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Jonathan J. (Joff) Silberg, Ph.D. - Publications

Affiliations: 
BioSciences Rice University, Houston, TX 
 1995-2000 University of California, Irvine, Irvine, CA 
Area:
Molecular Biology, Biochemistry
Website:
http://biosciences.rice.edu/facultydetail.aspx?riceid=22153
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52/71 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Kalvapalle PB, Sridhar S, Silberg JJ, Stadler LB. Long-duration environmental biosensing by recording analyte detection in DNA using recombinase memory. Applied and Environmental Microbiology. e0236323. PMID 38551351 DOI: 10.1128/aem.02363-23  0.63
2024 Coleman T, Shin J, Silberg JJ, Shamoo Y, Atkinson JT. The Biochemical Impact of Extracting an Embedded Adenylate Kinase Domain Using Circular Permutation. Biochemistry. PMID 38357768 DOI: 10.1021/acs.biochem.3c00605  0.727
2023 McGuinness KN, Fehon N, Feehan R, Miller M, Mutter AC, Rybak LA, Nam J, AbuSalim JE, Atkinson JT, Heidari H, Losada N, Kim JD, Koder RL, Lu Y, Silberg JJ, et al. The energetics and evolution of oxidoreductases in deep time. Proteins. PMID 37596815 DOI: 10.1002/prot.26563  0.738
2023 Truong A, Myerscough D, Campbell I, Atkinson J, Silberg JJ. A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase. Protein Science : a Publication of the Protein Society. e4746. PMID 37551563 DOI: 10.1002/pro.4746  0.72
2022 Atkinson JT, Su L, Zhang X, Bennett GN, Silberg JJ, Ajo-Franklin CM. Real-time bioelectronic sensing of environmental contaminants. Nature. PMID 36323787 DOI: 10.1038/s41586-022-05356-y  0.704
2022 Campbell IJ, Atkinson JT, Carpenter MD, Myerscough D, Su L, Ajo-Franklin CM, Silberg JJ. Determinants of Multiheme Cytochrome Extracellular Electron Transfer Uncovered by Systematic Peptide Insertion. Biochemistry. PMID 35687533 DOI: 10.1021/acs.biochem.2c00148  0.745
2022 Tseng CP, Liu F, Zhang X, Huang PC, Campbell I, Li Y, Atkinson JT, Terlier T, Ajo-Franklin CM, Silberg JJ, Verduzco R. Solution-Deposited and Patternable Conductive Polymer Thin Film Electrodes for Microbial Bioelectronics. Advanced Materials (Deerfield Beach, Fla.). e2109442. PMID 35088918 DOI: 10.1002/adma.202109442  0.673
2020 Del Valle I, Fulk EM, Kalvapalle P, Silberg JJ, Masiello CA, Stadler LB. Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences. Frontiers in Microbiology. 11: 618373. PMID 33633695 DOI: 10.3389/fmicb.2020.618373  0.618
2020 Campbell IJ, Kahanda D, Atkinson JT, Sparks ON, Kim J, Tseng CP, Verduzco R, Bennett GN, Silberg JJ. Recombination of 2Fe-2S Ferredoxins Reveals Differences in the Inheritance of Thermostability and Midpoint Potential. Acs Synthetic Biology. PMID 33226772 DOI: 10.1021/acssynbio.0c00303  0.748
2020 Fulk EM, Huh D, Atkinson JT, Lie M, Masiello CA, Silberg JJ. A Split Methyl Halide Transferase AND Gate That Reports by Synthesizing an Indicator Gas. Acs Synthetic Biology. PMID 33104325 DOI: 10.1021/acssynbio.0c00355  0.728
2020 Atkinson JT, Jones AM, Nanda V, Silberg JJ. Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts. Protein Engineering, Design & Selection : Peds. PMID 32626892 DOI: 10.1093/Protein/Gzaa012  0.792
2020 Campbell IJ, Olmos JL, Xu W, Kahanda D, Atkinson JT, Sparks ON, Miller MD, Phillips GN, Bennett GN, Silberg JJ. phage ferredoxin: Structural characterization and electron transfer to cyanobacterial sulfite reductases. The Journal of Biological Chemistry. PMID 32434930 DOI: 10.1074/Jbc.Ra120.013501  0.72
2019 Atkinson JT, Wu B, Segatori L, Silberg JJ. Overcoming component limitations in synthetic biology through transposon-mediated protein engineering. Methods in Enzymology. 621: 191-212. PMID 31128779 DOI: 10.1016/Bs.Mie.2019.02.014  0.761
