Cancer Program Publications

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Bioinformatics & Computational BiologyGISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
Craig Mermel, Steven Schumacher, Barbara Hill, Matthew Meyerson, Rameen Beroukhim, and Gad Getz
Mermel, C. H., Schumacher, S. E., Hill, B., Meyerson, M. L., Beroukhim, R., and Getz, G. (2011). GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol, 12(4), R41. doi: 10.1186/gb-2011-12-4-r41
 MicroRNA-Based Classification of Hepatocellular Carcinoma and Oncogenic Role of miR-517a
Toffanin S, Hoshida Y, Lachenmayer A, Villanueva A, Cabellos L, Minguez B, Savic R, Ward SC, Thung S, Chiang DY, Alsinet C, Tovar V, Roayaie S, Schwartz M, Bruix J, Waxman S, Friedman SL, Golub T, Mazzaferro V, Llovet JM
Gastroenterology. 2011
 Combining Clinical, Pathology, and Gene Expression Data to Predict Recurrence of Hepatocellular Carcinoma
Villanueva A, Hoshida Y, Battiston C, Tovar V, Sia D, Alsinet C, Cornella H, Liberzon A, Kobayashi M, Kumada H, Thung SN, Bruix J, Newell P, April C, Fan JB, Roayaie S, Mazzaferro V, Schwartz ME, Llovet JM
Gastroenterology. 2011
 Nearest Template Prediction: A Single-Sample-Based Flexible Class Prediction with Confidence Assessment
Yujin Hoshida
PLoS ONE 5(11): e15543
 Molecular sampling of prostate cancer: a dilemma for predicting disease progression
Andrea Sboner, Francesca Demichelis, Stefano Calza, Yudi Pawitan, Sunita R Setlur, Yujin Hoshida, Sven Perner, Hans-Olov Adami, Katja Fall, Lorelei A Mucci, Philip W Kantoff, Meir Stampfer, Swen-Olof Andersson, Eberhard Varenhorst, Jan-Erik Johansson, Mark B Gerstein, Todd R Golub, Mark A Rubin and Ove Andren
BMC Medical Genomics. 2010 Mar 16;3(1):8
 The landscape of somatic copy-number alteration across human cancers
Rameen Beroukhim*, Craig H. Mermel*, Dale Porter, Guo Wei, Soumya Raychaudhuri, Jerry Donovan, Jordi Barretina, Jesse S. Boehm, Jennifer Dobson, Mitsuyoshi Urashima, Kevin T. Mc Henry, Reid M. Pinchback, Azra H. Ligon, Yoon-Jae Cho, Leila Haery, Heidi Greulich, Michael Reich, Wendy Winckler, Michael S. Lawrence, Barbara A. Weir, Kumiko E. Tanaka, Derek Y. Chiang, Adam J. Bass, Alice Loo, Carter Hoffman, John Prensner, Ted Liefeld, Qing Gao, Derek Yecies, Sabina Signoretti, Elizabeth Maher, Frederic J. Kaye, Hidefumi Sasaki, Joel E. Tepper, Jonathan A. Fletcher, Josep Tabernero, Jose Baselga, Ming-Sound Tsao, Francesca DeMichelis, Mark A. Rubin, Pasi A. Janne, Mark J. Daly, Carmelo Nucera, Ross L. Levine, Benjamin L. Ebert, Stacey Gabriel, Anil K. Rustgi, Cristina R. Antonescu, Marc Ladanyi, Anthony Letai, Levi A. Garraway, Massimo Loda, David G. Beer, Lawrence D. True, Aikou Okamoto, Scott L. Pomeroy, Samuel Singer, Todd R. Golub, Eric S. Lander1, Gad Getz, William R. Sellers & Matthew Meyerson
Nature 463, 899-905(18 February 2010)
 Integrative Transcriptome Analysis Reveals Common Molecular Subclasses of Human Hepatocellular Carcinoma
Yujin Hoshida, Sebastian M.B. Nijman, Masahiro Kobayashi, Jennifer A. Chan, Jean-Philippe Brunet, Derek Y. Chiang, Augusto Villanueva, Philippa Newell, Kenji Ikeda, Masaji Hashimoto, Goro Watanabe, Stacey Gabriel, Scott L. Friedman, Hiromitsu Kumada, Josep M. Llovet, Todd R. Golub
Cancer Research 2009;69(18):7385-92
 Ultrasome: Efficient aberration caller for copy-number studies of ultra-high resolution
Bjorn Nilsson, Mikael Johansson, Fatima Al-Shahrour, Anne E. Carpenter, Benjamini L. Ebert
Bioinformatics (2009), in press.
 High-resolution mapping of copy-number alterations with massively parallel sequencing
Derek Y. Chiang, Gad Getz, David B. Jaffe, Michael J.T. O'Kelly, Xiaojun Zhao, Scott L. Carter, Carsten Russ, Chad Nusbaum, Matthew Meyerson, Eric S. Lander
Nature Methods 6:99-103
 Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma
Yujin Hoshida, Augusto Villanueva, Masahiro Kobayashi, Judit Peix, Derek Y. Chiang, Amy Camargo, Supriya Gupta, Jamie Moore, Matthew J. Wrobel, Jim Lerner, Michael Reich, Jennifer A. Chan, Jonathan N. Glickman, Kenji Ikeda, Masaji Hashimoto, Goro Watanabe, Maria G. Daidone, Sasan Roayaie, Myron Schwartz, Swan Thung, Helga B. Salvesen, Stacey Gabriel, Vincenzo Mazzaferro, Jordi Bruix, Scott L. Friedman, Hiromitsu Kumada, Josep M. Llovet, Todd R. Golub
N Engl J Med 2008;359:1995-2004
 CDK8 is a colorectal cancer oncogene that regulates bold beta-catenin activity
Firestein R, Bass AJ, Kim SY, Dunn IF, Silver SJ, Guney I, Freed E, Ligon AH, Vena N, Ogino S, Chheda MG, Tamayo P, Finn S, Shrestha Y, Boehm JS, Jain S, Bojarski E, Mermel C, Barretina J, Chan JA, Baselga J, Tabernero J, Root DE, Fuchs CS, Loda M, Shivdasani RA, Meyerson M, Hahn WC.
Firestein R, Bass AJ, Kim SY, Dunn IF, Silver SJ, Guney I, Freed E, Ligon AH, Vena N, Ogino S, Chheda MG, Tamayo P, Finn S, Shrestha Y, Boehm JS, Jain S, Bojarski E, Mermel C, Barretina J, Chan JA, Baselga J, Tabernero J, Root DE, Fuchs CS, Loda M, Shivdasani RA, Meyerson M, Hahn WC. CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity. Nature. 2008 Sep 25;455(7212):547-51. Epub 2008 Sep 14.
 Focal gains of VEGFA and molecular classification of hepatocellular carcinoma
Derek Y. Chiang, Augusto Villanueva, Yujin Hoshida, Judit Peix, Philippa Newell, Beatriz Minguez, Amanda LeBlanc, Diana Donovan, Swan Thung, Manel Sole, Victoria Tovar, Clara Alsinet, Alex Ramos, Jordi Barretina, Sasan Roayaie, Myron Schwartz, Samuel Waxman, Jordi Bruix, Vincenzo Mazzaferro, Azra Ligon, Vesna Najfeld, Scott Friedman, William Sellers, Matthew Meyerson, Josep Llovet
Cancer Res. 68(16):6779-88
 Carcinoma-Associated Fibroblast-Like Differentiation of Human Mesenchymal Stem Cells
Pravin J. Mishra, Prasun J. Mishra, Rita Humeniuk, Daniel J. Medina, Gabriela Alexe, Jill P. Mesirov, Sridhar Ganesan, John W. Glod and Debabrata Banerjee
Cancer Res 2008;68(11):4331-9
 Gene Expression Changes in an Animal Melanoma Model Correlate with Aggressiveness of Human Melanoma Metastases
Lei Xu, Steven S. Shen, Yujin Hoshida, Aravind Subramanian, Ken Ross, Jean-Philippe Brunet, Stephan N. Wagner, Sridhar Ramaswamy, Jill P. Mesirov, and Richard O. Hynes
Molecular Cancer Research 6, 760-769, May 1, 2008
 An erythroid differentiation signature predicts response to lenalidomide in Myelodysplastic Syndrome
Benjamin L. Ebert, Naomi Galili, Pablo Tamayo, Jocelyn Bosco, Raymond Mak, Jennifer Pretz, Christine Ladd-Acosta, Richard Stone, Todd R. Golub and Azra Raza.
 Identification of RPS14 as a 5q- syndrome gene by RNA interference screen
Benjamin L. Ebert, Jennifer Pretz, Jocelyn Bosco, Cindy Y. Chang, Pablo Tamayo, Naomi Galili, Azra Raza, David E. Root, Eyal Attar, Steven R. Ellis, and Todd R. Golub.
Nature 451, 335-339 (17 January 2008) | doi:10.1038/nature06494
 Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma
Rameen Beroukhim, Gad Getz, Leia Nghiemphu, Jordi Barretina, Teli Hsueh, David Linhart, Igor Vivanco, Jeffrey C. Lee, Julie H. Huang, Sethu Alexander, Jinyan Du, Tweeny Kau, Roman K. Thomas, Kinjal Shah, Horacio Soto, Sven Perner, John Prensner, Ralph M. Debiasi, Francesca Demichelis, Charlie Hatton, Mark A. Rubin, Levi A. Garraway, Stan F. Nelson, Linda Liau, Paul Mischel, Tim F. Cloughesy, Matthew Meyerson, Todd R. Golub, Eric S. Lander, Ingo K. Mellinghoff, William R. Sellers
Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):20007-12
 Subclass Mapping: Identifying Common Subtypes in Independent Disease Data Sets
Yujin Hoshida, Jean-Philippe Brunet, Pablo Tamayo, Todd R. Golub, Jill P. Mesirov
PLoS ONE 2(11): e1195, 2007
 High Expression of Lymphocyte-Associated Genes in Node-Negative HER2+ Breast Cancers Correlates with Lower Recurrence Rates
Gabriela Alexe, Gul S. Dalgin, Daniel Scanfeld, Pablo Tamayo, Jill P. Mesirov, Charles DeLisi, Lyndsay Harris, Nicola Barnard, Maritza Martel, Arnold J. Levine, Shridar Ganesan and Gyan Bhanot
Cancer Res. 2007;67(22):10669-76.
 Metagene projection for cross platform, cross species characterization of global transcriptional states
Pablo Tamayo, Daniel Scanfeld, Benjamin L. Ebert, Michael A. Gillette, Charles W. M. Roberts, and Jill P. Mesirov.
Proc. Natl. Acad. Sci. USA, 104: 5959-5964
 A transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent diffuse large B-cell lymphomas
Jose M. Polo, Przemyslaw Juszczynski, Stefano Monti, Leandro Cerchietti, Kenny Ye, John M. Greally, Margaret Shipp, Ari Melnick
PNAS 104(9): 3207-3212, 2007
 Gene Expression Profiling Reveals Reproducible Human Lung Adenocarcinoma Subtypes in Multiple Independent Patient Cohorts
DN Hayes, S Monti, G Parmigiani, CB Gilks, K Naoki, A Bhattacharjee, MA Socinski, C Perou and M Meyerson
J Clin Oncol, 24(31): 5079-5090, 2006.
 Comparative Gene Marker Selection Suite
Joshua Gould, Gad Getz, Stefano Monti, Michael Reich, Jill P. Mesirov
Bioinformatics 22(15): 1924-1925, 2006.
 GenePattern 2.0
Michael Reich, Ted Liefeld, Joshua Gould, Jim Lerner, Pablo Tamayo & Jill P Mesirov
Nat. Genet. 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500
 Allele-specific amplification in cancer revealed by SNP array analysis.
Thomas LaFramboise, Barbara A. Weir, Xiaojun Zhao, Rameen Beroukhim, Cheng Li, David Harrington, William R. Sellers, Matthew Meyerson
PLoS Comput Biol. 2005 Nov;1(6):e65.
 The impact of Life Science Identifiers on Informatics data
Martin, S., Hohmann, MM, Liefeld, T.
Drug Discovery Today. 2005 Nov 15;10(22):1566-72
 Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian, Pablo Tamayo, Vamsi K. Mootha, Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda Paulovich, Scott L. Pomeroy, Todd R. Golub, Eric S. Lander, and Jill P. Mesirov.
 GeneCruiser: a web service for the annotation of microarray data
Ted Liefeld, Michael Reich, Josh Gould, Peili Zhang, Pablo Tamayo, and Jill P. Mesirov
Bioinformatics, doi:10.1093/bioinformatics/bti587
 Molecular profiling of diffuse large B-cell lymphoma reveals a novel disease subtype with brisk host inflammatory response and distinct genetic features
Stefano Monti, Kerry J. Savage, Jeffery L. Kutok, Friedrich Feuerhake, Paul Kurtin, Martin Mihm, Bingyan Wu, Laura Pasqualucci, Donna Neuberg, Ricardo C.T. Aguiar, Paola Dal Cin, Christine Ladd, Geraldine S. Pinkus, Gilles Salles, Nancy L. Harris, Riccardo Dalla-Favera, Thomas Habermann, Jon C. Aster, Todd R. Golub, Margaret A. Shipp
Blood, 1 March 2005, Vol. 105, No. 5, pp. 1851-1861
 Erra and Gabpa/b specify PGC-1a-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle
Vamsi K. Mootha, Christoph Handschin, Dan Arlow, Xiaohui Xie, Julie St. Pierre, Smita Sihag, Wenli Yang, David Altshuler, Pere Puigserver, Nick Patterson, Patricia J. Willy, Ira G. Shulman, Richard A. Heyman, Eric S. Lander, and Bruce M. Spiegelman
Proc. Natl. Acad. Sci. USA
 Metagenes and molecular pattern discovery using matrix factorization
Jean-Philippe Brunet, Pablo Tamayo, Todd Golub, Jill Mesirov
Proc. Natl. Acad. Sci. USA 2004 101: 4164-4169
 Globally distributed object identification for biological knowledgebases
Clark T., Martin S., Liefeld T.
Briefings in Bioinformatics 5.1:59-70
 GeneCluster 2.0: An advanced toolset for bioarray analysis
M. Reich, K. Ohm, P. Tamayo, M. Angelo, J.P. Mesirov
Bioinformatics 2004; doi:10.1093/bioinformatics/bth138
 dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data.
Ming Lin, Lee-Jen Wei, William R. Sellers, Marshall Lieberfarb, Wing Hung Wong, and Cheng Li
Bioinformatics. 2004 May 22;20(8):1233-40.
 Microarray Data Mining: Facing the Challenges
Gregory Piatetsky-Shapiro and Pablo Tamayo
SIGKDD Explorations December 2003. Volume 5, Issue 2
 A Mechanism of Cyclin D1 Action Encoded in the Patterns of Gene Expression in Human Cancer
Justin Lamb, Sridhar Ramaswamy, Heide L. Ford, Bernardo Contreras, Robert V. Martinez, Frances S. Kittrell, Cynthia A. Zahnow, Nick Patterson, Todd R. Golub and Mark E. Ewen
Cell 114: 323-334 2003
 Estimating Dataset Size Requirements for Classifying DNA Microarray Data
Sayan Mukherjee, Pablo Tamayo, Simon Rogers, Ryan Rifkin, Anna Engle, Colin Campbell, Todd R. Golub and Jill P. Mesirov.
J. of Comp. Biol. vol 10, n2, p119-142 (2003)
 Consensus Clustering: A resampling-based method for class discovery and visualization of gene expression microarray data
Stefano Monti, Pablo Tamayo, Jill Mesirov, and Todd Golub
Machine Learning Journal, 52(1-2):91-118, 2003.
 An Analytical Method For Multi-class Molecular Cancer Classification
Ryan Rifkin, Sayan Mukherjee, Pablo Tamayo, Sridhar Ramaswamy, Chen-Hsiang Yeang, Michael Angelo, Michael Reich, Tomaso Poggio, Eric S. Lander, Todd R. Golub and Jill P. Mesirov.
SIAM Review, vol. 45, number 4, pp. 706-723 (2003).
Copyright ? 2003 by Society for Industrial and Applied Mathematics
 Evidence for a Molecular Signature of Metastasis in Primary Solid Tumors
Sridhar Ramaswamy, Ken N. Ross, Eric S. Lander, & Todd R. Golub
Nature Genetics, vol. 33, January 2003, pp. 49-54.
 A Strategy for Oligonucleotide Microarray Probe Reduction
Alena A. Antipova, Pablo Tamayo, and Todd R. Golub
Genome Biology 2002, 3(12):research0073.1?0073.4
 Multi-Class Cancer Diagnosis Using Tumor Gene Expression Signatures
Sridhar Ramaswamy, Pablo Tamayo, Ryan Rifkin, Sayan Mukherjee, Chen-Hsiang Yeang, Michael Angelo, Christine Ladd, Michael Reich, Eva Latulippe , Jill P. Mesirov, Tomaso Poggio, William Gerald , Massimo Loda, Eric S. Lander, Todd R. Golub
PNAS 98: 15149-15154
 Molecular Classification of Multiple Tumor Types
Chen-Hsiang Yeang, Sridhar Ramaswamy, Pablo Tamayo, Sayan Mukherjee, Ryan M. Rifkin, Michael Angelo, Michael Reich, Eric Lander, Jill P. Mesirov, and Todd Golub
Bioinformatics 17(Suppl. 1):S316-S322. 2001
 Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression
T.R. Golub, D.K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J.P. Mesirov, H. Coller, M. Loh, J.R. Downing, M.A. Caligiuri, C.D. Bloomfield, and E.S. Lander
Science 286:531-537. (1999).
 Interpreting patterns of gene expression with self-organizing maps
Pablo Tamayo, Donna Slonim, Jill Mesirov, Qing Zhu, Sutisak Kitareewan, Ethan Dmitrovsky, Eric S. Lander, and Todd R. Golub.
Proc. Natl. Acad. Sci. USA 96:2907-2912.

