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About FfAME Publications

All publications that have been produced by FfAME scientists can be found on this website. PDFs for most of these publications can be obtained by simply clicking on a publication's title. To view an individual scientist's publications, use the menu on the left. Below is a list of recent and notable FfAME publications.

Notable Publications

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Adsorption of RNA on mineral surfaces and mineral precipitates
Elisa Biondi, Yoshihiro Furukawa, Jun Kawai, and Steven A. Benner
Beilstein J. Org. Chem. , Beilstein Institute (2017) 13, 393-404
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Tautomeric equilibria of iso-guanine and related purine analogs
Nilesh B. Karalkar, Kshitij Khare, Robert Molt, and Steven A. Benner
Nuc. Nuc. Nuc. acids , Taylor & Francis Group (2017) Apr 3;36(4):256-274. doi: 10.1080/15257770.2016.1268694
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Assays To Detect the Formation of Triphosphates of Unnatural Nucleotides: Application to Escherichia coli Nucleoside Diphosphate Kinase
Mariko F. Matsuura, Ryan W. Shaw, Jennifer D. Moses, Hyo-Joong Kim, Myong-Jung Kim, Myong-Sang Kim, Shuichi Hoshika, Nilesh Karalkar, and Steven A. Benner
ACS Synthetic Biology , American Chemical Society (2016) 5 (3), pp 234-240 DOI: 10.1021/acssynbio.5b00172
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Synthesis and Enzymology of 2'-Deoxy-7-deazaisoguanosine Triphosphate and Its Complement: A Second Generation Pair in an Artificially Expanded Genetic Information System
Karalkar NB, Leal NA, Kim MS, Bradley KM, Benner SA
ACS Synthetic Biology , American Chemical Society (2016) doi: 10.1021/acssynbio.5b00276
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Standard and AEGIS nicking molecular beacons detect amplicons from the Middle East respiratory syndrome coronavirus
Ozlem Yaren, Lyudmyla G. Glushakova, Kevin M. Bradley, Shuichi Hoshika,Steven A. Benner
J Virol Methods (236) , Elsevier 54-61 (2016) doi:10.1016/j.jviromet.2016.07.008
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A norovirus detection architecture based on isothermal amplification and expanded genetic systems
Ozlem Yaren, Kevin M. Bradley, Patricia Moussatche, Shuichi Hoshika, Zunyi Yang,Shu Zhu, Stephanie M. Karst, Steven A. Benner
J Virol Methods (237) , Elsevier 64-71 (2016) doi: 10.1016/j.jviromet.2016.08.012
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Polymerase Interactions with Wobble Mismatches in Synthetic Genetic Systems and Their Evolutionary Implications
Christian B. Winiger, Myong-Jung Kim, Shuichi Hoshika, Ryan W. Shaw, Jennifer D. Moses, Mariko F. Matsuura, Dietlind L. Gerloff, and Steven A. Benner
Biochemistry 55 (28) 3847-3850 (2016) DOI: 10.1021/acs.biochem.6b00533
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Laboratory evolution of artificially expanded DNA gives redesignable aptamers that target the toxic form of anthrax protective antigen
Biondi E, Lane JD, Das D, Dasgupta S, Piccirilli JA, Hoshika S, Bradley KM, Krantz BA, Benner SA
Nucl. Acids Res. (2016) Oct 3. pii: gkw890. PubMed PMID: 27701076
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Crystal structures of deprotonated nucleobases from an expanded DNA alphabet
Mariko F. Matsuura, Hyo-Joong Kim, Daisuke Takahashi, Khalil A. Abboud and Steven A. Benner
