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250 entries

1.
Park JI, Semyonov J, Chang CL, Yi W, Warren W, Hsu SY.
Origin of INSL3-mediated testicular descent in therian mammals.
Genome Res. 2008 Jun;18(6):974-85. Epub 2008 May 7.
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2.
Whittington CM, Papenfuss AT, Bansal P, Torres AM, Wong ES, Deakin JE, Graves T, ...
Defensins and the convergent evolution of platypus and reptile venom genes.
Genome Res. 2008 Jun;18(6):986-94. Epub 2008 May 7.
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3.
Internal Medicine/Infectious Diseases Division, Washington University School of Medicine, Campus Mailbox 8051, 660 S. Euclid Avenue, St. Louis, MO 63110, USA.
Brugia malayi: whole genome amplification for genomic characterization of filarial parasites.
Exp Parasitol. 2008 Jun;119(2):256-63. Epub 2008 Feb 19.
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4.
Pasieka TJ, Lu B, Crosby SD, Wylie KM, Morrison LA, Alexander DE, Menachery VD, ...
Herpes simplex virus virion host shutoff attenuates establishment of the antiviral state.
J Virol. 2008 Jun;82(11):5527-35. Epub 2008 Mar 26.
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5.
Veyrunes F, Waters PD, Miethke P, Rens W, McMillan D, Alsop AE, Grützner F, ...
Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes.
Genome Res. 2008 Jun;18(6):965-73. Epub 2008 May 7.
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6.
Haddad GE, Saunders L, Carles M, Crosby SD, del Monte F, Macgillivray TE, Semigran MJ, ...
Fingerprint profile of alcohol-associated heart failure in human hearts.
Alcohol Clin Exp Res. 2008 May;32(5):814-21. Epub 2008 Mar 11.
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7.
Ordoñez GR, Hillier LW, Warren WC, Grützner F, López-Otín C, Puente XS.
Loss of genes implicated in gastric function during platypus evolution.
Genome Biol. 2008 May 15;9(5):R81. [Epub ahead of print]
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8.
Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, ...
Genome analysis of the platypus reveals unique signatures of evolution.
Nature. 2008 May 8;453(7192):175-83.
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9.
Xiang Z, Zhao Y, Mitaksov V, Fremont DH, Kasai Y, Molitoris A, Ries RE, ...
Identification of somatic JAK1 mutations in patients with acute myeloid leukemia.
Blood. 2008 May 1;111(9):4809-12. Epub 2007 Dec 26.
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10.
Tomasson MH, Xiang Z, Walgren R, Zhao Y, Kasai Y, Miner T, Ries RE, ...
Somatic mutations and germline sequence variants in the expressed tyrosine kinase genes of patients with de novo acute myeloid leukemia.
Blood. 2008 May 1;111(9):4797-808. Epub 2008 Feb 12.
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11.
Haddad GE, Saunders LJ, Crosby SD, Carles M, del Monte F, King K, Bristow MR, ...
Human cardiac-specific cDNA array for idiopathic dilated cardiomyopathy: sex-related differences.
Physiol Genomics. 2008 Apr 22;33(2):267-77. Epub 2008 Feb 26.
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12.
Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, Mardis ER, Sahinalp SC, ...
Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa.
Genome Res. 2008 Apr;18(4):571-84. Epub 2008 Mar 6.
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13.
Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI.
Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome.
Cell Host Microbe. 2008 Apr 17;3(4):213-23.
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14.
Van Tassell CP, Smith TP, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, ...
SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries.
Nat Methods. 2008 Mar;5(3):247-52. Epub 2008 Feb 24.
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15.
Abubucker S, Martin J, Yin Y, Fulton L, Yang SP, Hallsworth-Pepin K, Johnston JS, ...
The canine hookworm genome: analysis and classification of Ancylostoma caninum survey sequences.
Mol Biochem Parasitol. 2008 Feb;157(2):187-92. Epub 2007 Nov 9.
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16.
Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, ...
Whole-genome sequencing and variant discovery in C. elegans.
Nat Methods. 2008 Feb;5(2):183-8. Epub 2008 Jan 20.
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17.
Mardis ER.