Brain CancerAssessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma
Rameen Beroukhim, Gad Getz, Leia Nghiemphu, Jordi Barretina, Teli Hsueh, David Linhart, Igor Vivanco, Jeffrey C. Lee, Julie H. Huang, Sethu Alexander, Jinyan Du, Tweeny Kau, Roman K. Thomas, Kinjal Shah, Horacio Soto, Sven Perner, John Prensner, Ralph M. Debiasi, Francesca Demichelis, Charlie Hatton, Mark A. Rubin, Levi A. Garraway, Stan F. Nelson, Linda Liau, Paul Mischel, Tim F. Cloughesy, Matthew Meyerson, Todd R. Golub, Eric S. Lander, Ingo K. Mellinghoff, William R. Sellers
Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):20007-12
 Inactivation of the Snf5 tumor suppressor stimulates cell cycle progression and cooperates with p53 loss in oncogenic transformation
Michael S. Isakoff , Courtney G. Sansam , Pablo Tamayo , Aravind Subramanian , Julia A. Evans , Christine M. Fillmore , Xi Wang , Jaclyn A. Biegel , Scott L. Pomeroy , Jill P. Mesi Charles W. M. Roberts
Published online before print November 21, 2005, 10.1073/pnas.0509014102
 Gene expression-based classification of malignant gliomas correlates better with survival than histological classification
Catherine L. Nutt, D. R. Mani, Rebecca A. Betensky, Pablo Tamayo, J. Gregory Cairncross, Christine Ladd, Ute Pohl, Christian Hartmann, Margaret E. McLaughlin, Tracy T. Batchelor, Peter M. Black, Andreas von Deimling, Scott L. Pomeroy, Todd R. Golub, and David N. Louis
Cancer Research 63(7):1602-1607
 Gene Expression-Based Classification and Outcome Prediction of Central Nervous System Embryonal Tumors
Scott L. Pomeroy, Pablo Tamayo, Michelle Gaasenbeek, Lisa M. Sturla, Michael Angelo, Margaret E. McLaughlin, John Y.H. Kim, Liliana C. Goumnerova, Peter McL. Black, Ching Lau, Jeffrey C. Allen, David Zagzag, James M.Olson, Tom Curran, Cynthia Wetmore, Jaclyn A. Biegel, Tomaso Poggio, Shayan Mukherjee, Ryan Rifkin, Andrea Califano, Gustavo Stolovitzky, David N. Louis, Jill P. Mesirov, Eric S. Lander and Todd R. Golub
Nature, Vol 415, 24

Breast CancerSubclass Mapping: Identifying Common Subtypes in Independent Disease Data Sets
Yujin Hoshida, Jean-Philippe Brunet, Pablo Tamayo, Todd R. Golub, Jill P. Mesirov
PLoS ONE 2(11): e1195, 2007
 High Expression of Lymphocyte-Associated Genes in Node-Negative HER2+ Breast Cancers Correlates with Lower Recurrence Rates
Gabriela Alexe, Gul S. Dalgin, Daniel Scanfeld, Pablo Tamayo, Jill P. Mesirov, Charles DeLisi, Lyndsay Harris, Nicola Barnard, Maritza Martel, Arnold J. Levine, Shridar Ganesan and Gyan Bhanot
Cancer Res. 2007;67(22):10669-76.
 Portraits of breast cancer progression
Gul S Dalgin*, Gabriela Alexe*, Daniel Scanfeld, Pablo Tamayo, Jill P Mesirov, Shridar Ganesan, Charles DeLisi and Gyan Bhanot * Contributed equally
BMC Bioinformatics 2007, 8:291doi:10.1186/1471-2105-8-291
 Molecular characterization of the tumor microenvironment in breast cancer.
Minna Allinen, Rameen Beroukhim, Li Cai, Cameron Brennan, Jaana Lahti-Domenici, Haiyan Huang, Dale Porter, Min Hu, Lynda Chin, Andrea Richardson, Stuart Schnitt, William R. Sellers and Kornelia Polyak
Cancer Cell. 2004 Jul;6(1):17-32.
 Loss of heterozygosity and its correlation with expression profiles in subclasses of invasive breast cancers.
Zhigang C. Wang, Ming Lin, Lee-Jen Wei, Cheng Li, Alexander Miron, Gabriella Lodeiro, Lyndsay Harris, Sridhar Ramaswamy, David M. Tanenbaum, Matthew Meyerson, James D. Iglehart and Andrea Richardson
Cancer Res. 2004 Jan 1;64(1):64-71.

