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Director's Challenge PI Meeting Agenda Nov 3-5, 2004

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Director’s Challenge Bibliography
  • Adamson E, de Belle I, Mittal S, Wang Y, Hayakawa J, Korkmaz K, O'Hagan D, McClelland M, Mercola D. (2003). Egr1 signaling in prostate cancer.Cancer Biol Ther. 2:617-622.
  • Adamson ED, Mercola D.  (2002).  Egr1 transcription factor: multiple roles in prostate tumor cell growth and survival. Tumour Biol. 23:93-102. Review.
  • Agrawal D, Chen T, Irby R, Quackenbush J, Chambers AF, Szabo M, Cantor A, Coppola D, Yeatman TJ. (2002). Osteopontin identified as lead marker of colon cancer progression, using pooled sample expression profiling. J Natl Cancer Inst 94:513-521.
  • Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger, DD, Armitage JO, Warnke R, Staudt LM, et al. (2000). Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403:503-511.
  • Alter O, Brown PO, Botstein D. (2000). Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA 97:10101-10106.
  • Alter O, Brown PO, Botstein D. (2003). Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proc Natl Acad Sci USA 100: 3351-3356.
  • Arango D, Corner GA, Wadler S, Catalano PJ, Augenlicht LH. (2001). c-myc/p53 interaction determines sensitivity of human colon carcinoma cells to 5-fluorouracil in vitro and in vivo. Cancer Res. 61:4910-4915.
  • Arango D, Mariadason JM, Wilson AJ, Yang W, Corner GA, Nicholas C, Aranes MJ, Augenlicht LH. (2003) c-Myc overexpression sensitises colon cancer cells to camptothecin-induced apoptosis. Br J Cancer. 89:1757-1765.
  • Augenlicht LH, Mariadason JM, Wilson A, Arango D, Yang W, Heerdt BG, Velcich, A. (2002). Short chain Fatty acids and colon cancer.  J Nutr 132: 3804S-3808S.
  • Augenlicht LH, Velcich A, Klampfer L, Huang J, Corner G, Aranes M, Laboisse C, Rigas B, Lipkin M, Yang K, Shi Q, Lesser M, Heerdt B, Arango D, Yang W, Wilson A, Mariadason JM. (2003) Application of gene expression profiling to colon cell maturation, transformation and chemoprevention. J Nutr. 133:2410S-2416S.
  • Baggerly KA, Deng L, Morris JS, Aldaz CM. (2003). Differential expression in SAGE: accounting for normal between-library variation. Bioinformatics. 19:1477-1483.
  • Beer DG, Kardia SL, Huang CC, Giordano TJ, Levin AM, Misek DE, Lin L, Chen G, Gharib TG, Thomas DG, Lizyness ML, Kuick R, Hayasaka S, Taylor JM, Iannettoni MD, Orringer MB, Hanash S. (2002). Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med. 8:816-824.
  • Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark EJ, Lander ES, Wong W, Johnson BE, Golub TR, Sugarbaker DJ, Meyerson M. (2001). Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci USA. 98:13790-13795.
  • Bloom G, Yang IV, Boulware D, Kwong KY, Coppola D, Eschrich S, Quackenbush J, Yeatman TJ. (2004). Multi-platform, multi-site, microarray-based human tumor classification. Am J Pathol. 164:9-16.
  • Bohen SP, Troyanskaya OG, Alter O, Warnke R, Botstein D, Brown PO, Levy R. (2003). Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proc Natl Acad Sci USA. 100:1926-1930.
  • Boon K, Edwards JB, Siu IM, Olschner D, Eberhart CG, Marra MA, Strausberg RL, Riggins GJ. (2003). Comparison of medulloblastoma and normal neural transcriptomes identifies a restricted set of activated genes. Oncogene. 22:7687-7694.
  • Boon K, Osório EC, Greenhut SF, Schaefer CF, Shoemaker J, Polyak K, Morin PJ, Buetow KH, Strausberg RL, de Souza SJ, Riggins. GJ. (2002). An anatomy of normal and malignant gene expression. Proc Natl Acad Sci USA. 99:11287-11292.
  • Brooks JD. (2002) Microarray analysis in prostate cancer research. Curr Opin Urol. 12:395-399.