The impact of next-generation sequencing technology on genetics.
Trends Genet. 2008 Feb 8 [Epub ahead of print]
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18.
Drosophila 12 Genomes Consortium; Project Leaders, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, ...
Evolution of genes and genomes on the Drosophila phylogeny.
Nature. 2007 Nov 8;450(7167):203-218.
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19.
Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R, Lin WM, ...
Characterizing the cancer genome in lung adenocarcinoma.
Nature. 2007 Nov 4; [Epub ahead of print]
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20.
Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, ...
Genome-wide detection and characterization of positive selection in human populations.
Nature. 2007 Oct 18;449(7164):913-8.
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21.
International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, ...
A second generation human haplotype map of over 3.1 million SNPs.
Nature. 2007 Oct 18;449(7164):851-61.
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22.
Allen JO, Fauron CM, Minx P, Roark L, Oddiraju S, Lin GN, Meyer L, ...
Comparisons among two fertile and three male-sterile mitochondrial genomes of maize.
Genetics. 2007 Oct;177(2):1173-92. Epub 2007 Jul 29.
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23.
Schmidt CJ, Romanov M, Ryder O, Magrini V, Hickenbotham M, Glasscock J, McGrath S, ...
Gallus GBrowse: a unified genomic database for the chicken.
Nucleic Acids Res. 2007 Oct 11; [Epub ahead of print]
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24.
Elling AA, Mitreva M, Recknor J, Gai X, Martin J, Maier TR, McDermott JP, ...
Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycine.
Genome Biol. 2007 Oct 5;8(10):R211 [Epub ahead of print]
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25.
Laha T, Loukas A, Wattanasatitarpa S, Somprakhon J, Kewgrai N, Sithithaworn P, Kaewkes S, ...
The bandit, a New DNA Transposon from a Hookworm-Possible Horizontal Genetic Transfer between Host and Parasite.
PLoS Negl Trop Dis. 2007 Sep 27;1(1):e35.
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26.
Wendl MC.
H-index: however ranked, citations need context.
Nature. 2007 Sep 27;449(7161):403.
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27.
Wendl MC, Smith S, Pohl CS, Dooling DJ, Chinwalla AT, Crouse K, Hepler T, ...
Design and implementation of a generalized laboratory data model.
BMC Bioinformatics. 2007 Sep 26;8(1):362 [Epub ahead of print]
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28.
Jeck WR, Reinhardt JA, Baltrus DA, Hickenbotham MT, Magrini V, Mardis ER, Dangl JL, ...
Extending assembly of short DNA sequences to handle error.
Bioinformatics. 2007 Sep 24; [Epub ahead of print]
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29.
Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, ...
Draft genome of the filarial nematode parasite Brugia malayi.
Science. 2007 Sep 21;317(5845):1756-60.
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30.
Daniel C. Link, Ghada Kunter, Yumi Kasai, Yu Zhao, Tracie Miner, Michael D. McLellan, Rhonda E. Ries, ...
Distinct patterns of mutations occurring in de novo AML versus AML arising in the setting of severe congenital neutropenia.
Blood. 2007 Sep 1;110(5):1648-55. Epub 2007 May 9.
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31.
Mitreva M, Zarlenga DS, McCarter JP, Jasmer DP.
Parasitic nematodes - from genomes to control.
Vet Parasitol. 2007 Aug 19;148(1):31-42. Epub 2007 Jun 7.
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32.
Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, ...
Human genome ultraconserved elements are ultraselected.
Science. 2007 Aug 17;317(5840):915.
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33.
Hamvas A, Wegner DJ, Carlson CS, Bergmann KR, Trusgnich MA, Fulton L, Kasai Y, ...
Comprehensive genetic variant discovery in the surfactant protein B gene.
Pediatr Res. 2007 Aug;62(2):170-5.
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34.
Mardis ER.
ChIP-seq: welcome to the new frontier.
Nat Methods. 2007 Aug;4(8):613-4.
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35.
Hillier LW, Miller RD, Baird SE, Chinwalla A, Fulton LA, Koboldt DC, Waterston RH.
Comparison of C. elegans and C. briggsae Genome Sequences Reveals Extensive Conservation of Chromosome Organization and Synteny.
