Articles on Coccolithophorids

Articles on EST

Articles on Microarray

Articles on Coccolithophorids

2006:

1.                  Michael J. Allen, Declan C. Schroeder, Matthew T. G. Holden, and William H. Wilson. Evolutionary History of the Coccolithoviridae. Mol. Biol. Evol. 23(1):86-92. 2006

2005:

2.                  M. Virginia Sanchez Puerta, Tsvetan R. Bachvaroff, and Charles F. Delwiche. The Complete Plastid Genome Sequence of the Haptophyte Emiliania huxleyi: a Comparison to Other Plastid Genomes. DNA Research 12, 151-156 (2005)

3.                  Binh Nguyen, Robert M. Bowers, Thomas M. Wahlund, and Betsy A. Read. Suppressive Subtractive Hybridization of and Differences in Gene Expression Content of Calcifying and Noncalcifying Cultures of Emiliania huxleyi Strain 1516. Applied and Environmental Microbiology, May 2005, p. 2564-2575.

4.                  M. J. Allen, D. C. Schroeder, and W. H.Wilson, Preliminary characterization of repeat families in the genome of EhV-86, a giant algal virus that infects the marine microalga Emiliania huxleyi. Arch Virol (2005). Published online September 30, 2005 _c Springer-Verlag 2005

5.                  Shenglan Li, Tetyana Nosenko, Jeremiah D. Hackett, Debashish Bhattacharya. Phylogenomic Analysis Identifies Red Algal Genes of Endosymbiotic Origin in the Chromalveolates. MBE Advance Access published December 15, 2005

6.                  Hirokawa Y, Fujiwara S, Tsuzuki M. Three Types of Acidic Polysaccharides Associated with Coccolith of Pleurochrysis haptonemofera: Comparison with Pleurochrysis carterae and Analysis Using Fluorescein-Isothiocyanate-Labeled Lectins. Mar Biotechnol (NY). 2005 Nov-Dec;7(6):634-644.

7.                  Sorrosa JM, Satoh M, Shiraiwa Y. Low temperature stimulates cell enlargement and intracellular calcification of coccolithophorids. Mar Biotechnol (NY). 2005 Mar-Apr;7(2):128-133

8.                  Engel, A. et al. Testing the direct effect of CO2 concentration on a bloom of the coccolithophorid Emiliania huxleyi in mesocosm experiments. Limnology and Oceanography 50, 493-507 (2005).

9.                  Dupont, C. L. & Ahner, B. A. Effects of copper, cadmium, and zinc on the production and exudation of thiols by Emiliania huxleyi. Limnology and Oceanography 50, 508-515 (2005).

10.              Michael Wyman, John T. Davies,  Sylvia Hodgson,  Glen A. Tarran,  and Duncan A. Purdie. Dynamics of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase Gene Expression in the Coccolithophorid Coccolithus pelagicus during a Tracer Release Experiment in the Northeast Atlantic. Applied and Environmental Microbiology,  Mar. 2005, p. 1659-1661

2004:

11.              Emi Miyamoto, Fumio Watanabe, Yuji Yamaguchi, Hiroyuki Takenaka, Yoshihisa Nakano. Purification and characterization of methylmalonyl-CoA mutase from a photosynthetic coccolithophorid alga, Pleurochrysis carterae. Comparative Biochemistry and Physiology, Part B 138 (2004) 163-167.

12.              Schulz KG, Zondervan I, Gerringa LJ, Timmermans KR, Veldhuis MJ, Riebesell U. Effect of trace metal availability on coccolithophorid calcification. Nature. 2004 Aug 5; 430(7000):673-676.

13.              Wahlund, T. M., Zhang, X. Y. & Read, B. A. Expressed sequence tag profiles from calcifying and non- calcifying cultures of Emiliania huxleyi. Micropaleontology 50, 145-155 (2004).

14.              Putland, J. N., Whitney, F. A. & Crawford, D. W. Survey of bottom-up controls of Emiliania huxleyi in the Northeast Subarctic Pacific. Deep-Sea Research Part I-Oceanographic Research Papers 51, 1793-1802 (2004).

15.              Merico, A. et al. Modelling phytoplankton succession on the Bering Sea shelf: role of climate influences and trophic interactions in generating Emiliania huxleyi blooms 1997-2000. Deep-Sea Research Part I-Oceanographic Research Papers 51, 1803-1826 (2004).

16.              Herfort, L., Loste, E., Meldrum, F. & Thake, B. Structural and physiological effects of calcium and magnesium in Emiliania huxleyi (Lohmann) Hay and Mohler. Journal of Structural Biology 148, 307-314 (2004).

17.              Obata, T., Araie, H. & Shiraiwa, Y. Bioconcentration mechanism of selenium by a coccolithophorid, Emiliania huxleyi. Plant and Cell Physiology 45, 1434-1441 (2004).

18.              Dupont, C. L., Nelson, R. K., Bashir, S., Moffett, J. W. & Ahner, B. A. Novel copper-binding and nitrogen-rich thiols produced and exuded by Emiliania huxleyi. Limnology and Oceanography 49, 1754-1762 (2004).

19.              Vasconcelos, M., Lopez-Ruiz, J. L., Garcia, A., Leal, M. F. C. & Fachini, A. Effect of zeolites on cultures of the marine micro-algae Emiliania huxleyi. Aquacultural Engineering 31, 205-219 (2004).

20.              Crudeli, D. et al. Abnormal carbonate diagenesis in Holocene-late Pleistocene sapropel-associated sediments from the Eastern Mediterranean; evidence from Emiliania huxleyi coccolith morphology. Marine Micropaleontology 52, 217-240 (2004).

21.              Fachini, A., Leal, M. F. C. & Vasconcelos, M. Are zeolites capable of modifying the yield of marine micro- algae cultures? A case study with Emiliania huxleyi and a product of zeolitic nature. Aquaculture 237, 407-419 (2004).

22.              Wahlund, T. M. et al. Analysis of expressed sequence tags from calcifying cells of marine coccolithophorid (Emiliania huxleyi). Marine Biotechnology 6, 278-290 (2004).

23.              Sawada, K. & Shiraiwa, Y. Alkenone and alkenoic acid compositions of the membrane fractions of Emiliania huxleyi. Phytochemistry 65, 1299-1307 (2004).

24.              Denis, M. et al. Effect of elevated PCO2 on optical properties of the coccolithophorid Emiliania huxleyi grown under nitrate limitation. Cytometry Part A 59A, 105-105 (2004).

25.              Puerta, M. V. S., Bachvaroff, T. R. & Delwiche, C. F. The complete mitochondrial genome sequence of the haptophyte Emiliania huxleyi and its relation to heterokonts. DNA Research 11, 1-10 (2004).

26.              Puerta, M. V. S., Bachvaroff, T. R. & Delwiche, C. F. The complete mitochondrial genome sequence of the haptophyte Emiliania huxleyi and its relation to heterokonts (Supplement). DNA Research 11, 67-68 (2004).

27.              Obata, T. & Shiraiwa, Y. Identification of a novel selenoprotein in a coccolithophorid, Emiliania huxleyi. Plant and Cell Physiology 45, S141-S141 (2004).

28.              Engel, A. et al. Transparent exopolymer particles and dissolved organic carbon production by Emiliania huxleyi exposed to different CO2 concentrations: a mesocosm experiment. Aquatic Microbial Ecology 34, 93-104 (2004).

29.              Virginia Sanchez Puerta, Tsvetan Bachvaroff, and Charles Delwiche. The Complete Mitochondrial Genome Sequence of the Haptophyte Emiliania huxleyi and its relation to Heterokontos. DNA Research 11, page 1- 10, 2004

30.              Toshihiro Obata, Hiroya Araie and Yoshihiro Shiraiwa. Bioconcentration Mechanism of Selenium by a Coccolithophorid, Emiliania Huxleyi. Plant Cell Physiol. 45(10): 1434-1441 (2004)

2003:

31.              Yoshihiro Shiraiwa. Physiological regulation of carbon fixation in the photosynthesis and calcification of Coccolithophorids. Comparative Biochemistry and Physiology Part B 136 (2003) 775-783.

32.              Tchernov D, Silverman J, Luz B, Reinhold L, Kaplan A. Massive light-dependent cycling of inorganic carbon between oxygenic photosynthetic microorganisms and their surroundings. Photosynth Res. 2003;77(2-3):95-103.

33.              Sciandra, A. et al. Response of coccolithophorid Emiliania huxleyi to elevated partial pressure of CO2 under nitrogen limitation. Marine Ecology-Progress Series 261, 111-122 (2003).

34.              Dyhrman, S. T. & Palenik, B. Characterization of ectoenzyme activity and phosphate-regulated proteins in the coccolithophorid Emiliania huxleyi. Journal of Plankton Research 25, 1215-1225 (2003).

35.              Obata, T., Araie, H. & Shiraiwa, Y. Kinetic studies on bioconcentration mechanism of selenium by a coccolithophorid, Emiliania huxleyi. Plant and Cell Physiology 44, S43-S43 (2003).

36.              Buitenhuis, E. T., Timmermans, K. R. & de Baar, H. J. W. Zinc-bicarbonate colimitation of Emiliania huxleyi. Limnology and Oceanography 48, 1575-1582 (2003).

37.              Merico, A., Tyrrell, T., Brown, C. W., Groom, S. B. & Miller, P. I. Analysis of satellite imagery for Emiliania huxleyi blooms in the Bering Sea before 1997. Geophysical Research Letters 30, art. no.-1337 (2003).

38.              Schroeder, D. C., Oke, J., Hall, M., Malin, G. & Wilson, W. H. Virus succession observed during an Emiliania huxleyi bloom. Applied and Environmental Microbiology 69, 2484-2490 (2003).

39.              Harada, N., Shin, K. H., Murata, A., Uchida, M. & Nakatani, T. Characteristics of alkenones synthesized by a bloom of Emiliania huxleyi in the Bering Sea. Geochimica Et Cosmochimica Acta 67, 1507-1519 (2003).

40.              Strom, S. et al. Chemical defense in the microplankton I: Feeding and growth rates of heterotrophic protists on the DMS-producing phytoplankter Emiliania huxleyi. Limnology and Oceanography 48, 217-229 (2003).

41.              Herfort, L., Thake, B. & Roberts, J. Acquisition and use of bicarbonate by Emiliania huxleyi (vol 156, pg 427, 2002). New Phytologist 158, 225-225 (2003).

42.              Iwamoto, K. & Shiraiwa, Y. Characterization of NADH : nitrate reductase from the coccolithophorid Emiliania huxleyi (Lohman) Hay & Mohler (Haptophyceae). Marine Biotechnology 5, 20-26 (2003).

43.              Slezak, D. & Herndl, G. J. Effects of ultraviolet and visible radiation on the cellular concentrations of dimethylsulfoniopropionate (DMSP) in Emiliania huxleyi (strain L). Marine Ecology-Progress Series 246, 61-71 (2003).

44.              Alberto Saez, ian Probert, Markus Geisen, Patrick Quinn, Jeremy Young, and Linda Medlin. Psedudo-cryptic Speciation in Coccolithophores, Woods Hole Oceanographic Institute, Woods Hole, MA, April 19, 2003

45.              Declan C. Schroeder, Joanne Oke,1 Matthew Hall, Gillian Malin, and William H. Wilson. Virus Succession Observed during an Emiliania huxleyi Bloom Applied and Environmental Microbiology, May 2003, p. 2484-2490

2002:

46.              Emi Miyamoto, Fumio Watanabe, Hiroyuki Takenaka, and Yoshihisa Nakano. Uptake and Physiological Function of Vitamin B12 in a Photosynthetic Unicellular Coccolithopgorid alge, Pleurochrysis cartera. Biosci Biotechnol, Biochem., 65 (1), 195-198, 2002.

47.              Heather Stroll, Patricia Ziveri, Markus Geisen, Ian Probert, and Jeremy Young. Potential and Limitations of Sr/Ca rations in Coccolith carbonate: New Perspectives from Cultures and Monospecific Samples from Sediments, The Royal Society. Published online on March 18, 2002.

48.              Takahashi J, Fujiwara S, Kikyo M, Hirokawa Y, Tsuzuki M. Discrimination of the cell surface of the coccolithophorid Pleurochrysis haptonemofera from light scattering and fluorescence after fluorescein-isothiocyanate-labeled lectin staining measured by flow cytometry. Mar Biotechnol (NY). 2002 Jan;4(1):94-101.

49.              Smyth TJ, Moore GF, Groom SB, Land PE, Tyrrell T. Optical modeling and measurements of a coccolithophore bloom. Appl Opt. 2002 Dec 20;41(36):7679

50.              Iglesias-Rodriguez, M. D. et al. Polymorphic microsatellite loci in global populations of the marine coccolithophorid Emiliania huxleyi. Molecular Ecology Notes 2, 495-497 (2002).

51.              Olson, M. B. & Strom, S. L. Phytoplankton growth, microzooplankton herbivory and community structure in the southeast Bering Sea: insight into the formation and temporal persistence of an Emiliania huxleyi bloom. Deep-Sea Research Part Ii-Topical Studies in Oceanography 49, 5969-5990 (2002).

52.              Herfort, L., Thake, B. & Roberts, J. Acquisition and use of bicarbonate by Emiliania huxleyi. New Phytologist 156, 427-436 (2002).

53.              Colmenero-Hidalgo, E., Flores, J. A. & Sierro, F. J. Biometry of Emiliania huxleyi and its biostratigraphic significance in the Eastern North Atlantic Ocean and Western Mediterranean Sea in the last 20 000 years. Marine Micropaleontology 46, 247-263 (2002).

54.              Shin, K. H., Tanaka, N., Harada, N. & Marty, J. C. Production and turnover rates of C-37 alkenones in the eastern Bering Sea: implication for the mechanism of a long duration of Emiliania huxleyi bloom. Progress in Oceanography 55, 113-129 (2002).

55.              Rickaby, R. E. M., Schrag, D. P., Zondervan, I. & Riebesell, U. Growth rate dependence of Sr incorporation during calcification of Emiliania huxleyi. Global Biogeochemical Cycles 16, art. no.-1006 (2002).

56.              Van Rijssel, M. & Gieskes, W. W. C. Temperature, light, and the dimethylsulfoniopropionate (DMSP) content of Emiliania huxleyi (Prymnesiophyceae). Journal of Sea Research 48, 17-27 (2002).

57.              Schroeder, D. C., Oke, J., Malin, G. & Wilson, W. H. Coccolithovirus (Phycodnaviridae): Characterisation of a new large dsDNA algal virus that infects Emiliania huxleyi. Archives of Virology 147, 1685-1698 (2002).

58.              Castberg, T. et al. Isolation and characterization of a virus that infects Emiliania huxleyi (Haptophyta). Journal of Phycology 38, 767-774 (2002).

59.              Van Rijssel, M. & Buma, A. G. J. UV radiation induced stress does not affect DMSP synthesis in the marine prymnesiophyte Emiliania huxleyi. Aquatic Microbial Ecology 28, 167-174 (2002).

60.              Fileman, E. S., Cummings, D. G. & Llewllyn, C. A. Microplankton community structure and the impact of microzooplankton grazing during an Emiliania huxleyi bloom, off the Devon coast. Journal of the Marine Biological Association of the United Kingdom 82, 359-368 (2002).

