Genome sequence analysis - bip.weizmann.ac.il fileGenome Analyzer Selected Publications Genome sequence analysis McCutcheon,J.P.,Moran,N.A.(2007)Parallelgenomicevolutionandmetabolicinterdependenceinanancient

Genome AnalyzerSelected Publications

Genome sequence analysis


Stark, A., Lin, M., Kheradpour, P., Pedersen, J. S., Parts, L., Carlson, J. W., Crosby, M. A., Rasmussen, M. D.,

Roy, S., Deoras, A. N., Ruby, J. G., Brennecke, J., Harvard FlyBase curators, Berkeley Drosophila Genome

Project, Hodges, E., Hinrichs, A. S., Caspi, A., Paten, B., Park, S-W., Han, M. V., Maeder, M. L., Polansky, B. J.,

Robson, B. E., Aerts, S., van Helden, J., Hassan, B., Gilbert, D. G., Eastman, D. A., Rice, M., Weir, M., Hahn, M.

W., Park, Y.,Dewey, C. N., Pachter, L., Kent, W. J., Haussler, D., Lai, E. C., Bartel, D. P., Hannon, G. J.,

Kaufman, T. C., Eisen, M. B., Clark, A. G., Smith, D., Celniker, S. E., Gelbart, W. M., Kellis, M. (2007) Discovery of

functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450, 219-232.

Blow, M. J., Zhang, T., Woyke, T., Spelle, C. F., Krivoshapkin, A., Yang, D., Derevianko, A., Rubin, E. (2008)

Identification of the source of ancient remains through genomic sequencing. Genome Res. 18(8), 1347 - 1353.

Suchland RJ, Jeffrey BM, Xia M, Bhatia A, Chu HG, Rockey DD, Stamm WE (2008) Identification of concomitant

infection with Chlamydia trachomatis IncA-negative mutant and wild-type strains by genomic, transcriptional, and

biological characterizations. Infect Immun. 76(12), 5438-5446.

Amacher SL (2008) Emerging gene knockout technology in zebrafish: zinc-finger nucleases. Brief Funct Genomic

Proteomic. 7(6), 460-464.

Bennett, S. (2004) Solexa Ltd. Pharmacogenomics. 5, 433-438.

Blow, N. (2007) The Personal side of Genomics. Nature. 449, 627-630.

Hall, N. (2007) Advanced sequencing technologies and their wider impact in microbiology. J Exptl Biol. 209, 1518

-1525.

Hutchinson III, CA (2007) DNA sequencing: bench to bedside and beyond. Nucl Acids Res. 35(18), 6227-6237.

Mardis, E. R. (2006) Anticipating the 1,000 dollar genome. Genome Biol. 7, 112.

Pennisi, E. (2007) DNA SEQUENCING: A New Window on How Genomes Work. Science. 316(5828), 1120-1121.

Petretto, E., Liu, E. T., Aitman, T. J. (2007) A gene harvest revealing the archeology and complexity of human

disease. Nat Genetics. 39, 1299-1301.

Service, R. F. (2006) The Race for the $1000 Genome. Science. 311(5767), 1544-1546.

Shendure, J., Mitra, R. D., Varma, C., Church, G. M. (2004) Advanced Sequencing technologies: methods and

goals. Nat Genetics. 5, 335-344.

Wakefield M. J. (2006) Genomics--from Neanderthals to high-throughput sequencing. Genome Biol. 7(8), 326.

Ashburner, M. (2007) Drosophila Genomes by the Baker’s Dozen. Genetics. 177, 1263-1268.

Birney, A. (2007) Come fly with us. Nature. 450, 184-185.

Carter, D. M., Liti, G., Moses, A. M., Parts, L., James, S. A., Davey, R. P., Roberts, I. N., Blomberg, A., Warringer,

J., Burt, A., Koufopanou, V., Tsai, I. J., Bergman, C. M., Bensasson, D., O’Kelly, M. J. T., van Oudenaarden, A.,

Barton, D. B. H., Bailes, E., Jones, M., Quail, M. A., Goodhead, I., Sims, S., Smith, F., Richard Durbin, R., Loui, E.