PLoS Biol. 2007 Jul 3;5(7):e167 [Epub ahead of print]
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36.
Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B, Fulton R, Latreille P, ...
Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut.
Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10643-8. Epub 2007 Jun 11.
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37.
Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, ...
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
Genome Res. 2007 Jun;17(6):760-74.
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38.
ENCODE Project Consortium.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Nature. 2007 Jun 14;447(7146):799-816.
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39.
Elizur A, Orscheln RC, Ferkol TW, Atkinson JJ, Dunne WM, Buller RS, Armstrong JR, ...
Panton-Valentine Leukocidin-Positive Methicillin-Resistant Staphylococcus aureus Lung Infection in Patients With Cystic Fibrosis.
Chest. 2007 Jun;131(6):1718-25. Epub 2007 Mar 30.Click here to read
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40.
Jenifer L. Marks, Michael D. McLellan, Maureen F. Zakowski, Alex Lash, Yumi Kasai, Stephen Broderick, Inderpal S. Sarkaria, ...
Mutational Analysis of EGFR and Related Signaling Pathway Genes in Lung Adenocarcinomas Identifies a Novel Somatic Kinase Domain Mutation in FGFR4
PLoS ONE. 2007 May 9;2:e426.
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41.
Link DC, Kunter G, Kasai Y, Zhao Y, Miner T, McLellan MD, Ries RE, ...
Distinct patterns of mutations occurring in de novo AML versus AML arising in the setting of severe congenital neutropenia.
Blood. 2007 May 9; [Epub ahead of print]
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42.
Kistler AL, Webster DR, Rouskin S, Magrini V, Credle JJ, Schnurr DP, Boushey HA, ...
Genome-wide diversity and selective pressure in the human rhinovirus.
Virol J. 2007 May 3;4:40.
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43.
Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, ...
Evolutionary and biomedical insights from the rhesus macaque genome.
Science. 2007 Apr 13;316(5822):222-34.
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44.
Chen K, McLellan MD, Ding L, Wendl MC, Kasai Y, Wilson RK, Mardis ER.
PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data.
Genome Res. 2007 Apr 6;
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45.
Roberto R, Capozzi O, Wilson RK, Mardis ER, Lomiento M, Tuzun E, Cheng Z, ...
Molecular refinement of gibbon genome rearrangements.
Genome Res. 2007 Feb;17(2):249-57. Epub 2006 Dec 21.
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46.
Bieri T, Blasiar D, Ozersky P, Antoshechkin I, Bastiani C, Canaran P, Chan J, ...
WormBase: new content and better access.
Nucleic Acids Res. 2007 Jan;35(Database issue):D506-10. Epub 2006 Nov 11.
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47.
Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI.
An obesity-associated gut microbiome with increased capacity for energy harvest.
Nature. 2006 Dec 21;444(7122):1027-131.
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48.
Wendl MC.
A general coverage theory for shotgun DNA sequencing.
J Comput Biol. 2006 Jul-Aug;13(6):1177-96.
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49.
Mardis ER.
Anticipating the 1,000 dollar genome.
Genome Biol. 2006;7(7):112.
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50.
Field JJ, Mason PJ, An P, Kasai Y, McLellan M, Jaeger S, Barnes YJ, ...
Low frequency of telomerase RNA mutations among children with aplastic anemia or myelodysplastic syndrome.
J Pediatr Hematol Oncol. 2006 Jul;28(7):450-3.
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51.
Oh JD, Kling-Backhed H, Giannakis M, Xu J, Fulton RS, Fulton LA, Cordum HS, ...
The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression.
Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9999-10004. Epub 2006 Jun 20.Click here to read
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52.
Warren RL, Varabei D, Platt D, Huang X, Messina D, Yang SP, Kronstad JW, ...
Physical map-assisted whole-genome shotgun sequence assemblies.
Genome Res. 2006 Jun;16(6):768-75.
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53.
Wendl MC.
Occupancy Modeling of Coverage Distribution for Whole Genome Shotgun DNA Sequencing
Bulletin of Mathematical Biology, 68 (1), 179-196.
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54.
