Scientific Bibliography

Allinen M, Beroukhim R, Cai L, et al. Molecular characterization of the tumor microenvironment in breast cancer. Cancer Cell. 2004;6:17-32.

Bernstein BE, Kamal M, Lindblad-Toh K, et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell. 2005;120:169-181.

Buetow KH, Edmonson M, MacDonald R, et al. High-throughput development and characterization of a genome-wide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time of flight mass spectrometry. Proc Natl Acad Sci U S A. 2001;98:581-584.

Buetow KH, Klausner RD, Fine H, Kaplan R, Singer DS, Strausberg RL. Cancer Molecular Analysis Project: Weaving a rich cancer research tapestry. Cancer Cell. 2002;1:315-318.

Boon K, Osório EC, Greenhut SF, et al. An anatomy of normal and malignant gene expression. Proc Natl Acad Sci U S A. 2002;99:11287-11292.

Cawley S, Bekiranov S, Ng HH, et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell. 2004;116:499-509.

Cheng J, Kapranov P, Drenkow J, et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science. 2005;308:1149-1154.

Cheung VG, Nowak N, Jang W, et al. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 2001;409:953-958.

Egland KA, Vincent JJ, Strausberg R, Lee B, Pastan I. Discovery of the breast cancer gene BASE using a molecular approach to enrich for genes encoding membrane and secreted proteins. Proc Natl Acad Sci U S A. 2003;100:1099-1104.

Emmert-Buck MR, Strausberg RL, Krizman DB, et al. Molecular profiling of clinical tissues specimens: feasibility and applications. J Mol Diagn. 2000;2:60-66.

Emmert-Buck MR, Strausberg RL, Krizman DB, et al. Molecular profiling of clinical tissue specimens: feasibility and applications. Am J Pathol. 2000;156:1109-1115.

Fujii T, Dracheva T, Player A, et al. A transcriptome map of non-small cell lung cancer. Cancer Res. 2002;62:3340-3346.

Gerhard DS, Wagner L, Feingold EA, et al. The status, quality and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004;14:2121-2127.

Gillespie JW, Best CJM, Bichsel VE, et al. Evaluation of non-formalin tissue fixation for molecular profiling studies. Am J Pathol. 2002;160:449-457.

Gingeras TR. The multitasking genome. Nat Genet. 2006;38:608-609.

Iseli C, Stevenson BJ, de Souza SJ, et al. Long-range heterogeneity at the 3' ends of human mRNAs. Genome Res. 2002;12:1068-1074.

Jeon Y, Bekiranov S, Karnani N, et al. Temporal profile of replication of human chromosomes. Proc Natl Acad Sci U S A. 2005;102:6419-6424.

Jongeneel CV, Iseli C, Stevenson BJ, et al. Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing (MPSS). Proc Natl Acad Sci U S A. 2003;100:4702-4705.

Kampa D, Cheng J, Kapranov P, et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 2004;14:331-342.

Kapranov P, Cawley S, Drenkow J, et al. Large-scale transcriptional activity of the human genome revealed in chromosomes 21 and 22. Science. 2002;296:916-919.

Kapranov P, Drenkow J, Cheng J, et al. Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res. 2005;15:987-997.

Kirsch IR, Green ED, Yonescu R, et al. A systematic, high-resolution linkage of the cytogenetic and physical maps of the human genome. Nat Genet. 2000;24:339-340.

Klein SL, Strausberg RL, Wagner L, Pontius J, Clifton SW, Richardson P. Genetic and genomic tools for Xenopus research: The NIH Xenopus initiative: A peer reviewed forum. Developmental Dynamics. 2002;225:384-391.

Krizman DB, Wagner L, Lash A, Strausberg R, Emmert-Buck MR. The Cancer Genome Anatomy Project: EST sequencing and the genetics of cancer progression. Neoplasia. 1999;1:101-106.

Lal A, Lash A, Altschul S, et al. A public database for gene expression in human cancers. Cancer Res. 1999;59:5403-5407.

Lal A, Peters H, St Croix B, et al. Transcriptional response to hypoxia in human tumors. J Natl Cancer Inst. 2001;93:1337-1343.

Lash AE, Tolstoshev CM, Wagner L, et al. SAGEmap: a public gene expression resource. Genome Res. 2000;10:1051-1060.

Leethanakul C, Knezevic V, Patel V, et al. Gene discovery in oral squamous cell carcinoma through the Head and Neck Cancer Genome Anatomy Project: confirmation by microarray analysis. Oral Oncol. 2003;39:248-258.

Liu W, Putnam AL, Xu-Yu Z, et al. CD127 expression inversely correlates with FoxP3 and suppressive function of human CD4+ T reg cells. J Exp Med. 2006;203:1701-1711.

