Abstracts to publications by Rosetta Inpharmatics employees are available below. In some cases, supporting data is also available. Note: Current Rosetta Inpharmatics employees are shown in boldface type.

Design and implementation of microarray gene expression markup language (MAGE-ML) Genome Biology 2002, 3(9):research0046.1–0046.9

Paul T Spellman¹, Michael Miller², Jason Stewart³, Charles Troup⁴, Ugis Sarkans⁵, Steve Chervitz⁶, Derek Bernhart⁶, Gavin Sherlock⁷, Catherine Ball⁷, Marc Lepage⁸, Marcin Swiatek⁹, WL Marks¹⁰, Jason Goncalves¹⁰, Scott Markel¹¹, Daniel Iordan¹⁰, Mohammadreza Shojatalab⁵, Angel Pizarro¹², Joe White³, Robert Hubley¹⁴, Eric Deutsch¹⁴, Martin Senger⁵, Bruce J Aronow¹⁵, Alan Robinson⁵, Doug Bassett², Christian J Stoeckert Jr1² and Alvis Brazma⁵

Addresses:
¹Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, CA 94720-3206, USA.
²Rosetta Biosoftware, 113th Ave NE, Kirkland, WA 98034, USA.
³Open Informatics, Arizona St SE, Albuquerque, NM 87108, USA.
⁴BioscienceResearch - Agilent Technologies, Deer Creek Rd, Palo Alto, CA 94304, USA.
⁵European Bioinformatics Institute, EMBL Hinxton Outstation, Cambridge CB10 1SD, UK.
⁶Affymetrix, Inc., Vallejo St, Emeryville, CA 94608, USA.
⁷Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA.
⁸Molecular Mining Corporation, Rideau St, Kingston, ON K7K 2Z8, Canada.
⁹Imaging Research Inc., Glenridge Ave, St. Catharines, ON L2S 3A1, Canada.
¹⁰Iobion Informatics LLC, North Torrey Pines Road, La Jolla, CA 92037, USA.
¹¹LION bioscience Inc., Executive Drive, San Diego, CA 92121, USA.
¹²Center for Bioinformatics, University of Pennsylvania, Guardian Drive, Philadelphia, PA 19104, USA.
¹³The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850, USA.
¹⁴Computational Biology, Institute for Systems Biology, North 34th St, Seattle, WA 98103-8904, USA.
^15CHRF, Burnet Ave, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.

A gene-expression signature as a predictor of survival in breast cancer
New England Journal of Medicine 347, 1999-2009 (2002).

Marc J van de Vijver¹ ‡, M.D., Ph.D., Yudong D He²‡, Ph.D., Laura J van ’t Veer¹ ‡, Ph.D., Hongyue Dai², Ph.D., Augustinus A M Hart¹, M.Sc., Dorien Voskui¹, Ph.D., George J Schreiber2, M.Sc., Johannes L Peters¹, M.D., Chris Roberts², Ph.D., Matthew J Marton², Ph.D., Mark Parrish², Douwe Atsma¹, Anke Witteveen¹, Annuska Glas¹, Ph.D., Leonie Delahaye¹, Tony van der Velde¹, Harry Bartelink¹, M.D., Ph.D., Sjoerd Rodenhuis¹, M.D., Ph.D., Emiel Th Rutgers¹, M.D., Ph.D., Stephen Friend², M.D., Ph.D., and Rene Bernards¹ *, Ph.D.

¹ Divisions of Diagnostic Oncology, Radiotherapy and Molecular Carcinogenesis
and Center for Biomedical Genetics
The Netherlands Cancer Institute
121 Plesmanlaan
1066 CX Amsterdam
The Netherlands

² Rosetta Inpharmatics LLC*
12040 115th Avenue NE
Kirkland, Washington 98034
USA

‡ These authors contributed equally
* A wholly-owned subsidiary of Merck & Co., Inc.
# To whom correspondence should be addressed

Gene expression profiling predicts clinical outcome of breast cancer
Nature 415, 530 - 536 (2002)

Laura J. van ‘t Veer¹‡, Hongyue Dai² ‡, Marc J. van de Vijver1‡, Yudong D. He², Augustinus A.M. Hart¹, Mao Mao², Hans L. Peterse¹, Karin van der Kooy¹, Matthew J. Marton², Anke T. Witteveen¹, George J. Schreiber², Ron M. Kerkhoven¹, Chris Roberts², Peter S. Linsley², René Bernards¹ and Stephen H. Friend²#

¹ Divisions of Diagnostic Oncology, Radiotherapy and Molecular Carcinogenesis
and Center for Biomedical Genetics
The Netherlands Cancer Institute
121 Plesmanlaan
1066 CX Amsterdam
The Netherlands

² Rosetta Inpharmatics LLC*
12040 115th Avenue NE
Kirkland, Washington 98034
USA
‡ These authors contributed equally
* A wholly-owned subsidiary of Merck & Co., Inc.
# To whom correspondence should be addressed (stephen_friend@merck.com)

Early Growth Response Transcription Factors Are Required for Development of CD4(-) CD8(-) Thymocytes to the CD4(+) CD8(+) Stage
Journal of Immunology, 2002, 168: 1649-1658.