  • Brunschwig EB, Wilson K, Mack D, Dawson D, Lawrence E, Willson JK, Lu S, Nosrati A, Rerko RM, Swinler S, Beard L, Lutterbaugh JD, Willis J, Platzer P, Markowitz S. (2003). PMEPA1, a transforming growth factor-beta-induced marker of terminal colonocyte differentiation whose expression is maintained in primary and metastatic colon cancer. Cancer Res. 63:1568-1575.
  • Chang HY, Chi J-T, Dudoit S, Bondre C, van de Rijn M, Botstein D, Brown PO. (2002). Diversity, topographic differentiation, and positional memory in human fibroblasts. Proc Natl Acad Sci USA. 99: 12877-12882.
  • Chan WC, Hans CP. (2003). Genetic and molecular genetic studies in the diagnosis of T and NK cell neoplasia. Hum Pathol. 34:314-321.
  • Chan WC, Huang JZ. (2001). Gene expression analysis in aggressive NHL. Ann Hematol.  80 Suppl 3:B38-41.
  • Chang HY, Sneddon JB, Alizadeh AA, Sood R, West RB, Montgomery K, Chi JT, Rijn Mv M, Botstein D, Brown PO. (2004). Gene Expression Signature of Fibroblast Serum Response Predicts Human Cancer Progression: Similarities between Tumors and Wounds. PLoS Biol  2:E7. Epub.
  • Chen X, Cheung ST, So S, Fan ST, Barry C, Higgins J, Lai KM, Ji J, Dudoit S, Ng IO, Van De Rijn M, Botstein D, Brown PO. (2002). Gene expression patterns in human liver cancers. Mol Biol Cell. 13:1929-1939.
  • Chen G, Gharib TG, Huang CC, Taylor JM, Misek DE, Kardia SL, Giordano TJ, Iannettoni MD, Orringer MB, Hanash SM, Beer DG. (2002). Discordant protein and mRNA expression in lung adenocarcinomas. Mol Cell Proteomics 1:304-313.
  • Chen G, Gharib TG, Huang CC, Thomas DG, Shedden KA, Taylor JM, Kardia SL, Misek DE, Giordano TJ, Iannettoni MD, Orringer MB, Hanash SM, Beer DG. (2002). Proteomic analysis of lung adenocarcinoma: identification of a highly expressed set of proteins in tumors. Clin Cancer Res. 8:2298-2305.
  • Chen G, Gharib TG, Thomas DG, Huang CC, Misek DE, Kuick RD, Giordano TJ, Iannettoni MD, Orringer MB, Hanash SM, Beer DG. (2003). Proteomic analysis of eIF-5A in lung adenocarcinomas. Proteomics. 3:496-504.
  • Chen G, Gharib TG, Wang H, Huang CC, Kuick R, Thomas DG, Shedden KA, Misek DE, Taylor JM, Giordano TJ, Kardia SL, Iannettoni MD, Yee J, Hogg PJ, Orringer MB, Hanash SM, Beer DG. (2003 ). Protein profiles associated with survival in lung adenocarcinoma. Proc Natl Acad Sci USA. 100:13537-13542.
  • Chen X, Leung SY, Yuen ST, Chu KM, Ji J, Li R, Chan AS, Law S, Troyanskaya OG, Wong J, So S, Botstein D, Brown PO. (2003). Variation in gene expression patterns in human gastric cancers. Mol Biol Cell. 14:3208-3215.
  • Chen G, Wang H, Gharib TG, Huang CC, Thomas DG, Shedden KA, Kuick R, Taylor JM, Kardia SL, Misek DE, Giordano TJ, Iannettoni MD, Orringer MB, Hanash SM, Beer DG. (2003). Overexpression of oncoprotein 18 correlates with poor differentiation in lung adenocarcinomas. Mol Cell Proteomics. 2:107-116.
  • Chen G, Wang H, Miller CT, Thomas DG, Gharib TG, Misek DE, Giordano TJ, Orringer MB, Hanash SM, Beer DG. (2004). Reduced selenium-binding protein 1 expression is associated with poor outcome in lung adenocarcinomas. J Pathol 202:321-329.