Giannakis M, Stappenbeck TS, Mills JC, Leip DG, Lovett M, Clifton SW, Ippolito JE, ...
Molecular properties of adult mouse gastric and intestinal epithelial progenitors in their niches.
J Biol Chem. 2006 Apr 21;281(16):11292-300. Epub 2006 Feb 7.
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55.
Chen SL, Hung CS, Xu J, Reigstad CS, Magrini V, Sabo A, Blasiar D, ...
Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach.
Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):5977-82. Epub 2006 Apr 3.
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56.
Pham D, Kris MG, Riely GJ, Sarkaria IS, McDonough T, Chuai S, Venkatraman ES, ...
Use of cigarette-smoking history to estimate the likelihood of mutations in epidermal growth factor receptor gene exons 19 and 21 in lung adenocarcinomas.
J Clin Oncol. 2006 Apr 10;24(11):1700-4. Epub 2006 Feb 27.
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57.
Yin Y, Martin J, McCarter JP, Clifton SW, Wilson RK, Mitreva M.
Identification and analysis of genes expressed in the adult filarial parasitic nematode Dirofilaria immitis.
Int J Parasitol. 2006 Jun;36(7):829-39. Epub 2006 Mar 31.
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58.
Pham D, Kris MG, Riely GJ, Sarkaria IS, McDonough T, Chuai S, Venkatraman ES, ...
Use of cigarette-smoking history to estimate the likelihood of mutations in epidermal growth factor receptor gene exons 19 and 21 in lung adenocarcinomas.
J Clin Oncol. 2006 Apr 10;24(11):1700-4. Epub 2006 Feb 27.
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59.
Cliften PF, Fulton RS, Wilson RK, Johnston M.
After the duplication: gene loss and adaptation in Saccharomyces genomes.
Genetics. 2006 Feb;172(2):863-72. Epub 2005 Dec 1.
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60.
Huang X, Yang SP, Chinwalla AT, Hillier LW, Minx P, Mardis ER, Wilson RK.
Application of a superword array in genome assembly.
Nucleic Acids Res. 2006 Jan 5;34(1):201-5. Print 2006.
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61.
Schwarz EM, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Canaran P, Chan J, ...
WormBase: better software, richer content.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D475-8.Click here to read
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62.
Flowers SK, Easter C, Holmes A, Cohen B, Bednarski AE, Mardis ER, Wilson RK, ...
Genome science: a video tour of the Washington University Genome Sequencing Center for high school and undergraduate students.
Cell Biol Educ. 2005 Winter;4(4):291-7.
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63.
Wendl MC, Barbazuk WB.
Extension of Lander-Waterman theory for sequencing filtered DNA libraries.
BMC Bioinformatics. 2005 Oct 10;6:245.
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64.
Cheng Z, Ventura M, She X, Khaitovich P, Graves T, Osoegawa K, Church D, ...
A genome-wide comparison of recent chimpanzee and human segmental duplications.
Nature. 2005 Sep 1;437(7055):88-93.
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65.
Wendl MC.
Bioweapons could kill more in one strike than guns.
Nature. 2005 Sep 8;437(7056):192.
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66.
The Chimpanzee Sequencing and Analysis Consortium
Initial sequence of the chimpanzee genome and comparison with the human genome
Nature. 2005 Sep 1;437(7055):69-87.
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67.
Hughes JF, Skaletsky H, Pyntikova T, Minx PJ, Graves T, Rozen S, Wilson RK, ...
Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee.
Nature. 2005 Sep 1;437(7055):100-3.
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68.
Li BW, Rush AC, Crosby SD, Warren WC, Williams SA, Mitreva M, Weil GJ.
Profiling of gender-regulated gene transcripts in the filarial nematode Brugia malayi by cDNA oligonucleotide array analysis.
Mol Biochem Parasitol. 2005 Sep;143(1):49-57.
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69.
Walter MJ, Park JS, Ries RE, Lau SK, McLellan M, Jaeger S, Wilson RK, ...
Reduced PU.1 expression causes myeloid progenitor expansion and increased leukemia penetrance in mice expressing PML-RARalpha.
