Microarray

& Data

Analysis

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1999

1. U Alon, N Barkai, DA Notterman, K Gish, S Ybarra, D Mack, AJ Levine (1999),
   "Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays",
   Proceedings of the National Academy of Sciences, 96(12):6745-6750.
   [ companion webpage from the authors] [ Medline entry] [ PDF ]

2. T Akutsu, S Miyano, S Kuhara (1999)
   "Identification of genetic networks from a small number of gene expression patterns under the Boolean network model",
   PSB99
   [ PDF ]

3. Richard Baldock, Duncan Davidson (1999),
   "Gene expression databases",
   in Genetic Databases , ed Martin J Bishop pp.247-68 (Academic Press).
   [ from the publisher ]

4. Joel Lloyd Bellenson (1999)
   "Expression data and the bioinformatics challenges",
   in DNA Microarray (practical approach series, 205), ed. Mark Schena (Oxford Univ Press)
   [ from oxford ]

5. Amir Ben-Dor, Zohar Yakhini (1999),
   "Clustering gene expression patterns",
   Journal of Computational Biology, 6(3/4):281-298.
   [ PDF]
   [ companion webpage from the authors ]

6. M Bittner, Meltzer P, J Trent (1999),
   "Data analysis and integration: of steps and arrows",
   Nature Genetics, 22(3):213-215.
   (no abstract)

7. R Brent (1999),
   "Functional genomics: Learning to think about gene expression data",
   Current Biology, 9(9):R338-R341.
   (no abstract)

8. P Brown, D Bostein (1999),
   "Exploring the new world of the genome with DNA microarrays",
   Nature Genetics, 21(1 suppl):33-37.
   [ medline entry]

9. P Bucher (1999),
   "Regulatory elements and expression profiles",
   Current Opinion in Strctural Biology, 9(3):400-407.
   [ Medline entry]

10. Ting Chen, Vladimir Filkov, Steven S. Skiena (1999),
    "Identifying gene regulatory networks from experimental data",
    RECOMB99

11. Yidong Chen, Olga Ermolaeva, Michael L Bittner, Paul Meltzer, Jeffery Trent, Edward R Dougherty, Sinan Batman (1999),
    "Clustering analysis for gene expression data",
    Proceedings of SPIE, 3602:422-428.

12. JM Claverie (1999),
    "Computational methods for the identification of differential and coordinated gene expression",
    Human Molecular Genetics, 8(10):1821-1832.
    [ Medline entry]

13. C Debouck, PN Goodfellow (1999),
    "DNA microarrays in drug discovery and development",
    Nature Genetics, 21(1 suppl):48-50.
    [ Medline entry]

14. JL DeRisi, VR Iyer (1999),
    "Genomics and array technology",
    Current Opinion in Oncology, 11(1):76-79.
    [ medline entry]

15. P D'haeseleer, X Wen, S Fuhrman, R Somogyi (1999),
    "Linear modeling of mRNA expression levels during CNS developement and injury",
    PSB99
    [ html ]

16. DJ Duggan, M Bittner, Y Chen, P Meltzer, JM Trent (1999),
    "Expression profiling using cDNA microarrays",
    Nature Genetics, 21(1 suppl):10-14.

17. MB Eisen, PO Brown (1999),
    "DNA arrays for analysis of gene expression",
    Methods of Enzymology, 303:179-205.

18. R Ekins, FW Chu (1999),
    "Microarrays: their origins and applications",
    Trends in Biotechnology, 17:217-218.
    [ PDF]

19. RM Ewing, AB Kahla, O Poirot, F Lopez, S Audic, JM Claverie (1999),
    "Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression",
    Genome Research, 9:950-959.

20. D Gerhold, T Rushmore, CT Caskey (1999),
    "DNA chips: promising toys have become powerful tools",
    Trends in Biochemical Sciences, 24(5): 168-173.
    [ Medline entry]

21. TR Golub, DK Slonim, P Tamayo, C Huard, M Caasenbeek, JP Mesirov, H Coller, ML Loh, JR Downing, MA Caligiuri, CD Bloomfield, ES Lander (1999),
    "Molecular classification of cancer: class discovery and class prediction by gene expression monitoring",
    Science, 286:531-537.
    [ companion webpage from the authors] [ PDF ]

22. JG Hacia (1999),
    "Resequencing and mutational analysis using oligonucleotide microarrays",
    Nature Genetics, 21(1 suppl):42-47.
    [ Medline entry]

23. Erez Hartuv, Armin Schmitt, jorg Lange, Sebastian Meirer-Ewert, Hans Lehrach, Ron Shamir (1999),
    "An algorithm for clustinering cDNAs for gene expression analysis",
    RECOMB99

24. R Herwig, AJ Poustka, C Muller, C Bull, H Lehrach, J O'Brien (1999),
    "Large-scale clustering of cDNA-fingerprinting data",
    Genome Research, 9:1093-1105.

25. LJ Heyer, S Kruglyak, S Yooseph (1999),
    "Exploring expression data: identification and analysis of coexpressed genes",
    Genome Research, 9:1106-1115.