  • Chen T, Yang I, Irby R, Shain KH, Wang HG, Quackenbush J, Coppola D, Cheng JQ, Yeatman TJ. (2003). Regulation of caspase expression and apoptosis by adenomatous polyposis coli. Cancer Res. 63:4368-4374.
  • Chi JT, Chang HY, Haraldsen G, Jahnsen FL, Troyanskaya OG, Chang DS, Wang Z, Rockson SG, Van De Rijn M, Botstein D, Brown PO. (2003). Endothelial cell diversity revealed by global expression profiling. Proc Natl Acad Sci USA. 100:10623-10628.
  • Chi JT, Chang HY, Wang NN, Chang DS, Dunphy N, Brown PO. (2003). Genomewide view of gene silencing by small interfering RNAs. Proc Natl Acad Sci USA.100:6343-6346.
  • Choe G, Horvath S, Cloughesy TF, Crosby K, Seligson D, Palotie A, Inge L, Smith BL, Sawyers CL, Mischel PS. (2003). Analysis of the phosphatidylinositol 3'-kinase signaling pathway in glioblastoma patients in vivo. Cancer Res. 63:2742-2746.
  • Coppola D, Szabo M, Boulware D, Muraca P, Alsarraj M, Chambers AF, Yeatman TJ. (2004). Correlation of osteopontin protein expression and pathological stage across a wide variety of tumor histologies. Clin Cancer Res. 10:184-190.
  • Crawford EL, Peters GJ, Noordhuis P, Rots MG, Vondracek M, Grafstrom RC, Lieuallen K, Lennon G, Zahorchak RJ, Georgeson MJ, Wali A, Lechner JF, Fan PS, Kahaleh MB, Khuder SA, Warner KA, Weaver DA, Willey JC. (2001).  Reproducible gene expression measurement among multiple laboratories obtained in a blinded study using standardized RT (StaRT)-PCR. Mol Diagn. 6:217-225.
  • Crawford EL, Warner KA, Khuder SA, Zahorchak RJ, Willey JC. (2002).  Multiplex standardized RT-PCR for expression analysis of many genes in small samples. Biochem Biophys Res Commun. 293:509-516.
  • Creighton C, Hanash S, Beer D. (2003). Gene expression patterns define pathways correlated with loss of differentiation in lung adenocarcinomas. FEBS Lett. 540:167-170.
  • Cuezva JM, Chen G, Alonso AM, Isidoro A, Misek DE, Hanash SM, Beer DG. (2004). The bioenergetic signature of lung adenocarcinomas is a molecular marker of cancer diagnosis and prognosis. Carcinogenesis [Epub ahead of print]
  • Dave BJ, Nelson M, Pickering DL, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Sanger WG. (2002 ). Cytogenetic characterization of diffuse large cell lymphoma using multi-color fluorescence in situ hybridization. Cancer Genet Cytogenet. 132:125-132.
  • Davis RE, Staudt LM. (2002). Molecular diagnosis of lymphoid malignancies by gene expression profiling. Curr Opin Hematol. 9:333-338.
  • DePrimo SE, Diehn M, Nelson JB, Reiter RE, Matese J, Fero M, Tibshirani R,Brown PO, Brooks JD. (2002). Transcriptional programs activated by exposure of human prostate cancer cells to androgen. Genome Biol. 3:RESEARCH0032
  • Diehn M., Alizadeh AA, Brown PO. (2000). Examining the living genome in health and disease with DNA microarrays. JAMA. 283, 2298-2299.
  • Diehn M, Alizadeh AA, Rando  OJ, Liu CL, Stankunas K, Botstein D, Crabtree GR, Brown PO. (2002). Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation. Proc Natl Acad Sci USA. 99: 11796-11801.
  • Diehn M, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Sherlock G, Botstein D, Brown PO. (2003). SOURCE: A Unified Genomic Resource of Functional Annotations, Ontologies and Gene Expression Data.  Nucl. Acids Res. 31:219-223.
  • Fang NY, Greiner TC, Weisenburger DD, Chan WC, Vose JM, Smith LM, Armitage JO, Mayer RA, Pike BL, Collins FS, Hacia JG. (2003). Oligonucleotide microarrays demonstrate the highest frequency of ATM mutations in the mantle cell subtype of lymphoma. Proc Natl Acad Sci USA. 100:5372-5377.
