dChip: References and Acknowledgments

Manual References (Before 2002)

Affymetrix Inc. (1999) GeneChip ® Expression Analysis Algorithm Tutorial.

Cho RJ, Mingxia Huang, Michael J. Campbell, Helin Dong, Lars Steinmetz, Lisa Sapinoso, Garret Hampton, Stephen J. Elledge, Ronald W. Davis and David J. Lockhart (2001) Transcriptional regulation and function during the human cell cycle, Nature Genetics, Vol 27, 48-54.

Dudoit S., Juliet Popper Shaffer, and Jennifer C. Boldrick (2002b) Multiple Hypothesis Testing in Microarray Experiments. Technical report.

Eisen MB, Spellman PT, Brown PO and Botstein D. (1998). Cluster Analysis and Display of Genome-Wide Expression Patterns. Proc Natl Acad Sci U S A 95, 14863-14868.

Golub et al. (1999) Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring. Science, Vol 286, 531-537.

Hoffmann R, Thomas Seidl, Martin Dugas (2002) Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis. Genome Biology 2002 3(7): research0033.1-0033.11 (Compares different normalization methods and differential expression detection methods)

Irizarry, RA, B. M. Bolstad, F. Collin, L. M. Cope, B. Hobbs, and T. P. Speed. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003; 31(4): e15 - 15 (Compares MAS5, dChip and Robust Multichip Average)

Lemon WJ, Jeffrey J.T. Palatini, Ralf Krahe and Fred A. Wright (2002) Theoretical and experimental comparisons of gene expression indexes for oligonucleotide arrays. Bioinformatics. Vol 18, 1470-1476 (Compares AveDiff, reduced model and full model)

Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D, Siani-Rose MA: NetAffx: Affymetrix probesets and annotations. (2003) Nucleic Acids Res 2003, 31:82-86.

Naef, F., DA Lim, N Patil and M Magnasco (2001) From features to expression: high-density oligonucleotide arrays analysis revisted. Proceedings of the DIMACS Workshop on Analysis of Gene Expression Data, October 24-26.

Perou et al. Molecular portraits of human breast tumours (2000) Nature, Vol 406, 747-752.

Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander E, Golub T (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA, 96:2907-2912.

Tavazoie S., Jason D. Hughes, Michael J. Campbell, Raymond J. Cho, and George M. Church. (1999) Systematic determination of genetic network architecture. Nature Genetics, Vol 22, 281-285

Tusher VG, Tibshirani R and Chu G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA. 98, 5116-5121, 2001.

Zhou Y., Ruben Abagyan (2002) Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis. BMC Bioinformatics, 3:3.

Acknowledgments

[Acknowledgments after April 2003 can be found in the Update page]

We are also very grateful to our collaborators who kindly provided us with data, and to many dChip users who gave us valuable feedbacks, suggestions and help:

Eric Schadt, Scott Welford, Jih-tung Pai, Hajir Dadgostar, Sven de Vos, Dan Tang, Laura Block-Alper, Stan Nelson, Zugen Chen, Ruty Shai, Nik Brown, Jae K. Lee, Yaron Hakak, John Walker, Allen Fienberg, Arindam Bhattacharjee, Ruth Luthi-Carter, Leslie Thompson, Deming Wang, Elizabeth Winzeler, Scott Oakes, Martina Schinke, Robert Gentleman, Matthew Meyerson, Michael Zhang, Margaret Cam, Marquis Vawter, Matthew Tudor, Michael Angelo, Annick Peleraux, Mei Xu, Andrew Kirby, Elizabeth Robinson, Daniel Auclair, Scott Armstrong, Beth Wilmot, Steve Horvath, Patrick Jay, James Lederer, Yizheng Li, William Lemon, Fred Wright, Priya Sudarsanam, Mark Ettinger and Yan Cui. (April 01)

Victoria Perreau, Susan Hilsenbeck, Casper Frederiksen, Greer M. Murphy, Edward J. Oakeley, Anne Bowcock, Stephen Haggarty, Yingxi Lin, Simon M Lin, Florian Storch, Michael Boutros, Andrea Richardson, Catherine Gradek, Bradley Messmer, Tiago R Magalhaes, Elinor Dehan, Yoseph Barash, Sanjay Jain, Huan Dong, Miguel Ramalho Santos, Nikhil Munshi, John K. Park, Feng Wu, Stephen Henderson, Jenny Z. Xiang, Laura Forsberg, Richard Lempicki, Andrew Bent, Soemini Kasanmoentalib, Brain Yandell, Stefano Colella, Thomas Cappola, David Gerhold, Karen Vranizan, Adam Olshen, Michel Bellis, Thomas Seidl, Jason M. Laramie, Siming Shou, Wentian Li, Anthony Suffredini, Alex Owyang, Séverine Durier, Jane Staunton, Cyrus V. Hedvat, Eric Gerstenberger, Robert Mau and Isabella Tai. (Feb 02)

Chi Gu, Heiner Adams, Raphael Gottardo, Jianhua Hu, Chunfa Jie, Ken Aldape, Tiago Duarte, Igor Zwir, Dale Muzzey, Mayetri Gupta, Allen Day, Anna Tsimelzon, Kieran Holland, Yuval Kluger, Song Her, Frank Buxton, Dona Wu, Ming Lin, Xinmin Zhang, Igor Klacansky, Tao Shi, Joerg D. Becker, Edward Fox, Christine Konradi, Susan J. Miller, Reinhard Hoffmann, Laurent Gautier, James MacDonald, Yu Guo, John Okyere, Bill Sellers, Masood Shammas, Ryung Suk Kim, Jean-Phillippe Brunet, Tanya Logvinenko, Jeremy Erickson, Eric Libby, Xueqing Zhang, Tao Lu, Shahab Asgharzadeh, Keith Crist, Anyou Wang, Marco Wachtel, Wenhong Fan, Frank Millenaar, Bin Zhang, Rehannah Borup, Leighton Stein, David Lapointe (April 03).

Yu Qiu, Mike Wang, Robert Schoenfeld, Morgen Hickey, Marco Wachtel, Liselotte Folling, Ann Dring, Yuhyun Park.

This work is supported in part by NIH grant 1 RO1 HG02341-01 and NSF grant DBI-9904701. Some dChip codes are courtesy of Florian Schintke, Paul DiLascia, the independent JPEG team and the R development team.