Browsing HMS Scholarly Articles by Keyword "Functional Genomics"

Now showing items 1-15 of 15

    • Allele-Specific Methylation Occurs at Genetic Variants Associated with Complex Disease 

      Hutchinson, John N.; Raj, Towfique; Fagerness, Jes; Stahl, Eli; Viloria, Fernando T.; Gimelbrant, Alexander; Seddon, Johanna; Daly, Mark; Chess, Andrew; Plenge, Robert (Public Library of Science, 2014)
      We hypothesize that the phenomenon of allele-specific methylation (ASM) may underlie the phenotypic effects of multiple variants identified by Genome-Wide Association studies (GWAS). We evaluate ASM in a human population ...

    • Allelic Expression of Deleterious Protein-Coding Variants across Human Tissues 

      Kukurba, Kimberly R.; Zhang, Rui; Li, Xin; Smith, Kevin S.; Knowles, David A.; How Tan, Meng; Piskol, Robert; Lek, Monkol; Snyder, Michael; MacArthur, Daniel G.; Li, Jin Billy; Montgomery, Stephen B. (Public Library of Science, 2014)
      Personal exome and genome sequencing provides access to loss-of-function and rare deleterious alleles whose interpretation is expected to provide insight into individual disease burden. However, for each allele, accurate ...

    • Classify Hyperdiploidy Status of Multiple Myeloma Patients Using Gene Expression Profiles 

      Li, Yingxiang; Wang, Xujun; Zheng, Haiyang; Wang, Chengyang; Minvielle, Stéphane; Magrangeas, Florence; Avet-Loiseau, Hervé; Shah, Parantu K.; Zhang, Yong; Munshi, Nikhil C; Li, Cheng (Public Library of Science, 2013)
      Multiple myeloma (MM) is a cancer of antibody-making plasma cells. It frequently harbors alterations in DNA and chromosome copy numbers, and can be divided into two major subtypes, hyperdiploid (HMM) and non-hyperdiploid ...

    • Construction of a Global Pain Systems Network Highlights Phospholipid Signaling as a Regulator of Heat Nociception 

      Neely, G. Gregory; Rao, Shuan; Costigan, Michael; Mair, Norbert; Racz, Ildiko; Milinkeviciute, Giedre; Meixner, Arabella; Nayanala, Swetha; Griffin, Robert Stewart; Belfer, Inna; Dai, Feng; Smith, Shad; Diatchenko, Luda; Marengo, Stefano; Haubner, Bernhard J.; Novatchkova, Maria; Gibson, Dustin; Maixner, William; Pospisilik, J. Andrew; Hirsch, Emilio; Whishaw, Ian Q.; Zimmer, Andreas; Gupta, Vaijayanti; Sasaki, Junko; Kanaho, Yasunori; Sasaki, Takehiko; Kress, Michaela; Woolf, Clifford; Penninger, Josef M. (Public Library of Science, 2012)
      The ability to perceive noxious stimuli is critical for an animal's survival in the face of environmental danger, and thus pain perception is likely to be under stringent evolutionary pressure. Using a neuronal-specific ...

    • Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants 

      Du, Mengmeng; Jiao, Shuo; Bien, Stephanie A.; Gala, Manish; Abecasis, Goncalo; Bezieau, Stephane; Brenner, Hermann; Butterbach, Katja; Caan, Bette J.; Carlson, Christopher S.; Casey, Graham; Chang-Claude, Jenny; Conti, David V.; Curtis, Keith R.; Duggan, David; Gallinger, Steven; Haile, Robert W.; Harrison, Tabitha A.; Hayes, Richard B.; Hoffmeister, Michael; Hopper, John L.; Hudson, Thomas J.; Jenkins, Mark A.; Küry, Sébastien; Le Marchand, Loic; Leal, Suzanne M.; Newcomb, Polly A.; Nickerson, Deborah A.; Potter, John D.; Schoen, Robert E.; Schumacher, Fredrick R.; Seminara, Daniela; Slattery, Martha L.; Hsu, Li; Chan, Andrew T.; White, Emily; Berndt, Sonja I.; Peters, Ulrike (Public Library of Science, 2016)
      Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping ...

    • Gene and Genome Parameters of Mammalian Liver Circadian Genes (LCGs) 

      Wu, Gang; Zhu, Jiang; He, Fuhong; Wang, Weiwei; Hu, Songnian; Yu, Jun (Public Library of Science, 2012)
      The mammalian circadian system controls various physiology processes and behavior responses by regulating thousands of circadian genes with rhythmic expressions. In this study, we redefined circadian-regulated genes based ...

    • High Content Image Analysis Identifies Novel Regulators of Synaptogenesis in a High-Throughput RNAi Screen of Primary Neurons 

      Nieland, Thomas J. F.; Logan, David J.; Saulnier, Jessica; Lam, Daniel; Johnson, Caroline; Root, David E.; Carpenter, Anne E.; Sabatini, Bernardo L. (Public Library of Science, 2014)
      The formation of synapses, the specialized points of chemical communication between neurons, is a highly regulated developmental process fundamental to establishing normal brain circuitry. Perturbations of synapse formation ...

    • Histopathologic Alterations Associated with Global Gene Expression Due to Chronic Dietary TCDD Exposure in Juvenile Zebrafish 

      Liu, Qing; Spitsbergen, Jan M.; Cariou, Ronan; Huang, Chun-Yuan; Jiang, Nan; Goetz, Giles; Hutz, Reinhold J.; Tonellato, Peter J.; Carvan, Michael J. (Public Library of Science, 2014)
      The goal of this project was to investigate the effects and possible developmental disease implication of chronic dietary TCDD exposure on global gene expression anchored to histopathologic analysis in juvenile zebrafish ...