2019 Wu B, Atkinson JT, Kahanda D, Bennett GN, Silberg JJ. Combinatorial design of chemical‐dependent protein switches for controlling intracellular electron transfer Aiche Journal. 66. DOI: 10.1002/Aic.16796  0.712
2018 Atkinson JT, Campbell IJ, Thomas EE, Bonitatibus SC, Elliott SJ, Bennett GN, Silberg JJ. Metalloprotein switches that display chemical-dependent electron transfer in cells. Nature Chemical Biology. PMID 30559426 DOI: 10.1038/S41589-018-0192-3  0.746
2018 Zeng Y, Jones AM, Thomas EE, Nassif B, Silberg JJ, Segatori L. A split transcriptional repressor that links protein solubility to an orthogonal genetic circuit. Acs Synthetic Biology. PMID 30089365 DOI: 10.1021/Acssynbio.8B00129  0.614
2018 Atkinson JT, Jones AM, Zhou Q, Silberg JJ. Circular permutation profiling by deep sequencing libraries created using transposon mutagenesis. Nucleic Acids Research. PMID 29912470 DOI: 10.1093/Nar/Gky255  0.804
2017 Thomas EE, Pandey N, Knudsen S, Ball ZT, Silberg JJ. Programming Post-Translational Control over the Metabolic Labeling of Cellular Proteins with a Noncanonical Amino Acid. Acs Synthetic Biology. 6: 1572-1583. PMID 28419802 DOI: 10.1021/Acssynbio.7B00100  0.63
2017 Jones AM, Atkinson JT, Silberg JJ. PERMutation Using Transposase Engineering (PERMUTE): A Simple Approach for Constructing Circularly Permuted Protein Libraries. Methods in Molecular Biology (Clifton, N.J.). 1498: 295-308. PMID 27709583 DOI: 10.1007/978-1-4939-6472-7_19  0.805
2016 Atkinson JT, Campbell I, Bennett GN, Silberg JJ. Cellular Assays for Ferredoxins: A Strategy for Understanding Electron Flow through Protein Carriers That Link Metabolic Pathways. Biochemistry. 55: 7047-7064. PMID 27966889 DOI: 10.1021/Acs.Biochem.6B00831  0.73
2016 Pandey N, Kuypers BE, Nassif B, Thomas EE, Alnahhas RN, Segatori L, Silberg JJ. Tolerance of a Knotted Near-Infrared Fluorescent Protein to Random Circular Permutation. Biochemistry. 55: 3763-73. PMID 27304983 DOI: 10.1021/Acs.Biochem.6B00258  0.617
2016 Jones AM, Mehta MM, Thomas EE, Atkinson JT, Segall-Shapiro TH, Liu S, Silberg JJ. The Structure of a Thermophilic Kinase Shapes Fitness upon Random Circular Permutation. Acs Synthetic Biology. 5: 415-25. PMID 26976658 DOI: 10.1021/Acssynbio.5B00305  0.803
2015 Pandey N, Nobles CL, Zechiedrich L, Maresso AW, Silberg JJ. Combining random gene fission and rational gene fusion to discover near-infrared fluorescent protein fragments that report on protein-protein interactions. Acs Synthetic Biology. 4: 615-24. PMID 25265085 DOI: 10.1021/Sb5002938  0.657
2013 Mahdavi A, Segall-Shapiro TH, Kou S, Jindal GA, Hoff KG, Liu S, Chitsaz M, Ismagilov RF, Silberg JJ, Tirrell DA. A genetically encoded and gate for cell-targeted metabolic labeling of proteins. Journal of the American Chemical Society. 135: 2979-82. PMID 23406315 DOI: 10.1021/Ja400448F  0.642
2012 Judd J, Wei F, Nguyen PQ, Tartaglia LJ, Agbandje-McKenna M, Silberg JJ, Suh J. Random Insertion of mCherry Into VP3 Domain of Adeno-associated Virus Yields Fluorescent Capsids With no Loss of Infectivity. Molecular Therapy. Nucleic Acids. 1: e54. PMID 23629029 DOI: 10.1038/Mtna.2012.46  0.642
2012 Mehta MM, Liu S, Silberg JJ. A transposase strategy for creating libraries of circularly permuted proteins. Nucleic Acids Research. 40: e71. PMID 22319214 DOI: 10.1093/nar/gks060  0.32
2012 Vu MT, Zhai P, Lee J, Guerra C, Liu S, Gustin MC, Silberg JJ. The DNLZ/HEP zinc-binding subdomain is critical for regulation of the mitochondrial chaperone HSPA9. Protein Science : a Publication of the Protein Society. 21: 258-67. PMID 22162012 DOI: 10.1002/Pro.2012  0.777