61.              Wilson, W. H. et al. Isolation of viruses responsible for the demise of an Emiliania huxleyi bloom in the English Channel. Journal of the Marine Biological Association of the United Kingdom 82, 369-377 (2002).

62.              Lampert, L., Queguiner, B., Labasque, T., Pichon, A. & Lebreton, N. Spatial variability of phytoplankton composition and biomass on the eastern continental shelf of the Bay of Biscay (north-east Atlantic Ocean). Evidence for a bloom of Emiliania huxleyi (Prymnesiophyceae) in spring 1998. Continental Shelf Research 22, 1225-1247 (2002).

63.              Zondervan, I., Rost, B. & Riebesell, U. Effect of CO2 concentration on the PIC/POC ratio in the coccolithophore Emiliania huxleyi grown under light-limiting conditions and different daylengths. Journal of Experimental Marine Biology and Ecology 272, 55-70 (2002).

64.              Stoll, H. M., Rosenthal, Y. & Falkowski, P. Climate proxies from Sr/Ca of coccolith calcite: Calibrations from continuous culture of Emiliania huxleyi. Geochimica Et Cosmochimica Acta 66, 927-936 (2002).

65.              Vasconcelos, M., Leal, M. F. C. & van den Berg, C. M. G. Influence of the nature of the exudates released by different marine algae on the growth, trace metal uptake, and exudation of Emiliania huxleyi in natural seawater. Marine Chemistry 77, 187-210 (2002).

66.              Paasche, E. A review of the coccolithophorid Emiliania huxleyi (Prymnesiophyceae), with particular reference to growth, coccolith formation, and calcification-photosynthesis interactions. Phycologia 40, 503-529 (2001).

67.              Rost, B., Zondervan, I. & Riebesell, U. Light-dependent carbon isotope fractionation in the coccolithophorid Emiliania huxleyi. Limnology and Oceanography 47, 120-128 (2002).

2001:

68.              Noriaki Ozaki, Shohei Sakuda, and Hiromichi Nagasawa, Isolation and Some Characterization of an Acidic Polysaccharide with Anti-calcification Activity from Coccoliths if a Marine Alga, Pleurochrysis carterae, Biosci Biotechnol, Biochem., 65 (10), 2330-2333, 2001.

69.              Richard Laguna, Jesus Roma, betsy Read A. and Thomas Wahlund. Induction of Phase variation Events in the Life Cycle of the Marine Coccolithophorid Emiliania Huxley. Applied and Environmental Microbiology Sept 2001 p. 3824-3831.

70.              Emi Miyamoto, Fumio Watanabe,  Syuhei Ebara, Shigeo Takenaka, Hiroyuki Takenaka, Yuji Yamaguchi, Norihide Tanaka, Hiroshi Inui, and Yoshihisa Nakano. Characterization of a Vitamin B12 Compound from Unicellular Coccolithophorid Alga (Pleurochrysis carterae). J. Agric. Food Chem. 2001, 49, 3486-3489.

71.              Heldal HE, Stupakoff I, Fisher NS. Bioaccumulation of 137Cs and 57Co by five marine phytoplankton species. J Environ Radioact. 2001;57(3):231-236.

72.              Cokacar, T., Kubilay, N. & Oguz, T. Structure of Emiliania huxleyi blooms in the Black Sea surface waters as detected by SeaWIFS imagery. Geophysical Research Letters 28, 4607-4610 (2001).

73.              Castberg, T. et al. Microbial population dynamics and diversity during a bloom of the marine coccolithophorid Emiliania huxleyi (Haptophyta). Marine Ecology-Progress Series 221, 39-46 (2001).

74.              Buitenhuis, E. T., van der Wal, P. & de Baar, H. J. W. Blooms of Emiliania huxleyi are sinks of atmospheric carbon dioxide: A field and mesocosm study derived simulation. Global Biogeochemical Cycles 15, 577-587 (2001).

75.              Laguna, R., Romo, J., Read, B. A. & Wahlund, T. M. Induction of phase variation events in the life cycle of the marine coccolithophorid Emiliania huxleyi. Applied and Environmental Microbiology 67, 3824-3831 (2001).

76.              Gordon, H. R. & Du, T. Light scattering by nonspherical particles: Application to coccoliths detached from Emiliania huxleyi. Limnology and Oceanography 46, 1438-1454 (2001).

77.              Epstein, B. L., D'Hondt, S. & Hargraves, P. E. The possible metabolic role of C-37 alkenones in Emiliania huxleyi. Organic Geochemistry 32, 867-875 (2001).

78.              Vasconcelos, M. & Leal, M. F. C. Antagonistic interactions of Ph and Cd on Cu uptake, growth inhibition and chelator release in the marine algae Emiliania huxleyi. Marine Chemistry 75, 123-139 (2001).

79.              Timmermans, K. R., Snoek, J., Gerringa, L. J. A., Zondervan, I. & de Baar, H. J. W. Not all eukaryotic algae can replace zinc with cobalt: Chaetoceros calcitrans (Bacillariophyceae) versus Emiliania huxleyi (Prymnesiophyceae). Limnology and Oceanography 46, 699-703 (2001).

80.              Mouzdahir, A., Grossi, V., Bakkas, S. & Rontani, J. F. Visible light-dependent degradation of long-chain alkenes in killed cells of Emiliania huxleyi and Nannochloropsis salina. Phytochemistry 56, 677-684 (2001).

81.              Vasconcelos, M. & Leal, M. F. C. Adsorption and uptake of Cu by Emiliania huxleyi in natural seawater. Environmental Science & Technology 35, 508-515 (2001).

2000:

82.              S.B. Gulin. Recent changes of biogenic carbonate deposition in anoxic sediments of the Black Sea: sedimentary record and climatic implication Marine Environmental Research 49 (2000) 319-328.

83.              Vincent Grossia, Danielle Raphela, Claude Aubertb, Jean-Francois Rontani. The effect of growth temperature on the long-chain alkenes composition in the marine coccolithophorid Emiliania huxleyi. Phytochemistry 54 (2000) 393-399.

84.              Riebesell, U., Revill, A. T., Holdsworth, D. G. & Volkman, J. K. The effects of varying CO2 concentration on lipid composition and carbon isotope fractionation in Emiliania huxleyi. Geochimica Et Cosmochimica Acta 64, 4179-4192 (2000).

85.              Yamamoto, M., Shiraiwa, Y. & Inouye, I. Physiological responses of lipids in Emiliania huxleyi and Gephyrocapsa oceanica (Haptophyceae) to growth status and their implications for alkenone paleothermometry. Organic Geochemistry 31, 799-811 (2000).

86.              Wu, Q. Y., Shiraiwa, Y., Takeda, H., Sheng, G. Y. & Fu, J. M. Liquid-saturated hydrocarbons resulting from pyrolysis of the marine coccolithophores Emiliania huxleyi and Gephyrocapsa oceanica. Marine Biotechnology 1, 346-352 (1999).

87.              Boye, M. & van den Berg, C. M. G. Iron availability and the release of iron-complexing ligands by Emiliania huxleyi. Marine Chemistry 70, 277-287 (2000).

88.              Grossi, V., Raphel, D., Aubert, C. & Rontani, J. F. The effect of growth temperature on the long-chain alkenes composition in the marine coccolithophorid Emiliania huxleyi. Phytochemistry 54, 393-399 (2000).

89.              Jeffrey, S. W. & Anderson, J. M. Emiliania huxleyi (Haptophyta) holds promising insights for photosynthesis. Journal of Phycology 36, 449-452 (2000).

90.              Garrido, J. L., Otero, J., Maestro, M. A. & Zapata, M. The main nonpolar chlorophyll c from Emiliania huxleyi (Prymnesiophyceae) is a chlorophyll c(2)- monogalactosyldiacylglyceride ester: a mass spectrometry study. Journal of Phycology 36, 497-505 (2000).

91.              Stolte, W., Kraay, G. W., Noordeloos, A. A. M. & Riegman, R. Genetic and physiological variation in pigment composition of Emiliania huxleyi (Prymnesiophyceae) and the potential use of its pigment ratios as a quantitative physiological marker. Journal of Phycology 36, 529-539 (2000).

92.              Buma, A. G. J., van Oijen, T., van de Poll, W., Veldhuis, M. J. W. & Gieskes, W. W. C. The sensitivity of Emiliania huxleyi (Prymnesiophycea) to ultraviolet-B radiation. Journal of Phycology 36, 296-303 (2000).

93.              Garde, K. & Cailliau, C. The impact of UV-B radiation and different PAR intensities on growth, uptake of C-14, excretion of DOC, cell volume, and pigmentation in the marine prymnesiophyte, Emiliania huxleyi. Journal of Experimental Marine Biology and Ecology 247, 99-112 (2000).

94.              Riegman, R., Stolte, W., Noordeloos, A. A. M. & Slezak, D. Nutrient uptake, and alkaline phosphate (EC 3 : 1 : 3 : 1) activity of Emiliania huxleyi (Prymnesiophyceae) during growth under N and P limitation in continuous cultures. Journal of Phycology 36, 87-96 (2000).

 Before 2000:

95.              Paasche, E. Reduced coccolith calcite production under light-limited growth: a comparative study of three clones of Emiliania huxleyi (Prymnesiophyceae). Phycologia 38, 508-516 (1999).

96.              Buitenhuis, E. T., de Baar, H. J. W. & Veldhuis, M. J. W. Photosynthesis and calcification by Emiliania huxleyi (Prymnesiophyceae) as a function of inorganic carbon species. Journal of Phycology 35, 949-959 (1999).

97.              Leal, M. F. C., Vasconcelos, M. & van den Berg, C. M. G. Copper-induced release of complexing ligands similar to thiols by Emiliania huxleyi in seawater cultures. Limnology and Oceanography 44, 1750-1762 (1999).

98.              Varela, D. E. & Harrison, P. J. Effect of ammonium on nitrate utilization by Emiliania huxleyi, a coccolithophore from the oceanic northeastern Pacific. Marine Ecology-Progress Series 186, 67-74 (1999).

99.              Danbara, A. & Shiraiwa, Y. The requirement of selenium for the growth of marine coccolithophorids, Emiliania huxleyi, Gephyrocapsa oceanica and Helladosphaera sp (Prymnesiophyceae). Plant and Cell Physiology 40, 762-766 (1999).

100.          Wu, Q. Y., Dai, J. B., Shiraiwa, Y., Sheng, G. Y. & Fu, J. M. A renewable energy source - hydrocarbon gases resulting from pyrolysis of the marine nanoplanktonic alga Emiliania huxleyi. Journal of Applied Phycology 11, 137-142 (1999).

101.          Fritz, J. J. Carbon fixation and coccolith detachment in the coccolithophore Emiliania huxleyi in nitrate-limited cyclostats. Marine Biology 133, 509-518 (1999).

102.          Page, S., Hipkin, C. R. & Flynn, K. J. Interactions between nitrate and ammonium in Emiliania huxleyi. Journal of Experimental Marine Biology and Ecology 236, 307-319 (1999).

103.          Wu, Q. Y. & Shiraiwa, Y. Effects of HCO3- on surface calcification and CO2 fixation in marine Emiliania huxleyi. Acta Botanica Sinica 41, 285-289 (1999).

104.          Flynn, K. J., Page, S., Wood, G. & Hipkin, C. R. Variations in the maximum transport rates for ammonium and nitrate in the prymnesiophyte Emiliania huxleyi and the raphidophyte Heterosigma carterae. Journal of Plankton Research 21, 355-371 (1999).

105.          Steinke, M., Wolfe, G. V. & Kirst, G. O. Partial characterisation of dimethylsulfoniopropionate (DMSP) lyase isozymes in 6 strains of Emiliania huxleyi. Marine Ecology-Progress Series 175, 215-225 (1998).

106.          Teece, M. A., Getliff, J. M., Leftley, J. W., Parkes, R. J. & Maxwell, J. R. Microbial degradation of the marine prymnesiophyte Emiliania huxleyi under oxic and anoxic conditions as a model for early diagenesis: long chain alkadienes, alkenones and alkyl alkenoates. Organic Geochemistry 29, 863-880 (1998).

107.          Voss, K. J., Balch, W. M. & Kilpatrick, K. A. Scattering and attenuation properties of Emiliania huxleyi cells and their detached coccoliths. Limnology and Oceanography 43, 870-876 (1998).

108.          Rieley, G. & Campbell, C. Long-chain alkenes of the haptophytes Isochrysis galbana and Emiliania huxleyi (vol 33, pg 617, 1998). Lipids 33, 949-949 (1998).

109.          Corstjens, P. et al. GPA, a calcium-binding protein in the coccolithophorid Emiliania huxleyi (Prymnesiophyceae). Journal of Phycology 34, 622-630 (1998).

110.          Green, J. C., Heimdal, B. R., Paasche, E. & Moate, R. Changes in calcification and the dimensions of coccoliths of Emiliania huxleyi (Haptophyta) grown at reduced salinities. Phycologia 37, 121-131 (1998).

111.          Head, R. N. et al. The hydrography and biology of a bloom of the coccolithophorid Emiliania huxleyi in the northern North Sea. Journal of Sea Research 39, 255-266 (1998).

112.          Rieley, G. et al. Long-chain alkenes of the haptophytes Isochrysis galbana and Emiliania huxleyi. Lipids 33, 617-625 (1998).

113.          Laws, E. A., Thompson, P. A., Popp, B. N. & Bidigare, R. R. Sources of inorganic carbon for marine microalgal photosynthesis: A reassessment of delta C-13 data from batch culture studies of Thalassiosira pseudonana and Emiliania huxleyi. Limnology and Oceanography 43, 136-142 (1998).

114.          Paasche, E. Roles of nitrogen and phosphorus in coccolith formation in Emiliania huxleyi (Prymnesiophyceae). European Journal of Phycology 33, 33-42 (1998).

115.          Palenik, B. & Henson, S. E. The use of amides and other organic nitrogen sources by the phytoplankton Emiliania huxleyi. Limnology and Oceanography 42, 1544-1551 (1997).

116.          Maurin-Defossez, C. & Le Gal, Y. Diel periodicity of glutamine synthetase activity during the cell cycle of Emiliania huxleyi. Plant Physiology and Biochemistry 36, 233-236 (1998).

117.          Garrido, J. L. & Zapata, M. Detection of new pigments from Emiliania huxleyi (Prymnesiophyceae) by high-performance liquid chromatography, liquid chromatography-mass spectrometry, visible spectroscopy, and fast atom bombardment mass spectrometry. Journal of Phycology 34, 70-78 (1998).

118.          Conte, M. H., Thompson, A., Lesley, D. & Harris, R. P. Genetic and physiological influences on the alkenone/alkenoate versus growth temperature relationship in Emiliania huxleyi and Gephyrocapsa oceanica. Geochimica Et Cosmochimica Acta 62, 51-68 (1998).

119.          Sanders, R. & Purdie, D. A. Bacterial response to blooms dominated by diatoms and Emiliania huxleyi in nutrient-enriched mesocosms. Estuarine Coastal and Shelf Science 46, 35-48 (1998).

120.          Popp, B. N., Kenig, F., Wakeham, S. G., Laws, E. A. & Bidigare, R. R. Does growth rate affect ketone unsaturation and intracellular carbon isotopic variability in Emiliania huxleyi? Paleoceanography 13, 35-41 (1998).