  • Febbo PG, Sellers WR. (2003). Use of expression analysis to predict outcome after radical prostatectomy. J Urol. 170:S11-9; discussion S19-20.
  • Finlin BS, Gau CL, Murphy GA, Shao H, Kimel T, Seitz RS, Chiu YF, Botstein D, Brown PO, Der CJ, Tamanoi F, Andres DA, Perou CM. (2001). RERG is a novel ras-related, estrogen-regulated and growth-inhibitory gene in breast cancer. J Biol Chem. 276:42259-42267.
  • Friedman CP, Ozbolt JG, Masys DR. (2001). Toward a new culture for biomedical informatics: report of the 2001 ACMI symposium. J Am Med Inform Assoc. 8:519-526.
  • Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, van de Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, Petersen I. (2001). Diversity of gene expression in adenocarcinoma of the lung.  Proc Natl Acad Sci USA. 98:13784-13789.
  • Gascoyne RD, Lamant L, Martin-Subero JI, Lestou VS, Harris NL, Muller-Hermelink HK, Seymour JF, Horsman DE, Auvigne I, Espinos E, Siebert R, Delsol G. (2003). ALK-positive diffuse large B-cell lymphoma is associated with Clathrin-ALK rearrangements: report of six cases. Blood. 102:2568-2573.
  • Gerald WL. (2003). Genome-wide gene expression analysis of prostate carcinoma. Semin Oncol. 30:635-648. Review.
  • Gharib TG, Chen G, Wang H, Huang CC, Prescott MS, Shedden K, Misek DE, Thomas DG, Giordano TJ, Taylor JM, Kardia S, Yee J, Orringer MB, Hanash S, Beer DG. (2002). Proteomic analysis of cytokeratin isoforms uncovers association with survival in lung adenocarcinoma. Neoplasia  4:440-448.
  • Giordano TJ, Shedden KA, Schwartz DR, Kuick R, Taylor JM, Lee N, Misek DE, Greenson JK, Kardia SL, Beer DG, Rennert G, Cho KR, Gruber SB, Fearon ER, Hanash S. (2001). Organ-specific molecular classification of primary lung, colon, and ovarian  adenocarcinomas using gene expression profiles. Am J Pathol. 159:1231-1238.
  • Giordano TJ, Thomas DG, Kuick R, Lizyness M, Misek DE, Smith AL, Sanders D, Aljundi RT, Gauger PG, Thompson NM, Taylor JM, Hanash SM. (2003). Distinct transcriptional profiles of adenocortical tumors uncovered by DNA microarray analysis. Am J Pathol. 162:521-531.
  • Glinsky GV, Krones-Herzig A, Glinskii AB, Gebauer G. (2003). Microarray analysis of xenograft-derived cancer cell lines representing multiple experimental models of human prostate cancer. Mol Carcinog. 37:209-221.
  • Gollub J, Ball C, Binkley G, Demeter J, Hebert G, Hernandez-Boussard T, Jin H, Kaloper M, Matese J, Schroeder M, Brown PO, Botstein D, Sherlock G. (2003). The Stanford Microarray Database: Data Access and Quality Assessment Tools. Nucl. Acids Res. 31:94-96.
  • Haab BB, Dunham MJ, Brown PO. (2001). Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol 2, RESEARCH0004.
  • Hanash SM. (2001). Global profiling of gene expression in cancer using genomics and proteomics. Curr Opin Mol Ther. 3:538-545. Review.
  • Hanash SM, Bobek MP, Rickman DS, Williams T, Rouillard JM, Kuick R, Puravs E. (2002). Integrating cancer genomics and proteomics in the post-genome era. Proteomics. 2:69-75.
  • Hanash S, Brichory F, Beer D. (2001). A proteomic approach to the identification of lung cancer markers. Dis Markers. 17:295-300. Review.
  • Hanash S, Creighton C. (2003). Making sense of microarray data to classify cancer. Pharmacogenomics J. 3:308-311.
  • Hans CP, Weisenburger DD, Greiner TC, Gascoyne RD, Delabie J, Ott G, Muller-Hermelink HK, Campo E, Braziel RM, Jaffe ES, Pan Z, Farinha P, Smith LM, Falini B, Banham AH, Rosenwald A, Staudt LM, Connors JM, Armitage JO, Chan WC. (2004). Confirmation of the molecular classification of diffuse large B-cell lymphoma by immunohistochemistry using a tissue microarray. Blood. 103:275-282.