Cancer SusceptibilityCOT drives resistance to RAF inhibition through MAP kinase pathway reactivation
Cory M. Johannessen, Jesse S. Boehm, So Young Kim, Sapana R. Thomas, Leslie Wardwell, Laura A. Johnson, Caroline M. Emery, Nicolas Stransky, Alexandria P. Cogdill, Jordi Barretina, Giordano Caponigro, Haley Hieronymus, Ryan R. Murray, Kourosh Salehi-Ashtiani, David E. Hill, Marc Vidal, Jean J. Zhao, Xiaoping Yang, Ozan Alkan, Sungjoon Kim, Jennifer L. Harris, Christopher J. Wilson, Vic E. Myer, Peter M. Finan, David E. Root, Thomas M. Roberts, Todd Golub, Keith T. Flaherty, Reinhard Dummer, Barbara Weber, William R. Sellers, Robert Schlege, Jennifer A. Wargo, William C. Hahn, Levi A. Garraway
 Inactivation of the Snf5 tumor suppressor stimulates cell cycle progression and cooperates with p53 loss in oncogenic transformation
Michael S. Isakoff , Courtney G. Sansam , Pablo Tamayo , Aravind Subramanian , Julia A. Evans , Christine M. Fillmore , Xi Wang , Jaclyn A. Biegel , Scott L. Pomeroy , Jill P. Mesi Charles W. M. Roberts
Published online before print November 21, 2005, 10.1073/pnas.0509014102
 EBV Encoded LMP2A Induces Primary Epithelial Cell Migration and Invasion  Possible Role in Nasopharyngeal Carcinoma Metastasis.
Dirk M. Pegtel, Aravind Subramanian, Tzung-Shiahn Sheen, Ching-Hwa Tsai, Todd R. Golub and David A. Thorley-Lawson
 A zebrafish bmyb mutation causes genome instability and increased cancer susceptibility
Jennifer L. Shepard*, James F. Amatruda*, Howard M. Stern, Aravind Subramanian, David Finkelstein, James Ziai, K. Rose Finley, Kathleen L. Pfaff, Candace Hersey, Yi Zhou, Bruce Barut, Matthew Freedman, Charles Lee, Jan Spitsbergen, Donna Neuberg, Gerhard Weber, Todd R. Golub, Jonathan N. Glickman, Jeffery L. Kutok, Jon C. Aster, and Leonard I. Zon
 An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis
Alejandro Sweet-Cordero, Sayan Mukherjee, Aravind Subramanian, Han You, Jeffrey J Roix, Christine Ladd-Acosta, Jill Mesirov, Todd R Golub, & Tyler Jacks

Chemical GenomicsIdentification of AML1-ETO Modulators by Chemical Genomics
Steven M. Corsello, Giovanni Roti, Kenneth N. Ross, Kwan T. Chow, Ilene Galinsky, Richard M. Stone, Daniel J. DeAngelo, Andrew N. Kung, Todd R. Golub, and Kimberly Stegmaier
Blood. 2009 Jun 11;113(24):6193-205. Epub 2009 Apr 17.
 Expression-based Screening Identifies the Combination of Histone Deacetylase Inhibitors and Retinoids for Neuroblastoma Differentiation
Cynthia K. Hahn, Kenneth N. Ross, Ian Warrington, Ralph Mazitschek, Cindy M. Kanegai, Renee D. Wright, Andrew L. Kung, Todd R. Golub, and Kimberly Stegmaier
 Signature-Based Small Molecule Screening Identifies Cytosine Arabinoside as an EWS/FLI Modulator in Ewing Sarcoma
Kimberly Stegmaier, Jenny S. Wong, Kenneth N. Ross, Kwan T. Chow, David Peck, Renee D. Wright, Stephen L. Lessnick, Andrew L. Kung, Todd R. Golub
Stegmaier K, Wong JS, Ross KN, Chow KT, Peck D, et al. (2007) Signature-based small molecule screening identifies cytosine arabinoside as an EWS/FLI modulator in Ewing sarcoma. PLoS Med, Vol. 4, No. 4, e122 doi:10.1371/journal.pmed.0040122
 Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL-1 and glucocorticoid resistance in leukemia
Guo Wei, David Twomey, Justin Lamb, Krysta Schlis, Jyoti Agarwal, Ronald Stam, Joseph T. Opferman, Stephen E. Sallan, Monique L. den Boer, Rob Pieters, Todd R. Golub, Scott A. Armstrong.
CancerCell October 2006. 10.1016/j.ccr.2006.09.006
 The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease
Justin Lamb, Emily D. Crawford, David Peck, Joshua W. Modell, Irene C. Blat, Matthew J. Wrobel, Jim Lerner, Jean-Philippe Brunet, Aravind Subramanian, Kenneth N. Ross, Michael Reich, Haley Hieronymus, Guo Wei, Scott A. Armstrong, Stephen J. Haggarty, Paul A. Clemons, Ru Wei, Steven A. Carr, Eric S. Lander and Todd R. Golub
Science 313: 1929-1935 (2006)
 Gefitinib (Iressa) induces myeloid differentiation of acute myeloid leukemia
Kimberly Stegmaier, Steven M. Corsello, Kenneth N. Ross, Jenny S. Wong, Daniel J. DeAngelo, Todd R. Golub
Blood. 2005 Oct 15;106(8):2841-8.
 Gene Expression-Based High Throughput Screening (GE-HTS) and Application to Leukemia Differentiation
Kimberly Stegmaier, Kenneth N. Ross, Sierra A. Colavito, Shawn O'Malley, Brent R. Stockwell, and Todd R. Golub
Nature Genetics, Vol. 36, No. 3, 257-263, March 2004.
 Chemosensitivity Prediction by Transcriptional Profiling
Jane E. Staunton, Donna K. Slonim , Hilary A. Coller, Pablo Tamayo, Michael J. Angelo , Johnny Park , Uwe Scherf, Jae K. Lee, William O. Reinhold, John N. Weinstein, Jill P. Mesirov, Eric S. Landerand Todd R. Golub
Proc. Natl. Acad. Sci. USA 98: 0787-10792

Colon CancerCDK8 is a colorectal cancer oncogene that regulates bold beta-catenin activity
Firestein R, Bass AJ, Kim SY, Dunn IF, Silver SJ, Guney I, Freed E, Ligon AH, Vena N, Ogino S, Chheda MG, Tamayo P, Finn S, Shrestha Y, Boehm JS, Jain S, Bojarski E, Mermel C, Barretina J, Chan JA, Baselga J, Tabernero J, Root DE, Fuchs CS, Loda M, Shivdasani RA, Meyerson M, Hahn WC.
Firestein R, Bass AJ, Kim SY, Dunn IF, Silver SJ, Guney I, Freed E, Ligon AH, Vena N, Ogino S, Chheda MG, Tamayo P, Finn S, Shrestha Y, Boehm JS, Jain S, Bojarski E, Mermel C, Barretina J, Chan JA, Baselga J, Tabernero J, Root DE, Fuchs CS, Loda M, Shivdasani RA, Meyerson M, Hahn WC. CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity. Nature. 2008 Sep 25;455(7212):547-51. Epub 2008 Sep 14.

Endometrial cancerIntegrated genomic profiling of endometrial carcinoma associates aggressive tumors with indicators of PI3 kinase activation.
Salvesen HB, Carter SL, Mannelqvist M, Dutt A, Getz G, Stefansson IM, Raeder MB, Sos ML, Engelsen IB, Trovik J, Wik E, Greulich H, B?? TH, Jonassen I, Thomas RK, Zander T, Garraway LA, Oyan AM, Sellers WR, Kalland KH, Meyerson M, Akslen LA, Beroukhim R.
Proc. Natl. Acad. Sci. USA 106:4834-4839
 Drug-sensitive FGFR2 mutations in endometrial carcinoma
Dutt A, Salvesen HB, Chen TH, Ramos AH, Onofrio RC, Hatton C, Nicoletti R, Winckler W, Grewal R, Hanna M, Wyhs N, Ziaugra L, Richter DJ, Trovik J, Engelsen IB, Stefansson IM, Fennell T, Cibulskis K, Zody MC, Akslen LA, Gabriel S, Wong KK, Sellers WR, Meyerson M, Greulich H.
Proc. Natl. Acad. Sci. USA 105:8713-8717

HematopoiesismicroRNA-mediated control of cell fate in megakaryocyte-erythrocyte progenitors
Jun Lu, Shangqin Guo, Benjamin L. Ebert, Hao Zhang, Xiao Peng, Jocelyn Bosco, Jennifer Pretz, Rita Schlanger, Judy Y. Wang, Raymond H. Mak, David M. Dombkowski, Frederic I. Preffer, David T. Scadden and Todd R. Golub
Developmental Cell (2008), doi:10.1016/j.devcel.2008.03.012
 An erythroid differentiation signature predicts response to lenalidomide in Myelodysplastic Syndrome
Benjamin L. Ebert, Naomi Galili, Pablo Tamayo, Jocelyn Bosco, Raymond Mak, Jennifer Pretz, Christine Ladd-Acosta, Richard Stone, Todd R. Golub and Azra Raza.
 Identification of RPS14 as a 5q- syndrome gene by RNA interference screen
Benjamin L. Ebert, Jennifer Pretz, Jocelyn Bosco, Cindy Y. Chang, Pablo Tamayo, Naomi Galili, Azra Raza, David E. Root, Eyal Attar, Steven R. Ellis, and Todd R. Golub.
Nature 451, 335-339 (17 January 2008) | doi:10.1038/nature06494
 Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL-1 and glucocorticoid resistance in leukemia
Guo Wei, David Twomey, Justin Lamb, Krysta Schlis, Jyoti Agarwal, Ronald Stam, Joseph T. Opferman, Stephen E. Sallan, Monique L. den Boer, Rob Pieters, Todd R. Golub, Scott A. Armstrong.
CancerCell October 2006. 10.1016/j.ccr.2006.09.006
 Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9
Andrei Krivtsov, David Twomey, Zhaohui Feng, Matthew C. Stubbs, Yingzi Wang, Joerg Faber, Jason E. Levine, Jing Wang, William C. Hahn, D. Gary Gilliland, Todd R. Golub, Scott A. Armstrong
doi:10.1038/nature04980; Nature. 2006 Aug 17;442(7104):818-22. Epub 2006 Jul 16
 Identification of distinct molecular phenotypes in acute megakaryoblastic leukemia by gene expression profiling
Jean-Pierre Bourquin, Aravind Subramanian, Claudia Langebrake, Dirk Reinhardt, Olivier Bernard, Paola Ballerini , Andri Baruchel, Hilhne Cavi, Nicole Dastugue, Henrik Hasle , Gertjan L Kaspers, Michel Lessard, Lucienne Michaux, Elisabeth van Wering, Christian M Zwaan, Todd R.Golub and Stuart H. Orkin
 An RNA interference model of RPS19 deficiency in Diamond Blackfan Anemia recapitulates defective hematopoiesis and rescue by dexamethasone: identification of dexamethasone responsive genes by microarray
Benjamin L. Ebert, Michele M. Lee, Jennifer L. Pretz, Aravind Subramanian, Raymond Mak, Todd R. Golub, Colin A. Sieff
 Identification of endoglin as a functional marker that defines long-term repopulating hematopoietic stem cells
Chang-Zheng Chen, Min Li, David de Graaf, Stefano Monti, Berthold Gottgens, Maria-Jose Sanchez, Eric S. Lander, Todd R. Golub, Anthony R. Green and Harvey F. Lodish
PNAS 2002 99(24):15468-15473
 Interpreting patterns of gene expression with self-organizing maps
Pablo Tamayo, Donna Slonim, Jill Mesirov, Qing Zhu, Sutisak Kitareewan, Ethan Dmitrovsky, Eric S. Lander, and Todd R. Golub.
Proc. Natl. Acad. Sci. USA 96:2907-2912.