J. (2008) Population genomics of domestic and wild yeasts. Nat Precedings. Epub, hdl:10101/npre.2008.1988.1.

Margulies, E. H., Birney, E. (2008) Approaches to comparative sequence analysis: towards a functional view of

vertebrate genomes. Nat Genetics. 9, 303-313.

Ossowski, S., Schneeberger, K., Clark, R. M., Lanz, C., Warthmann, N., Weigel, D. (2008) Sequencing of natural

strains of Arabidopsis thaliana with short reads. Genome Res. 18(12), 2024-2033.

Hudson, M. E. (2008) Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol Ecol

Resources. 8(1), 3-17.

GA Publications www.illumina.com 12/4/2009



McCutcheon, J. P., Moran, N. A. (2007) Parallel genomic evolution and metabolic interdependence in an ancient

symbiosis. PNAS. 104(49), 19392-19397.

Millar, C. D., Huynen, L., Subramanian, S., Mohandesan, E. Lambert, D. M. (2008) New developments in ancient

genomics. Trends Eco Evol. 23(7), 386-393.

Rancati G, Pavelka N, Fleharty B, Noll A, Trimble R, Walton K, Perera A, Staehling-Hampton K, Seidel CW, Li R

(2008) Aneuploidy underlies rapid adaptive evolution of yeast cells deprived of a conserved cytokinesis motor.

Cell. 135(5), 879-893.

Sela DA, Chapman J, Adeuya A, Kim JH, Chen F, Whitehead TR, Lapidus A, Rokhsar DS, Lebrilla CB, German

JB, Price NP, Richardson PM, Mills DA (2008) The genome sequence of Bifidobacterium longum subsp. infantis

reveals adaptations for milk utilization within the infant microbiome. PNAS. Epub, doi: 10.1073/pnas.0809584105.

Blow, N. (2008) Exploring unseen communities. Nature. 453, 687-690.

Hugenholtz P, Tyson GW (2008) Microbiology: Metagenomics. Nature. 455(7212), 481-483.

Boonham, N., Glover, R., Tomlinson, J., Mumford, R. (2008) Exploiting generic platform technologies for the

detection and identification of plant pathogens. Eur J Plant Pathol. 121, 355-363.

Fidock DA, Eastman RT, Ward SA, Meshnick SR (2008) Recent highlights in antimalarial drug resistance and

chemotherapy research. Trends Parasitol. 24(12), 537-544.

Flintoft L (2008) Microbial genomics: Sequencing gets a handle on pathogen variation. Nat Rev Genetics. 9, .

Galperin, M. Y. (2008) Social bacteria and asocial eukaryotes. Environ Microbiol. 10(2), 281-288.

Holt KE, Thomson NR, Wain J, Langridge GC, Hasan R, Bhutta ZA, Quail MA, Norbertczak H, Walker D,

Simmonds M, White B, Bason N, Mungall K, Dougan G, Parkhill J (2009) Pseudogene accumulation in the

evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi. BMC Genomics. 10(1), 36.

Holt, K. E., Parkhill, J., Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J,

Dolecek C, Achtman M, Dougan G. (2008) High-throughput sequencing provides insights into genome variation

and evolution in Salmonella Typhi. Nat Genetics. 40(8), 987-93.

Kistler, A. L., Gancz, A., Clubb, S., Skewes-Cox, P., Fischer, K., Sorber, K., Chiu, C. Y., Lublin, A., Mechani, S.,

Farnoushi, Y., Greninger, A., Wen, C. C., Karlene, S. B., Ganem, D., DeRisi, J. L. (2008) Recovery of divergent

avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent.

Virol J. 5, 88.

Koenig R (2007) Tuberculosis. Few mutations divide some drug-resistant TB strains. Science. 318(5852), 901

-902.

