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Items: 1 to 20 of 29

1.

Target hub proteins serve as master regulators of development in yeast.

Borneman AR, Leigh-Bell JA, Yu H, Bertone P, Gerstein M, Snyder M.

Genes Dev. 2006 Feb 15;20(4):435-48. Epub 2006 Jan 31.

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Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences.

Hughes JR, Cheng JF, Ventress N, Prabhakar S, Clark K, Anguita E, De Gobbi M, de Jong P, Rubin E, Higgs DR.

Proc Natl Acad Sci U S A. 2005 Jul 12;102(28):9830-5. Epub 2005 Jul 5.

4.

DIP-chip: rapid and accurate determination of DNA-binding specificity.

Liu X, Noll DM, Lieb JD, Clarke ND.

Genome Res. 2005 Mar;15(3):421-7. Epub 2005 Feb 14.

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Computationally analyzing the possible biological function of YJL103C--an ORF potentially involved in the regulation of energy process in yeast.

Deng Y, He T, Wu Y, Vanka P, Yang G, Huang Y, Yao H, Brown SJ.

Int J Mol Med. 2005 Jan;15(1):123-7.

PMID:
15583838
7.

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.

Mukherjee S, Berger MF, Jona G, Wang XS, Muzzey D, Snyder M, Young RA, Bulyk ML.

Nat Genet. 2004 Dec;36(12):1331-9. Epub 2004 Nov 14.

8.

A gateway-compatible yeast one-hybrid system.

Deplancke B, Dupuy D, Vidal M, Walhout AJ.

Genome Res. 2004 Oct;14(10B):2093-101.

9.

Regulation of gene expression by a metabolic enzyme.

Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, Snyder M.

Science. 2004 Oct 15;306(5695):482-4.

10.

Combining phylogenetic data with co-regulated genes to identify regulatory motifs.

Wang T, Stormo GD.

Bioinformatics. 2003 Dec 12;19(18):2369-80.

11.

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.

Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH.

PLoS Biol. 2003 Nov;1(2):E45. Epub 2003 Nov 17.

12.

Finding functional features in Saccharomyces genomes by phylogenetic footprinting.

Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M.

Science. 2003 Jul 4;301(5629):71-6. Epub 2003 May 29.

13.

Sequencing and comparison of yeast species to identify genes and regulatory elements.

Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES.

Nature. 2003 May 15;423(6937):241-54.

PMID:
12748633
14.

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae.

Horak CE, Luscombe NM, Qian J, Bertone P, Piccirrillo S, Gerstein M, Snyder M.

Genes Dev. 2002 Dec 1;16(23):3017-33.

15.

Probabilistic code for DNA recognition by proteins of the EGR family.

Benos PV, Lapedes AS, Stormo GD.

J Mol Biol. 2002 Nov 1;323(4):701-27.

PMID:
12419259
16.

Functional profiling of the Saccharomyces cerevisiae genome.

Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, Dow S, Lucau-Danila A, Anderson K, André B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Güldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kötter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M.

Nature. 2002 Jul 25;418(6896):387-91.

PMID:
12140549
17.

High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites.

Roulet E, Busso S, Camargo AA, Simpson AJ, Mermod N, Bucher P.

Nat Biotechnol. 2002 Aug;20(8):831-5. Epub 2002 Jul 8.

PMID:
12101405
18.

Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range.

Dudley AM, Aach J, Steffen MA, Church GM.

Proc Natl Acad Sci U S A. 2002 May 28;99(11):7554-9.

19.

Assessing gene significance from cDNA microarray expression data via mixed models.

Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushel P, Afshari C, Paules RS.

J Comput Biol. 2001;8(6):625-37.

PMID:
11747616
20.

Global analysis of protein activities using proteome chips.

Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M.

Science. 2001 Sep 14;293(5537):2101-5. Epub 2001 Jul 26.

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