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Publications

"A split transcriptional repressor that links protein solubility to an orthogonal genetic circuit," Y. Zheng, A.M. Jones, B. Nassif, E.E. Thomas, J.J. Silberg, and L. Segatori, ACS Synthetic Biology, 2018, 7 (9), 2126-2138

"Circular permutation profiling by deep sequencing libraries created using transposon mutagenesis,” J.A. Atkinson, A.J. Jones, Q. Zhou, and J.J. Silberg, Nucleic Acids Research, 2018, 46(13), e76   

"Ratiometric gas reporting:  a non-disruptive approach to monitor gene expression in soils,” H.Y. Cheng, I. Del Valle, X. Gao, C.A. Masiello, G.N. Bennett, and J.J. Silberg, ACS Synthetic Biology, 2018, 7 (3), pp 903–911 

"Programming post-translational control over the metabolic labeling of cellular proteins with a non-canonical amino acid,” E.E. Thomas, N. Pandey, S.E. Knudsen, Z.T. Ball and J.J. Silberg, ACS Synthetic Biology, 2017, 6(8), pp 1572-1582

"PERMutation Using Transposase Engineering (PERMUTE):  a simple approach for constructing circularly permuted protein libraries,” A.M. Jones, J.T. Atkinson, and J. J. Silberg, Methods Molecular Biology, 2017, 1498, pp 295-308

Cellular assays for ferredoxins: a strategy to understand electron flow through protein carriers that link metabolic pathways,” J.T. Atkinson, I. Campbell, G.N. Bennett, and J. J. Silberg, Biochemistry, 2016, 55(51): pp 7047-7064 

Charcoal disrupts soil microbial communication through a combination of sorption and hydrolysis,” X. Gao, H.Y. Cheng, I Del Valle, S. Liu, C.A. Masiello, and J. J. Silberg, ACS Omega, 2016, 1(2), pp 226-233

Volatile gas production by methyl halide transferase:  an in situ reporter of microbial gene expression in soil,” H.S. Cheng, C.A. Masiello, G.N. Bennett, and J.J. Silberg, Environmental Science & Technology, 2016, 50(16), pp 8750-8759  

Tolerance of a knotted near infrared fluorescent protein to random circular permutation,” N. Pandey, B. Kuypers, B. Nassif, E. E. Thomas, R. N. Alnahhas, L. Segatori, and J. J. Silberg,  Biochemistry, 2016, 55(27), pp 3763-3773

The structure of a thermophilic kinase shapes fitness upon random circular permutation,” A.M. Jones, M.M. Mehta, E.E. Thomas, J.T. Atkinson, T.H. Segall-Shapiro, S. Liu, and J. J. Silberg, ACS Synthetic Biology, 20165(5), pp 415-425

"Combining random gene fission and rational gene fusion to discover near-infrared fluorescent protein fragments that report on protein-protein interactions," N. Pandey, C.L. Nobles, L. Zechiedrich, A.W. Maresso, and J.J. Silberg, ACS Synthetic Biology, 2015, 4(5), pp 615-624

Tunable protease-activatable virus nanonodes,"  J. Judd, M.L. Ho, A. Tiwari, E.J. Gomez, C. Dempsey, K. Van Vliet, O. Igoshin, J.J. Silberg, M. Agbandje-McKenna, and J. Suh, ACS Nano, 2014, 8(5), pp 4740-4746

"Sensitive detection of proteasomal activation using the Deg-On mammalian synthetic gene circuit," W. Zhao, M. Bonem, C. White, J.J. Silberg, and L. Segatori, Nature Communications, 2014, 5, pp 3612

SCHEMA computational design of virus capsid chimeras: calibrating how DNA packaging, protection, and transduction correlate with calculated disruption,” M.L. Ho, B. Adler, M. Torre, J.J. Silberg, and J. Suh. ACS Synthetic Biology, 2013, 2(12), 724-733

Biochar and microbial signaling:  production conditions determine effects on microbial communication,” C.A. Masiello, C. Ye, X. Gao, S. Liu, H.Y. Cheng, M.R. Bennett, J.A. Rudgers, D.S. Wagner, K. Zygourakis, and J.J. Silberg, Environmental Science & Technology, 2013, 47(20), pp 11496-11503 