Lamour KH, Win J, Kamoun S (2008) Oomycete genomics: new insights and future directions. FEMS Microbiol

Lett. 274(1), 1-8.

Loman, N. J., Pallen, M. J. (2008) XDR-TB genome sequencing: a glimpse of the microbiology of the future.

Future Microbiol. 3(2), 111-113.

Medini D, Serruto D, Parkhill J, Relman DA, Donati C, Moxon R, Falkow S, Rappuoli R (2008) Microbiology in the

post-genomic era. Nat Rev Microbiol. 6(6), 419-430.

Moran NA, McLaughlin HJ, Sorek R (2009) The Dynamics and Time Scale of Ongoing Genomic Erosion in

Symbiotic Bacteria. Science. 323(5912), 379-382.

Mwangi, M. M., Wu, S. W., Zhou, Y., Sieradzki, K., de Lencastre, H., Richardson, P., Bruce, D., Rubin, E., Myers,

E., Siggia, E. D., Tomasz, A. (2007) Tracking the in vivo evolution of multidrug resistance in Staphylococcus

aureus by whole-genome sequencing. PNAS. 104(22), 9451-9456.




Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, Warren RM, Hung DT, Birren BW, Lander ES, Jaffe DB

(2008) Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nat Methods.

Epub, DOI:10.1038/NMETH.1286.

Snyder LA, Loman N, Pallen MJ, Penn CW (2008) Next-Generation Sequencing-the Promise and Perils of

Charting the Great Microbial Unknown. Microb Ecol. Epub, 10.1007/s00248-008-9465-9.

Srivatsan, A., Han, Y., Peng, J., Tehranchi, A. K., Gibbs, R., Wang, J. D., Chen, R. (2008) High-precision, whole-

genome sequencing of laboratory strains facilitates genetic studies. PLoS Genetics. 4(8), e1000139.

Flintoft L (2008) Human genomics: Towards an individual view. Nat Rev Genetics. 9, 893.

Fox JL (2008) What price personal genome exploration?. Nat Biotech. 26(10), 1105-1108.

Pennisi E (2008) Personal genomics. Number of sequenced human genomes doubles.. Science. 322(5903), 838.

Bau S, Schracke N, Kränzle M, Wu H, Stähler PF, Hoheisel JD, Beier M, Summerer D (2008) Targeted next-

generation sequencing by specific capture of multiple genomic loci using low-volume microfluidic DNA arrays. Anal

Bioanal Chem. 393(1), 171-175.

Hardiman, G. (2008) Ultra-high-throughput sequencing, microarray-based genomic selection and

pharmacogenomics. Future Medicine. 9(1), 5-9.

Hodges, E., Xuan, Z., Balija, V., Kramer, M., Molla, M. N., Smith, S. W., Middle, C. M., Rodesch, M. J., Albert, T.

J., Hannon, G. J., McCombie, W. R. (2007) Genome-wide in situ exon capture for selective resequencing. Nat

Genetics. 39, 1522-1527.

Olson, M. (2007) Enrichment of super-sized resequencing targets from the human genome. Nat Methods. 4, 891

-892.

Porreca, G. J., Zhang, K., Li, J. B., Xie, B., Austin, D., Vassallo, S. L., Leproust, E. M., Peck, B. J., Emig, C. J.,

Dahl, F., Gao, Y., Church, G. M., Shendure, J. (2007) Multiplex amplification of large sets of human exons. Nat

Methods. 4, 931-936.

Rodriguez JA, Guiteau JJ, Nazareth L, Reid JG, Goss JA, Gibbs RA, Gingras MC (2008) Sequencing the Full-

Length of the Phosphatase and Tensin Homolog (PTEN) Gene in Hepatocellular Carcinoma (HCC) Using the 454

GS20 and Illumina GA DNA Sequencing Platforms.. World J Surg. Epub, 10.1007/s00268-008-9852-x.

Topol, E. J., Frazer, K. A. (2007) The resequencing imperative. Nat Genetics. 39, 439-440.

