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Items: 45

1.

Sequence variation, evolutionary constraint, and selection at the CD163 gene in pigs.

Johnsson M, Ros-Freixedes R, Gorjanc G, Campbell MA, Naswa S, Kelly K, Lightner J, Rounsley S, Hickey JM.

Genet Sel Evol. 2018 Dec 20;50(1):69. doi: 10.1186/s12711-018-0440-8.

2.

Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing.

Ros-Freixedes R, Battagin M, Johnsson M, Gorjanc G, Mileham AJ, Rounsley SD, Hickey JM.

Genet Sel Evol. 2018 Dec 13;50(1):64. doi: 10.1186/s12711-018-0436-4.

3.

Advances in Sequencing and Resequencing in Crop Plants.

Marri PR, Ye L, Jia Y, Jiang K, Rounsley SD.

Adv Biochem Eng Biotechnol. 2018;164:11-35. doi: 10.1007/10_2017_46.

PMID:
29516115
4.

QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii.

Nzuki I, Katari MS, Bredeson JV, Masumba E, Kapinga F, Salum K, Mkamilo GS, Shah T, Lyons JB, Rokhsar DS, Rounsley S, Myburg AA, Ferguson ME.

Front Plant Sci. 2017 Jul 21;8:1168. doi: 10.3389/fpls.2017.01168. eCollection 2017.

5.

Variations of five eIF4E genes across cassava accessions exhibiting tolerant and susceptible responses to cassava brown streak disease.

Shi S, Zhang X, Mandel MA, Zhang P, Zhang Y, Ferguson M, Amuge T, Rounsley S, Liu Z, Xiong Z.

PLoS One. 2017 Aug 3;12(8):e0181998. doi: 10.1371/journal.pone.0181998. eCollection 2017.

6.

Genome Sequence of Ophidiomyces ophiodiicola, an Emerging Fungal Pathogen of Snakes.

Ohkura M, Fitak RR, Wisecaver JH, DeBlasio D, Niazi F, Egholm M, Rounsley SD, Kodira CD, Orbach MJ.

Genome Announc. 2017 Jul 27;5(30). pii: e00677-17. doi: 10.1128/genomeA.00677-17.

7.

QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert.

Masumba EA, Kapinga F, Mkamilo G, Salum K, Kulembeka H, Rounsley S, Bredeson JV, Lyons JB, Rokhsar DS, Kanju E, Katari MS, Myburg AA, van der Merwe NA, Ferguson ME.

Theor Appl Genet. 2017 Oct;130(10):2069-2090. doi: 10.1007/s00122-017-2943-z. Epub 2017 Jul 13.

8.

DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses.

Wicker T, Yu Y, Haberer G, Mayer KF, Marri PR, Rounsley S, Chen M, Zuccolo A, Panaud O, Wing RA, Roffler S.

Nat Commun. 2016 Sep 7;7:12790. doi: 10.1038/ncomms12790.

9.

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity.

Bredeson JV, Lyons JB, Prochnik SE, Wu GA, Ha CM, Edsinger-Gonzales E, Grimwood J, Schmutz J, Rabbi IY, Egesi C, Nauluvula P, Lebot V, Ndunguru J, Mkamilo G, Bart RS, Setter TL, Gleadow RM, Kulakow P, Ferguson ME, Rounsley S, Rokhsar DS.

Nat Biotechnol. 2016 May;34(5):562-70. doi: 10.1038/nbt.3535. Epub 2016 Apr 18.

PMID:
27088722
10.

Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.

Guttikonda SK, Marri P, Mammadov J, Ye L, Soe K, Richey K, Cruse J, Zhuang M, Gao Z, Evans C, Rounsley S, Kumpatla SP.

PLoS One. 2016 Feb 23;11(2):e0149515. doi: 10.1371/journal.pone.0149515. eCollection 2016.

11.

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.

Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, Aury JM, Bento P, Bernard M, Bocs S, Campa C, Cenci A, Combes MC, Crouzillat D, Da Silva C, Daddiego L, De Bellis F, Dussert S, Garsmeur O, Gayraud T, Guignon V, Jahn K, Jamilloux V, Joët T, Labadie K, Lan T, Leclercq J, Lepelley M, Leroy T, Li LT, Librado P, Lopez L, Muñoz A, Noel B, Pallavicini A, Perrotta G, Poncet V, Pot D, Priyono, Rigoreau M, Rouard M, Rozas J, Tranchant-Dubreuil C, VanBuren R, Zhang Q, Andrade AC, Argout X, Bertrand B, de Kochko A, Graziosi G, Henry RJ, Jayarama, Ming R, Nagai C, Rounsley S, Sankoff D, Giuliano G, Albert VA, Wincker P, Lashermes P.

