6Department of Oncology (2009)
Justin Lamb, Sridhar Ramaswamy, Heide L. Ford, Bernardo Contreras, Robert V. Martinez, Frances S. Kittrell, ...
Here we describe how patterns of gene expression in human tumors have been deconvoluted to reveal a mechanism of action for the cyclin D1 oncogene. Com-putational analysis of the expression patterns...
Olson, Peter, Lu, Jun, Zhang, Hao, Shai, Anny, Chun, Matthew G., Wang, Yucheng, ...
While altered expression of microRNAs (miRs) in tumors has been well documented, it remains unclear how the miR transcriptome intersects neoplastic progression. By profiling the miR transcriptome we...
Stephen L. Lessnick, Caroline S. Dacwag, Todd R. Golub
Appendix 1: (below) Detailed description of the methods used in the microarray analyses. Appendix 2: Excel file containing the complete expression data from the tet-EF cell time course experiment....
Abstract Class Prediction and Discovery Using Gene Expression Data (2008)
Donna K. Slonim, Pablo Tamayo, Jill P. Mesirov, Todd R. Golub, Eric S. L
Classification of patient samples is a crucial aspect of cancer diagnosis and treatment. We present a method for classifying samples by computational analysis of gene expression data. We consider the...
Gene expression-based screening for inhibitors of PDGFR signaling (2008)
Antipova, Alena A, Stockwell, Brent R, Golub, Todd R
Abstract Here we describe a proof-of-concept experiment designed to explore the possibility of using gene expression-based high-throughput screening (GE-HTS) to find inhibitors of a signaling...
Benjamin L. Ebert, Naomi Galili, Pablo Tamayo, Jocelyn Bosco, Raymond Mak, Jennifer Pretz, ...
BackgroundLenalidomide is an effective new agent for the treatment of patients with myelodysplastic syndrome (MDS), an acquired hematopoietic disorder characterized by ineffective blood cell...
Modeling genomic diversity and tumor dependency in malignant melanoma (2008)
Lin, William M., Baker, Alissa C., Beroukhim, Rameen, Winckler, Wendy, Feng, Whei, Marmion, Jennifer M., ...
Estrogen-Dependent Signaling in a Molecularly Distinct Subclass of Aggressive Prostate Cancer (2008)
Setlur, Sunita R., Mertz, Kirsten D., Hoshida, Yujin, Demichelis, Francesca, Lupien, Mathieu, Perner, Sven, ...
Background The majority of prostate cancers harbor gene fusions of the 5′-untranslated region of the androgen-regulated transmembrane protease serine 2 (TMPRSS2) promoter with erythroblast...
SUPPLEMENTARY INFORMATION Multi-class Cancer Diagnosis Using Tumor Gene Expression Signatures (2007)
Sridhar Ramaswamy, Pablo Tamayo, Ryan Rifkin, Sayan Mukherjee, Hsiang Yeang, ...
This document provides supplementary information and details not included in the paper "Multiclass Cancer Diagnosis Using Tumor Gene Expression Signatures." Other sources of information can...
Kimberly Stegmaier, Jenny S. Wong, Kenneth N. Ross, Kwan T. Chow, David Peck, Renee D. Wright, ...
BackgroundThe presence of tumor-specific mutations in the cancer genome represents a potential opportunity for pharmacologic intervention to therapeutic benefit. Unfortunately, many classes of...
A method for high-throughput gene expression signature analysis (2006)
Peck, David, Crawford, Emily D, Ross, Kenneth N, Stegmaier, Kimberly, Golub, Todd R, Lamb, Justin
Abstract Genome-wide transcriptional profiling has shown that different biologic states (for instance, disease and response to pharmacologic manipulation) can be recognized by the expression pattern...
MPLW515L Is a Novel Somatic Activating Mutation in Myelofibrosis with Myeloid Metaplasia (2006)
Yana Pikman, Benjamin H. Lee, Thomas Mercher, Elizabeth McDowell, Benjamin L. Ebert, Maricel Gozo, ...
Activation of JAK-STAT signaling via a mutation - MPLW515L- in the thrombopoietin receptor seems to have a role in the pathogenesis of some patients with myelofibrosis.