2011 Zhai P, Vu MT, Hoff KG, Silberg JJ. A conserved histidine in human DNLZ/HEP is required for stimulation of HSPA9 ATPase activity. Biochemical and Biophysical Research Communications. 408: 589-94. PMID 21530495 DOI: 10.1016/J.Bbrc.2011.04.066  0.785
2011 Segall-Shapiro TH, Nguyen PQ, Dos Santos ED, Subedi S, Judd J, Suh J, Silberg JJ. Mesophilic and hyperthermophilic adenylate kinases differ in their tolerance to random fragmentation. Journal of Molecular Biology. 406: 135-48. PMID 21145325 DOI: 10.1016/J.Jmb.2010.11.057  0.652
2010 Silberg JJ, Nguyen PQ, Stevenson T. Computational design of chimeric protein libraries for directed evolution. Methods in Molecular Biology (Clifton, N.J.). 673: 175-88. PMID 20835798 DOI: 10.1007/978-1-60761-842-3_10  0.645
2010 Nguyen PQ, Silberg JJ. A selection that reports on protein-protein interactions within a thermophilic bacterium. Protein Engineering, Design & Selection : Peds. 23: 529-36. PMID 20418388 DOI: 10.1093/Protein/Gzq024  0.658
2009 Hoff KG, Culler SJ, Nguyen PQ, McGuire RM, Silberg JJ, Smolke CD. In vivo fluorescent detection of Fe-S clusters coordinated by human GRX2. Chemistry & Biology. 16: 1299-308. PMID 20064440 DOI: 10.1016/J.Chembiol.2009.11.011  0.742
2009 Hoff KG, Goodlitt R, Li R, Smolke CD, Silberg JJ. Fluorescence detection of a protein-bound 2Fe2S cluster. Chembiochem : a European Journal of Chemical Biology. 10: 667-70. PMID 19184988 DOI: 10.1002/Cbic.200800747  0.613
2008 Zhai P, Stanworth C, Liu S, Silberg JJ. The human escort protein Hep binds to the ATPase domain of mitochondrial hsp70 and regulates ATP hydrolysis. The Journal of Biological Chemistry. 283: 26098-106. PMID 18632665 DOI: 10.1074/Jbc.M803475200  0.694
2008 Nguyen PQ, Liu S, Thompson JC, Silberg JJ. Thermostability promotes the cooperative function of split adenylate kinases. Protein Engineering, Design & Selection : Peds. 21: 303-10. PMID 18287175 DOI: 10.1093/Protein/Gzn005  0.674
2005 Drummond DA, Silberg JJ, Meyer MM, Wilke CO, Arnold FH. On the conservative nature of intragenic recombination. Proceedings of the National Academy of Sciences of the United States of America. 102: 5380-5. PMID 15809422 DOI: 10.1073/Pnas.0500729102  0.728
2005 Bloom JD, Silberg JJ, Wilke CO, Drummond DA, Adami C, Arnold FH. Thermodynamic prediction of protein neutrality. Proceedings of the National Academy of Sciences of the United States of America. 102: 606-11. PMID 15644440 DOI: 10.1073/Pnas.0406744102  0.735
2004 Silberg JJ, Tapley TL, Hoff KG, Vickery LE. Regulation of the HscA ATPase reaction cycle by the co-chaperone HscB and the iron-sulfur cluster assembly protein IscU. The Journal of Biological Chemistry. 279: 53924-31. PMID 15485839 DOI: 10.1074/Jbc.M410117200  0.765
2004 Endelman JB, Silberg JJ, Wang ZG, Arnold FH. Site-directed protein recombination as a shortest-path problem. Protein Engineering, Design & Selection : Peds. 17: 589-94. PMID 15331774 DOI: 10.1093/Protein/Gzh067  0.718
2004 Silberg JJ, Endelman JB, Arnold FH. SCHEMA-guided protein recombination. Methods in Enzymology. 388: 35-42. PMID 15289059 DOI: 10.1016/S0076-6879(04)88004-2  0.749
2004 Otey CR, Silberg JJ, Voigt CA, Endelman JB, Bandara G, Arnold FH. Functional evolution and structural conservation in chimeric cytochromes p450: calibrating a structure-guided approach. Chemistry & Biology. 11: 309-18. PMID 15123260 DOI: 10.1016/J.Chembiol.2004.02.018  0.767
2004 Cupp-Vickery JR, Silberg JJ, Ta DT, Vickery LE. Crystal structure of IscA, an iron-sulfur cluster assembly protein from Escherichia coli. Journal of Molecular Biology. 338: 127-37. PMID 15050828 DOI: 10.1016/J.Jmb.2004.02.027  0.58