Hepatocellular carcinomaMicroRNA-Based Classification of Hepatocellular Carcinoma and Oncogenic Role of miR-517a
Toffanin S, Hoshida Y, Lachenmayer A, Villanueva A, Cabellos L, Minguez B, Savic R, Ward SC, Thung S, Chiang DY, Alsinet C, Tovar V, Roayaie S, Schwartz M, Bruix J, Waxman S, Friedman SL, Golub T, Mazzaferro V, Llovet JM
Gastroenterology. 2011
 Combining Clinical, Pathology, and Gene Expression Data to Predict Recurrence of Hepatocellular Carcinoma
Villanueva A, Hoshida Y, Battiston C, Tovar V, Sia D, Alsinet C, Cornella H, Liberzon A, Kobayashi M, Kumada H, Thung SN, Bruix J, Newell P, April C, Fan JB, Roayaie S, Mazzaferro V, Schwartz ME, Llovet JM
Gastroenterology. 2011
 IGF activation in a molecular subclass of hepatocellular carcinoma and pre-clinical efficacy of IGF-1R blockage
Victoria Tovar, Clara Alsinet, Augusto Villanueva, Yujin Hoshida, Derek Y. Chiang, Manel Sole, Swan Thung, Susana Moyano, Sara Toffanin, Beatriz M??nguez, Laia Cabellos, Judit Peix, Myron Schwartz, Vincenzo Mazzaferro, Jordi Bruix, Josep M. Llovet
Journal of Hepatology, 2010 in press
 Molecular Classification and Novel Targets in Hepatocellular Carcinoma: Recent Advancements
Yujin Hoshida, Sara Toffanin, Anja Lachenmayer, Augusto Villanueva, Beatriz Minguez, Josep M. Llovet
Seminars in Liver Disease, 30(1); 35, 2010
 Risk of recurrence in hepatitis B-related hepatocellular carcinoma: impact of viral load in late recurrence
Yujin Hoshida
Journal of Hepatology, 2009 Nov;51(5):842-4
 Integrative Transcriptome Analysis Reveals Common Molecular Subclasses of Human Hepatocellular Carcinoma
Yujin Hoshida, Sebastian M.B. Nijman, Masahiro Kobayashi, Jennifer A. Chan, Jean-Philippe Brunet, Derek Y. Chiang, Augusto Villanueva, Philippa Newell, Kenji Ikeda, Masaji Hashimoto, Goro Watanabe, Stacey Gabriel, Scott L. Friedman, Hiromitsu Kumada, Josep M. Llovet, Todd R. Golub
Cancer Research 2009;69(18):7385-92
 Ras pathway activation in hepatocellular carcinoma and anti-tumoral effect of combined sorafenib and rapamycin in vivo
Pippa Newell, Sara Toffanin, Augusto Villanueva, Derek Y. Chiang, Beatriz Minguez, Laia Cabellos, Radoslav Savic, Yujin Hoshida, Kiat Hon Lim, Pedro Melgar-Lesmes, Steven Yea, Judit Peix, Kemal Deniz, M. Isabel Fiel, Swan Thung, Clara Alsinet, Victoria Tovar, Vincenzo Mazzaferro, Jordi Bruix, Sasan Roayaie, Myron Schwartz, Scott L. Friedman, Josep M. Llovet
Journal of Hepatology, 2009;51(4): 725-733
 Lin28 promotes transformation and is associated with advanced human malignancies
Srinivas R Viswanathan, John T Powers, William Einhor, Yujin Hoshida, Tony L Ng, Sara Toffanin, Maureen O'Sullivan, Jun Lu, Letha A Phillips, Victoria L Lockhart, Samar P Shah, Pradeep S Tanwar, Craig H Mermel, Rameen Beroukhim, Mohammad Azam, Jose Teixeira, Matthew Meyerson, Timothy P Hughes, Josep M Llovet, Jerald Radich, Charles G Mullighan, Todd R Golub, Poul H Sorensen, George Q Daley
Nature Genetics, 2009 Jul;41(7):843-8
 Tumor-derived molecular information and outcome in hepatocellular carcinoma
Yujin Hoshida
Journal of Hepatology, 2009 Sep;51(3):595-6
 Molecular profiling to predict hepatocellular carcinoma outcome
Yujin Hoshida, Augusto Villanueva, Josep M. Llovet
Expert Rev Gastroenterol Hepatol. 2009 Apr;3(2):101-3
 Prolonged therapy for hepatitis C with low-dose peginterferon
Yujin Hoshida, Todd R. Golub
N Engl J Med. 2009 Mar 12;360(11):1152
 Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma
Yujin Hoshida, Augusto Villanueva, Masahiro Kobayashi, Judit Peix, Derek Y. Chiang, Amy Camargo, Supriya Gupta, Jamie Moore, Matthew J. Wrobel, Jim Lerner, Michael Reich, Jennifer A. Chan, Jonathan N. Glickman, Kenji Ikeda, Masaji Hashimoto, Goro Watanabe, Maria G. Daidone, Sasan Roayaie, Myron Schwartz, Swan Thung, Helga B. Salvesen, Stacey Gabriel, Vincenzo Mazzaferro, Jordi Bruix, Scott L. Friedman, Hiromitsu Kumada, Josep M. Llovet, Todd R. Golub
N Engl J Med 2008;359:1995-2004
 Pivotal Role of mTOR Signaling in Hepatocellular Carcinoma
Augusto Villanueva, Derek Y. Chiang, Pippa Newell, Judit Peix, Swan Thung, Clara Alsinet, Victoria Tovar, Sasan Roayaie, Beatriz Minguez, Manel Sole, Carlo Battiston, Stijn van Laarhoven, Maria I Fiel, Analisa Di Feo, Yujin Hoshida, Steven Yea, Sara Toffanin, Alex Ramos, John A. Martignetti, Vincenzo Mazzaferro, Jordi Bruix, Samuel Waxman, Myron Schwartz, Matthew Meyerson, Scott L. Friedman, Josep M. Llovet
Gastroenterology, 2008 Dec;135(6):1972-83
 Focal gains of VEGFA and molecular classification of hepatocellular carcinoma
Derek Y. Chiang, Augusto Villanueva, Yujin Hoshida, Judit Peix, Philippa Newell, Beatriz Minguez, Amanda LeBlanc, Diana Donovan, Swan Thung, Manel Sole, Victoria Tovar, Clara Alsinet, Alex Ramos, Jordi Barretina, Sasan Roayaie, Myron Schwartz, Samuel Waxman, Jordi Bruix, Vincenzo Mazzaferro, Azra Ligon, Vesna Najfeld, Scott Friedman, William Sellers, Matthew Meyerson, Josep Llovet
Cancer Res. 68(16):6779-88
 Genomics and signaling pathways in hepatocellular carcinoma
Augusto Villaneuva, Philippa Newell, Derek Y. Chiang, Scott Friedman, Josep Llovet
Semin. Liver Dis. 27(1): 55-76

Integrative Genomic AnalysisCOT drives resistance to RAF inhibition through MAP kinase pathway reactivation
Cory M. Johannessen, Jesse S. Boehm, So Young Kim, Sapana R. Thomas, Leslie Wardwell, Laura A. Johnson, Caroline M. Emery, Nicolas Stransky, Alexandria P. Cogdill, Jordi Barretina, Giordano Caponigro, Haley Hieronymus, Ryan R. Murray, Kourosh Salehi-Ashtiani, David E. Hill, Marc Vidal, Jean J. Zhao, Xiaoping Yang, Ozan Alkan, Sungjoon Kim, Jennifer L. Harris, Christopher J. Wilson, Vic E. Myer, Peter M. Finan, David E. Root, Thomas M. Roberts, Todd Golub, Keith T. Flaherty, Reinhard Dummer, Barbara Weber, William R. Sellers, Robert Schlege, Jennifer A. Wargo, William C. Hahn, Levi A. Garraway
 The landscape of somatic copy-number alteration across human cancers
Rameen Beroukhim*, Craig H. Mermel*, Dale Porter, Guo Wei, Soumya Raychaudhuri, Jerry Donovan, Jordi Barretina, Jesse S. Boehm, Jennifer Dobson, Mitsuyoshi Urashima, Kevin T. Mc Henry, Reid M. Pinchback, Azra H. Ligon, Yoon-Jae Cho, Leila Haery, Heidi Greulich, Michael Reich, Wendy Winckler, Michael S. Lawrence, Barbara A. Weir, Kumiko E. Tanaka, Derek Y. Chiang, Adam J. Bass, Alice Loo, Carter Hoffman, John Prensner, Ted Liefeld, Qing Gao, Derek Yecies, Sabina Signoretti, Elizabeth Maher, Frederic J. Kaye, Hidefumi Sasaki, Joel E. Tepper, Jonathan A. Fletcher, Josep Tabernero, Jose Baselga, Ming-Sound Tsao, Francesca DeMichelis, Mark A. Rubin, Pasi A. Janne, Mark J. Daly, Carmelo Nucera, Ross L. Levine, Benjamin L. Ebert, Stacey Gabriel, Anil K. Rustgi, Cristina R. Antonescu, Marc Ladanyi, Anthony Letai, Levi A. Garraway, Massimo Loda, David G. Beer, Lawrence D. True, Aikou Okamoto, Scott L. Pomeroy, Samuel Singer, Todd R. Golub, Eric S. Lander1, Gad Getz, William R. Sellers & Matthew Meyerson
Nature 463, 899-905(18 February 2010)
 Sanger Cell Line Project