MPLW515L Is a Novel Somatic Activating Mutation in Myelofibrosis with Myeloid Metaplasia (2006)
Yana Pikman, Benjamin H. Lee, Thomas Mercher, Elizabeth McDowell, Benjamin L. Ebert, Maricel Gozo, ...
Background The JAK2V617F allele has recently been identified in patients with polycythemia vera (PV), essential thrombocytosis (ET), and myelofibrosis with myeloid metaplasia (MF). Subsequent...
Wadleigh, Martha, Ebert, Benjamin L, Wernig, Gerlinde, Huntly, Brian J P, ...
Polycythemia vera (PV), essential thrombocythemia (ET), and myeloid metaplasia with myelofibrosis (MMM) are clonal disorders arising from hematopoietic progenitors. An internet-based protocol was...
Genomic Approaches to Hematologic Malignancies (2004)
Benjamin L Ebert, Todd R Golub, Benjamin L. Ebert, Todd R. Golub, Todd Golub
Information about reproducing this article in parts or in its entirety may be found online at:
Estimating dataset size requirements for classifying DNA Microarray data (2003)
Sayan Mukherjee, Pablo Tamayo, Simon Rogers, Ryan Rifkin, Anna Engle, Colin Campbell, ...
A statistical methodology for estimating dataset size requirements for classifying microarray data using learning curves is introduced. The goal is to use existing classi � cation results to...
An analytical method for multiclass molecular cancer classification (2003)
Ryan Rifkin, Sayan Mukherjee, Pablo Tamayo, Sridhar Ramaswamy, Chen-hsiang Yeang, Michael Angelo, ...
Abstract. Modern cancer treatment relies upon microscopic tissue examination to classify tumors according to anatomical site of origin. This approach is effective but subjective and variable even...
A strategy for oligonucleotide microarray probe reduction (2002)
Antipova, Alena A, Tamayo, Pablo, Golub, Todd R
Abstract Background One of the factors limiting the number of genes that can be analyzed on high-density oligonucleotide arrays is that each transcript is probed by multiple oligonucleotide probes....
Class Prediction and Discovery Using Gene Expression Data (2000)
Donna K. Slonim, Pablo Tamayo, Jill P. Mesirov, Todd R. Golub, Eric S. Lander, Eric S. L
Classification of patient samples is a crucial aspect of cancer diagnosis and treatment. We present a method for classifying samples by computational analysis of gene expression data. We consider the...
The TEL/ETV6 gene is required specifically for hematopoiesis in the bone marrow (1998)
Wang, Li Chun, Swat, Wojciech, Fujiwara, Yuko, Davidson, Laurie, Visvader, Jane, Kuo, Frank, ...
Tamayo, Pablo, Slonim, Donna, Mesirov, Jill, Zhu, Qing, Kitareewan, Sutisak, Dmitrovsky, Ethan, ...
Array technologies have made it straightforward to monitor simultaneously the expression pattern of thousands of genes. The challenge now is to interpret such massive data sets. The first step is to...
Coller, Hilary A., Grandori, Carla, Tamayo, Pablo, Colbert, Trent, Lander, Eric S., Eisenman, Robert N., ...
MYC affects normal and neoplastic cell proliferation by altering gene expression, but the precise pathways remain unclear. We used oligonucleotide microarray analysis of 6,416 genes and expressed...
Butte, Atul J., Tamayo, Pablo, Slonim, Donna, Golub, Todd R., Kohane, Isaac S.
In an effort to find gene regulatory networks and clusters of genes that affect cancer susceptibility to anticancer agents, we joined a database with baseline expression levels of 7,245 genes...
Chemosensitivity prediction by transcriptional profiling
Staunton, Jane E., Slonim, Donna K., Coller, Hilary A., Tamayo, Pablo, Angelo, Michael J., Park, Johnny, ...
In an effort to develop a genomics-based approach to the prediction of drug response, we have developed an algorithm for classification of cell line chemosensitivity based on gene expression profiles...
Bhattacharjee, Arindam, Richards, William G., Staunton, Jane, Li, Cheng, Monti, Stefano, Vasa, Priya, ...
We have generated a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, we analyzed mRNA expression levels...
