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Items: 27


Corrigendum: Engineering and optimising deaminase fusions for genome editing.

Yang L, Briggs AW, Chew WL, Mali P, Guell M, Aach J, Goodman DB, Cox D, Kan Y, Lesha E, Soundararajan V, Zhang F, Church G.

Nat Commun. 2017 Oct 9;8:16169. doi: 10.1038/ncomms16169.


Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data.

Gupta NT, Adams KD, Briggs AW, Timberlake SC, Vigneault F, Kleinstein SH.

J Immunol. 2017 Mar 15;198(6):2489-2499. doi: 10.4049/jimmunol.1601850. Epub 2017 Feb 8.


Engineering and optimising deaminase fusions for genome editing.

Yang L, Briggs AW, Chew WL, Mali P, Guell M, Aach J, Goodman DB, Cox D, Kan Y, Lesha E, Soundararajan V, Zhang F, Church G.

Nat Commun. 2016 Nov 2;7:13330. doi: 10.1038/ncomms13330. Erratum in: Nat Commun. 2017 Oct 09;8:16169.


A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data.

Cui A, Di Niro R, Vander Heiden JA, Briggs AW, Adams K, Gilbert T, O'Connor KC, Vigneault F, Shlomchik MJ, Kleinstein SH.

J Immunol. 2016 Nov 1;197(9):3566-3574. Epub 2016 Oct 5.


Genetic Evidence of Human Adaptation to a Cooked Diet.

Carmody RN, Dannemann M, Briggs AW, Nickel B, Groopman EE, Wrangham RW, Kelso J.

Genome Biol Evol. 2016 Apr 13;8(4):1091-103. doi: 10.1093/gbe/evw059.


Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing.

Tsioris K, Gupta NT, Ogunniyi AO, Zimnisky RM, Qian F, Yao Y, Wang X, Stern JN, Chari R, Briggs AW, Clouser CR, Vigneault F, Church GM, Garcia MN, Murray KO, Montgomery RR, Kleinstein SH, Love JC.

Integr Biol (Camb). 2015 Dec;7(12):1587-97. doi: 10.1039/c5ib00169b. Epub 2015 Oct 20.


Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers.

Spencer SJ, Tamminen MV, Preheim SP, Guo MT, Briggs AW, Brito IL, A Weitz D, Pitkänen LK, Vigneault F, Juhani Virta MP, Alm EJ.

ISME J. 2016 Feb;10(2):427-36. doi: 10.1038/ismej.2015.124. Epub 2015 Sep 22.


Optimization of scarless human stem cell genome editing.

Yang L, Guell M, Byrne S, Yang JL, De Los Angeles A, Mali P, Aach J, Kim-Kiselak C, Briggs AW, Rios X, Huang PY, Daley G, Church G.

Nucleic Acids Res. 2013 Oct;41(19):9049-61. doi: 10.1093/nar/gkt555. Epub 2013 Jul 31.


A high-coverage genome sequence from an archaic Denisovan individual.

Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S.

Science. 2012 Oct 12;338(6104):222-6. doi: 10.1126/science.1224344. Epub 2012 Aug 30.


Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers.

Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM.

Nucleic Acids Res. 2012 Aug;40(15):e117. doi: 10.1093/nar/gks624. Epub 2012 Jun 26.


Stable gene targeting in human cells using single-strand oligonucleotides with modified bases.

Rios X, Briggs AW, Christodoulou D, Gorham JM, Seidman JG, Church GM.

PLoS One. 2012;7(5):e36697. doi: 10.1371/journal.pone.0036697. Epub 2012 May 14.


Preparation of next-generation sequencing libraries from damaged DNA.

Briggs AW, Heyn P.

Methods Mol Biol. 2012;840:143-54. doi: 10.1007/978-1-61779-516-9_18.


Rapid retrieval of DNA target sequences by primer extension capture.

Briggs AW.

