Now showing items 1-20 of 26

    • Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease 

      Bradner, James Elliott; Mak, Raymond Heungwing; Tanguturi, Shyam Kumar; Mazitschek, Ralph; Haggarty, Stephen John; Ross, Kenneth N; Chang, Cindy Y.; Bosco, Jocelyn; West, Nathan; Morse, Elizabeth; Lin, Katherine; Shen, John Paul; Kwiatkowski, Nicholas Paul; Gheldof, Nele; Dekker, Job; DeAngelo, Daniel J.; Carr, Steven A.; Schreiber, Stuart L.; Golub, Todd Robert; Ebert, Benjamin L. (Proceedings of the National Academy of Sciences, 2010)
      The worldwide burden of sickle cell disease is enormous, with over 200,000 infants born with the disease each year in Africa alone. Induction of fetal hemoglobin is a validated strategy to improve symptoms and complications ...
    • Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq 

      Venteicher, Andrew S; Tirosh, Itay; Hebert, Christine; Yizhak, Keren; Neftel, Cyril Ralf Alexander; Filbin, Mariella Gruber; Hovestadt, Volker; Escalante, Leah; Shaw, McKenzie; Rodman, Christopher Jiahn-Leh; Gillespie, Shawn; Dionne, Danielle; Luo, Christina; Ravichandran, Hiranmayi; Mylvaganam, Ravindra; Mount, Christopher; Onozato, Maristela Lika; Nahed, Brian Vala; Wakimoto, Hiroaki; Curry, William Thomas; Iafrate, Anthony John; Rivera, Miguel Nicolas; Frosch, Matthew P.; Golub, Todd Robert; Brastianos, Priscilla Kalliope; Getz, Gad A; Patel, Anoop Premswaroop; Monje, Michelle; Cahill, Daniel P.; Rozenblatt-Rosen, Orit; Louis, David N.; Bernstein, Bradley E.; Regev, Aviv; Suvà, Mario (American Association for the Advancement of Science (AAAS), 2017)
    • Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis 

      Novershtern, Noa; Subramanian, Aravind; Lawton, Lee N.; Mak, Raymond Heungwing; Haining, William Nicholas; McConkey, Marie E.; Habib, Naomi; Yosef, Nir; Chang, Cindy Hsin-Yu; Shay, Tal; Frampton, Garrett M.; Drake, Adam C.B.; Leskov, Ilya; Nilsson, Bjorn; Preffer, Frederic Ira; Dombkowski, David; Evans, John W.; Liefeld, Ted; Smutko, John S.; Chen, Jianzhu; Friedman, Nir; Young, Richard A.; Golub, Todd Robert; Regev, Aviv; Ebert, Benjamin L. (Elsevier BV, 2011)
      While many individual transcription factors are known to regulate hematopoietic differentiation, major aspects of the global architecture of hematopoiesis remain unknown. Here, we profiled gene expression in 38 distinct ...
    • Discovery and saturation analysis of cancer genes across 21 tumor types 

      Lawrence, Michael S.; Stojanov, Petar; Mermel, Craig H.; Garraway, Levi A.; Golub, Todd R.; Meyerson, Matthew; Gabriel, Stacey B.; Lander, Eric S.; Getz, Gad (2014)
      Summary While a few cancer genes are mutated in a high proportion of tumors of a given type (>20%), most are mutated at intermediate frequencies (2–20%). To explore the feasibility of creating a comprehensive catalog of ...
    • Dual Suppression of the Cyclin-Dependent Kinase Inhibitors CDKN2C and CDKN1A in Human Melanoma 

      Jalili, Ahmad; Wagner, Christine; Pashenkov, Mikhail; Pathria, Gaurav; Mertz, Kirsten D.; Widlund, Hans R.; Lupien, Mathieu; Brunet, Jean- Philippe; Golub, Todd R.; Stingl, Georg; Fisher, David Erich; Ramaswamy, Sridhar; Wagner, Stephan N. (Oxford University Press, 2012)
      Resistance to BRAFV600E inhibitors is associated with reactivation of mitogen-activated protein kinase (MAPK) signaling at different levels in melanoma. To identify downstream effectors of MAPK signaling that could be used ...
    • Empirical Bayes Analysis of Quantitative Proteomics Experiments 