Multiclass cancer diagnosis using tumor gene expression signatures
Ramaswamy, Sridhar, Tamayo, Pablo, Rifkin, Ryan, Mukherjee, Sayan, Yeang, Chen-Hsiang, Angelo, Michael, ...
The optimal treatment of patients with cancer depends on establishing accurate diagnoses by using a complex combination of clinical and histopathological data. In some instances, this task is...
c-Myc Is a Critical Target for C/EBPα in Granulopoiesis
Johansen, Lisa M., Iwama, Atsushi, Lodie, Tracey A., Sasaki, Koichi, Felsher, Dean W., Golub, Todd R., ...
CCAAT/enhancer binding protein α (C/EBPα) is an integral factor in the granulocytic developmental pathway, as myeloblasts from C/EBPα-null mice exhibit an early block in differentiation. Since...
Kitareewan, Sutisak, Pitha-Rowe, Ian, Sekula, David, Lowrey, Christopher H., Nemeth, Michael J., Golub, Todd R., ...
All-trans-retinoic acid (RA) treatment induces remissions in acute promyelocytic leukemia (APL) cases expressing the t(15;17) product, promyelocytic leukemia (PML)/RA receptor α (RARα). Microarray...
Abnormal gene expression in cloned mice derived from embryonic stem cell and cumulus cell nuclei
Humpherys, David, Eggan, Kevin, Akutsu, Hidenori, Friedman, Adam, Hochedlinger, Konrad, Yanagimachi, Ryuzo, ...
To assess the extent of abnormal gene expression in clones, we assessed global gene expression by microarray analysis on RNA from the placentas and livers of neonatal cloned mice derived by nuclear...
Peng, Tao, Golub, Todd R., Sabatini, David M.
RAFT1/FRAP/mTOR is a key regulator of cell growth and division and the mammalian target of rapamycin, an immunosuppressive and anticancer drug. Rapamycin deprivation and nutrient deprivation have...
Chen, Chang-Zheng, Li, Min, De Graaf, David, Monti, Stefano, Göttgens, Berthold, Sanchez, Maria-Jose, ...
We describe a strategy to obtain highly enriched long-term repopulating (LTR) hematopoietic stem cells (HSCs) from bone marrow side-population (SP) cells by using a transgenic reporter gene driven by...
A strategy for oligonucleotide microarray probe reduction
Antipova, Alena A, Tamayo, Pablo, Golub, Todd R
One of the factors limiting the number of genes that can be analyzed on high-density oligonucleotide arrays is that each transcript is probed by multiple oligonucleotide probes. To reduce the number...
Prostate intraepithelial neoplasia induced by prostate restricted Akt activation: The MPAKT model
Majumder, Pradip K., Yeh, Jen Jen, George, Daniel J., Febbo, Phillip G., Kum, Jennifer, Xue, Qi, ...
To determine whether Akt activation was sufficient for the transformation of normal prostate epithelial cells, murine prostate restricted Akt kinase activity was generated in transgenic mice (MPAKT...
The TEL/ETV6 gene is required specifically for hematopoiesis in the bone marrow
Wang, Li Chun, Swat, Wojciech, Fujiwara, Yuko, Davidson, Laurie, Visvader, Jane, Kuo, Frank, ...
The TEL (translocation–Ets–leukemia or ETV6) locus, which encodes an Ets family transcription factor, is frequently rearranged in human leukemias of myeloid or lymphoid origins. By gene targeting...
Metagenes and molecular pattern discovery using matrix factorization
Brunet, Jean-Philippe, Tamayo, Pablo, Golub, Todd R., Mesirov, Jill P.
We describe here the use of nonnegative matrix factorization (NMF), an algorithm based on decomposition by parts that can reduce the dimension of expression data from thousands of genes to a handful...
The Six1 homeoprotein stimulates tumorigenesis by reactivation of cyclin A1
Coletta, Ricardo D., Christensen, Kimberly, Reichenberger, Kelly J., Lamb, Justin, Micomonaco, Damian, Huang, Lili, ...
Homeobox genes constitute a large family of transcription factors that are essential during normal development and are often dysregulated in cancer. However, the molecular mechanisms by which...
Conditional MLL-CBP targets GMP and models therapy-related myeloproliferative disease
Wang, Jing, Iwasaki, Hiromi, Krivtsov, Andrei, Febbo, Phillip G, Thorner, Aaron R, Ernst, Patricia, ...