Science. 2014 Sep 5;345(6201):1181-4. doi: 10.1126/science.1255274. Epub 2014 Sep 4.

12.

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication.

Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, de Baynast K, Golser W, Wissotski M, Kim W, Sanchez P, Ndjiondjop MN, Sanni K, Long M, Carney J, Panaud O, Wicker T, Machado CA, Chen M, Mayer KF, Rounsley S, Wing RA.

Nat Genet. 2014 Sep;46(9):982-8. doi: 10.1038/ng.3044. Epub 2014 Jul 27.

PMID:
25064006
13.

Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.

Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC, Wing RA, Xiao N, Moore R, Soltis PS, Soltis DE, Barbazuk WB.

Science. 2013 Dec 20;342(6165):1516-7. doi: 10.1126/science.1241130.

PMID:
24357320
14.

Agriculture: Feeding the future.

McCouch S, Baute GJ, Bradeen J, Bramel P, Bretting PK, Buckler E, Burke JM, Charest D, Cloutier S, Cole G, Dempewolf H, Dingkuhn M, Feuillet C, Gepts P, Grattapaglia D, Guarino L, Jackson S, Knapp S, Langridge P, Lawton-Rauh A, Lijua Q, Lusty C, Michael T, Myles S, Naito K, Nelson RL, Pontarollo R, Richards CM, Rieseberg L, Ross-Ibarra J, Rounsley S, Hamilton RS, Schurr U, Stein N, Tomooka N, van der Knaap E, van Tassel D, Toll J, Valls J, Varshney RK, Ward J, Waugh R, Wenzl P, Zamir D.

Nature. 2013 Jul 4;499(7456):23-4. doi: 10.1038/499023a. No abstract available.

PMID:
23823779
15.

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses.

O'Connell RJ, Thon MR, Hacquard S, Amyotte SG, Kleemann J, Torres MF, Damm U, Buiate EA, Epstein L, Alkan N, Altmüller J, Alvarado-Balderrama L, Bauser CA, Becker C, Birren BW, Chen Z, Choi J, Crouch JA, Duvick JP, Farman MA, Gan P, Heiman D, Henrissat B, Howard RJ, Kabbage M, Koch C, Kracher B, Kubo Y, Law AD, Lebrun MH, Lee YH, Miyara I, Moore N, Neumann U, Nordström K, Panaccione DG, Panstruga R, Place M, Proctor RH, Prusky D, Rech G, Reinhardt R, Rollins JA, Rounsley S, Schardl CL, Schwartz DC, Shenoy N, Shirasu K, Sikhakolli UR, Stüber K, Sukno SA, Sweigard JA, Takano Y, Takahara H, Trail F, van der Does HC, Voll LM, Will I, Young S, Zeng Q, Zhang J, Zhou S, Dickman MB, Schulze-Lefert P, Ver Loren van Themaat E, Ma LJ, Vaillancourt LJ.

Nat Genet. 2012 Sep;44(9):1060-5. doi: 10.1038/ng.2372. Epub 2012 Aug 12.

PMID:
22885923
16.

The Cassava Genome: Current Progress, Future Directions.

Prochnik S, Marri PR, Desany B, Rabinowicz PD, Kodira C, Mohiuddin M, Rodriguez F, Fauquet C, Tohme J, Harkins T, Rokhsar DS, Rounsley S.

Trop Plant Biol. 2012 Mar;5(1):88-94. Epub 2012 Jan 5.

17.

Plantagora: modeling whole genome sequencing and assembly of plant genomes.

Barthelson R, McFarlin AJ, Rounsley SD, Young S.

PLoS One. 2011;6(12):e28436. doi: 10.1371/journal.pone.0028436. Epub 2011 Dec 12.

18.

A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure.

Zuccolo A, Bowers JE, Estill JC, Xiong Z, Luo M, Sebastian A, Goicoechea JL, Collura K, Yu Y, Jiao Y, Duarte J, Tang H, Ayyampalayam S, Rounsley S, Kudrna D, Paterson AH, Pires JC, Chanderbali A, Soltis DE, Chamala S, Barbazuk B, Soltis PS, Albert VA, Ma H, Mandoli D, Banks J, Carlson JE, Tomkins J, dePamphilis CW, Wing RA, Leebens-Mack J.

Genome Biol. 2011;12(5):R48. doi: 10.1186/gb-2011-12-5-r48. Epub 2011 May 27.

19.

Genome sequencing reveals widespread virulence gene exchange among human Neisseria species.

Marri PR, Paniscus M, Weyand NJ, Rendón MA, Calton CM, Hernández DR, Higashi DL, Sodergren E, Weinstock GM, Rounsley SD, So M.