Zhu, C., Gore, M.,Buckler, E. S., Yu, J. (2008) Status and Prospects of Association Mapping in Plants. Plant

Genome. 1(1), 5-20.

Aury J-M, Cruaud C, Barbe V, Rogier O, Mangenot S, Samson G, Poulain P, Anthouard V, Scarpelli C,

Artiguenave F, Wincker P (2008) High quality draft sequences for prokaryotic genomes using a mix of new

sequencing technologies. BMC Genomics. 9, 603.

Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008)

Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One. 3(10), e3376.

Baker, S., Holt, K., Whitehead, S., Goodhead, I., Perkins, T., Stocker, B., Hardy, J., Dougan, G. (2007) A linear

plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi. Molecular

Microbiology. 66(5), 1207-1218.

Bansal, A. T., Barnes, M. R. (2008) Genomics in drug discovery: the best things come to those who wait. Curr

Opin Drug Discov Devel. 11(3), 303-311.

Beals JK () Genomes of Asian and African Individuals Sequenced Using Less Costly Approach. Medscape. , .




Beck J, Urnovitz HB, Riggert J, Clerici M, Schütz E (2009) Profile of the Circulating DNA in Apparently Healthy

Individuals. Clin Chem. Epub, 10.1373/clinchem.2008.113597.

Becker, N. S., Rodriguez, J. A., Gingras, M-C., Reid, J. G., Brunicardi, F. C., Goss, J. A., Gibbs, R. A. (2008)

QS445. Phosphatase and Tensin Homolog (PTEN) Mutation Detection in Hepatocellular Carcinoma Using The

454 GS and Solexa DNA Sequencing Platforms. J Surgical Res. 144(2), 444-445.

Bennett, S. T., Barnes, C., Cox, A., Davies, L., Brown, C. (2005) Toward the 1,000 dollars human genome.

Pharmacogenomics. 6, 373-382.

Bentley DR, Balasubramanian S, Swerdlow HP et al (2008) Accurate whole human genome sequencing using

reversible terminator chemistry. Nature. 456(7218), 53-59.

Bentley, D. R. (2006) Whole-genome re-sequencing. Curr Opin Genet Dev. 16, 545-552.

Campbell, P. J., Stephens, P. J., Pleasance, E. D., O’Meara, S., Li, H., Santarius, T., Stebbings, L. A., Leroy, C.,

Edkins, S., Hardy, C., Teague, J. W., Menzies, A., Goodhead, I., Turner, D. J., Clee, C. M., Quail, M. A., Cox, A.,

Brown, C., Durbin, R., Hurles, M. E., Edwards, P. A. W., Bignell, G. R., Stratton, M. R., Futreal, P. A. (2008)

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end

sequencing. Nat Genetics. 40(6), 722-729.

Chen, W., Kalscheu, V., Tzschach, A., Menzel, C., Ullmann, R., Schulz, M., Erdogan, F., Li, N., Kijas, Z.,

Arkesteijn, G., Pajares, I. L., Goetz-Sothmann, M., Heinrich, U., Rost, I., Dufke, A., Grasshoff, U., Glaeser, B. G.,

Vingron, M., Ropers, H. H. (2008) Mapping translocation breakpoints by next-generation sequencing. Genome

Res. 18(7), 1143-1149.

Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES

(2008) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods.

Epub, .

Chiu RWK, Chan KCA, Gao Y, Lau VYM, Zheng W, Leung TY, Foo CHFF, Xie B, Tsui NBY, Lun FMF, Zee BCY,

Lau TK, Cantor CR, Lo YMD (2008) Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively

parallel genomic sequencing of DNA in maternal plasma. PNAS. 105(51), 20458–20463.

Craig, D. W., Pearson, J. V., Szelinger, S., Sekar. A., Redman, M., Corneveaux, J. J., Pawlowski, T. L., Laub, T.,

Nunn, G., Stephan, D. A., Homer, N., Huentelman, M. J. (2008) Identification of genetic variants using bar-coded

multiplexed sequencing. Nat Methods. 5(10), 887-893.