121.          Maurin, C. & Le Gal, Y. Isoforms of glutamine synthetase in the marine coccolithophorid Emiliania huxleyi (Prymnesiophyceae). Comparative Biochemistry and Physiology B-Biochemistry & Molecular Biology 118, 903-912 (1997).

122.          Maranon, E. & Gonzalez, N. Primary production, calcification and macromolecular synthesis in a bloom of the coccolithophore Emiliania huxleyi in the North Sea. Marine Ecology-Progress Series 157, 61-77 (1997).

123.          Nielsen, M. V. Growth, dark respiration and photosynthetic parameters of the coccolithophorid Emiliania huxleyi (Prymnesiophyceae) acclimated to different day length-irradiance combinations. Journal of Phycology 33, 818-822 (1997).

124.          Rontani, J. F., Cuny, P., Grossi, V. & Beker, B. Stability of long-chain alkenones in senescing cells of Emiliania huxleyi: effect of photochemical and aerobic microbial degradation on the alkenone unsaturation ratio (U- 37(k')). Organic Geochemistry 26, 503-509 (1997).

125.          Crawford, D. W. & Purdie, D. A. Increase of PCO2 during blooms of Emiliania huxleyi: Theoretical considerations on the asymmetry between acquisition of HCO3- and respiration of free CO2. Limnology and Oceanography 42, 365-372 (1997).

126.          Batvik, H., Heimdal, B. R., Fagerbakke, K. M. & Green, J. C. Effects of unbalanced nutrient regime on coccolith morphology and size in Emiliania huxleyi (Prymnesiophyceae). European Journal of Phycology 32, 155-165 (1997).

127.          Nejstgaard, J. C., Gismervik, I. & Solberg, P. T. Feeding and reproduction by Calanus finmarchicus, and microzooplankton grazing during mesocosm blooms of diatoms and the coccolithophore Emiliania huxleyi. Marine Ecology-Progress Series 147, 197-217 (1997).

128.          Maurin, C. & LeGal, Y. Glutamine synthetase in the marine coccolithophorid Emiliania huxleyi (Prymnesiophyceae): Regulation of activity in relation to light and nitrogen availability. Plant Science 122, 61-69 (1997).

129.          Fernandez, E., Maranon, E., Harbour, D. S., Kristiansen, S. & Heimdal, B. R. Patterns of carbon and nitrogen uptake during blooms of Emiliania huxleyi in two Norwegian fjords. Journal of Plankton Research 18, 2349-2366 (1996).

130.          Wolfe, G. V. & Steinke, M. Grazing-activated production of dimethyl sulfide (DMS) by two clones of Emiliania huxleyi. Limnology and Oceanography 41, 1151-1160 (1996).

131.          Fritz, J. J. & Balch, W. M. A light-limited continuous culture study of Emiliania huxleyi: Determination of coccolith detachment and its relevance to cell sinking. Journal of Experimental Marine Biology and Ecology 207, 127-147 (1996).

132.          Fernandez, E., Fritz, J. J. & Balch, W. M. Chemical composition of the coccolithophorid Emiliania huxleyi under light-limited steady state growth. Journal of Experimental Marine Biology and Ecology 207, 149-160 (1996).

133.          Sawada, K., Handa, N., Shiraiwa, Y., Danbara, A. & Montani, S. Long-chain alkenones and alkyl alkenoates in the coastal and pelagic sediments of the northwest North Pacific, with special reference to the reconstruction of Emiliania huxleyi and Gephyrocapsa oceanica ratios. Organic Geochemistry 24, 751-764 (1996).

134.          Buitenhuis, E., vanBleijswijk, J., Bakker, D. & Veldhuis, M. Trends in inorganic and organic carbon in a bloom of Emiliania huxleyi in the North Sea. Marine Ecology-Progress Series 143, 271-282 (1996).

135.          GarciaSoto, C., Sinha, B. & Pingree, R. D. Mapping a bloom of the coccolithophorid Emiliania huxleyi from airborne thematic mapper (ATM) data. Journal of the Marine Biological Association of the United Kingdom 76, 839-849 (1996).

136.          Balch, W. M., Fritz, J. & Fernandez, E. Decoupling of calcification and photosynthesis in the coccolithophore Emiliania huxleyi under steady-state light- limited growth. Marine Ecology-Progress Series 142, 87-97 (1996).

137.          Levasseur, M. et al. Production of DMSP and DMS during a mesocosm study of an Emiliania huxleyi bloom: Influence of bacteria and Calanus finmarchicus grazing. Marine Biology 126, 609-618 (1996).

138.          Sekino, K. & Shiraiwa, Y. Evidence for the involvement of mitochondrial respiration in calcification in a marine coccolithophorid, Emiliania huxleyi. Plant and Cell Physiology 37, 1030-1033 (1996).

139.          Nimer, N. A., Merrett, M. J. & Brownlee, C. Inorganic carbon transport in relation to culture age and inorganic carbon concentration in a high-calcifying strain of Emiliania huxleyi (Prymnesiophyceae). Journal of Phycology 32, 813-818 (1996).

140.          Harris, R. P. Coccolithophorid dynamics: The European Emiliania huxleyi programme, EHUX. Journal of Marine Systems 9, 1-11 (1996).

141.          Medlin, L. K. et al. Genetic characterisation of Emiliania huxleyi (Haptophyta). Journal of Marine Systems 9, 13-31 (1996).

142.          Green, J. C., Course, P. A. & Tarran, G. A. The life-cycle of Emiliania huxleyi: A brief review and a study of relative ploidy levels analysed by flow cytometry. Journal of Marine Systems 9, 33-44 (1996).

143.          Fernandez, E., Maranon, E. & Balch, W. M. Intracellular carbon partitioning in the coccolithophorid Emiliania huxleyi. Journal of Marine Systems 9, 57-66 (1996).

144.          Nanninga, H. J., Ringenaldus, P. & Westbroek, P. Immunological quantitation of a polysaccharide formed by Emiliania huxleyi. Journal of Marine Systems 9, 67-74 (1996).

145.          Bratbak, G., Wilson, W. & Heldal, M. Viral control of Emiliania huxleyi blooms? Journal of Marine Systems 9, 75-81 (1996).

146.          Tyrrell, T. & Taylor, A. H. A modelling study of Emiliania huxleyi in the NE Atlantic. Journal of Marine Systems 9, 83-112 (1996).

147.          Pond, D. W. & Harris, R. P. The lipid composition of the coccolithophore Emiliania huxleyi and its possible ecophysiological significance. Journal of the Marine Biological Association of the United Kingdom 76, 579-594 (1996).

148.          Nimer, N. A. & Merrett, M. J. The development of a CO2-concentrating mechanism in Emiliania huxleyi. New Phytologist 133, 383-389 (1996).

149.          Hansen, F. C., Witte, H. J. & Passarge, J. Grazing in the heterotrophic dinoflagellate Oxyrrhis marina: Size selectivity and preference for calcified Emiliania huxleyi cells. Aquatic Microbial Ecology 10, 307-313 (1996).

150.          Nanninga, H. J. & Tyrrell, T. Importance of light for the formation of algal blooms by Emiliania huxleyi. Marine Ecology-Progress Series 136, 195-203 (1996).

151.          Brussaard, C. P. D., Kempers, R. S., Kop, A. J., Riegman, R. & Heldal, M. Virus-like particles in a summer bloom of Emiliania huxleyi in the North Sea. Aquatic Microbial Ecology 10, 105-113 (1996).

152.          Sekino, K., Kobayashi, H. & Shiraiwa, Y. Role of coccoliths in the utilization of inorganic carbon by a marine unicellular coccolithophorid, Emiliania huxleyi: A survey using intact cells and protoplasts. Plant and Cell Physiology 37, 123-127 (1996).

153.          Maranon, E., Fernandez, E., Harris, R. P. & Harbour, D. S. Effects of the diatom-Emiliania huxleyi succession on photosynthesis, calcification and carbon metabolism by size- fractionated phytoplankton. Hydrobiologia 317, 189-199 (1996).

154.          Lecourt, M., Muggli, D. L. & Harrison, P. J. Comparison of growth and sinking rates of non-coccolith- and coccolith-forming strains of Emiliania huxleyi (Prymnesiophyceae) grown under different irradiances and nitrogen sources. Journal of Phycology 32, 17-21 (1996).

155.          Muggli, D. L. & Harrison, P. J. Effects of nitrogen source on the physiology and metal nutrition of Emiliania huxleyi grown under different iron and light conditions. Marine Ecology-Progress Series 130, 255-267 (1996).

156.          Bell, M. V. & Pond, D. Lipid composition during growth of motile and coccolith forms of Emiliania huxleyi. Phytochemistry 41, 465-471 (1996).

157.          Davis, S. A., Young, J. R. & Mann, S. Electron microscopy studies of shield elements of Emiliania huxleyi coccoliths. Botanica Marina 38, 493-497 (1995).

158.          Bratbak, G. et al. Viral activity in relation to Emiliania huxleyi blooms: A mechanism of DMSP release? Marine Ecology-Progress Series 128, 133-142 (1995).

159.          Rhodes, L. L., Peake, B. M., Mackenzie, A. L. & Marwick, S. Coccolithophores Gephyrocapsa-Oceanica and Emiliania-Huxleyi (Prymnesiophyceae Equals Haptophyceae) in New-Zealand Coastal Waters - Characteristics of Blooms and Growth in Laboratory Culture. New Zealand Journal of Marine and Freshwater Research 29, 345-357 (1995).

160.          Tyrrell, T. & Taylor, A. H. Latitudinal and Seasonal-Variations in Carbon-Dioxide and Oxygen in the Northeast Atlantic and the Effects on Emiliania- Huxleyi and Other Phytoplankton. Global Biogeochemical Cycles 9, 585-604 (1995).

161.          Nielsen, M. V. Photosynthetic Characteristics of the Coccolithophorid Emiliania-Huxleyi (Prymnesiophyceae) Exposed to Elevated Concentrations of Dissolved Inorganic Carbon. Journal of Phycology 31, 715-719 (1995).

162.          Garrido, J. L., Zapata, M. & Muniz, S. Spectral Characterization of New Chlorophyll-C Pigments Isolated from Emiliania-Huxleyi (Prymnesiophyceae) by High- Performance Liquid-Chromatography. Journal of Phycology 31, 761-768 (1995).

163.          Vanderwal, P., Kempers, R. S. & Veldhuis, M. J. W. Production and Downward Flux of Organic-Matter and Calcite in a North-Sea Bloom of the Coccolithophore Emiliania-Huxleyi. Marine Ecology-Progress Series 126, 247-265 (1995).

164.          Gayoso, A. M. Bloom of Emiliania-Huxleyi (Prymnesiophyceae) in Western South- Atlantic Ocean. Journal of Plankton Research 17, 1717-1722 (1995).

165.          Thompson, P. A. & Calvert, S. E. Carbon-Isotope Fractionation by Emiliania-Huxleyi. Limnology and Oceanography 40, 673-679 (1995).

166.          Takano, H. et al. Increased Coccolith Production by Emiliania-Huxleyi Cultures Enriched with Dissolved Inorganic Carbon. Applied Microbiology and Biotechnology 43, 460-465 (1995).

167.          Vanbleijswijk, J. D. L. & Veldhuis, M. J. W. In-Situ Gross Growth-Rates of Emiliania-Huxleyi in Enclosures with Different Phosphate Loadings Revealed by Diel Changes in DNA Content. Marine Ecology-Progress Series 121, 271-277 (1995).

168.          Conte, M. H., Thompson, A., Eglinton, G. & Green, J. C. Lipid Biomarker Diversity in the Coccolithophorid Emiliania- Huxleyi (Prymnesiophyceae) and the Related Species Gephyrocapsa-Oceanica. Journal of Phycology 31, 272-282 (1995).

169.          Heimdal, B. R., Egge, J. K., Veldhuis, M. J. W. & Westbroek, P. The 1992 Norwegian Emiliania-Huxleyi Experiment - an Overview. Sarsia 79, 285-290 (1994).

170.          Aksnes, D. L., Egge, J. K., Rosland, R. & Heimdal, B. R. Representation of Emiliania-Huxleyi in Phytoplankton Simulation-Models - a 1st Approach. Sarsia 79, 291-300 (1994).

171.          Barker, G. L. A., Green, J. C., Hayes, P. K. & Medlin, L. K. Preliminary-Results Using the Rapd Analysis to Screen Bloom Populations of Emiliania-Huxleyi (Haptophyta). Sarsia 79, 301-306 (1994).

172.          Vanbleijswijk, J. D. L. et al. Standing Stocks of Pic, Poc, Pon and Emiliania-Huxleyi Coccospheres and Liths in Sea-Water Enclosures with Different Phosphate Loadings. Sarsia 79, 307-317 (1994).

173.          Conte, M. H., Thompson, A. & Eglinton, G. Primary Production of Lipid Biomarker Compounds by Emiliania- Huxleyi - Results from an Experimental Mesocosm Study in Fjords of Southwestern Norway. Sarsia 79, 319-331 (1994).

174.          Egge, J. K. & Heimdal, B. R. Blooms of Phytoplankton Including Emiliania-Huxleyi (Haptophyta) - Effects of Nutrient Supply in Different N-P Ratios. Sarsia 79, 333-348 (1994).

175.          Fagerbakke, K. M., Heldal, M., Norland, S., Heimdal, B. R. & Batvik, H. Emiliania-Huxleyi - Chemical-Composition and Size of Coccoliths from Enclosure Experiments and a Norwegian Fjord. Sarsia 79, 349-355 (1994).

176.          Kristiansen, S., Thingstad, T. F., Vanderwal, P., Farbrot, T. & Skjoldal, E. F. An Emiliania-Huxleyi Dominated Subsurface Bloom in Samnangerfjorden, Western Norway - Importance of Hydrography and Nutrients. Sarsia 79, 357-368 (1994).

177.          Nejstgaard, J. C., Witte, H. J., Vanderwal, P. & Jacobsen, A. Copepod Grazing During a Mesocosm Study of an Emiliania-Huxleyi (Prymnesiophyceae) Bloom. Sarsia 79, 369-377 (1994).

178.          Vanderwal, P., Vanbleijswijk, J. D. L. & Egge, J. K. Primary Productivity and Calcification Rate in Blooms of the Coccolithophorid Emiliania-Huxleyi (Lohmann) Hay-Et-Mohler Developing in Mesocosms. Sarsia 79, 401-408 (1994).

179.          Young, J. R. Variation in Emiliania-Huxleyi Coccolith Morphology in Samples from the Norwegian Ehux Experiment, 1992. Sarsia 79, 417-425 (1994).

180.          Didymus, J. M., Young, J. R. & Mann, S. Construction and Morphogenesis of the Chiral Ultrastructure of Coccoliths from the Marine Alga Emiliania-Huxleyi. Proceedings of the Royal Society of London Series B-Biological Sciences 258, 237-245 (1994).

181.          Spooner, N. et al. Formation of Mesopyrophaeophorbide a During Anaerobic Bacterial-Degradation of the Marine Prymnesiophyte Emiliania- Huxleyi. Organic Geochemistry 22, 225-229 (1995).

