nature Methods 7, S5 - S15.
- Eid, J, et al. (2009) Real-Time DNA sequencing from single polymerase molecules. Science 323: 133-138.
- Warren RL, Varabei D, Platt D, Huang X, Messina D, Yang SP, Kronstad JW, Krzywinski M, Warren WC, Wallis JW, Hillier LW, Chinwalla AT, Schein JE, Siddiqui AS, Marra MA, Wilson RK, Jones SJ. (2006) Physical map-assisted whole-genome shotgun sequence assemblies. Genome Res. 16: 768-75.
- Gordon D, Desmarais C, Green P. (2001) Automated Finishing with Autofinish. Genome Res. 11: 614-625.
- Gordon D, Abajian C, Green P. (1998) Consed: A graphical tool for sequence finishing. Genome Res. 8: 195-202.
Understanding Chromatin Structure
- Kharchenko, PV, ..., M Kellis, SCR Elgin, MI Kuroda, V Pirrotta, G Karpen, PJ Park. (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471: 480-5.
- Riddle, NC, ..., SCR Elgin, GH Karpen (2011) Plasticity in patterns of histone modifications and chromosomal proteins in the Drosophila heterochromatin. Genome Res 21: 147-63.
- Grewal, SIS (2010) RNAi-dependent formation of heterochromatin and its diverse functions. Curr Opin Genet Dev 20: 134-41.
- Haynes KA, Caudy AA, Collins L, Elgin SC. (2006) Element 1360 and RNAi Components Contribute to HP1-Dependent Silencing of a Pericentric Reporter. Curr Biol. 16: 2222-7.
- Felsenfeld G, Groudine M (2003) Controlling the double helix, Nature 421: 448-453.
- Grewal SIS, Elgin, SCR. (2002) Heterochromatin: new possibilities for the inheritance of structure, Curr. Opin. Genetics & Develop. 12: 178-187.
Human Genomics
- Altshuler, D.M., et al. (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467, 52-58.
- Conrad, D.F., et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature 464, 704-712.
- Ding, L, Wendl MC, Koboldt DC, Mardis ER (2010) Analysis of next-generation genomic data in cancer: accomplishments and challenges. Hum Mol Genet 19: R188-96.
- Ding, L. et al. (2010) Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 464: 999-1005.
- Edwards JR, O'Donnell AH, Rollins RA, Peckham HE, Lee C, Milekic MH, Chanrion B, Fu Y, Su T, Hibshoosh H, Gingrich JA, Haghighi F, Nutter R, Bestor TH. (2010) Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns. Genome Res 20: 972-80.
- Schuster, S.C., et al (2010) Complete Khosian and Bantu genomes from southern Africa. Nature 463, 943-947.
- Sudmant, P.H., et al. (2010) Diversity of human copy number variation and multicopy genes. Science 330, 641-646.
- Mardis, E.R. et al. (2009). Recurring mutations found by sequencing an acute myeloid leukemia genome. N. Engl. J. Med. 2009; 361(11): 1058-66.
- Ley, T. et al. (2008). DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456: 66-72.
- Webber C, Ponting CP. (2004) Genes and homology. Curr Biol 14: R332-R333.
- Hardison RC. (2003) Comparative Genomics. PloS Biology 1: 156-160.
Finding Genes in Drosophila
- Timothy R. Dreszer, et al. (2012) The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res 40(D1): D918-D923.
- Irwin Jungreis, Michael F. Lin, Rebecca Spokony, Clara S. Chan, Nicolas Negre, Alec Victorsen, Kevin P. White, and Manolis Kellis. (2011) Evidence of abundant stop codon readthrough in Drosophila and other metazoa. Genome Res. 21: 2096-2113.
- Peter McQuilton, Susan E. St. Pierre, Jim Thurmond, and the FlyBase Consortium. (2011) FlyBase 101 - the basics of navigating FlyBase. Nucleic Acids Res 39:21.
- Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, Brenner JC, Laxman B, Asangani IA, Grasso CS, Kominsky HD, Cao X, Jing X, Wang X, Siddiqui J, Wei JT, Robinson D, Iyer HK, Palanisamy N, Maher CA, Chinnaiyan AM. (2011) Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol. 2011 Jul 31;29(8):742-9
- Weinstock, GM. (2011) The volatile microbiome. Genome Biol. 12: 114.
