Collins FS, Green ED, Guttmacher AE, Guyer MS: A vision for the future of genomics research. Nature. 2003, 422: 835-847. 10.1038/nature01626.
Article
CAS
PubMed
Google Scholar
Schuster SC: Next-generation sequencing transforms today’s biology. Nat Methods. 2008, 5: 16-18.
Article
CAS
PubMed
Google Scholar
Metzker ML: Applications of next-generation sequencing technologies - the next generation. Nat Rev Genet. 2010, 11: 31-46. 10.1038/nrg2626.
Article
CAS
PubMed
Google Scholar
von Bubnoff A: Next-generation sequencing: the race is on. Cell. 2008, 132: 721-723. 10.1016/j.cell.2008.02.028.
Article
CAS
PubMed
Google Scholar
Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M: SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics. 2010, 26: 730-736. 10.1093/bioinformatics/btq040.
Article
PubMed Central
CAS
PubMed
Google Scholar
Walter MJ, Graubert TA, Dipersio JF, Mardis ER, Wilson RK, Ley TJ: Next-generation sequencing of cancer genomes: back to the future. Pers Med. 2009, 6: 653-10.2217/pme.09.52.
Article
CAS
Google Scholar
Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O: Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet. 2009, 41: 1061-1067. 10.1038/ng.437.
Article
PubMed Central
CAS
PubMed
Google Scholar
Uchiyama T, Miyazaki K: Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr Opin Biotech. 2009, 20: 616-622. 10.1016/j.copbio.2009.09.010.
Article
CAS
PubMed
Google Scholar
Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L: Functional metagenomic profiling of nine biomes. Nature. 2008, 452: 629-632. 10.1038/nature06810.
Article
CAS
PubMed
Google Scholar
Chi KR: The sequencer: rapid technological developments have spurred big changes in the requisite genome-sequencing jobs. Nature. 2010, 456: 256-257.
Article
Google Scholar
Haspel RL, Arnaout R, Briere L, Kantarci S, Marchand K, Tonellato P, Connolly J, Boguski MS, Saffitz JE: A call to action: training pathology residents in genomics and personalized medicine. Am J Clin Pathol. 2010, 133: 832-834. 10.1309/AJCPN6Q1QKCLYKXM.
Article
PubMed
Google Scholar
Council NR: The new science of metagenomics: revealing the secrets of our microbial planet. 2007, DC: National Academies Press
Google Scholar
Fambrough D: Review of Bio2010: transforming undergraduate education for foture research biologists, by the national research council. Cell Biol Educ. 2003, 2: 92-93. 10.1187/cbe.03-03-0015.
Article
PubMed Central
PubMed
Google Scholar
Lopatto D, Alvarez C, Barnard D, Chandrasekaran C, Chung HM, Du C, Eckdahl T, Goodman AL, Hauser C, Jones CJ: Undergraduate research. Genomics education partnership. Science. 2008, 322: 684-685. 10.1126/science.1165351.
Article
PubMed Central
CAS
PubMed
Google Scholar
Temple L, Cresawn SG, Monroe JD: Genomics and bioinformatics in undergraduate curricula: contexts for hybrid laboratory/lecture courses for entering and advanced science students. Biochem Molecul Biol Educ. 2010, 38: 23-28. 10.1002/bmb.20359.
Article
CAS
Google Scholar
Lau JM, Robinson DL: Effectiveness of a cloning and sequencing exercise on student learning with subsequent publication in the national center for biotechnology information, GenBank. CBE Life Sci Educ. 2009, 8: 326-337. 10.1187/cbe.09-05-0036.
Article
PubMed Central
PubMed
Google Scholar
Kerfeld CA, Simons RW: The undergraduate genomics research initiative. PLoS Biol. 2007, 5: e141-10.1371/journal.pbio.0050141.
Article
PubMed Central
PubMed
Google Scholar
Shaffer CD, Alvarez C, Bailey C, Barnard D, Bhalla S, Chandrasekaran C, Chandrasekaran V, Chung HM, Dorer DR, Du C: The genomics education partnership: successful integration of research into laboratory classes at a diverse group of undergraduate institutions. CBE Life Sci Educ. 2010, 9: 55-69. 10.1187/09-11-0087.
Article
PubMed Central
PubMed
Google Scholar
Hanauer DI, Jacobs-Sera D, Pedulla ML, Cresawn SG, Hendrix RW, Hatfull GF: Teaching scientific inquiry. Science. 2006, 314: 1880-1881. 10.1126/science.1136796.
Article
CAS
PubMed
Google Scholar
Dymond JS, Scheifele LZ, Richardson S, Lee P, Chandrasegaran S, Bader JS, Boeke JD: Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary build-a-genome course. Genet. 2009, 181: 13-21.
Article
CAS
Google Scholar
Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, Ford ME, Gonda RM, Houtz JM, Hryckowian AJ, Kelchner VA: Exploring the mycobacteriophage metaproteome: Phage genomics as an educational platform. PLoS Genet. 2006, 2: 835-847.
Article
CAS
Google Scholar
Denofrio LA, Russell B, Lopatto D, Lu Y: Linking student interests to science curricula. Science. 2007, 318: 1872-1873. 10.1126/science.1150788.
Article
CAS
PubMed
Google Scholar
Howard DR, Miskowski JA, Grunwald SK, Abler ML: Assessment of a bioinformatics across life science curricula initiative. Biochem Molecul Biol Educ. 2007, 35: 16-23. 10.1002/bmb.13.
