Browsing HMS Scholarly Articles by Title

Now showing items 7010-7029 of 17922

    • Genome-wide Co-occurrence of Promoter Elements Reveals a cis-Regulatory Cassette of rRNA Transcription Motifs in Saccharomyces cerevisiae 

      Sudarsanam, Priya; Pilpel, Yitzhak; Church, George (Cold Spring Harbor Laboratory, 2002-11-01)
      Combinatorial regulation is an important feature of eukaryotic transcription. However, only a limited number of studies have characterized this aspect on a whole-genome level. We have conducted a genome-wide computational ...

    • Genome-wide common and rare variant analysis provides novel insights into clozapine-associated neutropenia 

      Legge, Sophie E; Hamshere, Marian L; Ripke, Stephan; Pardinas, Antonio F; Goldstein, Jacqueline I; Rees, Elliott; Richards, Alexander L; Leonenko, Ganna; Jorskog, L Fredrik; Chambert, Kimberly D; Collier, David A; Genovese, Giulio; Giegling, Ina; Holmans, Peter; Jonasdottir, Adalbjorg; Kirov, George; McCarroll, Steven A; MacCabe, James H; Mantripragada, Kiran; Moran, Jennifer L; Neale, Benjamin M; Stefansson, Hreinn; Rujescu, Dan; Daly, Mark J; Sullivan, Patrick F; Owen, Michael J; O’Donovan, Michael C; Walters, James T R (2016)
      The antipsychotic clozapine is uniquely effective in the management of schizophrenia, but its use is limited by its potential to induce agranulocytosis. The causes of this, and of its precursor neutropenia, are largely ...

    • Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method 

      Tan, Li; Xiong, Lijun; Xu, Wenqi; Wu, Feizhen; Huang, Ning; Xu, Yufei; Kong, Lingchun; Zheng, Lijuan; Schwartz, Lisa; Shi, Yang; Shi, Yujiang (Oxford University Press, 2013)
      The genome-wide distribution patterns of the ‘6th base’ 5-hydroxymethylcytosine (5hmC) in many tissues and cells have recently been revealed by hydroxymethylated DNA immunoprecipitation (hMeDIP) followed by high throughput ...

    • Genome-wide copy number variant analysis for congenital ventricular septal defects in Chinese Han population 

      An, Yu; Duan, Wenyuan; Huang, Guoying; Chen, Xiaoli; Li, Li; Nie, Chenxia; Hou, Jia; Gui, Yonghao; Wu, Yiming; Zhang, Feng; Shen, Yiping; Wu, Bailin; Wang, Hongyan (BioMed Central, 2016)
      Background: Ventricular septal defects (VSDs) constitute the most prevalent congenital heart disease (CHD), occurs either in isolation (isolated VSD) or in combination with other cardiac defects (complex VSD). Copy number ...

    • Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis 

      Chen, Sidi; Sanjana, Neville; Zheng, Kaijie; Shalem, Ophir; Lee, Kyungheon; Shi, Xi; Scott, David; Song, Jun; Pan, Jen; Weissleder, Ralph; Lee, Hakho; Zhang, Feng; Sharp, Phillip (Elsevier (Cell Press), 2015)
      Genetic screens are powerful tools for identifying genes responsible for diverse phenotypes. Here we describe a genome-wide CRISPR/Cas9-mediated loss-of-function screen in tumor growth and metastasis. We mutagenized a ...

    • Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases 

      Frock, Richard L.; Hu, Jiazhi; Meyers, Robin M.; Ho, Yu-Jui; Kii, Erina; Alt, Frederick W. (2014)
      Although great progress has been made in the characterization of off-target effects of engineered nucleases, sensitive and unbiased genome-wide methods for the detection of off-target cleavage events and potential collateral ...

    • Genome-wide determination of drug localization 

      Anders, Lars; Guenther, Matthew G.; Qi, Jun; Fan, Zi Peng; Marineau, Jason J.; Rahl, Peter B.; Lovén, Jakob; Sigova, Alla A.; Smith, William B.; Lee, Tong Ihn; Bradner, James E.; Young, Richard A. (2014)
      A vast number of small-molecule ligands, including therapeutic drugs under development and in clinical use, elicit their effects by binding specific proteins associated with the genome. An ability to map the direct ...