182.          Fernandez, E., Balch, W. M., Maranon, E. & Holligan, P. M. High-Rates of Lipid Biosynthesis in Cultured, Mesocosm and Coastal Populations of the Coccolithophore Emiliania-Huxleyi. Marine Ecology-Progress Series 114, 13-22 (1994).

183.          Paasche, E. & Brubak, S. Enhanced Calcification in the Coccolithophorid Emiliania- Huxleyi (Haptophyceae) under Phosphorus Limitation. Phycologia 33, 324-330 (1994).

184.          Teece, M. A., Getliff, J. M., Parkes, R. J., Leftley, J. W. & Maxwell, J. R. Microbial-Degradation of the Marine Prymnesiophyte Emiliania- Huxleyi and Significance for Sediment Studies. Abstracts of Papers of the American Chemical Society 208, 96-GEOC (1994).

185.          Wolfe, G. V., Sherr, E. B. & Sherr, B. F. Release and Consumption of Dmsp from Emiliania-Huxleyi During Grazing by Oxyrrhis-Marina. Marine Ecology-Progress Series 111, 111-119 (1994).

186.          Townsend, D. W., Keller, M. D., Holligan, P. M., Ackleson, S. G. & Balch, W. M. Blooms of the Coccolithophore Emiliania-Huxleyi with Respect to Hydrography in the Gulf of Maine. Continental Shelf Research 14, 979-1000 (1994).

187.          Nimer, N. A., Brownlee, C. & Merrett, M. J. Carbon-Dioxide Availability, Intracellular Ph and Growth-Rate of the Coccolithophore Emiliania-Huxleyi. Marine Ecology-Progress Series 109, 257-262 (1994).

188.          Harris, R. P. Zooplankton Grazing on the Coccolithophore Emiliania-Huxleyi and Its Role in Inorganic Carbon Flux. Marine Biology 119, 431-439 (1994).

189.          Nimer, N. A., Guan, Q. & Merrett, M. J. Extracellular and Intracellular Carbonic-Anhydrase in Relation to Culture Age in a High-Calcifying Strain of Emiliania-Huxleyi Lohmann. New Phytologist 126, 601-607 (1994).

190.          Vanbleijswijk, J. D. L., Kempers, R. S., Veldhuis, M. J. & Westbroek, P. Cell and Growth-Characteristics of Type-a and Type-B of Emiliania-Huxleyi (Prymnesiophyceae) as Determined by Flow- Cytometry and Chemical-Analyses. Journal of Phycology 30, 230-241 (1994).

191.          Sekino, K. & Shiraiwa, Y. Accumulation and Utilization of Dissolved Inorganic Carbon by a Marine Unicellular Coccolithophorid, Emiliania-Huxleyi. Plant and Cell Physiology 35, 353-361 (1994).

192.          Merrett, M. J., Dong, L. F. & Nimer, N. A. Nitrate Availability and Calcite Production in Emiliania- Huxleyi Lohmann. European Journal of Phycology 28, 243-246 (1993).

193.          Brown, C. W. & Yoder, J. A. Blooms of Emiliania-Huxleyi (Prymnesiophyceae) in Surface Waters of the Nova-Scotian Shelf and the Grand Bank. Journal of Plankton Research 15, 1429-1438 (1993).

194.          Ding-Kwo Chang and Garry C. King. Isolation and Characterization of a Novel Acidic Polysaccharide Containing Tartrate and Glyoxylate Residues from the Mineralized Scales of a Unicellular Coccolithophorid Alga Pleurochrysis curterae. The Journal of Biological Chemistry  Vol. 267, No . 28, Issue of October 5. PP . 20507-2051’2,1992.

Articles on EST

2006:

1.                  Zongyuan Ma, Jun Yu, and Le Kang. LocustDB: a relational database for the transcriptome and biology of the migratory locust (Locusta migratoria) BMC Genomics 2006, 7:11 doi:10.1186/1471-2164-7-11.

2.                  Neil F Lobo, Susanta K Behura, Rajat Aggarwal, Ming-Shun Chen, Frank H Collins, and Jeff J Stuart. Genomic analysis of a 1 Mb region near the telomere of Hessian fly chromosome X and avirulence gene vH13. BMC Genomics 2006, 7:7 doi:10. 1186/1471-2164-7-7

 2005:

3.                  Yixing ZHOU, Michele R. WING, John SONDEK and T. Kendall Harden. Molecular cloning and characterization of PLC-η2. Biochem. J. (2005) 391-667

4.                  Xin Wu, Michael G. Walker, Jingchu Luo, and Liping Wei.  GBA server: EST-based digital gene expression. Profiling. Nucleic Acids Research, 2005, Vol. 33, Web Server issue W673-W676

5.                  Katie Fraass Wlaschin,1 Peter Morin Nissom, Marcela de Leon Gatti, Peh Fern Ong, Sanny Arleen, Kher Shing Tan, Anette Rink, Breana Cham, Kathy Wong, Miranda Yap, Wei-Shou Hu. EST Sequencing for Gene Discovery in Chinese Hamster Ovary Cells. Published online 7 July 2005 in Wiley InterScience (www.interscience.wiley.com).

6.                  Jing-Ke Weng, Milos Tanurdzic, and Clint Chapple. Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii. BMC Genomics 2005, 6:85, pp 2164-6-85

7.                  Manuel J Torres, Alexey A Tomilov, Natalya Tomilova, Russell L Reagan and John I Yoder. Pscroph, a parasitic plant EST database enriched for parasite associated transcripts. BMC Plant Biology 2005, 5:24 doi:10.1186/1471-2229-5-24

8.                  Parantu K. Shah, Lars J. Jensen, Ste´phanie Boue, and Peer Bork. Extraction of Transcript Diversity from Scientific Literature PLoS Computational Biology. June 2005 Vol 1 Issue 1 e10

9.                  Kristian R von Schalburg, Matthew L Rise, Glenn A Cooper, Gordon D Brown, A Ross Gibbs, Colleen C Nelson, William S Davidson and Ben F Koop. Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics 2005, 6:126 doi:10.1186/1471-2164-6-126

10.              Nathalie Pavy, Charles Paule, Lee Parsons, John A Crow, Marie-Josee Morency, Janice Cooke, James E Johnson, Etienne Noumen, Carine Guillet-Claude, Yaron Butterfield, Sarah Barber, George Yang, Jerry Liu, Jeff Stott, Robert Kirkpatrick, Asim Siddiqui, Robert Holt, Marco Marra, Armand Seguin, Ernest Retzel, Jean Bousquet and John MacKay. Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics 2005, 6:144 doi:10.1186/1471-2164-6-144

11.              Osamu Ogasawara, Makiko Otsuji, Kouji Watanabe, Takayasu Iizuka, Takuro Tamura, Teruyoshi Hishiki, Shoko Kawamoto and Kousaku Okubo. BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression. D628-D63 Nucleic Acids Research, 2006, Vol. 34, Database issue doi:10.1093/nar/gkj137

12.              Bao-Long NIU, Zhi-Qi MENG, Yue-Zhi TAO, Shun-Lin LU, Hong-Biao WENG, Li-Hua HE, and Wei-Feng SHEN. Cloning and Alternative Splicing Analysis of Bombyx mori Transformer-2 Gene using Silkworm EST Database. Acta Biochimica et Biophysica Sinica 2005, 37(11): 728-736

13.              Xiang Jia Min, Gregory Butler, Reginald Storms, and Adrian Tsang. OrfPredictor: predicting protein-coding regions in EST-derived sequences Nucleic Acids Research, 2005, Vol. 33, Web Server issue W677-W680

14.              Xiang Jia Min, Gregory Butler, Reginald Storms, and Adrian Tsang. Target Identifier: a webserver for identifying full-length cDNAs from EST sequences. Nucleic Acids Research, 2005, Vol. 33, Web Server issue W669-W672

15.              Adam J. Liska, Shami Sunyaev, Ignat N. Shilov, Dan A. Schaeffer and Andrej Shevchenko. Error-tolerant EST database searches by tandem mass spectrometry and multiTag software. Proteomics 2005, 5, 4118-4122

16.              Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Alessandra Stella, Luciano Milanesi and Carlo Pozzi. ESTree db: a Tool for Peach Functional Genomics. BMC Bioinformatics 2005, 6(Suppl 4):S16

17.              Giovanni Lavorgna, Riccardo Triunfo, Federico Santoni, Ugo Orfanelli, Sara Noci, Alessandro Bulfone, Gianluigi Zanetti and Giorgio Casari. AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts Nucleic Acids Research, 2005, Vol. 33, Web Server issue W665-W668

18.              Heidi Hagen-Larsen, Jon K Laerdahl, Frank Panitz, Alexei Adzhubei,  and Bjorn Hoyheim. An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar). BMC Genomics 2005, 6:171 doi:10.1186/1471-2164-6-171

19.              Anyuan Guo, Kun He, Di Liu, Shunong Bai, Xiaocheng Gu, Liping Wei, and Jingchu Luo, DATF: A database of Arabidopsis transcription factors BIOINFORMATICS APPLICATIONS NOTE Vol. 21 no. 10, 2005, pages 2568-2569

20.              Jerome Grimplet, JoseWalter Gaspar, Anne-Laure Gancel, Franc¸ois-Xavier Sauvage and Charles Romieu. Including mutations from conceptually translated expressed sequence tags into orthologous proteins improves the preliminary assignment of peptide mass fingerprints on non-model genomes. Proteomics 2005, 5, 2769-2777

21.              Munirathinam Gnanasekar, Balumuri Padmavathi, and Kalyanasundaram Ramaswamy. Cloning and characterization of a novel immunogenic protein 3 (NIP3) from Brugia malayi by immuno screening of a phagedisplay cDNA expression library.  Parasitol Res. 2005 August ; 97(1): 49-58.

22.              Xiang Jia Min, Gregory Butler, Reginald Storms, and Adrian Tsang. OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Research, 2005, Vol. 33, Web Server issue W677-W680

23.              Xiang Jia Min, Gregory Butler, Reginald Storms, and Adrian Tsang. TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences. Nucleic Acids Research, 2005, Vol. 33, Web Server issue W669-W672.

24.              Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Alessandra Stella, Luciano Milanesi and Carlo Pozzi. ESTree db: a Tool for Peach Functional Genomics. BMC Bioinformatics 2005, 6(Suppl 4):S16.

25.              Giovanni Lavorgna, Riccardo Triunfo, Federico Santoni, Ugo Orfanelli, Sara Noci, Alessandro Bulfone, Gianluigi Zanetti and Giorgio Casari. AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts. Nucleic Acids Research, 2005, Vol. 33, Web Server issue W665-W668.

26.              J. A. Holzwarth. P. Middleton, M. Roberts,  R. Mansourian, F. Raymond AND S. S. Hannah. The Development of a High-Density Canine Microarray. Journal of Heredity 2005:96(7):817-820.

27.              Heidi Hagen-Larsen, Jon K Laerdah, Frank Panitz, Alexei Adzhubei, and Bjorn Hoyheim. An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar). BMC Genomics 2005, 6:171.

28.              Anyuan Guo, Kun He, Di Liu, Shunong Bai, Xiaocheng Gu, Liping Wei, and Jingchu Luo. Databases and ontologies DATF: a database of Arabidopsis transcription factors BIOINFORMATICS APPLICATIONS NOTE. Vol. 21 no. 10 2005, pages 2568-2569.

29.              Jerome Grimplet, JoseWalter Gaspar, Anne-Laure Gancel, Franc¸ois-Xavier Sauvage, and Charles Romieu. Including mutations from conceptually translated expressed sequence tags into orthologous proteins improves the preliminary assignment of peptide mass fingerprints on non-model genomes. Proteomics 2005, 5, 2769-2777.

30.              Munirathinam Gnanasekar, Balumuri Padmavathi, and Kalyanasundaram Ramaswamy. Cloning and characterization of a novel immunogenic protein 3 (NIP3) from Brugia malayi by immuno screening of a phagedisplay cDNA expression library.Parasitol Res. 2005 August ; 97(1): 49-58.

31.              Bing Ge, Scott Gurd, Tiffany Gaudin, Carole Dore, Pierre Lepage, Eef Harmsen, Thomas J. Hudson and Tomi Pastinen. Survey of allelic expression using EST mining. Genome Res. 2005 15: 1584-1591.

32.              Zhangjun Fei, Xuemei Tang, Rob Alba,  and James Giovannoni. Tomato Expression Database (TED): a suite of data presentation and analysis tools. D766-D770 Nucleic Acids Research, 2006, Vol. 34.

33.              Uma Maheswari, Anton Montsant, Johannes Goll, S. Krishnasamy5, K. R. Rajyashri, Villoo Morawala Patell and Chris Bowler. The Diatom EST Database. D344-D347 Nucleic Acids Research, 2005, Vol. 33.

34.              Nunzio D Agostino, Mario Aversano, and Maria Luisa Chiusano. ParPEST: a pipeline for EST data analysis based on parallel Computing. BMC Bioinformatics 2005, 6(Suppl 4):S9.

35.              Marcus Bräutigam, Angelica Lindlöf, Shakhira Zakhrabekova, Gokarna Gharti-Chhetri, Björn Olsson and Olof Olsson. Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa.BMC Plant Biology 2005, 5:18 doi:10.1186/1471-2229-5-18.

36.              Paola Bonizzoni, Raffaella Rizzi and Graziano Pesole. ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences. BMC Bioinformatics 2005, 6:244.

37.              James D Wasmuth, and Mark L Blaxter. Prot4EST: Translating Expressed Sequence Tags from neglected genomes. BMC Bioinformatics 2004, 5:187. Y. Lee, J. Tsai, S. Sunkara, S. Karamycheva, G. Pertea, R. Sultana, V. Antonescu, A. Chan, F. Cheung and J. Quackenbush. The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Research, 2005, Vol. 33, Database issue D71D74.

38.              Rex T. Nelson, David Grant and Randy C. Shoemaker. USDA-ARS, CICGR, Ames, IA, USA ESTminer: a suite of programs for gene and allele Identification. BIOINFORMATICS APPLICATIONS NOTE Vol. 21 no. 5 2005, pages 691-693.

39.              Uma Maheswari, Anton Montsant, Johannes Goll, S. Krishnasamy5, K. R. Rajyashri, Villoo Morawala Patell and Chris Bowler. The Diatom EST Database. D344-D347 Nucleic Acids Research, 2005, Vol. 33.

40.              Stephen Rudd. openSputnik—a database to ESTablish comparative plant genomics using unsaturated sequence collections. D622-D627 Nucleic Acids Research, 2005, Vol. 33.

41.              C. Kunne, M. Lange, T. Funke, H. Miehe, T. Thiel, I. Grosse and U. Scholz. CR-EST: a resource for crop ESTs. Nucleic Acids Research, 2005, Vol. 33, Database issue D619-D621.

42.              Yecheng Huang, Janie Pumphrey, and Alan R. Gingle. ESTminer: a Web interface for mining EST contig and cluster databases. BIOINFORMATICS APPLICATIONS NOTE Vol. 21 no. 5, 2005, pages 669-670.

43.              Binh Nguyen, Robert M. Bowers, Thomas M. Wahlund, and Betsy A. Read. Suppressive Subtractive Hybridization of and Differences in Gene Expression Content of Calcifying and Noncalcifying Cultures of Emiliania huxleyi Strain 1516. Applied and Environmental Microbiology, May 2005, p. 2564-2575.