Article
CAS
Google Scholar
Rice DW, Lawrence SL: Marine mammals of the world: systematics and distribution. Special publications of the society for marine mammals. The Society for Marine Mammalogy. 1998, Lawrence KS, USA: Alan Press, 1-891276-03-04, vol. 4
Google Scholar
Department of Commerce, NOAA, National Marine Fisheries Service: Impacts of california sea lions and pacific harbor seals on salmonids and west coast ecosystems. Report by dept. Commerce. 1999, U.S: Department of Commerce
Google Scholar
Wolf JB, Tautz D, Trillmich F: Galapagos and Californian sea lions are separate species: genetic analysis of the genus zalophus and its implications for conservation management. Frontiers Zool. 2007, 4: 20-10.1186/1742-9994-4-20.
Article
Google Scholar
Kirkness EF, Bafna V, Halpern AL, Levy S, Remington K, Rusch DB, Delcher AL, Pop M, Wang W, Fraser CM: The dog genome: survey sequencing and comparative analysis. Science. 2003, 301: 1898-1903. 10.1126/science.1086432.
Article
PubMed
Google Scholar
Li RQ, Fan W, Tian G, Zhu HM, He L, Cai J, Huang QF, Cai QL, Li B, Bai YQ: The sequence and de novo assembly of the giant panda genome. Nature. 2010, 463: 311-317. 10.1038/nature08696.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W: Initial sequencing and analysis of the human genome. Nature. 2001, 409: 860-921. 10.1038/35057062.
Article
CAS
PubMed
Google Scholar
Batzer MA, Deininger PL: Alu repeats and human genomic diversity. Nat Rev Genet. 2002, 3: 370-379. 10.1038/nrg798.
Article
CAS
PubMed
Google Scholar
Roy-Engel AM, Carroll ML, El-Sawy M, Salem AH, Garber RK, Nguyen SV, Deininger PL, Batzer MA: Non-traditional Alu evolution and primate genomic diversity. J Mol Biol. 2002, 316: 1033-1040. 10.1006/jmbi.2001.5380.
Article
CAS
PubMed
Google Scholar
Dinsdale EA, Edwards RA, Bailey BA, Tuba I, Akhter S, McNair K, Schmieder R, Apkarian N, Creek M, Guan E: Multivariate analysis of functional metagenomes. Frontiers Genet Stat Analysis. 2013, 4: 41-10.3389/fgene.2013.00041.
CAS
Google Scholar
Dinsdale EA, Pantos O, Smriga S, Edwards RA, Angly F, Wegley L, Hatay M, Hall D, Brown E, Haynes M: Microbial ecology of four coral atolls in the Northern Line Islands. Plos One. 2008, 3: e1584-10.1371/journal.pone.0001584.
Article
PubMed Central
PubMed
Google Scholar
Hanna LF, Matthews TD, Dinsdale EA, Hasty D, Edwards RA: Characterization of the ELPhiS Prophage from Salmonella enterica serovar Enteritidis Strain LK5. Appl Environ Microb. 2012, 78: 1785-1793. 10.1128/AEM.07241-11.
Article
CAS
Google Scholar
Bruce T, Meirelles P, Garcia G, Paranhos R, Rezende C, de Moura R, Francini Filho R, Tereza Vasconcelos A, Amado Filho G, Hatay M: Abrolhos reef Bank health evaluated by means of water quality, microbial diversity, benthic cover, and fish biomass data. PLoS One. 2012, 7: e36687-10.1371/journal.pone.0036687.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hagen M, McNair K, Carolina A, Adegbemle F, Agarwal N, Aguinaldo K, Andrews J, Arciniega J, Arnoult M, Avila V: Complete genome sequences of Vibrio alginolyticus spp. 2013, Stand Genomic Sci: Miyuksis, in review
Google Scholar
Carolino A, McNair K, Adegbemle F, Agarwal N, Aguinaldo K, Andrews J, Arciniega J, Arnoult M, Avila V, Badeanlou L: Draft genome sequence of Vibrio sp strain 624788. Stand Genomic Sci. 2013, in review
Google Scholar
Jurkowski A, Reid AH, Labov JB: Metagenomics: a call for bringing a new science into the classroom (while it’s still new). CBE Life Sci Educ. 2007, 6: 260-265. 10.1187/cbe.07-09-0075.
Article
PubMed Central
PubMed
Google Scholar
Tibell LA, Rundgren CJ: Educational challenges of molecular life science: characteristics and implications for education and research. CBE Life Sci Educ. 2010, 9: 25-33. 10.1187/cbe.08-09-0055.
Article
PubMed Central
PubMed
Google Scholar
Thompson JD, Higgins DG, Gibson TJ: Clustal-W - Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680. 10.1093/nar/22.22.4673.
Article
PubMed Central
CAS
PubMed
Google Scholar
Felsenstein J: PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics. 1989, 5: 164-166.
Google Scholar
Darling AC, Mau B, Blattner FR, Perna NT: Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004, 14: 1394-1403. 10.1101/gr.2289704.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tempel S: Using and understanding RepeatMasker. Methods Mol Biol. 2012, 859: 29-51. 10.1007/978-1-61779-603-6_2.
Article
CAS
PubMed
Google Scholar
Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD: SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models. Plos One. 2012, 7 (10): 10.1371/journal.pone.0048053.
Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A: The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008, 9: 386-10.1186/1471-2105-9-386.
Article
PubMed Central
CAS
PubMed
Google Scholar
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M: The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008, 9: 75-10.1186/1471-2164-9-75.
Article
PubMed Central
PubMed
Google Scholar