 GenePattern 2.0
Michael Reich, Ted Liefeld, Joshua Gould, Jim Lerner, Pablo Tamayo & Jill P Mesirov
Nat. Genet. 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500

LeukemiaIdentification of AML1-ETO Modulators by Chemical Genomics
Steven M. Corsello, Giovanni Roti, Kenneth N. Ross, Kwan T. Chow, Ilene Galinsky, Richard M. Stone, Daniel J. DeAngelo, Andrew N. Kung, Todd R. Golub, and Kimberly Stegmaier
Blood. 2009 Jun 11;113(24):6193-205. Epub 2009 Apr 17.
 Identification of RPS14 as a 5q- syndrome gene by RNA interference screen
Benjamin L. Ebert, Jennifer Pretz, Jocelyn Bosco, Cindy Y. Chang, Pablo Tamayo, Naomi Galili, Azra Raza, David E. Root, Eyal Attar, Steven R. Ellis, and Todd R. Golub.
Nature 451, 335-339 (17 January 2008) | doi:10.1038/nature06494
 Metagene projection for cross platform, cross species characterization of global transcriptional states
Pablo Tamayo, Daniel Scanfeld, Benjamin L. Ebert, Michael A. Gillette, Charles W. M. Roberts, and Jill P. Mesirov.
Proc. Natl. Acad. Sci. USA, 104: 5959-5964
 Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL-1 and glucocorticoid resistance in leukemia
Guo Wei, David Twomey, Justin Lamb, Krysta Schlis, Jyoti Agarwal, Ronald Stam, Joseph T. Opferman, Stephen E. Sallan, Monique L. den Boer, Rob Pieters, Todd R. Golub, Scott A. Armstrong.
CancerCell October 2006. 10.1016/j.ccr.2006.09.006
 Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9
Andrei Krivtsov, David Twomey, Zhaohui Feng, Matthew C. Stubbs, Yingzi Wang, Joerg Faber, Jason E. Levine, Jing Wang, William C. Hahn, D. Gary Gilliland, Todd R. Golub, Scott A. Armstrong
doi:10.1038/nature04980; Nature. 2006 Aug 17;442(7104):818-22. Epub 2006 Jul 16
 Identification of distinct molecular phenotypes in acute megakaryoblastic leukemia by gene expression profiling
Jean-Pierre Bourquin, Aravind Subramanian, Claudia Langebrake, Dirk Reinhardt, Olivier Bernard, Paola Ballerini , Andri Baruchel, Hilhne Cavi, Nicole Dastugue, Henrik Hasle , Gertjan L Kaspers, Michel Lessard, Lucienne Michaux, Elisabeth van Wering, Christian M Zwaan, Todd R.Golub and Stuart H. Orkin
 Gefitinib (Iressa) induces myeloid differentiation of acute myeloid leukemia
Kimberly Stegmaier, Steven M. Corsello, Kenneth N. Ross, Jenny S. Wong, Daniel J. DeAngelo, Todd R. Golub
Blood. 2005 Oct 15;106(8):2841-8.
 Gene Expression-Based High Throughput Screening (GE-HTS) and Application to Leukemia Differentiation
Kimberly Stegmaier, Kenneth N. Ross, Sierra A. Colavito, Shawn O'Malley, Brent R. Stockwell, and Todd R. Golub
Nature Genetics, Vol. 36, No. 3, 257-263, March 2004.
 MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia
Scott A. Armstrong, Jane E. Staunton, Lewis B. Silverman, Rob Pieters, Monique L. den Boer, Mark D. Minden, Stephen E. Sallan, Eric S. Lander, Todd R. Golub, and Stanley J. Korsemeyer
Nature Genetics 30, pp 41 - 47 (2002)
 c-Myc is a critical target for c/EBPalpha in granulopoiesis.
Johansen LM, Iwama A, Lodie TA, Sasaki K, Felsher DW, Golub TR, Tenen DG
Molecular and Cellular Biology, June 2001, p. 3789-3806, Vol. 21, No. 11
 Class prediction and discovery using gene expression data
Donna K. Slonim, Pablo Tamayo, Jill P. Mesirov, Todd R. Golub and Eric S. Lander
RECOMB 2000, p263-272, 2000
 Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression
T.R. Golub, D.K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J.P. Mesirov, H. Coller, M. Loh, J.R. Downing, M.A. Caligiuri, C.D. Bloomfield, and E.S. Lander
Science 286:531-537. (1999).
 Interpreting patterns of gene expression with self-organizing maps
Pablo Tamayo, Donna Slonim, Jill Mesirov, Qing Zhu, Sutisak Kitareewan, Ethan Dmitrovsky, Eric S. Lander, and Todd R. Golub.
Proc. Natl. Acad. Sci. USA 96:2907-2912.

Lung CancerSystematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1.
David A. Barbie, Pablo Tamayo, Jesse S. Boehm, So Young Kim, Susan E. Moody, Ian F. Dunn, Anna C. Schinzel, Peter Sandy, Etienne Meylan, Claudia Scholl, Stefan Frohling, Edmond M. Chan, Martin L. Sos, Kathrin Michel, Craig Mermel, Serena J. Silver, Barbara A. Weir, Jan H. Reiling, Qing Sheng, Piyush B. Gupta, Raymond C. Wadlow, Hanh Le, Sebastian Hoersch, Ben S. Wittner, Sridhar Ramaswamy, David M. Livingston, David M. Sabatini, Matthew Meyerson, Roman K. Thomas, Eric S. Lander, Jill P. Mesirov, David E. Root, D. Gary Gilliland, Tyler Jacks & William C. Hahn
Nature 462(7269),108-112
 Characterizing the cancer genome in lung adenocarcinoma
Barbara A. Weir, Michele S. Woo, Gad Getz, Sven Perner, Li Ding, Rameen Beroukhim, William M. Lin, Michael A. Province, Aldi Kraja, Laura A. Johnson, Kinjal Shah, Mitsuo Sato, Roman K. Thomas, Justine A. Barletta, Ingrid B. Borecki, Stephen Broderick, Andrew C. Chang, Derek Y. Chiang, Lucian R. Chirieac, Jeonghee Cho, Yoshitaka Fujii, Adi F. Gazdar, Thomas Giordano, Heidi Greulich, Megan Hanna, Bruce E. Johnson, Mark G. Kris, Alex Lash, Ling Lin, Neal Lindeman, Elaine R. Mardis, John D. McPherson, John Minna, Margaret B. Morgan, Mark Nadel, Mark B. Orringer, John R. Osborne, Brad Ozenberger, Alex H. Ramos, James Robinson, Jack A. Roth, Valerie Rusch, Hidefumi Sasaki, Frances Shepherd, Carrie Sougnez, Margaret R. Spitz, Ming-Sound Tsao, David Twomey, Roel Verhaak, George M. Weinstock, David A. Wheeler, Wendy Winckler, Akihiko Yoshizawa, Soyoung Yu, Maureen F. Zakowski, Qunyuan Zhang, David G. Beer, Ignacio I. Wistuba, Mark A. Watson, Levi A. Garraway, Marc Ladanyi, William D. Travis, William Pao, Mark A. Rubin, Stacey B. Gabriel, Richard A. Gibbs, Harold E. Varmus, Richard K. Wilson, Eric S. Lander & Matthew Meyerson
Nature 450, 893-898 (06 December 2007)
 Metagene projection for cross platform, cross species characterization of global transcriptional states
Pablo Tamayo, Daniel Scanfeld, Benjamin L. Ebert, Michael A. Gillette, Charles W. M. Roberts, and Jill P. Mesirov.
Proc. Natl. Acad. Sci. USA, 104: 5959-5964
 Impaired microRNA processing enhances cellular transformation and tumorigenesis
Madhu S. Kumar, Jun Lu, Kim L. Mercer, Todd R. Golub, and Tyler Jacks
Nat Genet. 2007 May;39(5):673-7. Epub 2007 Apr 1
 Gene Expression Profiling Reveals Reproducible Human Lung Adenocarcinoma Subtypes in Multiple Independent Patient Cohorts
DN Hayes, S Monti, G Parmigiani, CB Gilks, K Naoki, A Bhattacharjee, MA Socinski, C Perou and M Meyerson
J Clin Oncol, 24(31): 5079-5090, 2006.
 Oncogenic transformation by inhibitor-sensitive and -resistant EGFR mutants.
Greulich H, Chen TH, Feng W, Janne PA, Alvarez JV, Zappaterra M, Bulmer SE, Frank DA, Hahn WC, Sellers WR, Meyerson M.
PLoS Medicine 2:e313
 Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis.
Xiaojun Zhao, Barbara A. Weir, Thomas LaFramboise, Ming Lin, Rameen Beroukhim, Levi Garraway, Javad Beheshti, Jeffrey C. Lee, Katsuhiko Naoki, William G. Richards, David Sugarbaker, Fei Chen, Mark A. Rubin, Pasi A. Janne, Luc Girard, John Minna, David Christiani, Cheng Li, William R. Sellers and Matthew Meyerson
Cancer Res. 2005 Jul 1;65(13):5561-70.
 An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis
Alejandro Sweet-Cordero, Sayan Mukherjee, Aravind Subramanian, Han You, Jeffrey J Roix, Christine Ladd-Acosta, Jill Mesirov, Todd R Golub, & Tyler Jacks
 A Transcriptional Profiling Study of CAAT/Enhancer Binding Protein Targets Identifies Hepatocyte Nuclear Factor 3beta as a Novel Tumor Suppressor in Lung Cancer
Balazs Halmos, Daniela S. Basseres, Stefano Monti, Francesco D'Alo, Tajhal Dayaram, Katalin Ferenczi, Bas J. Wouters, Claudia S. Huettner, Todd R. Golub and Daniel G. Tenen
Cancer Research 64, 4137-4147, June 15, 2004
 High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines.
Pasi A Janne, Cheng Li, Xiaojun Zhao, Luc Girard, Tzu-Hsiu Chen, John Minna, David C Christiani, Bruce E Johnson, and Matthew Meyerson
Oncogene (2004) 23, 2716-2726
 Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes
Arindam Bhattacharjee, William G. Richards, Jane Staunton, Cheng Li, Stefano Monti, Priya Vasa, Christine Ladd, Javad Beheshti, Raphael Bueno, Michael Gillette, Massimo Loda, Griffin Weber, Eugene J. Mark, Eric S. Lander, Wing Wong, Bruce E. Johnson, Todd R. Golub, David J. Sugarbaker, and Matthew Meyerson
Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 24, 13790-13795, November 20, 2001
 Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays.
Kerstin Lindblad-Toh, David M. Tanenbaum, Mark J. Daly, Ellen Winchester, Weng-Onn Lui, Anuradha Villapakkam, Sasha E. Stanton, Catharina Larsson, Thomas J. Hudson, Bruce E. Johnson, Eric S. Lander & Matthew Meyerson
Nat Biotechnol. 2000 Sep;18(9):1001-5.