    • Identification of Novel Type 2 Diabetes Candidate Genes Involved in the Crosstalk between the Mitochondrial and the Insulin Signaling Systems 

      Mercader, Josep M.; Puiggros, Montserrat; Segrè, Ayellet V.; Planet, Evarist; Sorianello, Eleonora; Sebastian, David; Rodriguez-Cuenca, Sergio; Ribas, Vicent; Bonàs-Guarch, Sílvia; Draghici, Sorin; Yang, Chenjing; Mora, Sílvia; Vidal-Puig, Antoni; Dupuis, Josée; Zorzano, Antonio; Torrents, David; Florez, Jose Carlos (Public Library of Science, 2012)
      Type 2 Diabetes (T2D) is a highly prevalent chronic metabolic disease with strong co-morbidity with obesity and cardiovascular diseases. There is growing evidence supporting the notion that a crosstalk between mitochondria ...

    • Regulation of Gene Expression in Autoimmune Disease Loci and the Genetic Basis of Proliferation in CD4+ Effector Memory T Cells 

      Hu, Xinli; Kim, Hyun; Raj, Towfique; Brennan, Patrick J.; Trynka, Gosia; Teslovich, Nikola; Slowikowski, Kamil; Chen, Wei-Min; Onengut, Suna; Baecher-Allan, Clare; De Jager, Philip L.; Rich, Stephen S.; Stranger, Barbara E.; Brenner, Michael B.; Raychaudhuri, Soumya (Public Library of Science, 2014)
      Genome-wide association studies (GWAS) and subsequent dense-genotyping of associated loci identified over a hundred single-nucleotide polymorphism (SNP) variants associated with the risk of rheumatoid arthritis (RA), type ...

    • An RNA Interference Lethality Screen of the Human Druggable Genome to Identify Molecular Vulnerabilities in Epithelial Ovarian Cancer 

      Sethi, Geetika; Pathak, Harsh B.; Zhang, Hong; Zhou, Yan; Einarson, Margret B.; Vathipadiekal, Vinod; Gunewardena, Sumedha; Birrer, Michael James; Godwin, Andrew K. (Public Library of Science, 2012)
      Targeted therapies have been used to combat many tumor types; however, few have effectively improved the overall survival in women with epithelial ovarian cancer, begging for a better understanding of this deadly disease ...

    • Software for Computing and Annotating Genomic Ranges 

      Lawrence, Michael; Huber, Wolfgang; Pagès, Hervé; Aboyoun, Patrick; Carlson, Marc; Gentleman, Robert; Morgan, Martin T.; Carey, Vincent J. (Public Library of Science, 2013)
      We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure ...

    • Stable Gene Targeting in Human Cells Using Single-Strand Oligonucleotides with Modified Bases 

      Rios, Xavier; Briggs, Adrian; Christodoulou, Danos C.; Gorham, Josh McClean; Seidman, Jonathan G.; Church, George McDonald (Public Library of Science, 2012)
      Recent advances allow multiplexed genome engineering in E. coli, employing easily designed oligonucleotides to edit multiple loci simultaneously. A similar technology in human cells would greatly expedite functional genomics, ...

    • Susceptibility to Chronic Mucus Hypersecretion, a Genome Wide Association Study 

      Dijkstra, Akkelies E.; Smolonska, Joanna; van den Berge, Maarten; Wijmenga, Ciska; Zanen, Pieter; Luinge, Marjan A.; Platteel, Mathieu; Lammers, Jan-Willem; Dahlback, Magnus; Tosh, Kerrie; Hiemstra, Pieter S.; Sterk, Peter J.; Spira, Avi; Vestbo, Jorgen; Nordestgaard, Borge G.; Benn, Marianne; Nielsen, Sune F.; Dahl, Morten; Verschuren, W. Monique; Picavet, H. Susan J.; Smit, Henriette A.; Owsijewitsch, Michael; Kauczor, Hans U.; de Koning, Harry J.; Nizankowska-Mogilnicka, Eva; Mejza, Filip; Nastalek, Pawel; van Diemen, Cleo C.; Cho, Michael H.; Silverman, Edwin K.; Crapo, James D.; Beaty, Terri H.; Lomas, David A.; Bakke, Per; Gulsvik, Amund; Bossé, Yohan; Obeidat, M. A.; Loth, Daan W.; Lahousse, Lies; Rivadeneira, Fernando; Uitterlinden, Andre G.; Hofman, Andre; Stricker, Bruno H.; Brusselle, Guy G.; van Duijn, Cornelia M.; Brouwer, Uilke; Koppelman, Gerard H.; Vonk, Judith M.; Nawijn, Martijn C.; Groen, Harry J. M.; Timens, Wim; Boezen, H. Marike; Postma, Dirkje S. (Public Library of Science, 2014)
      Background: Chronic mucus hypersecretion (CMH) is associated with an increased frequency of respiratory infections, excess lung function decline, and increased hospitalisation and mortality rates in the general population. ...

    • Systematic Dissection of Roles for Chromatin Regulators in a Yeast Stress Response 

      Weiner, Assaf; Chen, Hsiuyi V.; Liu, Chih Long; Rahat, Ayelet; Klien, Avital; Soares, Luis; Gudipati, Mohanram; Pfeffner, Jenna; Regev, Aviv; Buratowski, Stephen; Pleiss, Jeffrey A.; Friedman, Nir; Rando, Oliver J. (Public Library of Science, 2012)
      Packaging of eukaryotic genomes into chromatin has wide-ranging effects on gene transcription. Curiously, it is commonly observed that deletion of a global chromatin regulator affects expression of only a limited subset ...