PLoS One. 2010 Jul 28;5(7):e11835. doi: 10.1371/journal.pone.0011835.

20.

Scaffold filling, contig fusion and comparative gene order inference.

Muñoz A, Zheng C, Zhu Q, Albert VA, Rounsley S, Sankoff D.

BMC Bioinformatics. 2010 Jun 4;11:304. doi: 10.1186/1471-2105-11-304.

21.

Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control.

Neafsey DE, Barker BM, Sharpton TJ, Stajich JE, Park DJ, Whiston E, Hung CY, McMahan C, White J, Sykes S, Heiman D, Young S, Zeng Q, Abouelleil A, Aftuck L, Bessette D, Brown A, FitzGerald M, Lui A, Macdonald JP, Priest M, Orbach MJ, Galgiani JN, Kirkland TN, Cole GT, Birren BW, Henn MR, Taylor JW, Rounsley SD.

Genome Res. 2010 Jul;20(7):938-46. doi: 10.1101/gr.103911.109. Epub 2010 Jun 1.

22.

Shotguns and SNPs: how fast and cheap sequencing is revolutionizing plant biology.

Rounsley SD, Last RL.

Plant J. 2010 Mar;61(6):922-7. doi: 10.1111/j.1365-313X.2009.04030.x. Review.

23.

Development of a rapid, cost-effective TaqMan Real-Time PCR Assay for identification and differentiation of Coccidioides immitis and Coccidioides posadasii.

Sheff KW, York ER, Driebe EM, Barker BM, Rounsley SD, Waddell VG, Beckstrom-Sternberg SM, Beckstrom-Sternberg JS, Keim PS, Engelthaler DM.

Med Mycol. 2010 May;48(3):466-9. doi: 10.3109/13693780903218990.

PMID:
20370360
24.

The subtelomere of Oryza sativa chromosome 3 short arm as a hot bed of new gene origination in rice.

Fan C, Zhang Y, Yu Y, Rounsley S, Long M, Wing RA.

Mol Plant. 2008 Sep;1(5):839-50. doi: 10.1093/mp/ssn050. Epub 2008 Aug 22.

25.

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives.

Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung CY, McMahan C, Muszewska A, Grynberg M, Mandel MA, Kellner EM, Barker BM, Galgiani JN, Orbach MJ, Kirkland TN, Cole GT, Henn MR, Birren BW, Taylor JW.

Genome Res. 2009 Oct;19(10):1722-31. doi: 10.1101/gr.087551.108. Epub 2009 Aug 28.

26.

The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion.

Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, Schmutz J, Taga M, White GJ, Zhou S, Schwartz DC, Freitag M, Ma LJ, Danchin EG, Henrissat B, Coutinho PM, Nelson DR, Straney D, Napoli CA, Barker BM, Gribskov M, Rep M, Kroken S, Molnár I, Rensing C, Kennell JC, Zamora J, Farman ML, Selker EU, Salamov A, Shapiro H, Pangilinan J, Lindquist E, Lamers C, Grigoriev IV, Geiser DM, Covert SF, Temporini E, Vanetten HD.

PLoS Genet. 2009 Aug;5(8):e1000618. doi: 10.1371/journal.pgen.1000618. Epub 2009 Aug 28.

27.

Genomic and population analyses of the mating type loci in Coccidioides species reveal evidence for sexual reproduction and gene acquisition.

Mandel MA, Barker BM, Kroken S, Rounsley SD, Orbach MJ.

Eukaryot Cell. 2007 Jul;6(7):1189-99. Epub 2007 May 18.

28.

Uneven chromosome contraction and expansion in the maize genome.

Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, Pontaroli AC, Wei F, Haberer G, Fuks G, Du C, Raymond C, Estep MC, Liu R, Bennetzen JL, Chan AP, Rabinowicz PD, Quackenbush J, Barbazuk WB, Wing RA, Birren B, Nusbaum C, Rounsley S, Mayer KF, Messing J.

Genome Res. 2006 Oct;16(10):1241-51. Epub 2006 Aug 10.

29.

Comparative sequencing of plant genomes: choices to make.

Jackson S, Rounsley S, Purugganan M.

Plant Cell. 2006 May;18(5):1100-4. No abstract available.

30.

Analysis of the DNA sequence and duplication history of human chromosome 15.

