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NGEC Publications

The interdisciplinary work of the Northwest Genome Engineering Consortium (NGEC) has led to considerable scientific progress. As of December 2012, 38 publications are directly attributable to the work in the seven consortium laboratories.

In addition, the laboratories funded through the NGEC Pilot Project grants have published at least thirteen manuscripts that can be found here.

 

2013

Baxter SK, Lambert AR, Scharenberg AM, Jarjour J.  2013.  Flow Cytometric Assays for Interrogating LAGLIDADG Homing Endonuclease DNA-Binding and Cleavage Properties.. Methods Mol Biol. 978:45-61.

2012

Certo MT, Gwiazda KS, Kuhar R, Sather B, Curinga G, Mandt T, Brault M, Lambert AR, Baxter SK, Jacoby K et al..  2012.  Coupling endonucleases with DNA end-processing enzymes to drive gene disruption.. Nat Methods.
Taylor GK, Petrucci LH, Lambert AR, Baxter SK, Jarjour J, Stoddard BL.  2012.  LAHEDES: the LAGLIDADG homing endonuclease database and engineering server.. Nucleic acids research.
Humbert O, Davis L, Maizels N.  2012.  Targeted gene therapies: tools, applications, optimization.. Critical reviews in biochemistry and molecular biology. 47(3):264-81.
Taylor GK, Stoddard BL.  2012.  Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms.. Nucleic acids research.
Li H, Ulge UY, Hovde BT, Doyle LA, Monnat RJ.  2012.  Comprehensive homing endonuclease target site specificity profiling reveals evolutionary constraints and enables genome engineering applications.. Nucleic acids research. 40(6):2587-98.
Thyme SB, Baker D, Bradley P.  2012.  Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design.. Journal of molecular biology. 419(3-4):255-74.
Baxter S, Lambert AR, Kuhar R, Jarjour J, Kulshina N, Parmeggiani F, Danaher P, Gano J, Baker D, Stoddard BL et al..  2012.  Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases.. Nucleic acids research.
Jacoby K, Metzger M, Shen BW, Certo MT, Jarjour J, Stoddard BL, Scharenberg AM.  2012.  Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space.. Nucleic acids research. 40(11):4954-64.
Muñoz NM, Beard BC, Ryu BY, Luche RM, Trobridge GD, Rawlings DJ, Scharenberg AM, Kiem H-P.  2012.  Novel reporter systems for facile evaluation of I-SceI-mediated genome editing.. Nucleic acids research. 40(2):e14.
Mak AN-S, Bradley P, Cernadas RA, Bogdanove AJ, Stoddard BL.  2012.  The crystal structure of TAL effector PthXo1 bound to its DNA target.. Science (New York, N.Y.). 335(6069):716-9.
Mak AN-S, Bradley P, Bogdanove AJ, Stoddard BL.  2012.  TAL effectors: function, structure, engineering and applications.. Curr Opin Struct Biol.
Humbert O, Maizels N.  2012.  Epigenetic modification of the repair donor regulates targeted gene correction.. Mol Ther Nucleic Acids. 1:e49.

2011

Szeto MD, Boissel SJS, Baker D, Thyme SB.  2011.  Mining endonuclease cleavage determinants in genomic sequence data.. The Journal of biological chemistry. 286(37):32617-27.
Bandaranayake AD, Correnti C, Ryu BY, Brault M, Strong RK, Rawlings DJ.  2011.  Daedalus: a robust, turnkey platform for rapid production of decigram quantities of active recombinant proteins in human cell lines using novel lentiviral vectors.. Nucleic acids research. 39(21):e143.
Ulge UY, Baker DA, Monnat RJ.  2011.  Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering.. Nucleic acids research. 39(10):4330-9.
Paddock MN, Bauman AT, Higdon R, Kolker E, Takeda S, Scharenberg AM.  2011.  Competition between PARP-1 and Ku70 control the decision between high-fidelity and mutagenic DNA repair.. DNA repair. 10(3):338-43.
Stoddard BL.  2011.  Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification.. Structure (London, England : 1993). 19(1):7-15.
Taylor GK, Heiter DF, Pietrokovski S, Stoddard BL.  2011.  Activity, specificity and structure of I-Bth0305I: a representative of a new homing endonuclease family.. Nucleic acids research. 39(22):9705-19.
Takeuchi R, Lambert AR, Mak AN-S, Jacoby K, Dickson RJ, Gloor GB, Scharenberg AM, Edgell DR, Stoddard BL.  2011.  Tapping natural reservoirs of homing endonucleases for targeted gene modification.. Proceedings of the National Academy of Sciences of the United States of America. 108(32):13077-82.
Certo MT, Ryu BY, Annis JE, Garibov M, Jarjour J, Rawlings DJ, Scharenberg AM.  2011.  Tracking genome engineering outcome at individual DNA breakpoints.. Nature methods. 8(8):671-6.
Davis L, Maizels N.  2011.  G4 DNA: at risk in the genome.. The EMBO journal. 30(19):3878-9.
Davis L, Maizels N.  2011.  DNA nicks promote efficient and safe targeted gene correction.. PloS one. 6(9):e23981.

