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Cancer Program Publications/Projects
Project	Publication
Bioinformatics & Computational Biology	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
	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)
	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
	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.
	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 Cancer	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
Cancer Susceptibility	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 zebrafish bmyb mutation causes genome instability and increased cancer susceptibility Jennifer L. Shepard*, James F. Amatruda*, Howard M. Stern, 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, Aravind Subramanian, Todd R. Golub, Jonathan N. Glickman, Jeffery L. Kutok, Jon C. Aster, and Leonard I. Zon
Chemical Genomics	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
Consensus Clustering	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.
Hematopoiesis	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.
Leukemia	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 Cancer	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
	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
Lymphoma	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
Melanoma	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 Diseases	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
	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.
Metastasis	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
Multi-Class Diagnosis	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
NMF	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
Prostate Cancer	mTOR inhibition reverses Akt-dependent prostate intraepithelial neoplasia through regulation of apoptotic and HIF-1-dependent pathways Nature Medicine 10, 594 - 601 (2004)
	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/Commentary	Genomic Approaches to Hematologic Malignancies 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.
Sarcoma	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
Self-Organizing Maps: Methods and Applications	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.
Signal Transduction	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
Transcriptional Regulation	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