LymphomaSYK-dependent Tonic B-cell Signaling is a Rational Treatment Target in Diffuse Large B-cell Lymphoma
Linfeng Chen, Stefano Monti, Przemyslaw Juszczynski, Yasumichi Hitoshi, Wen Chen, Jeffery L. Kutok, Margaret A. Shipp
Blood, 111(4): 2230-2237, 2008
 Integrative analysis reveals 53BP1 copy loss and decreased expression in a subset of human diffuse large B-cell lymphoma
K Takeyama, S Monti, J P Manis, P Dal Cin, G Getz, R Beroukhim, S Dutt, J C Aster, F W Alt, T R Golub, and M A Shipp
Oncogene 27(3):318-322, 2007
 Subclass Mapping: Identifying Common Subtypes in Independent Disease Data Sets
Yujin Hoshida, Jean-Philippe Brunet, Pablo Tamayo, Todd R. Golub, Jill P. Mesirov
PLoS ONE 2(11): e1195, 2007
 Lesional gene expression profiling in cutaneous T-cell lymphoma reveals natural clusters associated with disease outcome
Jessica Shin, Stefano Monti, Daniel J Aires, Madeleine Duvic, Todd Golub, David A Jones, and Thomas S Kupper
Blood, 110(8): 3015-3027, 2007
 The AP1-dependent secretion of galectin-1 by Reed-Sternberg cells fosters immune privilege in classical Hodgkin lymphoma
Przemyslaw Juszczynski, Jing Ouyang, Stefano Monti, Scott J. Rodig, Kunihiko Takeyama, Jeremy Abramson, Wen Chen, Jeffery L. Kutok, Gabriel A. Rabinovich, and Margaret A. Shipp
Proc. Natl. Acad. Sci. USA 104(32):13134-13139, 2007
 A transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent diffuse large B-cell lymphomas
Jose M. Polo, Przemyslaw Juszczynski, Stefano Monti, Leandro Cerchietti, Kenny Ye, John M. Greally, Margaret Shipp, Ari Melnick
PNAS 104(9): 3207-3212, 2007
 NFkB activity, function and target gene signatures in primary mediastinal large B-cell lymphoma and diffuse large B-cell lymphoma subtypes
Friedrich Feuerhake, Jeffery L. Kutok, Stefano Monti, Wen Chen, Ann S. LaCasce, Giorgio Cattoretti, Paul Kurtin, Geraldine S. Pinkus, Laurence de Leval, Nancy L. Harris, Kerry J. Savage, Donna Neuberg, Thomas M. Habermann, Riccardo Dalla-Favera, Todd R. Golub, Jon C. Aster, Margaret A. Shipp
Blood, 2005. 106(4): p.1392-1399.
 Molecular profiling of diffuse large B-cell lymphoma reveals a novel disease subtype with brisk host inflammatory response and distinct genetic features
Stefano Monti, Kerry J. Savage, Jeffery L. Kutok, Friedrich Feuerhake, Paul Kurtin, Martin Mihm, Bingyan Wu, Laura Pasqualucci, Donna Neuberg, Ricardo C.T. Aguiar, Paola Dal Cin, Christine Ladd, Geraldine S. Pinkus, Gilles Salles, Nancy L. Harris, Riccardo Dalla-Favera, Thomas Habermann, Jon C. Aster, Todd R. Golub, Margaret A. Shipp
Blood, 1 March 2005, Vol. 105, No. 5, pp. 1851-1861
 The molecular signature of mediastinal large B-cell lymphoma differs from that of other diffuse large B-cell lymphomas and shares features with classical Hodgkin lymphoma
Kerry J. Savage, Stefano Monti, Jeffery L. Kutok, Giorgio Cattoretti, Donna Neuberg, Laurence de Leval, Paul Kurtin, Paola Dal Cin, Christine Ladd, Friedrich Feuerhake, Ricardo C. T. Aguiar, Sigui Li, Gilles Salles, Francoise Berger, Wen Jing, Geraldine S. Pinkus, Thomas Habermann, Riccardo Dalla-Favera, Nancy Lee Harris, Jon C. Aster, Todd R. Golub and Margaret A. Shipp
Blood, 1 December 2003, Vol. 102, No. 12, pp. 3871-3879.
 Diffuse Large B-Cell Lymphoma Outcome Prediction by Gene Expression Profiling and Supervised Machine Learning
M A Shipp, K N Ross, P Tamayo, A P Weng, J L Kutok, R C T Aguiar, M Gaasenbeek, M Angelo, M Reich, G S Pinkus, T S Ray, M A Koval, K W Last, A Norton, T A Lister, J Mesirov, D S Neuberg, E S Lander, J C Aster & T R Golub
Nature Medicine January 2002 Volume 8 Number 1 pp 68 - 74

MelanomaCOT drives resistance to RAF inhibition through MAP kinase pathway reactivation
Cory M. Johannessen, Jesse S. Boehm, So Young Kim, Sapana R. Thomas, Leslie Wardwell, Laura A. Johnson, Caroline M. Emery, Nicolas Stransky, Alexandria P. Cogdill, Jordi Barretina, Giordano Caponigro, Haley Hieronymus, Ryan R. Murray, Kourosh Salehi-Ashtiani, David E. Hill, Marc Vidal, Jean J. Zhao, Xiaoping Yang, Ozan Alkan, Sungjoon Kim, Jennifer L. Harris, Christopher J. Wilson, Vic E. Myer, Peter M. Finan, David E. Root, Thomas M. Roberts, Todd Golub, Keith T. Flaherty, Reinhard Dummer, Barbara Weber, William R. Sellers, Robert Schlege, Jennifer A. Wargo, William C. Hahn, Levi A. Garraway
 Gene Expression Changes in an Animal Melanoma Model Correlate with Aggressiveness of Human Melanoma Metastases
Lei Xu, Steven S. Shen, Yujin Hoshida, Aravind Subramanian, Ken Ross, Jean-Philippe Brunet, Stephan N. Wagner, Sridhar Ramaswamy, Jill P. Mesirov, and Richard O. Hynes
Molecular Cancer Research 6, 760-769, May 1, 2008
 Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma.
Levi A. Garraway, Hans R. Widlund, Mark A. Rubin, Gad Getz, Aaron J. Berger, Sridhar Ramaswamy, Rameen Beroukhim, Danny A. Milner, Scott R. Granter, Jinyan Du, Charles Lee, Stephan N. Wagner, Cheng Li, Todd R. Golub, David L. Rimm, Matthew L. Meyerson, David E. Fisher and William R. Sellers
Nature. 2005 Jul 7;436(7047):117-22.
 Genomic analysis of metastasis reveals an essential role for RhoC
Edwin A. Clark, Todd R. Golub, Eric S. Lander and Richard O. Hynes.
Nature 406:532-535

Metabolic DiseasesErra and Gabpa/b specify PGC-1a-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle
Vamsi K. Mootha, Christoph Handschin, Dan Arlow, Xiaohui Xie, Julie St. Pierre, Smita Sihag, Wenli Yang, David Altshuler, Pere Puigserver, Nick Patterson, Patricia J. Willy, Ira G. Shulman, Richard A. Heyman, Eric S. Lander, and Bruce M. Spiegelman
Proc. Natl. Acad. Sci. USA
 Integrated Analysis of Protein Composition, Tissue Diversity, and Gene Regulation in Mouse Mitochondria
Vamsi K. Mootha, Jakob Bunkenborg, Jesper V. Olsen, Majbrit Hjerrild, Jacek R. Wisniewski, Erich Stahl, Marjan S. Bolouri, Heta N. Ray, Smita Sihag, Michael Kamal, Nick Patterson, Eric S. Lander, and Matthias Mann
Cell 115: 629-640
 PGC-1a Responsive Genes Involved in Oxidative Phosphorylation are Coordinately Downregulated in Human Diabetes
Vamsi K. Mootha, Cecilia M. Lindgren, Karl-Fredrik Eriksson, Aravind Subramanian, Smita Sihag, Joseph Lehar, Pere Puigserver, Emma Carlsson, Martin Ridderstr?le, Esa Laurila, Nicholas Houstis, Mark J. Daly, Nick Patterson, Jill P. Mesirov, Todd R. Golub, Pablo Tamayo, Bruce Spiegelman, Eric S. Lander, Joel N. Hirschhorn, David Altshuler, and Leif C. Groop
Nature Nature Genet. 15 June 2003, vol. 34 no. 3 pp 267 ? 273.

MetastasisGene Expression Changes in an Animal Melanoma Model Correlate with Aggressiveness of Human Melanoma Metastases
Lei Xu, Steven S. Shen, Yujin Hoshida, Aravind Subramanian, Ken Ross, Jean-Philippe Brunet, Stephan N. Wagner, Sridhar Ramaswamy, Jill P. Mesirov, and Richard O. Hynes
Molecular Cancer Research 6, 760-769, May 1, 2008
 EBV Encoded LMP2A Induces Primary Epithelial Cell Migration and Invasion  Possible Role in Nasopharyngeal Carcinoma Metastasis.
Dirk M. Pegtel, Aravind Subramanian, Tzung-Shiahn Sheen, Ching-Hwa Tsai, Todd R. Golub and David A. Thorley-Lawson
 Evidence for a Molecular Signature of Metastasis in Primary Solid Tumors
Sridhar Ramaswamy, Ken N. Ross, Eric S. Lander, & Todd R. Golub
Nature Genetics, vol. 33, January 2003, pp. 49-54.
 Genomic analysis of metastasis reveals an essential role for RhoC
Edwin A. Clark, Todd R. Golub, Eric S. Lander and Richard O. Hynes.
Nature 406:532-535

microRNAMicroRNA Dynamics in the Stages of Tumorigenesis Correlate with Hallmark Capabilities of Cancer

 Lin28 promotes transformation and is associated with advanced human malignancies
Srinivas R Viswanathan, John T Powers, William Einhor, Yujin Hoshida, Tony L Ng, Sara Toffanin, Maureen O'Sullivan, Jun Lu, Letha A Phillips, Victoria L Lockhart, Samar P Shah, Pradeep S Tanwar, Craig H Mermel, Rameen Beroukhim, Mohammad Azam, Jose Teixeira, Matthew Meyerson, Timothy P Hughes, Josep M Llovet, Jerald Radich, Charles G Mullighan, Todd R Golub, Poul H Sorensen, George Q Daley
Nature Genetics, 2009 Jul;41(7):843-8
 microRNA-mediated control of cell fate in megakaryocyte-erythrocyte progenitors
Jun Lu, Shangqin Guo, Benjamin L. Ebert, Hao Zhang, Xiao Peng, Jocelyn Bosco, Jennifer Pretz, Rita Schlanger, Judy Y. Wang, Raymond H. Mak, David M. Dombkowski, Frederic I. Preffer, David T. Scadden and Todd R. Golub
Developmental Cell (2008), doi:10.1016/j.devcel.2008.03.012
 Impaired microRNA processing enhances cellular transformation and tumorigenesis
Madhu S. Kumar, Jun Lu, Kim L. Mercer, Todd R. Golub, and Tyler Jacks
Nat Genet. 2007 May;39(5):673-7. Epub 2007 Apr 1
 MicroRNA Expression Profiles Classify Human Cancers
Jun Lu, Gad Getz, Eric A. Miska, Ezequiel A. Alvarez-Saavedra, Justin Lamb, David Peck, Alejandro Sweet-Cordero, Benjamin L. Ebert, Raymond H. Mak, Adolfo A. Ferrando, James R. Downing, Tyler Jacks, H. Robert Horvitz and Todd R. Golub
Nature 435, 834-838 (9 June 2005)
 Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
Xiaohui Xie, Jun Lu, E. J. Kulbokas, Todd R. Golub, Vamsi Mootha, Kerstin Lindblad-Toh, Eric S. Lander and Manolis Kellis
Nature. 2005 Mar 17;434(7031):338-45

