Bibliography

This bibliography is work in progress, and will be expanded as the quarter progresses. It is divided into two sections: one (class reading) are scientific papers which we will discuss in class, plus a representative book chapter or review as grounding for the empirical paper. These items will also be linked from the syllabus page.

The second section is background reading, that is, it is meant as a recommended papers and chapters which you can consult if you are interested in specific topics. The publications are likely to be very relevant for you if you want to write your proposal in the respective area.

Class Reading

Week 1: Introduction

Background reading:

Carlson R (2003) The pace and proliferation of biological techniques. Biosecurity and Bioterrorism: Biodefense Strategy, Practice and Science 1, 1-12

Week 2: Detecting diversity - direct sequencing

Papers discussed:

Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu PG, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380.

Sogin ML, Morrison HG, Huber JA, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings Of The National Academy Of Sciences Of The United States Of America 103, 12115.

Background reading:

Taubenberger JK, Reid AH, Lourens RM, Wang RX, Jin GZ, Fanning TG (2005) Characterization of the 1918 influenza virus polymerase genes. Nature 437, 889-893.

Chan EY (2005) Advances in sequencing technology. Mutation Research-Fundamental And Molecular Mechanisms Of Mutagenesis 573, 13-40.

Metzker ML (2005) Emerging technologies in DNA sequencing. Genome Research 15, 1767-1776.

Shendure J, Mitra RD, Varma C, Church GM (2004) Advanced sequencing technologies: Methods and goals. Nature Reviews Genetics 5, 335-344.

Kelley, et al. (2004) Molecular Analysis of Shower Curtain Biofilm Microbes. Appl. Environ. Microbiol. 70: 4187-4192.

Week 3: Whole Genome Sequencing

Paper discussed

Clark AG (2006) Genomics of the evolutionary process. Trends In Ecology & Evolution 21, 316-321.

Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D (2006) Genetic evidence for complex speciation of humans and chimpanzees. Nature 441, 1103.

Background reading

Mikkelsen TS, Hillier LW, Eichler EE, Zody MC, Jaffe DB, Yang SP, Enard W, Hellmann I, Lindblad-Toh K, Altheide TK, Archidiacono N, Bork P, Butler J, Chang JL, Cheng Z, Chinwalla AT, deJong P, Delehaunty KD, Fronick CC, Fulton LL, Gilad Y, Glusman G, Gnerre S, Graves TA, Hayakawa T, Hayden KE, Huang XQ, Ji HK, Kent WJ, King MC, Kulbokas EJ, Lee MK, Liu G, Lopez-Otin C, Makova KD, Man O, Mardis ER, Mauceli E, Miner TL, Nash WE, Nelson JO, Paabo S, Patterson NJ, Pohl CS, Pollard KS, Prufer K, Puente XS, Reich D, Rocchi M, Rosenbloom K, Ruvolo M, Richter DJ, Schaffner SF, Smit AFA, Smith SM, Suyama M, Taylor J, Torrents D, Tuzun E, Varki A, Velasco G, Ventura M, Wallis JW, Wendl MC, Wilson RK, Lander ES, Waterston RH (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69-87.

Perna NT, Plunkett G, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, Posfai G, Hackett J, Klink S, Boutin A, Shao Y, Miller L, Grotbeck EJ, Davis NW, Limk A, Dimalanta ET, Potamousis KD, Apodaca J, Anantharaman TS, Lin JY, Yen G, Schwartz DC, Welch RA, Blattner FR (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157: H7. Nature 409, 529-533.

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu DY, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74.

Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, Chisholm SW (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424, 1042-1047.

Week 4: Detecting diversity - indirect

Paper discussed:

Schlötterer C (2004) The evolution of molecular markers - just a matter of fashion? Nature Reviews Genetics 5, 63-69.

Buonaccorsi VP, Kimbrell CA, Lynn EA, Vetter RD (2006) Limited realized dispersal and introgressive hybridization influence genetic structure and conservation strategies for brown rockfish, Sebastes auriculatus. Conservation Genetics, in press.

Background reading:

deBruin A, Ibelings BW, van Donk E (2003) Molecular techniques in phytoplankton research: from allozyme electrophoresis to genomics. Hydrobiologia 491, 47-63.

Selkoe KA, Toonen RJ (2006) Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecology Letters 9, 615.

Week 5: Estimating relationships among species

Paper discussed:

Baldauf SL (2003) Phylogeny for the faint of heart: a tutorial. Trends In Genetics 19, 345.

Shaw KL (2002) Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: What mtDNA reveals and conceals about modes of speciation in Hawaiian crickets. Proceedings Of The National Academy Of Sciences Of The United States Of America 99, 16122-16127.

Week 6: Genome scans

Paper discussed

Luikart G, England PR, Tallmon D, Jordan S, Taberlet P (2003) The power and promise of population genomics: From genotyping to genome typing. Nature Reviews Genetics 4, 981-994.

Nair S, Williams JT, Brockman A, Paiphun L, Mayxay M, Newton PN, Guthmann JP, Smithuis FM, Hien TT, White NJ, Nosten F, Anderson TJC (2003) A selective sweep driven by pyrimethamine treatment in southeast Asian malaria parasites. Molecular Biology and Evolution 20, 1526-1536.

Background reading

Other reviews:

Black WC, Baer CF, Antolin MF, DuTeau NM (2001) Population genomics: Genome-wide sampling of insect populations. Annual Review of Entomology 46, 441-469.

Storz JF (2005) Using genome scans of DNA polymorphism to infer adaptive population divergence. Molecular Ecology 14, 671-688.

