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Steven Benner

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

Research Profile (preview)

Phenomena

Concepts & Ideas

Chemicals & Drugs

Genes & Molecular Sequences

Procedures

Sequence Alignment

Occupations

Computational Biology

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Co-Publications
Name
13
Gaucher, Eric
8
Sismour, Michael
7
Hutter, Daniel
6
Liberles, David
6
Ricardo, Alonso
4
Schreiber, David
4
Lutz, Michael
4
Miyamoto, Michael
4
Carrigan, Matthew
4
Chamberlin, Stephen
4
Yang, Zunyi
3
Thomson, Michael
3
Haugg, M
3
Knecht, L
3
Li, Tang

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Publications

TOP 3
Johnson Richard J; Sautin Yuri Y; Oliver William J; Roncal Carlos; Mu Wei; Gabriela Sanchez-Lozada L; Rodriguez-Iturbe Bernardo; Nakagawa Takahiko; Benner Steven A
Lessons from comparative physiology: could uric acid represent a physiologic alarm signal gone awry in western society?
Sheng Pinpin; Yang Zunyi; Kim Youngmi; Wu Yanrong; Tan Weihong; Benner Steven A
Design of a novel molecular beacon: modification of the stem with artificially genetic alphabet.
Havemann Stephanie A; Hoshika Shuichi; Hutter Daniel; Benner Steven A
Incorporation of multiple sequential pseudothymidines by DNA polymerases and their impact on DNA duplex structure.