Chromosomal translocations that fuse the mixed lineage leukemia (MLL) gene with multiple partners typify acute leukemias of infancy as well as therapy-related leukemias. We utilized a conditional...
A zebrafish bmyb mutation causes genome instability and increased cancer susceptibility
Shepard, Jennifer L., Amatruda, James F., Stern, Howard M., Subramanian, Aravind, Finkelstein, David, Ziai, James, ...
A major goal of cancer research has been to identify genes that contribute to cancer formation. The similar pathology between zebrafish and human tumors, as well as the past success of large-scale...
Pegtel, Dirk M., Subramanian, Aravind, Sheen, Tzung-Shiahn, Tsai, Ching-Hwa, Golub, Todd R., Thorley-Lawson, David A.
Nonkeratinizing nasopharyngeal carcinomas (NPC) are >95% associated with the expression of the Epstein-Barr virus (EBV) LMP2A latent protein. However, the role of EBV, in particular, LMP2A, in tumor...
Subramanian, Aravind, Tamayo, Pablo, Mootha, Vamsi K., Mukherjee, Sayan, Ebert, Benjamin L., Gillette, Michael A., ...
Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a...
MPLW515L Is a Novel Somatic Activating Mutation in Myelofibrosis with Myeloid Metaplasia
Pikman, Yana, Lee, Benjamin H, Mercher, Thomas, McDowell, Elizabeth, Ebert, Benjamin L, Gozo, Maricel, ...
Activation of JAK-STAT signaling via a mutation - MPLW515L- in the thrombopoietin receptor seems to have a role in the pathogenesis of some patients with myelofibrosis.
Bourquin, Jean-Pierre, Subramanian, Aravind, Langebrake, Claudia, Reinhardt, Dirk, Bernard, Olivier, Ballerini, Paola, ...
Individuals with Down syndrome (DS) are predisposed to develop acute megakaryoblastic leukemia (AMKL), characterized by expression of truncated GATA1 transcription factor protein (GATA1s) due to...
Tamayo, Pablo, Slonim, Donna, Mesirov, Jill, Zhu, Qing, Kitareewan, Sutisak, Dmitrovsky, Ethan, ...
Array technologies have made it straightforward to monitor simultaneously the expression pattern of thousands of genes. The challenge now is to interpret such massive data sets. The first step is to...
Coller, Hilary A., Grandori, Carla, Tamayo, Pablo, Colbert, Trent, Lander, Eric S., Eisenman, Robert N., ...
MYC affects normal and neoplastic cell proliferation by altering gene expression, but the precise pathways remain unclear. We used oligonucleotide microarray analysis of 6,416 genes and expressed...
Butte, Atul J., Tamayo, Pablo, Slonim, Donna, Golub, Todd R., Kohane, Isaac S.
In an effort to find gene regulatory networks and clusters of genes that affect cancer susceptibility to anticancer agents, we joined a database with baseline expression levels of 7,245 genes...
Chemosensitivity prediction by transcriptional profiling
Staunton, Jane E., Slonim, Donna K., Coller, Hilary A., Tamayo, Pablo, Angelo, Michael J., Park, Johnny, ...
In an effort to develop a genomics-based approach to the prediction of drug response, we have developed an algorithm for classification of cell line chemosensitivity based on gene expression profiles...
Bhattacharjee, Arindam, Richards, William G., Staunton, Jane, Li, Cheng, Monti, Stefano, Vasa, Priya, ...
We have generated a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, we analyzed mRNA expression levels...
Multiclass cancer diagnosis using tumor gene expression signatures
Ramaswamy, Sridhar, Tamayo, Pablo, Rifkin, Ryan, Mukherjee, Sayan, Yeang, Chen-Hsiang, Angelo, Michael, ...
The optimal treatment of patients with cancer depends on establishing accurate diagnoses by using a complex combination of clinical and histopathological data. In some instances, this task is...
c-Myc Is a Critical Target for C/EBPα in Granulopoiesis
Johansen, Lisa M., Iwama, Atsushi, Lodie, Tracey A., Sasaki, Koichi, Felsher, Dean W., Golub, Todd R., ...