Structural Chemistry , Acta Crystallographica (2016) C72, 952-959. doi: 10.1107/S2053229616017071
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A Single Deoxynucleoside Kinase Variant from Drosophila melanogaster Synthesizes Monophosphates of Nucleosides That Are Components of an Expanded Genetic System
Mariko F. Matsuura, Christian B. Winiger, Ryan W. Shaw, Myong-Jung Kim, Myong-Sang Kim, Ashley B. Daugherty, Fei Chen, Patricia Moussatche, Jennifer D. Moses, Stefan Lutz, and Steven A. Benner
ACS Synthetic Biology , American Chemical Society (2016) DOI: 10.1021/acssynbio.6b00228
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Evolution of functional six-nucleotide DNA
Zhang, L., Yang, Z., Sefah, K., Bradley, K. M., Hoshika, S., Kim, M-J,. Kim, H-J., Zhu., Jimenez, E., Cansiz, S., Teng, I-T., Champanhac, C, McLendon, C., Liu, C., Zhang, W., Gerloff, D. L., Huang, Z., Tan, W., Benner, S. A.
J. Am. Chem. Soc. (2015) DOI: 10.1021/jacs.5b02251
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Pooled assembly of marine metagenomic datasets: enriching annotation through chimerism
Jonathan D. Magasin and Dietlind L. Gerloff
Bioinformatics (2015) 31:311-317
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Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA
Lyudmyla G. Glushakova, Nidhi Sharma, Shuichi Hoshika, Andrea C. Bradley, Kevin M. Bradley, Zunyi Yang, Steven A. Benner
Anal Biochem , Elsevier (2015) Nov 15;489:62-72. doi: 10.1016/j.ab.2015.08.015
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High-throughput multiplexed xMAP Luminex array panel for detection of twenty two medically important mosquito-borne arboviruses based on innovations in synthetic biology
Lyudmyla G. Glushakova, Andrea Bradley, Kevin M. Bradley, Barry W. Alto, Shuichi Hoshika, Daniel Hutter, Nidhi Sharma, Zunyi Yang, Myong-Jung Kim, Steven A. Benner
J Virol Methods 214 , Elsevier 60-74 (2015) doi: 10.1016/j.jviromet.2015.01.003
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Ribonucleosides for an Artificially Expanded Genetic Information System
Hyo-Joong Kim, Nicole A. Leal, Shuichi Hoshika, Steven A. Benner
J. Org. Chem. (2014) 79 (7), pp 3194-3199
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Hominids adapted to metabolize ethanol long before human-directed fermentation
Matthew A. Carrigan, Oleg Uryasev, Carole B. Frye, Blair L. Eckman, Candace R. Myers, Thomas D. Hurley, and Steven A. Benner
Proc. Natl. Acad. Sci. USA 112 (2) 458-463 (2014) doi: 10.1073/pnas.1404167111
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MaGnET: Malaria Genome Exploration Tool
Sharman JL and Gerloff DL
Bioinformatics (2013) 2350-2352
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Directed Evolution of Polymerases To Accept Nucleotides with Nonstandard Hydrogen Bond Patterns
Laos R, Shaw R, Leal NA, Gaucher E, Benner S.
Biochemistry (2013) 52, 5288-5294
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Conversion strategy using an expanded genetic alphabet to assay nucleic acids
Yang, Z., Durante, M., Glushakova, L., Sharma, N., Leal, N., Bradley, K., Chen, F., Benner, S. A.
Anal. Chem. (2013) 85(9):4705-12
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Use of codon models in molecular dating and functional analysis
Steven A. Benner
Codon Evolution , ed. Gina M Cannarozzi, Adrian Scheider , Oxford University Press 133-144 (2012)