- Chen, K, and L Pachter (2010) Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Computational Biology 1: 106-12.
- Gertz, J. et al. (2010). Epistasis in a quantitative trait captured by a molecular model of transcription factor interactions. Theor. Popul. Biol. 77(1): 1-5.
- Human Microbiome Consortium (Nelson KE, et al). (2010) A catalog of reference genomes from the human microbiome. Science 328: 994-9.
- Leung, W, CD Shaffer, T Cordonnier, J Wong, MS Itano, EE Slawson-Tempel, E Kellmann, DM Desruisseau, C Cain, R Carrasquillo, TM Chusak, K Falkowska, KD Grim, R Guan, J Honeybourne, S Khan, L Lo, R McGaha, J Plunkett, JM Richner, R Richt, L Sabin, A Shah, A Sharma, S Singhal, F Song, C Swope, CB Wilen, J Buhler, ER Mardis, SCR Elgin (2010) Evolution of a Distinct Genomic Domain in Drosophila: Comparative Analysis of the Dot Chromosome in Drosophila melanogaster and Drosophila virilis. Genetics 185: 1519-1534.
- Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielson C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SSJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF. (2010) Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466: 253-257.
- Gerke J, Lorenz K and B. Cohen (2009). Genetic interactions between transcription factors cause natural variation in yeast. Science 323: 498-501.
- Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, Luo S, Khrebtukova I, Barrette T, Quist C, Yu J, Lonigro R, Schroth G, Kumar-Sinha C and Chinnaiyan A. (2009) Chimera transcript discovery using paired-end transcriptome sequencing. Proc Natl Acad Sci USA 106: 12353-8.
- Brent MR (2008). Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nat Rev Genet. 9: 62-73.
- Stark et al (2008) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450: 219-32.
- Birney E. (2007) Come fly with us. Nature 450: 5-6 (reprint).
- Drosophila 12 Genomes Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
- Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D (2007) Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci U S A 104:18613-18618.
- Ashburner M, Bergman CM. (2005) Drosophila melanogaster: a case study of a model genomic sequence and its consequences. Genome Res. 15:1661-1667.
- Kondrashov AS. (2005) Evolutionary biology: fruitfly genome is not junk. Nature 437:1106.
- Eddy, S. (2004) What is a hidden Markov model? Nature Biotech. 22: 1315-16.
- Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M. (2003). Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
- Dermitzakis ET, Reymond A, Scamuffa N, Ucla C, Kirkness E, Rossier C, Antonarakis SE. (2003) Evolutionary discrimination of mammalian Conserved Non-Genic sequences (CNGs), Science 302:1033-1035.
- W. James Kent, Charles W. Sugnet, Terrence S. Furey, Krishna M. Roskin, Tom H. Pringle, Alan M. Zahler1, and David Haussler. (2002) The Human Genome Browser at UCSC. Genome Res. 12: 996-1006.
Additional Suggested Readings
- Hoskins RA, Carlson JW, Kennedy C, Acevedo D, Evans-Holm M, Frise E, Wan KH, Park S, Mendez-Lago M, Rossi F, Villasante A, Dimitri P, Karpen GH, Celniker SE. (2007) Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science 316: 1625-8.
- Smith CD, Shu S, Mungall CJ, Karpen GH. (2007) The Release 5.1 annotation of Drosophila melanogaster heterochromatin. Science 316: 1586-91.
- Yang H-P, Hung T-L, You T-L, Yang T-H. (2006) Genome-wide comparative analysis of the highly abundant transposable element DINE-1 suggests a recent transpositional burst in Drosophila yakuba. Genetics, 173: 189-96.
- Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, Anxolabehere D. (2005) Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol. 1:166-75.
- Celniker SE, Rubin GM. (2003) The Drosophila melanogaster genome. Annu Rev Genomics Hum Genet. 4: 89-117.
- Bartolome C, Maside X, Charlesworth B. (2002) On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster. Mol Biol Evol. 19: 926-37.
- Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE. (2002) The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 3:RESEARCH0084. PMID: 12537573