CCAAT/enhancer binding protein α (C/EBPα) is an integral factor in the granulocytic developmental pathway, as myeloblasts from C/EBPα-null mice exhibit an early block in differentiation. Since...
Kitareewan, Sutisak, Pitha-Rowe, Ian, Sekula, David, Lowrey, Christopher H., Nemeth, Michael J., Golub, Todd R., ...
All-trans-retinoic acid (RA) treatment induces remissions in acute promyelocytic leukemia (APL) cases expressing the t(15;17) product, promyelocytic leukemia (PML)/RA receptor α (RARα). Microarray...
Abnormal gene expression in cloned mice derived from embryonic stem cell and cumulus cell nuclei
Humpherys, David, Eggan, Kevin, Akutsu, Hidenori, Friedman, Adam, Hochedlinger, Konrad, Yanagimachi, Ryuzo, ...
To assess the extent of abnormal gene expression in clones, we assessed global gene expression by microarray analysis on RNA from the placentas and livers of neonatal cloned mice derived by nuclear...
Peng, Tao, Golub, Todd R., Sabatini, David M.
RAFT1/FRAP/mTOR is a key regulator of cell growth and division and the mammalian target of rapamycin, an immunosuppressive and anticancer drug. Rapamycin deprivation and nutrient deprivation have...
Chen, Chang-Zheng, Li, Min, De Graaf, David, Monti, Stefano, Göttgens, Berthold, Sanchez, Maria-Jose, ...
We describe a strategy to obtain highly enriched long-term repopulating (LTR) hematopoietic stem cells (HSCs) from bone marrow side-population (SP) cells by using a transgenic reporter gene driven by...
A strategy for oligonucleotide microarray probe reduction
Antipova, Alena A, Tamayo, Pablo, Golub, Todd R
One of the factors limiting the number of genes that can be analyzed on high-density oligonucleotide arrays is that each transcript is probed by multiple oligonucleotide probes. To reduce the number...
Prostate intraepithelial neoplasia induced by prostate restricted Akt activation: The MPAKT model
Majumder, Pradip K., Yeh, Jen Jen, George, Daniel J., Febbo, Phillip G., Kum, Jennifer, Xue, Qi, ...
To determine whether Akt activation was sufficient for the transformation of normal prostate epithelial cells, murine prostate restricted Akt kinase activity was generated in transgenic mice (MPAKT...
The TEL/ETV6 gene is required specifically for hematopoiesis in the bone marrow
Wang, Li Chun, Swat, Wojciech, Fujiwara, Yuko, Davidson, Laurie, Visvader, Jane, Kuo, Frank, ...
The TEL (translocation–Ets–leukemia or ETV6) locus, which encodes an Ets family transcription factor, is frequently rearranged in human leukemias of myeloid or lymphoid origins. By gene targeting...
Metagenes and molecular pattern discovery using matrix factorization
Brunet, Jean-Philippe, Tamayo, Pablo, Golub, Todd R., Mesirov, Jill P.
We describe here the use of nonnegative matrix factorization (NMF), an algorithm based on decomposition by parts that can reduce the dimension of expression data from thousands of genes to a handful...
The Six1 homeoprotein stimulates tumorigenesis by reactivation of cyclin A1
Coletta, Ricardo D., Christensen, Kimberly, Reichenberger, Kelly J., Lamb, Justin, Micomonaco, Damian, Huang, Lili, ...
Homeobox genes constitute a large family of transcription factors that are essential during normal development and are often dysregulated in cancer. However, the molecular mechanisms by which...
Conditional MLL-CBP targets GMP and models therapy-related myeloproliferative disease
Wang, Jing, Iwasaki, Hiromi, Krivtsov, Andrei, Febbo, Phillip G, Thorner, Aaron R, Ernst, Patricia, ...
Chromosomal translocations that fuse the mixed lineage leukemia (MLL) gene with multiple partners typify acute leukemias of infancy as well as therapy-related leukemias. We utilized a conditional...
A zebrafish bmyb mutation causes genome instability and increased cancer susceptibility
Shepard, Jennifer L., Amatruda, James F., Stern, Howard M., Subramanian, Aravind, Finkelstein, David, Ziai, James, ...