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Synthesis and Properties of 5-Cyano-Substituted Nucleoside Analog with a Donor-Donor-Acceptor Hydrogen-Bonding Pattern
Hyo-Joong Kim, Fei Chen, and Steven A. Benner
J. Org. Chem. (2012)
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The Natural History of Class I Primate Alcohol Dehydrogenases Includes Gene Duplication, Gene Loss, and Gene Conversion
Matthew A. Carrigan, Oleg Uryasev, Ross P. Davis, LanMin Zhai, Thomas D. Hurley, Steven A. Benner
PLOS One 7 (7) , Public Library of Science (2012)

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Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity.
Chen, F; Yang, ZY; Yan, M; Alvarado, JB; Wang, G; Benner, SA
Nucl. Acids Res. 39 (9) 3949-3961 (2011)
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Synthetic Biology, Tinkering Biology, and Artificial Biology: A Perspective from Chemistry
Benner, SA; Chen, F; Yang, ZY
Chemical Synthetic Biology , ed. Pier Luigi Luisi and Cristiano Chiarabelli , Wiley 69-106 (2011)

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Setting the Stage: The History, Chemistry, and Geobiology behind RNA
Benner, SA; Kim, HJ; Yang, ZY
RNA Worlds: From Life's Origins to Diversity in Gene Regulation , ed. John F. Atkins, Raymond F. Gesteland, Thomas R. Cech , Cold Spring Harbor Laboratory Press 7-19 (2011)

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Amplification, Mutation, and Sequencing of a Six-Letter Synthetic Genetic System
Yang, Z; Chen, F; Alvarado, JB; Benner, SA
J. Am. Chem. Soc. 133 (38) 15105-15112 (2011) dx.doi.org/10.1021/ja204910n
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Labeled nucleoside triphosphates with reversibly terminating aminoalkoxyl groups
Hutter, D; Kim, MJ; Karalkar, N; Leal, NA; Chen, F; Guggenheim, E; Visalakshi, V; Olejnik, J; Gordon, S; Benner, SA
Nuc. Nuc. Nuc. acids 29 (11) , Taylor & Francis Group 879-895 (2010)
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Expanded Genetic Alphabets in the Polymerase Chain Reaction
Yang, ZY; Chen, F; Chamberlin, SG; Benner, SA
Angew. Chem. Int. Ed. 49 (1) 177-180 (2010)

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Artificial Genetic Systems: Self-Avoiding DNA in PCR and Multiplexed PCR
Hoshika, S; Chen, F; Leal, NA; Benner, SA
Angew. Chem. Int. Ed. 49 (32) 5554-5557 (2010)

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Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection
Chen, F; Gaucher, EA; Leal, NA; Hutter, D; Havemann, SA; Govindarajan, S; Ortlund, EA; Benner, SA
Proc. Natl. Acad. Sci. USA 107 (5) 1948-1953 (2010)

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Chemistry, Life, and the Search for Aliens
Benner, SA
Proc. SPIE 7819 (10) 1-12 (2010)
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Interview with Steven Benner
Impey, C; Benner, SA
Talking about Life: Conversations on Astrobiology , ed. Chris Impey , Cambridge University Press 58-68 (2010)

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Q&A: Life, synthetic biology and risk
Benner, SA
BMC Biology 8 (77) (2010) doi:10.1186/1741-7007-8-77

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2'-Deoxy-1-methylpseudocytidine, a stable analog of 2'-deoxy-5-methylisocytidine
Kim, HJ; Leal, NA; Benner, SA
Bioorg. Med. Chem. 17 (10) 3728-3732 (2009)
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A Convenient Synthesis of N,N'-dibenzyl-2,4-diaminopyrimidine-2'-deoxyribonucleoside and 1-Methyl-2'-Deoxypseudoisocytidine
Wellington, KW; Ooi, HC; Benner, SA
Nuc. Nuc. Nuc. acids 28 (4) , Taylor & Francis Group 275-291 (2009)
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Signatures of a Shadow Biosphere
Davies, PCW; Benner, SA; Cleland, CE; Lineweaver, CH; McKay, CP; Wolfe-Simon, F
Astrobiology 9 (2) 241-249 (2009)
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The challenges of sequencing by synthesis
Fuller, CW; Middendorf, LR; Benner, SA; Church, GM; Harris, T; Huang, XH; Jovanovich, SB; Nelson, JR; Schloss, JA; Schwartz, DC; Vezenov, DV
Nat. Biotechnol. 27 (11) 1013-1023 (2009)
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Design of a novel molecular beacon: modification of the stem with artificially genetic alphabet
Sheng, PP; Yang, ZY; Kim, YM; Wu, YR; Tan, WH; Benner, SA
Chem. Comm. (41) 5128-5130 (2008)
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The planetary biology of ascorbate and uric acid and their relationship with the epidemic of obesity and cardiovascular disease
Johnson, RJ; Gaucher, EA; Sautin, YY; Henderson, GN; Angerhofer, AJ; Benner, SA
Medical Hypotheses 71 (1) 22-31 (2008)
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Self-Avoiding Molecular Recognition Systems (SAMRS)
Hoshika, S; Chen, F; Leal, NA; Benner, SA
Nucleic Acids Symp. Ser. 52 (1) 129-130 (2008)

