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Items: 20

1.

Gibbon genome and the fast karyotype evolution of small apes.

Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA.

Nature. 2014 Sep 11;513(7517):195-201. doi: 10.1038/nature13679.

2.

Using mitogenomic and nuclear ribosomal sequence data to investigate the phylogeny of the Xiphinema americanum species complex.

Zasada IA, Peetz A, Howe DK, Wilhelm LJ, Cheam D, Denver DR, Smythe AB.

PLoS One. 2014 Feb 27;9(2):e90035. doi: 10.1371/journal.pone.0090035. eCollection 2014.

3.

Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa.

Vining K, Pomraning KR, Wilhelm LJ, Ma C, Pellegrini M, Di Y, Mockler TC, Freitag M, Strauss SH.

BMC Plant Biol. 2013 Jun 25;13:92. doi: 10.1186/1471-2229-13-92.

4.

Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence.

Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, Berlin AM, Figueroa M, Freitag M, Hane JK, Henrissat B, Holman WH, Kodira CD, Martin J, Oliver RP, Robbertse B, Schackwitz W, Schwartz DC, Spatafora JW, Turgeon BG, Yandava C, Young S, Zhou S, Zeng Q, Grigoriev IV, Ma LJ, Ciuffetti LM.

G3 (Bethesda). 2013 Jan;3(1):41-63. doi: 10.1534/g3.112.004044. Epub 2013 Jan 1.

5.

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa.

Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler TC, Freitag M, Geraldes A, El-Kassaby YA, Mansfield SD, Cronk QC, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA.

New Phytol. 2012 Nov;196(3):713-25. doi: 10.1111/j.1469-8137.2012.04258.x. Epub 2012 Aug 3.

6.

Host-selective toxins of Pyrenophora tritici-repentis induce common responses associated with host susceptibility.

Pandelova I, Figueroa M, Wilhelm LJ, Manning VA, Mankaney AN, Mockler TC, Ciuffetti LM.

PLoS One. 2012;7(7):e40240. doi: 10.1371/journal.pone.0040240. Epub 2012 Jul 6.

7.

Variation in base-substitution mutation in experimental and natural lineages of Caenorhabditis nematodes.

Denver DR, Wilhelm LJ, Howe DK, Gafner K, Dolan PC, Baer CF.

Genome Biol Evol. 2012;4(4):513-22. doi: 10.1093/gbe/evs028. Epub 2012 Mar 20.

8.

Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression.

Vining KJ, Pomraning KR, Wilhelm LJ, Priest HD, Pellegrini M, Mockler TC, Freitag M, Strauss SH.

BMC Genomics. 2012 Jan 17;13:27. doi: 10.1186/1471-2164-13-27.

9.

GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.

Cumbie JS, Kimbrel JA, Di Y, Schafer DW, Wilhelm LJ, Fox SE, Sullivan CM, Curzon AD, Carrington JC, Mockler TC, Chang JH.

PLoS One. 2011;6(10):e25279. doi: 10.1371/journal.pone.0025279. Epub 2011 Oct 6.

10.

The genome of woodland strawberry (Fragaria vesca).

Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJ, Williams KP, Holt SH, Ruiz Rojas JJ, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW Jr, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Lopez Girona E, Zdepski A, Wang W, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM.

Nat Genet. 2011 Feb;43(2):109-16. doi: 10.1038/ng.740. Epub 2010 Dec 26.

11.

Selective sweeps and parallel mutation in the adaptive recovery from deleterious mutation in Caenorhabditis elegans.

Denver DR, Howe DK, Wilhelm LJ, Palmer CA, Anderson JL, Stein KC, Phillips PC, Estes S.

Genome Res. 2010 Dec;20(12):1663-71. doi: 10.1101/gr.108191.110. Epub 2010 Oct 29.

12.

Analysis of transcriptome changes induced by Ptr ToxA in wheat provides insights into the mechanisms of plant susceptibility.

Pandelova I, Betts MF, Manning VA, Wilhelm LJ, Mockler TC, Ciuffetti LM.

Mol Plant. 2009 Sep;2(5):1067-83. doi: 10.1093/mp/ssp045. Epub 2009 Jul 7.

13.

A genome-wide view of Caenorhabditis elegans base-substitution mutation processes.

Denver DR, Dolan PC, Wilhelm LJ, Sung W, Lucas-Lledó JI, Howe DK, Lewis SC, Okamoto K, Thomas WK, Lynch M, Baer CF.

Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16310-4. doi: 10.1073/pnas.0904895106. Epub 2009 Sep 10.

14.

Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea.

Sowell SM, Wilhelm LJ, Norbeck AD, Lipton MS, Nicora CD, Barofsky DF, Carlson CA, Smith RD, Giovanonni SJ.

ISME J. 2009 Jan;3(1):93-105. doi: 10.1038/ismej.2008.83. Epub 2008 Sep 4.

PMID:
18769456
15.

SAR11 marine bacteria require exogenous reduced sulphur for growth.

Tripp HJ, Kitner JB, Schwalbach MS, Dacey JW, Wilhelm LJ, Giovannoni SJ.

Nature. 2008 Apr 10;452(7188):741-4. doi: 10.1038/nature06776. Epub 2008 Mar 12.

PMID:
18337719
16.

Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data.

Wilhelm LJ, Tripp HJ, Givan SA, Smith DP, Giovannoni SJ.

Biol Direct. 2007 Nov 7;2:27.

17.

The phylogeny of endolithic microbes associated with marine basalts.

Mason OU, Stingl U, Wilhelm LJ, Moeseneder MM, Di Meo-Savoie CA, Fisk MR, Giovannoni SJ.

Environ Microbiol. 2007 Oct;9(10):2539-50.

PMID:
17803778
18.

High intraspecific recombination rate in a native population of Candidatus pelagibacter ubique (SAR11).

Vergin KL, Tripp HJ, Wilhelm LJ, Denver DR, Rappé MS, Giovannoni SJ.

Environ Microbiol. 2007 Oct;9(10):2430-40.

PMID:
17803769
19.

Proteorhodopsin in the ubiquitous marine bacterium SAR11.

Giovannoni SJ, Bibbs L, Cho JC, Stapels MD, Desiderio R, Vergin KL, Rappé MS, Laney S, Wilhelm LJ, Tripp HJ, Mathur EJ, Barofsky DF.

Nature. 2005 Nov 3;438(7064):82-5.

PMID:
16267553
20.

RNA binding properties of the coat protein from bacteriophage GA.

Gott JM, Wilhelm LJ, Uhlenbeck OC.

Nucleic Acids Res. 1991 Dec 11;19(23):6499-503.

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