A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Boutz PL, Stoilov P, Li Q, Lin CH, Chawla G, Ostrow K, Shiue L, Ares M Jr, Black DL. Genes Dev. 2007 Jul 1;21(13):1636-52.

Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Ni JZ, Grate L, Donohue JP, Preston C, Nobida N, O'Brien G, Shiue L, Clark TA, Blume JE, Ares M Jr. Genes Dev. 2007 Mar 15;21(6):708-18.

Cell type and culture condition-dependent alternative splicing in human breast cancer cells revealed by splicing-sensitive microarrays. Li C, Kato M, Shiue L, Shively JE, Ares M Jr, Lin RJ. Cancer Res. 2006 Feb 15;66(4):1990-9.

Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Davis CA, Ares M Jr. Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3262-7.

Unusual intron conservation near tissue-regulated exons found by splicing microarrays. Sugnet CW, Srinivasan K, Clark TA, O'Brien G, Cline MS, Wang H, Williams A, Kulp D, Blume JE, Haussler D, Ares M Jr. PLoS Comput Biol. 2006 Jan;2(1):e4.

Prp43p is a DEAH-box spliceosome disassembly factor essential for ribosome biogenesis. Combs DJ, Nagel RJ, Ares M Jr, Stevens SW. Mol Cell Biol. 2006 Jan;26(2):523-34.

Detection and measurement of alternative splicing using splicing-sensitive microarrays. Srinivasan K, Shiue L, Hayes JD, Centers R, Fitzwater S, Loewen R, Edmondson LR, Bryant J, Smith M, Rommelfanger C, Welch V, Clark TA, Sugnet CW, Howe KJ, Mandel-Gutfreund Y, Ares M Jr. Methods. 2005 Dec;37(4):345-59.

Analysis of a splice array experiment elucidates roles of chromatin elongation factor Spt4-5 in splicing. Xiao Y, Yang YH, Burckin TA, Shiue L, Hartzog GA, Segal MR. PLoS Comput Biol. 2005 Sep;1(4):e39.

Exploring functional relationships between components of the gene expression machinery. Burckin T, Nagel R, Mandel-Gutfreund Y, Shiue L, Clark TA, Chong JL, Chang TH, Squazzo S, Hartzog G, Ares M Jr. Nat Struct Mol Biol. 2005 Feb;12(2):175-82.

Molecular analysis of rugosity in a Vibrio cholerae O1 El Tor phase variant. Yildiz FH, Liu XS, Heydorn A, Schoolnik GK. Mol Microbiol. 2004 Jul;53(2):497-515.

Transcriptome and genome conservation of alternative splicing events in humans
and mice. Sugnet CW, Kent WJ, Ares M Jr, Haussler D. Pac Symp Biocomput. 2004:66-77.

Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Clark TA, Sugnet CW, Ares M Jr. Science. 2002 May 3;296(5569):907-10.

Knowledge-based analysis of microarray gene expression data using support vector machines. Brown MPS, Grundy WN, Lin D, Cristianini N, Sugnet C, Furey TS, Ares M Jr, Haussler D. Proc Natl Acad Sci USA. 2000 January 4; 97(1):262-267.