Zody MC, Garber M, Sharpe T, Young SK, Rowen L, O'Neill K, Whittaker CA, Kamal M, Chang JL, Cuomo CA, Dewar K, FitzGerald MG, Kodira CD, Madan A, Qin S, Yang X, Abbasi N, Abouelleil A, Arachchi HM, Baradarani L, Birditt B, Bloom S, Bloom T, Borowsky ML, Burke J, Butler J, Cook A, DeArellano K, DeCaprio D, Dorris L 3rd, Dors M, Eichler EE, Engels R, Fahey J, Fleetwood P, Friedman C, Gearin G, Hall JL, Hensley G, Johnson E, Jones C, Kamat A, Kaur A, Locke DP, Madan A, Munson G, Jaffe DB, Lui A, Macdonald P, Mauceli E, Naylor JW, Nesbitt R, Nicol R, O'Leary SB, Ratcliffe A, Rounsley S, She X, Sneddon KM, Stewart S, Sougnez C, Stone SM, Topham K, Vincent D, Wang S, Zimmer AR, Birren BW, Hood L, Lander ES, Nusbaum C.

Nature. 2006 Mar 30;440(7084):671-5.

PMID:
16572171
31.

Structure and architecture of the maize genome.

Haberer G, Young S, Bharti AK, Gundlach H, Raymond C, Fuks G, Butler E, Wing RA, Rounsley S, Birren B, Nusbaum C, Mayer KF, Messing J.

Plant Physiol. 2005 Dec;139(4):1612-24.

32.

Sharing the wealth. The mechanics of a data release from industry.

Rounsley S.

Plant Physiol. 2003 Oct;133(2):438-40. No abstract available.

33.

Arabidopsis map-based cloning in the post-genome era.

Jander G, Norris SR, Rounsley SD, Bush DF, Levin IM, Last RL.

Plant Physiol. 2002 Jun;129(2):440-50. Review.

34.

Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.

Lin X, Kaul S, Rounsley S, Shea TP, Benito MI, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, Feldblyum TV, Buell CR, Ketchum KA, Lee J, Ronning CM, Koo HL, Moffat KS, Cronin LA, Shen M, Pai G, Van Aken S, Umayam L, Tallon LJ, Gill JE, Adams MD, Carrera AJ, Creasy TH, Goodman HM, Somerville CR, Copenhaver GP, Preuss D, Nierman WC, White O, Eisen JA, Salzberg SL, Fraser CM, Venter JC.

Nature. 1999 Dec 16;402(6763):761-8.

PMID:
10617197
35.

Large-scale sequencing of plant genomes.

Rounsley S, Lin X, Ketchum KA.

Curr Opin Plant Biol. 1998 Apr;1(2):136-41.

PMID:
10066574
36.

High throughput direct end sequencing of BAC clones.

Kelley JM, Field CE, Craven MB, Bocskai D, Kim UJ, Rounsley SD, Adams MD.

Nucleic Acids Res. 1999 Mar 15;27(6):1539-46.

37.

Genome maps 9. Arabidopsis thaliana. Wall chart.

Rhee SY, Weng S, Flanders D, Cherry JM, Dean C, Lister C, Anderson M, Koornneef M, Meinke DW, Nickle T, Smith K, Rounsley SD.

Science. 1998 Oct 23;282(5389):663-7. No abstract available.

PMID:
9841422
38.

Arabidopsis thaliana: a model plant for genome analysis.

Meinke DW, Cherry JM, Dean C, Rounsley SD, Koornneef M.

Science. 1998 Oct 23;282(5389):662, 679-82. Review.

PMID:
9784120
39.

Targeted disruption in Arabidopsis.

Kempin SA, Liljegren SJ, Block LM, Rounsley SD, Yanofsky MF, Lam E.

Nature. 1997 Oct 23;389(6653):802-3. No abstract available.

PMID:
9349810
40.

The construction of Arabidopsis expressed sequence tag assemblies. A new resource to facilitate gene identification.

Rounsley SD, Glodek A, Sutton G, Adams MD, Somerville CR, Venter JC, Kerlavage AR.

Plant Physiol. 1996 Nov;112(3):1177-83.

41.

Diverse roles for MADS box genes in Arabidopsis development.

Rounsley SD, Ditta GS, Yanofsky MF.

Plant Cell. 1995 Aug;7(8):1259-69.

42.
43.

Molecular evolution of flower development: diversification of the plant MADS-box regulatory gene family.

Purugganan MD, Rounsley SD, Schmidt RJ, Yanofsky MF.

Genetics. 1995 May;140(1):345-56.

44.

Isolation of the tomato AGAMOUS gene TAG1 and analysis of its homeotic role in transgenic plants.

Pnueli L, Hareven D, Rounsley SD, Yanofsky MF, Lifschitz E.

Plant Cell. 1994 Feb;6(2):163-73.

45.

The use of the polymerase chain reaction in plant transformation studies.

Hamill JD, Rounsley S, Spencer A, Todd G, Rhodes MJ.

Plant Cell Rep. 1991 Aug;10(5):221-4. doi: 10.1007/BF00232562.

PMID:
24221583

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