A genetically encoded and gate for cell-targeted metabolic labeling of proteins,” A. Mahdavi, T.H. Segall-Shapiro, S. Kou, G.A. Jindal, K.G. Hoff, S. Liu, M. Chitsaz, R.F. Ismagilov, J.J. SIlberg, and D.A. Tirrell, Journal of the American Chemical Society 2013, 135, pp 2979-2982  

Nitrogen, Biochar, and Mycorrhizae: Alteration of the Symbiosis and Oxidation of the Char Surface,” C. LeCroy, C.A. Masiello, J.A. Rudgers, W.C. Hockaday, and J.J. Silberg, Soil Biology & Biochemistry 2013, 58, pp 248-254

Random insertion of mCherry into the VP3 domain of adeno-associated virus (AAV) yields fluorescent capsids with no loss of infectivity,” J. Judd, F. Wei, P.Q. Nguyen, L.J. Tartaglia, M. Agbandje-McKenna, J.J. Silberg, and J. Suh, Molecular Therapy – Nucleic Acids, 2012, 1, pp e1

"A transposase strategy for creating libraries of circularly permuted proteins," M. M. Mehta, S. Liu, and J. J. Silberg, Nucleic Acids Research, 2012, 40(9), pp e71

"The DNLZ/HEP zinc-binding subdomain supports the solubility of the mitochondrial chaperone HSPA9," M. Vu, P. Zhai, J. Lee, C. Guerra, S. Liu, M. C. Gustin, and J. J. Silberg, Protein Science 2012, 21(2), pp 258-267

"Selective cell-surface labeling of the molecular motor prestin," R. M. McGuire, J. J. Silberg, F. R. Pereira, and R. M. Raphael, Biochemical and Biophysical Research Communications. 2011, 410(1), pp 134-139

A conserved histidine in human DNLZ/HEP is required for stimulation of HSPA9 ATPase activity," P. Zhai, M. Vu, K. G. Hoff, and J. J. Silberg, Biochemical and Biophysical Research Communications. 2011, 408(4), pp 589-594

"Mesophilic and thermophilic adenylate kinases differ in their tolerance to random fragmentation," T. H. Segall-Shapiro, P. Q. Nguyen, E. Dos Santos, S. Subedi, J. Judd, J. Suh, and J. J. Silberg, Journal of Molecular Biology, 2011, 406(1), pp 135-148

"A selection that reports on protein–protein interactions within a thermophilic bacterium," P.Q. Nguyen and J. J. Silberg, Protein Engineering Design & Selection, 2010, 23(7), pp 529-536

"Computational methods for directed protein evolution," J. J. Silberg and P. Q. Nguyen, Methods in Molecular Biology, Topics in Computational Biology, D. Fenyo, Ed., 2010, 673, pp 175-188

"In vivo fluorescent detection of Fe-S clusters coordinated by human GRX2," K. G. Hoff, S. J. Culler, P.Q. Nguyen, R. McGuire, J. J. Silberg, C. D. Smolke, Chemistry & Biology 2009, 16(12), pp 1299-1308

"Fluorescent detection of a protein-bound 2Fe2S cluster," K. G. Hoff, R. Liu, Goodlitt, R., Smolke, C. D., and J. J. Silberg, ChemBioChem 2009, 10(4), pp 667-670

"Models predicting optimized strategies for protein evolution," J. J. Silberg and P. Q. Nguyen, The Metabolic Pathway Engineering Handbook, C. D. Smolke, Ed., 2, (2009) Chapter 5

"The human hsp70 escort protein Hep binds to the ATPase domain of mitochondrial Hsp70 and regulates nucleotide hydrolysis," P. Zhai, C. Stanworth, S. Liu, and J. J. Silberg, Journal of Biological Chemistry, 2008, 283, pp 26098-26106

"Thermostability promotes the cooperative function of split adenylate kinases," P. Q. Nguyen, J. Thompson, S. Liu, and J. J. Silberg, Protein Engineering Design & Selection, 2008, 21(5), 303-310

"On the conservative nature of intragenic recombination," D. A. Drummond, J. J. Silberg, C. O. Wilke, M. M. Meyer, and F. H. Arnold, Proc. Nat'l. Acad. Sci. U.S.A. 2005, 102(15), pp 5380-5385

"Thermodynamic prediction of protein neutrality," J. D. Bloom, J. J. Silberg, C. Wilke, D. A. Drummond, C. Adami, and F. H. Arnold, Proc. Nat'l. Acad. Sci. U.S.A. 2005, 102(3), pp 606-611 (2005)