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Incorporation of Multiple Sequential Pseudothymidines by DNA Polymerases and Their Impact on DNA Duplex Structure
Havemann, SA; Hoshika, S; Hutter, D; Benner, SA
Nuc. Nuc. Nuc. acids 27 (3) , Taylor & Francis Group 261-278 (2008)
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Synthesis of pyrophosphates for in vitro selection of catalytic RNA molecules
Kim, HJ; Kim, MJ; Karalkar, N; Hutter, D; Benner, SA
Nuc. Nuc. Nuc. acids 27 , Taylor & Francis Group 43-56 (2008)

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Synthetic Biology for Improved Personalized Medicine
Benner, SA; Hoshika, S; Sukeda, M; Hutter, D; Leal, NA; Yang, ZY; Chen, F
Nucleic Acids Symp. Ser. 52 (1) 243-244 (2008) doi: 10.1093/nass/nrn123
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Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters
Danchin, EGJ; Gaucher, EA; Pontarotti, P
Ancestral Sequence Reconstruction , ed. David A. Liberles , Oxford University Press 139-150 (2007)

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Experimental resurrection of ancient biomolecules: gene synthesis, heterologous protein expression, and functional assays
Gaucher, EA
Ancestral Sequence Reconstruction , ed. David A. Liberles , Oxford University Press 153-163 (2007)

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Ancestral sequence reconstruction as a tool to understand natural history and guide synthetic biology: realizing and extending the vision of Zuckerkandl and Pauling
Gaucher, EA
Ancestral Sequence Reconstruction , ed. David A. Liberles , Oxford University Press 20-33 (2007)

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A thermophilic last universal ancestor inferred from its estimated amino acid composition
Brooks, DJ; Gaucher, EA
Ancestral Sequence Reconstruction , ed. David A. Liberles , Oxford University Press 200-207 (2007)

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The resurrection of ribonucleases from mammals: from ecology to medicine
Sassi, SO; Benner, SA
Ancestral Sequence Reconstruction , ed. David A. Liberles , Oxford University Press 208-224 (2007)

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The early days of paleogenetics: connecting molecules to the planet
Benner, SA
Ancestral Sequence Reconstruction , ed. David A. Liberles , Oxford University Press 3-19 (2007)

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Leishmania promastigotes activate PI3K/Akt signalling to confer host cell resistance to apoptosis
Ruhland, A; Leal, N; Kima, PE
Cell Microbiol. 9 (1) 84-96 (2007)
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PduL is an evolutionarily distinct phosphotransacylase involved in B-12-dependent 1,2-propanediol degradation by Salmonella enterica serovar typhimurium LT2
Liu, Y; Leal, NA; Sampson, EM; Johnson, CLV; Havemann, GD; Bobik, TA
J. Bacteriol. 189 (5) 1589-1596 (2007)
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In vivo expression of human ATP : cob(I)atamin adenosyltransferase (ATR) using recombinant adeno-associated virus (rAAV) serotypes 2 and 8
Erger, KE; Conlon, TJ; Leal, NA; Zori, R; Bobik, TA; Flotte, TR
J. Gene Med. 9 (6) 462-469 (2007)
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The evolution of seminal ribonuclease: Pseudogene reactivation or multiple gene inactivation events?
Sassi, SO; Braun, EL; Benner, SA
Mol. Biol. Evol. 24 (4) 1012-1024 (2007)
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Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages
Yang, ZY; Sismour, AM; Benner, SA
Nucl. Acids Res. 35 (9) 3118-3127 (2007)
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Enzymatic incorporation of a third nucleobase pair
Yang, ZY; Sismour, AM; Sheng, PP; Puskar, NL; Benner, SA
Nucl. Acids Res. 35 (13) 4238-4249 (2007)
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The origin of proteins and nucleic acids
Ricardo, A; Benner, SA
Planets and Life: The Emerging Science of Astrobiology , ed. Woodruff T. Sullivan and John A. Baross , Cambridge University Press 154-173 (2007)