2004:

44.              Steven P. Wilder, Marie-Therese Bihoreau, Karene Argoud, Takeshi K. Watanabe, Mark Lathrop and Dominique Gauguier. Integration of the Rat Recombination and EST Maps in the Rat Genomic Sequence and Comparative Mapping Analysis With the Mouse Genome. Genome Res. 2004 14: 758-765.

45.              Kristin Whitworth, Gordon K. Springer, L. Joe Forrester, William G. Spollen, Jim Ries, William R. Lamberson, Nathan Bivens,  Clifton N. Murphy,3 Nagappan Mathialigan,  Jonathan A. Green, and Randall S. Prather. Developmental Expression of 2489 Gene Clusters During Pig Embryogenesis: An Expressed Sequence Tag Project. Biology of reproduction 71, 1230-1243 (2004).

46.              Michel Seve, Fabrice Chimienti, Severine Devergnas, and Alain Favier. In silico identification and expression of SLC30 family genes: An expressed sequence tag data mining strategy for the characterization of zinc transporters' tissue expression. BMC Genomics 2004, 5:32.

47.              Matthew L. Rise, Kristian R. von Schalburg, Gordon D. Brown, Melanie A. Mawer, Robert H. Devlin, Nathanael Kuipers, Maura Busby, Marianne Beetz-Sargent, Roberto Alberto, A. Ross Gibbs, Peter Hunt, Robert Shukin, Jeffrey A. Zeznik, Colleen Nelson, Simon R.M. Jones, Duane E. Smailus, Steven J.M. Jones, Jacqueline E. Schein, Marco A. Marra, Yaron S.N. Butterfield, Jeff M. Stott, Siemon H.S. Ng, William S. Davidson and Ben F. Koop. Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics. Genome Res. 2004 14: 478-490.

48.              Srikrishna Putta, Jeramiah J Smith, John A Walker, Mathieu Rondet, David W Weisrock, James Monaghan, Amy K Samuels, Kevin Kump, David C King, Nicholas J Maness, Bianca Habermann5, Elly Tanaka6, Susan V Bryant, David M Gardiner, David M Parichy7 and S Randal Voss. From biomedicine to natural history research: EST resources for ambystomatid salamanders. BMC Genomics 2004, 5:54.

49.              R Henrik Nilsson, Balaji Rajashekar, Karl-Henrik Larsson and Björn M Ursing. galaxieEST: addressing EST identity through automated phylogenetic analysis. BMC Bioinformatics 2004, 5:87.

50.              Afshin Nadershahi, Scott C Fahrenkrug and Lynda BM Ellis. Comparison of computational methods for identifying translation initiation sites in EST data.BMC Bioinformatics 2004, 5:14.

51.              Shobhit Gupta, Dorothea Zink, Bernhard Korn, Martin Vingron and Stefan A Haas. Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing. Published: 28 September 2004 BMC Genomics 2004, 5:72.

52.              S. Gupta, D. Zink, B. Korn, M. Vingron and S. A. Haas.Genome wide identification and classification of alternative splicing based on EST data. Vol. 20 no. 16 2004, pages 2579-2585.

53.              Vivek Gopalan, Tin Wee Tan, Bernett T. K. Lee and Shoba Ranganathan. Xpro: database of eukaryotic protein-encoding genes. Nucleic Acids Research, 2004, Vol. 32, Database issue D59-D63.

54.              Charu G Kumar, Richard LeDuc, George Gong, Levan Roinishivili, Harris A Lewin and Lei Liu. ESTIMA, a tool for EST management in a multi-project Environment. BMC Bioinformatics 2004, 5:176.

55.              Junichi Watanabe , Yutaka Suzuki, Masahide Sasaki and Sumio Sugano. Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species. D334-D338 Nucleic Acids Research, 2004, Vol. 32.

56.              Hirohide Uenishi, Tomoko Eguchi, Kohei Suzuki, Tetsuya Sawazaki, Daisuke Toki, Hiroki Shinkai, Naohiko Okumura, Noriyuki Hamasima, and Takashi Awata. PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries. D484-D488 Nucleic Acids Research, 2004, Vol. 32.

57.              T. A. Thanaraj, Stefan Stamm, Francis Clark, Jean-Jack Riethoven, Vincent Le Texier and Juha Muilu. ASD: the Alternative Splicing Database. D64-D69 Nucleic Acids Research, 2004, Vol. 32.

58.              Peter Sperisen, Christian Iseli, Marco Pagni, Brian J. Stevenson, Philipp Bucher, and C. Victor Jongeneel. trome, trEST and trGEN: databases of predicted protein sequences. Nucleic Acids Research, 2004, Vol. 32, Database issue D509-D511.

59.              Heike Pospisil, Alexander Herrmann, Ralf H. Bortfeldt and Jens G. Reich. EASED: Extended Alternatively Spliced EST Database. D70-D74 Nucleic Acids Research, 2004, Vol. 32.

60.              John Parkinson, Claire Whitton, Ralf Schmid, Marian Thomson and Mark Blaxter. NEMBASE: a resource for parasitic nematode ESTs. Nucleic Acids Research, 2004, Vol. 32, Database issue D427-D430.

61.              Christiane Hertz-Fowler, Chris S. Peacock, Valerie Wood, Martin Aslett, Arnaud Kerhornou, Paul Mooney, Adrian Tivey, Matthew Berriman, Neil Hall, Kim Rutherford, Julian Parkhill, Alasdair C. Ivens, Marie-Adele Rajandream and Bart Barrell. GeneDB: a resource for prokaryotic and eukaryotic Organisms. Nucleic Acids Research, 2004, Vol. 32, Database issue D339-D343.

62.              Qunfeng Dong, Shannon D. Schlueter, and Volker Brendel. PlantGDB, plant genome database and analysis tools. D354-D359 Nucleic Acids Research, 2004, Vol. 32.

63.              Li Li, Jonathan Crabtree, Steve Fischer, Deborah Pinney, Christian J. Stoeckert Jr, L. David Sibley and David S. Roos. ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites. D326-D328 Nucleic Acids Research, 2004, Vol. 32.

64.              Nadim W. Alkharouf, and Benjamin F. Matthews. SGMD: the Soybean Genomics and Microarray Database. D398-D400 Nucleic Acids Research, 2004, Vol. 32.

2003:

65.              Hao Xu, Ling He, Yuanzhong Zhu, Wei Huang, Lijun Fang, Lin Tao, Yuedong Zhu, Lin Cai, Huayong Xu, Liang Zhang, Hong Yu, and Yan Zhou. EST Pipeline System: Detailed and Automated EST Data Processing and Mining. Geno., Prot. & Bioinfo. Vol. 1 No. 3 August 2003.

66.              Reinhardt, Ralf Herwig, Georgia Panopoulou and Hans Lehrach Albert J. Poustka, Detlef Groth, Steffen Hennig, Sabine Thamm, Andrew Cameron, Alfred Beck, Richard. Generation, Annotation, Evolutionary Analysis, and Database Integration of 20,000 Unique Sea Urchin EST Clusters. Genome Res. 2003 13: 2736-2746.

67.              Jane Lo, Sorcheng Lee, Min Xu, Feng Liu, Hua Ruan, Alvin Eun, Yawen He, Weiping Ma, Weefuen Wang, Zilong Wen and Jinrong Peng. 15,000 Unique Zebrafish EST Clusters and Their Future Use in Microarray for Profiling Gene Expression Patterns During Embryogenesis.Genome Res. 2003 13: 455-466.

68.              Li Li, Brian P. Brunk, Jessica C. Kissinger, Deana Pape, Keliang Tang, Robert H. Cole, John Martin, Todd, Wylie, Mike Dante, Steven J. Fogarty, Daniel K. Howe, Paul Liberator, Carmen Diaz, Jennifer Anderson, Michael White, Maria E. Jerome, Emily A. Johnson, Jay A. Radke, Christian J. Stoeckert, Jr., Robert H. Waterston, Sandra W. Clifton, David S. Roos and L. David Sibley. Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database. Genome Res. 2003 13: 443-454.

69.              W. B. Hunter, P.M. Dang, M.G. Bausher, J. X. Chaparro, W. McKendree, R.G. Shatters, Jr., C.L. McKenzie and X.H. Sinisterra. Aphid biology: Expressed genes from alate Toxoptera citricida, the brown. Journal of Insect Science Published 31 July 2003.

70.              Melody S. Clark, Yvonne J.K. Edwards, Dan Peterson, Sandra W. Clifton, Amanda J. Thompson, Masahide, Sasaki, Yutaka Suzuki, Kiyoshi Kikuchi, Shugo Watabe, Koichi Kawakami, Sumio Sugano, Greg Elgar and Stephen L. Johnson. Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation. Genome Res. 2003 13: 2747-2753; originally published online Nov 12, 2003.

71.              Hidemasa Bono, Ken Yagi, Takeya Kasukawa, Itoshi Nikaido, Naoko Tominaga, Rika Miki, Yosuke Mizuno, Yasuhiro Tomaru, Hitoshi Goto, Hiroyuki Nitanda, Daisuke Shimizu, Hirochika Makino, Tomoyuki Morita, Junshin Fujiyama, Takehito Sakai, Takashi Shimoji, David A. Hume, Yoshihide Hayashizaki and Yasushi Okazaki. Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays. Genome Res. 2003 13: 1318-1323.

72.              Frederic Beisson, Abraham J.K. Koo, Sari Ruuska, Jorg Schwender, Mike Pollard, Jay J. Thelen, Troy Paddock, Joaquın J. Salas, Linda Savage, Anne Milcamps, Vandana B. Mhaske, Younghee Cho, and John B. Ohlrogge. Arabidopsis Genes Involved in Acyl Lipid Metabolism. A 2003 Census of the Candidates, a Study of the Distribution of Expressed Sequence Tags in Organs, and a Web-Based Database. Plant Physiology, June 2003, Vol. 132, pp. 681-697.

2002:

73.              Graeme Wistow, Steven L. Bernstein,M. Keith Wyatt, Robert N. Fariss, Amita Behal,1Jeffrey W. Touchman, Gerard Bouffard, Don Smith, Katherine Peterson. Expressed sequence tag analysis of human RPE/choroid for the NEIBank Project: Over 6000 non-redundant transcripts, novel genes and splice variants. Molecular Vision 2002; 8:205-20.

74.              Julio Escribano, and Miguel Coca-Prados. Bioinformatics and reanalysis of subtracted expressed sequence tags from the human ciliary body: Identification of novel biological functions. Molecular Vision 2002; 8:315-32.

75.              Rehannah HA Borup, Stefano Toppo, Yi-Wen Chen, Tanya M Teslovich, Gerolamo Lanfranchi, Giorgio Valle, and Eric P Hoffman. Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs. BMC Bioinformatics 2002, 3:33.

Before 2000:

76.              C. Victor Jongeneel. Searching the expressed sequence tag (EST) databases: Panning for genes. 1467-5463. Briefings in Bioinformaticsl 76 1. no1. 76-92. Feb 2000.

77.              Igor Abdrakhmanov, Dmitry Lodygin, Paul Geroth, Hiroshi Arakawa, Andy Law, Jiri Plachy, Berndt Korn and Jean-Marie Buerstedde. A Large Database of Chicken Bursal ESTs as a Resource for the Analysis of Vertebrate Gene Function. Genome Res. 2000 10: 2062-2069.

78.              Brian Palenik and Sarah E. Henson. The use of amides and other organic nitrogen sources by the phytoplankton Emiliania huxleyi. Limnol. Oceanogr., 42(7), 1997, 1544-1551.

Articles on Microarray

 2006:

1.                  Zengjun Xu1, Tucker A Patterson1, Jonathan D Wren2, Tao Han3, Leming Shi3, Helen Duhart1, Syed F Ali1 and William Slikker Jr. A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools. BMC Bioinformatics 2005, 6(Suppl 2):S8 doi:10.1186/1471-2105-6-S2-S8.

2.                  Anfosso L, Efferth T, Albini A, Pfeffer U. Microarray expression profiles of angiogenesis-related genes predict tumor cell response to artemisinins. Experimental Oncology A, National Cancer Research Institute, Genova, Italy. PMID: 16432535. Pharmacogenomics J. 2006 Jan 24;

3.                  Cottee PA, Nisbet AJ, El-Osta YG, Webster TL, Gasser RB. Construction of gender-enriched cDNA archives for adult Oesophagostomum dentatum by suppressive-subtractive hybridization and a microarray analysis of expressed sequence tags. Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia. PMID: 16426483. Parasitology. 2006 Jan 23; 1-18.

4.                  Zhang JS, Liu Q, Li YM, Hall SH, French FS, Zhang YL. Genome-wide profiling of segmental-regulated transcriptomes in human epididymis using oligo microarray. State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China. PMID: 16412555, Elsevier, Mol Cell Endocrinal. 2006 Jan 10

5.                  Jakupovic M, Heintz M, Reichmann P, Mendgen K, Hahn M. Microarray analysis of expressed sequence tags from haustoria of the rust fungus Uromyces fabae. Department of Biology, University of Kaiserslautern, Post Box 3049, 67653 Kaiserslautern, Germany PMID: 16289953. Fungal Genet Biol. 2006 Jan;43(1):8-19

6.                  Novak BA, Jain AN. Pathway recognition and augmentation by computational analysis of microarray expression data. UCSF Cancer Research Institute and Comprehensive Cancer Center, University of California at San Francisco San Francisco, CA 94143-0128, USA. PMID: 16278238. Bioinformatics. 2006 Jan 15;22(2):233-41

2005:

7.                  Li X, Quigg RJ. An integrated strategy for the optimization of microarray data interpretation. Functional Genomics Facility, Division of Biological Sciences, The University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637, USA. xli@medicine.bsd.uchicago.edu. PMID: 16355722. Gene Expr. 2005;12(4-6):223-30.

8.                  Yang CW, Hsiao CF, Chou CK. Evaluation of experimental designs for two-color cDNA microarrays. Institute of Biochemistry, National Yang-Ming University, Shih-Pai, Taipei 112, Taiwan, R.O.C. PMID: 16305329. J Comput Biol. 2005 Nov;12(9): 1202-20.