26. S Huang (1999),
    "Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery",
    Journal of Molecular Medicine, 77(6):469-480.
    [ Medline entry]

27. A Isaksson, U Landegren (1999),
    "Accessing genomic information: alternatives to PCR",
    Current Opinion in Biotechnology, 10(1):11-15.
    [ PDF]

28. EG Jennings, RA Young (1999),
    "Genome expression on the world wide web",
    Trends in Genetics, 15(5):202-204.

29. CM Kao (1999),
    "Functional genomic technologies: Creating new paradigms for fundamental and applied biology",
    Biotechnology Progress,15(3):304-311.

30. Richard M Karp, KaYee Yeung (1999),
    "Algorithms for choosing differential gene expression experiments",
    RECOMB99

31. L Khan, ML Bittner, Y Chen, PS Meltzer, JM Trent (1999)
    "DNA microarray technology: the anticipated impact on the study of human disease",
    Biochim Biophys Acta, 1423(2):M17-M28.
    [ Medline entry]

32. DH Kozian, BJ Kirschbaum (1999),
    "Comparative gene-expression analysis",
    Trends in Biotechnology, 17(2):73-78.
    [ Medline entry]

33. Mitsuteru Nakao, Hidemasa Bono, Shuichi Kawashima, Tomomi Kamiya, Kazushige Sato, Susumu Goto, Minoru Kanehisa (1999),
    "Genome-scale gene expression analysis and pathway reconstruction in KEGG",
    Genome Informatics, 10:94-103.

34. P Ross-Macdonald, PSR Coelho, T Roemer, S Agarwal, A Kumar, R Jansen, KH Cheung, A Sheehan, D Symoniatis, L Umansky, M Heidtman, FK Nelsen, H Iwasaki, K Hager, M Gerstein, P Miller, GS Roeder, M Snyder (1999),
    "Large-scale analysis of the yeast genome by transposon tagging and gene disruption",
    Nature, 402:413-418.

35. MG Samsonova, VN Serov (1999)
    "NetWork: An interactive interface to the tools for analysis of genetic network structure and dynamics",
    PSB99
    [ PDF ]

36. RJ Sapolsky, L Hsie , A Berno , G Ghandour , M Mittmann , JB Fan (1999),
    "High-throughput polymorphism screening and genotyping with high-density oligonucleotide arrays",
    Genetic Analysis, 14(5-6):187-192.
    [ Medline entry]

37. Roland Somogyi (1999),
    "Making sense of gene-expression data",
    Pharmainformatics (a Trends Guide), 17-24.

38. E Southern, K Mir, M Shchepinov (1999),
    "Molecular interactions on microarrays",
    Nature Genetics, 21(1 suppl):5-9.
    [ Medline entry]

39. Z Szallasi (1999),
    "Genetic network analysis in light of massively parallel biological data acquisition",
    PSB99
    [ Medline entry] [ PDF ]

40. P Tamayo, D Slonim, J Mesirov, Q Zhu, S Kitareewan, E Dmitrovsky, ES Lander, TR Golub (1999),
    "Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation",
    Proceedings of the National Academy of Sciences, 96(6):2907-2912.
    [ PDF ]
    
    [ Medline entry]
    [ GENECLUSTER program]

41. L Tanabe, LH Smith, JK Lee, U Scherf, L Hunter, JN Weinstein (1999),
    "MedMiner: An internet tool for filtering and organizing biomedical information, with application to gene expression profiling",
    BioTechniques, 27:1210-1217.

42. S Tavazoie, JD Hughes, MJ Campbell, RJ Cho, GM Church (1999),
    "Systematic determination of genetic network architecture",
    Nature Genetics, 22(3):281-285.

43. R Tibshirani, T Hastie, M Eisen, D Ross, D Botstein, P Brown (1999),
    "Clustering methods for the analysis of DNA microarray data",
    Technical Report, Stanford University.
    [ PDF - a big 11.4 Mb file!]

44. P Toronen, M Kolehmainen, G Wong, E Castren (1999),
    "Analysis of gene expression data using self-organizing maps",
    FEBS Letters, 451(2):142-146.
    [ Medline entry]

45. D Warburton (1999),
    "Comparative genomic hybridization: FISH and chips in our future? ",
    Teratology, 59(5):321-322.

46. SJ Watson, H Akil (1999),
    "Gene chips and arrays revealed: a primer on their power and their uses",
    Biol Psychiatry, 45(5):533-543.

47. DC Weaver, CT Workman, GD Stormo (1999),
    "Modeling regulatory networks with weight matrices",
    PSB99
    [ PDF ]

48. J Wittes, HP Friedman (1999),
    "Searching for evidence of altered gene expression: a comment on statistical analysis of microarray data",
    Journal of National Cancer Institute, 91(5):400-401.
    [ Medline entry]

49. MQ Zhang (1999),
    "Large-scale gene expression data analysis: A new challenge to computational biologists",
    Genome Research, 9(8):681-688.
    [ Medline entry]

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