Browsing FAS Scholarly Articles by Title

Now showing items 6520-6539 of 18292

    • Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues 

      Zhu, Jiang; Adli, Mazhar; Zou, James Y.; Verstappen, Griet; Coyne, Michael J.; Zhang, Xiaolan; Durham, Timothy; Miri, Mohammad; Deshpande, Vikram; De Jager, Philip L.; Bennett, David A.; Houmard, Joseph A.; Muoio, Deborah M.; Onder, Tamer T.; Camahort, Raymond; Cowan, Chad A.; Meissner, Alexander; Epstein, Charles B.; Shoresh, Noam; Bernstein, Bradley E. (Elsevier BV, 2013)
      Differences in chromatin organization are key to the multiplicity of cell states that arise from a single genetic background, yet the landscapes of in vivo tissues remain largely uncharted. Here, we mapped chromatin ...

    • Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell 

      Zong, Chenghang; Chapman, Alec Randolph; Xie, Xiaoliang Sunney (American Association for the Advancement of Science, 2012)
      Kindred cells can have different genomes because of dynamic changes in DNA. Single cell sequencing is needed to characterize these genomic differences but has been hindered by whole-genome amplification bias, resulting in ...

    • 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 evidence for speciation with gene flow in Heliconius butterflies 

      Martin, S. H.; Dasmahapatra, K. K.; Nadeau, N. J.; Salazar, C.; Walters, J. R.; Simpson, F.; Blaxter, M.; Manica, A.; Mallet, James; Jiggins, C. D. (Cold Spring Harbor Laboratory Press, 2013)
      Most speciation events probably occur gradually, without complete and immediate reproductive isolation, but the full extent of gene flow between diverging species has rarely been characterized on a genome-wide scale. ...

    • Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response 

      Zhong, Mei; Niu, Wei; Lu, Zhi John; Sarov, Mihail; Janette, Judith; Raha, Debasish; Sheaffer, Karyn L.; Lam, Hugo Y. K.; Preston, Elicia; Slightham, Cindie; Hillier, LaDeana W.; Agarwal, Ashish; Auerbach, Raymond; Hyman, Anthony A.; Gerstein, Mark; Kim, Stuart K.; Waterston, Robert H.; Reinke, Valerie; Snyder, Michael; Murray, John I.; Mango, Susan; Brock, Trisha Jane (Public Library of Science, 2010)
      Transcription factors are key components of regulatory networks that control development, as well as the response to environmental stimuli. We have established an experimental pipeline in Caenorhabditis elegans that permits ...

    • Genome-wide identification of microRNAs regulating cholesterol and triglyceride homeostasis 

      Wagschal, Alexandre; Najafi-Shoushtari, S Hani; Wang, Lifeng; Goedeke, Leigh; Sinha, Sumita; deLemos, Andrew S; Black, Josh C; Ramírez, Cristina M; Li, Yingxia; Tewhey, Ryan; Hatoum, Ida; Shah, Naisha; Lu, Yong; Kristo, Fjoralba; Psychogios, Nikolaos; Vrbanac, Vladimir; Lu, Yi-Chien; Hla, Timothy T; de Cabo, Rafael; Tsang, John S; Schadt, Eric; Sabeti, Pardis Christine; Kathiresan, Sekar; Cohen, David E; Whetstine, Johnathan; Chung, Raymond Taeyong; Fernández-Hernando, Carlos; Kaplan, Lee Michael; Bernards, Andre; Gerszten, Robert Edgardo; Naar, Anders Michael (Springer Nature, 2015)
      Genome-wide association studies (GWASs) have linked genes to various pathological traits. However, the potential contribution of regulatory noncoding RNAs, such as microRNAs (miRNAs), to a genetic predisposition to ...

    • Genome-wide introgression among distantly related Heliconius butterfly species 

      Zhang, Wei; Dasmahapatra, Kanchon K.; Mallet, James; Moreira, Gilson R. P.; Kronforst, Marcus R. (BioMed Central, 2016)
      Background: Although hybridization is thought to be relatively rare in animals, the raw genetic material introduced via introgression may play an important role in fueling adaptation and adaptive radiation. The butterfly ...

    • Genome-wide Map of Quantified Epigenetic Changes during In vitro Chondrogenic Differentiation of Primary Human Mesenchymal Stem Cells 

      Herlofsen, Sarah; Bryne, Jan Christian; Høiby, Torill; Wang, Li; Issner, Robbyn; Zhang, Xiaolan; Coyne, Michael J.; Boyle, Patrick; Gu, Hongcang; Meza-Zepeda, Leonardo A; Collas, Philippe; Mikkelsen, Tarjei Sigurd; Brinchmann, Jan E (BioMed Central, 2013)
      Background: For safe clinical application of engineered cartilage made from mesenchymal stem cells (MSCs), molecular mechanisms for chondrogenic differentiation must be known in detail. Changes in gene expression and ...

