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Papers authored by Benner SA

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The challenges of sequencing by synthesis.

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Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, Jovanovich SB, Nelson JR, Schloss JA, Schwartz DC, and Vezenov DV

Nature biotechnology 27(11):1013-23, 2009 Nov - Who cited this? | PubMed ID: 19898456 | Fulltext

2'-deoxy-1-methylpseudocytidine, a stable analog of 2'-deoxy-5-methylisocytidine.

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Kim HJ, Leal NA, and Benner SA

Bioorganic & medicinal chemistry 17(10):3728-32, 2009 May 15 - Who cited this? | PubMed ID: 19394831 | Fulltext

Signatures of a shadow biosphere.

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Davies PC, Benner SA, Cleland CE, Lineweaver CH, McKay CP, and Wolfe-Simon F

Astrobiology 9(2):241-9, 2009 Mar - Who cited this? | PubMed ID: 19292603 | Fulltext

Design of a novel molecular beacon: modification of the stem with artificially genetic alphabet.

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Sheng P, Yang Z, Kim Y, Wu Y, Tan W, and Benner SA

Chemical communications (Cambridge, England)(41):5128-30, 2008 Nov 7 - Who cited this? | PubMed ID: 18956044 | Fulltext

The potential and challenges of nanopore sequencing.

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Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, Di Ventra M, Garaj S, Hibbs A, Huang X, Jovanovich SB, Krstic PS, Lindsay S, Ling XS, Mastrangelo CH, Meller A,

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Nature biotechnology 26(10):1146-53, 2008 Oct - Who cited this? | PubMed ID: 18846088 | Fulltext

Lessons from comparative physiology: could uric acid represent a physiologic alarm signal gone awry in western society?.

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Johnson RJ, Sautin YY, Oliver WJ, Roncal C, Mu W, Gabriela Sanchez-Lozada L, Rodriguez-Iturbe B, Nakagawa T, and Benner SA

Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology, 2008 Jul 23 - Who cited this? | PubMed ID: 18649082 | Fulltext

Incorporation of multiple sequential pseudothymidines by DNA polymerases and their impact on DNA duplex structure.

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Havemann SA, Hoshika S, Hutter D, and Benner SA

Nucleosides, nucleotides & nucleic acids 27(3):261, 2008 Mar - Who cited this? | PubMed ID: 18260010 | Fulltext

Synthetic biology for improved personalized medicine.

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Benner SA, Hoshika S, Sukeda M, Hutter D, Leal N, Yang Z, and Chen F

Nucleic acids symposium series (2004)(52):243, 2008 - Who cited this? | PubMed ID: 18776344 | Fulltext

Synthesis of pyrophosphates for in vitro selection of catalytic RNA molecules.

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Kim HJ, Kim MJ, Karalkar N, Hutter D, and Benner SA

Nucleosides, nucleotides & nucleic acids 27(1):43-56, 2008 - Who cited this? | PubMed ID: 18188769 | Fulltext

The planetary biology of ascorbate and uric acid and their relationship with the epidemic of obesity and cardiovascular disease.

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Johnson RJ, Gaucher EA, Sautin YY, Henderson GN, Angerhofer AJ, and Benner SA

Medical hypotheses 71(1):22-31, 2008 - Who cited this? | PubMed ID: 18331782 | Fulltext

Self-Avoiding molecular Recognition Systems (SAMRS).

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Hoshika S, Chen F, Leal NA, and Benner SA

Nucleic acids symposium series (2004)(52):129-30, 2008 - Who cited this? | PubMed ID: 18776287 | Fulltext

The evolution of seminal ribonuclease: pseudogene reactivation or multiple gene inactivation events?.

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Sassi SO, Braun EL, and Benner SA

Molecular biology and evolution 24(4):1012, 2007 Apr - Who cited this? | PubMed ID: 17267422 | Fulltext

Enzymatic incorporation of a third nucleobase pair.

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Yang Z, Sismour AM, Sheng P, Puskar NL, and Benner SA

Nucleic acids research 35(13):4238, 2007 - Who cited this? | PubMed ID: 17576683 | Fulltext

Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages.

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Yang Z, Sismour AM, and Benner SA

Nucleic acids research 35(9):3118, 2007 - Who cited this? | PubMed ID: 17452363 | Fulltext

Molecular paleoscience: systems biology from the past.

