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Items: 26

1.

Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence.

Rands CM, Darling A, Fujita M, Kong L, Webster MT, Clabaut C, Emes RD, Heger A, Meader S, Hawkins MB, Eisen MB, Teiling C, Affourtit J, Boese B, Grant PR, Grant BR, Eisen JA, Abzhanov A, Ponting CP.

BMC Genomics. 2013 Feb 12;14:95. doi: 10.1186/1471-2164-14-95.

2.

Progressive genome-wide introgression in agricultural Campylobacter coli.

Sheppard SK, Didelot X, Jolley KA, Darling AE, Pascoe B, Meric G, Kelly DJ, Cody A, Colles FM, Strachan NJ, Ogden ID, Forbes K, French NP, Carter P, Miller WG, McCarthy ND, Owen R, Litrup E, Egholm M, Affourtit JP, Bentley SD, Parkhill J, Maiden MC, Falush D.

Mol Ecol. 2013 Feb;22(4):1051-64. doi: 10.1111/mec.12162. Epub 2012 Dec 20.

3.

Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici.

Lamour KH, Mudge J, Gobena D, Hurtado-Gonzales OP, Schmutz J, Kuo A, Miller NA, Rice BJ, Raffaele S, Cano LM, Bharti AK, Donahoo RS, Finley S, Huitema E, Hulvey J, Platt D, Salamov A, Savidor A, Sharma R, Stam R, Storey D, Thines M, Win J, Haas BJ, Dinwiddie DL, Jenkins J, Knight JR, Affourtit JP, Han CS, Chertkov O, Lindquist EA, Detter C, Grigoriev IV, Kamoun S, Kingsmore SF.

Mol Plant Microbe Interact. 2012 Oct;25(10):1350-60. doi: 10.1094/MPMI-02-12-0028-R.

4.

The genome sequence of the wine yeast VIN7 reveals an allotriploid hybrid genome with Saccharomyces cerevisiae and Saccharomyces kudriavzevii origins.

Borneman AR, Desany BA, Riches D, Affourtit JP, Forgan AH, Pretorius IS, Egholm M, Chambers PJ.

FEMS Yeast Res. 2012 Feb;12(1):88-96. doi: 10.1111/j.1567-1364.2011.00773.x. Epub 2011 Dec 23.

5.

Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development.

Holder JW, Ulrich JC, DeBono AC, Godfrey PA, Desjardins CA, Zucker J, Zeng Q, Leach AL, Ghiviriga I, Dancel C, Abeel T, Gevers D, Kodira CD, Desany B, Affourtit JP, Birren BW, Sinskey AJ.

PLoS Genet. 2011 Sep;7(9):e1002219. doi: 10.1371/journal.pgen.1002219. Epub 2011 Sep 8.

6.

Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae.

Borneman AR, Desany BA, Riches D, Affourtit JP, Forgan AH, Pretorius IS, Egholm M, Chambers PJ.

PLoS Genet. 2011 Feb 3;7(2):e1001287. doi: 10.1371/journal.pgen.1001287.

7.

The genome of the domesticated apple (Malus × domestica Borkh.).

Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R.

Nat Genet. 2010 Oct;42(10):833-9. doi: 10.1038/ng.654. Epub 2010 Aug 29.

PMID:
20802477
8.

A draft sequence of the Neandertal genome.

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S.

Science. 2010 May 7;328(5979):710-722. doi: 10.1126/science.1188021.

9.

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins.

Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F, Affourtit J, Egholm M, Henrissat B, Knight R, Gordon JI.

Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7503-8. doi: 10.1073/pnas.1002355107. Epub 2010 Apr 2.

10.

Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium.

Tripp HJ, Bench SR, Turk KA, Foster RA, Desany BA, Niazi F, Affourtit JP, Zehr JP.

Nature. 2010 Mar 4;464(7285):90-4. doi: 10.1038/nature08786. Epub 2010 Feb 21.

PMID:
20173737
11.

Cdcs1 a major colitis susceptibility locus in mice; subcongenic analysis reveals genetic complexity.

Bleich A, Büchler G, Beckwith J, Petell LM, Affourtit JP, King BL, Shaffer DJ, Roopenian DC, Hedrich HJ, Sundberg JP, Leiter EH.

Inflamm Bowel Dis. 2010 May;16(5):765-75. doi: 10.1002/ibd.21146.

12.

Mutation discovery in the mouse using genetically guided array capture and resequencing.

D'Ascenzo M, Meacham C, Kitzman J, Middle C, Knight J, Winer R, Kukricar M, Richmond T, Albert TJ, Czechanski A, Donahue LR, Affourtit J, Jeddeloh JA, Reinholdt L.

Mamm Genome. 2009 Jul;20(7):424-36. doi: 10.1007/s00335-009-9200-y. Epub 2009 Jul 21.