Cronn, R., Liston, A., Parks, M., Gernandt, D. S., Shen, R., Mockler, T. (2008) Multiplex sequencing of plant

chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucl Acids Res. 36(19), e122.

Darby AC, Hall N (2008) Fast forward genetics. Nat Biotech. 26(11), 1248-1249.

Enserink M (2008) Genomics. Read all about it--the first female genome! Or is it?. Science. 320(5881), 1274.

Estivill, X., Armengol, L. (2007) Copy Number Variants and Common Disorders: Filling the Gaps and Exploring

Complexity in Genome-Wide Association Studies. PLoS Genetics. 3(10), 1787-1799.

Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR (2008) Noninvasive diagnosis of fetal aneuploidy by

shotgun sequencing DNA from maternal blood. PNAS. 105(42), 16266-16271.

Fay DS (2008) Classical genetics goes high-tech. Nat Methods. 5, 863-864.

Ganal MW, Altmann T, Röder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol. Epub,

doi:10.1016/j.pbi.2008.12.009.

Goodier JL, Kazazian HH Jr (2008) Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell.

135(1), 23-35.




Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME (2009) Genomic selection in dairy cattle: Progress and

challenges. J Dairy Sci. 92, 433-443.

Hayton K, Su XZ (2008) Drug resistance and genetic mapping in Plasmodium falciparum. Curr Genetics. 54(5),

223-239.

Hillier, L. W., Marth, G. T., Quinlan, A. R., Dooling, D., Fewell, G., Barnett, D., Fox, P., Glasscock, J. I.,

Hickenbotham, M., Huang, W., Magrini, V. J., Richt, R. J., Sander, S. N., Stewart, D. A., Stromberg, M., Tsung, E.

F., Wylie, T., Schedl, T., Wilson, R. K., Mardis, E. R. (2008) Whole-genome sequencing and variant discovery in

C. elegans. Nat Methods. 5, 183-188.

Jao LE, Maddison L, Chen W, Burgess SM (2008) Using retroviruses as a mutagenesis tool to explore the

zebrafish genome. Brief Funct Genomic Proteomic. Epub, doi:10.1093/bfgp/eln038 .

Käller M, Lundeberg J, Ahmadian A (2008) Arrayed identification of DNA signatures. Expert Rev Mol Diagn. 7(1),

65-76.

Lang L (2008) Three Sequencing Companies Join the 1000 Genomes Project. Gastroenterology. 135(2), 336-337.

Levy S, Strausberg RL (2008) Human genetics: Individual genomes diversify. Nature. 456(7218), 49-51.

Ley TJ, Mardis ER, Ding L et al (2008) DNA sequencing of a cytogenetically normal acute myeloid leukaemia

genome. Nature. 456(7218), 66-72.

Li B, Leal SM (2008) Methods for detecting associations with rare variants for common diseases: application to

analysis of sequence data. Am J Hum Genet. 83(3), 311-321.

Lin, J., Li, M. (2008) Molecular profiling in the age of cancer genomics. Expert Rev Mol Diagn. 8(3), 263-276.

Maher B (2008) Personal genomes: The case of the missing heritability. Nature. 456(7218), 18-21.

Marguerat S, Wilhelm BT, Bähler J (2008) Next-generation sequencing: applications beyond genomes. Biochem

Soc Trans. 36(Pt 5), 1091-1096.

Messing J (2009) Synergy of Two Reference Genomes for the Grass Family. Plant Physiol. 149, 117-124.

Moens CB, Donn TM, Wolf-Saxon ER, Ma TP (2008) Reverse genetics in zebrafish by TILLING. Brief Funct

Genomic Proteomic. Epub, .

Moerman DG, Barstead RJ (2008) Towards a mutation in every gene in Caenorhabditis elegans. Brief Funct

Genomic Proteomic. 7(3), 195-204.