  • Hastie T, Tibshirani R, Botstein D, Brown P. (2001). Supervised harvesting of expression trees. Genome Biol 2, RESEARCH0003.
  • Hastie T, Tibshirani R, Eisen MB, Alizadeh A, Levy R, Staudt L, Chan WC, Botstein D, Brown P. (2000). 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns.  Genome Biol 1, RESEARCH0003.
  • Hegde P, Qi R, Gaspard R, Abernathy K, Dharap S, Earle-Hughes J, Gay C, Nwokekeh NU, Chen T, Saeed AI, Sharov V, Lee NH, Yeatman TJ, Quackenbush J. (2001). Identification of tumor markers in models of human colorectal cancer using a 19,200-element complementary DNA microarray. Cancer Res. 61:7792-7797.
  • Higgins JP, Montgomery K, Wang L, Domanay E, Warnke RA, Brooks JD, van de Rijn M. (2003). Expression of FKBP12 in benign and malignant vascular endothelium: an immunohistochemical study on conventional sections and tissue microarrays. Am J Surg Pathol. 27:58-64.
  • Higgins JT, Shinghal R, Gill H, Reese JH, Terris M, Cohen RJ, Fero M, Pollack JR, van de Rijn M, Brooks JD. (2003). Gene Expression Patterns in Renal Cell Carcinoma Assessed by Complementary DNA Microarray. Am J Pathol. 162: 925-932.
  • Higgins JP, Wang L, Kambham N, Montgomery K, Mason V, Vogelmann SU, Lemley KV, Brown PO, Brooks JD, van de Rijn M. (2004). Gene expression in the normal adult human kidney assessed by complementary DNA microarray. Mol Biol Cell. 15:649-656.
  • Hinoi T, Lucas PC, Kuick R, Hanash S, Cho KR, Fearon ER. (2002). CDX2 regulates liver intestine-cadherin expression in normal and malignant colon epithelium and intestinal metaplasia. Gastroenterology. 123:1565-1577.
  • Holterhus PM, Hiort O, Demeter J, Brown PO, Brooks JD. (2003). Differential gene-expression patterns in genital fibroblasts of normal males and 46,XY females with androgen insensitivity syndrome: evidence for early programming involving the androgen receptor. Genome Biol. 4:R37.
  • Holzbeierlein J, Lal P, LaTulippe E, Smith A, Satagopan J, Zhang L, Ryan C, Smith S, Scher H, Scardino P, Reuter V, Gerald WL. (2004). Gene expression analysis of human prostate carcinoma during hormonal therapy identifies androgen-responsive genes and mechanisms of therapy resistance. Am J Pathol. 164:217-227.
  • Horsman DE, Okamoto I, Ludkovski O, Le N, Harder L, Gesk S, Siebert R, Chhanabhai M, Sehn L, Connors JM, Gascoyne RD. (2003). Follicular lymphoma lacking the t(14;18)(q32;q21): identification of two disease subtypes. British Journal of Haematology. 120:424-433.
  • Huang J, Qi R, Quackenbush J, Dauway E, Lazaridis E, Yeatman T. (2001). Effects of ischemia on gene expression. J Surg Res. 99:222-227.
  • Huang JZ, Sanger WG, Greiner TC, Staudt LM, Weisenburger DD, Pickering DL, Lynch JC, Armitage JO, Warnke RA, Alizadeh AA, Lossos IS, Levy R, Chan WC. (2002). The t(14;18) defines a unique subset of diffuse large B-cell lymphoma with a germinal center B-cell gene expression profile. Blood 99:2285-2290.
  • Iacobuzio-Donahue CA, Maitra A, Olsen M, Lowe AW, van Heek NT, Rosty C, Walter K, Sato N, Parker A, Ashfaq R, Jaffee E, Ryu B, Jones J, Eshleman JR, Yeo CJ, Cameron JL, Kern SE, Hruban RH, Brown PO, Goggins M. (2003). Exploration of global gene expression patterns in pancreatic adenocarcinoma using cDNA microarrays. Am J Pathol. 162:1151-1162.
