Browsing HMS Scholarly Articles by Title

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    • Genomic profiling distinguishes familial multiple and sporadic multiple meningiomas 

      Engler, David A; Roy, Jennifer; Shen, Yiping; Nunes, Fabio Pereira; Stemmer-Rachamimov, Anat; James, Marianne F.; Mohapatra, Gayatry; Plotkin, Scott Randall; Betensky, Rebecca Aubrey; Ramesh, Vijaya; Gusella, James Francis (BioMed Central, 2009)
      Background: Meningiomas may occur either as familial tumors in two distinct disorders, familial multiple meningioma and neurofibromatosis 2 (NF2), or sporadically, as either single or multiple tumors in individuals with ...

    • Genomic Screening in Family-Based Association Testing 

      Murphy, Amy; McQueen, Matthew B; Su, Jessica Ann Lasky; Kraft, Peter; Lazarus, Ross; Laird, Nan M.; Lange, Christoph; Van Steen, Kristel (BioMed Central, 2005)
      Due to the recent gains in the availability of single-nucleotide polymorphism data, genome-wide association testing has become feasible. It is hoped that this additional data may confirm the presence of disease susceptibility ...

    • Genomic Screening with RNAi: Results and Challenges 

      Mohr, Stephanie; Bakal, Chris; Perrimon, Norbert (Annual Reviews, 2010)
      RNA interference (RNAi) is an effective tool for genome-scale, high-throughput analysis of gene function. In the past five years, a number of genome-scale RNAi high-throughput screens (HTSs) have been done in both Drosophila ...

    • Genomic Sequencing 

      Church, George; Gilbert, Walter (National Academy of Sciences, 1984-04-01)
      Unique DNA sequences can be determined directly from mouse genomic DNA. A denaturing gel separates by size mixtures of unlabeled DNA fragments from complete restriction and partial chemical cleavages of the entire genome. ...

    • Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations 

      Brastianos, Priscilla K.; Horowitz, Peleg M.; Santagata, Sandro; Jones, Robert T.; McKenna, Aaron; Getz, Gad; Ligon, Keith L.; Palescandolo, Emanuele; Van Hummelen, Paul; Ducar, Matthew D.; Raza, Alina; Sunkavalli, Ashwini; MacConaill, Laura E.; Stemmer-Rachamimov, Anat O.; Louis, David N.; Hahn, William C.; Dunn, Ian F.; Beroukhim, Rameen (2013)
      Meningiomas are the most common primary nervous system tumor. The tumor suppressor NF2 is disrupted in approximately half of meningiomas1 but the complete spectrum of genetic changes remains undefined. We performed ...

    • Genomic Signatures Characterize Leukocyte Infiltration in Myositis Muscles 

      Zhu, Wei; Streicher, Katie; Shen, Nan; Higgs, Brandon W; Morehouse, Chris; Greenlees, Lydia; Amato, Anthony A.; Ranade, Koustubh; Richman, Laura; Fiorentino, David; Jallal, Bahija; Greenberg, Steven A.; Yao, Yihong (BioMed Central, 2012)
      Background: Leukocyte infiltration plays an important role in the pathogenesis and progression of myositis, and is highly associated with disease severity. Currently, there is a lack of: efficacious therapies for myositis; ...

    • A Genomic Storm in Critically Injured Humans 

      Mindrinos, Michael N.; Seok, Junhee; Cuschieri, Joseph; Cuenca, Alex G.; Hayden, Douglas L.; Hennessy, Laura; Moore, Ernest E.; Minei, Joseph P.; Bankey, Paul E.; Sperry, Jason; Nathens, Avery B.; Billiar, Timothy R.; Brownstein, Bernard H.; Mason, Philip H.; Baker, Henry V.; Finnerty, Celeste C.; Jeschke, Marc G.; López, M. Cecilia; Klein, Matthew B.; Gamelli, Richard L.; Gibran, Nicole S.; Arnoldo, Brett; Xu, Weihong; Zhang, Yuping; Calvano, Steven E.; McDonald-Smith, Grace P.; Storey, John D.; Moldawer, Lyle L.; Herndon, David N.; Lowry, Stephen F.; Maier, Ronald V.; Davis, Ronald W.; Xiao, Wenzhong; Gao, Hong; Johnson, Jeffrey L.; West, Michael A.; Schoenfeld, David Alan; Cobb, Joseph Perren; Warren, H. Shaw; Tompkins, Ronald Gary (The Rockefeller University Press, 2011)
      Human survival from injury requires an appropriate inflammatory and immune response. We describe the circulating leukocyte transcriptome after severe trauma and burn injury, as well as in healthy subjects receiving low-dose ...