    • Genome-Wide Diet-Gene Interaction Analyses for Risk of Colorectal Cancer 

      Figueiredo, Jane C.; Hsu, Li; Hutter, Carolyn M.; Lin, Yi; Campbell, Peter T.; Baron, John A.; Berndt, Sonja I.; Jiao, Shuo; Casey, Graham; Fortini, Barbara; Chan, Andrew T.; Cotterchio, Michelle; Lemire, Mathieu; Gallinger, Steven; Harrison, Tabitha A.; Le Marchand, Loic; Newcomb, Polly A.; Slattery, Martha L.; Caan, Bette J.; Carlson, Christopher S.; Zanke, Brent W.; Rosse, Stephanie A.; Brenner, Hermann; Giovannucci, Edward L.; Wu, Kana; Chang-Claude, Jenny; Chanock, Stephen J.; Curtis, Keith R.; Duggan, David; Gong, Jian; Haile, Robert W.; Hayes, Richard B.; Hoffmeister, Michael; Hopper, John L.; Jenkins, Mark A.; Kolonel, Laurence N.; Qu, Conghui; Rudolph, Anja; Schoen, Robert E.; Schumacher, Fredrick R.; Seminara, Daniela; Stelling, Deanna L.; Thibodeau, Stephen N.; Thornquist, Mark; Warnick, Greg S.; Henderson, Brian E.; Ulrich, Cornelia M.; Gauderman, W. James; Potter, John D.; White, Emily; Peters, Ulrike (Public Library of Science, 2014)
      Dietary factors, including meat, fruits, vegetables and fiber, are associated with colorectal cancer; however, there is limited information as to whether these dietary factors interact with genetic variants to modify risk ...

    • Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings 

      Schubert, Benjamin; Maddamsetti, Rohan; Nyman, Jackson; Farhat, Maha; Marks, Debora S. (Springer Science and Business Media LLC, 2018-12-03)
      Genome analysis should allow the discovery of interdependent loci that together cause antibiotic resistance. In practice however, the vast number of possible epistatic interactions erodes statistical power. Here, we extend ...

    • Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture 

      Haber, Marc; Gauguier, Dominique; Youhanna, Sonia; Patterson, Nick; Moorjani, Priya; Botigué, Laura R.; Platt, Daniel E.; Matisoo-Smith, Elizabeth; Soria-Hernanz, David F.; Wells, R. Spencer; Bertranpetit, Jaume; Tyler-Smith, Chris; Comas, David; Zalloua, Pierre A. (Public Library of Science, 2013)
      The Levant is a region in the Near East with an impressive record of continuous human existence and major cultural developments since the Paleolithic period. Genetic and archeological studies present solid evidence placing ...

    • Genome-wide DNA methylation analysis identifies a metabolic memory profile in patient-derived diabetic foot ulcer fibroblasts 

      Park, Lara K; Maione, Anna G; Smith, Avi; Gerami-Naini, Behzad; Iyer, Lakshmanan K; Mooney, David J; Veves, Aristidis; Garlick, Jonathan A (Taylor & Francis, 2014)
      Diabetic foot ulcers (DFUs) are a serious complication of diabetes. Previous exposure to hyperglycemic conditions accelerates a decline in cellular function through metabolic memory despite normalization of glycemic control. ...

    • Genome-Wide Enhancer Maps Link Risk Variants to Disease Genes 

      Nasser, Joseph; Bergman, Drew T.; Fulco, Charles P.; Guckelberger, Philine; Doughty, Benjamin; Patwardhan, Tejal A.; Jones, Thouis; Nguyen, Tung; Ulirsch, Jacob; Lekschas, Fritz; Mualim, Kristy; Natri, Heini M.; Weeks, Elle M.; Munson, Glen; Kane, Michael; Kang, Helen Y.; Cui, Ang; Ray, John P.; Eisenhaure, Thomas M.; Collins, Ryan; Dey, Kushal; Pfister, Hanspeter; Price, Alkes; Epstein, Charles; Kundaje, Anshul; Xavier, Ramnik; Daly, Mark; Huang, Hailiang; Finucane, Hilary; Hacohen, Nir; Lander, Eric; Engreitz, Jesse (Springer Science and Business Media LLC, 2021-04-07)

    • Genome-wide enrichment analysis between endometriosis and obesity-related traits reveals novel susceptibility loci 

      Rahmioglu, Nilufer; Macgregor, Stuart; Drong, Alexander W.; Hedman, Åsa K.; Harris, Holly R.; Randall, Joshua C.; Prokopenko, Inga; Nyholt, Dale R.; Morris, Andrew P.; Montgomery, Grant W.; Missmer, Stacey A.; Lindgren, Cecilia M.; Zondervan, Krina T. (2015)
      Endometriosis is a chronic inflammatory condition in women that results in pelvic pain and subfertility, and has been associated with decreased body mass index (BMI). Genetic variants contributing to the heritable component ...

