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Items: 16

1.

Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays.

Li L, He H, Zhang J, Wang X, Bai S, Stolc V, Tongprasit W, Young ND, Yu O, Deng XW.

Genome Biol. 2008;9(3):R57. doi: 10.1186/gb-2008-9-3-r57. Epub 2008 Mar 19.

2.

High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression.

Li X, Wang X, He K, Ma Y, Su N, He H, Stolc V, Tongprasit W, Jin W, Jiang J, Terzaghi W, Li S, Deng XW.

Plant Cell. 2008 Feb;20(2):259-76. doi: 10.1105/tpc.107.056879. Epub 2008 Feb 8.

3.

In-depth query of large genomes using tiling arrays.

Samanta MP, Tongprasit W, Stolc V.

Methods Mol Biol. 2007;377:163-74. Review.

PMID:
17634616
4.

Global identification and characterization of transcriptionally active regions in the rice genome.

Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M, Deng XW.

PLoS One. 2007 Mar 14;2(3):e294.

5.

Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development.

Lee J, He K, Stolc V, Lee H, Figueroa P, Gao Y, Tongprasit W, Zhao H, Lee I, Deng XW.

Plant Cell. 2007 Mar;19(3):731-49. Epub 2007 Mar 2.

6.

A core transcriptional network for early mesoderm development in Drosophila melanogaster.

Sandmann T, Girardot C, Brehme M, Tongprasit W, Stolc V, Furlong EE.

Genes Dev. 2007 Feb 15;21(4):436-49.

7.

The transcriptome of the sea urchin embryo.

Samanta MP, Tongprasit W, Istrail S, Cameron RA, Tu Q, Davidson EH, Stolc V.

Science. 2006 Nov 10;314(5801):960-2.

8.

The genome of the sea urchin Strongylocentrotus purpuratus.

Sea Urchin Genome Sequencing Consortium, Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Bellé R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevière AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallböök F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Röttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R.

Science. 2006 Nov 10;314(5801):941-52. Erratum in: Science. 2007 Feb 9;315(5813):766.

9.

Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway.

Samanta MP, Tongprasit W, Sethi H, Chin CS, Stolc V.

Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4192-7. Epub 2006 Mar 6.

10.

Genome-wide transcription analyses in rice using tiling microarrays.

Li L, Wang X, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J, Deng XW.

Nat Genet. 2006 Jan;38(1):124-9. Epub 2005 Dec 20.

PMID:
16369532
11.

A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.

Stolc V, Li L, Wang X, Li X, Su N, Tongprasit W, Han B, Xue Y, Li J, Snyder M, Gerstein M, Wang J, Deng XW.

Plant Mol Biol. 2005 Sep;59(1):137-49.

PMID:
16217608
12.

Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays.

Stolc V, Samanta MP, Tongprasit W, Sethi H, Liang S, Nelson DC, Hegeman A, Nelson C, Rancour D, Bednarek S, Ulrich EL, Zhao Q, Wrobel RL, Newman CS, Fox BG, Phillips GN Jr, Markley JL, Sussman MR.

Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4453-8. Epub 2005 Mar 8.

13.

Genome-wide transcriptional analysis of flagellar regeneration in Chlamydomonas reinhardtii identifies orthologs of ciliary disease genes.

Stolc V, Samanta MP, Tongprasit W, Marshall WF.

Proc Natl Acad Sci U S A. 2005 Mar 8;102(10):3703-7. Epub 2005 Feb 28.

14.

Global identification of human transcribed sequences with genome tiling arrays.

Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M.

Science. 2004 Dec 24;306(5705):2242-6. Epub 2004 Nov 11.

15.

A gene expression map for the euchromatic genome of Drosophila melanogaster.

Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, Rifkin SA, Hua S, Herreman T, Tongprasit W, Barbano PE, Bussemaker HJ, White KP.

Science. 2004 Oct 22;306(5696):655-60.

16.

Characterization of synthetic DNA bar codes in Saccharomyces cerevisiae gene-deletion strains.

Eason RG, Pourmand N, Tongprasit W, Herman ZS, Anthony K, Jejelowo O, Davis RW, Stolc V.

Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):11046-51. Epub 2004 Jul 16.

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