Loging WT, Lal A, Siu I-M, et al. Identifying potential tumor markers and antigens by database mining and rapid expression screening. Genome Res. 2000;10:1393-1402.

The Mammalian Gene Collection Program Team. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences by the Mammalian Gene Collection Program. Proc Natl Acad Sci U S A. 2002;99:16899-16903.

Manak J R, Dike S, Sementchenko V, et al. Functional roles of unannotated intergenic transcription revealed by genome-wide transcription maps of Drosophila melanogaster during embryonic development. Nat Genet. 2006;In press.

Morin RD, Chang E, Petrescu A, et al. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res. 2006;16:796-803.

Packer BR, Yeager M, Staats B, et al. SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes. Nucleic Acids Res. 2004;32:D528-D532.

Packer BR, Yeager M, Burdett L, et al. SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes. Nucleic Acids Res. 2006;34:D617-D621.

Porter D, Lahti-Domenici J, Keshaviah A, et al. Molecular markers in ductal carcinoma in situ of the breast. Mol Cancer Res. 2003;1:362-375.

Rangel LB, Sherman-Baust CA, Wernyj RP, Schwartz DR, Cho KR, Morin PJ. Characterization of novel human ovarian cancer-specific transcripts (HOSTs) identified by serial analysis of gene expression. Oncogene. 2003;22:7225-7232.

Riggins GJ, Strausberg RL. Genome and genetic resources from the Cancer Genome Anatomy Project. Hum Mol Genet. 2001;10:663-667.

Sakabe NJ, de Souza JE, Galante PA, et al. ORESTES are enriched in rare exon usage variants affecting the encoded proteins. C R Biol. 2003;32:979-985.

Schaefer C, Grouse L, Buetow K, Strausberg RL. A new Cancer Genome Anatomy Project web resource for the community. Cancer J. 2001;7:52-60.

Shillitoe EJ, May M, Patel V, et al. Genome-wide analysis of oral cancer - early results from the Cancer Genome Anatomy Project. Oral Oncol. 2000;36:8-16.

Siddiqui AS, Khattra J, Delaney AD, et al. A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci U S A. 2005;102:18485-18490.

Strausberg RL. The Cancer Genome Anatomy Project: building a new information and technology platform for cancer research. In: Srivastava S, Henson DE, Gazdar A, eds. Molecular Pathology of Early Cancer. Amsterdam: IOS Press; 1999:365-370.

Strausberg RL. Talkin' omics. Dis Markers. 2001;17:39.

Strausberg RL. The Cancer Genome Anatomy Project: new resources for reading the molecular signatures of cancer. J Pathol. 2001;195:31-40.

Strausberg RL, Austin MJF. Functional genomics: technological challenges and opportunities. Physiol Genomics 1999;1:25-32.

Strausberg RL, Buetow KH, Emmert-Buck M, Klausner RD. The Cancer Genome Anatomy Project: building an annotated gene index. Trends Genet. 2000;16:103-106.

Strausberg RL, Camargo AA, Riggins GJ, et al. An international database and integrated analysis tools for the study of cancer gene expression.
Pharmacogenomics J. 2002;2:156-164.

Strausberg RL, Feingold EA, Klausner RD, Collins FS. The Mammalian Gene Collection. Science. 1999;286:455-457.

Strausberg RL, Greenhut SF, Grouse LH, Schaefer CF, Buetow KH. In silico analysis of molecular signatures of cancer through the Cancer Genome Anatomy Project. Trends Cell Biol. 2001;11:S66-S71.

Strausberg RL, Greenhut SF, Grouse LH, Schaefer CF, Buetow KH. The Cancer Genome Anatomy Project: Online resources for reading molecular signatures of cancer. Cancer Invest. 2002;20:1038-1050.

Strausberg RL, Klausner RD. Reading the molecular signatures of cancer. In: Warrington, Wong, Todd, eds. Microarrays and Cancer. Westboro MA: Eaton Publishing; 2002:xi-xvi.

Strausberg RL, Riggins GJ. Navigating the human transcriptome. Proc Natl Acad Sci U S A. 2001;98:11837-11838.

Strausberg RL, Schreiber SL. From knowing to controlling: a path from genomics to drugs using small molecule probes. Science. 2003;300:294-295.

Tolliday, N, Clemons, PA, Ferraiolo, P, Koehler, AN, Lewis, TA, Li, X, Schreiber, SL, Gerhard, DS, Eliasof, S. Small Molecules, Big Players: the National Cancer Institute's Initiative for Chemical Genetics. Cancer Research 2006; 66:8935-8942.

Willingham AT, Gingeras TR. TUF love for “junk” DNA. Cell. 2006;125:1215-1220.

Back to Top