    • Genome-Wide Expression Profiling of Five Mouse Models Identifies Similarities and Differences with Human Psoriasis 

      Swindell, William R.; Johnston, Andrew; Carbajal, Steve; Han, Gangwen; Wohn, Christian; Lu, Jun; Xing, Xianying; Nair, Rajan P.; Voorhees, John J.; Elder, James T.; Wang, Xiao-Jing; Sano, Shigetoshi; Prens, Errol P.; DiGiovanni, John; Pittelkow, Mark R.; Ward, Nicole L.; Gudjonsson, Johann E. (Public Library of Science, 2011)
      Development of a suitable mouse model would facilitate the investigation of pathomechanisms underlying human psoriasis and would also assist in development of therapeutic treatments. However, while many psoriasis mouse ...

    • Genome-wide gene-based analysis suggests an association between Neuroligin 1 (NLGN1) and post-traumatic stress disorder 

      Kilaru, V; Iyer, S V; Almli, L M; Stevens, J S; Lori, A; Jovanovic, T; Ely, T D; Bradley, B; Binder, E B; Koen, N; Stein, D J; Conneely, K N; Wingo, A P; Smith, A K; Ressler, K J (Nature Publishing Group, 2016)
      Post-traumatic stress disorder (PTSD) develops in only some people following trauma exposure, but the mechanisms differentially explaining risk versus resilience remain largely unknown. PTSD is heritable but candidate gene ...

    • Genome-wide germline correlates of the epigenetic landscape of prostate cancer 

      Houlahan, Kathleen E.; Shiah, Yu-Jia; Gusev, Alexander; Yuan, Jiapei; Ahmed, Musaddeque; Ramanand, Susmita G.; Yao, Cindy Q.; Bell, Connor; O’Connor, Edward; Huang, Vincent; Fraser, Michael; Heisler, Lawrence E.; Livingstone, Julie; Yamaguchi, Takafumi N.; Rouette, Alexandre; Foucal, Adrien; Espiritu, Shadrielle Melijah G.; Sinha, Ankit; Sam, Michelle; Timms, Lee; Johns, Jeremy; Wong, Ada; Murison, Alex; Orain, Michèle; Picard, Valérie; Hovington, Hélène; Bergeron, Alain; Lacombe, Louis; Lupien, Mathieu; Fradet, Yves; Têtu, Bernard; McPherson, John D.; Pasaniuc, Bogdan; Kislinger, Thomas; Chua, Melvin L. K.; Pomerantz, Mark; van der Kwast, Theodorus; Freedman, Matthew; Mani, Ram S.; He, Housheng H.; Bristow, Robert G.; Boutros, Paul C.; Shetty, Anamay (Springer Science and Business Media LLC, 2019-10)
      Cancer initiation and progression are driven by germline, environmental and stochastic factors. How these interact to produce the molecular phenotypes of primary human tumours remains unknown. To better understand the role ...

    • Genome-wide high-throughput screens in functional genomics 

      Friedman, Adam; Perrimon, Norbert (Elsevier, 2004)
      The availability of complete genome sequences from many organisms has yielded the ability to perform high-throughput, genome-wide screens of gene function. Within the past year, rapid advances have been made towards this ...

    • Genome-Wide Identification of Calcium-Response Factor (CaRF) Binding Sites Predicts a Role in Regulation of Neuronal Signaling Pathways 

      Pfenning, Andreas R.; Spotts, James M.; Su, Dan; West, Anne E.; Nitabach, Michael N.; Kim, Tae-Hyun; Hemberg, Martin (Public Library of Science, 2010)
      Calcium-Response Factor (CaRF) was first identified as a transcription factor based on its affinity for a neuronal-selective calcium-response element (CaRE1) in the gene encoding Brain-Derived Neurotrophic Factor (BDNF). ...

    • Genome-Wide Identification of Functionally Distinct Subsets of Cellular mRNAs Associated with Two Nucleocytoplasmic-Shuttling Mammalian Splicing Factors 

      Gama-Carvalho, Margarida; Barbosa-Morais, Nuno L; Brodsky, Alexander S; Silver, Pamela A.; Carmo-Fonseca, Maria (BioMed Central, 2006)
      Background: Pre-mRNA splicing is an essential step in gene expression that occurs co-transcriptionally in the cell nucleus, involving a large number of RNA binding protein splicing factors, in addition to core spliceosome ...

    • Genome-wide Identification of microRNA Expression Quantitative Trait Loci 

      Huan, Tianxiao; Rong, Jian; Liu, Chunyu; Zhang, Xiaoling; Tanriverdi, Kahraman; Joehanes, Roby; Chen, Brian H.; Murabito, Joanne M.; Yao, Chen; Courchesne, Paul; Munson, Peter J.; O’Donnell, Christopher J.; Cox, Nancy; Johnson, Andrew D.; Larson, Martin G.; Levy, Daniel; Freedman, Jane E. (2015)
      Identification of microRNA expression quantitative trait loci (miR-eQTL) can yield insights into regulatory mechanisms of microRNA transcription, and can help elucidate the role of microRNA as mediators of complex traits. ...