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Publications

Journal of computational biology : a journal of computational molecular cell biology. 2005-06-01; 12.5: 497-513.
A tool for analyzing mate pairs in assemblies (TAMPA)
Dew IM, Walenz B, Sutton G
PMID: 15952874
Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 2005-05-20; 23.15: 3526-35.
Molecular staging for survival prediction of colorectal cancer patients
Eschrich S, Yang I, Bloom G, Kwong KY, Boulware D, Cantor A, Coppola D, Kruhøffer M, Aaltonen L, Orntoft TF, Quackenbush J, Yeatman TJ
PMID: 15908663
Proceedings of the National Academy of Sciences of the United States of America. 2005-05-17; 102.20: 7315-20.
Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella
Schmidt EW, Nelson JT, Rasko DA, Sudek S, Eisen JA, Haygood MG, Ravel J
PMID: 15883371
Bioinformatics (Oxford, England). 2005-05-01; 21.9: 1782-8.
Efficient implementation of a generalized pair hidden Markov model for comparative gene finding
Majoros WH, Pertea M, Salzberg SL
PMID: 15691859
Plant physiology. 2005-05-01; 138.1: 18-26.
The institute for genomic research Osa1 rice genome annotation database
Yuan Q, Ouyang S, Wang A, Zhu W, Maiti R, Lin H, Hamilton J, Haas B, Sultana R, Cheung F, Wortman J, Buell CR
PMID: 15888674
Applied and environmental microbiology. 2005-05-01; 71.5: 2530-8.
DNA microarray analysis of nitrogen fixation and Fe(III) reduction in Geobacter sulfurreducens
Methé BA, Webster J, Nevin K, Butler J, Lovley DR
PMID: 15870343
Nature methods. 2005-05-01; 2.5: 345-50.
Multiple-laboratory comparison of microarray platforms
Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martínez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W
PMID: 15846361
Medical mycology. 2005-05-01; 43 Suppl 1.S313-9.
The ergosterol biosynthesis pathway, transporter genes, and azole resistance in Aspergillus fumigatus
Ferreira ME, Colombo AL, Paulsen I, Ren Q, Wortman J, Huang J, Goldman MH, Goldman GH
PMID: 16110826
International journal of systematic and evolutionary microbiology. 2005-05-01; 55.Pt 3: 1021-6.
Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales
Badger JH, Eisen JA, Ward NL
PMID: 15879228
Nature methods. 2005-05-01; 2.5: 351-6.
Standardizing global gene expression analysis between laboratories and across platforms
Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, Bumgarner RE, Bushel PR, Chaturvedi K, Choi D, Cunningham ML, Deng S, Dressman HK, Fannin RD, Farin FM, Freedman JH, Fry RC, Harper A, Humble MC, Hurban P, Kavanagh TJ, Kaufmann WK, Kerr KF, Jing L, Lapidus JA, Lasarev MR, Li J, Li YJ, Lobenhofer EK, Lu X, Malek RL, Milton S, Nagalla SR, O'malley JP, Palmer VS, Pattee P, Paules RS, Perou CM, Phillips K, Qin LX, Qiu Y, Quigley SD, Rodland M, Rusyn I, Samson LD, Schwartz DA, Shi Y, Shin JL, Sieber SO, Slifer S, Speer MC, Spencer PS, Sproles DI, Swenberg JA, Suk WA, Sullivan RC, Tian R, Tennant RW, Todd SA, Tucker CJ, Van Houten B, Weis BK, Xuan S, Zarbl H, Members of the Toxicogenomics Research Consortium
PMID: 15846362