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Benner SA, Sassi SO, and Gaucher EA

Advances in enzymology and related areas of molecular biology 75:1-132, xi, 2007 - Who cited this? | PubMed ID: 17124866 | Fulltext

2-Hydroxymethylboronate as a reagent to detect carbohydrates: application to the analysis of the formose reaction.

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Ricardo A, Frye F, Carrigan MA, Tipton JD, Powell DH, and Benner SA

The Journal of organic chemistry 71(25):9503-5, 2006 Dec 8 - Who cited this? | PubMed ID: 17137382 | Fulltext

Application of DETECTER, an evolutionary genomic tool to analyze genetic variation, to the cystic fibrosis gene family.

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Gaucher EA, De Kee DW, and Benner SA

BMC genomics 7:44, 2006 - Who cited this? | PubMed ID: 16522197 | Fulltext

Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics.

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Li T, Chamberlin SG, Caraco MD, Liberles DA, Gaucher EA, and Benner SA

BMC evolutionary biology 6:25, 2006 - Who cited this? | PubMed ID: 16545144 | Fulltext

Integrating protein structures and precomputed genealogies in the Magnum database: examples with cellular retinoid binding proteins.

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Bradley ME and Benner SA

BMC bioinformatics 7:89, 2006 - Who cited this? | PubMed ID: 16504077 | Fulltext

Dynamic assembly of primers on nucleic acid templates.

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Leal NA, Sukeda M, and Benner SA

Nucleic acids research 34(17):4702-10, 2006 - Who cited this? | PubMed ID: 16963776 | Fulltext

A review: synthesis of aryl C-glycosides via the heck coupling reaction.

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Wellington KW and Benner SA

Nucleosides, nucleotides & nucleic acids 25(12):1309-33, 2006 - Who cited this? | PubMed ID: 17067955 | Fulltext

Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern.

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Yang Z, Hutter D, Sheng P, Sismour AM, and Benner SA

Nucleic acids research 34(21):6095-101, 2006 - Who cited this? | PubMed ID: 17074747 | Fulltext

Locked nucleic acid molecular beacons.

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Wang L, Yang CJ, Medley CD, Benner SA, and Tan W

Journal of the American Chemical Society 127(45):15664-5, 2005 Nov 16 - Who cited this? | PubMed ID: 16277483 | Fulltext

Synthetic biology.

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Sismour AM and Benner SA

Expert opinion on biological therapy 5(11):1409, 2005 Nov - Who cited this? | PubMed ID: 16255644 | Fulltext

Desorption/ionization on porous silicon mass spectrometry studies on pentose-borate complexes.

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Li Q, Ricardo A, Benner SA, Winefordner JD, and Powell DH

Analytical chemistry 77(14):4503-8, 2005 Jul 15 - Who cited this? | PubMed ID: 16013866 | Fulltext

Synthetic biology.

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Benner SA and Sismour AM

Nature reviews. Genetics 6(7):533, 2005 Jul - Who cited this? | PubMed ID: 15995697 | Fulltext

Resurrecting ancestral alcohol dehydrogenases from yeast.

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Thomson JM, Gaucher EA, Burgan MF, De Kee DW, Li T, Aris JP, and Benner SA

Nature genetics 37(6):630-5, 2005 Jun - Who cited this? | PubMed ID: 15864308 | Fulltext

Planetary systems biology.

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Benner SA and Ricardo A

Molecular cell 17(4):471, 2005 Feb 18 - Who cited this? | PubMed ID: 15721248 | Fulltext

The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system.

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Sismour AM and Benner SA

Nucleic acids research 33(17):5640, 2005 - Who cited this? | PubMed ID: 16192575 | Fulltext

Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

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Bradley ME and Benner SA

BMC evolutionary biology 5(1):22, 2005 - Who cited this? | PubMed ID: 15752422 | Fulltext

Is there a common chemical model for life in the universe?.

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Benner SA, Ricardo A, and Carrigan MA

Current opinion in chemical biology 8(6):672-89, 2004 Dec - Who cited this? | PubMed ID: 15556414 | Fulltext

Multiplexed genetic analysis using an expanded genetic alphabet.

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Johnson SC, Marshall DJ, Harms G, Miller CM, Sherrill CB, Beaty EL, Lederer SA, Roesch EB, Madsen G, Hoffman GL, Laessig RH, Kopish GJ, Baker MW, Benner SA, Farrell PM, and Prudent JR

Clinical chemistry 50(11):2019-27, 2004 Nov - Who cited this? | PubMed ID: 15319316 | Fulltext

Chemistry. Redesigning genetics.