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Alien biochemistries
Ward, PD; Benner, SA
Planets and Life: The Emerging Science of Astrobiology , ed. Woodruff T. Sullivan and John A. Baross , Cambridge University Press 537-544 (2007)

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Inferred thermophily of the Last Universal Ancestor based on estimated amino acid composition
Brooks, DJ; Gaucher, EA
Ancestral Sequence Reconstruction , ed. David A. Liberles , Oxford University Press 200-207 (2007)
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Molecular Paleoscience: Systems Biology from the Past
Benner, SA; Sassi, SO; Gaucher, EA
Adv. Enzymol. Relat. Areas Mol. Biol. 75 (2006)

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Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins
Bradley, ME; Benner, SA
BMC Bioinformatics 7 89 (2006)
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Application of DETECTER, an Evolutionary Genomic Tool to Analyze Genetic Variation, to the Cystic Fibrosis Gene Family
Gaucher, EA; DeKee, DW; Benner, SA
BMC Genomics 7 44 (2006)
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The diverse biological functions of phosphatidylinositol transfer proteins in eukaryotes
Phillips, SE; Vincent, P; Rizzieri, KE; Schaaf, G; Bankaitis, VA; Gaucher, EA
Crit. Rev. Biochem. Mol. Biol. 41 (1) 21-49 (2006)
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2-Hydroxymethylboronate as a Reagent To Detect Carbohydrates: Application to the Analysis of the Formose Reaction
Ricardo, A; Frye, F; Carrigan, MA; Tipton, JD; Powell, DH; Benner, SA
J. Org. Chem. 71 (25) 9503-9505 (2006)
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Dynamic assembly of primers on nucleic acid templates
Leal, NA; Sukeda, M; Benner, SA
Nucl. Acids Res. 34 4702-4710 (2006)
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Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern
Yang, ZY; Hutter, D; Sheng, PP; Sismour, AM; Benner, SA
Nucl. Acids Res. 34 (21) 6095-6101 (2006)
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A review: Synthesis of aryl C-glycosides via the heck coupling reaction
Wellington, KW; Benner, SA
Nuc. Nuc. Nuc. acids 25 (12) , Taylor & Francis Group 1309-1333 (2006)
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Desorption/ionization on porous silicon mass spectrometry studies on pentose-borate complexes
Li, Q; Ricardo, A; Benner, SA; Winefordner, JD; Powell, DH
Anal. Chem. 77 (14) 4503-4508 (2005)
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Synthetic biology
Sismour, AM; Benner, SA
Expert Opin. Biol. Ther. 5 (11) 1409-1414 (2005)
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A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous
Gaucher, EA; Miyamoto, MM
Mol. Phylogenet. Evol. 37 (3) 928-931 (2005)
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The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system
Sismour, AM; Benner, SA
Nucl. Acids Res. 33 5640-5646 (2005)
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Resurrecting ancestral alcohol dehydrogenases from yeast
Thomson, JM; Gaucher, EA; Burgan, MF; De Kee, DW; Li, T; Aris, JP; Benner, SA
Nature Genet. 37 (6) 630-635 (2005)
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Synthetic Biology
Sismour, AM; Benner, SA
Nat. Rev. Genet. 6 533-543 (2005)
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Cytoplasmic glycosylation of protein-hydroxyproline and its relationship to other glycosylation pathways
West, CM; van der Wel, H; Sassi, S; Gaucher, EA
Biochim. Biophys. Acta 1673 29-44 (2004)
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The planetary biology of cytochrome P450 aromatases
Gaucher, EA; Graddy, LG; Li, T; Simmen, RC; Simmen, FA; Schreiber, DR; Liberles, DA; Janis, CM; Benner, SA
BMC Biology 2 (1) 19 (2004)
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Significance of cytoplasmic prolyl hydroxylation and complex glycosylation in the cellular slime mold Dictyostelium
West, CM; van der Wel, H; Sassi, S; Gaucher, E; Ercan, A
Glycobiology 14 (11) 1063-1063 (2004)