Morozova, O., Marra, M. A. (2008) From cytogenetics to next-generation sequencing technologies: advances in

the detection of genome rearrangements in tumors1. Biochem Cell Biol. 86, 81-91.

Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ (2008) A large genome

center's improvements to the Illumina sequencing system. Nat Methods. 5, 1005-1010.

Ropers HH (2007) New Perspectives for the Elucidation of Genetic Disorders. Am J Hum Genet. 81(2), 199-207.

Sarin, S., Prabhu, S., O'Meara, M. M., Pe'er, I., Hobert, O. (2008) Caenorhabditis elegans mutant allele

identification by whole-genome sequencing. Nat Methods. 5(10), 865-867.

Schuster SC (2008) Next-generation sequencing transforms today’s biology. Nat Methods. 5(1), 16-18.

Sellner EM, Kim JW, McClure MC, Taylor KH, Schnabel RD, Taylor JF (2007) Board-invited review: Applications

of genomic information in livestock. J Anim Sci. 85(12), 3148-3158.

Shen Y, Sarin S, Liu Y, Hobert O, Pe'er I (2008) Comparing Platforms for C. elegans Mutant Identification Using

High-Throughput Whole-Genome Sequencing. PLoS One. 3(12), e4012.




Smith, D. R., Quinlan, A. R., Peckham, H. E., Makowsky, K., Tao, W., Woolf, B., Shen, L., Donahue, W. F.,

Tusneem, N., Stromberg, M. P., Stewart, D. A., Zhang, L., Ranade, S. S., Warner, J. B., Lee, C. C., Coleman, B.

E., Zhang, Z., McLaughlin, S. F., Malek, J. A., Sorenson, J. M., Blanchard, A. P., Chapman, J., Hillman, D., Chen,

F., Rokhsar, D. S., McKernan, K. J., Jeffries, T. W., Marth, G. T., Richardson, P. M. (2008) Rapid whole-genome

mutational profiling using next-generation sequencing technologies. Genome Res. Epub,

doi:10.1101/gr.077776.108.

Sturre MJG, Shirzadian-Khorramabad R, Schippers JHM, Chin-A-Woeng TFC, Hille J, Dijkwel PP (2008) Method

for the identification of single mutations in large genomic regions using massive parallel sequencing. Mol

Breeding. 23(1), 51-59.

Takahashi JS, Shimomura K, Kumar V (2008) Searching for genes underlying behavior: lessons from circadian

rhythms. Science. 322(5903), 909-912.

van Ommen GJ (2008) Popper revisited: GWAS here, last year. Eur J Hum Genet. 16(1), 1-2.

Van Tassell, C. P., Smith, T. P. L., Matukumalli, L. K., Taylor, J. F., Schnabel, R. D., Lawley, C. T., Haudenschild,

C. D., Moore, S. S., Warren, W. C., Sonstegard, T. S. (2008) SNP discovery and allele frequency estimation by

deep sequencing of reduced representation libraries. Nat Methods. 5, 247 - 252.

Voisey, J., Morris, C. P. (2008) SNP technologies for drug discovery: a current review. Curr Drug Discov Technol.

5(3), 230-235.

Wang J, Wang W, Li R et al (2008) The diploid genome sequence of an Asian individual. Nature. 456(7218), 60

-65.

Wendl, M.C., Wilson, R. K. (2008) Aspects of coverage in medical DNA sequencing. BMC Bioinformatics. 9, 239

(doi:10.1186/1471-2105-9-239).

Wicker T, Narechania A, Sabot F, Stein J, Vu GT, Graner A, Ware D, Stein N (2008) Low-pass shotgun

sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and

novel repeats. BMC Genomics. 9(1), 518.