A major goal of cancer research has been to identify genes that contribute to cancer formation. The similar pathology between zebrafish and human tumors, as well as the past success of large-scale...
Subramanian, Aravind, Tamayo, Pablo, Mootha, Vamsi K., Mukherjee, Sayan, Ebert, Benjamin L., Gillette, Michael A., ...
Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a...
Pegtel, Dirk M., Subramanian, Aravind, Sheen, Tzung-Shiahn, Tsai, Ching-Hwa, Golub, Todd R., Thorley-Lawson, David A.
Nonkeratinizing nasopharyngeal carcinomas (NPC) are >95% associated with the expression of the Epstein-Barr virus (EBV) LMP2A latent protein. However, the role of EBV, in particular, LMP2A, in tumor...
Bourquin, Jean-Pierre, Subramanian, Aravind, Langebrake, Claudia, Reinhardt, Dirk, Bernard, Olivier, Ballerini, Paola, ...
Individuals with Down syndrome (DS) are predisposed to develop acute megakaryoblastic leukemia (AMKL), characterized by expression of truncated GATA1 transcription factor protein (GATA1s) due to...
MPLW515L Is a Novel Somatic Activating Mutation in Myelofibrosis with Myeloid Metaplasia
Pikman, Yana, Lee, Benjamin H, Mercher, Thomas, McDowell, Elizabeth, Ebert, Benjamin L, Gozo, Maricel, ...
Activation of JAK-STAT signaling via a mutation - MPLW515L- in the thrombopoietin receptor seems to have a role in the pathogenesis of some patients with myelofibrosis.
A method for high-throughput gene expression signature analysis
Peck, David, Crawford, Emily D, Ross, Kenneth N, Stegmaier, Kimberly, Golub, Todd R, Lamb, Justin
A new method for cost-effective high-throughput gene expression signature analysis is described.
Stegmaier, Kimberly, Wong, Jenny S, Ross, Kenneth N, Chow, Kwan T, Peck, David, Wright, Renee D, ...
Todd Golub and colleagues show that a gene expression-based screen of small-molecule libraries can identify candidate drugs that modulate cancer-associated oncoproteins.
Ebert, Benjamin L., Lee, Michele M., Pretz, Jennifer L., Subramanian, Aravind, Mak, Raymond, Golub, Todd R., ...
Diamond-Blackfan anemia (DBA), a congenital erythroblastopenia, is a model disease for the study of erythroid differentiation but is poorly understood. RPS19 is the only gene yet to have been...
Gefitinib induces myeloid differentiation of acute myeloid leukemia
Stegmaier, Kimberly, Corsello, Steven M., Ross, Kenneth N., Wong, Jenny S., DeAngelo, Daniel J., Golub, Todd R.
Cure rates for patients with acute myeloid leukemia (AML) remain low despite ever-increasing dose intensity of cytotoxic therapy. In an effort to identify novel approaches to AML therapy, we recently...
Subclass Mapping: Identifying Common Subtypes in Independent Disease Data Sets
Hoshida, Yujin, Brunet, Jean-Philippe, Tamayo, Pablo, Golub, Todd R., Mesirov, Jill P.
Whole genome expression profiles are widely used to discover molecular subtypes of diseases. A remaining challenge is to identify the correspondence or commonality of subtypes found in multiple,...
An Erythroid Differentiation Signature Predicts Response to Lenalidomide in Myelodysplastic Syndrome
Ebert, Benjamin L, Galili, Naomi, Tamayo, Pablo, Bosco, Jocelyn, Mak, Raymond, Pretz, Jennifer, ...
Using gene expression profiling, Azra Raza and colleagues identified a molecular signature that predicts response to lenalidomide in patients without Chromosome 5q deletions, which suggests that...
Semiautomated Multiplexed Quantum Dot-Based in Situ Hybridization and Spectral Deconvolution
Byers, Richard J., Di Vizio, Dolores, O’Connell, Fionnuala, Tholouli, Eleni, Levenson, Richard M., Gossard, Kirk, ...
Gene expression profiling has identified several potentially useful gene signatures for predicting outcome or for selecting targeted therapy. However, these signatures have been developed in fresh or...