      Margolin, Adam A.; Ong, Shao-En; Schenone, Monica; Gould, Robert; Schreiber, Stuart L.; Carr, Steven A.; Golub, Todd R. (Public Library of Science, 2009)
      Background: Advances in mass spectrometry-based proteomics have enabled the incorporation of proteomic data into systems approaches to biology. However, development of analytical methods has lagged behind. Here we describe ...
    • An Erythroid Differentiation Signature Predicts Response to Lenalidomide in Myelodysplastic Syndrome 

      Galili, Naomi; Tamayo, Pablo; Bosco, Jocelyn; Ladd-Acosta, Christine; Raza, Azra; Ebert, Benjamin L.; Mak, Raymond Heungwing; Pretz, Jennifer Lee; Tanguturi, Shyam Kumar; Stone, Richard Maury; Golub, Todd R. (Public Library of Science, 2008)
      Background: Lenalidomide is an effective new agent for the treatment of patients with myelodysplastic syndrome (MDS), an acquired hematopoietic disorder characterized by ineffective blood cell production and a predisposition ...
    • Exome and whole genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity 

      Dulak, Austin M.; Stojanov, Petar; Peng, Shouyong; Lawrence, Michael S.; Fox, Cameron; Stewart, Chip; Bandla, Santhoshi; Imamura, Yu; Schumacher, Steven E.; Shefler, Erica; McKenna, Aaron; Cibulskis, Kristian; Sivachenko, Andrey; Carter, Scott L.; Saksena, Gordon; Voet, Douglas; Ramos, Alex H.; Auclair, Daniel; Thompson, Kristin; Sougnez, Carrie; Onofrio, Robert C.; Guiducci, Candace; Beroukhim, Rameen; Zhou, David; Lin, Lin; Lin, Jules; Reddy, Rishindra; Chang, Andrew; Luketich, James D.; Pennathur, Arjun; Ogino, Shuji; Golub, Todd R.; Gabriel, Stacey B.; Lander, Eric S.; Beer, David G.; Godfrey, Tony E.; Getz, Gad; Bass, Adam J. (2013)
      The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years. With a five-year survival rate of 15%, identification of new therapeutic targets for EAC is greatly important. We analyze the mutation ...
    • Gene Expression-Based Screening for Inhibitors of PDGFR Signaling 

      Antipova, Alena A.; Stockwell, Brent R.; Golub, Todd R. (BioMed Central, 2008)
      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 cascade, using platelet derived growth ...
    • The Genomic Landscape of Juvenile Myelomonocytic Leukemia 

      Stieglitz, Elliot; Taylor-Weiner, Amaro N.; Chang, Tiffany Y.; Gelston, Laura C.; Wang, Yong-Dong; Mazor, Tali; Esquivel, Emilio; Yu, Ariel; Seepo, Sara; Olsen, Scott; Rosenberg, Mara; Archambeault, Sophie L.; Abusin, Ghada; Beckman, Kyle; Brown, Patrick A.; Briones, Michael; Carcamo, Benjamin; Cooper, Todd; Dahl, Gary V.; Emanuel, Peter D.; Fluchel, Mark N.; Goyal, Rakesh K.; Hayashi, Robert J.; Hitzler, Johann; Hugge, Christopher; Liu, Y. Lucy; Messinger, Yoav H.; Mahoney, Donald H.; Monteleone, Philip; Nemecek, Eneida R.; Roehrs, Philip A.; Schore, Reuven J.; Stine, Kimo C.; Takemoto, Clifford M.; Toretsky, Jeffrey A.; Costello, Joseph F.; Olshen, Adam B.; Stewart, Chip; Li, Yongjin; Ma, Jing; Gerbing, Robert B.; Alonzo, Todd A.; Getz, Gad; Gruber, Tanja; Golub, Todd; Stegmaier, Kimberly; Loh, Mignon L. (2015)
      Juvenile myelomonocytic leukemia (JMML) is a myeloproliferative neoplasm (MPN) of childhood with a poor prognosis. Mutations in NF1, NRAS, KRAS, PTPN11 and CBL occur in 85% of patients, yet there are currently no risk ...
    • Identification of RPS14 as a 5q- syndrome gene by RNA interference screen 