Emprical papers:

Bensch S, Akesson S, Irwin DE (2002) The use of AFLP to find an informative SNP: genetic differences across a migratory divide in willow warblers. Molecular Ecology 11, 2359-2366.

Nicod JC, Largiader CR (2003) SNPs by AFLP (SBA): a rapid SNP isolation strategy for non-model organisms. Nucleic Acids Research 31.

Canino MF, O'Reilly PT, Hauser L, Bentzen P (2005) Genetic differentiation in walleye pollock (Theragra chalcogramma) in response to selection at the pantophysin (PanI) locus. Canadian Journal of Fisheries and Aquatic Sciences 62, 2519-2529.

Week 7: Estimating abundance - qPCR

Paper discussed

Wong ML, Medrano JF (2005) Real-time PCR for mRNA quantitation. BioTechniques 39, 75-85.

Thompson JR, Pacocha S, Pharino C, Klepac-Ceraj V, Hunt DE, Benoit J, Sarma-Rupavtarm R, Distel DL, Polz MF (2005) Genotypic diversity within a natural coastal bacterioplankton population. Science 307, 1311-1313.

Background reading

Vadopalas B, Bouma JV, Jackels CR, Friedman CS (2006) Application of real-time PCR for simultaneous identification and quantification of larval abalone. Journal of Experimental Marine Biology and Ecology 334 (2): 219-228

Week 8: Selection / Proposal Reviews

Review on Selection

Nielsen R (2005) Molecular signatures of natural selection. Annual Review Of Genetics 39, 197.

Background reading (on ITS, for Eric)

Alvarez I, Wendel JF (2003) Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29, 417-434.

Week 9: Gene expression

Paper discussed

Rensink WA, Buell CR (2005) Microarray expression profiling resources for plant genomics. Trends In Plant Science 10, 603-609.

Gracey AY, Troll JV, Somero GN (2001) Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Proceedings Of The National Academy Of Sciences Of The United States Of America 98, 1993-1998.

Background reading

Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JG, Sabet H, Tran T, Yu X, Powell JI, Yang LM, Marti GE, Moore T, Hudson J, Lu LS, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403, 503-511.

Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo SJ, McCurdy S, Foy M, Ewan M, Roth R, George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J, Fearon K, Mao J, Corcoran K (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnology 18, 630-634.

David JP, Strode C, Vontas J, Nikou D, Vaughan A, Pignatelli PM, Louis C, Hemingway J, Ranson H (2005) The Anopheles gambiae detoxification chip: A highly specific microarray to study metabolic-based insecticide resistance in malaria vectors. Proceedings Of The National Academy Of Sciences Of The United States Of America 102, 4080-4084.

Halitschke R, Gase K, Hui DQ, Schmidt DD, Baldwin IT (2003) Molecular interactions between the specialist herbivore Manduca sexta (Lepidoptera, Sphingidae) and its natural host Nicotiana attenuata. VI. Microarray analysis reveals that most herbivore-specific transcriptional changes are mediated by fatty acid-amino acid conjugates. Plant Physiology 131, 1894-1902.

Lettieri T (2006) Recent applications of DNA microarray technology to toxicology and ecotoxicology. Environmental Health Perspectives 114, 4-9.

Meyers BC, Galbraith DW, Nelson T, Agrawal V (2004) Methods for transcriptional profiling in plants. Be fruitful and replicate. Plant Physiology 135, 637-652.

Oleksiak MF, Roach JL, Crawford DL (2005) Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus. Nature Genetics 37, 67-72.

Sarropoulou E, Kotoulas G, Power DM, Geisler R (2005) Gene expression profiling of gilthead sea bream during early development and detection of stress-related genes by the application of cDNA microarray technology. Physiological Genomics 23, 182-191.

Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, Pergamenschikov A, Lee JCE, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, Brown PO (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nature Genetics 24, 227-235.

Tittiger C (2004) Functional genomics and insect chemical ecology. Journal Of Chemical Ecology 30, 2335-2358.

Week 10: Integration

Paper discussed

Vasemagi A, Primmer CR (2005) Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies. Molecular Ecology 14, 3623-3642.

Background reading

 

General Textbooks

Gibson G, Muse SV (2002) A Primer to Genome Science. Sinauer Assoc., Sunderland, MA.
Excellent introduction to many of the emergent approaches we discussed, with a good description of principles and not too much technical detail.

Avise JC (2004) Molecular Markers, Natural History and Evolution. Chapman & Hall, London.
Excellent book on molecular markers in general. Not a lot about microsatellites, but the other markers are well covered. Good discussion on applications.

Hillis D.M., Moritz C., Mable B.K. (eds., 1996) Molecular Systematics. Sinauer Associates, Sunderland, Massachusetts
A collection of very useful chapters dealing with molecular markers. Now ten years old, but still very useful for more traditional techniques. If you want to buy a book for this class, it's probably this one.

Graur D., Li W.-H. (2000) Fundamentals of Molecular Evolution. Sinauer Associates, Sunderland, Massachusetts
Excellent textbook covering patterns and rates of mutation and phylogenetic reconstruction

Baker AJ (ed. 2000) Molecular Methods in Ecology. Blackwell Science, Malden MA.
Nice textbook also covering not too common methods such as MHC, minisatellites and DNA-DNA hybridization

Sambrook J, Russell DW (2001) Molecular Clonin: a laboratory manual. Cold Spring HArbor Laboratory Press, Cold Spring Harbor, New York.
The central 'cook book' for most molecular laboratories. Contains invaluable recipes, protocols and background info. See also http://www.molecularcloning.com.

Russel PJ (2002) iGenetics, Benjamin Cummings, San Francisco.
Excellent undergraduate textbook covering all the basics of genetics, including applications. Use this book to firm up your basic knowledge.