2003 Meyer MM, Silberg JJ, Voigt CA, Endelman JB, Mayo SL, Wang ZG, Arnold FH. Library analysis of SCHEMA-guided protein recombination. Protein Science : a Publication of the Protein Society. 12: 1686-93. PMID 12876318 DOI: 10.1110/Ps.0306603  0.796
2003 Meinhold P, Joern JM, Silberg JJ. Analysis of shuffled libraries by oligonucleotide probe hybridization. Methods in Molecular Biology (Clifton, N.J.). 231: 177-87. PMID 12824614 DOI: 10.1385/1-59259-395-X:177  0.726
2003 Udit AK, Silberg JJ, Sieber V. Sequence homology-independent protein recombination (SHIPREC). Methods in Molecular Biology (Clifton, N.J.). 231: 153-63. PMID 12824612 DOI: 10.1385/1-59259-395-X:153  0.729
2002 Hoff KG, Ta DT, Tapley TL, Silberg JJ, Vickery LE. Hsc66 substrate specificity is directed toward a discrete region of the iron-sulfur cluster template protein IscU. The Journal of Biological Chemistry. 277: 27353-9. PMID 11994302 DOI: 10.1074/Jbc.M202814200  0.777
2001 Urbina HD, Silberg JJ, Hoff KG, Vickery LE. Transfer of sulfur from IscS to IscU during Fe/S cluster assembly. The Journal of Biological Chemistry. 276: 44521-6. PMID 11577100 DOI: 10.1074/Jbc.M106907200  0.781
2001 Silberg JJ, Hoff KG, Tapley TL, Vickery LE. The Fe/S assembly protein IscU behaves as a substrate for the molecular chaperone Hsc66 from Escherichia coli. The Journal of Biological Chemistry. 276: 1696-700. PMID 11053447 DOI: 10.1074/Jbc.M009542200  0.791
2000 Hoff KG, Silberg JJ, Vickery LE. Interaction of the iron-sulfur cluster assembly protein IscU with the Hsc66/Hsc20 molecular chaperone system of Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 97: 7790-5. PMID 10869428 DOI: 10.1073/Pnas.130201997  0.754
2000 Silberg JJ, Vickery LE. Kinetic characterization of the ATPase cycle of the molecular chaperone Hsc66 from Escherichia coli. The Journal of Biological Chemistry. 275: 7779-86. PMID 10713091 DOI: 10.1074/Jbc.275.11.7779  0.573
1998 Silberg JJ, Hoff KG, Vickery LE. The Hsc66-Hsc20 chaperone system in Escherichia coli: chaperone activity and interactions with the DnaK-DnaJ-grpE system. Journal of Bacteriology. 180: 6617-24. PMID 9852006 DOI: 10.1128/Jb.180.24.6617-6624.1998  0.758
1997 Vickery LE, Silberg JJ, Ta DT. Hsc66 and Hsc20, a new heat shock cognate molecular chaperone system from Escherichia coli. Protein Science : a Publication of the Protein Society. 6: 1047-56. PMID 9144776 DOI: 10.1002/Pro.5560060511  0.61
Low-probability matches (unlikely to be authored by this person)
2019 Mutter AC, Tyryshkin AM, Campbell IJ, Poudel S, Bennett GN, Silberg JJ, Nanda V, Falkowski PG. De novo design of symmetric ferredoxins that shuttle electrons in vivo. Proceedings of the National Academy of Sciences of the United States of America. PMID 31262814 DOI: 10.1073/Pnas.1905643116  0.273
1995 Arai A, Silberg J, Kessler M, Lynch G. Effect of thiocyanate on AMPA receptor mediated responses in excised patches and hippocampal slices. Neuroscience. 66: 815-27. PMID 7544449 DOI: 10.1016/0306-4522(94)00616-D  0.248
2019 Campbell IJ, Bennett GN, Silberg JJ. Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers. Frontiers in Energy Research. 7. PMID 32095484 DOI: 10.3389/fenrg.2019.00079  0.237
1995 Arai A, Silberg J, Lynch G. Differences in the refractory properties of two distinct inhibitory circuitries in field CA1 of the hippocampus. Brain Research. 704: 298-306. PMID 8788926 DOI: 10.1016/0006-8993(95)01137-4  0.226
2011 McGuire RM, Silberg JJ, Pereira FA, Raphael RM. Selective cell-surface labeling of the molecular motor protein prestin. Biochemical and Biophysical Research Communications. 410: 134-9. PMID 21651892 DOI: 10.1016/J.Bbrc.2011.05.121  0.214