      Ebert, Benjamin L.; Pretz, Jennifer; Bosco, Jocelyn; Chang, Cindy Y.; Tamayo, Pablo; Galili, Naomi; Raza, Azra; Root, David E.; Attar, Eyal; Ellis, Steven R.; Golub, Todd R. (2013)
      Somatic chromosomal deletions in cancer are thought to indicate the location of tumor suppressor genes, whereby complete loss of gene function occurs through biallelic deletion, point mutation, or epigenetic silencing, ...
    • Integrative Genome Comparison of Primary and Metastatic Melanomas 

      Kabbarah, Omar; Nogueira, Cristina; Feng, Bin; Bosenberg, Marcus; Scott, Kenneth L.; Xiao, Yonghong; Cordon-Cardo, Carlos; Wagner, Stephan N.; Brennan, Cameron; Nazarian, Rosalynn; Wu, Min; Kwong, Lawrence Noc-Woon; Granter, Scott R.; Ramaswamy, Sridhar; Golub, Todd R.; Duncan, Lyn M.; Chin, Lynda (Public Library of Science, 2010)
      A cardinal feature of malignant melanoma is its metastatic propensity. An incomplete view of the genetic events driving metastatic progression has been a major barrier to rational development of effective therapeutics and ...
    • The landscape of chromosomal aberrations in breast cancer mouse models reveals driver-specific routes to tumorigenesis 

      Ben-David, Uri; Ha, Gavin; Khadka, Prasidda; Jin, Xin; Wong, Bang; Franke, Lude; Golub, Todd R. (Nature Publishing Group, 2016)
      Aneuploidy and copy-number alterations (CNAs) are a hallmark of human cancer. Although genetically engineered mouse models (GEMMs) are commonly used to model human cancer, their chromosomal landscapes remain underexplored. ...
    • Melanoma genome sequencing reveals frequent PREX2 mutations 

      Berger, Michael F.; Hodis, Eran; Heffernan, Timothy P.; Deribe, Yonathan Lissanu; Lawrence, Michael S.; Protopopov, Alexei; Ivanova, Elena; Watson, Ian R.; Nickerson, Elizabeth; Ghosh, Papia; Zhang, Hailei; Zeid, Rhamy; Ren, Xiaojia; Cibulskis, Kristian; Sivachenko, Andrey Y.; Wagle, Nikhil; Sucker, Antje; Sougnez, Carrie; Onofrio, Robert; Ambrogio, Lauren; Auclair, Daniel; Fennell, Timothy; Carter, Scott L.; Drier, Yotam; Stojanov, Petar; Singer, Meredith A.; Voet, Douglas; Jing, Rui; Saksena, Gordon; Barretina, Jordi; Ramos, Alex H.; Pugh, Trevor J.; Stransky, Nicolas; Parkin, Melissa; Winckler, Wendy; Mahan, Scott; Ardlie, Kristin; Baldwin, Jennifer; Wargo, Jennifer; Schadendorf, Dirk; Meyerson, Matthew; Gabriel, Stacey B.; Golub, Todd R.; Wagner, Stephan N.; Lander, Eric S.; Getz, Gad; Chin, Lynda; Garraway, Levi A. (2012)
      Melanoma is notable for its metastatic propensity, lethality in the advanced setting, and association with ultraviolet (UV) exposure early in life1. To obtain a comprehensive genomic view of melanoma, we sequenced the ...
    • A Method for High-Throughput Gene Expression Signature Analysis 

      Peck, David; Crawford, Emily D; Ross, Kenneth N; Stegmaier, Kimberly; Golub, Todd R.; Lamb, Justin (BioMed Central, 2006)
      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 of relatively small numbers of ...
    • MicroRNA miR-125a Controls Hematopoietic Stem Cell Number 

      Guo, Shangqin; Lu, Jun; Schlanger, Rita; Zhang, Hao; Wang, Judy Y.; Fox, Michelle Caroline; Purton, Louise E.; Fleming, Heather H.; Cobb, Bradley; Merkenschlager, Matthias; Golub, Todd R.; Scadden, David Thomas (National Academy of Sciences, 2010)
      MicroRNAs influence hematopoietic differentiation, but little is known about their effects on the stem cell state. Here, we report that the microRNA processing enzyme Dicer is essential for stem cell persistence in vivo ...
    • MicroRNA-Mediated Control of Cell Fate in Megakaryocyte-Erythrocyte Progenitors 