"Site-directed protein recombination as a shortest-path problem," J. B. Endelman, J. J. Silberg, Z. G. Wang, and F. H. Arnold, Protein Engineering Design & Selection, 2004, 17(7), pp 589-594

"Functional evolution and structural conservation in chimeric cytochromes P450: calibrating a structure-guided approach," C. Otey, J. J. Silberg, J. B. Endelman, G. Bandara, C. A. Voigt, and F. H. Arnold, Chemistry & Biology, 2004, 11(3), pp 309-318

"Regulation of the HscA ATPase reaction cycle by the J-type cochaperone HscB and the iron-sulfur escort protein IscU," J. J. Silberg, T. L. Tapley, K. G. Hoff, and L. E. Vickery, Journal of Biological Chemistry, 2004, 279, pp 53924-53931

"Crystal structure of IscA, an iron-sulfur cluster assembly protein from Escherichia coli," J. R. Cupp-Vickery, J. J. Silberg, D. T. Ta, and L. E. Vickery, Journal of Molecular Biology, 2004, 338(1), pp 127-137

"SCHEMA-guided protein recombination," J. J. Silberg, J. B. Endelmen, and F. H. Arnold, Methods Enzymology, D. Robertson and J.P. Noel, Eds., 2004, 388, pp 35-42

"Library analysis of SCHEMA-guided recombination," M. M. Meyer, J. J. Silberg, C. A. Voigt, J. B. Endelman, S. L. Mayo, Z. G. Wang, and F. H. Arnold, Protein Science, 2003, 12(8), pp 1686-1693

"Sequence homology-independent protein recombination, SHIPREC," A.K. Udit, J. J. Silberg, and V. Sieber, Methods in Molecular Biology, F. H. Arnold and G. Georgiou, Eds., 2003, 231, pp 153-164

"Analysis of shuffled libraries by oligonucleotide probe hybridization," P. Meinhold, J. Joern, and J.J. Silberg, Methods in Molecular Biology, F. H. Arnold and G. Georgiou, Eds., 2003, 231, pp 177-188

"Hsc66 substrate specificity is directed towards a discrete region of the Fe/S template protein IscU," K. G. Hoff, D. T. Ta, T. L. Tapley, J. J. Silberg, and L. E. Vickery, Journal of Biological Chemistry, 2002, 277, pp 27353-27359

"Transfer of sulfur from IscS to IscU during Fe/S cluster assembly," H. D. Urbina, J. J. Silberg, K. G. Hoff, and L. E. Vickery, Journal of Biological Chemistry, 2001, 276, pp 44521-44526

"The Fe/S-escort protein IscU behaves as a substrate for the molecular chaperone Hsc66 from Escherichia coli," J. J. Silberg, K. G. Hoff, T. L. Tapley, and L. E. Vickery, Journal of Biological Chemistry, 2001, 276, pp 1696-1700

"Kinetic characterization of the ATPase cycle of the molecular chaperone Hsc66 from Escherichia coli," J. J. Silberg and L. E. Vickery, Journal of Biological Chemistry, 2000, 275, pp 7779-7786

"Interaction of the iron-sulfur cluster assembly protein IscU with the Hsc66/Hsc20 molecular chaperone system in Escherichia coli," K. G. Hoff, J. J. Silberg, and L. E. Vickery, Proc. Nat'l. Acad. Sci. U.S.A., 2000, 97, pp 7790-7795

"The Hsc66-Hsc20 Chaperone System in Escherichia coli: Chaperone Activity and Interactions with the DnaK-DnaJ-GrpE System," J. J. Silberg, K. G. Hoff, and L. E. Vickery, Journal of Bacteriology, 1998, 180, pp 6617-6624

"Hsc66 and Hsc20, a new heat shock cognate molecular chaperone system from Escherichia coli," L. E. Vickery, J. J. Silberg, and D. T. Ta, Protein Science, 1997, 6, pp 1047-1056

"Effect of thiocyanate on AMPA receptor mediated responses in excised patches and hippocampal slices," A. Arai, J. Silberg, M. Kessler, and G. Lynch, Neuroscience 1995, 66, pp 815-827

"Differences in the refractory properties of two distinct inhibitory circuitries in field CA1 of the hippocampus," A. Arai, J. Silberg, and G. Lynch, Brain Research, 1995, 704, pp 298-306

Rice University, Biosciences Department, 6100 Main Street MS-140, Houston TX, 77005-1892