Now showing items 1-20 of 104

    • 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 ...
    • 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. ...
    • 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 ...
    • 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 ...
    • 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 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering 

      Mali, Prashant; Aach, John; Stranges, P. Benjamin; Esvelt, Kevin M.; Moosburner, Mark; Kosuri, Sriram; Yang, Luhan; Church, George M. (2013)
      Prokaryotic type II CRISPR-Cas systems can be adapted to enable targeted genome modifications across a range of eukaryotes.1–7. Here we engineer this system to enable RNA-guided genome regulation in human cells by tethering ...
    • CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing 

      Montague, Tessa G.; Cruz, José M.; Gagnon, James A.; Church, George M.; Valen, Eivind (Oxford University Press, 2014)
      Major advances in genome editing have recently been made possible with the development of the TALEN and CRISPR/Cas9 methods. The speed and ease of implementing these technologies has led to an explosion of mutant and ...
    • Comparative Analysis of Cas9 Activators Across Multiple Species 

      Chavez, Alejandro; Tuttle, Marcelle; Pruitt, Benjamin W; Ewen-Campen, Ben; Chari, Raj; Ter-Ovanesyan, Dmitry; Haque, Sabina J; Cecchi, Ryan J; Kowal, Emma J K; Buchthal, Joanna; Housden, Benjamin E; Perrimon, Norbert; Collins, James J; Church, George (2016)
      Several groups have generated programmable transcription factors based on the versatile Cas9 protein, yet their relative potency and effectiveness across various cell types and species remain unexplored. Here, we compare ...
    • Computational discovery of sense-antisense transcription in the human and mouse genomes 

      Shendure, Jay; Church, George McDonald (BioMed Central, 2002)
      Background: Overlapping but oppositely oriented transcripts have the potential to form senseantisense perfect double-stranded (ds) RNA duplexes. Over recent years, the number and variety of examples of mammalian ...
    • Concerning RNA-guided gene drives for the alteration of wild populations 

      Esvelt, Kevin M; Smidler, Andrea L; Catteruccia, Flaminia; Church, George M (eLife Sciences Publications, Ltd, 2014)
      Gene drives may be capable of addressing ecological problems by altering entire populations of wild organisms, but their use has remained largely theoretical due to technical constraints. Here we consider the potential for ...
    • CRISPR/Cas9-Mediated Phage Resistance Is Not Impeded by the DNA Modifications of Phage T4 

      Yaung, Stephanie J.; Esvelt, Kevin M.; Church, George M. (Public Library of Science, 2014)
      Bacteria rely on two known DNA-level defenses against their bacteriophage predators: restriction-modification and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) systems. Certain ...
    • Designing Scalable Biological Interfaces 

      Marblestone, Adam Henry (2014-06-06)
      This thesis presents the analysis and design of biological interfacing technologies in light of a need for radical improvements in scalability. It focuses primarily on structural and functional neural data acquisition, but ...
    • Development of Human Genome Editing Tools for the Study of Genetic Variations and Gene Therapies 

      Yang, Luhan (2013-10-17)
      The human genome encodes information that instructs human development, physiology, medicine, and evolution. Massive amount of genomic data has generated an ever-growing pool of hypothesis. Genome editing, broadly defined ...
    • Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human 

      Zhang, Kun; Li, Jin Billy; Gao, Yuan; Egli, Dieter; Xie, Bin; Deng, Jie; Li, Zhe; Lee, Je-Hyuk; Aach, John Dennis; Leproust, Emily M; Eggan, Kevin Carl; Church, George McDonald (Nature Publishing Group, 2009)
      We developed a digital RNA allelotyping method for quantitatively interrogating allele-specific gene expression. This method involves ultra-deep sequencing of padlock captured SNPs from the transcriptome. We characterized ...
    • Direct Mutagenesis of Thousands of Genomic Targets Using Microarray-Derived Oligonucleotides 

      Bonde, Mads T.; Kosuri, Sriram; Genee, Hans J.; Sarup-Lytzen, Kira; Church, George M.; Sommer, Morten O.A.; Wang, Harris H. (American Chemical Society, 2014)
      Multiplex Automated Genome Engineering (MAGE) allows simultaneous mutagenesis of multiple target sites in bacterial genomes using short oligonucleotides. However, large-scale mutagenesis requires hundreds to thousands of ...
    • Discovery and Functional Interpretation of Genetic Risk in Autoimmune Diseases 

      Hu, Xinli (2015-05-08)
      Autoimmune diseases are chronic and debilitating conditions arising from abnormal immune responses directed against normal body tissues; they collectively affect the lives of 5-10% of the world population. These diseases ...