  • James AC, Veitch JG, Zareh AR, Triche T. (2004). Sensitivity and specificity of five abundance estimators for high-density oligonucleotide microarrays. Bioinformatics. [Epub ahead of print]
  • Jazaeri AA, Yee CJ, Sotiriou C, Brantley KR, Boyd J, Liu ET. (2002). Gene expression profiles of BRCA1-linked, BRCA2-linked, and sporadic ovarian cancers. J Natl Cancer Inst. 94:990-1000.
  • Kachman MT, Wang H, Schwartz DR, Cho KR, Lubman DM. (2002). A 2-D liquid separations/mass mapping method for interlysate comparison of ovarian cancers. Anal Chem. 74:1779-1791.
  • Kari L, Loboda A, Nebozhyn M, Rook AH, Vonderheid EC, Nichols C, Virok D, Chang C, Horng WH, Johnston J, Wysocka M, Showe MK, Showe LC. (2003). Classification and prediction of survival in patients with the leukemic phase of cutaneous T cell lymphoma. J Exp Med. 197:1477-1488.
  • Khoury H, Lestou VS, Gascoyne RD, Bruyere H, Li CH, Nantel SH, Dalal BI, Naiman SC, Horsman DE. (2003). Multicolor karyotyping and clinicopathological analysis of three intravascular lymphoma cases. Mod Pathol. 16:716-724.
  • Kim PJ, Plescia J, Clevers H, Fearon ER, Altieri DC. (2003). Survivin and molecular pathogenesis of colorectal cancer. Lancet. 362:205-209.
  • Klampfer L, Huang J, Corner G, Mariadason J, Arango D, Sasazuki T, Shirasawa S, Augenlicht L. (2003). Oncogenic k-ras inhibits the expression of IFN-responsive genes through inhibition of STAT1 and STAT2 expression. J Biol Chem. 278:46278-46287.
  • Klampfer L, Huang J, Sasazuki T, Shirasawa S, Augenlicht L. (2003). Inhibition of interferon gamma signaling by the short chain fatty acid butyrate. Mol Cancer Res. 1:855-862.
  • Ladanyi M, Chan W C, Triche T J, Gerald W L. (2001). Expression profiling of human tumors: the end of surgical pathology? J Mol Diagn. 3:92-97.
  • Lal A, Glazer CA, Martinson HM, Friedman HS, Archer GE, Sampson JH, Riggins GJ. (2002). Mutant Epidermal Growth Factor Receptor Up-Regulates Molecular Effectors of Tumor Invasion. Cancer Res. 62:3335-3339.
  • Lamant L, Gascoyne RD, Duplantier MM, Armstrong F, Raghab A, Chhanabhai M, Rajcan-Separovic E, Raghab J, Delsol G, Espinos E. (2003). Non-muscle myosin heavy chain (MYH9): a new partner fused to ALK in anaplastic large cell lymphoma. Genes Chromosomes Cancer. 37:427-432.
  • Lapointe J, Li C, Higgins JP, van de Rijn M, Bair E, Montgomery K, Ferrari M, Egevad L, Rayford W, Bergerheim U, Ekman P, DeMarzo AM, Tibshirani R, Botstein D, Brown PO, Brooks JD, Pollack JR. (2004). Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci USA. 101:811-816.
  • LaTulippe E, Satagopan J, Smith A, Scher H, Scardino P, Reuter V, Gerald WL. (2002). Comprehensive gene expression analysis of prostate cancer reveals distinct transcriptional programs associated with metastatic disease. Cancer Res. 62:4499-4506.
  • Lau CC, Harris CP, Lu XY, Perlaky L, Gogineni S, Chintagumpala M, Hicks J, Johnson ME, Davino NA, Huvos AG, Meyers PA, Healy JH, Gorlick R, Rao PH. (2004). Frequent amplification and rearrangement of chromosomal bands 6p12-p21 and 17p11.2 in osteosarcoma. Genes Chromosomes Cancer. 39:11-21.