    • Genomic Studies with Escherichia coli MelR Protein: Applications of Chromatin Immunoprecipitation and Microarrays 

      Grainger, DC; Overton, TW; Reppas, N; Wade, JT; Tamai, E; Hobman, JL; Constantinidou, C; Struhl, Kevin; Church, George; Busby, SJW (American Society for Microbiology, 2004)
      Escherichia coli MelR protein is a transcription activator that is essential for melibiose-dependent expression of the melAB genes. We have used chromatin immunoprecipitation to study the binding of MelR and RNA polymerase ...

    • The genomic substrate for adaptive radiation in African cichlid fish 

      Brawand, David; Wagner, Catherine E.; Li, Yang I.; Malinsky, Milan; Keller, Irene; Fan, Shaohua; Simakov, Oleg; Ng, Alvin Y.; Lim, Zhi Wei; Bezault, Etienne; Turner-Maier, Jason; Johnson, Jeremy; Alcazar, Rosa; Noh, Hyun Ji; Russell, Pamela; Aken, Bronwen; Alföldi, Jessica; Amemiya, Chris; Azzouzi, Naoual; Baroiller, Jean-François; Barloy-Hubler, Frederique; Berlin, Aaron; Bloomquist, Ryan; Carleton, Karen L.; Conte, Matthew A.; D'Cotta, Helena; Eshel, Orly; Gaffney, Leslie; Galibert, Francis; Gante, Hugo F.; Gnerre, Sante; Greuter, Lucie; Guyon, Richard; Haddad, Natalie S.; Haerty, Wilfried; Harris, Rayna M.; Hofmann, Hans A.; Hourlier, Thibaut; Hulata, Gideon; Jaffe, David B.; Lara, Marcia; Lee, Alison P.; MacCallum, Iain; Mwaiko, Salome; Nikaido, Masato; Nishihara, Hidenori; Ozouf-Costaz, Catherine; Penman, David J.; Przybylski, Dariusz; Rakotomanga, Michaelle; Renn, Suzy C. P.; Ribeiro, Filipe J.; Ron, Micha; Salzburger, Walter; Sanchez-Pulido, Luis; Santos, M. Emilia; Searle, Steve; Sharpe, Ted; Swofford, Ross; Tan, Frederick J.; Williams, Louise; Young, Sarah; Yin, Shuangye; Okada, Norihiro; Kocher, Thomas D.; Miska, Eric A.; Lander, Eric S.; Venkatesh, Byrappa; Fernald, Russell D.; Meyer, Axel; Ponting, Chris P.; Streelman, J. Todd; Lindblad-Toh, Kerstin; Seehausen, Ole; Di Palma, Federica (2014)
      Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes ...

    • Genomic testing to determine drug response: measuring preferences of the public and patients using Discrete Choice Experiment (DCE) 

      Najafzadeh, Mehdi; Johnston, Karissa M; Peacock, Stuart J; Connors, Joseph M; Marra, Marco A; Lynd, Larry D; Marra, Carlo A (BioMed Central, 2013)
      Background: The extent to which a genomic test will be used in practice is affected by factors such as ability of the test to correctly predict response to treatment (i.e. sensitivity and specificity of the test), invasiveness ...

    • Genomic transition of enterococci from gut commensals to leading causes of multidrug-resistant hospital infection in the antibiotic era 

      Gilmore, Michael S.; Lebreton, Francois Herve; van Schaik, Willem (Elsevier BV, 2013)
      The enterococci evolved over eons as highly adapted members of gastrointestinal consortia of a wide variety of hosts, but for reasons that are not entirely clear, emerged in the 1970s as leading causes of multidrug resistant ...

    • Genomic variation landscape of the human gut microbiome 

      Schloissnig, Siegfried; Arumugam, Manimozhiyan; Sunagawa, Shinichi; Mitreva, Makedonka; Tap, Julien; Zhu, Ana; Waller, Alison; Mende, Daniel R.; Kultima, Jens Roat; Martin, John; Kota, Karthik; Sunyaev, Shamil R.; Weinstock, George M.; Bork, Peer (2012)
      While large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the latter is largely unexplored in the human microbiome. We therefore developed a framework for metagenomic ...

    • Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System 

      Pecora, Nicole D.; Li, Ning; Allard, Marc; Li, Cong; Albano, Esperanza; Delaney, Mary; Dubois, Andrea; Onderdonk, Andrew B.; Bry, Lynn (American Society of Microbiology, 2015)
      ABSTRACT Carbapenem-resistant Enterobacteriaceae (CRE) are an urgent public health concern. Rapid identification of the resistance genes, their mobilization capacity, and strains carrying them is essential to direct hospital ...

