Now showing items 21-40 of 104

    • The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies 

      Sok, Devin; Laserson, Uri; Laserson, Jonathan; Liu, Yi; Vigneault, Francois; Julien, Jean-Philippe; Briney, Bryan; Ramos, Alejandra; Saye, Karen F.; Le, Khoa; Mahan, Alison; Wang, Shenshen; Kardar, Mehran; Yaari, Gur; Walker, Laura M.; Simen, Birgitte B.; St. John, Elizabeth P.; Chan-Hui, Po-Ying; Swiderek, Kristine; Kleinstein, Stephen H.; Alter, Galit; Seaman, Michael S.; Chakraborty, Arup K.; Koller, Daphne; Wilson, Ian A.; Church, George M.; Burton, Dennis R.; Poignard, Pascal (Public Library of Science, 2013)
      Broadly neutralizing HIV antibodies (bnAbs) are typically highly somatically mutated, raising doubts as to whether they can be elicited by vaccination. We used 454 sequencing and designed a novel phylogenetic method to ...
    • Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription 

      Zhang, Feng; Cong, Le; Lodato, Simona; Kosuri, Sriram; Church, George McDonald; Arlotta, Paola (Nature Publishing Group, 2011)
      The ability to direct functional proteins to specific DNA sequences is a long-sought goal in the study and engineering of biological processes. Transcription activator–like effectors (TALEs) from Xanthomonas sp. are ...
    • Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection 

      Carr, Peter A.; Wang, Harris He; Sterling, Bram; Isaacs, Farren J.; Lajoie, Marc Joseph; Xu, George Jing; Church, George McDonald; Jacobson, Joseph M. (Oxford University Press, 2012)
      Genome-scale engineering of living organisms requires precise and economical methods to efficiently modify many loci within chromosomes. One such example is the directed integration of chemically synthesized single-stranded ...
    • Evidence for Large Diversity in the Human Transcriptome Created by Alu RNA Editing 

      Barak, Michal; Levanon, Erez Y.; Eisenberg, Eli; Paz, Nurit; Rechavi, Gideon; Church, George McDonald; Mehr, Ramit (Oxford University Press, 2009)
      Adenosine-to-inosine (A-to-I) RNA editing alters the original genomic content of the human transcriptome and is essential for maintenance of normal life in mammals. A-to-I editing in Alu repeats is abundant in the human ...
    • Expression Dynamics of a Cellular Metabolic Network 

      Kharchenko, Peter Vasili; Church, George McDonald; Vitkup, Dennis (Nature Publishing Group, 2005)
      Toward the goal of understanding system properties of biological networks, we investigate the global and local regulation of gene expression in the Saccharomyces cerevisiae metabolic network. Our results demonstrate ...
    • Extensive sequencing of seven human genomes to characterize benchmark reference materials 

      Zook, Justin M.; Catoe, David; McDaniel, Jennifer; Vang, Lindsay; Spies, Noah; Sidow, Arend; Weng, Ziming; Liu, Yuling; Mason, Christopher E.; Alexander, Noah; Henaff, Elizabeth; McIntyre, Alexa B.R.; Chandramohan, Dhruva; Chen, Feng; Jaeger, Erich; Moshrefi, Ali; Pham, Khoa; Stedman, William; Liang, Tiffany; Saghbini, Michael; Dzakula, Zeljko; Hastie, Alex; Cao, Han; Deikus, Gintaras; Schadt, Eric; Sebra, Robert; Bashir, Ali; Truty, Rebecca M.; Chang, Christopher C.; Gulbahce, Natali; Zhao, Keyan; Ghosh, Srinka; Hyland, Fiona; Fu, Yutao; Chaisson, Mark; Xiao, Chunlin; Trow, Jonathan; Sherry, Stephen T.; Zaranek, Alexander W.; Ball, Madeleine; Bobe, Jason; Estep, Preston Wayne; Church, George McDonald; Marks, Patrick; Kyriazopoulou-Panagiotopoulou, Sofia; Zheng, Grace X.Y.; Schnall-Levin, Michael; Ordonez, Heather S.; Mudivarti, Patrice A.; Giorda, Kristina; Sheng, Ying; Rypdal, Karoline Bjarnesdatter; Salit, Marc (Springer Nature, 2016)
      The Genome in a Bottle Consortium, hosted by the National Institute of Standards and Technology (NIST) is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and ...
    • Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues 

      Lee, Je Hyuk; Daugharthy, Evan R; Scheiman, Jonathan; Kalhor, Reza; Ferrante, Thomas Charles; Terry, Richard; Turczyk, Brian M; Yang, Joyce L; Lee, Ho Suk; Aach, John Dennis; Zhang, Kun; Church, George McDonald (Springer Nature, 2015)
      RNA sequencing measures the quantitative change in gene expression over the whole transcriptome, but it lacks spatial context. On the other hand, in situ hybridization provides the location of gene expression, but only for ...
    • A Functional Metagenomic Approach for Expanding the Synthetic Biology Toolbox for Biomass Conversion 

      Sommer, Morten OA; Church, George McDonald; Dantas, Gautam (Nature Publishing Group, 2010)
      Sustainable biofuel alternatives to fossil fuel energy are hampered by recalcitrance and toxicity of biomass substrates to microbial biocatalysts. To address this issue, we present a culture-independent functional metagenomic ...
    • A general strategy to construct small molecule biosensors in eukaryotes 