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All Publications

2009: Johnson Richard J; Sautin Yuri Y; Oliver William J; Roncal Carlos; Mu Wei; Gabriela Sanchez-Lozada L; Rodriguez-Iturbe Bernardo; Nakagawa Takahiko; Benner Steven A
Lessons from comparative physiology: could uric acid represent a physiologic alarm signal gone awry in western society?
Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology 2009;179(1):67-76.
2008: Sheng Pinpin; Yang Zunyi; Kim Youngmi; Wu Yanrong; Tan Weihong; Benner Steven A
Design of a novel molecular beacon: modification of the stem with artificially genetic alphabet.
Chemical communications (Cambridge, England) 2008;(41):5128-30.
2008: Havemann Stephanie A; Hoshika Shuichi; Hutter Daniel; Benner Steven A
Incorporation of multiple sequential pseudothymidines by DNA polymerases and their impact on DNA duplex structure.
Nucleosides, nucleotides & nucleic acids 2008;27(3):261-78.
2008: Kim Hyo-joong; Kim Myong Jung; Karalkar Nilesh; Hutter Daniel; Benner Steven A
Synthesis of pyrophosphates for in vitro selection of catalytic RNA molecules.
Nucleosides, nucleotides & nucleic acids 2008;27(1):43-56.
2008: Benner Steven A; Hoshika Shuichi; Sukeda Makoto; Hutter Daniel; Leal Nicole; Yang Zunyi; Chen Fei
Synthetic biology for improved personalized medicine.
Nucleic acids symposium series (2004) 2008;(52):243-4.
2008: Hoshika Shuichi; Chen Fei; Leal Nicole A; Benner Steven A
Self-Avoiding Molecular Recognition Systems (SAMRS).
Nucleic acids symposium series (2004) 2008;(52):129-30.
2008: Johnson Richard J; Gaucher Eric A; Sautin Yuri Y; Henderson George N; Angerhofer Alex J; Benner Steven A
The planetary biology of ascorbate and uric acid and their relationship with the epidemic of obesity and cardiovascular disease.
Medical hypotheses 2008;71(1):22-31.
2007: Sassi Slim O; Braun Edward L; Benner Steven A
The evolution of seminal ribonuclease: pseudogene reactivation or multiple gene inactivation events?
Molecular biology and evolution 2007;24(4):1012-24.
2007: Yang Zunyi; Sismour A Michael; Sheng Pinpin; Puskar Nyssa L; Benner Steven A
Enzymatic incorporation of a third nucleobase pair.
Nucleic acids research 2007;35(13):4238-49.
2007: Yang Zunyi; Sismour A Michael; Benner Steven A
Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages.
Nucleic acids research 2007;35(9):3118-27.
2007: Benner Steven A; Sassi Slim O; Gaucher Eric A
Molecular paleoscience: systems biology from the past.
Advances in enzymology and related areas of molecular biology 2007;75():1-132, xi.
2006: Ricardo Alonso; Frye Fabianne; Carrigan Matthew A; Tipton Jeremiah D; Powell David H; Benner Steven A
2-Hydroxymethylboronate as a reagent to detect carbohydrates: application to the analysis of the formose reaction.
The Journal of organic chemistry 2006;71(25):9503-5.
2006: Yang Zunyi; Hutter Daniel; Sheng Pinpin; Sismour A Michael; Benner Steven A
Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern.
Nucleic acids research 2006;34(21):6095-101.
2006: Wellington Kevin W; Benner Steven A
A review: synthesis of aryl C-glycosides via the heck coupling reaction.
Nucleosides, nucleotides & nucleic acids 2006;25(12):1309-33.
2006: Li Tang; Chamberlin Stephen G; Caraco M Daniel; Liberles David A; Gaucher Eric A; Benner Steven A
Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics.
BMC evolutionary biology 2006;6():25.
2006: Gaucher Eric A; De Kee Danny W; Benner Steven A
Application of DETECTER, an evolutionary genomic tool to analyze genetic variation, to the cystic fibrosis gene family.
BMC genomics 2006;7():44.
2006: Bradley Michael E; Benner Steven A
Integrating protein structures and precomputed genealogies in the Magnum database: examples with cellular retinoid binding proteins.
BMC bioinformatics 2006;7():89.
2005: Sismour A Michael; Benner Steven A
Synthetic biology.
Expert opinion on biological therapy 2005;5(11):1409-14.
2005: Li Qian; Ricardo Alonso; Benner Steve A; Winefordner James D; Powell David H
Desorption/ionization on porous silicon mass spectrometry studies on pentose-borate complexes.
Analytical chemistry 2005;77(14):4503-8.
2005: Benner Steven A; Sismour A Michael
Synthetic biology.
Nature reviews. Genetics 2005;6(7):533-43.
2005: Thomson J Michael; Gaucher Eric A; Burgan Michelle F; De Kee Danny W; Li Tang; Aris John P; Benner Steven A
Resurrecting ancestral alcohol dehydrogenases from yeast.
Nature genetics 2005;37(6):630-5.
2005: Benner Steven A; Ricardo Alonso
Planetary systems biology.
Molecular cell 2005;17(4):471-2.
2005: Sismour A Michael; Benner Steven A
The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system.
Nucleic acids research 2005;33(17):5640-6.
2005: Bradley Michael E; Benner Steven A
Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.
BMC evolutionary biology 2005;5(1):22.
2004: Benner Steven A; Ricardo Alonso; Carrigan Matthew A