Identification of prostate cancer modifier pathways using parental strain expression mapping
Xu, Qing, Majumder, Pradip K., Ross, Kenneth, Shim, Yeonju, Golub, Todd R., Loda, Massimo, ...
Inherited genetic risk factors play an important role in cancer. However, other than the Mendelian fashion cancer susceptibility genes found in familial cancer syndromes, little is known about risk...
Gene expression-based screening for inhibitors of PDGFR signaling
Antipova, Alena A, Stockwell, Brent R, Golub, Todd R
Inhibitors of the platelet derived growth factor receptor (PDGFR) signaling pathway are isolated using gene expression-based high-throughput screening (GE-HTS), a method that is applicable to other...
Mi, Shuangli, Lu, Jun, Sun, Miao, Li, Zejuan, Zhang, Hao, Neilly, Mary Beth, ...
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer, whereas acute myeloid leukemia (AML) is the most common acute leukemia in adults. In general, ALL has a better prognosis than...
Hahn, Cynthia K., Ross, Kenneth N., Warrington, Ian M., Mazitschek, Ralph, Kanegai, Cindy M., Wright, Renee D., ...
The discovery of new small molecules and their testing in rational combination poses an ongoing problem for rare diseases, in particular, for pediatric cancers such as neuroblastoma. Despite maximal...
Id1 is a common downstream target of oncogenic tyrosine kinases in leukemic cells
Tam, Winnie F., Gu, Ting-Lei, Chen, Jing, Lee, Benjamin H., Bullinger, Lars, Fröhling, Stefan, ...
Oncogenic tyrosine kinases, such as BCR-ABL, TEL-ABL, TEL-PDGFβR, and FLT3-ITD, play a major role in the development of hematopoietic malignancy. They activate many of the same signal transduction...
Distinct microRNA expression profiles in acute myeloid leukemia with common translocations
Li, Zejuan, Lu, Jun, Sun, Miao, Mi, Shuangli, Zhang, Hao, Luo, Roger T., ...
MicroRNAs (miRNAs) are postulated to be important regulators in cancers. Here, we report a genome-wide miRNA expression analysis in 52 acute myeloid leukemia (AML) samples with common translocations,...
Highly parallel identification of essential genes in cancer cells
Luo, Biao, Cheung, Hiu Wing, Subramanian, Aravind, Sharifnia, Tanaz, Okamoto, Michael, Yang, Xiaoping, ...
More complete knowledge of the molecular mechanisms underlying cancer will improve prevention, diagnosis and treatment. Efforts such as The Cancer Genome Atlas are systematically characterizing the...
Identifying the proteins to which small-molecule probes and drugs bind in cells
Ong, Shao-En, Schenone, Monica, Margolin, Adam A., Li, Xiaoyu, Do, Kathy, Doud, Mary K., ...
Most small-molecule probes and drugs alter cell circuitry by interacting with 1 or more proteins. A complete understanding of the interacting proteins and their associated protein complexes, whether...
microRNA Expression during Trophectoderm Specification
Viswanathan, Srinivas R., Mermel, Craig H., Lu, Jun, Lu, Chi-Wei, Golub, Todd R., Daley, George Q.
Identification of AML1-ETO modulators by chemical genomics
Corsello, Steven M., Roti, Giovanni, Ross, Kenneth N., Chow, Kwan T., Galinsky, Ilene, DeAngelo, Daniel J., ...
Somatic rearrangements of transcription factors are common abnormalities in the acute leukemias. With rare exception, however, the resultant protein products have remained largely intractable as...
Ikeda, Sadakatsu, He, Aibin, Kong, Sek Won, Lu, Jun, Bejar, Rafael, Bodyak, Natalya, ...
Calcium signaling is a central regulator of cardiomyocyte growth and function. Calmodulin is a critical mediator of calcium signals. Because the amount of calmodulin within cardiomyocytes is...
MicroRNA dynamics in the stages of tumorigenesis correlate with hallmark capabilities of cancer
Olson, Peter, Lu, Jun, Zhang, Hao, Shai, Anny, Chun, Matthew G., Wang, Yucheng, ...
While altered expression of microRNAs (miRs) in tumors has been well documented, it remains unclear how the miR transcriptome intersects neoplastic progression. By profiling the miR transcriptome we...