Prostate CancerSMAD4-dependent barrier constrains prostate cancer growth and metastatic progression
Ding Z, Wu CJ, Chu GC, Xiao Y, Ho D, Zhang J, Perry SR, Labrot ES, Wu X, Lis R, Hoshida Y, Hiller D, Hu B, Jiang S, Zheng H, Stegh AH, Scott KL, Signoretti S, Bardeesy N, Wang YA, Hill DE, Golub TR, Stampfer MJ, Wong WH, Loda M, Mucci L, Chin L, DePinho RA
Nature. 2011 Feb 10;470(7333):269-73
 Molecular sampling of prostate cancer: a dilemma for predicting disease progression
Andrea Sboner, Francesca Demichelis, Stefano Calza, Yudi Pawitan, Sunita R Setlur, Yujin Hoshida, Sven Perner, Hans-Olov Adami, Katja Fall, Lorelei A Mucci, Philip W Kantoff, Meir Stampfer, Swen-Olof Andersson, Eberhard Varenhorst, Jan-Erik Johansson, Mark B Gerstein, Todd R Golub, Mark A Rubin and Ove Andren
BMC Medical Genomics. 2010 Mar 16;3(1):8
 Estrogen-Dependent Signaling in a Molecularly Distinct Subclass of Aggressive Prostate Cancer
Sunita R. Setlur , Kirsten D. Mertz , Yujin Hoshida , Francesca Demichelis , Mathieu Lupien , Sven Perner , Andrea Sboner , Yudi Pawitan , Ove Andrin , Laura A. Johnson , Jeff Tang , Hans-Olov Adami , Stefano Calza , Arul M. Chinnaiyan , Daniel Rhodes , Scott Tomlins , Katja Fall , Lorelei A. Mucci , Philip W. Kantoff , Meir J. Stampfer , Swen-Olof Andersson , Eberhard Varenhorst , Jan-Erik Johansson , Myles Brown , Todd R. Golub , Mark A. Rubin
J Natl Cancer Inst 2008;100: 815  825
 TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort
F Demichelis, K Fall, S Perner, O Andre4n, F Schmidt, SR Setlur, Y Hoshida, J-M Mosquera, Y Pawitan, C Lee, H-O Adami, LA Mucci, PW Kantoff, S-O Andersson, AM Chinnaiyan, J-E Johansson, MA Rubin
Oncogene. 2007 Jul 5;26(31):4596-9
 Gene Expression Correlates of Clinical Prostate Cancer Behavior
Dinesh Singh, Phillip G. Febbo, Kenneth Ross, Donald G. Jackson, Judith Manola, Christine Ladd, Pablo Tamayo, Andrew A. Renshaw, Anthony V. D'Amico, Jerome P. Richie, Eric S. Lander, Massimo Loda, Philip W. Kantoff, Todd R. Golub, William R. Sellers.
Cancer Cell: March 2002, Vol. 1.

Reviews/CommentaryMolecular Classification and Novel Targets in Hepatocellular Carcinoma: Recent Advancements
Yujin Hoshida, Sara Toffanin, Anja Lachenmayer, Augusto Villanueva, Beatriz Minguez, Josep M. Llovet
Seminars in Liver Disease, 30(1); 35, 2010
 Risk of recurrence in hepatitis B-related hepatocellular carcinoma: impact of viral load in late recurrence
Yujin Hoshida
Journal of Hepatology, 2009 Nov;51(5):842-4
 Tumor-derived molecular information and outcome in hepatocellular carcinoma
Yujin Hoshida
Journal of Hepatology, 2009 Sep;51(3):595-6
 Molecular profiling to predict hepatocellular carcinoma outcome
Yujin Hoshida, Augusto Villanueva, Josep M. Llovet
Expert Rev Gastroenterol Hepatol. 2009 Apr;3(2):101-3
 Prolonged therapy for hepatitis C with low-dose peginterferon
Yujin Hoshida, Todd R. Golub
N Engl J Med. 2009 Mar 12;360(11):1152
 Genomics and signaling pathways in hepatocellular carcinoma
Augusto Villaneuva, Philippa Newell, Derek Y. Chiang, Scott Friedman, Josep Llovet
Semin. Liver Dis. 27(1): 55-76
 Gene Expression Profiling Reveals Reproducible Human Lung Adenocarcinoma Subtypes in Multiple Independent Patient Cohorts
DN Hayes, S Monti, G Parmigiani, CB Gilks, K Naoki, A Bhattacharjee, MA Socinski, C Perou and M Meyerson
J Clin Oncol, 24(31): 5079-5090, 2006.
 Genomic Approaches to Hematologic Malignancies
Benjamin L. Ebert and Todd R. Golub
Blood. 2004; 104: 923-932
 Microarray Data Mining: Facing the Challenges
Gregory Piatetsky-Shapiro and Pablo Tamayo
SIGKDD Explorations December 2003. Volume 5, Issue 2
 DNA Microarrays in Cancer: Realising the Promise of Personalised Medicine
Sridhar Ramaswamy, Charles M. Perou
Lancet 361:1576-1577
 Cancer Genomics and Molecular Pattern Recognition
Pablo Tamayo and Sridhar Ramaswamy
Expression profiling of human tumors: diagnostic and research applications. Marc Ladanyi and William Gerald eds. Humana Press (2003).
 DNA Microarrays in Clinical Oncology
Sridhar Ramaswamy, Todd R. Golub
Journal of Clinical Oncology 20, 1932-1941
 Genome-Wide Views of Cancer
Todd Golub
N Engl J Med 2001; 344:601-602
 GENOMICS: Journey to the Center of Biology
Eric S. Lander and Robert A. Weinberg
Science 2000 March 10; 287: 1777-1782
 Array of Hope
Eric S Lander
The Chipping Forecast (1999) Special Supplement. Nature Genet. 21:January 1999.

RNAiSystematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1.
David A. Barbie, Pablo Tamayo, Jesse S. Boehm, So Young Kim, Susan E. Moody, Ian F. Dunn, Anna C. Schinzel, Peter Sandy, Etienne Meylan, Claudia Scholl, Stefan Frohling, Edmond M. Chan, Martin L. Sos, Kathrin Michel, Craig Mermel, Serena J. Silver, Barbara A. Weir, Jan H. Reiling, Qing Sheng, Piyush B. Gupta, Raymond C. Wadlow, Hanh Le, Sebastian Hoersch, Ben S. Wittner, Sridhar Ramaswamy, David M. Livingston, David M. Sabatini, Matthew Meyerson, Roman K. Thomas, Eric S. Lander, Jill P. Mesirov, David E. Root, D. Gary Gilliland, Tyler Jacks & William C. Hahn
Nature 462(7269),108-112

SarcomaSignature-Based Small Molecule Screening Identifies Cytosine Arabinoside as an EWS/FLI Modulator in Ewing Sarcoma
Kimberly Stegmaier, Jenny S. Wong, Kenneth N. Ross, Kwan T. Chow, David Peck, Renee D. Wright, Stephen L. Lessnick, Andrew L. Kung, Todd R. Golub
Stegmaier K, Wong JS, Ross KN, Chow KT, Peck D, et al. (2007) Signature-based small molecule screening identifies cytosine arabinoside as an EWS/FLI modulator in Ewing sarcoma. PLoS Med, Vol. 4, No. 4, e122 doi:10.1371/journal.pmed.0040122
 Expression profiling of EWS/FLI identifies NKX2.2 as a critical target gene in Ewing's sarcoma
Richard Smith, Leah A. Owen, Deborah J. Trem, Jenny S. Wong, Jennifer S. Whangbo, Todd R. Golub, and Stephen L. Lessnick
Cancer Cell (2006) 9:405-416
 The Ewing's Sarcoma Oncoprotein EWS/FLI Induces a p53-Dependent Growth Arrest in Primary Human Fibroblasts
Stephen L. Lessnick, Caroline S. Dacwag, and Todd R. Golub
Cancer Cell 1, 393-401

Signal TransductionCOT drives resistance to RAF inhibition through MAP kinase pathway reactivation
Cory M. Johannessen, Jesse S. Boehm, So Young Kim, Sapana R. Thomas, Leslie Wardwell, Laura A. Johnson, Caroline M. Emery, Nicolas Stransky, Alexandria P. Cogdill, Jordi Barretina, Giordano Caponigro, Haley Hieronymus, Ryan R. Murray, Kourosh Salehi-Ashtiani, David E. Hill, Marc Vidal, Jean J. Zhao, Xiaoping Yang, Ozan Alkan, Sungjoon Kim, Jennifer L. Harris, Christopher J. Wilson, Vic E. Myer, Peter M. Finan, David E. Root, Thomas M. Roberts, Todd Golub, Keith T. Flaherty, Reinhard Dummer, Barbara Weber, William R. Sellers, Robert Schlege, Jennifer A. Wargo, William C. Hahn, Levi A. Garraway
 Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1.
David A. Barbie, Pablo Tamayo, Jesse S. Boehm, So Young Kim, Susan E. Moody, Ian F. Dunn, Anna C. Schinzel, Peter Sandy, Etienne Meylan, Claudia Scholl, Stefan Frohling, Edmond M. Chan, Martin L. Sos, Kathrin Michel, Craig Mermel, Serena J. Silver, Barbara A. Weir, Jan H. Reiling, Qing Sheng, Piyush B. Gupta, Raymond C. Wadlow, Hanh Le, Sebastian Hoersch, Ben S. Wittner, Sridhar Ramaswamy, David M. Livingston, David M. Sabatini, Matthew Meyerson, Roman K. Thomas, Eric S. Lander, Jill P. Mesirov, David E. Root, D. Gary Gilliland, Tyler Jacks & William C. Hahn
Nature 462(7269),108-112
 Diverse Signaling Pathways Activated by Growth Factor Receptors Induce Broadly Overlapping, Rather Than Independent, Sets
Douglas Fambrough, Kimberly McClure, Andrius Kazlauskas, and Eric S. Lander.
Cell, Vol. 97, 727?741, June, 1999