Wicker W, Krattinger S, Lagudah ES, Komatsuda T, Pourkheirandish M, Matsumoto T, Cloutier S, Reiser L,

Kanamori H, Sato K, Perovic D, Stein N, Keller B (2008) Analysis of intraspecies diversity in wheat and barley

genomes identifies breakpoints of ancient haplotypes and provides insight in the structure of diploid and hexaploid

Triticeae gene pools. Plant Physiol. Epub, 10.1104/pp.108.129734.

Woods IG, Schier AF (2008) Targeted mutagenesis in zebrafish. Nat Biotech. 26(6), 650-651.



Epigenome analysis

Epigenome analysis

Rouhi, A., Mager, D. L., Humphries, R. K., Kuchenbauer, F. (2008) MiRNAs, epigenetics, and cancer. Mamm

Genome. epub, 10.1007/s00335-008-9133-x.

Bock, C., Lengauer, T. (2007) Computational epigenetics. Bioinformatics. 24(1), 1-10.

Appasani, K. (2007) Epigenomics and sequencing: an intertwined and emerging big science of the next decade.

Pharmacogenomics. 8(9), 1109-1113.

Baylin SB, Schuebel KE (2007) Genomic biology: the epigenomic era opens. Nature. 448(7153), 548-549.

Beck, S., Rakyan, V. K. (2008) The methylome: approaches for global DNA methylation profiling. Trends Genet.

24(5), 231-237.

Bonetta, L. (2008) Epigenomics: Detailed analysis. Nature. 454, 795-798.

Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, Hannon GJ (2008) An epigenetic role for

maternally inherited piRNAs in transposon silencing. Science. 322(5906), 1387-92.

Cokus, S. J., Feng, S., Zhang, X., Chen, Z., Merriman, B., Haudenschild, C. D., Pradhan, S., Nelson, S. F.,

Pellegrini, M., Jacobsen, S. E. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA

methylation patterning. Nature. 452(7184), 215-219.

Jeddeloh, J. A., Greally, J. M., Rando, O. J. (2008) Reduced-representation methylation mapping. Genome Biol. 9

(8), 231.

Lister, R., O'Malley, R. C., Tonti-Filippini, J., Gregory, B. D., Berry, C. C., Millar, A. H., Ecker, J. R. (2008) Highly

integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 133(3), 523-536.

Meissner A, Bernstein BE (2008) Sequencing the Epigenome. Epigenomics. 10.1007/978-1-4020-9187-2, 19-35.

Meissner, A., Mikkelsen, T. S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B. E.,

Nusbaum, C., Jaffe, D. B., Gnirke, A., Jaenisch, R., Lander, E. S. (2008) Genome-scale DNA methylation maps of

pluripotent and differentiated cells. Nature. 454(7205), 766-770.

Muhonen P, Holthofer H (2009) Epigenetic and microRNA-mediated regulation in diabetes. Nephrol Dial

Transplant. Epub, doi:10.1093/ndt/gfn728.

Pflumm, M. (2008) Tuning in to flower power. Nat Methods. 5, 463.

Pomraning KR, Smith KM, Freitag M (2008) Genome-wide high throughput analysis of DNA methylation in

eukaryotes. Methods. Epub, .

Rusk N (2008) Mapping the plant methylome. Nat Methods. 5(4), 284-285.

Stöger R (2008) Epigenetics and obesity. Pharmacogenomics. 9(12), 1851-1860.

Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev

Genetics. 9(6), 465-476.

Zhang, X. (2008) The Epigenetic Landscape of Plants. Science. 320(5875), 489-492.

Zhu, J. K. (2008) Epigenome sequencing comes of age. Cell. 133(3), 395-397.

Zilberman, D., Henikoff, S. (2007) Genome-wide analysis of DNA methylation patterns. Development. 134, 3959

-3965.

Goymer, P. (2007) Mapping the methylome without chips. Nat Genetics. 8, 489 - 489.



Epigenome analysis

Henderson, I. R., Jacobsen, S. E. (2008) Tandem repeats upstream of the Arabidopsis endogene SDC recruit

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Transcriptome analysis


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Protein-nucleic acid interactions


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