    • Genome-wide meta-analysis reveals common splice site acceptor variant in CHRNA4 associated with nicotine dependence 

      Hancock, D B; Reginsson, G W; Gaddis, N C; Chen, X; Saccone, N L; Lutz, S M; Qaiser, B; Sherva, R; Steinberg, S; Zink, F; Stacey, S N; Glasheen, C; Chen, J; Gu, F; Frederiksen, B N; Loukola, A; Gudbjartsson, D F; Brüske, I; Landi, M T; Bickeböller, H; Madden, P; Farrer, L; Kaprio, J; Kranzler, H R; Gelernter, J; Baker, T B; Kraft, P; Amos, C I; Caporaso, N E; Hokanson, J E; Bierut, L J; Thorgeirsson, T E; Johnson, E O; Stefansson, K (Nature Publishing Group, 2015)
      We conducted a 1000 Genomes–imputed genome-wide association study (GWAS) meta-analysis for nicotine dependence, defined by the Fagerström Test for Nicotine Dependence in 17 074 ever smokers from five European-ancestry ...

    • Genome-wide patterns of selection in 230 ancient Eurasians 

      Mathieson, Iain; Lazaridis, Iosif; Rohland, Nadin; Mallick, Swapan; Patterson, Nick; Roodenberg, Songül Alpaslan; Harney, Eadaoin; Stewardson, Kristin; Fernandes, Daniel; Novak, Mario; Sirak, Kendra; Gamba, Cristina; Jones, Eppie R.; Llamas, Bastien; Dryomov, Stanislav; Pickrel, Joseph; Arsuaga, Juan Luís; de Castro, José María Bermúdez; Carbonell, Eudald; Gerritsen, Fokke; Khokhlov, Aleksandr; Kuznetsov, Pavel; Lozano, Marina; Meller, Harald; Mochalov, Oleg; Moiseyev, Vayacheslav; Rojo Guerra, Manuel A.; Roodenberg, Jacob; Vergès, Josep Maria; Krause, Johannes; Cooper, Alan; Alt, Kurt W.; Brown, Dorcas; Anthony, David; Lalueza-Fox, Carles; Haak, Wolfgang; Pinhasi, Ron; Reich, David (2016)
      Ancient DNA makes it possible to directly witness natural selection by analyzing samples from populations before, during and after adaptation events. Here we report the first scan for selection using ancient DNA, capitalizing ...

    • A Genome-Wide Screen to Identify Transcription Factors Expressed in Pelvic Ganglia of the Lower Urinary Tract 

      Wiese, Carrie B.; Ireland, Sara; Fleming, Nicole L.; Georgas, Kylie; Chiu, Han Sheng; Brennan, Jane; Armstrong, Jane; Little, Melissa H.; Southard-Smith, E. Michelle; Yu, Jing; Valerius, Michael Todd; McMahon, Andrew P. (Frontiers Research Foundation, 2012)
      Relative positions of neurons within mature murine pelvic ganglia based on expression of neurotransmitters have been described. However the spatial organization of developing innervation in the murine urogenital tract (UGT) ...

    • Genome-wide significant association between a ‘negative mood delusions' dimension in bipolar disorder and genetic variation on chromosome 3q26.1 

      Meier, S.; Mattheisen, M.; Vassos, E.; Strohmaier, J.; Treutlein, J.; Josef, F.; Breuer, R.; Degenhardt, F.; Mühleisen, T. W.; Müller-Myhsok, B.; Steffens, M.; Schmael, C.; McMahon, F. J.; Nöthen, M. M.; Cichon, S.; Schulze, T. G.; Rietschel, M. (Elsevier, 2012)
      Research suggests that clinical symptom dimensions may be more useful in delineating the genetics of bipolar disorder (BD) than standard diagnostic models. To date, no study has applied this concept to data from genome-wide ...