2010

Ashworth J, Taylor GK, Havranek JJ, Quadri AS, Stoddard BL, Baker D.  2010.  Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs.. Nucleic acids research. 38(16):5601-8.
Mak AN-S, Lambert AR, Stoddard BL.  2010.  Folding, DNA recognition, and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI.. Structure (London, England : 1993). 18(10):1321-31.
Paddock MN, Buelow BD, Takeda S, Scharenberg AM.  2010.  The BRCT domain of PARP-1 is required for immunoglobulin gene conversion.. PLoS biology. 8(7):e1000428.

2009

Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D.  2009.  Exploitation of binding energy for catalysis and design.. Nature. 461(7268):1300-4.
Kaiser BK, Clifton MC, Shen BW, Stoddard BL.  2009.  The structure of a bacterial DUF199/WhiA protein: domestication of an invasive endonuclease.. Structure (London, England : 1993). 17(10):1368-76.
Jarjour J, West-Foyle H, Certo MT, Hubert CG, Doyle L, Getz MM, Stoddard BL, Scharenberg AM.  2009.  High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display.. Nucleic acids research. 37(20):6871-80.
Beard BC, Sud R, Keyser KA, Ironside C, Neff T, Gerull S, Trobridge GD, Kiem H-P.  2009.  Long-term polyclonal and multilineage engraftment of methylguanine methyltransferase P140K gene-modified dog hematopoietic cells in primary and secondary recipients.. Blood. 113(21):5094-103.
Trobridge GD, Allen J, Peterson L, Ironside C, Russell DW, Kiem H-P.  2009.  Foamy and lentiviral vectors transduce canine long-term repopulating cells at similar efficiency.. Human gene therapy. 20(5):519-23.
McConnell Smith A, Takeuchi R, Pellenz S, Davis L, Maizels N, Monnat RJ, Stoddard BL.  2009.  Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease.. Proceedings of the National Academy of Sciences of the United States of America. 106(13):5099-104.
Ashworth J, Baker D.  2009.  Assessment of the optimization of affinity and specificity at protein-DNA interfaces.. Nucleic acids research. 37(10):e73.
Zhao L, Pellenz S, Stoddard BL.  2009.  Activity and specificity of the bacterial PD-(D/E)XK homing endonuclease I-Ssp6803I.. Journal of molecular biology. 385(5):1498-510.
Takeuchi R, Certo M, Caprara MG, Scharenberg AM, Stoddard BL.  2009.  Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation.. Nucleic acids research. 37(3):877-90.
Li H, Pellenz S, Ulge U, Stoddard BL, Monnat RJ.  2009.  Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins.. Nucleic acids research. 37(5):1650-62.
Ordinario EC, Yabuki M, Handa P, Cummings JW, Maizels N.  2009.  RAD51 paralogs promote homology-directed repair at diversifying immunoglobulin V regions.. BMC molecular biology. 10:98.

2008

Nomura N, Nomura Y, Sussman D, Klein D, Stoddard BL.  2008.  Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases.. Nucleic acids research. 36(22):6988-98.
Cummings JW, Bednarski DW, Maizels N.  2008.  Genetic variation stimulated by epigenetic modification.. PloS one. 3(12):e4075.



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