Now showing items 1-20 of 193

    • A prudent path forward for genomic engineering and germline gene modification 

      Baltimore, D; Berg, P; Botchan, M; Carroll, D; Charo, A; Church, G; Daley, G; Doudna, J; Fenner, M; Greely, H; Jinek, M; Martin, G; Penhoet, E; Puck, J; Sternberg, S; Weissman, J; Yamamoto, K
      A framework for open discourse on the use of CRISPR-Cas9 technology to manipulate the human genome is urgently needed
    • Accurate Whole Genome Sequencing as the Ultimate Genetic Test 

      Drmanac, R.; Peters, B. A.; Church, George McDonald; Reid, Clifford; Xu, Xun (American Association for Clinical Chemistry (AACC), 2014)
    • Accurate Whole-Genome Sequencing and Haplotyping from 10 to 20 Human Cells 

      Peters, Brock A.; Kermani, Bahram G.; Sparks, Andrew B.; Alferov, Oleg; Hong, Peter; Alexeev, Andrei; Jiang, Yuan; Dahl, Fredrik; Tang, Y. Tom; Haas, Juergen; Robasky, Kimberly J.; Lee, Je-Hyuk; Peterson, Joseph E.; Perazich, Helena; Yeung, George; Liu, Jia; Chen, Linsu; Kennemer, Michael I.; Pothuraju, Kaliprasad; Konvicka, Karel; Tsoupko-Sitnikov, Mike; Pant, Krishna P.; Ebert, Jessica C.; Nilsen, Geoffrey B.; Baccash, Jonathan; Halpern, Aaron L.; Church, George McDonald; Drmanac, Radoje; Zaranek, Alexander Wait; Ball, Madeleine Price (Nature Publishing Group, 2012)
      Recent advances in whole genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context ...
    • The Amino-Acid Mutational Spectrum of Human Genetic Disease 

      Vitkup, Dennis; Sander, Chris; Church, George McDonald (BioMed Central, 2003)
      Background: Nonsynonymous mutations in the coding regions of human genes are responsible for phenotypic differences between humans and for susceptibility to genetic disease. Computational methods were recently used to ...
    • Analyses of Human–Chimpanzee Orthologous Gene Pairs to Explore Evolutionary Hypotheses of Aging 

      de Magalhães, João Pedro; Church, George (Elsevier BV, 2007-05)
      Compared to chimpanzees (Pan troglodytes), the onset of aging appears to be delayed in the human species. Herein, we studied human-chimpanzee orthologous gene pairs to investigate the selective forces acting on genes ...
    • An Analysis and Validation Pipeline for Large-Scale RNAi-Based Screens 

      Plank, Michael; Hu, Guang; Silva, A. Sofia; Wood, Shona H.; Hesketh, Emily E.; Janssens, Georges; Macedo, André; de Magalhães, João Pedro; Church, George (Springer Science and Business Media LLC, 2013-01-16)
      Large-scale RNAi-based screens are a major technology, but require adequate prioritization and validation of candidate genes from the primary screen. In this work, we performed a large-scale pooled shRNA screen in mouse ...
    • Analysis of optimality in natural and perturbed metabolic networks 

      Segre, Daniel; Vitkup, Dennis; Church, George (Proceedings of the National Academy of Sciences, 2002-11)
      An important goal of whole-cell computational modeling is to integrate detailed biochemical information with biological intuition to produce testable predictions. Based on the premise that prokaryotes such as Escherichia ...
    • An Analysis of the Relationship Between Metabolism, Developmental Schedules, and Longevity Using Phylogenetic Independent Contrasts 

      Costa, Joana; Church, George; de Magalhães, João Pedro (Gerontological Society of America, 2007-02)
      Comparative studies of aging are often difficult to interpret because of the different factors that tend to correlate with longevity. We used the AnAge database to study these factors, particularly metabolism and developmental ...
    • Application of a synthetic human proteome to autoantigen discovery through PhIP-Seq 

      Larman, H. Benjamin; Zhao, Zhenming; Laserson, Uri; Li, Mamie Z.; Ciccia, Alberto; Gakidis, M. Angelica Martinez; Church, George M.; Kesari, Santosh; LeProust, Emily M.; Solimini, Nicole L.; Elledge, Stephen J. (2011)
      In this study, we improve on current autoantigen discovery approaches by creating a synthetic representation of the complete human proteome, the T7 “peptidome” phage display library (T7-Pep), and use it to profile the ...
    • Automated Modelling of Signal Transduction Networks 

      Steffen, Martin; Petti, Allegra; Aach, John Dennis; D'haeseleer, Patrik; Church, George McDonald (BioMed Central, 2002)
      Background: Intracellular signal transduction is achieved by networks of proteins and small molecules that transmit information from the cell surface to the nucleus, where they ultimately effect transcriptional changes. ...
    • B Cells Populating the Multiple Sclerosis Brain Mature in the Draining Cervical Lymph Nodes 