  • Lestou VS, Gascoyne RD, Sehn L, Ludkovski O, Chhanabhai M, Klasa RJ, Husson H, Freedman AS, Connors JM, Horsman DE. (2003). Multicolour fluorescence in situ hybridization analysis of t(14;18)-positive follicular lymphoma and correlation with gene expression data and clinical outcome. Br J Haematol. 122:745-759.
  • Lestou VS, Ludkovski O, Connors JM, Gascoyne RD, Lam WL, Horsman DE. (2003). Characterization of the recurrent translocation t(1;1)(p36.3;q21.1-2) in non-Hodgkin lymphoma by multicolor banding and fluorescence in situ hybridization analysis. Genes Chromosomes Cancer. 36:375-381.
  • Leung JY, Kolligs FT, Wu R, Zhai Y, Kuick R, Hanash S, Cho KR, Fearon ER.  (2002). Activation of AXIN2 expression by beta-catenin-T cell factor. A feedback repressor pathway regulating Wnt signaling. J Biol Chem. 277:21657-21665.
  • Leung SY, Chen X, Chu KM, Yuen ST, Mathy J, Ji J, Chan ASY, Li R, Law S, Troyanskaya OG, Tum I-P, Wong J, So S, Botstein D, Brown PO. (2002). Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis. Proc Natl Acad Sci USA. 99:16203-16208.
  • Lieberfarb ME, Lin M, Lechpammer M, Li C, Tanenbaum DM, Febbo PG, Wright RL, Shim J, Kantoff PW, Loda M, Meyerson M, Sellers WR. (2003). Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP.  Cancer Res. 63:4781-4785.
  • Lin F, Yu YP, Woods J, Cieply K, Gooding B, Finkelstein P, Dhir R, Krill D, Becich MJ, Michalopoulos G, Finkelstein S, Luo JH. (2001). Myopodin, a synaptopodin homologue, is frequently deleted in invasive prostate cancers. Am J Pathol. 159:1603-1612.
  • Lindblad-Toh K, Tanenbaum DM, Daly MJ, Winchester E, Lui WO, Villapakkam A, Stanton SE, Larsson C, Hudson TJ, Johnson BE, Lander ES, Meyerson M. (2000). Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat Biotechnol. 18:1001-1005.
  • Linn SC, West RB, Pollack JR, Zhu S, Hernandez-Boussard T, Nielsen TO, Rubin BP, Patel R, Goldblum JR, Siegmund D, Botstein D, Brown PO, Gilks CB, van de Rijn M. (2003). Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans. Am J Pathol. 163:2383-2395.
  • Liu CL, Prapong W, Natkunam Y, Alizadeh A, Montgomery K, Gilks CB, van de Rijn M. (2002). Software Tools for High-Throughput Analysis and Archiving of Immunohistochemistry Staining Data Obtained with Tissue Microarrays. Am J Pathol. 161: 1557-1565.
  • Logsdon CD, Simeone DM, Binkley C, Arumugam T, Greenson JK, Giordano TJ, Misek DE, Kuick R, Hanash S. (2003). Molecular profiling of pancreatic adenocarcinoma and chronic pancreatitis identifies multiple genes differentially regulated in pancreatic cancer. Cancer Res. 63:2649-2657.
  • Lonning PE, Sorlie T, Perou CM, Brown PO, Botstein D, Borresen-Dale AL.  (2001). Microarrays in primary breast cancer--lessons from chemotherapy studies. Endocr Relat Cancer. 8:259-263.
  • Lossos IS, Alizadeh AA, Eisen MB, Chan WC, Brown PO, Botstein D, Staudt LM, Levy R. (2000). Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas. Proc Natl Acad Sci USA. 97:10209-10213.
  • Luo JH. (2002). Gene expression alterations in human prostate cancer. Drugs Today. 38:713-719. Review.
  • Lu KV, Jong KA, Rajasekaran AK, Cloughesy TF, Mischel PS. (2004) Upregulation of tissue inhibitor of metalloproteinases (TIMP)-2 promotes matrix metalloproteinase (MMP)-2 activation and cell invasion in a human glioblastoma cell line. Lab Invest. 84:8-20.
  • Luo JH, Yu YP, Cieply K, Lin F, Deflavia P, Dhir R, Finkelstein S, Michalopoulos G, Becich M. (2002). Gene expression analysis of prostate cancers. Mol Carcinog. 33:25-35.
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