      Lu, Jun; Guo, Shangqin; Ebert, Benjamin L.; Zhang, Hao; Peng, Xiao; Bosco, Jocelyn; Pretz, Jennifer Lee; Schlanger, Rita; Wang, Judy Y.; Mak, Raymond Heungwing; Dombkowski, David M.; Preffer, Frederic Ira; Scadden, David Thomas; Golub, Todd Robert (Elsevier BV, 2008)
      Lineage specification is a critical issue in developmental and regenerative biology. We hypothesized that microRNAs (miRNAs) are important participants in that process and used the poorly-understood regulation of ...
    • Molecular Sampling of Prostate Cancer: A Dilemma for Predicting Disease Progression 

      Sboner, Andrea; Demichelis, Francesca; Calza, Stefano; Pawitan, Yudi; Hoshida, Yujin; Perner, Sven; Andersson, Swen-Olof; Varenhorst, Eberhard; Johansson, Jan-Erik; Gerstein, Mark B; Rubin, Mark A; Andrén, Ove; Setlur, Sunita Ramakrishna; Adami, Hans-Olov; Fall, Katja; Mucci, Lorelei Ann; Kantoff, Philip Wayne; Stampfer, Meir; Golub, Todd R. (BioMed Central, 2010)
      Background: Current prostate cancer prognostic models are based on pre-treatment prostate specific antigen (PSA) levels, biopsy Gleason score, and clinical staging but in practice are inadequate to accurately predict disease ...
    • Multiplex Cytological Profiling Assay to Measure Diverse Cellular States 

      Gustafsdottir, Sigrun M.; Ljosa, Vebjorn; Sokolnicki, Katherine L.; Anthony Wilson, J.; Walpita, Deepika; Kemp, Melissa M.; Petri Seiler, Kathleen; Carrel, Hyman A.; Golub, Todd R.; Schreiber, Stuart L.; Clemons, Paul A.; Carpenter, Anne E.; Shamji, Alykhan F. (Public Library of Science, 2013)
      Computational methods for image-based profiling are under active development, but their success hinges on assays that can capture a wide range of phenotypes. We have developed a multiplex cytological profiling assay that ...
    • Mutational heterogeneity in cancer and the search for new cancer genes 

      Lawrence, Michael S.; Stojanov, Petar; Polak, Paz; Kryukov, Gregory V.; Cibulskis, Kristian; Sivachenko, Andrey; Carter, Scott L.; Stewart, Chip; Mermel, Craig H.; Roberts, Steven A.; Kiezun, Adam; Hammerman, Peter S.; McKenna, Aaron; Drier, Yotam; Zou, Lihua; Ramos, Alex H.; Pugh, Trevor J.; Stransky, Nicolas; Helman, Elena; Kim, Jaegil; Sougnez, Carrie; Ambrogio, Lauren; Nickerson, Elizabeth; Shefler, Erica; Cortés, Maria L.; Auclair, Daniel; Saksena, Gordon; Voet, Douglas; Noble, Michael; DiCara, Daniel; Lin, Pei; Lichtenstein, Lee; Heiman, David I.; Fennell, Timothy; Imielinski, Marcin; Hernandez, Bryan; Hodis, Eran; Baca, Sylvan; Dulak, Austin M.; Lohr, Jens; Landau, Dan-Avi; Wu, Catherine J.; Melendez-Zajgla, Jorge; Hidalgo-Miranda, Alfredo; Koren, Amnon; McCarroll, Steven A.; Mora, Jaume; Crompton, Brian; Onofrio, Robert; Parkin, Melissa; Winckler, Wendy; Ardlie, Kristin; Gabriel, Stacey B.; Roberts, Charles W. M.; Biegel, Jaclyn A.; Stegmaier, Kimberly; Bass, Adam J.; Garraway, Levi A.; Meyerson, Matthew; Golub, Todd R.; Gordenin, Dmitry A.; Sunyaev, Shamil; Lander, Eric S.; Getz, Gad (2014)
      Major international projects are now underway aimed at creating a comprehensive catalog of all genes responsible for the initiation and progression of cancer. These studies involve sequencing of matched tumor–normal samples ...