      Stern, Joel N. H.; Yaari, Gur; Vander Heiden, Jason A.; Church, George; Donahue, William F.; Hintzen, Rogier Q.; Huttner, Anita J.; Laman, Jon D.; Nagra, Rashed M.; Nylander, Alyssa; Pitt, David; Ramanan, Sriram; Siddiqui, Bilal A.; Vigneault, Francois; Kleinstein, Steven H.; Hafler, David A.; O’Connor, Kevin C. (American Association for the Advancement of Science (AAAS), 2014-08-06)
      Multiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS) characterized by autoimmune mediated demyelination and neurodegeneration. The CNS of patients with MS harbors expanded clones of ...
    • Barcoding Bias in High-Throughput Multiplex Sequencing of miRNA 

      Alon, Shahar; Vigneault, Francois; Eminaga, Seda; Christodoulou, Danos; Seidman, Jonathan; Church, George; Eisenberg, Eli (Cold Spring Harbor Laboratory, 2011-09)
      Second-generation sequencing is gradually becoming the method of choice for miRNA detection and expression profiling. Given the relatively small number of miRNAs and improvements in DNA sequencing technology, studying miRNA ...
    • Barcoding cells using cell-surface programmable DNA-binding domains 

      Mali, Prashant; Aach, John; Lee, Jehyuk; Levner, Daniel; Nip, Lisa; Church, George M. (2013)
      We develop here a novel approach to barcode large numbers of cells through cell-surface expression of programmable zinc-finger DNA-binding domains (sZFs). We show sZFs enable double-stranded DNA to sequence-specifically ...
    • A BioBrick compatible strategy for genetic modification of plants 

      Boyle, Patrick M; Burrill, Devin Rene; Inniss, Mara Christine; Agapakis, Christina M; Deardon, Aaron; dewerd, Jonathan G; Gedeon, Michael A; Quinn, Jacqueline Y; Paull, Morgan L; Raman, Anugraha M; Theilmann, Mark R; Wang, Lu; Winn, Julia C; Medvedik, Oliver; Schellenberg, Kurt William; Haynes, Karmella; Viel, Alain; Brenner, Tamara Jane; Church, George McDonald; Shah, Jagesh V.; Silver, Pamela A. (BioMed Central, 2012)
      Background: Plant biotechnology can be leveraged to produce food, fuel, medicine, and materials. Standardized methods advocated by the synthetic biology community can accelerate the plant design cycle, ultimately making ...
    • Biocontainment of Genetically Modified Organisms by Synthetic Protein Design 

      Mandell, Daniel; Lajoie, Marc J.; Mee, Michael T.; Takeuchi, Ryo; Kuznetsov, Gleb; Norville, Julie; Gregg, Christopher J.; Stoddard, Barry L.; Church, George (Nature Research, 2015-02-05)
      Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. ...
    • Biosensing for Multiplexed Genome Engineering: Applications in Renewable Chemical Production 

      Rogers, Jameson Kerr (2015-05-15)
      Engineered biological systems are increasingly used to produce fuels, pharmaceuticals and industrial chemicals. While transforming cells into renewable chemical factories presents an enormous opportunity, development ...
    • The Brain Activity Map Project and the Challenge of Functional Connectomics 

      Alivisatos, A. Paul; Chun, Miyoung; Church, George; Greenspan, Ralph J.; Roukes, Michael L.; Yuste, Rafael (Elsevier BV, 2012-06-21)
      The function of neural circuits is an emergent property that arises from the coordinated activity of large numbers of neurons. To capture this, we propose launching a large-scale, international public effort, the Brain ...
    • Building Next-Generation Technologies for Low-Cost Gene Synthesis and High-Accuracy Genome Engineering 

      Eroshenko, Nikolai A. (2014-11-21)
      The technologies that enable writing and editing of DNA form the foundation of modern molecular biology and biotechnology. However, a number of methodological barriers have limited the widespread adoption of both high-throughput ...
    • Cas9 as a Versatile Tool for Engineering Biology 

      Mali, Prashant; Esvelt, Kevin M.; Church, George (Springer Science and Business Media LLC, 2013-10)
      RNA-guided Cas9 nucleases derived from clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have dramatically transformed our ability to edit the genomes of diverse organisms. We believe tools and ...
    • Cas9 gRNA Engineering for Genome Editing, Activation and Repression 

      Kiani, Samira; Chavez, Alejandro; Tuttle, Marcelle; Hall, Richard N; Chari, Raj; Ter-Ovanesyan, Dmitry; Qian, Jason; Pruitt, Benjamin W; Beal, Jacob; Vora, Suhani; Buchthal, Joanna; Kowal, Emma J K; Ebrahimkhani, Mohammad R; Collins, James; Weiss, Ron; Church, George (Springer Science and Business Media LLC, 2015-11)
      We demonstrate that by altering the length of Cas9-associated guide RNA(gRNA) we were able to control Cas9 nuclease activity and simultaneously perform genome editing and transcriptional regulation with a single Cas9 ...