    • Genomically Recoded Organisms Expand Biological Functions 

      Lajoie, Marc J.; Rovner, Alexis J.; Goodman, Daniel B.; Aerni, Hans-Rudolf; Haimovich, Adrian D.; Kuznetsov, Gleb; Mercer, Jaron A.; Wang, Harris H.; Carr, Peter A.; Mosberg, Joshua A.; Rohland, Nadin; Schultz, Peter G.; Jacobson, Joseph M.; Rinehart, Jesse; Church, George; Isaacs, Farren J. (American Association for the Advancement of Science (AAAS), 2013-10-18)
      We describe the construction and characterization of a genomically recoded organism (GRO). We replaced all known UAG stop codons in Escherichia coli MG1655 with synonymous UAA codons, which permitted the deletion of release ...

    • Genomics of Drug Sensitivity in Cancer (GDSC): a Resource for Therapeutic Biomarker Discovery in Cancer Cells 

      Yang, Wanjuan; Soares, Jorge; Greninger, Patricia; Edelman, Elena J.; Lightfoot, Howard; Forbes, Simon; Bindal, Nidhi; Beare, Dave; Smith, James A.; Thompson, I. Richard; Ramaswamy, Sridhar; Futreal, P. Andrew; Haber, Daniel Arie; Stratton, Michael R.; Benes, Cyril Henri; McDermott, Ultan; Garnett, Mathew J. (Oxford University Press, 2012)
      Alterations in cancer genomes strongly influence clinical responses to treatment and in many instances are potent biomarkers for response to drugs. The Genomics of Drug Sensitivity in Cancer (GDSC) database (www.cancerRxgene.org) ...

    • Genomics of Loa loa, a Wolbachia-free filarial parasite of humans 

      Desjardins, Christopher A.; Cerqueira, Gustavo C.; Goldberg, Jonathan M.; Hotopp, Julie C. Dunning; Haas, Brian J.; Zucker, Jeremy; Ribeiro, Jose’ M.C.; Saif, Sakina; Levin, Joshua Z.; Fan, Lin; Zeng, Qiandong; Russ, Carsten; Wortman, Jennifer R.; Fink, Doran L.; Birren, Bruce W.; Nutman, Thomas B. (2014)
      Loa loa, the African eyeworm, is a major filarial pathogen of humans. Unlike most filariae, Loa loa does not contain the obligate intracellular Wolbachia endosymbiont. We describe the 91.4 Mb genome of Loa loa, and the ...

    • Genotator: A Disease-Agnostic Tool for Genetic Annotation of Disease 

      Wall, Dennis Paul Paul; Pivovarov, Rimma; Tong, Mark; Jung, Jae-Yoon; Fusaro, Vincent Alfred; DeLuca, Todd; Tonellato, Peter J (BioMed Central, 2010)
      Background: Disease-specific genetic information has been increasing at rapid rates as a consequence of recent improvements and massive cost reductions in sequencing technologies. Numerous systems designed to capture and ...

    • Genotype Directed Therapy in Murine Mismatch Repair Deficient Tumors 

      Kucherlapati, Melanie H.; Esfahani, Shadi; Habibollahi, Peiman; Wang, Junning; Still, Eric R.; Bronson, Roderick T.; Mahmood, Umar; Kucherlapati, Raju S. (Public Library of Science, 2013)
      The PI3K/AKT/mTOR pathway has frequently been found activated in human tumors. We show that in addition to Wnt signaling dysfunction, the PI3K/AKT/mTOR pathway is often upregulated in mouse Msh2−/− initiated intestinal ...

    • Genotypic and Functional Impact of HIV-1 Adaptation to Its Host Population during the North American Epidemic 

      Cotton, Laura A.; Kuang, Xiaomei T.; Le, Anh Q.; Carlson, Jonathan M.; Chan, Benjamin; Chopera, Denis R.; Brumme, Chanson J.; Markle, Tristan J.; Martin, Eric; Shahid, Aniqa; Anmole, Gursev; Mwimanzi, Philip; Nassab, Pauline; Penney, Kali A.; Rahman, Manal A.; Milloy, M.-J.; Schechter, Martin T.; Markowitz, Martin; Carrington, Mary; Walker, Bruce D.; Wagner, Theresa; Buchbinder, Susan; Fuchs, Jonathan; Koblin, Beryl; Mayer, Kenneth H.; Harrigan, P. Richard; Brockman, Mark A.; Poon, Art F. Y.; Brumme, Zabrina L. (Public Library of Science, 2014)
      HLA-restricted immune escape mutations that persist following HIV transmission could gradually spread through the viral population, thereby compromising host antiviral immunity as the epidemic progresses. To assess the ...

    • Genotyping Analyses of Tuberculosis Cases in U.S.- and Foreign-Born Massachusetts Residents 

      Sharnprapai, Sharon; Miller, Ann C.; Suruki, Robert; Corkren, Edward; Etkind, Sue; Driscoll, Jeffrey; McGarry, Michael; Nardell, Edward Anthony (Centers for Disease Control and Prevention, 2002)
      We used molecular genotyping to further understand the epidemiology and transmission patterns of tuberculosis (TB) in Massachusetts. The study population included 983 TB patients whose cases were verified by the Massachusetts ...