    • Genome-Wide SNP Genotyping Highlights the Role of Natural Selection in Plasmodium Falciparum Population Divergence 

      Wirth, Dyann F.; Sabeti, Pardis C.; Lander, Eric S.; Birren, Bruce W.; Hartl, Daniel; Wiegand, Roger; Chitnis, Chetan E.; Dash, Aditya P.; do Lago Moraes, Sandra; Ferreira, Marcelo U.; Mboup, Soulyemane; Ndir, Omar; Ndiaye, Daouda; Ousmane, Sarr; Stange-Thomann, Nicole; Gates, Casey; Tyndall, Erin; Cortese, Joseph F.; Houde, Nathan; Daniels, Rachel; Rosen, David; Lukens, Amanda; Milner, Danny; Montgomery, Philip; Park, Daniel; Volkman, Sarah K.; Schaffner, Stephen F.; Neafsey, Daniel (BioMed Central, 2008)
      Background: The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity in P. falciparum have begun ...

    • Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells 

      Kleinstiver, Benjamin P.; Tsai, Shengdar Q.; Prew, Michelle S.; Nguyen, Nhu T.; Welch, Moira M.; Lopez, Jose M.; McCaw, Zachary R.; Aryee, Martin J.; Joung, J. Keith (2016)
      The activities and genome-wide specificities of CRISPR-Cas Cpf1 nucleases1 are not well defined. We show that two Cpf1 nucleases from Acidaminococcus sp. BV3L6 and Lachnospiraceae bacterium ND2006 (AsCpf1 and LbCpf1, ...

    • Genome-Wide Study of mRNA Degradation and Transcript Elongation in Escherichia coli 

      Chen, Huiyi; Shiroguchi, Katsuyuki; Ge, Hao; Xie, Xiaoliang Sunney (EMBO, 2015)
      An essential part of gene expression is the coordination of RNA synthesis and degradation, which occurs in the same cellular compartment in bacteria. Here, we report a genome‐wide RNA degradation study in Escherichia coli ...

    • Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains 

      Rheinbay, Esther; Endoh, Mitsuhiro; Mikkelsen, Tarjei S.; Nusbaum, Chad; Xie, Xiaohui; Adli, Mazhar; Kasif, Simon; Ptaszek, Leon M.; Koseki, Haruhiko; van Steensel, Bas; Ku, Manching; Koche, Richard Patrick; Mendenhall, Eric M; Presser, Aviva; Chi, Andrew S.; Cowan, Chad A.; Lander, Eric Steven; Bernstein, Bradley E. (Public Library of Science, 2008)
      In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 ...

    • Genomewide studies of histone deacetylase function in yeast 

      Bernstein, Bradley; Tong, Jeffrey; Schreiber, Stuart (National Academy of Sciences, 2000)
      The trichostatin A (TSA)-sensitive histone deacetylase (HDAC) Rpd3p exists in a complex with sin3p and Sap30p in yeast that is recruited to target promoters by transcription factors including Ume6p. Sir2p is a TSA-resistant ...

    • Genomic Analysis Identifies Targets of Convergent Positive Selection in Drug Resistant Mycobacterium tuberculosis 

      Farhat, Maha R; Shapiro, B Jesse; Kieser, Karen J; Sultana, Razvan; Jacobson, Karen R; Victor, Thomas C; Warren, Robin M; Streicher, Elizabeth M; Calver, Alistair; Sloutsky, Alex; Kaur, Devinder; Posey, Jamie E; Plikaytis, Bonnie; Oggioni, Marco R; Gardy, Jennifer L; Johnston, James C; Rodrigues, Mabel; Tang, Patrick K C; Kato-Maeda, Midori; Borowsky, Mark L; Muddukrishna, Bhavana; Kreiswirth, Barry N; Kurepina, Natalia; Galagan, James; Gagneux, Sebastien; Birren, Bruce; Rubin, Eric J; Lander, Eric S; Sabeti, Pardis C; Murray, Megan (2013)
      Mycobacterium tuberculosis is successfully evolving antibiotic resistance, threatening attempts at tuberculosis epidemic control. Mechanisms of resistance, including the genetic changes favored by selection in resistant ...

    • A genomic and evolutionary approach reveals non-genetic drug resistance in malaria 

      Herman, Jonathan D; Rice, Daniel P; Ribacke, Ulf; Silterra, Jacob; Deik, Amy A; Moss, Eli L; Broadbent, Kate M; Neafsey, Daniel E; Desai, Michael M; Clish, Clary B; Mazitschek, Ralph; Wirth, Dyann F (BioMed Central, 2014)
      Background: Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis ...

    • Genomic Evidence of Gene Flow During Reinforcement in Texas Phlox 

      Roda, Federico; Mendes, Fabio; Hahn, Matthew W.; Hopkins, Robin (Wiley, 2017-03-06)
      Gene flow can impede the evolution of reproductive isolating barriers between species. Reinforcement is the process by which prezygotic reproductive isolation evolves in sympatry due to selection to decrease costly ...