Michael Carleton^2,*, Mariëlle C. Haks^2,*,†, Sigrid A. A. Smeele^†, Allan Jones‡, Stanley M. Belkowski^*, Marc A. Berger^4,*, Peter Linsley^s‡, Ada M. Kruisbeek^‡ and David L. Wiest^3,*

^* Immunobiology Working Group, Division of Basic Sciences, Fox Chase Cancer Center, Philadelphia, PA 19111; ^† Division of Immunology, The Netherlands Cancer Institute, Amersterdam, The Netherlands; and ^‡ Rosetta Inpharmatics, Kirkland, WA 98034

2 M.C. and M.C.H. contributed equally to this work.
3 Address correspondence and reprint requests to: Dr. David L. Wiest, Fox Chase Cancer Center, Division of Basic Sciences, Immunobiology Working Group, 7701 Burholme Avenue, Philadelphia, PA 19111. E-mail address: DL_Wiest@FCCC.edu
4 Current address: Purdue BioPharma, Princeton, NJ 08540.

Modulation of TCR-induced transcriptional profiles by ligation of CD28, ICOS, and CTLA-4 receptors
PNAS, 2002. 99(18): p. 11790-5.

James L. Riley* †‡ , Mao Mao §, Sumire Kobayashi §, Matt Biery §, Julja Burchard §, Guy Cavet §, Brian P. Gregson*, Carl H. June*, and Peter S. Linsley †‡§

*Abramson Family Cancer Research Institute and Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160; and § Rosetta Inpharmatics, Kirkland, WA 98034

† J.L.R. and P.S.L. contributed equally to this work
‡ To whom reprint requests may be addressed at: Abramson Family Cancer Research Institute, 508 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104 (J.L.R.) or Rosetta Inpharmatics, 12040 115th Avenue Northeast, Kirkland, WA 98034 (P.S.L.). E-mail: rileyj@mail.med.upenn.edu or peter_linsley@merck.com.

Communicated by Gerald R. Crabtree, Stanford University School of Medicine, Stanford, CA, June 17, 2002 (received for review February 15, 2002)

Identification of genes over-expressed in small cell lung carcinoma using suppression subtractive hybridization and cDNA microarray expression analysis.
Oncogene. 2002 May 23;21(23):3814-25.

¹Bangur CS, Switzer A, Fan L, Marton MJ, Meyer MR, Wang T.

¹Tumor Antigen Discovery
Corixa Corporation
1124 Columbia Street
Seattle, Washington WA 98104, USA.
bangur@corixa.com

Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters.
Nat Genet. 2002 Jul;31(3):255-65.

Lani F. Wu ¹,³ *, Timothy R. Hughes¹,² *, Armaity P. Davierwala ², Mark D. Robinson ², Roland Stoughton ¹ &
Steven J. Altschuler ¹,³
*These authors contributed equally to this manuscript.

¹ Rosetta Inpharmatics LLC, Kirkland, Washington, USA.
² Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada.
³ Current address: Bauer Center for Genomics Research, Harvard University, Cambridge, Massachusetts, USA.
Correspondence should be addressed to S.J.A. (e-mail:saltschuler@cgr.harvard.edu).

Toxicogenomics and drug discovery: will new technologies help us produce better drugs?
Nature Reviews Drug Discovery 1, 84 -88 (2002)

Ulrich R, Friend SH¹.

¹Rosetta Inpharmatics LLC
12040 115th Avenue NE
Kirkland, Washington 98034, USA.
roger_ulrich@merck.com

Recent developments in DNA microarrays
Curr Opin Microbiol. 2002 Jun;5(3):334-7. Review.

Shoemaker DD¹, Linsley PS¹.

¹Rosetta Inpharmatics LLC
12040 115th Avenue North East
Kirkland, Washington 98034, USA.
daniel_shoemaker@merck.com

Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays.
Nucleic Acids Reserach. 2002 Aug 15;30(16):e86.

Hongyue Dai¹, Michael Meyer¹, Sergey Stepaniants¹, Michael Ziman, Ronald Stoughton¹

¹Rosetta Inpharmatics LLC
12040 115th Avenue North East
Kirkland, Washington 98034, USA.
email: ronald_stoughton@merck.com