Publications:

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

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

• Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D.
  The human genome browser at UCSC.
  Genome Res. 2002 Jun;12(6):996-1006.

• Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ.
  The UCSC Table Browser data retrieval tool.
  Nucleic Acids Res. 2004 Jan 1;32 Database issue:D493-6.

• Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ; University of California Santa Cruz.
  The UCSC Genome Browser Database.
  Nucleic Acids Res. 2003 Jan 1;31(1):51-4.

• Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES; Mouse Genome Sequencing Consortium.
  Initial sequencing and comparative analysis of the mouse genome.
  Nature. 2002 Dec 5;420(6915):520-62.

• Burns CG, Ohi R, Mehta S, O'Toole ET, Winey M, Clark TA, Sugnet CW, Ares M Jr, Gould KL.
  Removal of a single alpha-tubulin gene intron suppresses cell cycle arrest phenotypes of splicing factor mutations in Saccharomyces cerevisiae.
  Mol Cell Biol. 2002 Feb;22(3):801-15.

• Lewis MT, Ross S, Strickland PA, Sugnet CW, Jimenez E, Hui C, Daniel CW.
  The Gli2 transcription factor is required for normal mouse mammary gland development.
  Dev Biol. 2001 Oct 1;238(1):133-44.

• Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M Jr, Haussler D.
  Knowledge-based analysis of microarray gene expression data by using support vector machines.
  Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):262-7.

• Lewis MT, Ross S, Strickland PA, Sugnet CW, Jimenez E, Scott MP, Daniel CW.
  Defects in mouse mammary gland development caused by conditional haploinsufficiency of Patched-1.
  Development. 1999 Nov;126(22):5181-93.