13.

A core gut microbiome in obese and lean twins.

Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI.

Nature. 2009 Jan 22;457(7228):480-4. doi: 10.1038/nature07540. Epub 2008 Nov 30.

14.

Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II.

Zehr JP, Bench SR, Carter BJ, Hewson I, Niazi F, Shi T, Tripp HJ, Affourtit JP.

Science. 2008 Nov 14;322(5904):1110-2. doi: 10.1126/science.1165340.

15.

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history.

Kim PM, Lam HY, Urban AE, Korbel JO, Affourtit J, Grubert F, Chen X, Weissman S, Snyder M, Gerstein MB.

Genome Res. 2008 Dec;18(12):1865-74. doi: 10.1101/gr.081422.108. Epub 2008 Oct 8.

16.

Applying gene expression, proteomics and single-nucleotide polymorphism analysis for complex trait gene identification.

Stylianou IM, Affourtit JP, Shockley KR, Wilpan RY, Abdi FA, Bhardwaj S, Rollins J, Churchill GA, Paigen B.

Genetics. 2008 Mar;178(3):1795-805. doi: 10.1534/genetics.107.081216. Epub 2008 Feb 3.

17.

Oocyte regulation of metabolic cooperativity between mouse cumulus cells and oocytes: BMP15 and GDF9 control cholesterol biosynthesis in cumulus cells.

Su YQ, Sugiura K, Wigglesworth K, O'Brien MJ, Affourtit JP, Pangas SA, Matzuk MM, Eppig JJ.

Development. 2008 Jan;135(1):111-21. Epub 2007 Nov 28.

18.

A mouse model of conditional lipodystrophy.

Kim S, Huang LW, Snow KJ, Ablamunits V, Hasham MG, Young TH, Paulk AC, Richardson JE, Affourtit JP, Shalom-Barak T, Bult CJ, Barak Y.

Proc Natl Acad Sci U S A. 2007 Oct 16;104(42):16627-32. Epub 2007 Oct 5.

19.

Paired-end mapping reveals extensive structural variation in the human genome.

Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M.

Science. 2007 Oct 19;318(5849):420-6. Epub 2007 Sep 27.

20.

The nonhomologous end joining factor Artemis suppresses multi-tissue tumor formation and prevents loss of heterozygosity.

Woo Y, Wright SM, Maas SA, Alley TL, Caddle LB, Kamdar S, Affourtit J, Foreman O, Akeson EC, Shaffer D, Bronson RT, Morse HC 3rd, Roopenian D, Mills KD.

Oncogene. 2007 Sep 6;26(41):6010-20. Epub 2007 Mar 26.

PMID:
17384673
21.

Selective degradation of transcripts during meiotic maturation of mouse oocytes.

Su YQ, Sugiura K, Woo Y, Wigglesworth K, Kamdar S, Affourtit J, Eppig JJ.

Dev Biol. 2007 Feb 1;302(1):104-17. Epub 2006 Sep 12.

22.

Inheritance patterns of transcript levels in F1 hybrid mice.

Cui X, Affourtit J, Shockley KR, Woo Y, Churchill GA.

Genetics. 2006 Oct;174(2):627-37. Epub 2006 Aug 3.

23.

Transcriptional profile of mouse pre-granulosa and Sertoli cells isolated from early-differentiated fetal gonads.

Bouma GJ, Affourtit JP, Bult CJ, Eicher EM.

Gene Expr Patterns. 2007 Jan;7(1-2):113-23. Epub 2006 Jun 6.

PMID:
16839824
24.

A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms.

Woo Y, Affourtit J, Daigle S, Viale A, Johnson K, Naggert J, Churchill G.

J Biomol Tech. 2004 Dec;15(4):276-84.

25.

Expression profiling using a hexamer-based universal microarray.

Roth ME, Feng L, McConnell KJ, Schaffer PJ, Guerra CE, Affourtit JP, Piper KR, Guccione L, Hariharan J, Ford MJ, Powell SW, Krishnaswamy H, Lane J, Guccione L, Intrieri G, Merkel JS, Perbost C, Valerio A, Zolla B, Graham CD, Hnath J, Michaelson C, Wang R, Ying B, Halling C, Parman CE, Raha D, Orr B, Jedrzkiewicz B, Liao J, Tevelev A, Mattessich MJ, Kranz DM, Lacey M, Kaufman JC, Kim J, Latimer DR, Lizardi PM.

Nat Biotechnol. 2004 Apr;22(4):418-26. Epub 2004 Mar 14.

PMID:
15024387
26.

Distribution of Nitrogen-Fixing Microorganisms along the Neuse River Estuary, North Carolina.

Affourtit J, Zehr JP, Paerl HW.

Microb Ecol. 2001 Feb;41(2):114-123.

PMID:
12032616

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