Proc Natl Acad Sci U S A. 2005 Aug 30;102(35):12513-8. Epub 2005 Aug 19.
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70.
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, ...
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
Genome Res. 2005 Jul 15;
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71.
Horvath JE, Gulden CL, Vallente RU, Eichler MY, Ventura M, McPherson JD, Graves TA, ...
Punctuated duplication seeding events during the evolution of human chromosome 2p11.
Genome Res. 2005 Jul;15(7):914-27. Epub 2005 Jun 17.
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72.
Wendl MC.
The question of forbidden knowledge.
Science. 2005 Jun 10;308(5728):1549-50.
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73.
Wendl MC.
Probabilistic assessment of clone overlapsin DNA fingerprint mapping via a priori models.
J Comput Biol. 2005 Apr;12(3):283-97.
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74.
Mitreva M, McCarter JP, Arasu P, Hawdon J, Martin J, Dante M, Wylie T, ...
Investigating hookworm genomes by comparative analysis of two Ancylostoma species.
BMC Genomics. 2005 Apr 26;6(1):58.
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75.
Katari MS, Balija V, Wilson RK, Martienssen RA, McCombie WR.
Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana.
Genome Res. 2005 Apr;15(4):496-504.
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76.
Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, ...
Generation and annotation of the DNA sequences of human chromosomes 2 and 4.
Nature. 2005 Apr 7;434(7034):724-31.
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77.
Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, Platzer M, ...
The DNA sequence of the human X chromosome.
Nature. 2005 Mar 17;434(7031):325-37.
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78.
Chen N, Harris TW, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, ...
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics.
Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D383-9.
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79.
Ding L, Sabo A, Berkowicz N, Meyer RR, Shotland Y, Johnson MR, Pepin KH, ...
EAnnot: a genome annotation tool using experimental evidence.
Genome Res. 2004 Dec;14(12):2503-9.
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80.
International Chicken Genome Sequencing Consortium
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
Nature. 2004 Dec 9;432(7018):695-716.
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81.
Wallis JW, Aerts J, Groenen MA, Crooijmans RP, Layman D, Graves TA, Scheer DE, ...
A physical map of the chicken genome.
Nature. 2004 Dec 9;432(7018):679-80.
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82.
Wong GK, Liu B, Wang J, Zhang Y, Yang X, Zhang Z, Meng Q, ...
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.
Nature. 2004 Dec 9;432(7018):717-22.
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83.
Parkinson J, Mitreva M, Whitton C, Thomson M, Daub J, Martin J, Schmid R, ...
A transcriptomic analysis of the phylum Nematoda
Nat Genet. 2004 Dec;36(12):1259-67. Epub 2004 Dec.
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84.
C. Fauron, J. Allen, S. Clifton, K. Newton
2004 Plant mitochondrial genomes, pp. 155-171 in Molecular Biology and Biotechnology of Plant Organelles, edited by H. Daniell and C. Chase. Kluwer Academic Publishing.
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85.
McClelland M, Sanderson KE, Clifton SW, Latreille P, Porwollik S, Sabo A, Meyer R, ...
Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid
Nat Genet. 2004 Dec;36(12):1268-74. Epub 2004 Dec.
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86.
Sandra W. Clifton, Patrick Minx, Christiane M.-R. Fauron, Michael Gibson, James O. Allen, Hui Sun, Melissa Thompson, ...
Sequence and Comparative Analysis of the Maize NB Mitochondrial Genome
Plant Physiol. 2004 Nov;136(3):3486-503.
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87.
A list of authors and their affiliations appears in the Supplementary Information
Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stages.
Mol Biochem Parasitol. 2004 Oct;137(2):277-91.
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88.
Jasmer DP, Mitreva MD, McCarter JP.
mRNA sequences for Haemonchus contortus intestinal cathepsin B-like cysteine proteases display an extreme in abundance and diversity compared with other adult mammalian parasitic nematodes.
Mol Biochem Parasitol. 2004 Oct;137(2):297-305.
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89.
A list of authors and their affiliations appears in the Supplementary Information
Finishing the euchromatic sequence of the human genome
Nature. 2004 Oct 21;431(7011):931-45.
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90.
McCarter, J. P.