Is there a common chemical model for life in the universe?
Current opinion in chemical biology 2004;8(6):672-89.
2004: Benner Steven A
Chemistry. Redesigning genetics.
Science (New York, N.Y.) 2004;306(5696):625-6.
2004: Benner Steven A
Understanding nucleic acids using synthetic chemistry.
Accounts of chemical research 2004;37(10):784-97.
2004: Carrigan Matthew A; Ricardo Alonso; Ang Darwin N; Benner Steven A
Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selection.
Biochemistry 2004;43(36):11446-59.
2004: Chang Mike S S; Benner Steven A
Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments.
Journal of molecular biology 2004;341(2):617-31.
2004: Martinot Theodore A; Benner Steven A
Artificial genetic systems: exploiting the "aromaticity" formalism to improve the tautomeric ratio for isoguanosine derivatives.
The Journal of organic chemistry 2004;69(11):3972-5.
2004: Roychowdhury Abhijit; Illangkoon Heshan; Hendrickson Cynthia L; Benner Steven A
2'-deoxycytidines carrying amino and thiol functionality: synthesis and incorporation by Vent (exo-) polymerase.
Organic letters 2004;6(4):489-92.
2004: Ricardo A; Carrigan M A; Olcott A N; Benner S A
Borate minerals stabilize ribose.
Science (New York, N.Y.) 2004;303(5655):196.
2004: Gaucher Eric A; Graddy Logan G; Li Tang; Simmen Rosalia C M; Simmen Frank A; Schreiber David R; Liberles David A; Janis Christine M; Benner Steven A
The planetary biology of cytochrome P450 aromatases.
BMC biology 2004;2():19.
2004: Hendrickson Cynthia L; Devine Kevin G; Benner Steven A
Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2'-deoxyadenosine.
Nucleic acids research 2004;32(7):2241-50.
2004: Sismour A Michael; Lutz Stefan; Park Jeong-Ho; Lutz Michael J; Boyer Paul L; Hughes Stephen H; Benner Steven A
PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1.
Nucleic acids research 2004;32(2):728-35.
2003: Geyer C Ronald; Battersby Thomas R; Benner Steven A
Nucleobase pairing in expanded Watson-Crick-like genetic information systems.
Structure (London, England : 1993) 2003;11(12):1485-98.
2003: Hutter Daniel; Benner Steven A
Expanding the genetic alphabet: non-epimerizing nucleoside with the pyDDA hydrogen-bonding pattern.
The Journal of organic chemistry 2003;68(25):9839-42.
2003: Gaucher Eric A; Thomson J Michael; Burgan Michelle F; Benner Steven A
Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins.
Nature 2003;425(6955):285-8.
2003: Held Heike A; Roychowdhury Abhijit; Benner Steven A
C-5 modified nucleosides: direct insertion of alkynyl-thio functionality in pyrimidines.
Nucleosides, nucleotides & nucleic acids 2003;22(4):391-404.
2003: Gaucher Eric A; Miyamoto Michael M; Benner Steven A
Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein.
Genetics 2003;163(4):1549-53.
2003: Benner Steven A
Synthetic biology: Act natural.
Nature 2003;421(6919):118.
2003: Benner Steven A; Hutter Daniel; Sismour A Michael
Synthetic biology with artificially expanded genetic information systems. From personalized medicine to extraterrestrial life.
Nucleic acids research. Supplement (2001) 2003;(3):125-6.
2003: Benner Steven A
Interpretive proteomics--finding biological meaning in genome and proteome databases.
Advances in enzyme regulation 2003;43():271-359.
2002: Wigger Maria; Eyler John R; Benner Steven A; Li Weiqun; Marshall Alan G
Fourier transform-ion cyclotron resonance mass spectrometric resolution, identification, and screening of non-covalent complexes of Hck Src homology 2 domain receptor and ligands from a 324-member peptide combinatorial library.
Journal of the American Society for Mass Spectrometry 2002;13(10):1162-9.
2002: Held Heike A; Benner Steven A
Challenging artificial genetic systems: thymidine analogs with 5-position sulfur functionality.
Nucleic acids research 2002;30(17):3857-69.
2002: Gaucher Eric A; Gu Xun; Miyamoto Michael M; Benner Steven A
Predicting functional divergence in protein evolution by site-specific rate shifts.
Trends in biochemical sciences 2002;27(6):315-21.
2002: Huang Zhen; Benner Steven A
Oligodeoxyribonucleotide analogues with bridging dimethylene sulfide, sulfoxide, and sulfone groups. Toward a second-generation model of nucleic acid structure.
The Journal of organic chemistry 2002;67(12):3996-4013.
2002: Benner Steven A; Caraco M Daniel; Thomson J Michael; Gaucher Eric A
Planetary biology--paleontological, geological, and molecular histories of life.
Science (New York, N.Y.) 2002;296(5569):864-8.
2002: Benner Steven A
The past as the key to the present: resurrection of ancient proteins from eosinophils.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(8):4760-1.
2002: Gaucher Eric A; Das Ujjwal K; Miyamoto Michael M; Benner Steven A
The crystal structure of eEF1A refines the functional predictions of an evolutionary analysis of rate changes among elongation factors.
Molecular biology and evolution 2002;19(4):569-73.
2002: Benner Steven A; Hutter Daniel