2013 Ho ML, Adler BA, Torre ML, Silberg JJ, Suh J. SCHEMA computational design of virus capsid chimeras: calibrating how genome packaging, protection, and transduction correlate with calculated structural disruption. Acs Synthetic Biology. 2: 724-33. PMID 23899192 DOI: 10.1021/Sb400076R  0.192
2014 Zhao W, Bonem M, McWhite C, Silberg JJ, Segatori L. Sensitive detection of proteasomal activation using the Deg-On mammalian synthetic gene circuit. Nature Communications. 5: 3612. PMID 24710080 DOI: 10.1038/Ncomms4612  0.165
2014 Judd J, Ho ML, Tiwari A, Gomez EJ, Dempsey C, Van Vliet K, Igoshin OA, Silberg JJ, Agbandje-McKenna M, Suh J. Tunable protease-activatable virus nanonodes. Acs Nano. 8: 4740-6. PMID 24796495 DOI: 10.1021/Nn500550Q  0.146
2018 Cheng HY, Masiello CA, Del Valle I, Gao X, Bennett GN, Silberg JJ. Ratiometric gas reporting: a non-disruptive approach to monitor gene expression in soils. Acs Synthetic Biology. PMID 29366321 DOI: 10.1021/Acssynbio.7B00405  0.139
2013 Masiello CA, Chen Y, Gao X, Liu S, Cheng HY, Bennett MR, Rudgers JA, Wagner DS, Zygourakis K, Silberg JJ. Biochar and microbial signaling: production conditions determine effects on microbial communication. Environmental Science & Technology. 47: 11496-503. PMID 24066613 DOI: 10.1021/Es401458S  0.118
2023 Goldman AL, Fulk EM, Momper LM, Heider C, Mulligan J, Osburn M, Masiello CA, Silberg JJ. Microbial sensor variation across biogeochemical conditions in the terrestrial deep subsurface. Msystems. e0096623. PMID 38059636 DOI: 10.1128/msystems.00966-23  0.094
2016 Gao X, Cheng HY, Del Valle I, Liu S, Masiello CA, Silberg JJ. Charcoal Disrupts Soil Microbial Communication through a Combination of Signal Sorption and Hydrolysis. Acs Omega. 1: 226-233. PMID 29938248 DOI: 10.1021/acsomega.6b00085  0.082
2016 Cheng HY, Masiello CA, Bennett GN, Silberg JJ. Volatile Gas Production by Methyl Halide Transferase: An In Situ Reporter Of Microbial Gene Expression In Soil. Environmental Science & Technology. 50: 8750-9. PMID 27415416 DOI: 10.1021/Acs.Est.6B01415  0.078
2020 Tseng CP, Silberg JJ, Bennett GN, Verduzco R. 100th Anniversary of Macromolecular Science Viewpoint: Soft Materials for Microbial Bioelectronics. Acs Macro Letters. 9: 1590-1603. PMID 35617074 DOI: 10.1021/acsmacrolett.0c00573  0.073
2023 Kim J, Lu LC, Gao X, Hofmockel KS, Masiello CA, Silberg JJ. Using Methyl Bromide for Interspecies Cell-Cell Signaling and As a Reporter in a Model Soil Consortium. Acs Synthetic Biology. PMID 37991716 DOI: 10.1021/acssynbio.3c00559  0.072
2020 Del Valle I, Webster TM, Cheng HY, Thies JE, Kessler A, Miller MK, Ball ZT, MacKenzie KR, Masiello CA, Silberg JJ, Lehmann J. Soil organic matter attenuates the efficacy of flavonoid-based plant-microbe communication. Science Advances. 6: eaax8254. PMID 32064339 DOI: 10.1126/Sciadv.Aax8254  0.069
2013 LeCroy C, Masiello CA, Rudgers JA, Hockaday WC, Silberg JJ. Nitrogen, biochar, and mycorrhizae: Alteration of the symbiosis and oxidation of the char surface Soil Biology and Biochemistry. 58: 248-254. DOI: 10.1016/J.Soilbio.2012.11.023  0.064
2022 Fulk EM, Gao X, Lu LC, Redeker KR, Masiello CA, Silberg JJ. Nondestructive Chemical Sensing within Bulk Soil Using 1000 Biosensors Per Gram of Matrix. Acs Synthetic Biology. PMID 35715210 DOI: 10.1021/acssynbio.2c00083  0.061
2022 Del Valle I, Gao X, Ghezzehei TA, Silberg JJ, Masiello CA. Artificial Soils Reveal Individual Factor Controls on Microbial Processes. Msystems. e0030122. PMID 35880897 DOI: 10.1128/msystems.00301-22  0.055
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