Methods Mol Biol. 2011;772:145-54. doi: 10.1007/978-1-61779-228-1_8.


Genetic history of an archaic hominin group from Denisova Cave in Siberia.

Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, Pääbo S.

Nature. 2010 Dec 23;468(7327):1053-60. doi: 10.1038/nature09710.


Road blocks on paleogenomes--polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA.

Heyn P, Stenzel U, Briggs AW, Kircher M, Hofreiter M, Meyer M.

Nucleic Acids Res. 2010 Sep;38(16):e161. doi: 10.1093/nar/gkq572. Epub 2010 Jun 28.


Targeted investigation of the Neandertal genome by array-based sequence capture.

Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PL, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Albert FW, de la Rasilla M, Fortea J, Rosas A, Lachmann M, Hannon GJ, Pääbo S.

Science. 2010 May 7;328(5979):723-5. doi: 10.1126/science.1188046.


A draft sequence of the Neandertal genome.

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S.

Science. 2010 May 7;328(5979):710-722. doi: 10.1126/science.1188021.


A complete mtDNA genome of an early modern human from Kostenki, Russia.

Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N, Derevianko A, Pääbo S.

Curr Biol. 2010 Feb 9;20(3):231-6. doi: 10.1016/j.cub.2009.11.068. Epub 2009 Dec 31.


Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA.

Briggs AW, Stenzel U, Meyer M, Krause J, Kircher M, Pääbo S.

Nucleic Acids Res. 2010 Apr;38(6):e87. doi: 10.1093/nar/gkp1163. Epub 2009 Dec 22.


Primer extension capture: targeted sequence retrieval from heavily degraded DNA sources.

Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Pääbo S.

J Vis Exp. 2009 Sep 3;(31):1573. doi: 10.3791/1573.


The Neandertal genome and ancient DNA authenticity.

Green RE, Briggs AW, Krause J, Prüfer K, Burbano HA, Siebauer M, Lachmann M, Pääbo S.

EMBO J. 2009 Sep 2;28(17):2494-502. doi: 10.1038/emboj.2009.222. Epub 2009 Aug 6. Review.


Targeted retrieval and analysis of five Neandertal mtDNA genomes.

Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Schmitz R, Doronichev VB, Golovanova LV, de la Rasilla M, Fortea J, Rosas A, Pääbo S.

Science. 2009 Jul 17;325(5938):318-21. doi: 10.1126/science.1174462.


A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing.

Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PL, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano HA, Ronan M, Rothberg JM, Egholm M, Rudan P, Brajković D, Kućan Z, Gusić I, Wikström M, Laakkonen L, Kelso J, Slatkin M, Pääbo S.

Cell. 2008 Aug 8;134(3):416-26. doi: 10.1016/j.cell.2008.06.021.


Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary.

Krause J, Unger T, Noçon A, Malaspinas AS, Kolokotronis SO, Stiller M, Soibelzon L, Spriggs H, Dear PH, Briggs AW, Bray SC, O'Brien SJ, Rabeder G, Matheus P, Cooper A, Slatkin M, Pääbo S, Hofreiter M.

BMC Evol Biol. 2008 Jul 28;8:220. doi: 10.1186/1471-2148-8-220.


From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing.

Meyer M, Briggs AW, Maricic T, Höber B, Höffner B, Krause J, Weihmann A, Pääbo S, Hofreiter M.

Nucleic Acids Res. 2008 Jan;36(1):e5. Epub 2007 Dec 15.


Patterns of damage in genomic DNA sequences from a Neandertal.

Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, Prüfer K, Meyer M, Krause J, Ronan MT, Lachmann M, Pääbo S.

Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14616-21. Epub 2007 Aug 21.


Analysis of one million base pairs of Neanderthal DNA.

Green RE, Krause J, Ptak SE, Briggs AW, Ronan MT, Simons JF, Du L, Egholm M, Rothberg JM, Paunovic M, Pääbo S.

Nature. 2006 Nov 16;444(7117):330-6.


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