9.                  Zheng CL, Kwon YS, Li HR, Zhang K, Coutinho-Mansfield G, Yang C, Nair TM, Gribskov M, Fu XD. MAASE: an alternative splicing database designed for supporting splicing microarray applications. Biomedical Sciences Graduate Program, University of California-San Diego, La Jolla, CA 92093-0651, USA. PMID: 16251387. RNA. 2005 Dec;11(12):1767-76

10.              York TP, Plymate SR, Nelson PS, Eaves LJ, Webb HD, Ware JL. cDNA microarray analysis identifies genes induced in common by peptide growth factors and androgen in human prostate epithelial cells. Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA. PMID: 16240454 Mol Carcinog. 2005 Dec;44(4):242-51

11.              Samuel Lattimore B, van Dongen S, Crabbe MJ. GeneMCL in microarray analysis. School of Animal and Microbial Sciences, University of Reading, Whiteknights, Reading RG6 6AJ, UK. PMID: 16172020  Comput Biol Chem. 2005 Oct;29(5):354-9

12.              Wilson WH, Schroeder DC, Allen MJ, Holden MT, Parkhill J, Barrell BG, Churcher C, Hamlin N, Mungall K, Norbertczak H, Quail MA, Price C, Rabbinowitsch E, Walker D, Craigon M, Roy D, Ghazal P. Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK. whw@pml.ac.uk . PMID: 16099989. Science. 2005 Aug 12;309(5737):1090-2

13.              Gary L Argraves, Saurin Jani, Jeremy L Barth and W Scott Argraves, ArrayQuest: a web resource for the analysis of DNA microarray data, BMC Bioinformatics 2005, 6:287 doi:10.1186/1471-2105-6-287

14.              Sarah Burgarella†, Dario Cattaneo, Francesco Pinciroli and Marco Masseroli, MicroGen: a MIAME compliant web system for microarray experiment information and workflow management, BMC Bioinformatics 2005, 6(Suppl 4):S6 doi:10.1186/1471-2105-6-S4-S6

15.              Giacomo Finocchiaro, Francesco Mancuso,  and Heiko Muller, Mining published lists of cancer related microarray experiments: Identification of a gene expression signature having a critical role in cell-cycle control, BMC Bioinformatics 2005, 6(Suppl 4):S14 doi:10.1186/1471-2105-6-S4-S14

16.              Leslie R Grate, Many accurate small-discriminatory feature subsets exist in microarray transcript data: biomarker discovery BMC Bioinformatics 2005, 6:97 doi:10.1186/1471-2105-6-97

17.              Matthew A Hibbs,  Nathaniel C Dirksen, Kai Li, and Olga G Troyanskaya, Visualization methods for statistical analysis of microarray clusters, BMC Bioinformatics 2005, 6:115, doi:10.1186/1471-2105-6-115

18.              Hua Liu, Sergey Tarima1, Aaron S Borders, Thomas V Getchell, Marilyn L Getchell, and Arnold J Stromberg, Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments, BMC Bioinformatics 2005, 6:106 doi:10.1186/1471-2105-6-106

19.              Tim Lu, Christine M Costello, Peter JP Croucher, Robert Hasler, Gunther Deuschl, and Stefan Schreiber, Can Zipf's law be adapted to normalize microarrays? BMC Bioinformatics 2005, 6:37 doi:10.1186/1471-2105-6-37

20.              Michael Maurer, Robert Molidor, Alexander Sturn, Juergen Hartler, Hubert Hackl, Gernot Stocker, Andreas Prokesch, Marcel Scheideler and Zlatko Trajanoski,  MARS: Microarray analysis, retrieval, and storage system, BMC Bioinformatics 2005, 6:101 doi:10.1186/1471-2105-6-101

21.              Bjorn Menten, Filip Pattyn, Katleen De Preter, Piet Robbrecht, Evi Michels, Karen Buysse, Geert Mortier, Anne De Paepe, Steven van Vooren, Joris Vermeesch, Yves Moreau, Bart De Moor, Stefan Vermeulen, Frank Speleman,  and Jo Vandesompele,  arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays, BMC Bioinformatics 2005, 6:124 doi:10.1186/1471-2105-6-124

22.              Alexander Ploner, Lance D Miller, Per Hall, Jonas Bergh and Yudi Pawitan, Correlation test to assess low-level processing of high-density oligonucleotide microarray data, BMC Bioinformatics 2005, 6:80 doi:10.1186/1471-2105-6-80

23.              Leming Shi, Weida Tong, Hong Fang, Uwe Scherf, Jing Han, Raj K Puri, Felix W Frueh, Federico M Goodsaid, Lei Guo, Zhenqiang Su, Tao Han, James C Fuscoe, Z Alex Xu, Tucker A Patterson, Huixiao Hong, Qian Xie, Roger G Perkins, James J Chen, and Daniel A Casciano, Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential, BMC Bioinformatics 2005, 6(Suppl 2):S12 doi:10.1186/1471-2105-6-S2-S12

24.              John R Stevens, and RW Doerge,  Combining Affymetrix microarray results, BMC Bioinformatics 2005, 6:57 doi:10.1186/1471-2105-6-57

25.              Thanyaluk Jirapech-Umpai,  and Stuart Aitken, Feature selection and classification for microarray data analysis: Evolutionary methods for identifying predictive genes, BMC Bioinformatics 2005, 6:148 doi:10.1186/1471-2105-6-148

26.              Zengjun Xu, Tucker A Patterson1, Jonathan D Wren, Tao Han, Leming Shi, Helen Duhart, Syed F Ali and William Slikker Jr, A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools, BMC Bioinformatics 2005, 6(Suppl 2):S8 doi:10.1186/1471-2105-6-S2-S8

2002:

27.              Selection bias in gene extraction on the basis of microarray gene-expression data, Christophe Ambroise,  and Geoffrey J. McLachlan, www.pnas.org_cgi_doi_10.1073_pnas.102102699, PNAS May 14, 2002 vol. 99 no. 10 pp 6562-6566

28.              Igor Aizenberg, Ekaterina Myasnikova, Maria Samsonova and John Reinitz (2002), "Temporal classification of Drosophila segmentation gene expression patterns by the multi-valued neural recognition method", Mathematical Biosciences, 176(1):145-159.

29.              DB Allison, CS Coffey (2002), "Two-stage testing in microarray analysis: what is gained?", Journal of Gerontology: Biological Sciences, 57(5):B189-192.

30.              DB Allison, GL Gadbury, M Heo, JR Fernández, CK Lee, TA Prolla, R Weindruch (2002), "A mixture model approach for the analysis of microarray gene expression data",Computational Statistics & Data Analysis.

31.              C Ambroise, GJ McLachlan (2002), "Selection bias in gene extraction on the basis of microarray gene-expression data.", Proceedings of the National Academy of Sciences, 99(10):6562-6566.

32.              Virginie Aris, Michael Recce (2002), "A method to improve detection of disease using selective expressed genes in microarray data", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 69-80.

33.              F Azuaje (2002), "A cluster validity framework for genome expression data ",
Bioinformatics, 18:319-320.

34.              Marina Bakay , Yi-Wen Chen , Rehannah Borup , Po Zhao , Kanneboyina Nagaraju, Eric Hoffman (2002), "Sources of variability and effect of experimental approach on expression profiling data interpretation", BMC Bioinformatics, 3:4?.

35.              Z Bar-Joseph, G Gerber, DK Gifford, TS Jaakkola, I Simon (2002), "A new approach to analyzing gene expression time series data", in RECOMB 2002: Proceedings of the Sixth Annual International Conference on Computational Biology , ?-? (ACM Press).

36.              Y Barash, N Friedman (2002), "Context-specific Bayesian clustering for gene expression data", Journal of Computational Biology, 9(2):169-192.

37.              JA Bernstein, AB Khodursky, PH Lin, S Lin-Chao, SN Cohen (2002), "Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays", Proceedings of the National Academy of Sciences, 99(15):9697-9702.

38.              D Berrar, W Dubitzky, M Granzow, R Eils (2002), "Analysis of gene expression and drug activity data by knowledge-based association mining", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

39.              Ghislain Bidaut, Jeffrey Grant, Thomas Moloshok, Frank Manion, Michael Ochs (2002), "Application of Bayesian decomposition to gene expression analysis of deletion mutation data", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

40.              M Bilban, LK Buehler, S Head, G Desoye, V Quaranta (2002), "Defining signal thresholds in DNA microarrays: exemplary application for invasive cancer", BMC Genomics, 3:19.

41.              T Bo, I Jonassen (2002), "New feature subset selection procedures for classification of expression profiles", Genome Biology, 3(4):research0017.

42.              Michael Bober, Kevin Wiehe, Christina Yung, Tugba Onal Suzek, Matthew Lin, William Baumgartner, Jr, and Raimond Winslow (2002), "CaGE: Cardiac gene expression knowledgebase", Bioinformatics, 18:1013-1014.

43.              Christopher MLS Bouton, Jonathan Pevsner (2002), "DRAGON View: information visualization for annotated microarray data ", Bioinformatics, 18:323-324.

44.              Daniel Bozinov and Jörg Rahnenführer (2002), "Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering ", Bioinformatics, 18:747-756.

45.              Vanessa M Brown, Alex Ossadtchi, Arshad H Khan, Simon R Cherry, Richard M Leahy, Desmond J Smith (2002), "High-throughput imaging of brain gene expression ", Genome Research, 12:244-254.

46.              Jenny Bryan, Katherine S Pollard, Mark J van der Laan (2002), "Paired and unpaired comparison and clustering with gene expression data", Statistica Sinica, 12:87-110.

47.              Klaus Bumm, Mingzhong Zheng, Clyde Bailey, Fenghuang Zhan, M Chiriva-Internati, Paul Eddlemon, Julian Terry, Bart Barlogie, John D Shaughnessy, Jr (2002), "CGO: utilizing and integrating gene expression microarray data in clinical research and data management", Bioinformatics, 18:327-328.

48.              Jeong-Ho Chang, Kyu-Baek Hwang, Byoung-Tak Zhang (2002), "Analysis of gene expression profiles and drug activity patterns for the molecular pharmacology of cancer (data set 2)", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

49.              Scott Chapman, Peer Schenk, Kemal Kazan, John Manners (2002), "Using biplots to interpret gene expression patterns in plants ", Bioinformatics, 18:202-204.

50.              Damien Chaussabel, Alan Sher (2002), "Mining microarray expression data by literature profiling", Genome Biology, 3(10):research0055.1-0055.16.

51.              G Chen, N Banerjee, SA Jaradat, TS Tanaka, MSH Ko, Zhang MQ (2002), "Cluster analysis of microarray gene expression data: application to and evaluation with NIA mouse 15K array on ES cell differentiation", Statistica Sinica, 12:241-262.

52.              Y Chen, V Kamat, ER Dougherty, ML Bittner, PS Meltzer, JM Trent (2002), "Ratio statistics of gene expression levels and applications to microarray data analysis", Bioinformatics, 18(9):1207-1215.

53.              Francesca Chiaromonte, JessicaA Martinelli (2002), "Dimension reduction strategies for analyzing global gene expression data with a response", Mathematical Biosciences, 176(1):123-144.

54.              A Chilingaryan, N Gevorgyan, A Vardanyan, D Jones, A Szabo (2002), "Multivariate approach for selecting sets of differentially expressed genes", Mathematical Biosciences, 176(1):59-69.

55.              Tzu-Ming Chu, Bruce Weir and Russ Wolfinger (2002), "A systematic statistical linear modeling approach to oligonucleotide array experiments", Mathematical Biosciences, 176(1):35-51.

56.              C Colantuoni, G Henry, S Zeger, J Pevsner (2002), "SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis", Bioinformatics, 18(11):1540-1541.

57.              Charles J Colbourn, Alan C H Ling, Martin Tompa (2002), "Construction of optimal quality control for oligo arrays ", Bioinformatics, 18:529-535.

58.              L Conde, A Mateos, J Herrero, J Dopazo (2002), "Unsupervised reduction of the dimensionality followed by supervised learning with a perceptron improves the classification of conditions in DNA microarray gene expression data", Neural Networks for Signal Processing XII (IEEE Press) eds. Boulard, Adali, Bengio, Larsen, Douglas. pp. 77-86.

59.              T Conway, B Kraus, DL Tucker, DJ Smalley, AF Dorman, L McKibben (2002), "DNA array analysis in a Microsoft Windows environment", Biotechniques, 32(1):110, 112-4, 116, 118-9.

60.              Kevin R Coombes, Keith A. Baggerly, David N. Stivers, Jing Wang, David Gold, His-Guan Sung, Sang-Joon Lee (2002), "Biology-Driven clustering of microarray data: applications to the NCI60 data set", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

61.              KD Dahlquist, N Salomonis, K Vranizan, SC Lawlor, BR Conklin (2002), "GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways", Nature Genetics, 31(1):19-20.

62.              Dennise D Dalma-Weiszhausz, Marina E Chicurel, Thomas R Gingeras (2002), "Microarrays and genetic epidemiology: A multipurpose tool for a multifaceted field", Genetic Epidemiology, 23(1):4-20.

63.              Nilanjan Dasgupta, Simon M Lin, Lawrence Carin (2002), "Modeling pharmacogenomics of the NCI-60 anticancer data set: utilizing kernel PLS to correlate the microarray data to therapeutic responses", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ??.

64.              S Datta, J Arnold (2002), "Some comparisons of clustering and classification techniques applied to transcriptional profiling data", in Advances in Statistics, Combinatorics and Related Areas (World Scientific), to appear.

65.              Frank De Smet, Janick Mathys, Kathleen Marchal, Gert Thijs, Bart De Moor, and Yves Moreau (2002), "Adaptive quality-based clustering of gene expression profiles", Bioinformatics, 18:735-746.

66.              G Didier, P Brezellec, E Remy, A Henaut (2002), "Gene-ANOVA - gene expression analysis of variance", Bioinformatics, in press.

67.              CHQ Ding (2002), "Analysis of gene expression profiles: class discovery and leaf ordering", in RECOMB 2002: Proceedings of the Sixth Annual International Conference on Computational Biology , 127-136 (ACM Press). [ webpage from the author] [PDF]

68.              K Dobbin, R Simon (2002),"Comparison of microarray designs for class comparison and class discovery", Bioinformatics, 18(11):1438-1445.

69.              JM Dodson, PT Charles, DA Stenger, JJ Pancrazio (2002), "Quantitative assessment of filter-based cDNA microarrays: gene expression profiles of human T-lymphoma cell lines", Bioinformatics, 18:953-960.

70.              J Dopazo (2002) "Microarray data processing and analysis", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. 43-63.

71.              ER Dougherty, J Barrera, M Brun, S Kim, RM Cesar, Y Chen, M Bittner, JM Trent (2002), "Inference from clustering with application to gene-expression microarrays", Journal of Computational Biology, 9(1):105-126.

72.              S Draghici (2002), "Statistical intelligence: effective analysis of high-density microarray data", Drug Discovery Today, in press.

73.              S Draghici (2002), "Data analysis and visualization in DNA microarrays", in Introduction to Bioinformatics: A Theoretical and Practical Approach, eds. S Krawetz and D Womble (Humana Press). (to be published in Aug 2002)

74.              RO Dror, JG Murnick, NA Rinaldi (2002), "A Bayesian approach to transcript estimation from gene array data: The BEAM technique", in RECOMB 2002: Proceedings of the Sixth Annual International Conference on Computational Biology , ?-? (ACM Press).

75.              W Dubitzky, M Granzow, D Berrar (2002), "Data mining and machine learning methods for microarray analysis", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 5-22.

76.              W Dubitzky, D Berrar, M Granzow, R Eils (2002), "Detecting broad-band and selective correlation patters among gene expression and drug activity data", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

77.              W Dubitzky, M Granzow, D Berrar (2002), "Comparing symbolic and subsymbolic machine learning approaches to classification of cancer and gene indentification", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 151-166.

78.              Aimee M Dudley, John Aach, Martin A Steffen, George M Church (2002), "Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range", Proceedings of the National Academy of Sciences, 99(11):7554-7559.

79.              Sandrine Dudoit, Jane Fridlyand (2002), "A prediction-based resampling method to estimate the number of clusters in a dataset", Genome Biology, 3(7):0036.1-0036.21.