Phosphates, DNA, and the search for nonterrean life: a second generation model for genetic molecules.
Bioorganic chemistry 2002;30(1):62-80.
2001: Rao P; Benner S A
Fluorescent charge-neutral analogue of xanthosine: synthesis of a 2'-deoxyribonucleoside bearing a 5-aza-7-deazaxanthine base.
The Journal of organic chemistry 2001;66(15):5012-5.
2001: Benner S A; Gaucher E A
Evolution, language and analogy in functional genomics.
Trends in genetics : TIG 2001;17(7):414-8.
2001: Gaucher E A; Miyamoto M M; Benner S A
Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(2):548-52.
2001: Benner S A
Natural progression.
Nature 2001;409(6819):459.
2001: Liberles D A; Schreiber D R; Govindarajan S; Chamberlin S G; Benner S A
The adaptive evolution database (TAED).
Genome biology 2001;2(8):RESEARCH0028.
2001: Liberles D A; Schreiber D R; Govindarajan S; Chamberlin S G; Benner S A
The Adaptive Evolution Database (TAED).
Genome biology 2001;2(4):PREPRINT0003.
2000: Peltier M R; Raley L C; Liberles D A; Benner S A; Hansen P J
Evolutionary history of the uterine serpins.
The Journal of experimental zoology 2000;288(2):165-74.
2000: Benner S A; Chamberlin S G; Liberles D A; Govindarajan S; Knecht L
Functional inferences from reconstructed evolutionary biology involving rectified databases--an evolutionarily grounded approach to functional genomics.
Research in microbiology 2000;151(2):97-106.
2000: Benner S A; Devine K G; Matveeva L N; Powell D H
The missing organic molecules on Mars.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(6):2425-30.
1999: Lutz S; Burgstaller P; Benner S A
An in vitro screening technique for DNA polymerases that can incorporate modified nucleotides. Pseudo-thymidine as a substrate for thermostable polymerases.
Nucleic acids research 1999;27(13):2792-8.
1999: Soucek J; Raines R T; Haugg M; Raillard-Yoon S A; Benner S A
Structural changes to ribonuclease A and their effects on biological activity.
Comparative biochemistry and physiology. Part C, Pharmacology, toxicology & endocrinology 1999;123(2):103-11.
1999: Lutz M J; Will D W; Breipohl G; Benner S A; Uhlmann E
Synthesis of a monocharged peptide nucleic acid (PNA) analog and its recognition as substrate by DNA polymerases.
Nucleosides & nucleotides 1999;18(3):393-401.
1999: Lutz S; Benner S A
Simple one-pot synthesis of a 2'-tritium labeled C-deoxynucleoside.
Bioorganic & medicinal chemistry letters 1999;9(5):723-6.
1999: Battersby T R; Ang D N; Burgstaller P; Jurczyk S C; Bowser M T; Buchanan D D; Kennedy R T; Benner S A
Quantitative analysis of receptors for adenosine nucleotides obtained via in vitro selection from a library incorporating a cationic nucleotide analog.
Journal of the American Chemical Society 1999;121(42):9781-9.
1998: Lutz M J; Horlacher J; Benner S A
Recognition of a non-standard base pair by thermostable DNA polymerases.
Bioorganic & medicinal chemistry letters 1998;8(10):1149-52.
1998: Huang Z; Benner S A
Functionalization of nucleoside analogs: regiospecific conversion of 4"-hydroxyl groups to thioesters and deoxygenation of 3'-hydroxyl groups.
Nucleosides & nucleotides 1998;17(5):895-9.
1998: Lutz M J; Horlacher J; Benner S A
Recognition of 2'-deoxyisoguanosine triphosphate by HIV-1 reverse transcriptase and mammalian cellular DNA polymerases.
Bioorganic & medicinal chemistry letters 1998;8(5):499-504.
1998: Opitz J G; Ciglic M I; Haugg M; Trautwein-Fritz K; Raillard S A; Jermann T M; Benner S A
Origin of the catalytic activity of bovine seminal ribonuclease against double-stranded RNA.
Biochemistry 1998;37(12):4023-33.
1998: Ciglic M I; Jackson P J; Raillard S A; Haugg M; Jermann T M; Opitz J G; Trabesinger-Rüf N; Benner S A
Origin of dimeric structure in the ribonuclease superfamily.
Biochemistry 1998;37(12):4008-22.
1998: Eschgfäller B; König M; Boess F; Boelsterli U A; Benner S A
Synthesis and biodistribution of a short nonionic oligonucleotide analogue in mouse with a potential to mimic peptides.
Journal of medicinal chemistry 1998;41(3):276-83.
1998: Benner S A; Trabesinger N; Schreiber D
Post-genomic science: converting primary structure into physiological function.
Advances in enzyme regulation 1998;38():155-80.
1998: Chelvanayagam G; Knecht L; Jenny T; Benner S A; Gonnet G H
A combinatorial distance-constraint approach to predicting protein tertiary models from known secondary structure.
Folding & design 1998;3(3):149-60.
1997: Chelvanayagam G; Eggenschwiler A; Knecht L; Gonnet G H; Benner S A
An analysis of simultaneous variation in protein structures.
Protein engineering 1997;10(4):307-16.
1997: Wigger M; Nawrocki J P; Watson C H; Eyler J R; Benner S A
Assessing enzyme substrate specificity using combinatorial libraries and electrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry.
Rapid communications in mass spectrometry : RCM 1997;11(16):1749-52.

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