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Benner SA

Science (New York, N.Y.) 306(5696):625, 2004 Oct 22 - Who cited this? | PubMed ID: 15499002 | Fulltext

Understanding nucleic acids using synthetic chemistry.

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Benner SA

Accounts of chemical research 37(10):784, 2004 Oct - Who cited this? | PubMed ID: 15491125 | Fulltext

Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selection.

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Carrigan MA, Ricardo A, Ang DN, and Benner SA

Biochemistry 43(36):11446-59, 2004 Sep 14 - Who cited this? | PubMed ID: 15350131 | Fulltext

Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments.

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Chang MS and Benner SA

Journal of molecular biology 341(2):617-31, 2004 Aug 6 - Who cited this? | PubMed ID: 15276848 | Fulltext

Artificial genetic systems: exploiting the "aromaticity" formalism to improve the tautomeric ratio for isoguanosine derivatives.

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Martinot TA and Benner SA

The Journal of organic chemistry 69(11):3972-5, 2004 May 28 - Who cited this? | PubMed ID: 15153036 | Fulltext

2'-deoxycytidines carrying amino and thiol functionality: synthesis and incorporation by Vent (exo-) polymerase.

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Roychowdhury A, Illangkoon H, Hendrickson CL, and Benner SA

Organic letters 6(4):489-92, 2004 Feb 19 - Who cited this? | PubMed ID: 14961605 | Fulltext

Borate minerals stabilize ribose.

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Ricardo A, Carrigan MA, Olcott AN, and Benner SA

Science (New York, N.Y.) 303(5655):196, 2004 Jan 9 - Who cited this? | PubMed ID: 14716004 | Fulltext

Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2'-deoxyadenosine.

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Hendrickson CL, Devine KG, and Benner SA

Nucleic acids research 32(7):2241, 2004 - Who cited this? | PubMed ID: 15107492 | Fulltext

PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1.

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Sismour AM, Lutz S, Park JH, Lutz MJ, Boyer PL, Hughes SH, and Benner SA

Nucleic acids research 32(2):728, 2004 - Who cited this? | PubMed ID: 14757837 | Fulltext

The planetary biology of cytochrome P450 aromatases.

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Gaucher EA, Graddy LG, Li T, Simmen RC, Simmen FA, Schreiber DR, Liberles DA, Janis CM, and Benner SA

BMC biology 2:19, 2004 - Who cited this? | PubMed ID: 15315709 | Fulltext

Expanding the genetic alphabet: non-epimerizing nucleoside with the pyDDA hydrogen-bonding pattern.

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Hutter D and Benner SA

The Journal of organic chemistry 68(25):9839-42, 2003 Dec 12 - Who cited this? | PubMed ID: 14656120 | Fulltext

Nucleobase pairing in expanded Watson-Crick-like genetic information systems.

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Geyer CR, Battersby TR, and Benner SA

Structure (London, England : 1993) 11(12):1485-98, 2003 Dec - Who cited this? | PubMed ID: 14656433 | Fulltext

Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins.

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Gaucher EA, Thomson JM, Burgan MF, and Benner SA

Nature 425(6955):285-8, 2003 Sep 18 - Who cited this? | PubMed ID: 13679914 | Fulltext

C-5 modified nucleosides: direct insertion of alkynyl-thio functionality in pyrimidines.

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Held HA, Roychowdhury A, and Benner SA

Nucleosides, nucleotides & nucleic acids 22(4):391-404, 2003 Apr - Who cited this? | PubMed ID: 12885121 | Fulltext

Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein.

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Gaucher EA, Miyamoto MM, and Benner SA

Genetics 163(4):1549-53, 2003 Apr - Who cited this? | PubMed ID: 12702697 | Fulltext

Synthetic biology: Act natural.

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Benner SA

Nature 421(6919):118, 2003 Jan 9 - Who cited this? | PubMed ID: 12520282 | Fulltext

Synthetic biology with artificially expanded genetic information systems. From personalized medicine to extraterrestrial life.

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Benner SA, Hutter D, and Sismour AM

Nucleic acids research. Supplement (2001)(3):125, 2003 - Who cited this? | PubMed ID: 14510412 | Fulltext

Interpretive proteomics--finding biological meaning in genome and proteome databases.

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Benner SA

Advances in enzyme regulation 43:271-359, 2003 - Who cited this? | PubMed ID: 12791396 | Fulltext

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