80.              Sandrine Dudoit, Jane Fridlyand, Terry Speed (2002), "Comparison of discrimination methods for the classification of tumors using gene expression data", Journal of the American Statistical Association, 97(457):77-87.

81.              Sandrine Dudoit, YH Yang (2002), "Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data", in The Analysis of Gene Expression Data: Methods and Software, eds. G Parmigiani, ES Garrett, RA Irizarry and SL Zeger (Springer), to appear.

82.              Sandrine Dudoit, YH Yang, B Bolstad (2002), "Using R for the analysis of DNA microarray data", R News (online newsletter), 2(1):24-32.

83.              Sandrine Dudoit, Yee Hwa Yang, Terry Speed, Matthew J Callow (2002) "Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments", Statistica Sinica, 12(1):111-139.

84.              BP Durbin, JS Hardin, DM Hawkins, DM Rocke (2002), "A variance-stabilizing transformation for gene-expression microarray data", Bioinformatics, 18:105S-110S.

85.              Mary E Edgerton, Ronald Taylor, John I Powell, Lawrence Hunter, Richard Simon, Edison T Liu (2002), "A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis", Bioinformatics, 18:774-775.

86.              Bradley Efron, Robert Tibshirani (2002), "Empirical bayes methods and false discovery rates for microarrays", Genetic Epidemiology, 23(1):70-86.

87.              Kurt Fellenberg, Nicole C. Hauser, Benedikt Brors, Jörg D. Hoheisel, Martin Vingron (2002), "Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis", Bioinformatics, 18:423-433.

88.              V Filkov, S Skiena, J Zhi (2002), "Analysis techniques for microarray time-series data", Journal of Computational Biology, 9(2):317-330.

89.              David B Finkelstein, Rob Ewing, Jeremy Gollub, Fredrik Sterky, Shauna Somerville, J Michael Cherry (2002), "Iterative linear regression by sector", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 57-68.

90.              GS Firestein, DS Pisetsky (2002), "DNA microarrays: boundless technology or bound by technology? Guidelines for studies using microarray technology" (editorial), Arthritis & Rheumatism, 46(4):859-861. [ PDF]

91.              Charless Fowlkes, Qun Shan, Serge Belongie, Jitendra Malik (2002), "Applying classification separability analysis to microarray data", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ??.

92.              D Gershon (2002), "Microarray technology: an array of opportunities", Nature, 416:885-891. [ PDF]

93.              D Ghosh (2002), "Singular value decomposition regression models for classification of tumors from microarray experiments", PSB02

94.              D Ghosh (2002), "Resampling methods for variance estimation of singular value decomposition analyses from microarray experiments", Functional and Integrative Genomics, to appear.

95.              Debashis Ghosh, Arul M Chinnaiyan (2002), "Mixture modelling of gene expression data from microarray experiments", Bioinformatics, 18:275-286.

96.              DR Goldstein, E Conlon, D Ghosh (2002), "Statistical issues in the clustering of gene expression data", Statistica Sinica, 12(1):219-240.

97.              GJ Gordon, RV Jensen, LL Hsiao, SR Gullans, JE Blumenstock, S Ramaswamy, WG Richards, DJ Sugarbaker , R Bueno (2002), "Translation of microarray data into clinically relevant cancer diagnostic tests using gene expression ratios in lung cancer and mesothelioma", Cancer Research, 62(17):4963-4967.

98.              G Grant, E Manduchi, C Stoeckert Jr. (2002), "Using non-parametric methods in the context of multiple testing to determine differentially expressed genes", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 37-56. preprint version: [ PDF]

99.              Paul Grosu, Jeffrey P Townsend, Daniel L Hartl, Duccio Cavalieri (2002), "Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks", Genome Research, 12:1121-1126.

100.          Chi C Gu, DC Rao, Gary Stormo, Chindo Hicks, Michael A Province (2002), "Role of gene expression microarray analysis in finding complex disease genes", Genetic Epidemiology, 23(1):37-56.

101.          AJ Hartemink, DK Gifford, TS Jaakkola, RA Young (2002), "Combining location and expression data for principled discovery of genetic regulatory network models ", PSB02

102.          J Herrero, R Diaz-Uriarte, J Dopazo (2002), "An approach to inferring transcriptional regulation among genes from large-scale expression data", Comparative and Functional Genomics, in press.

103.          J Herrero, J Dopazo (2002), "Combining hierarchical clustering and self-organizing maps for exploratory analysis of gene expression patterns", Journal of Proteome Research, 1(5):467-470.

104.          KR Hess (2002), "Coming to grips with microarray data analysis", Trends in Biotechnology, 20(5):226-227.

105.          Reinhard Hoffmann, Thomas Seidl, Martin Dugas (2002), "Profound effect of normalization on detection of differentially expressed genes in oligonucleotide", Genome Biology , 3(7):research0033.1 - 0033.11

106.          DC Hoyle, M Rattray, R Jupp, A Brass (2002), "Making sense of mRNA abundance distributions from microarray data", Bioinformatics, 18:576-584. [ PDF ]

107.          W Huber, A von Heydebreck, H Sültmann, A Poustka, M Vingron (2002), "Variance stabilization applied to microarray data calibration and to the quantification of differential expression", Bioinformatics, to appear.

108.          LL Hsiao, RV Jensen, T Yoshida, KE Clark, JE Blumenstock, SR Gullans (2002), "Correcting for signal saturation errors in the analysis of microarray data", Biotechniques, 32:330-336.

109.          X Huang, W Pan (2002), "Comparing three methods for variance estimation with duplicated high density oligonucleotide arrays", Functional & Integrative Genomics, to appear.

110.          Kyu-Baek Hwang, Dong-Yeon Cho, Sang-Wook Park, Sung-Dong Kim, Byoung-Tak Zhang (2002), "Applying machine learning techniques to analysis of gene expression data: cancer diagnosis", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 167-182.

111.          Rafael A Irizarry, Bridget Hobbs, Francois Collin, Yasmin D Beazer-Barclay, Kristen J Antonellis, Uwe Scherf, Terence P Speed (2002), "Exploration, normalization, adn summaries of high density oligonucleotide array probe level data", Biostatistics, to appear.

112.          Christian Iseli, Brian J Stevenson, Sandro J de Souza, Helena B Samaia, Anamaria A Camargo, Kenneth H Buetow, Robert L Strausberg, Andrew JG Simpson, Philipp Bucher, C Victor Jongeneel (2002), "Long-range heterogeneity at the 3' ends of human mRNAs", Genome Research, 12:1068-1074.

113.          Ajay N Jain, Taku A Tokuyasu, Antoine M Snijders, Richard Segraves, Donna G Albertson, Daniel Pinkel (2002), "Fully automatic quantification of microarray image data", Genome Research, 12:325-332.

114.          Ronald Jansen, Dov Greenbaum, Mark Gerstein (2002), "Relating whole-genome expression data with protein-protein interactions", Genome Research, 12:37-46.

115.          Thomas B Kepler, Lynn Crosby, Kevin T Morgan (2002), "Normalization and analysis of DNA microarray data by self-consistency and local regression", Genome Biology, 3(7):research0037.1 - 0037.12

116.          M Kathleen Kerr, Cindy Afshari, Lee Bennett, Pierre Bushel, Jeanelle Martinez, Nigel Walker, Gary A Churchill (2002), "Statistical analysis of a gene expression microarray experiment with replication", Statistica Sinica, 12(1):203-218.

117.          Purvesh Khatri, Sorin Draghici, G Charles Ostermeier, Stephen A Krawetz (2002), "Profiling gene expression using onto-express", Genomics, 79(2):266-270

118.          Isaac S Kohane, Alvin Kho, Atul J Butte (2002),
Microarrays for an Integrative Genomics
(MIT Press).

119.          C Kooperberg, TG Fazzio, JJ Delrow, T Tsukiyama (2002), "Improved background correction for spotted DNA microarrays",Journal of Computational Biology, 9(1):55-66.

120.          Charles Kooperberg, Simonetta Sipione, Michael L LeBlanc, Andrew D Strand, Elena Cattaneo, James M Olson (2002), "Human evaluating test-statistics to select interesting genes in microarray experiments", Molecular Genetics, to appear.

121.          Ravi Kothapalli, Sean J Yoder, Shrikant Mane, Thomas P Loughran Jr (2002), "Microarray results: how accurate are they? ", BMC Bioinformatics, 3:22. [ abstract]

122.          P Krajewski, J Bocianowski (2002), "Statistical methods for microarray assays", Journal of Applied Genetics, 43(3):269-278.

123.          TC Kroll, S Wölfl (2002), "Ranking: a closer look on globalisation methods for normalisation of gene expression arrays", Nucleic Acids Research, 30(11):e50.[ PDF ]

124.          VA Kuznetsov, GD Knott, RF Bonner (2002), "General statistics of stochastic process of gene expression in eukaryotic cells", Genetics, 161(3):1321-1332.

125.          Winston Patrick Kuo, Tor-Kristian Jenssen, Atul J Butte, Lucila Ohno-Machado, Isaac S. Kohane (2002), "Analysis of matched mRNA measurements from two different microarray technologies ", Bioinformatics, 18:405-412.

126.          MP Kurhekar, S Adak, S Jhunjhunwala, K Raghupathy (2002),"Genome-wide pathway analysis and visualization using gene expression data ", PSB02

127.          J Landgrebe, W Wurst, G Welzl (2002), "Permutation-validated principal components analysis of microarray data", Genome Biology, 3(4):research0019.

128.          CJ Langmead, AK Yan, CR McClung, BR Donald (2002), "Phase-independent rhythmic analysis of genome-wide expression patterns", in RECOMB 2002: Proceedings of the Sixth Annual International Conference on Computational Biology , ?-? (ACM Press).

129.          Emmanuel N Lazaridis, Dominic Sinibaldi, Gregory Bloom, Shrikant Mane, Richard Jove (2002), "A simple method to improve probe set estimates from oligonucleotide arrays", Mathematical Biosciences, 176(1):53-58.

130.          Laura Lazzeroni, Art Owen (2002), "Plaid models for gene expression data", Statistica Sinica, 12(1):61-86.

131.          ML Lee, W Lu, GA Whitmore, D Beier (2002), "Models for microarray gene expression data", Journal of Biopharm Stat., 12(1):1-19.

132.          Peter D Lee, Robert Sladek, Celia MT Greenwood, Thomas J Hudson (2002), "Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies", Genome Research, 12:292-297.

133.          YF Leung (2002), "Microarray data analysis for dummies... and experts too?", Trends in Biochemical Sciences, 27:433-434.

134.          YF Leung (2002), "Unravel the mystery of microarray data analysis", Trends in Biotechnology, 20(9):366.

135.          Ker-Chau Li, Ming Yan, Shinsheng Yuan (2002), "A simple statistical model for depicting the CDC15-synchronized yeast cell-cycle regulated gene expression data", Statistica Sinica, 12(1):141-158.

136.          Jinyan Li, Limsoon Wong (2002), "Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patterns", Bioinformatics, 18:725-734.

137.          Leping Li, Lee G Pedersen, Thomas A Darden, Clarice Weinberg (2002), "Computational analysis of leukemia microarray expression data using the GA/KNN method", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 81-96.

138.          Yi-Ju Li, Ling Zhang, Marcy Speer, Eden Martin (2002), "Evaluation of current methods of testing differential gene expression and beyond", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

139.          Wentian Li, Yaning Yang (2002) "Zipf's law in importance of genes for cancer classification using microarray Data", Journal of Theoretical Biology, 219(4):539-551. [PDF].

140.          Wentian Li, Yaning Yang (2002), "How many genes are needed for a discriminant microarray data analysis?", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 137-150. preprint version: [ MS-WORD]

141.          Wuju Li, Momiao Xiong (2002), "Tclass: tumor classification system based on gene expression profile", Bioinformatics, 18:325-326.

142.          X Li, W Gu, S Mohan, DJ Baylink (2002), "DNA microarrays: their use and misuse", Microcirculation, 9(1):13-22.

143.          Wolfram Liebermeister (2002), "Linear modes of gene expression determined by independent component analysis", Bioinformatics, 18:51-60.

144.          Simon M Lin, Kimberly F Johnson (2002), Methods of Microarray Data Analysis: Papers from CAMDA'00 (Kluwer Academic). [ link to amazon ]

145.          Simon M Lin, Xuejun Liao, Patrick McConnell, Korkut Vata, Lawrence Carin, Pascal Goldschmidt (2002), "Using functional genomic units to corroborate user experiments with the Rosetta compendium", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. 91-103.

146.          I Lonnstedt, T Speed (2001), "Replicated microarray data", Statistica Sinica, 12(1):31-46.

147.          Brad Love, David R Rank, Sharron G Penn, David A Jenkins, Russell S Thomas (2002), "A conditional density error model for the statistical analysis of microarray data", Bioinformatics, 18:1064-1072.

148.          J Lu, S Hardy, W Tao, S Muse, B Weir, S Spruill (2002), "Classical statistical approaches to molecular classification of cancer from gene expression profiling", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 97-108.

149.          Philippe Marc and Claude Jacq (2002), "Arrayplot for visualization and normalization of cDNA microarray data ", Bioinformatics, 18:888-889.

150.          DR Masys (2002), "Database designs for microarray data", Pharmacogenomics, 1(4):232-233.

151.          A Mateos, J Herrero, J Dopazo (2002), "Using perceptrons for supervised classification of DNA microarray samples: obtaining the optimal level of information and finding differentially expressed genes", Artifitial Neural Networks - ICANN 2002 (Springer), pp. 577-582.

152.          A Mateos, J Herrero, J Tamames, J Dopazo (2002) "Supervised neural networks for clustering conditions in DNA array data after reducing noise by clustering gene expression profiles", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. 91-103.

153.          GJ McLachlan, RW Bean, D Peel (2002), "A mixture model-based approach to the clustering of microarray expression data", Bioinformatics, 18:413-422.

154.          MA Mendez, C Hodar, C Vulpe, M Gonzalez, V Cambiazo (2002), "Discriminant analysis to evaluate clustering of gene expression data", FEBS Letts, 522(1-3):24-28.

155.          Jatin Misra, William Schmitt, Daehee Hwang, Li-Li Hsiao, Steve Gullans, George Stephanopoulos, Gregory Stephanopoulos (2002) "Interactive exploration of microarray gene expression patterns in a reduced dimensional space", Genome Research, 12:1112-1120.

156.          Madhusmita Mitra, Nigam Shah, Lukas Mueller, Scuth Pin, Nina Fedoroff (2002), "StressDB: A locally installable web-based relational microarray database designed for small user communities", Comparative and Functional Genomics, 3(2):91-96.

157.          TD Moloshok, RR Klevecz, JD Grant, FJ Manion, WF Speier, IV, MF Ochs (2002), "Application of Bayesian Decomposition for analysing microarray data ", Bioinformatics, 18:566-575.

158.          Jason H Moore, Joel S Parker (2002), "Evolutionary computation in microarray data analysis", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 23-36.

159.          Jason H. Moore, Joel S Parker, Nancy J Olsen, Thomas M Aune (2002), "Symbolic discriminant analysis of microarray data in autoimmune disease", Genetic Epidemiology, 23(1):57-69.

160.          M Nees, CD Woodworth (2002), "Microarrays: spotlight on gene function and pharmacogenomics", Current Cancer Drug Targets, 1(2):155-175.