SNP AnalysisThe landscape of somatic copy-number alteration across human cancers
Rameen Beroukhim*, Craig H. Mermel*, Dale Porter, Guo Wei, Soumya Raychaudhuri, Jerry Donovan, Jordi Barretina, Jesse S. Boehm, Jennifer Dobson, Mitsuyoshi Urashima, Kevin T. Mc Henry, Reid M. Pinchback, Azra H. Ligon, Yoon-Jae Cho, Leila Haery, Heidi Greulich, Michael Reich, Wendy Winckler, Michael S. Lawrence, Barbara A. Weir, Kumiko E. Tanaka, Derek Y. Chiang, Adam J. Bass, Alice Loo, Carter Hoffman, John Prensner, Ted Liefeld, Qing Gao, Derek Yecies, Sabina Signoretti, Elizabeth Maher, Frederic J. Kaye, Hidefumi Sasaki, Joel E. Tepper, Jonathan A. Fletcher, Josep Tabernero, Jose Baselga, Ming-Sound Tsao, Francesca DeMichelis, Mark A. Rubin, Pasi A. Janne, Mark J. Daly, Carmelo Nucera, Ross L. Levine, Benjamin L. Ebert, Stacey Gabriel, Anil K. Rustgi, Cristina R. Antonescu, Marc Ladanyi, Anthony Letai, Levi A. Garraway, Massimo Loda, David G. Beer, Lawrence D. True, Aikou Okamoto, Scott L. Pomeroy, Samuel Singer, Todd R. Golub, Eric S. Lander1, Gad Getz, William R. Sellers & Matthew Meyerson
Nature 463, 899-905(18 February 2010)
 Integrative analysis reveals 53BP1 copy loss and decreased expression in a subset of human diffuse large B-cell lymphoma
K Takeyama, S Monti, J P Manis, P Dal Cin, G Getz, R Beroukhim, S Dutt, J C Aster, F W Alt, T R Golub, and M A Shipp
Oncogene 27(3):318-322, 2007
 Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma
Rameen Beroukhim, Gad Getz, Leia Nghiemphu, Jordi Barretina, Teli Hsueh, David Linhart, Igor Vivanco, Jeffrey C. Lee, Julie H. Huang, Sethu Alexander, Jinyan Du, Tweeny Kau, Roman K. Thomas, Kinjal Shah, Horacio Soto, Sven Perner, John Prensner, Ralph M. Debiasi, Francesca Demichelis, Charlie Hatton, Mark A. Rubin, Levi A. Garraway, Stan F. Nelson, Linda Liau, Paul Mischel, Tim F. Cloughesy, Matthew Meyerson, Todd R. Golub, Eric S. Lander, Ingo K. Mellinghoff, William R. Sellers
Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):20007-12
 Characterizing the cancer genome in lung adenocarcinoma
Barbara A. Weir, Michele S. Woo, Gad Getz, Sven Perner, Li Ding, Rameen Beroukhim, William M. Lin, Michael A. Province, Aldi Kraja, Laura A. Johnson, Kinjal Shah, Mitsuo Sato, Roman K. Thomas, Justine A. Barletta, Ingrid B. Borecki, Stephen Broderick, Andrew C. Chang, Derek Y. Chiang, Lucian R. Chirieac, Jeonghee Cho, Yoshitaka Fujii, Adi F. Gazdar, Thomas Giordano, Heidi Greulich, Megan Hanna, Bruce E. Johnson, Mark G. Kris, Alex Lash, Ling Lin, Neal Lindeman, Elaine R. Mardis, John D. McPherson, John Minna, Margaret B. Morgan, Mark Nadel, Mark B. Orringer, John R. Osborne, Brad Ozenberger, Alex H. Ramos, James Robinson, Jack A. Roth, Valerie Rusch, Hidefumi Sasaki, Frances Shepherd, Carrie Sougnez, Margaret R. Spitz, Ming-Sound Tsao, David Twomey, Roel Verhaak, George M. Weinstock, David A. Wheeler, Wendy Winckler, Akihiko Yoshizawa, Soyoung Yu, Maureen F. Zakowski, Qunyuan Zhang, David G. Beer, Ignacio I. Wistuba, Mark A. Watson, Levi A. Garraway, Marc Ladanyi, William D. Travis, William Pao, Mark A. Rubin, Stacey B. Gabriel, Richard A. Gibbs, Harold E. Varmus, Richard K. Wilson, Eric S. Lander & Matthew Meyerson
Nature 450, 893-898 (06 December 2007)
 Allele-specific amplification in cancer revealed by SNP array analysis.
Thomas LaFramboise, Barbara A. Weir, Xiaojun Zhao, Rameen Beroukhim, Cheng Li, David Harrington, William R. Sellers, Matthew Meyerson
PLoS Comput Biol. 2005 Nov;1(6):e65.
 Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma.
Levi A. Garraway, Hans R. Widlund, Mark A. Rubin, Gad Getz, Aaron J. Berger, Sridhar Ramaswamy, Rameen Beroukhim, Danny A. Milner, Scott R. Granter, Jinyan Du, Charles Lee, Stephan N. Wagner, Cheng Li, Todd R. Golub, David L. Rimm, Matthew L. Meyerson, David E. Fisher and William R. Sellers
Nature. 2005 Jul 7;436(7047):117-22.
 Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis.
Xiaojun Zhao, Barbara A. Weir, Thomas LaFramboise, Ming Lin, Rameen Beroukhim, Levi Garraway, Javad Beheshti, Jeffrey C. Lee, Katsuhiko Naoki, William G. Richards, David Sugarbaker, Fei Chen, Mark A. Rubin, Pasi A. Janne, Luc Girard, John Minna, David Christiani, Cheng Li, William R. Sellers and Matthew Meyerson
Cancer Res. 2005 Jul 1;65(13):5561-70.
 Molecular characterization of the tumor microenvironment in breast cancer.
Minna Allinen, Rameen Beroukhim, Li Cai, Cameron Brennan, Jaana Lahti-Domenici, Haiyan Huang, Dale Porter, Min Hu, Lynda Chin, Andrea Richardson, Stuart Schnitt, William R. Sellers and Kornelia Polyak
Cancer Cell. 2004 Jul;6(1):17-32.
 Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification.
J. Guillermo Paez, Ming Lin, Rameen Beroukhim, Jeffrey C. Lee, Xiaojun Zhao, Daniel J. Richter, Stacey Gabriel, Paula Herman, Hidefumi Sasaki, David Altshuler, Cheng Li, Matthew Meyerson, and William R. Sellers
Nucleic Acids Res. 2004 May 18;32(9):e71.
 An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays.
Xiaojun Zhao, Cheng Li, J. Guillermo Paez, Koei Chin, Pasi A. Janne, Tzu-Hsiu Chen, Luc Girard, John Minna, David Christiani, Chris Leo, Joe W. Gray, William R. Sellers and Matthew Meyerson
Cancer Res. 2004 May 1;64(9):3060-71.
 High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines.
Pasi A Janne, Cheng Li, Xiaojun Zhao, Luc Girard, Tzu-Hsiu Chen, John Minna, David C Christiani, Bruce E Johnson, and Matthew Meyerson
Oncogene (2004) 23, 2716-2726
 dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data.
Ming Lin, Lee-Jen Wei, William R. Sellers, Marshall Lieberfarb, Wing Hung Wong, and Cheng Li
Bioinformatics. 2004 May 22;20(8):1233-40.
 Loss of heterozygosity and its correlation with expression profiles in subclasses of invasive breast cancers.
Zhigang C. Wang, Ming Lin, Lee-Jen Wei, Cheng Li, Alexander Miron, Gabriella Lodeiro, Lyndsay Harris, Sridhar Ramaswamy, David M. Tanenbaum, Matthew Meyerson, James D. Iglehart and Andrea Richardson
Cancer Res. 2004 Jan 1;64(1):64-71.
 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.
Marshall E. Lieberfarb, Ming Lin, Mirna Lechpammer, Cheng Li, David M. Tanenbaum, Phillip G. Febbo, Renee L. Wright, Judy Shim, Philip W. Kantoff, Massimo Loda, Matthew Meyerson and William R. Sellers
Cancer Res. 2003 Aug 15;63(16):4781-5.
 Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays.
Kerstin Lindblad-Toh, David M. Tanenbaum, Mark J. Daly, Ellen Winchester, Weng-Onn Lui, Anuradha Villapakkam, Sasha E. Stanton, Catharina Larsson, Thomas J. Hudson, Bruce E. Johnson, Eric S. Lander & Matthew Meyerson
Nat Biotechnol. 2000 Sep;18(9):1001-5.

Transcriptional RegulationExpression profiling of EWS/FLI identifies NKX2.2 as a critical target gene in Ewing's sarcoma
Richard Smith, Leah A. Owen, Deborah J. Trem, Jenny S. Wong, Jennifer S. Whangbo, Todd R. Golub, and Stephen L. Lessnick
Cancer Cell (2006) 9:405-416
 Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
Xiaohui Xie, Jun Lu, E. J. Kulbokas, Todd R. Golub, Vamsi Mootha, Kerstin Lindblad-Toh, Eric S. Lander and Manolis Kellis
Nature. 2005 Mar 17;434(7031):338-45
 The Six1 Homeoprotein Stimulates Tumorigenesis via Reactivation of Cyclin A1
Ricardo D. Coletta, Kimberly Christensen, Kelly Jansky Reichenberger, Justin Lamb, Damian Micomonaco, Lili Huang, Douglas M. Wolf, Carsten M?ller-Tidow, Todd R. Golub, Kiyoshi Kawakami and Heide L. Ford
Proc. Natl. Acad. Sci. USA 101: 6478-6483
 Erra and Gabpa/b specify PGC-1a-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle
Vamsi K. Mootha, Christoph Handschin, Dan Arlow, Xiaohui Xie, Julie St. Pierre, Smita Sihag, Wenli Yang, David Altshuler, Pere Puigserver, Nick Patterson, Patricia J. Willy, Ira G. Shulman, Richard A. Heyman, Eric S. Lander, and Bruce M. Spiegelman
Proc. Natl. Acad. Sci. USA
 A Mechanism of Cyclin D1 Action Encoded in the Patterns of Gene Expression in Human Cancer
Justin Lamb, Sridhar Ramaswamy, Heide L. Ford, Bernardo Contreras, Robert V. Martinez, Frances S. Kittrell, Cynthia A. Zahnow, Nick Patterson, Todd R. Golub and Mark E. Ewen
Cell 114: 323-334 2003
 The Ewing's Sarcoma Oncoprotein EWS/FLI Induces a p53-Dependent Growth Arrest in Primary Human Fibroblasts
Stephen L. Lessnick, Caroline S. Dacwag, and Todd R. Golub
Cancer Cell 1, 393-401
 c-Myc is a critical target for c/EBPalpha in granulopoiesis.
Johansen LM, Iwama A, Lodie TA, Sasaki K, Felsher DW, Golub TR, Tenen DG
Molecular and Cellular Biology, June 2001, p. 3789-3806, Vol. 21, No. 11
 Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion
Hilary A. Coller, Carla Grandori, Pablo Tamayo, Trent Colbert, Eric S. Lander, Robert N. Eisenman and Todd R. Golub
Proc. Natl. Acad. Sci. USA, Vol. 97, Issue 7, 3260-3265, March 28, 2000