      Feng, Justin; Jester, Benjamin W; Tinberg, Christine E; Mandell, Daniel J; Antunes, Mauricio S; Chari, Raj; Morey, Kevin J; Rios, Xavier; Medford, June I; Church, George M; Fields, Stanley; Baker, David (eLife Sciences Publications, Ltd, 2015)
      Biosensors for small molecules can be used in applications that range from metabolic engineering to orthogonal control of transcription. Here, we produce biosensors based on a ligand-binding domain (LBD) by using a method ...
    • Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels 

      Petit, Elsa; Coppi, Maddalena V.; Hayes, James C.; Tolonen, Andrew C.; Warnick, Thomas; Latouf, William G.; Amisano, Danielle; Biddle, Amy; Mukherjee, Supratim; Ivanova, Natalia; Lykidis, Athanassios; Land, Miriam; Hauser, Loren; Kyrpides, Nikos; Henrissat, Bernard; Lau, Joanne; Schnell, Danny J.; Church, George M.; Leschine, Susan B.; Blanchard, Jeffrey L. (Public Library of Science, 2015)
      Clostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual ...
    • Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems 

      DiCarlo, James; Norville, Julie; Mali, Prashant; Rios Villanueva, Xavier; Aach, John Dennis; Church, George McDonald (Oxford University Press, 2013)
      Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) systems in bacteria and archaea use RNA-guided nuclease activity to provide adaptive immunity against invading foreign nucleic ...
    • Genome Engineering Technologies to Change the Genetic Code 

      Lajoie, Marc Joseph (2014-02-25)
      New technologies are making it possible to engineer organisms with fundamentally new and useful properties. In vivo genome engineering technologies capable of manipulating genomes from the nucleotide to the megabase scale ...
    • Genome Engineering Technology and Its Application in Mammalian Cells 

      Cong, Le (2014-06-06)
      The advancement of high-throughput, large-scale biochemical, biophysical, and genetic technologies has enabled the generation of massive amounts of biological data and allowed us to synthesize various types of biomaterial ...
    • Genome-Scale Promoter Engineering by Coselection MAGE 

      Wang, Harris He; Kim, Hwangbeom; Cong, Le; Jeong, Jaehwan; Bang, Duhee; Church, George McDonald (Nature Publishing Group, 2012)
      Multiplex Automated Genome Engineering (MAGE) employs short oligonucleotides to scarlessly modify genomes. However, insertions of >10 bases are still inefficient, but can be improved substantially by selection of highly ...
    • Genome-wide inactivation of porcine endogenous retroviruses (PERVs) 

      Yang, Luhan; Guell, Marc; Niu, D.; George, H.; Lesha, E.; Grishin, Dennis; Aach, John Dennis; Shrock, Ellen Lee; Xu, W.; Poci, Jurgen; Cortazio, R.; Wilkinson, R. A.; Fishman, Jay Alan; Church, George McDonald (American Association for the Advancement of Science (AAAS), 2015)
      The shortage of organs for transplantation is a major barrier to the treatment of organ failure. While porcine organs are considered promising, their use has been checked by concerns about transmission of porcine endogenous ...
    • Genomic Analysis of the Hydrocarbon-Producing, Cellulolytic, Endophytic Fungus Ascocoryne sarcoides 

      Sboner, Andrea; Kodira, Chinnappa; Egholm, Michael; Church, George McDonald; Gianoulis, Tara A.; Griffin, Meghan A.; Spakowicz, Daniel J.; Dunican, Brian F.; Alpha, Cambria J.; Sismour, A. Michael; Gerstein, Mark B.; Strobel, Scott A. (Public Library of Science, 2012)
      The microbial conversion of solid cellulosic biomass to liquid biofuels may provide a renewable energy source for transportation fuels. Endophytes represent a promising group of organisms, as they are a mostly untapped ...
    • Harvard Personal Genome Project: lessons from participatory public research 

      Ball, Madeleine P; Bobe, Jason R; Chou, Michael F; Clegg, Tom; Estep, Preston W; Lunshof, Jeantine E; Vandewege, Ward; Zaranek, Alexander Wait; Church, George M (BioMed Central, 2014)
      Background: Since its initiation in 2005, the Harvard Personal Genome Project has enrolled thousands of volunteers interested in publicly sharing their genome, health and trait data. Because these data are highly identifiable, ...
    • Heritable genome editing in C. elegans via a CRISPR-Cas9 system 

      Friedland, Ari E.; Tzur, Yonatan B.; Esvelt, Kevin M.; Colaiácovo, Monica P.; Church, George M.; Calarco, John A. (2013)
      CRISPR-Cas systems have been used with single-guide RNAs for accurate gene disruption and conversion in multiple biological systems. Here we report the use of the endonuclease Cas9 to target genomic sequences in the C. ...
    • Hippocrates Revisited? Old Ideals and New Realities 

      Lunshof, Jeantine E.; Chadwick, Ruth; Church, George McDonald (Springer Verlag, 2008)
      Individual genomics has arrived, personal decisions to make use of it are a new reality. What are the implications for the patient–physician relationship? In this article we address three factors that call the traditional ...
    • How Accurate Can Genetic Predictions Be? 

      Dreyfuss, Jonathan M; Levner, Daniel; Galagan, James E; Church, George McDonald; Ramoni, Marco F (BioMed Central, 2012)
      Background: Pre-symptomatic prediction of disease and drug response based on genetic testing is a critical component of personalized medicine. Previous work has demonstrated that the predictive capacity of genetic testing ...