161.          Danh V Nguyen, David M Rocke (2002) "Classification of acute leukemia based on DNA microarray gene expressions using partial least squares", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 109-124.

162.          Danh Nguyen, David Rocke (2002) "Partial least squares proportional hazard regression for application to DNA microarray survival data", Bioinformatics, to appear.

163.          Danh Nguyen, David Rocke (2002) "Multi-class cancer classification via partial least squares using gene expression profiles", Bioinformatics, 18:1216-1226.

164.          Danh Nguyen, David Rocke (2002) "Tumor classification by partial least squares using microarray gene expression data", Bioinformatics, 18(1):39-50.

165.          HB Nielsen, S Knudsen (2002), "Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays ", Bioinformatics, 18:321-322.

166.          Jaroslav P Novak, Robert Sladek, Thomas J Hudson (2002), "Characterization of variability in large-scale gene expression data: implications for study design ", Genomics, 79(1):104-113.

167.          Adam B Olshen, Ajay N Jain (2002), "Deriving quantitative conclusions from microarray expression data", Bioinformatics, 18:961-970.

168.          G Parmigiani, ES Garrett, R Anbazhagan and E Gabrielson (2002), "A statistical framework for expression-based molecular classification in cancer", Journal of Royal Statistical Society B, 64(4): to appear. [PDF ] [ supplemental material from the authors ]

169.          Kuang-Hung Pan, Chih-Jian Lih, Stanley N Cohen (2002), "Analysis of DNA microarrays using algorithms that employ rule-based expert knowledge", Proceedings of the National Academy of Sciences, 99(4):2118-2123.

170.          W Pan (2002), "A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments", Bioinformatics, 18:536-545.

171.          W Pan, J Lin, C Le (2002), "Model-based cluster analysis of microarray gene expression data", Genome Biology, 3 (2): research0009.1-0009.8

172.          W Pan, J Lin, C Le, "How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach", Genome Biology, to appear.

173.          P Pavlidis, DP Lewis, WS Noble (2002), "Exploring gene expression data with class scores", PSB02

174.          Leif E Peterson (2002), "CLUSFAVOR 5.0: hierarchical cluster and principal-component analysis of microarray-based transcriptional profiles", Genome Biology,3(7):software0002.1 - 0002.8

175.          Katherine S Pollard, Mark J Van Der Laan (2002), "Statistical inference for simultaneous clustering of gene expression data", Mathematical Biosciences, 176(1):99-121.

176.          Scott L Pomeroy, Pablo Tamayo, Michelle Gaasenbeek, Lisa M Sturla, Michael Angelo, Margaret E McLaughlin, John YH Kim, Liliana C Goumnerova, Peter M Black, Ching Lau, Jeffrey C Allen, David Zagzag, James M Olson, Tom Curran, Cynthia Wetmore, Jaclyn A Biegel, Tomaso Poggio, Shayan Mukherjee, Ryan Rifkin, Andrea Califano, Gustavo Stolovitzky, David N Louis, Jill P Mesirov, Eric S Lander, Todd R Golub (2002), "Prediction of central nervous system embryonal tumour outcome based on gene expression", Nature, 415:436-442.

177.          MD Radmacher, LM McShane, R Simon (2002), "A paradigm for class prediction using gene expression profiles", Journal of Computational Biology, 9(3):505-512.

178.          A Relógio, C Schwager, A Richter, W Ansorge, J Valcárcel (2002), "Optimization of oligonucleotide-based DNA microarrays", Nucleic Acids Research, 30(11):e51.

179.          Ramoni MF, Sebastiani P, Kohane IS (2002), "Cluster analysis of gene expression dynamics", Proceedings of the National Academy of Sciences, 99(14):9121-9126.

180.          Daniel R Rhodes, Jeremy C Miller, Brian B Haab, Kyle A. Furge (2002), "CIT: identification of differentially expressed clusters of genes from microarray data ", Bioinformatics, 18:205-206.

181.          Jean-Marie Rouillard, Christopher J. Herbert, Michael Zuker (2002), "OligoArray: genome-scale oligonucleotide design for microarrays ", Bioinformatics, 18:486-487.

182.          Lao H Saal, Carl Troein, Johan Vallon-Christersson, Sofia Gruvberger, Åke Borg, Carsten Peterson (2002), "BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data", Genome Biology, 3(8):software0003.1 - 0003.6

183.          Chiara Sabatti, Stanislav L Karsten, Daniel Geschwind (2002), "Thresholding rules for recovering a sparse signal from microarray experiments", Mathematical Biosciences, 176(1):17-34. [ PDF (preprint version) ]

184.          JJ Schageman, M Basit, TD Gallardo, HR Garner, RV Shohet (2002), "MarC-V: a spreadsheet-based tool for analysis, normalization, and visualization of single cDNA microarray experiments", Biotechniques, 32:338-344.

185.          Daniel J Schaid (2002), "Genetic epidemiology and microarrays", Genetic Epidemiology, 23(1):1-3.

186.          E Segal, Y Barash, I Simon, N Friedman, D Koller (2002), "Discovering active transcription factors in gene expression", in RECOMB 2002: Proceedings of the Sixth Annual International Conference on Computational Biology , ?-? (ACM Press).

187.          R Sengupta, M Tompa (2002), "Quality control in manufacturing oligo arrays: combinatorial design approach", Journal of Computational Biology, 9(1):1-22.

188.          William D. Shannon, Mark A. Watson, Arie Perry, Keith Rich (2002), "Mantel statistics to correlate gene expression levels from microarrays with clinical covariates", Genetic Epidemiology, 23(1):87-96.

189.          Kerby Shedden (2002), "Modeling the influence of disease processes on gene expression", Statistica Sinica, 12:263-272.

190.          M A Shipp, K N Ross, P Tamayo, A P Weng, J L Kutok, R C T Aguiar, M Gaasenbeek, M Angelo, M Reich, G S Pinkus, T S Ray, M A Koval, K W Last, A Norton, T A Lister, J Mesirov, D S Neuberg, E S Lander, J C Aster, T R Golub (2002), "Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning", Nature Medicine, 8(1):68-74. [webpage: http://www-genome.wi.mit.edu/mpr/lymphoma/]

191.          Ilya Shmulevich and Wei Zhang (2002) "Binary analysis and optimization-based normalization of gene expression data", Bioinformatics, 18:555-565.

192.          J Shrager, P Langley, A Pohorille (2002), "Guiding revision of regulatory models with expression data", PSB02

193.          Richard Simon, Michael D. Radmacher, Kevin Dobbin (2002), "Design of studies using DNA microarrays", Genetic Epidemiology, 23(1):21-36.

194.          James P Sluka (2002), "Extracting knowledge from genomic experiments by incorporating the biomedical literature", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

195.          Terry Speed, YH Yang (2002), "Direct versus indirect design for cDNA microarray experiments", Sankhya Series A, to appear.

196.          Paul T Spellman, Michael Miller, Jason Stewart, Charles Troup, Ugis Sarkans, Steve Chervitz, Derek Bernhart, Gavin Sherlock, Catherine Ball, Marc Lepage, et al (2002), "Design and implementation of microarray gene expression markup language (MAGE-ML)", Genome Biology, 3(9):research0046.1 - 0046.9

197.          Rainer Spang, Harry Zuzan, Mike West, Joseph Nevins, Carrie Blanchette, Jeffrey R Marks (2002), "Prediction and uncertainty in the analysis of gene expression profiles", In Silico Biology, 2:0033.

198.          Gregory Stephanopoulos, Daehee Hwang, William A Schmitt, Jatin Misra, George Stephanopoulos (2002), "Mapping physiological states from microarray expression measurements", Bioinformatics, 18:1054-1063.

199.          JD Storey, R Tibshirani (2002), "Statistical methods for detecting differential gene expression", Journal of Molecular Biology (special issue), to appear.

200.          Andrew D Strand, James M Olson, Charles Kooperberg (2002), "Estimating significance levels for gene expression changes observed with oligonucleotide arrays", Human Molecular Genetics, to appear.

201.          Alexander Sturn, John Quackenbush, Zlatko Trajanoski (2002), "Genesis: cluster analysis of microarray data ", Bioinformatics, 18:207-208.

202.          A Szabo, K Boucher, WL Carroll, LB Klebanov, AD Tsodikov, AY Yakovlev (2002), "Variable selection and pattern recognition with gene expression data generated by the microarray technology", Mathematical Biosciences, 176(1):71-98.

203.          J Tamames, D Clark, J Herrero, J Dopazo, C Blaschke, JM Fernández, JC Oliveros, A Valencia (2002) "Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction", Journal of Biotechnology, 98(2-3):269-283.

204.          A Tefferi, ME Bolander, SM Ansell, ED Wieben, TC Spelsberg (2002), "Primer on medical genomics. Part III: Microarray experiments and data analysis", Mayo Clinic Proceedings, 77(9):927-490. [PDF ]

205.          MF Templin, D Stoll, M Schrenk, PC Traub, CF Vohringer, TO Joos (2002), "Protein microarray technology", Trends in Biotechnology, 20(4):160-166.

206.          Terry Therneau, Renee C Tschumper, Diane Jelinek (2002), "Sharpening spots: correcting for bleedover in cDNA array images ", Mathematical Biosciences, 176(1):1-15.

207.          R Tibshirani, T Hastie, B Narasimhan, G Chu (2002), "Diagnosis of multiple cancer types by shrunken centroids of gene expression", Proceedings of the National Academy of Sciences, 99(10):6567-6572.

208.          Robert Tibshirani, Trevor Hastie, Balasubramanian Narasimhan, Michael Eisen, Gavin Sherlock, Pat Brown, David Botstein (2002), "Exploratory screening of genes and clusters from microarray experiments", Statistica Sinica, 12:47-59.

209.          Shuta Tomida, Taizo Hanai, Hiroyuki Honda, Takeshi Kobayashi (2002), "Analysis of expression profile using fuzzy adaptive resonance theory", Bioinformatics, 18:1073-1083.

210.          OG Troyanskaya, ME Garber, PO Brown, D Botstein, RB Altman (2002), "Nonparametric methods for identifying differentially expressed genes in microarray data", Bioinformatics, 18(11):1454-1461.

211.          A Tsodikov, A Szabo, D Jones (2002), "Adjustments and measures of differential expression for microarray data ", Bioinformatics, 18:251-260.

212.          R Michael Van Dam, Stephen R. Quake (2002), "Gene expression analysis with universal n-mer arrays", Genome Research, 12:145-152.

213.          Junbai Wang, Vigdis Nygaard, Birgitte Smith-Sørensen, Eivind Hovig, Ola Myklebost (2002), "MArray: analysing single, replicated or reversed microarray experiments", Bioinformatics, 18: 1139-1140.

214.          Pinglang Wang, Fei Ding, Hsienyuan Chiang, Robert C. Thompson, Stanley J. Watson, Fan Meng (2002), "ProbeMatchDB-a web database for finding equivalent probes across microarray platforms and species ", Bioinformatics, 18:488-489.

215.          Y Wang, CL Liu, JD Storey, RJ Tibshirani, D Herschlag, PO Brown (2002), "Precision and functional specificity in mRNA decay", Proceedings of the National Academy of Sciences, 99:5860-5865.

216.          Y Wang, J Lu, R Lee, Z Gu, R Clarke (2002), "Iterative normalization of cDNA microarray data", IEEE Transactions on Information Technology in Biomedicine, 6(1):29-37.

217.          ML Wayne, LM McIntyre (2002), "Combining mapping and arraying: An approach to candidate gene identification", Proceedings of the National Academy of Sciences, to appear.

218.          Weinstein JN, Scherf U, Lee JK, Nishizuka S, Gwadry F, Bussey AK, Kim S, Smith LH, Tanabe L, Richman S, Alexander J, Kouros-Mehr H, Maunakea A, Reinhold WC (2002), "The bioinformatics of microarray gene expression profiling", Cytometry, 47(1):46-49.

219.          Stephen Welle, Andrew I Brooks, Charles A Thornton (2002), "Computational method for reducing variance with Affymetrix microarrays", BMC Bioinformatics, 3:23. [abstract]

220.          Christopher Workman, Lars Jensen, Hanne Jarmer, Randy Berka, Laurent Gautier, Henrik Nielser, Hans-Henrik Saxild, Claus Nielsen, Søren Brunak, Steen Knudsen (2002), "A new non-linear normalization method for reducing variability in DNA microarray experiments", Genome Biology, 3(9):research0048.1 - 0048.16

221.          Thomas D Wu (2002), "Large-scale analysis of gene expression profiles", Briefings in Bioinformatics, 3(1):7-17.

222.          Ying Xu, Victor Olman, and Dong Xu (2002), "Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees ", Bioinformatics, 18:536-545.

223.          YH Yang, MJ Buckley, S Dudoit, TP Speed (2002), "Comparison of methods for image analysis on cDNA microarray data", Journal of Computational and Graphic Statistics, 11:108-136.

224.          YH Yang, T Speed (2002), "Design issues for cDNA microarray experiments", Nature Reviews Genetics, 3(8):579-588.

225.          YH Yang, S Dudoit, P Luu, DM Lin, V Peng, J Ngai, TP Speed, "Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation", Nucleic Acids Research, 30(4):e15. [PDF ]

226.          MK Yeung, J Tegner, JJ Collins (2002), "Reverse engineering gene networks using singular value decomposition and robust regression", Proceedings of the National Academy of Sciences, 99(9):6163-6168.

227.          C Yoo, V Thorsson, GF Cooper (2002), "Discovery of causal relationships in a gene-regulation pathway from a mixture of experimental and observational DNA microarray data", PSB02

228.          Tony Yuen, Elisa Wurmbach, Robert L Pfeffer, Barbara J Ebersole, Stuart C Sealfon (2002), "Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays", Nucleic Acids Research, 30(10):e48. [PDF ]

229.          Matthew A Zapala, Daniel J Lockhart, Daniel G Pankratz, Anthony J Garcia, Carrolee Barlow, David J Lockhart (2002), "Software and methods for oligonucleotide and cDNA array data analysis", Genome Biology ,3(6):software0001.1 - 0001.9

230.          H Zhang, CY Yu (2002), "Tree-based analysis of microarray data for classifying breast cancer", Front. Biosci. 7:C63-C67.

231.          MQ Zhang (2002), "Extracting functional information from microarrays: a challenge for functional genomics", Proceedings of the National Academy of Sciences, in press.

232.          Zhen Zhang, Grier Page, Hong Zhang (2002), "Applying classification separability analysis to microarray data", in Methods of Microarray Data Analysis , eds. SM Lin, KF Johnson (Kluwer Academic), pp. 125-136.

233.          Zhen Zhang, Grier Page, Hong Zhang (2002), "Fishing expedition - a supervised approach to extract patterns from a compendium of expression profiles", in Microarray data analysis II, ed. SM Lin and KF Johnson (Kluwer Academic), pp. ?-?.

234.          Yingyao Zhou, Ruben Abagyan (2002), "Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis", BMC Bioinformatics, 3:3. [ abstract] [ PDF]

235.          A Zien, J Fluck, R Zimmer, T Lengauer (2002), "Microarrays: How many do you need?", in RECOMB 2002: Proceedings of the Sixth Annual International Conference on Computational Biology , ?-? (ACM Press).