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Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments
Chang, MSS; Benner, SA
J. Mol. Biol. 341 (2) 617-631 (2004)
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Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein
Gaucher, EA; Miyamoto, MM; Benner, SA
Genetics 163 (4) 1549-1553 (2003)
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Initiation of mucin-type O-glycosylation in lower eukaryotes (O-alpha-GlcNAc-type) and higher eukaryotes (O-alpha-GalNAc-type) is homologous
West, CM; Wang, F; van der Wel, H; Gaucher, E; Sassi, S; Metcalf, T; Heise, N; Mendonca-Previato, L; Previato, JO
Glycobiology 13 (11) 875-876 (2003)

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Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
Gaucher, EA; Thomson, JM; Burgan, MF; Benner, SA
Nature 425 (6955) 285-288 (2003)
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Complex glycosylation of Skp1 in Dictyostelium: implications for the modification of other eukaryotic cytoplasmic and nuclear proteins
West, CM; van der Wel, H; Gaucher, EA
Glycobiology 12 (2) (2002)
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Identification of a Golgi-associated UDP-GlcNAc : polypeptide mucin-type alpha-N-acetylglucosaminyltransferase that modifies cell surface proteins in Dictyostelium
West, CM; van der Wel, H; Metcalf, T; Kaplan, L; Gaucher, EA
Glycobiology 12 (10) 697-697 (2002)

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Evolution - Planetary biology - Paleontological, geological, and molecular histories of life
Benner, SA; Caraco, MD; Thomson, JM; Gaucher, EA
Science 296 (5569) 864-868 (2002)
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Predicting functional divergence in protein evolution by site-specific rate shifts
Gaucher, EA; Gu, X; Miyamoto, MM; Benner, SA
Trends Biochem. Sci. 27 (6) 315-321 (2002)
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A bifunctional diglycosyltransferase forms the Fuca1,2Galb,3-disaccharide on Skp1 in the cytoplasm of Dictyostelium
van der Wel, H; Fisher, SZ; Gaucher, EA; West, CM
Glycobiology 11 (10) 884-884 (2001)

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Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors
Gaucher, EA; Miyamoto, MM; Benner, SA
Proc. Natl. Acad. Sci. USA 98 (2) 548-552 (2001)
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Evolution, language and analogy in functional genomics
Benner, SA; Gaucher, EA
Trends in Genetics 17 (7) 414-418 (2001)
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Functional inferences from reconstructed evolutionary biology involving rectified databases. An evolutionarily-grounded approach to functional genomics.
Benner, SA; Chamberlin, SG; Liberles, DA; Govindarajan, S; Knecht, L
Res. MicroBiol. 151 (2) 97-106 (2000)
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Chance and Necessity in Biomolecular Chemistry - Is Life as We Know It Universal?
Benner, SA; Switzer, CY
Simplicity and Complexity in Proteins and Nucleic Acids , ed. H. Frauenfelder, J. Deisenhofer, P.G. Wolynes , Dahlem University Press 339-363 (1999)

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How small can a microorganism be?
Benner, SA
Size Limits of Very Small Microorganisms: Proceedings of a Workshop, Steering Group on Astrobiology of the Space Studies Board , National Research Council 126-135 (1999)

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